Thursday, February 08, 2007

Inside the Cell.

David Goodsell is a biochemist who is also an excellent artist. He has combined these skills in the production of beautiful paintings which seek to portray an idea of the molecular biology of the cell. More of his illustrations are here. He kindly gave me permission to use these pictures here:




This picture shows part of a bacterium.

(Can you spot the motor? :-) )



This one shows a section across a red blood cell with the blood serum outside the cell.


This is an enlargement of a small part of the same picture.

This picture shows an HIV virus particle under attack from the immune system.

(Thanks to Tony Jackson for the original link.)


69 Comments:

Blogger Tony Jackson said...

Hmmm. I see no mousetraps....

Andrew, rememeber what I said in the other thread: the real cell is a very crowded place with molecules darting hither and thither in endless chaos. And to repeat the point I made previously:

"even these paintings are simplified abstractions. Goodsell is careful for example to omit all the ions, small molecular weight compounds (glucose, amino acids etc) and of course water itself. If he didn’t, his paintings would be an utterly impenetrable mess."

This is what Sydney Brenner meant when he talked about macromolecules as 'anarchic demons'. There is no hint here of any thing resembling macroscopic man-made objects.

4:50 pm  
Anonymous Sparky said...

"This is what Sydney Brenner meant when he talked about macromolecules as 'anarchic demons'. There is no hint here of any thing resembling macroscopic man-made objects." I disagree. It seems cell functions painted or not are essential to the cell's survival, (and reproduction and all that good stuff) if you were to stop one part of cellular respiration say only one part of kreb's cycle you kill the cell. period. dead. sounds like a bit of a mousetrap to me, and thats only one example. A cell is like an entire city with tiny machines for building proteins. How can you see no mousetraps?

7:59 pm  
Blogger Tony Jackson said...

Sparky

Pay attention at the back of the class!

Re-read my other posts about this stuff on the previous thread.

"Possible Pathways for the evolution of intracellular transport."

8:21 pm  
Blogger Tony Jackson said...

sparky. In all seriousness, it just isn't true that knocking out say a TCA cycle enzyme is necessarily always lethal.

The cell-as-factory image is deeply, deeply misguided and no serious biochemist or cell biologist believes it literally. This isn't big news. It's been well understood in mainstream biochemistry for forty or more years.

You're thinking like Behe wants you to think. One of the reasons that those (relatively few) biochemists that have even heard of Behe are so irritated by his book is because he has quite deliberately (and I would say quite cynically) presented a view of biochemistry that is just plain wrong. In that respect, I think he has done enormous damage to the scientific understanding of the general public.

10:27 pm  
Blogger Andrew Rowell said...

Tony,
"The cell-as-factory image is deeply, deeply misguided."

Why?

10:43 pm  
Blogger Tony Jackson said...

Come on Andrew, we've been over this before. See previous posts on other threads from smokey, umbjm, myself and others.....

9:42 am  
Blogger Andrew Rowell said...

Tony,

It is not a perfect analogy but I would not go as far as to say "deeply deeply misguided" would you say that it is a serious educational mistake to use the analogy at all? You used the analogy of motorways and A roads. Some of the factory analogy is ingrained in the very terminology we use. I still think it is a useful analogy even after all the discussions in the previous threads. I think it is misguided to call it "deeply deeply misguided."

10:36 am  
Blogger Tony Jackson said...

Andrew,

There’s nothing wrong with using analogies. In fact, when dealing with this weird stuff, it’s probably essential at some level. But you have to keep things very clearly in mind. All analogies break down if you push them too far or if you interpret them too literally. A good analogy should capture vividly some key, but limited aspect of an unusual process is more familiar terms. So for example, I’ve previously mentioned Jacob’s use of the ‘tinkerer’ analogy, which is a very popular one amongst biologists because it captures rather well a key feature of the evolutionary process. But of course Jacob didn’t believe there is a literal tinkerer out there.

Ditto Brenner and his ‘anarchic demons’ analogy. Umbjm’s analogy of the secretory pathway in terms of dumb postmen repeatedly banging at your door asking ‘is this yours?’ is another example of how a good analogy should work. Yes, I once used the roadway system as a rough analogy to make the point that there are many different ways for proteins to get from A to B in a cell, but again, there aren’t any literal motorways with traffic cops in the cell.

I worry that Behe - either deliberately or through sloppy prose - is spreading the idea among those who do not know much biochemistry or cell biology that the cell really is a literal factory, and in that sense, it isn’t.

12:26 pm  
Anonymous Anonymous said...

FWIW I typed "Cell Factory Analogy" into Google and did find evidence from various sources that the idea not at all novel to Behe. As a biological layman I appreciate the analogy will break down at some level but I must confess for me personally it is helpful and not misguided.

2:06 pm  
Anonymous Sparky said...

"sparky. In all seriousness, it just isn't true that knocking out say a TCA cycle enzyme is necessarily always lethal."

Tony, that is very interesting. You have my curiosity piqued. Could I see a peer-reviewed source?

Also, do you believe this is the case with electron transport as well?

3:28 pm  
Anonymous Sparky said...

Tony, I am also curious as to how you would respond to the defense of an "irreducible core".

3:30 pm  
Blogger Smokey said...

Andrew asked:
"Why?"

Because analogies are explanatory devices that help us to comprehend bits of biology.

What Behe omits is that the analogies always break down, and we'll use multiple analogies to describe different facets of a single mechanism, or even a single molecule.

That's why substituting analogy for hypothesis-testing is pathetic.

6:46 pm  
Blogger Tony Jackson said...

Sparky: why don’t you re-read what’s already been said about irreducible complexity on other threads eg “Intracellular Transport systems” and “Possible Pathways for the evolution of intracellular transport.”

Behe wants you to think that eg knockout experiments are always black and white, but they’re not.

Actually, the specific example you ask about is a good example of this, and in fact forms the basis of an undergraduate class practical we run here. Take some yeast and knockout a TCA cycle enzyme or an electron transport protein. If you feed this mutant only acetate as sole carbon source, it won’t grow, but if you feed it glycerol it will grow (why is this by the way?). That’s what I mean by context-dependence, and it’s absolutely central to the proper interpretation of knockouts.

Really, believe me, this isn’t controversial. It’s bread and butter stuff and it’s one of the reasons why professional biologists/biochemists regard Behe at best as a bit of a joke and at worse as a bloody menace.

Anonymous: If to get started, you just want to say, “the ribosome is like a factory” well OK (I suppose). But the problem here is that if you look a bit more closely, you’ll find other aspects of protein synthesis and secretion that are decidedly un-factory-like (see my previous post on the “Possible Pathways for the evolution of intracellular transport” thread). In other words, at very best it’s a limited analogy and it does have the potential to seriously mislead if you’re not careful.

Analogies can be useful to explain unfamiliar concepts, but in and of themselves they cannot be used to draw scientific conclusions. That way, madness lies.

8:40 pm  
Anonymous kairosfocus said...

Onlookers:

There is so much that is misleading in the comments I saw on glancing at this thread that I cannot but remark on a few points:

1] The cell is not a factory

Of course it isn't.

It is a self-replicating, self-maintaining automaton that takes in energy and materials, uses molecular nanotechnologty to process them, synthesises components based on stored, coded data and in general shows itself to be a massively functionally specified information-rich complex system far beond the credible reach of chance + necessity alone on the gamut of the observed cosmos.

THAT is why the evolutionary materialistic OOL models are in deep and increasing trouble. In turn that is why there is a convenient attempted delimitaiton of discussions on evolution to exclude OOL issues when they come up.

But in the end that does not wash, as there is a major linked problem: body-plan level macroevolution requires the same creation of massive amounts of functionally specified, coordinated andintegrated algorithmic information that rapidly exhausts the credible probabilistic resources of the observed cosmos.

That is, ont he assumptiont ha tit originated by chance plus necessity, in Monod's phrase. But we know that FSCI of enormous complexcity -- if not yet the spophistication that we see int he cell -- is routinely produced by intelligent agents. So, based on what we do know the best explanation forthe FSCI int he cell is justthat: intelligent -- as opposed to supernatural -- agents.

2] Analogies break down . . .

So what?

Analogies often work, too; and have been enormously fruitful in science across the ages.

Just one instance: it was Galileo's observation that Jupiter had an orbiting cluster of satellites, that materially helped make the Copernican sytem plausible.

Reasoning by analogy is a species of inductive argument,and is deeply tied to its power:

A, B, C, D have similar characteristics 1, 2,3, 4.

E is similar to these so it is likely to have the same characteristics.

The issue is, whether the features beign compared are relevant, and the underlying point that we are dealing with defeatable reasoning, and provisional results. But that is all we can do once we coem into that messy world of perceptions and facts . . .

So, to use such reasoning in science generally then to dismiss it on grounds that it does not always work is selective hyperskepticism. Use it when it suits you, complain on its usewhen it does not suit you. What does that tell us about the state of the thinking at work?

And, recall, deductive arguments do not contain anything inthe conclusion that was not in the premises. I.e. it is inductive reasoning in whatever form [including Abduction] that is whatis creative in discovering new potential knowledge that can be provisionally tested and accepted as credible . . .

Science cannot escape the issues of induction. (And all that stuff about hypothetico-deductive reasoning runs intotheproblem that if H implies obseefvations O1, O2, O3 etc,adn we test them a finite number of times, we have not tested ALL possible outcomes,a nd cannot for we are finite and fallible, even when testing. So, we are STILL making an induction thatthe principle in question is trustworthy inother untested cases, provisional though it is. Of course,when worldviews such as evolutionary materialism are at stake, there is too often resistance tothe point hatthe science is provisional,a nd thatright now it is runing into a mounting pile of anomalies tied to the issue of FSCI . . .]

3] Digital, algorithmic information in life systems -- FSCI as an issue

Much of the argument above by TJ and co is -- to be frank -- manipulative adn misleading, given that TJ is a knowledgeable professional by his own admission. He MUST know better than he has argued.

The above plays on general ignorance of the relevant discrete state, algorighmic information stored in key life molecules and used in the synthesis and functioning of proteins, the workhorse molecules of the cell.

Sure, the cell does not LOOK -- notice the appeal to dis-analogy here [i.e. geometrically unlike the linear, right-angle and circles full machinery we make on the much bigger scale] -- like say a PC does if you rip open its guts; which look rather messy too, BTW. [Part of why we put tem in a nice looking case . . .]

But what is relevant is that DNA, in real life something like 300 - 500 K to 3 - 4 thousand million monomer elements -- is a molecular data storage technology based on a partly decoded system.

So we know that in each position there are 4 states [GCAT sometimes U] and that these function materially like letters in our own text-based systems,or on/off elements in a computer. Thus we see that in 300k DNA storage elements we have a data storage potential of 4^300k = 9.94*10^180,617 possible states. That is a huge data storage potential,adn a confu=igutration spavce that bogglesthe imagination [within which biofunctional states are sparse, so this means that random search strategies, such as trial and error are maximally inefficient].

This storage is used to generate the coding for protein molecules which have precise chains of monomers based on a 20-state element, based on 3-letter DNA codons [64 possible states per codon, most of which code for varios amino acids . . . but include start/stop] In turn the code is sentitive to the sequence or it will often fail to fold properly, leading to failing to fuction, sometimes just one amino acid monomer in error leads to failure to fuction, sometimes partial sometimes total. And much more.

But the bottomline is plain, we are not dealing here with a mere whimsical analogy, but with an information processing system of enormous sophistication, one that can be compared to the concept of the automated digitally controlled factory of the future. But all within maybe 1 - 10 microns of scale, and based on molecular nanotechnology. So Denton's 1986 factory analogy is not to besimply dismissed based onthe fact that analogies sometimes break down.

Indeed, BTW there is interest in reverse engineering lifeformas at cellular level and using the resutls for further industrial development [and unfortunately, war too ].

Tervors and Abel discuss the implications in two peer reviewed papers here and here.

_________

Go here to see what has happened so far when I have directly challenged TJ to answer the issues linked to getting to such FSCI based systems, after he tried to dismiss Minnich as a way to distract from the issue of ausive secularist commentary.

Misleading remarks as I just pointed outabove are slo abusive, TJ. [NB: My name links an introductory level survey with much more.]

Bottomline: there is a lot more to this issue than meets the eye; and, do not allow yourselves to be misled by secularist dismissive and distracting or accusatory rhetoric.

Cheerio

TKI

10:28 am  
Blogger Tony Jackson said...

Kairosfocus: If you want to discuss the origin of life, ask Andrew to start another thread. Here, the issue is the appropriate use of analogies. I think we all agree that they are helpful, but our point is that they need to be used with caution and Behe has (to put it mildly) been rather cavalier in this department.

“Reasoning by analogy is a species of inductive argument, and is deeply tied to its power:
A, B, C, D have similar characteristics 1, 2,3, 4. E is similar to these so it is likely to have the same characteristics.”

This is similar to the sort of reasoning Behe makes eg:

i) A mousetrap is ‘irreducibly complex’
ii) A mousetrap was designed.
iii) The blood clotting cascade is ‘irreducibly complex’
iv) Therefore blood clotting was also designed.

But this is a fallacy. If X is like Y, then that just means that X and Y share some conceptual properties, perhaps in a quite limited way. It most certainly does not mean that X and Y have all the same properties.

Since you mentioned the other thread, let me also add this: Over there I made the simple point that I couldn’t see anything in Minnich’s papers that provided direct evidence for the existence of an intelligent designer. Moreover, to the extent that any ID advocate has proposed any ID theory at all, so far we’ve just got some wild speculations from Behe and Davison which are very clearly contradicted by the avialable data.

You responded to this by throwing a hissy fit, which isn’t helpful.

8:28 pm  
Anonymous kairosfocus said...

Onlookers:

I see, sadly, TJ has time to comment on the remarks I made overnight but no time to address the major concerns in the previous threads, including especially abusive commentary.

I will remarks on points of the issue of inductive logic and other matters that are illustrative of the underlying problems:

1] TJ: If you want to discuss the origin of life, ask Andrew to start another thread. Here, the issue is the appropriate use of analogies.

Coming from someone who sought to divert the thread just linked, that is rich.

Moreover, it is inaccurate, as Andrew in his post was speaking of the complex functional information and systems in the cell, which makes the origin of such material to the issue. Analogy as a question in logic and epistemology is at best incidental, at worst, diversionary.

But in fact I am not primarily addressing OOL, but the underlying common core issue in all of these things: the known origin of functuionally specific complex information, FSCI and the special case, irreducible complexity, IC. OOL and body plan level or molecular nanotech cellular machines are empirically testable and illustrative cases in point of the underlying information generation issue. I contend – giving my reasoning at introductory technical level -- that FSCI simply does not credibly arise from lucky noise.

In particular, we rapidly run out of the probabilistic resources of the known universe to account for such FSCI on a basis of chance + necessity only. But, we know that FSCI and IC are routinely produced by intelligent agents, and that we are looking at the most sophisticated known cases of FSCI.

Thus, it seem to me that the points of comparison are relevant to the inferences being drawn. Very relevant.

2] If X is like Y, then that just means that X and Y share some conceptual properties, perhaps in a quite limited way. It most certainly does not mean that X and Y have all the same properties.

And so?

If X and Y share very evidently relevant properties in common -- FSCI, IC -- but not rather irrelevant ones -- e.g. not having the same look of being based on straight lines, circles and right angles that is common in human artifacts based on our specific technologies and relatively unsophisticated materials -- then the analogies and indeed more than analogies will tell. The similarities are dynamical, the dissimilarities are those of mere appearance. We are asking about the dynamics at work, not issues of appearance.

Onlookers, note that indeed, we are in fact looking at points of identity not mere analogy on the issue of linear arrays of discrete state elements used to encode information in identifiable codes and to drive a sequential, step by step process that pursues solutions/caries out processes of transformation. That is, we are looking at algorithmically functional information in both cases.

To illustrate, here is a recent comment on that, as nanotech seeks to use reverse engineering of live to synthesise novel systems:

>>Biochip platforms that work as artificial cells are attractive for medical diagnostics, interrogation of biological processes, and for the production of important biomolecules. However, to match the complexity of nature, the biochips need to be designed such that proteins, DNA, and other important biological components can be located in specific, spatially well-defined regions on the chips.

This allows these devices to mimic the complex, sequential, and often cascaded events involved in biological processes. Now, in a major breakthrough, a group of researchers at the Weizmann Institute of Science in Israel, led by Roy Bar-Ziv, in collaboration with Margherita Morpurgo from the University of Padova in Italy, have designed a molecule affectionately called the “daisy” that is able to bind genes onto chips in miniature patterned arrays.

Bar-Ziv and co-workers have been able to use the daisy to pattern tiny regions of double-stranded DNA onto silicon dioxide surfaces. Indeed, these immobilized genes are able to conduct their business on patterned silicon substrates without the need for living cells. These biochips can act as protein microtraps, selectively trapping specific proteins from crude cell extracts with high spatial resolution. Moreover, the gene sequences immobilized on the biochips can be used for the on-chip production of proteins by transcription/translation processes such as those occurring within cells.>>

Observe the highlight that shows the algorithmic, complex nature of the biofunctional information in DNA.

3] Induction and analogy

More generally, arguments by induction are a form of defeatable reasoning: they do not always work; so the objection that they do not always work is pointless or selectively hyperskeptical, as we routinely use inductive reasoning to create and test knowledge and to go on to apply such knowledge to influence or control the world in desirable ways.

Of course, such knowledge claims are provisional, subject to further testing, and so we inevitably come back tot he need to take that step of faith to trust and use them even though they are not certain. Popper et al have even made virtue out of that necessity by using the idea of falsification at some level as one way to tell good from bad science -- follow up Lakatos and many others to see the limitations on falsificationism. (BTW, I observe how TJ resorts to phil issues when it suits him but then ducks out when he is challenged to seriously work through the thorny phil of sci challenges that lurk beneath the points he raises. But then most practising scientists today are not well equipped to address the phil of sci issues that arise in times of scientific crisis and nascent revolution.)

Since that limitation applies to the trustworthiness of the air we breathe, the food and drink we consume, the seats we sit on, the cars we drive, the senses that we use to do these things and more, the objection is pointless or worse.

Instead, what we have done in developing common sense and scientific methods is that we apply the principles of inference to best explanation and abduction to see that we have at any given point the best reasonable explanation that gives satisfactory results relative to our formal and informal world models.

On this case, the best known situation is that we have knowledge of a great many cases of the origin of FSCI and IC systems. Without exception to date, they originate in intelligent action, where we directly know the cause. So, what is the most credible explanation for the most sophisticated observed cases, absent worldview level question-begging that artificially excludes it?

That answer is quite obvious: intelligent agents.

4] I made the simple point that I couldn’t see anything in Minnich’s papers that provided direct evidence for the existence of an intelligent designer. Moreover, to the extent that any ID advocate has proposed any ID theory at all, so far we’ve just got some wild speculations from Behe and Davison which are very clearly contradicted by the avialable data. You responded to this by throwing a hissy fit, which isn’t helpful.

More accurately, you sought to divert the course of a thread on the subject of abusive commentary without being willing to acknowledge -- much less apologise for -- your own guilt in the matter.

Moreover, your "hissy fit" remark just excerpted shows that you are still in the thought police mentality and, sadly, frankly plainly lack the broughtupcy to see that you need to be accountable over misbehaviour and apologise then amend your ways. FOR SHAME!

In specific, to correct the misrepresentation for onlookers:

* I respondede to the claim by U: "empirically anchored" falls far short of real science. One has to test predictions from the inference to be doing science, and to date, every ID proponent on the planet lacks the courage/faith/integrity to do so. [NB: it seems that permalinks to comments don't work, at least in Firefox]

* I took this slanderous claim up by pointing to the csacade of thought and empirical research that goes Behe -> Miller -> Minnich et al, on the bacterial flagellum, first noting that Mr Minnich is a well-published lab based scientist who openly – that is an issue givent he thought police mentality and tactics we are increasingly seeing on display -- works in the Design theory paradigm. [That is, I showed that U's comment is ill-informed and/or slanderous.]

* To support this, I linked the ID Research Wiki -- which should be a first reference for factual adequacy on such claims as U made and others often make. (Note, no-one has taken up the challenge to examine what is seen there and show that it fails to answer to U's claim. No prizes for guessing why. BTW, U has been missing in action since.]

* In that context, I also linked Mr Minnich's resume and some excerpts therefrom. TJ pounced on the publications so listed in the excerpt as not being on ID specifically and explicitly; in reply to which I noted that I was simply showing his basic credentials as a scientist; and posted first a reference then an excerpt to the peer-reviewed paper presented at the conference on Nature and Design and appearing in the proceedings.

* TJ also attempted to imply/suggest that the article in question was not peer reviewed, and then that conferences are not a suitable medium, both in utter disconnect from the real world of practical science.

* I pointed out through highlights that the article in question reports in part on Minnich's lab work. He tried to go on the further rabbit trail that "only" Fig 2 seems to be coming out of his lab work [neatly omitting that a lot of lab work often goes into a little bit of reporting], not noticing that that is in itself enough to make my point that there are such things as Scientists working in the design paradigm who are doing lab based research that is relevant to tests of the design inference.

* He also tried to suggest that the material identified and excerpted was just assertions, not cogent evidence. So, I took the time to lay out the context of the debate as just noted [with onward links] and to highlight the underlying issue: the origin of FSCI and IC in living systems, especially at cellular level.

* In particular, I have pointed out that the reported findings of fact in the article -- i.e. public domain information -- include that the TTSS is expressed by implementing a subset of the present but inactive set of genes for the flagellum. That means that the code for the flagellum embeds a secondary program for creating the TTSS as in Y pestis etc.

* Such code reuse is one of the highest forms aod the art of writing software at machine code level, as I know from observation and experience of writing such software for far less sophisticated systems.

* Indeed, the implied constraint that the genes for the flagellum include code for an unexpressed subprogram to drive creation of the TTSS which appearsin bacteria that use only a part of the code in the whole, itself is a mind-boggling challenge for NDT-style mechanisms to account for the complexity without appealing to foresight.

* I therefore challenged him that it is he and his party who have a huge, unmet burden of proof so the attempt to shift that burden is out of order, especially since he is insistent in refusing to address the issue in the main for the thread: abusive commentary -- which he further exemplified there and here.

* Next, this is what Mr Minnich claims to have done in his lab and in analysis based on that lab work, in outline:

>>Abstract: . . . Our interest in the Yersinia centers on the coordinate genetic regulation between flagellum biosynthesis and virulence TTSS expression. Y. enterocolitica, for example operates three TTSSs (motility, Ysa, and Yop), but each is expressed under defined mutually exclusive conditions. Y. pestis has lost the ability to assemble flagella (the genes are present on the chromosome) and expresses only the Yop system at 37oC, mammalian temperature. Using a combination of microarray analysis, genetic fusions, and behaviors of specific engineered mutants, we demonstrate how environmental factors influence gene expression of these multigene families, where the influence is exerted within each system, and propose why segregating these systems is critical for the organism. Our model further offers an explanation as to why an important subset of human pathogens has lost motility during their histories >>

* On the flagellum and the algorithmic processes, he reports:

>>The rotary engine comprising the bacterial flagellum has been studied as a model for organelle development and assembly. Approximately 30 genes are involved in coding for its individual parts with another 10 genes regulating expression and assembly and 10 more for sensory perception or chemotaxis. These 50 genes constitute roughly one percent of the Escherichia coli or Salmonella typhimurium genome, a modest but significant information investment. . . . . Viewed as a whole, the flagellum is a true nanomachine of remarkable complexity in structure and assembly control. This macromolecular machine self-assembles [which is relevant to the issue on the TTSS as seen below] and repairs, displays assembly control and processing, operates with two gears, is fueled by proton motive force, and the apparatus is ‘hardwired’ to a sensory apparatus that functions on short term memory (chemotaxis). Rotor speeds for E. coli are estimated at 17,000 rpm but motors of some marine vibrios have been clocked upwards of 100,000 rpms [2]."

* on the TTSS:

>>In the early 1990s, several observations intimated the reciprocal temperature requirements of flagellar biosynthesis and Yop expression were more than coincidental effects. In the dissection of the mechanism of temperature regulation, Rohde et al. [4] isolated several spontaneous mutants that showed loss of motility and Yop synthesis suggesting regulatory coordination of these two disparate systems. Ramakrishnan et .al. [5], and Sanders et. al. [6] also found that the sequence of the Caulobacter crescentus flhA flagellar gene showed predicted sequence similarity to pYV-encoded LcrD. Soon thereafter another set of Caulobacter flagellar genes showed sequence similarity to additional ysc and lcr genes [7]. The common denominator for this association identified both sets of genes as required for protein secretion in each process, flagellar assembly or Yop secretion. It was this association that led to the recognition that virulence protein secretion and flagellar protein assembly involved similar mechanisms now classed as type III secretion systems>>

* On the hyp to be tested in his lab:

.. Before the separate parallel nature of the flagellar and Yop systems was dissected, our laboratory proposed that the simplest explanation for temperature regulation of these systems was a direct overlap in function. Thus, the flagellum in our view could be used not only as a propulsion machine, but a dedicated highly efficient protein secretory machine for the Yops . . . . This hypothesis was testable by the following predictions. [Cf U's remark!!!] First, nonmotile Y. pestis would also have to contain a set of flagellar genes, some of which would be expressed. Second, it predicted that both Y. enterocolitica and Y. pseudotuberculosis would maintain expression of a subset of flagellar genes even at the nonpermissive temperature (37oC) for motility. Finally, it suggested that a subclass of mutants should be defective in both Yop secretion and motility. Using genetic fusion with a reporter gene (lacZ) and northern blot assays, it was determined that at 37oC Y. enterocolitica continues to synthesize Class I and Class II flagellar genes. The loss of motility appears to be due to the immediate transcriptional arrest of Class III genes (25-30 fold repression) on exposure to 37oC [9]. A subset set of flagellar gene transposon insertionally inactivated genes were mapped to flagellar genes and also fail to secrete Yops. Finally, Y. pestis does contain a complete set of flagellar genes, and using RT PCR, some are transcribed [10] [Lab work stage 1] . . . . [After some back-forth on further issues and questions] Schneewind and co-workers [13] showed that TTSS proteins of plant pathogens were recognized and secreted by Y. enterocolitica and vice versa. This suggested that the secretory signal of TTS proteins was conserved across genera. Based on this observation, we came full circle back to our original hypothesis [i.e it had been in abeyance for a time, pending resolution of issues] of dual function of the flagellar basal body structure. Expression of multiple TTSSs in the same organism by mutually exclusive environmental conditions prevents cross contamination of secreted proteins. That is to say, if flagellum biosynthesis were expressed simultaneously with the Yop TTSS, flagellin monomers may be exported out the ‘needle-like’ structure as well as the flagellar basal body and vice versa in regard to Yops. Efficiency of both systems would suffer as a consequence.>>

* Further testing, lab work stage II in Minnich's lab, stage V overall if the work leading to the issues an then to the circling back are reckoned with :

>>To test the above hypothesis, a flagellin and two Yop genes (fleB and, yopD and yopM respectively) were cloned and fused to the inducible ptac promoter. By placing these plasmid constructs in various mutant strains lacking either a flagellum TTSS (flhD-, flhB-) or Yop TTSS (yscE-, pYV-), expression and secretion of FleB, YopM, and YopD could be examined under conditions when these proteins are not normally expressed . . . . As can be seen in Figure 2, it was found that FleB is indeed secreted by the Yop TTSS and even the Ysa TTSS (low temperature, high salt). Conversely, it has been shown that YopM is recognized by both the Ysa and flagellar TTSSs. The overall view of Y. enterocolitica type III segregation is illustrated in Figure 3.>>

* Thus, Minnich has done at least two relevant stages of lab work and is only reporting his latest findings in Fig 2, all in a context that rationalises why this is all relevant to the issues outlined above on the IC nature of the flagellum. In particular, we can see the ebb and flow of hypothesising, prediction, and testing across something like five stages of lab work, two in Minnich's lab, leading tot he conclusions summarised in the abstract as cited.

In short, TJ has again seriously misrepresented the situation, and unfortunately, has also repeatedly acted in an abusive fashion.

__________

Onlookers, take notice on the misleading and abusive rhetorical tactics being used by the advocates of Evo mat in this and other threads as has now been repeatedly shown. Observe that such tactics coming from that side of the debate are all too common – as many others have documented.

Then, use common sense in evaluating your own final conclusions on the matters in the main.

Note on this that there is a KNOWN routinely acting source of FSCI and IC, intelligent agents, and that the basic reason that it is being resisted on the case of life nanotechnology etc is that it challenges the underlying worldviews and agendas of evolutionary materialism which has been so bold as to try to redefine science in defiance of history and of related phil of sci issues, in terms of so-called methodological naturalism.

TKI

11:29 am  
Anonymous kairosfocus said...

A footnote:

IC -- defn:

>>DEMBSKI: "A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system's basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system."

BEHE: "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway." >>

In the case of TJ's strawman argument:

>>) A mousetrap is ‘irreducibly complex’
ii) A mousetrap was designed.
iii) The blood clotting cascade [note the shift in case] is ‘irreducibly complex’
iv) Therefore blood clotting was also designed.

But this is a fallacy. If X is like Y, then that just means that X and Y share some conceptual properties, perhaps in a quite limited way. It most certainly does not mean that X and Y have all the same properties. >>

COMMENTS:

1] A mousetrap is IC, containing a core set of mutually interacting parts, all of which are necessary to its proper function.

2] the flagellum or the blood clotting cascade, et c etc arguably contain similar IC cores [and note the point on CORE TJ, before rushing off to is it the Dolphin's blood clotting system. Onlookers, guess why he is introducing a new example not the flagellum . . . no prizes]

+++++++++

Suppressed points:

a] IC systems are well known in many cases, and are in every case where we do know the cause directly, are the product of intelligent agency. [Have a look at the price of car parts and computer components to see what I mean. Once you buy you are locked in if a key part goes bad. So I just spent 1/20th what I spent on a whole car for two minor parts, comparing shipping etc. And the parts in question were not actually part of the critical subsystems that make the car work or fail -- just one was annoying and the other could damage such IC core, namely engine, parts.]

b] The elements of the cascade are produced by cellular nanotechnology driven by algorithmic information stored in DNA

c] The required amount of FSCI to get the system as a whole is comfortably beyond the reach of chance and natural regularities in the scope of the observed cosmos; probably by thousands of orders of magnitude

d] We routinely use this criterion intuitively or explicitly in commonplace commonsense reasoning andin science, e.g in statistical inference on hypothesis testing

e] The reason why this is suppressed is that there is a worldview adn agenda at stake here, evolutionary materialism

++++++

3] Like mousetraps etc as an IC system on the evidence in hand, adn in light of the evidence on the source of such IC, the flagellum and the BC cascade etc adn a lot of other cellular nanotechnology, were probably the work of intelligent agents.

4] Such an inductive conclusion is subject to defeat by provision of further empirical evidence and/or the provision of sound corrective analysis on induction. That is, it is an inference to best explanation and is provisional as is the work of science in general.

I suspect hat TJ's summary of the "fallacy" takes on a very different colour now.

TKI

12:02 pm  
Blogger Tony Jackson said...

Kairosfocus: “But in fact I am not primarily addressing OOL, but the underlying common core issue in all of these things: the known origin of functionally specific complex information, FSCI and the special case, irreducible complexity,”

We’ve dealt with ‘irreducible complexity’ before, but what exactly is ‘functionally specific complex information’ (FSCI)?

When faced with a new concept that might be important in my field, I first ask my colleagues to find out what they think. So I did that today at tea time but nobody had even heard of ‘functionally specific complex information’.

OK, well next you could go to PubMed and see how many researchers are mentioning this concept in the published biomedical literature. Typing ‘functionally specific complex information’, I got nothing. Typing FSCI, I got four hits, none of them relevant (I don’t think ‘facial skin care index’ is quite what we’re after).

Ah, well, er...perhaps kairosfocus means ‘complex specified information’ which I remember William Dembski mentioning. This time on PubMed I got one hit. That was a review in the ‘Annual Review of Genomics and Human Genetics’. Unfortunately for kairosfocus, it was a thorough smack-down of creationism and the modern intelligent design movement - not exactly the ringing endorsement that I think he would like.

But maybe I’m still missing something. As I understand it, ‘complex specified information’ is something Dembski makes a big song and dance about based on his interpretation of a bit of mathematics called the ‘No-Free-Lunch Theorems’. I’m not a mathematician, so in these matters I think it’s sensible to be guided by what other mathematical experts think. In particular David Wolpert, who first derived the ‘No-Free-Lunch Theorems’, seems like a good person to consult.

What does he think of Dembski’s maths?

If you go to:

http://www.talkreason.org/articles/jello.cfm

You’ll discover that the answer is: ‘not much’.

4:22 pm  
Anonymous kairosfocus said...

Andrew & Onlookers:

Observe the continued refusal on the part of evo mat advocates to face serious ethical issues raised by their insistent misrepresentations of people and issues, sometimes to the level of slander or even workplace harassment and career busting. This should warn us that something very wrong is happening.

Observe also how often they fall silent on a topic once their rhetoric is exposed as fallacious, then rush on to the next objection or assertion, without responsible accountability for their too often uncivil tactics.

We should draw appropriate conclusions from such tactics.

Now, on points raised that are worth a further comment:

1] TJ: what exactly is ‘functionally specific complex information’ (FSCI)? . . . .[attempts to ridicule] . . . . well, er...perhaps kairosfocus means ‘complex specified information’ which I remember William Dembski mentioning.

Had TJ bothered to simply follow up links long since made copiously [I have explicitly given a phrase and given the abbreviation; so he has no basis for pretending that I am not using my own terms and giving opportunity to see what I mean by them . . . for shame, that's basic reading skills here!!!!], he would have seen my own discussion of what I have termed functionally specified, complex information is.

In effect, based on discussions in other threads in other blogs over the course of about a year, I found that by augmenting the commonly used ID term complex specified information in my discussion, I was able to clarify the core issue for those willing to learn.

Further to this, had he bothered to see what design thinkers have to say for themselves -- instead of following what is now plainly calculated rhetorically distorted misrepresentations [and talkorigins, talkreason, Wikipedia, NCSE, BCSE, ACLU and the like ilk are especially heinous offenders in this -- I am not impressed by TJ's use of such a link] -- he would have easily enough seen the following definition, in the very first featured article:

Specified Complexity is a dual-pronged criterion for objectively detecting the effects of certain types of intelligent activity without first hand evidence of the cause of the event in question.[1] It consists of two important components, both of which are essential for inferring design reliably. The first component is the criterion of complexity or improbability. The second is the criterion of specificity, which is an independently given, detachable pattern.

An onward link would have given more on the technical issues of definition of this key concept.

But, my own note on this is that the core idea is long since a commonplace from OOL research, going back to the early 1980's, as can be seen from TMLO, ch 8, by Thaxton et al (it is not even exclusively a design theorists' concept!).

2] TMLO, 1984, on Specified complexity:

I reproduce the relevant section of TMLO ch 8 in toto, as it is so tellingly relevant to exposing the longstanding misleading and distorting rhetorical games that are being played by those who have led TJ to imagine that pretending that FSCI/CSI is an ill-defined empirically empty concept, is a useful tactic in persuading the public to reject design thought:

>>Order vs. Complexity in the Question of Information

Only recently has it been appreciated that the distinguishing feature of living systems is complexity rather than order.4 This distinction has come from the observation that the essential ingredients for a replicating system---enzymes and nucleic acids---are all information-bearing molecules. In contrast, consider crystals. They are very orderly, spatially periodic arrangements of atoms (or molecules) but they carry very little information. Nylon is another example of an orderly, periodic polymer (a polyamide) which carries little information. Nucleic acids and protein are aperiodic polymers, and this aperiodicity is what makes them able to carry much more information. By definition then, a periodic structure has order. An aperiodic structure has complexity. In terms of information, periodic polymers (like nylon) and crystals are analogous to a book in which the same sentence is repeated throughout. The arrangement of "letters" in the book is highly ordered, but the book contains little information since the information presented---the single word or sentence---is highly redundant.

It should be noted that aperiodic polypeptides or polynucleotides do not necessarily represent meaningful information or biologically useful functions. A random arrangement of letters in a book is aperiodic but contains little if any useful information since it is devoid of meaning.

[NOTE: H.P. Yockey, personal communication, 9/29/82. Meaning is extraneous to the sequence, arbitrary, and depends on some symbol convention. For example, the word "gift," which in English means a present and in German poison, in French is meaningless].

Only certain sequences of letters correspond to sentences, and only certain sequences of sentences correspond to paragraphs, etc. In the same way only certain sequences of amino acids in polypeptides and bases along polynucleotide chains correspond to useful biological functions. Thus, informational macro-molecules may be described as being and in a specified sequence.5 Orgel notes:

Living organisms are distinguished by their specified complexity. Crystals fail to qualify as living because they lack complexity; mixtures of random polymers fail to qualify because they lack specificity.6

Three sets of letter arrangements show nicely the difference between order and complexity in relation to information:

1. An ordered (periodic) and therefore specified arrangement:

THE END THE END THE END THE END

Example: Nylon, or a crystal.

[NOTE: Here we use "THE END" even though there is no reason to suspect that nylon or a crystal would carry even this much information. Our point, of course, is that even if they did, the bit of information would be drowned in a sea of redundancy].

2. A complex (aperiodic) unspecified arrangement:

AGDCBFE GBCAFED ACEDFBG

Example: Random polymers (polypeptides).

3. A complex (aperiodic) specified arrangement:

THIS SEQUENCE OF LETTERS CONTAINS A MESSAGE!

Example: DNA, protein.

Yockey7 and Wickens5 develop the same distinction, that "order" is a statistical concept referring to regularity such as could might characterize a series of digits in a number, or the ions of an inorganic crystal. On the other hand, "organization" refers to physical systems and the specific set of spatio-temporal and functional relationships among their parts. Yockey and Wickens note that informational macromolecules have a low degree of order but a high degree of specified complexity. In short, the redundant order of crystals cannot give rise to specified complexity of the kind or magnitude found in biological organization; attempts to relate the two have little future.>>

Once the information in question is encoded in a linear sequence of discrete state elements, it can be assessed in terms of sparseness in the configuration space. For instance, DNA elements are 4-state [GCAT] and the chaining chemistry is essentially irrelevant to the information stored therein. That implies by basic digital analysis that an N-element DNA chain has information carrying capacity, 4^N. In practice, the DNA monomers are in part at least clustered in 3-element tricodons using a highly sophisticated and subtle code, which specify the 20 amino acids used in proteins and give certain control information e.g. start/stop.

3] ‘complex specified information’ is something Dembski makes a big song and dance about based on his interpretation of a bit of mathematics called the ‘No-Free-Lunch Theorems’.

Onlookers, observe the continued tone of misrepresentation and dismissal through here ridicule and distortion of the facts.

I observe in particular the insistence on dismissive reference to Mr Dembski and to the rhetorically deceptive conflation of two highly distinct movements, Design thought and Biblical Creationism.Mr Dembski, FYI, TJ, holds two relevant doctorates, in philosophy [relevant to science in crisis stages as Kuhn and Lakatos counsel us], and in Mathematics. He has given mathematical form to some of the ideas summarised in the above discussion, related to compressibility of digital strings to express complexity, and to also address functional specification and the inefficiency of random or otherwise undirected search strategies for such sparse functional and complex states.

The basic point is as noted long since [as is also quite plain from the simple discussion in TMLO as excerpted, cf the already repeatedly linked Trevors and Abel here and here for a more technical peer-reviewed discussion in the OOL and related contexts; one of which appears directly in of course Pub Med . . .], that functional states are so sparse in the configuration space that random walks or similar but modified blind searches end up in a consistent problem of that sparseness, so that there is no free lunch. That is, one cannot credibly count on lucky noise to generate information, nor can one credibly assert that absent demonstrative proof to the contrary one must assume that lucky noise best explains a case of complex, specified information. [Cf Dembski's recent discussions here [which addresses Wolpert's, Fogel's and MacReady's claims] and here and here on the more general issues on specification.]

In short, this is not a matter for the selectively hyperskeptical rhetoric of dismissal, driven by an underlying attitude of zealous contempt for those who differ with the secularist, evolutionary materialist agenda and worldview claims.

4] http://www.talkreason.org/articles/jello.cfm

What happens here is that Mr Wolpert seems to assume that only Bayesian inference is relevant to scientific work.

Unfortunately, in the real world it is Fisherian inference by elimination of null hyps that is far more common, and in fact the Bayesian approach is arguably -- cf Demsbski's discussion here -- derivative from it. In short, there is more than one side to a story,and dismissing ones interlocuter in the literature as speaking "jello" hardly counts as anything more than petty name-calling.

Let's go back to what has already been pointed out above:

* biofunctional states are quite sparse relative to the configuration space for reasonable length biopolymers.

* These bipopolymers exhibit functionally specified [and macroscopically observable -- works/doesn't] complex information. [That is, we see here that by comparison with the statistical weight of the random polymer macrostate, that of the biofunctional macrostate is tiny. This is the heart of the TMLO's stat mech based reasoning that leads to the not significantly different from zero equilibrium conc of such functional macromolecules in generous prebiotic soups, based on the relevant thermodynamics. Of course, as Brillouin showed (as linked and excerpted in an earlier thread now so tellingly abandoned by evo mat advocates who one so boldly dismissed thermodynamics issues until the issues were seriously addressed) and as Jaynes and others subsequently developed, there is a credible link between entropy and information.]

* That information is comfortably beyond the reach of chance plus necessity alone in the gamut of he observed cosmos, usually estimated at ~ 13.7 BY, 10^80 atoms, leading to a reasonable estimate of the number of quantum states accessible in that gamut [actually across the full estimated lifetime, about twice as long], ~ 10^150.

* Odds sufficiently beyond about 1 in 10^150 are credibly beyond the reach of chance and natural regularities acting alone, but entities exhibiting that sort of FSCI are routinely produced by intelligent agents. (Resort to the speculative quasi-infinite cosmos as a whole in which an array of sub cosmi have random physics and situations in which life can emerge and evolve by chance are quire obviously ad hoc metaphysical resorts to try to save an otherwise in trouble worldview; absent serious observational evidence we need not entertain such.)

On an inference to best explanation basis similar to that which we intuitively and routinely use when we infer that messages such as this post are produced by agents not lucky noise and the physics of the Internet generally, the credible best current explanation for the information-rich nanotechnology of life forms at cellular level is intelligent agency. [This of course assumes that we are not asserting the grossest of selectively hyperskeptical inconsistency.]

Similarly, the same inference to agency best explains the bodyplan level diversity of life forms in the current biosphere and across the fossil record.

Thirdly, this explanation is also credibly the best one for the fine tuned, life-facilitating cosmos we observe.

__________

It is obvious that we are dealing with the thought police mentality, and that the driving attitude of cynically manipulative contempt for the ill-informed, entertainment-drugged public leads evo mat advocates to systematically misrepresent movements, concepts, issues and persons, the latter to the point of not just ridicule based on strawman attacks but also even demonstrable unapologised for slander; sometimes, outright persecution.

This is irresponsible and uncivil conduct that is enormously damaging in the long run not only tot he reputation of science but to society itself.

Let us draw appropriate conclusions and beware of such men and their schemes,which will end in no good. Then, let us wake up, rise up and defend ourselves and our civilisation before it is too late.

TKI

6:10 am  
Anonymous merkur said...

"Andrew & Onlookers... Then, let us wake up, rise up and defend ourselves and our civilisation before it is too late."

Hi, I'm one of the Onlookers. I just wanted to let you know that, not only did you lose this argument on points, but you also come across as being paranoid and pompous.

Oh, and by the way, I quite reasonably feel that referring to me as one of the "ill-informed, entertainment-drugged public" also identifies you as being patronising.

8:14 am  
Anonymous kairosfocus said...

Hi Merkur (and other onlookers):

I am sorry to see that you have taken offense at some of what I had to say; perhaps I should not have been as blunt as that. Sorry on my tone, which may indeed have been too cutting.

Howbeit, on substance: I think that on the merits, the issue of entertainment drugging of the culture is a major one, right up there with the tabloidising of news and the spin vs straight news and views problem.

Indeed, it may come as a surprise to you that the distinction between rhetorical level debating and critically aware dialogue [dialectic, in the old terminology] is the issue of level of preparation to address issues on comparative difficulties and the like. That has been so in western discourse since the days of Plato's Republic and Aristotle's the Rhetoric. Indeed, excerpting my intro lecture on a philosopher's toolkit in citing Ari, on how arguments work:

>>Aristotle, in his The Rhetoric[1], aptly but wryly observes:

"Of the modes of persuasion furnished by the spoken word there are three kinds. The first kind depends on the personal character of the speaker [ethos]; the second on putting the audience into a certain frame of mind [pathos]; the third on the proof, or apparent proof, provided by the words of the speech itself [logos]. Persuasion is achieved by the speaker's personal character when the speech is so spoken as to make us think him credible . . . Secondly, persuasion may come through the hearers, when the speech stirs their emotions. Our judgements when we are pleased and friendly are not the same as when we are pained and hostile . . . Thirdly, persuasion is effected through the speech itself when we have proved a truth or an apparent truth by means of the persuasive arguments suitable to the case in question . . . ."

Thus, a clear distinction has long since been drawn between persuasion by proof (or apparent proof) and that by appeals to emotions and/or to the credibility of an authority or speaker, not to mention, outright spin/propaganda tactics. Since, there is a common tendency to either blindly follow emotions or authorities on the one hand, or else to -- equally blindly -- dismiss them when they do not tell us what we wish to hear on the other, it is worth pausing to remark further on this pattern of appeals to ethos, pathos, and logos . . .>>

I see also your comment as an onlooker, that in your opinion, I have lost on the points.

I suspect, though, that other onlookers (some of whom may be intimidated by the sort of brutal rhetoric that has marred discussion in this blog) may have a very different view than you do.

To see why, why not summarise and post just what points I have made that have failed, just why; giving credible onward links. (In short, open refereeing only, please: you are not God with a right to simply rule with finality but no explanation. Even God, at least in the Judaeo-Christian tradition, often explains himself.)

Then, finally, you have accused me of paranoia.

Perhaps, you have not monitored several recent threads to see just why I have made a point of highlighting a major ethical problem, especially this one where the blog owner had to take up the issue of abusive commentary and slanderous namecalling himself.

Then, compare what has been going on in the threads here and here, and come back to me on whether or not my call for recognising and admitting abuse, apologising for it and turning from it are warranted or no. Also, observe that it is not just repeated insistent slanders and misrepresentations, but up to and including supporting evident workplace harassment and career busting, as was just linked of those who have oin any serious way challenged or -- in this case -- simply published a peer-reviewed ID supportive article. (Notice BTW, how there has never been an admission of serious wrongdoing by the evo mat advocates across these threads, including this one, in which the misrepresentations and slanders continue.)

After that, come back to me on the paranoia question again. Or, do you APPROVE of the tactics being used by the evo mat advocates?

I trust that this is helpful to you and to other onlookers.

Cheerio

TKI

11:02 am  
Anonymous merkur said...

You might want to go back and read my post. I said that you come across as being pompous and paranoid, not that you are pompous and paranoid. A subtle distinction, sure, but there you go.

However I will continue to accuse being patronising. "It may come as a surprise to you..."? Please spare me.

12:44 pm  
Anonymous merkur said...

Apologies for the lapse in grammar in my previous post. Oh, and Kairofocus - the link to that article on WorldNetDaily is broken, so could you repost it?

I love WorldNetDaily, but mainly because it's such a transparently poor excuse for "journalism". My most favoritest article was the one that claimed that Soy is making kids 'gay'.

12:51 pm  
Blogger Tony Jackson said...

kairosfocus, with respect to Dembski's maths, why do you think it is that none of my biochemist colleagues are using ideas like ‘functionally specific complex information’ or ‘complex specified information’ in their research?

I suppose that you’d say we biochemists just don’t understand cutting edge mathematics or that we’re deliberately ignoring or even censoring such work because it threatens our precious theories. But in that case, you should ask yourself why Dembski has similarly failed to convince his fellow mathematicians. After all, they have no emotional attachment to the theory of evolution, yet most mathematicians regard Dembski in the same way that most biochemists regard Behe.

Could it be that both Dembski and Behe are not only wrong in their details, but worse, they are actively promoting serious misunderstandings?

Here’s a short article in ‘The Mathematical Intelligencer’, Vol. 23, No. 4, pp. 3-8. (2001) entitled: ‘How anti-evolutionists abuse mathematics’.

http://www.math.jmu.edu/~rosenhjd/sewell.pdf

Note in particular this bit from the final section:

“When scientists are presented with subjects that invoke the terminology of science to defend nonsense, like astrology or creationism, they use the term pseudoscience. I suggest we need a similar term, pseudomathematics perhaps, to describe mathematical formalism, used to promote bad arguments.”

5:51 pm  
Anonymous kairosfocus said...

Onlookers:

Let's begin with a fresh illustration.

A glance at the presentation of a current Sci Am article by famous OOL researcher Robert Shapiro will serve very well indeed to highlight the pattern of misleading icons and assertions commonly met with in popular and even semi-popular literature on evolution:

1] The article prominently features a photo of the Miller-Urey "icon" with a caption that reads in part: "The famous Miller-Urey experiment showed how inanimate nature could have produced amino acids in Earth's primordial atmosphere . . ."

--> Of course, it has long been pointed out that the reducing atmosphere used in the 1953 experiment [convenient for the chemistry required] is implausible for the early earth's atmosphere, e.g. by Wells in the early 2000's, and of course in details in the TMLO that Mr Shapiro gave such a respectful review to in 1984.

--> Indeed, in the very same article in Sci Am, Shapiro makes the telling acknowledgment: some writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case . . . . inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life. (When larger carbon-containing molecules are produced, they tend to be insoluble, hydrogen-poor substances that organic chemists call tars.) I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

--> In short, there ias an obvious gap between the detailed article, 8 pp in the online version, and the easy to see photo and caption. That looks a lot like spin rather than straight dope to me. The rhetorical premise being, that more will look at the caption than at the article in details. Somehow, responsibility to the truth is lost in the shuffle.

3] Shapiro then goes on to a withering review of most OOL research to date, including the basic implausibilities of the popular RNA world. Then, he makes an interesting acknowledgment, in listing requisites for his metabolism first relatively simple molecules proposal, on the requisites for life: A boundary is needed to separate life from non-life . . . . n energy source is needed to drive the organization process . . . . A coupling mechanism must link the release of energy to the organization process that produces and sustains life . . . . A chemical network must be formed, to permit adaptation and evolution . . . . The network must grow and reproduce

--> Observe the distinction between order and ORGANISATION that appears, and the need for an energy coupling mechanism. These are of course precisely where the big challenges are, and are precisely the points long made by the despised Creationists and ID thinkers. Indeed, they are often mocked for making points very similar to this distinguished OOL researcher – as e.g. Happens with Granville at the hands of his critical reviewer in the Mathematical Intelligencer, ands as Tj cites with approval. .

--> In particular, let us observe: Shapiro's unmet challenge amounts to getting to energy converters that implement the algorithmic, information-driven processes of life by lucky noise. [He applies this same knife to other scenarios, but seems unaware that it speaks with force to his own case too . . .]

4] This comment in the sci am piece is thus rather inadvertently ironic: The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

In short, we see that the issues I have pointed out, and the problems over misleading rhetoric, are real.

Now, on points worth a few comments:

1] M: No response on the merits, just more rhetoric and attempted ridicule.

The Cashill link? This is the report by Cashill, on the Sternberg case - I seem to have inadvertently clipped off a digit, apologies.

Here is the Congressional report, and here is the appendix with facts, esp. the telling emails. Also, the OSC letter. (I think the investigative news report in question backed up by a staff report for the chair of the relevant Congressional oversight sub committee and the report of an official investigation is a bit different from say Mr Rutz' personal comments in an opinion column.)

Similarly, Mr Klinghoffer's report in that trashy tabloid, Jerusalem Post, makes interesting reading, as did his original article in that fish-wrapper, Wall Street Journal.

The issue in short is not going to go away through dismissal rhetoric.

2] TJ: I suppose that you’d say we biochemists just don’t understand cutting edge mathematics or that we’re deliberately ignoring or even censoring such work because it threatens our precious theories.

First, fact-check: some qualified biochemists are using FSCI in their work. For instance, it so happens that Mr Behe, onlookers, is a biochemist. He is in fact, Professor Biochemistry Department of Biological Sciences at LeHigh university, PA, USA.

And since Mr Behe's book is the most famous on the Irreducible Complexity [IC] concept, which TJ made reference to above, we can take it that TJ knows that Behe is by qualification and professorial appointment in a credible university, precisely a biochemist. TJ is in effect begging a very big question here by resorting to the classic No True Scotsman fallacy or a kissing cousin thereof.

IC is of course, explicitly a form of the same issue of complex specified information I have adverted to and others, a great many others.

Similarly, one may wish to look at the Trevors and Axe peer-reviewed journal papers as repeatedly linked, here and here.

These last raise the specific problem of getting to algorithmic information and the associated complex chemical nanotechnology of life by in effect lucky noise, and show why such a proposal is maximally unlikely to succeed.

In short, TJ is here implicitly slandering Mr Behe and others, as not being "real" biochemists. He is as is now patently usual, studiously avoiding the matter on the real merits and is resorting instead to a subtle form of the abusive rhetoric of dismissal, namecalling and ridicule.

3] http://www.math.jmu.edu/~rosenhjd/sewell.pdf

And, here is Sewell's original piece and his reply to his critics is here. An inspection of the back-forth will readily show that the issue is not the one-sided caricature that TJ imagines and has linked. Just ask yourself, who is indulging in dismissive rhetoric based on namecalling and general claims of authority and who is actually dealing with the central questions on the merits?

The article TJ links is based on a classic literature bluff making reference to a vast darwinian lit but not engaging the precise issue of accounting in detail and not by just so stories for the FSCI actually observed in the evidently IC systems of nature. It also fails utterly to realise that the problem starts long before we get to life forms, with the sort of issues that Shapiro summarises above which have led to the current impasse where there is no robust and credible theory of OOL on the premise of chance plus necessity only in plausible pre-biotic scenarios.

Onlookers, observe again the ad hominem tactics that are being used quite generally to try to poison the atmosphere of the discussion.

In short there is a serious issue here,one that Shapiro acknowledged in the current article above on getting to life forms, the need for getting a coupling mechanism to convert energy into organisation, which implies the set of issues I have raised.

4: Citing the paper: “When scientists are presented with subjects that invoke the terminology of science to defend nonsense, like astrology or creationism, they use the term pseudoscience. I suggest we need a similar term, pseudomathematics perhaps, to describe mathematical formalism, used to promote bad arguments.”

A capital example of the name-calling rhetoric of dismissal.

Onlookers, observe carefully: the serious issues are simply being ducked and dodged behind a cloud of personalities and namecalling.

That is precisely the issue that I have raised in speaking to the obvious and persistent ethical breakdown that characterises the evolutionary materialist advocacy we are seeing in the general and even professional literature.

We must do a lot better than this. Or, eventually, the public backlash is going to be terrible, and will not do the reputation of science in general any good..

_____________

Finally, observe that I have long since repeatedly invited serious addressing of an introductory survey that I have linked through my name in EVERY post in this blog. To date, no response on the merits.

What should that tell the fair-minded onlooker on the balance of the real case on the merits?

Cheerio

TKI

9:26 am  
Anonymous kairosfocus said...

H'mm:

I think a PS is in order, given that TJ refers to himself above as "we" in the context "biochemists."

I presume that implies he has domne one or more thermodynamics courses as a part of the chemistry part, so should b eable to address the below -- which I have raised in the earlier thread on the second law and which is the precise point I link in my name in every post:

_________

From my page Info Design & Science, Appendix I:

On Thermodynamics, Information and Design

1] TMLO: In 1984, this well-received work provided the breakthrough critical review on the origin of life that led to the modern design school of thought in science. The three online chapters, here, should be carefully read to understand why design thinkers think that the origin of FSCI in biology is a significant and unmet challenge to neo-darwinian thought . . . .

2] But open systems can increase their order [NB I am using the terminology where OS imports both mass and energy, closed ones energy only, isolated ones neither]: This is the "standard" dismissal argument on thermodynamics, but it is both fallacious and often resorted to by those who should know better. My own note on why this argument should be abandoned is:

a] Clausius is the founder of the 2nd law, and the first standard example of an isolated system -- one that allows neither energy nor matter to flow in or out -- is instructive, given the "closed" subsystems [i.e. allowing energy to pass in or out] in it. Pardon the substitute for a real diagram, for now:

Isol System:

| | (A, at Thot) --> d'Q, heat --> (B, at T cold) | |

b] Now, we introduce entropy change dS >/= d'Q/T . . . "Eqn" A.1

c] So, dSa >/= -d'Q/Th, and dSb >/= +d'Q/Tc, where Th > Tc

d] That is, for system, dStot >/= dSa + dSb >/= 0, as Th > Tc . . . "Eqn" A.2

e] But, observe: the subsystems A and B are open to energy inflows and outflows, and the entropy of B RISES DUE TO THE IMPORTATION OF RAW ENERGY.

f] The key point is that when raw energy enters a body, it tends to make its entropy rise. For the injection of energy to instead do something useful, it needs to be coupled to an energy conversion device.

g] When such devices, as in the cell, exhibit FSCI, the question of their origin becomes material, and in that context, their spontaneous origin is strictly logically possible but negligibly different from zero probability on the gamut of the observed cosmos.

h] Now, certain bodies have in them energy conversion devices: they COUPLE input energy to subsystems that harvest some of the energy to do work, exhausting sufficient waste energy to a heat sink that the overall entropy of the system is increased. Illustratively:

| | (A, heat source: Th): d'Qi --> (B', heat engine, Te): -->

d'W [work done on say D] + d'Qo --> (C, sink at Tc) | |

i] A's entropy: dSa >/= - d'Qi/Th

j] C's entropy: dSc >/= + d'Qo/Tc

k] The rise in entropy in B, C and in the object on which the work is done, D, say, compensates for that lost from A. The second law holds for heat engines.

l] However for B since it now couples energy into work and exhausts waste heat, does not necessarily undergo a rise in entropy having imported d'Qi. [The problem is to explain the origin of the heat engine -- or more generally, energy converter -- that does this, if it exhibits FSCI.]

m] There is also a material difference between the sort of heat engine [an instance of the energy conversion device mentioned] that forms spontaneously as in a hurricane [directly driven by boundary conditions in a convective system on the planetary scale, i.e. an example of order], and the sort of energy conversion device found in living cells [the DNA-RNA-Ribosome-Enzyme system, which exhibits massive FSCI].

n] In short, the root problem is the ORIGIN of such a FSCI-based energy converter through causal mechanisms traceable only to chance conditions and undirected [non-purposive] natural forces. This problem yields a conundrum for chem evo scenarios, such that inference to agency as the probable cause of such FSCI -- on the analogy of the cases where we do directly know the causal story -- becomes the better explanation. As TBO say, in bridging from a survey of the basic thermodynamics of living systems in CH 7, to that more focussed discussion in ch's 8 - 9:

While the maintenance of living systems is easily rationalized in terms of thermodynamics, the origin of such living systems is quite another matter. Though the earth is open to energy flow from the sun, the means of converting this energy into the necessary work to build up living systems from simple precursors remains at present unspecified (see equation 7-17). The "evolution" from biomonomers of to fully functioning cells is the issue. Can one make the incredible jump in energy and organization from raw material and raw energy, apart from some means of directing the energy flow through the system? In Chapters 8 and 9 we will consider this question, limiting our discussion to two small but crucial steps in the proposed evolutionary scheme namely, the formation of protein and DNA from their precursors.

It is widely agreed that both protein and DNA are essential for living systems and indispensable components of every living cell today.11 Yet they are only produced by living cells. Both types of molecules are much more energy and information rich than the biomonomers from which they form. Can one reasonably predict their occurrence given the necessary biomonomers and an energy source? Has this been verified experimentally? These questions will be considered . . . [Bold emphasis added. Cf summary in the peer-reviewed journal of the American Scientific Affiliation, "Thermodynamics and the Origin of Life," in Perspectives on Science and Christian Faith 40 (June 1988): 72-83, pardon the poor quality of the scan. NB:as the journal's online issues will show, this is not necessarily a "friendly audience."]

3] So far we have worked out a classical view of the subject. But, to explore such a question, we need to look at the microscopic level. Happily, there is a link from macroscopic thermodynamic concepts to the microscopic, molecular view of matter, as worked out by Boltzmann and others, leading to the key equation:

s = k ln w . . . Eqn.A.3

That is, entropy of a specified macrostate [in effect, macrsocopic description or specification] is a constant times a log measure of the number of ways matter and energy can be distributed at the micro-level consistent with that state [i.e. the number of associated microstates; aka "the statistical weight of the macrostate," aka "thermodynamic probability"]. The point is, that there are as a rule a great many ways for energy and matter to be arranged at micro level relative to a given macro-state. That is, there is a "loss of information" issue here. Thence, we can see that if we do not know the microstates, we have to more or less treat the micro-distributions of matter and energy as random, leading to acting as though they are disordered. Or, as Leon Brillouin, one of the foundational workers in modern information theory, put it in his 1962 Science and Information Theory, Second Edition:

How is it possible to formulate a scientific theory of information? The first requirement is to start from a precise definition. . . . . We consider a problem involving a certain number of possible answers, if we have no special information on the actual situation. When we happen to be in possession of some information on the problem, the number of possible answers is reduced, and complete information may even leave us with only one possible answer. Information is a function of the ratio of the number of possible answers before and after, and we choose a logarithmic law in order to insure additivity of the information contained in independent situations [as seen above in the main body, section A] . . . .

Physics enters the picture when we discover a remarkable likeness between information and entropy. This similarity was noticed long ago by L. Szilard, in an old paper of 1929, which was the forerunner of the present theory. In this paper, Szilard was really pioneering in the unknown territory which we are now exploring in all directions. He investigated the problem of Maxwell's demon, and this is one of the important subjects discussed in this book. The connection between information and entropy was rediscovered by C. Shannon in a different class of problems, and we devote many chapters to this comparison. We prove that information must be considered as a negative term in the entropy of a system; in short, information is negentropy. The entropy of a physical system has often been described as a measure of randomness in the structure of the system. We can now state this result in a slightly different way:

Every physical system is incompletely defined. We only know the values of some macroscopic variables, and we are unable to specify the exact positions and velocities of all the molecules contained in a system. We have only scanty, partial information on the system, and most of the information on the detailed structure is missing. Entropy measures the lack of information; it gives us the total amount of missing information on the ultramicroscopic structure of the system.

This point of view is defined as the negentropy principle of information [added links: cf. explanation here and "onward" discussion here -- noting on the brief, dismissive critique of Brillouin there, that you never get away from the need to provide information -- there is "no free lunch," as Dembski has pointed out ; ->) ], and it leads directly to a generalization of the second principle of thermodynamics, since entropy and information must, be discussed together and cannot be treated separately. This negentropy principle of information will be justified by a variety of examples ranging from theoretical physics to everyday life. The essential point is to show that any observation or experiment made on a physical system automatically results in an increase of the entropy of the laboratory. It is then possible to compare the loss of negentropy (increase of entropy) with the amount of information obtained. The efficiency of an experiment can be defined as the ratio of information obtained to the associated increase in entropy. This efficiency is always smaller than unity, according to the generalized Carnot principle. Examples show that the efficiency can be nearly unity in some special examples, but may also be extremely low in other cases.

This line of discussion is very useful in a comparison of fundamental experiments used in science, more particularly in physics. It leads to a new investigation of the efficiency of different methods of observation, as well as their accuracy and reliability . . . . [From an online excerpt of the Dover Reprint, here. Emphases, links and bracketed comment added.]

4] This sort of thinking has led to the rise of a school of thought -- note, much spoken against in some quarters, but I think they clearly have a point -- that ties information and thermodynamics together. Robertson presents their case; in summary:

. . . It has long been recognized that the assignment of probabilities to a set represents information, and that some probability sets represent more information than others . . . if one of the probabilities say p2 is unity and therefore the others are zero, then we know that the outcome of the experiment . . . will give [event] y2. Thus we have complete information . . . if we have no basis . . . for believing that event yi is more or less likely than any other [we] have the least possible information about the outcome of the experiment . . . . A remarkably simple and clear analysis by Shannon [1948] has provided us with a quantitative measure of the uncertainty, or missing pertinent information, inherent in a set of probabilities [NB: i.e. a probability should be seen as, in part, an index of ignorance] . . . .

[deriving informational entropy, cf. discussions here, here, here, here and here; also Sarfati's discussion of debates and open systems here; the debate here is eye-opening on rhetorical tactics used to cloud this and related issues . . . ]

S({pi}) = - C [SUM over i] pi*ln pi, [. . . "my" Eqn A.4]

[where [SUM over i] pi = 1, and we can define also parameters alpha and beta such that: (1) pi = e^-[alpha + beta*yi]; (2) exp [alpha] = [SUM over i](exp - beta*yi) = Z [Z being in effect the partition function across microstates, the "Holy Grail" of statistical thermodynamics]. . . .[pp.3 - 6]

S, called the information entropy, . . . correspond[s] to the thermodynamic entropy, with C = k, the Boltzmann constant, and yi an energy level, usually ei, while [BETA] becomes 1/kT, with T the thermodynamic temperature . . . A thermodynamic system is characterized by a microscopic structure that is not observed in detail . . . We attempt to develop a theoretical description of the macroscopic properties in terms of its underlying microscopic properties, which are not precisely known. We attempt to assign probabilities to the various microscopic states . . . based on a few . . . macroscopic observations that can be related to averages of microscopic parameters. Evidently the problem that we attempt to solve in statistical thermophysics is exactly the one just treated in terms of information theory. It should not be surprising, then, that the uncertainty of information theory becomes a thermodynamic variable when used in proper context [p. 7] . . . .

Jayne's [summary rebuttal to a typical objection] is ". . . The entropy of a thermodynamic system is a measure of the degree of ignorance of a person whose sole knowledge about its microstate consists of the values of the macroscopic quantities . . . which define its thermodynamic state. This is a perfectly 'objective' quantity . . . it is a function of [those variables] and does not depend on anybody's personality. There is no reason why it cannot be measured in the laboratory." . . . . [p. 36.]

[Robertson, Statistical Thermophysics, Prentice Hall, 1993. (NB: Sorry for the math and the use of text for symbolism. However, it should be clear enough that Robserson first summarises how Shannon derived his informational entropy [though Robertson uses s rather than the usual H for that information theory variable, average information per symbol], then ties it to entropy in the thermodynamic sense using another relation that is tied to the Boltzmann relationship above. This context gives us a basis for looking at the issues that surface in prebiotic soup or similar models as we try to move from relatively easy to form monomers to the more energy- and information- rich, far more complex biofunctional molecules.)]

5] What is the result of applying such a view of the link between entropy and information to the issue of the suggested spontaneous origin of life? TBO in CH 8 set up a model prebiotic soup, on a planetary scale, with quite generous unimolar concentrations of the required amino acids [L-form only] to give rise to a hypothetical, relatively simple 100-link, 101-monomer biofunctional protein. This yields -- through basic equilibrium of chemical reaction thermodynamics and the Brillouin information measure which contributes to estimating the relevant Gibbs free energies (and with some empirical results on energies of formation etc) -- an expected protein concentration of ~10^-338 molar, i.e. far, far less than one molecule per planet. (There may be about 10^80 atoms in the observed universe, with Carbon a rather small fraction thereof; and 1 mole of atoms is ~ 6.02*10^23 atoms. ) Recall, known lifeforms routinely use dozens to hundreds of such information-rich macromolecules, in close proximity in an integrated self-replicating information system on the scale of about 10^-6 m.

6] Ch 9 extends the discussion by exploring different scenarios for gettig the required synthesis through spontaneous mechanisms, circa 1984: chance, prebiotic "natural selection," self-ordering tendencies, mineral catalysis, nonlinear non-equilibrium processes, experimental thermal synthesis, solar energy, energy-rich condensing agents, and energy-rich precursor molecules. The results are uniformaly fruitless as soon as degree of invcestigator involvement is reduced to a credible one relative to the proposed prebiotic type environment. In the twenty or so years since, the manner of addressing the issue has generally shifted towards discussing information and probabilities more directly: complex, specified information, probability filters, etc., but the result is still more or less the same. (Cf. the recent peer-reviewed, scientific discussions here and here, by Abel and Trevors, in the context of the origin of the molecular nanotechnology of life.)

7] In short summary: thermodynamics issues tied to the second law are both relevant and strongly adverse for the proposed spontaneous [chance + necessity only] origin of life in prebiotic conditions; rhetoric to the contrary notwithstanding. But, at he same time, we know that FSCI, the key factor in driving that adverse thermodynamics, is routinely produced by intelligent agents. Thus, based on what we do directly know about the source of FSCI in every case where we observe or experience its origin, the origin of the FSCI-rich nanotechnologies of life in the cell is best explained as the product of agency. (The further issue of identification of the agency/agencies directly or indirectly involved, of course, is not currently within the ambit of science, proper. A suggestive clue, however is to be found in the similarly fine-tuned observed comsos, which is "set" so that biological life as we know it becomes possible . . . )

________

THis is of course closely related tothe issues logn since raised by TBO in TMLO, by Granville inthe above linked, and by Dhapiro as linked and excerpted currentrly.

TJ seems to have the qualifications to address them. Let us therefore hear his response on the merits.

Cheerio

TKI

10:12 am  
Blogger Tony Jackson said...

Gordon, you’ve surpassed yourself. I reckon those last two posts amount to 4,678 words – which is a record even for you.

For your own sake, try not to be prolix.

“famous OOL researcher Robert Shapiro”.

Are you trying to insinuate that Robert Shapiro supports ID? I have a copy of ‘Origins’, his book on the origin of life. Although he does have issues with current origin of life scenarios (he’s an advocate of the minority ‘metabolism first’ school of thought) he’s resolutely anti-creationism or any other form of supernaturalism.

“some qualified biochemists are using FSCI in their work. For instance, it so happens that Mr Behe, onlookers, is a biochemist. He is in fact, Professor Biochemistry Department of Biological Sciences at LeHigh university, PA, USA.”

If you go to the Lehigh Department of Biological Sciences web site, you’ll see that each member of the faculty has an individual page devoted to their particular research interests, their lab members (ie graduate students and post-doctoral researchers etc), funding and a publication list. Almost every member of the Lehigh faculty runs an active lab and generates publications in good-quality peer-reviewed scientific journals.

However, there is one glaring exception. If you look at Michael Behe’s page, you’ll get a very different impression. There’s just some old-hat about mousetraps. Tellingly, there’s no mention of students or post-docs. His publication list consists of 11 references, but only one of these is to a published scientific paper (done three years ago, and that was a rather poor mathematical model of protein evolution thoroughly discredited at the time).

That’s it as far as the science goes. He’s padded-out the rest of the references with his book, philosophical stuff about ID, and even popular articles in the New York Times!

The claim that Behe is “using FSCI” in his research is false, because Behe isn’t doing any current research.

4:40 pm  
Blogger Tony Jackson said...

And by the way, your second post is a classic example of exactly the point Jason Rosenhouse was making in his article in the Mathematical Intelligencer about ‘pseudo-mathematics’.

Look, your gibberish is an example of misdirection. Nowhere in the Laws of Thermodynamics will you find any reference to the mechanisms involved in any “energy conversion device.”

With respect to the origin of life: At this point, the origin of life is indeed a mystery. I don’t know how life got started (and neither by the way do you).

In science, it’s OK to say: “we don’t know”. But to just throw our hands up and say “therefore Goddidit” is to change the rules of the game half way through the match.

4:42 pm  
Anonymous kairosfocus said...

Onlookers:

Observe again the Sci Am excerpt from Shapiro, an outstanding OOL researcher, on the pre-requisites for life:

>>A boundary is needed to separate life from non-life . . . . An energy source is needed to drive the organization process . . . . A coupling mechanism must link the release of energy to the organization process that produces and sustains life . . . . A chemical network must be formed, to permit adaptation and evolution . . . . The network must grow and reproduce >>

In short, energetics and the issues that link to energetics are critical to the move from pre-biotic chemistry to life. And, the central issue of that energetics is that the energy influx to the process must be coupled to ordering and/or shaft work, not simply dumped into the system, which will simply lead to an increment in entropy, i.e. disorder, by virtue of positive signs on the d'Q and T terms in ds >/= d'Q/T; as Clausius discussed long ago. Further to this, for that ordering and/or shaft work to occur, there must be an exhausting of energy to a heat sink that allows compensation for the injection of energy into the entity containing the energy converter. And so, when such an energy converter exhibits functionally specific, complex [often irreducibly so] information -- especially algorithmic processing steps -- then we have reason to note that the only directly known source of such FSCI is intelligent agents, and that "lucky noise" is not a credible substitute for that.

Why? Because precisely, the relevant odds of getting to such FSCI by such lucky noise are maximally low relative to the probabilistic resources of the observed cosmos. (The only semi-credible escape from this is the resort to the quasi-infinite cosmos as a whole in which there are enough sub-cosmi to swamp the odds; but that is a departure from observationally anchored science into what is arguably an ad hoc metaphysical philosophical patchwork.]

Indeed,this is the apparent context of the OOL Foundation's put-up or shut-up prize offer:

>>"The Origin-of-Life Prize" (hereafter called "the Prize") will be awarded for proposing a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. To win, the explanation must be consistent with empirical biochemical, kinetic, and thermodynamic concepts as further delineated herein, and be published in a well-respected, peer-reviewed science journal(s).
The one-time Prize will be paid to the winner(s) as a twenty-year annuity in hopes of discouraging theorists' immediate retirement from productive careers. The annuity consists of $50,000.00 (U.S.) per year for twenty consecutive years, totalling one million dollars in payments . . . .

Applicants must provide
A. a well-conceived, detailed hypothetical mechanism explaining how the rise of genetic instructions sufficient to give rise to life as defined in "Definitions" below might have occurred in Nature by natural processes, and an
B. empirical correlation to the real world of biochemistry and molecular biology - not just mathematical or computer models - of how the prescriptive information characteristic of all known living organisms might have arisen.
The mechanism must address four topics:
* The simplest known genome's apparent anticipation and directing of future events toward biological ends, both metabolic and structural;
* The ability of the genome to convey instructions, deliver orders, and actually produce the needed biological end-products;
* The indirectness of recipe-like biological "linguistic" message code - the gap between genotypic prescriptive information (instruction) and phenotypic expression. How did the first genetic instruction arise in its coded format prior to phenotypic realization of progeny from which the environment could select? If a protobiont's genetic code and phenotype were one and the same, how did such a simple system self-organize to meet the nine minimum conditions of "life" enumerated below under "Definitions"? How did stellar energy, the four known forces of physics (strong and weak nuclear forces, electromagnetic force, and gravity), and natural processes produce initial prescriptive information (instruction/recipe) using direct or indirect code?
* The bizarre concentration of singlehanded optical isomers (homochirality of enantiomers) in living things - how did a relatively pure population of left-handed amino acids or right-handed sugars arise out of a chemical environment wherein reactions ordinarily give rise to roughly equal numbers of both right- and left-handed optical isomers? >>

NB: The Abel of Trevors and Abel frequently mentioned above directs the Gene Emergence Project also underwritten by said foundation. Notice how TJ has consistently avoided addressing the remarks made by Trevors and Abel. I excerpt the abstract from one of the peer-reviewed papers, “Chance and necessity do not explain the origin of life“:

>>Where and how did the complex genetic instruction set programmed into DNA come into existence? The genetic set may have arisen elsewhere and was transported to the Earth. If not, it arose on the Earth, and became the genetic code in a previous lifeless, physical-chemical world. Even if RNA or DNA were inserted into a lifeless world, they would not contain any genetic instructions unless each nucleotide selection in the sequence was programmed for function. Even then, a predetermined communication system would have had to be in place for any message to be understood at the destination. Transcription and translation would not necessarily have been needed in an RNA world. Ribozymes could have accomplished some of the simpler functions of current protein enzymes. Templating of single RNA strands followed by retemplating back to a sense strand could have occurred. But this process does not explain the derivation of ‘‘sense’’ in any strand. ‘‘Sense’’ means algorithmic function achieved through sequences of certain decision-node switch-settings. These particular primary structures determine secondary and tertiary structures. Each sequence determines minimum-free-energy folding propensities, binding site specificity, and function. Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic e that is, it is programmatically and algorithmically organized and controlled.  2004 International Federation for Cell Biology. Published by Elsevier Ltd. All rights reserved.>>


Kindly bear that in mind as we look at TJ's responses to my remarks yesterday:

1] TJ: Are you trying to insinuate that Robert Shapiro supports ID?

Observe, TJ is here creating a handy accusatory strawman by putting words in my mouth that do not belong there.

I noted specifically from a context that makes it plain that Mr Shapiro is a metabolism first OOL researcher, commenting that his viewpoint is also subject to the stricture that he put up for the more popular RNA World scenario:

>>My introduction to his position: he makes an interesting acknowledgment, in listing requisites for his metabolism first relatively simple molecules proposal, on the requisites for life . . . [above cluster of Shapiro's preconditions follows] . . . .

Then, I excerpted further from Shapiro: >> The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck. >>

Notice, again, TJ's "standard" rhetorical ploy: attack the man instead of dealing with the issue, by misrepresenting the situation. That, again, on track record, is a major ethical challenge for the evo mat advocates. This is not mere paranoia, or what walks and talks/quacks like paranoia.

2] there is one glaring exception. If you look at Michael Behe’s page . . .

Again, notice the attack-the-man rhetorical ploy: in response to TJ's implicit accusation that Behe et al are not "true" biochemists [as "true" biochemists do not use FSCI in their work] , I noted that Behe is an example of a professor of Biochemistry at a credible university and plainly uses FSCI and its derivative concept, IC, in his work. That is I cited a specific empirical counter-example to a false and accusatory claim. (i also pointed to the work of Trevors and Abel, now excerpted above, which TJ of course ignores as that would not fit his purpose.)

Predictably, TJ rushes off track to accuse the man; this time, of being "unproductive." [In the background are two highly relevant factors that TJ does not report: (a) the censorship of access to publication for those working in an explicit ID frame, to the level of persecution of journal editors who break ranks [which from previous interaction, TJ excuses and indeed perhaps defends or approves]; (b) the basic fact that one does not become a professor without having a significant track record of professional publication -- especially if one is a controversial figure.)

In that context, a look at the relevant page will show that Behe has indeed got a list of selected -- i.e not exhaustive [TJ is reading into the evidence here] -- publications, including [with my bracketed notes – NB this focuses on his IC related work]:

>>Selected Publications

Behe, M.J. 2005. Design for Living. New York Times, February 7, p. A21. [Newspaper of record, USA]

Behe M.J., Snoke D.W. 2004. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci13:2651-2664. [Peer reviewed]

Behe, M.J. 2004. "Irreducible Complexity: Obstacle to Darwinian Evolution." In Debating Design: from Darwin to DNA, Ruse, M. and Dembski, W.A., eds., Cambridge University Press, pp. 352-370. [Peer reviewed]

Behe, M.J. 2003. "Design in the Details: The Origin of Biomolecular Machines." In Darwinism, Design & Public Education, Campbell, J.A. and Meyer, S.C. eds., Michigan State University Press, pp. 287-302. [Peer reviewed]

Behe, M.J. 2003. "The Modern Intelligent Design Hypothesis: Breaking Rules." In God and Design: The Teleological Argument and Modern Science , Neil Manson, ed., Routledge, pp. 277-291.

Behe, M.J. 2002. The challenge of irreducible complexity. Natural History 111, 74.

Behe, M.J. 2001. Reply to My Critics: A Response to Reviews of Darwin’s Black Box: The Biochemical Challenge to Evolution, Biology and Philosophy16, 685-709.

Behe, M.J. 2000. Self-Organization and Irreducibly Complex Systems: A Reply to Shanks and Joplin. Philosophy of Science 67, 155-162.

Behe, M.J. 1999. Teach Evolution—And Ask Hard Questions. New York Times, August 13, p. A21.

Behe, M.J. 1996a. Darwin Under the Microscope, New York Times, October 29, p. A25.

Behe, M.J. 1996b. Darwin’s Black Box: The Biochemical Challenge to Evolution, The Free Press, New York.>>

His DI Senior Fellow bio note states:

>>Michael J. Behe is Professor of Biological Sciences at Lehigh University in Pennsylvania. He received his Ph.D. in Biochemistry from the University of Pennsylvania in 1978. Behe's current research involves delineation of design and natural selection in protein structures.

In addition to publishing over 35 articles in refereed biochemical journals, he has also written editorial features in Boston Review, American Spectator, and The New York Times. His book, Darwin's Black Box discusses the implications for neo-Darwinism of what he calls "irreducibly complex" biochemical systems. The book was internationally reviewed in over one hundred publications and recently named by National Review and World magazine as one of the 100 most important books of the 20th century.>>

In short, he has a significant list of publications, and has made a significant impact on the intellectual climate, in the context of his background as a biochemist.

3] The claim that Behe is “using FSCI” in his research is false, because Behe isn’t doing any current research.

Let's see, folks: "It all depends on what the meaning of is, is." I would think, onlookers, that it should be plain that Behe is a credentialled Biochemist and uses FSCI in his work, whatever TJ may think of it -- and TJ is not exactly an objective, unbiased observer. That is the material fact. Further tot his, I have no good reason to doubt the self testimony in the resumes that Behe is continuing to do research, in the precise paradigm he announced. NB: research is not equivalent to publication, even if there are in fact no more recent published articles than 2004 on his account relating to IC, especially given the situation since – why, August 2004, with Mr Sternberg.

The complaint of censors and their applauders that high profile ID researchers are not breaking through their censorship since they made a horrible example – through workplace harrassment, attempted firing, slander and now demotion -- of a fair-minded journal editor who published an article that passed “proper peer review” by a panel of “renowned scientists,” is less than a genuine objection, methinks.

TJ, predictably is abusing a list of selected publications over the span of a bout a decade, to infer that Mr Behe is not doing any research currently. Then he jumps to the "support" of his earlier conclusion that presto, here we have proof that "no true biochemists" use the FSCI concept in their work. In short, No True Scotsman, classic form.

(He is also tellingly failing to observe that for instance the already linked work in the peer reviewed papers by Trevors and Abel etc are riddled with biochemistry that passed peer review.)

4] . . .your gibberish is an example of misdirection. Nowhere in the Laws of Thermodynamics will you find any reference to the mechanisms involved in any “energy conversion device.”

Excuse me -- have you done a first course in thermodynamics, at least far enough to get to the example no 2, the heat engine?

Are you aware that "engine" is of course directly related to the term, "engineering"?

That in turn, both are related to the concept "ingenuity," i.e an acknowledgment of the creative intervention of intelligent agents in the setting up of interesting and even paradigmatic exemplars in thermodynamics, namely, Sadi Carnot's studies of the C18 - early C19 steam engine? [Note the significance of the Carnot theorem on the efficiency of such a heat engine, which is a precursor to the issues that led to the concept of entropy.]

In short, instead of addressing the issue that, as Shapiro pointed out [along with a great many others], energy conversion is a relevant consideration in OOL, and that when the observed energy converters exhibit FSCI -- as opposed to the relatively simple convection structures in say a hurricane -- we have an origin of energy converter problem at stake, TJ resorts to personal abuse.

So, let the record reflect: when challenged to address the relevant thermodynamics and information generation challenged, TJ resorted to personal abuse and citation of an abusive advocate.

Indeed, let us observe what Mr Sewell -- note again TJ's usual absence of apology for slander -- had to tellingly say in his response to his critics, regarding Mr Rosenhouse [apparently one of the Darwinist advocates to be observed at the consistently over the top Panda's Thumb]:

>>One critic [Jason Rosenhouse, "How Anti-Evolutionists Abuse Mathematics," The Mathematical Intelligencer 23 , number 4, 3-8, 2001] wrote "His claim that 'natural forces do not cause extremely improbable things to happen' is pure gibberish. Does Sewell invoke supernatural forces to explain the winning numbers in last night's lottery?" But getting the right number on 5 or 6 balls is not extremely improbable, in thermodynamics "extremely improbable" events involve getting the "right number" on 100,000,000,000,000,000,000,000 or so balls! If every atom on Earth bought one ticket every second since the big bang (about 10^70 tickets) there is virtually no chance than any would ever win even a 100-ball lottery, much less this one. And since the second law derives its authority from logic alone, and thus cannot be overturned by future discoveries, Sir Arthur Eddington called it the "supreme" law of Nature [The Nature of the Physical World, McMillan, 1929].

Although it is true that we sometimes are not sure what the second law predicts, it is not true that there are so many macroscopically describable phenomena that the second law cannot be expected to hold when applied to all of them---there are relatively few macroscopically describable phenomena. It is not true, as the new argument asserts, that there are so many types of order that computers and TV sets need no explanation. >>

First, observe the very familiar terminology, misrepresentations and unwarranted accusatory inferences.

In short, we see just who is guilty of misdirection, and in addition of personal abuse. [Note: the mathematics involved in my remarks and in Sewell's remarks are NOT gibberish, as a consultation of the relevant texts in thermodynamics, classical and statistical, will immediately show. Similarly, the design inference as long since pointed out is to AGENCY in light of relevant empirical data, not "the supernatural." Nor, is it an appeal to ignorance, since we know full well the generally observed source of FSCI.]

Why such tactics by evo mat advocates?

Because the issue at stake is fatal for the underlying evolutionary materialistic claim: the cosmos, from hydrogen to humans can be explained on the basis of chance plus necessity only, without agency save as these emerged from the first two causal forces by evolutionary processes.

This will come out as we see TJ's onward remark . . .

5] At this point, the origin of life is indeed a mystery. I don’t know how life got started (and neither by the way do you).

In short, there is a major, unanswered anomaly for the evo mat cluster of evolutions: cosmological, chemical, macro-biological.

What is it?

That we have in life forms, sophisticated energy conversion devices based on FSCI stored in DNA and associated codes and algorithms implemented by sophisticated molecular machines. As a cluster, they implement a class of machine we have been able to analyse since the 1930s or so, but not to actually design and develop to date: a self-replicating, self-maintaining automaton.

It is the general argument of the evo mat view that life forms that embed this sort of system are the products of chance plus necessity only without agency, i.e. that they are the product of lucky noise and associated boundary conditions that accidentally obtained in the prebiotic world.

But, on examination of the details, there is a mounting pile of anomalies relative to the assumptions of evo mat, i.e it has a major factual adequacy problem as the spontaneous origin of such machines and systems is maximally improbable relative to the probabilistic resources on the scope of the observed cosmos.

But on the other hand, absent worldview and agenda-driven censorship and question-begging, we have a well-known source of FSCI, routinely directly observed to generate such specified complexity and associated irreducibly complex systems and fine-tumed tightly integrated systems. Namely, intelligent agents.

So,the claim to “ignorance” on the origin of FSCI is not innocent, it is the product of an intent to protect a worldview and associated scientific paradigm from effective challenge.

Absent that intent, the unprejudiced mind would have long since accepted the obvious: we have in the case of the nanotechnology of life, just that: a technology, the artifacts of the work of intelligent agency beyond our current -- but not conceivable [and thereby hangs perhaps the most ambitious scientific programme ever to be embarked upon!] -- capacity.

__________

Onlookers, it should be plain that the balance on the merits is simply not in favour of the evo mat advocates, and so they have resorted to the rhetoric of personal attack and misrepresentation.

That is an ethical challenge in the end, as the insistence by evo mat advocates -- and here they speak as advocates for a peculiar worldview, not scientists -- such a resort in the teeth of evident facts and their implications absent a prior worldview-level commitment and indeed question-begging shows that the approach is that of persuasion by any tactics, not serious open-minded dialogue towards scientifically credible truth.

Let us observe and learn from that habitual resort to attacking the messenger instead of addressing the issue on the merits, once their assertions were subjected to challenge on the merits.

Cheerio

TKI

7:16 am  
Anonymous kairosfocus said...

H'mm:

I think we should also explicitly address the insistent misrepresentation in:

TJ: In science, it’s OK to say: “we don’t know”. But to just throw our hands up and say “therefore Goddidit” is to change the rules of the game half way through the match.

1] The rhetoric of the accusatory strawman:

First, there is a very plain and public definition of Design Theory, already repeatedly linked. Here is the one from the Research ID wiki, in excerpt:

>>Intelligent design is the scientific investigation of intelligent causation and subsequent novel data, hypotheses, experiments, and practical applications that are derived by viewing specific phenomena in the universe as designed . . . .

Intelligent design (also known as "ID") proposes that specific physical phenomena in nature are better explained as being designed by intelligence. This is inferred by detecting the types of physical effects known to be produced by intelligent agents when they act. The goal is to understand intelligence working in the context of the physical world, and infer intelligent activity by observation and analysis of data . . . . Simply stated, ID asks, "Can we scientifically detect if something was designed by intelligence?"

Proponents of ID are compelled by physical evidence, seen through the application of induction, inference, and statistical probability, that detecting design is a scientific possibility, and this ability is essential for a proper contextual study of the universe.

Additionally, intelligent design has been applied in the form of working scientific hypothetical research programs by which novel data, hypotheses, experiments, and practical applications are derived by hypothetically viewing phenomena in the universe as designed, whether the researcher holds that the objects of study are actually designed or not.>>

That definition is explicit that inference to agency is just that: an empirically anchored inference that certain features of the observed world on reasonable criteria of inference, show themselves to be the artifacts of intelligent action. This is obviously and even explicitly not the same as inference to the supernatural, etc.

It is therefore an insistent, deliberate, and deceptive misrepresentation to keep on saying this in the teeth of the plain facts.

2] The Question-begging attempted redefintion of science:

TJ's remark "to change the rules of the game" is also extremely revealing. For, here, again he blunders into the history and philosophy of science, i.e we see here again the attempted redefinition of science as methodological naturalism, i.e. in effect that scientific thought must only infer ultimately to chance plus necessity as root causes.

But in fact, historically and even currently this is false to the praxis of science. Just to cite the most famous scientist of all time, Newton was a design thinker, and certainly was not in agreement with materialism, evolutionary or no.

Second, the imposition of the criterion that in effect we may only infer to chance plus necessity, especially on matters relating to origins of the cosmos and life, is an imposition of a question-begging definition, as I have long since repeatedly pointed out and linked. But, let us follow Plantinga this time around to see what is really going on:

* let us for argument accept that "science" is methodologically naturalistic, as a "rule" of the game. [BTW, set by whose authority? Is that definition beyond revision? What then of the vaunted self-critical nature of science?]

* Now, let us propose SIENZE, which is pronounced the same way, but which permits us to on a case by case basis empirically investigate causes in light of chance, necessity and agency, using relevant statistical etc techniques such as Fisherian hypothesis testing and probabilistic assessments.

* Why -- apart from reasons of worldview agendas -- should one prefer "science" to "sienze"? [In short, it is substance, not labels that count.]

3] The accusatory inference to God:

Isn't it interesting that so often evo mat advocates immediately infer that inference to agency on matters of origins is an inference to God? [Especially in a context where so many of them are staunch even fiery advocates of atheism, and wish to use evolutionary science as a prop for their worldviews . . . ?]

By sharp contrast, design theory is about whether intelligent agents leave empirically detectable traces, as we routinely infer in both common-sense and scientific contexts. For instance, as have repeatedly highlighted, we do not infer as the default that postings to this thread are lucky noise absent absolute proof tot he contrary. If a posting is sufficiently complex and functional in the communicative context, it is intuitively accepted as a product of an agent.

Design theory in effect makes a more systematic approach tot hat inference, and applies the principles to a certain similar case: the molecular nanotechnology of life, inter alia.

So what is going on here is that eh evo mat advocates are being inconsistent when it suits their worldview and agenda.

4] The science stopper accusation:

Why, specifically, should the defeatable inference that one or more intelligent agents have had something to do with the origin of he molecular nanotechnologies of life stop scientific work on such systems?

Wouldn't it rather stimulate efforts to reverse engineer life systems and apply the results to related classes of FSCI-using systems, e.g. starting with computers? (hasn't it also stirred up a current wave of attempts to empirically refute the inference, i.e the actions as opposed to the rhetoric shows that he inference to design is falsifiable in principle but obviously not in fact to date.)

And, if the inference were that eh agent in question can be identified with the God of the theistic worldviews, given the distinguished track record of theistic scientists across the ages and even currently [i.e up to the level of Nobel Prize winners; indeed isn't eh inventor of the gene gun a YEC, yet alone an ID thinker?], why would that be a science stopper?

4] That's giving up . . .

In effect TJ asserts that the only credible inferences to causal forces on matters of origins are to chance + necessity. That is we are looking at worldview level question-begging.

But in fact, the three causal forces stand at the same epistemic status as explaining influences. Taking an example from my online notes:

* heavy objects tend to fall under the natural regularity we call gravity.

* if the object in question is a die, it will tumble in effect at random to a face from the set {1,2,3,4,5,6}.

* If the die is being tossed as part of a game, then intelligent agents are using chance and natural regularities to pursue their goals.

--> Plainly, each of these three causal/explanatory factors is relevant to the situation!

--> Plainly, each adds something more to our understanding!

--> Plainly, each is a relevant causal factor, and the "giving up" would be on the part of one who insisted that we cannot bring to bear he traces that point to a game being played!!!!!

--> Let us recall the classical view that causes lie in efficient, material, purposive and originating/agent forms. That is agents can act to effect an outcome in pursuit of a goal, taking advantage of the materials and forces and phenomena of nature in so doing. The agents originate, they actuate the outcome, they do this in pursuit of a goal, and they use the material conditions of nature in that pursuit. Each of these four is a causal factor.

___________

In short, we again see the usual breakdown on the merits and the usual misrepresentations and accusations. Rhetoric not serious dialogue.

TKI

8:35 am  
Anonymous merkur said...

Kairofocus: you've clearly misunderstood my point, so I'll lay it out clearly:

1. You continually appeal to onlookers like me to consider your arguments.
2. Your arguments are presented in a way that makes them difficult to read, difficult to comprehend once read, and difficult to accept because of your patronising style.

I am suggesting that you try to present your arguments in a different manner, otherwise you are unlikely to win over onlookers like me who are interested in learning more about these issues.

8:49 am  
Blogger Tony Jackson said...

I stand by what I said about Behe. Indeed, you make my case for me by reprinting his so-called publication list from his departmental site. Remember, this is supposed to be a selected list of academic publications. Citing articles from the New York Times, when other faculty members can happily quote their papers in Nature, Science or PNAS smacks to me of desperation on Behe’s part.

It isn’t ad hominem to point this out. On the contrary, scientists make these judgements calls all the time to assess someone’s productivity.

And what am I supposed to conclude from the Trevors and Abel paper in ‘Cell Biology International’ other than the origin of life is a very difficult problem indeed? I knew that already - which is why I choose not to work in that field:-).

Incidentally, I notice D.L. Abel gives his affiliation as something called ‘the Origin of Life Foundation’, which I’ve never heard of before, but whose web site is careful to state:

“The Origin-of-Life Foundation should not be confused with "creation science" groups. It has no religious affiliations of any kind, nor are we connected in any way with any New Age, Gaia, or "Science and Spirit" groups. The Origin-of-Life Foundation, Inc. is a science and education foundation encouraging the pursuit of natural-process explanations and mechanisms within nature.” (my emphasis).

Re your thermodynamics. Tell you what Gordon, you write this all up and submit it to the ‘Journal of Theoretical Biology’ or even ‘Cell Biology International’. I’m perfectly, totally serious. If you really do believe you’ve got an important insight, then you’re simply wasting your time talking about it on this blog or on your web site.

The only way you’re going to get noticed by the wider scientific community is by dissemination in the peer-reviewed literature and that’s the honest bottom line.

Don’t be put off by the fact that you’re not at an academic institution. Remember, Einstein himself was a lowly patent clerk when he sent his manuscripts to ‘Annalen der Physik’…….

9:08 am  
Anonymous kairosfocus said...

Andrew:

I see, sadly, the issue of refusing to respect commenters has again come up on TJ's part. (Just possibly he did not mean it maliciously.)

Onlookers:

I will further remark:

1] M: You continually appeal to onlookers like me to consider your arguments.

M, "to consider" is not at all the same as "to dismiss" through rhetorical devices.

If in your opinion I have "lost on points," just how relative to the merits on fact and logic? [In other words, onlookers, if one side is cogently addressing on facts and logic, the other side does not "win" by making dismissive rhetorical appeals that major on ad hominems.]

That is not a question of style, but of substance. [M has it ever occurred to you that those who present their arguments by misrepresentations and slanders are a little more than merely condescending or “patronising”? Observe above and in previous threads just how often evo mat advocates have done that, and how often I and others -- up to and including the blog owner, have had to speak to it.]

3] TJ: I stand by what I said about Behe

In other words, you continue to insist that he, a PhD biochemist, working in the field to the tune of 35+ articles in the peer reviewed biochem lit, who has feathered in his faculty bio page a precis of his work in the area of ID, is not a case of a biochemist who is using the concept IC, and thus FSCI , in his work.

Sorry, that makes my case. (Besides, all of this is on a side issue based on yet another ad hominem.)

3] what am I supposed to conclude from the Trevors and Abel paper in ‘Cell Biology International’ other than the origin of life is a very difficult problem indeed?

Why, not just that, but that there is a basic problem with the chance + necessity argument, which is why this is a "difficult" field. Thus the peer reviewed abstract for the paper as just cited this morning reads:

>>Where and how did the complex genetic instruction set programmed into DNA come into existence? The genetic set may have arisen elsewhere and was transported to the Earth. If not, it arose on the Earth, and became the genetic code in a previous lifeless, physical-chemical world. Even if RNA or DNA were inserted into a lifeless world, they would not contain any genetic instructions unless each nucleotide selection in the sequence was programmed for function. Even then, a predetermined communication system would have had to be in place for any message to be understood at the destination. Transcription and translation would not necessarily have been needed in an RNA world. Ribozymes could have accomplished some of the simpler functions of current protein enzymes. Templating of single RNA strands followed by retemplating back to a sense strand could have occurred. But this process does not explain the derivation of ‘‘sense’’ in any strand. ‘‘Sense’’ means algorithmic function achieved through sequences of certain decision-node switch-settings. These particular primary structures determine secondary and tertiary structures. Each sequence determines minimum-free-energy folding propensities, binding site specificity, and function. Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic -- that is, it is programmatically and algorithmically organized and controlled. 2004 International Federation for Cell Biology. Published by Elsevier Ltd. All rights reserved.>>

In short, relative to what we do know, algorithmically functional information is an artifact of intelligent action. We see here just such algorithmic functionality, and so absent compelling reasons to the contrary, we would conclude that the relevant situation is an artifact of intelligent agency.

4] “The Origin-of-Life Foundation . . . is a science and education foundation encouraging the pursuit of natural-process explanations and mechanisms within nature.”

Yes indeed, and that means that it has put up a US$1 mn offer -- find such an explanation. It then requires addressing the precise questions that the design theorists are putting up on this topic: there is evidence that under other circustances we would and in fact routinely do ascribe to intelligent agency. So, if there is no existing solution and an unclaimed million dollar reward is floating out there long enough, why is there such an assertion that those who infer to the obvious are wrong to the point where it is routinely asserted that they are ignorant,stupid, insane or wicked?

5] Re your thermodynamics. Tell you what . . .. you write this all up and submit it to the ‘Journal of Theoretical Biology’ or even ‘Cell Biology International’.

First, you have again used my personal name without permission, Kindly desist.

Second, I claim no originality in what I have to say on the topic. (Indeed, I am making remarks around the 20+ year old TMLO, which BTW was quite favourably reviewed by Shapiro, on pretty much the same grounds that he in the Sci Am semi popular article has challenged the popular RNA world scenarios. Of course the same arguments also hold for his metabolism first alternative.)

Trevors and Abel in their two papers are saying pretty much the same [though at a higher technical level], and on the specifically thermodynamic side the points are straightforward applications and observations of basic thermodynamics. Indeed – though I think I would have used somewhat different terms [especially on isol/closed/open systems – tough some engineers seem to speak in his terms], Sewell is making the same basic point.

I have merely put up an introductory level survey that someone with basic college physics and chem and enough algebra can follow, perhaps with the aid of a basic primer on thermodynamics. (And yes the issue is not at the level of the classic intelligent 12 yo, more like the intelligent A level graduate in Math-Physics-Chem or the like, with help as noted..)

The underlying point is this: thermodynamics is relevant to energy converters including those that exhibit FSCI, so the "open systems can increase their order" claim is irrelevant to the core issue. For, right in the first example for the 2nd law, we see how merely dumping raw energy into a subsystem tends to increase its disorder. Then, energy converting subsystems which can use such energy have a coupling structure.

The point is that unlike hurricanes and Prigogine's dissipative structures in general, we are looking at FSCI rich systems. Their origin by chance + necessity only within the gamut of the probabilstic resources of the observed cosmos is maximally improbable.

And, that is long before we get to the censorship issue!

6] The only way you’re going to get noticed by the wider scientific community is by dissemination in the peer-reviewed literature and that’s the honest bottom line.

On this topic I have utterly no interest in being noticed by any peer reviewed community, nor do I claim any originality, just basic common sense to apply basic physics, and enough philosophical insight not to do something utterly foolish, like beg the question by imposing methodological naturalism.

(My peer reviewed papers have been on things like moving the Caribbean's industrial and associated technology and technology education base to a more likely to succeed one: mechatronics plus ICTs with a migration to mass customisation, or on renewable technologies vs energy efficiency and their likely potential in this region, or on education in the world of ICTs in that context, even on the sustainability paradigm as an ethical construct related to Kant's categorical imperative and Jesus' Golden Rule. The cluster is energy-technology-development-strategic change- and associated tertiary educational transformation in the sustainability paradigm.)

As to Einstein, he was in fact submitting papers to a NON-peer reviewed Journal, which Annalen was at the time. Four papers in 1905, each worth the Nobel Prize. [And the prize was NOT given for his relativity either!]

___________


I think the issue is clear enough for onlookers to see for themselves what lies at stake and that those who stand within the design paradigm are not just idiots or worse.

TKI

12:19 pm  
Blogger Tony Jackson said...

Alright, I’ll try one more time, very slowly. Believe me, I’m not being harder on Behe that I would be on any other scientist.

To fund our research, we scientists have to formally apply to grant bodies – say the Medical Research Council or whatever. The committee that decides whether to fund takes a number of factors into account – the scientific quality of the application certainly, but also the track record of the applicant is important too. The committee want to be sure that their money has a good chance of not being wasted. That’s why it’s important for active scientists to keep a consistent stream of publications going.

There’s nothing wrong with Behe writing articles for the New York Times, but when this happens at the expense, or instead of writing serious peer-reviewed papers in the scientific literature, then I for one conclude that Behe is no-longer interested in doing serious scientific research.

And frankly, Behe himself must know this too.

3:33 pm  
Blogger Smokey said...

Gordon wrote:
"Analogies often work, too; and have been enormously fruitful in science across the ages.

"Just one instance: it was Galileo's observation that Jupiter had an orbiting cluster of satellites, that materially helped make the Copernican sytem plausible."

In what way is that an analogy? Try to keep your answer to a single paragraph.

"This storage is used to generate the coding for protein molecules which have precise chains of monomers based on a 20-state element,..."

Absolutely false. Proteins are SYNTHESIZED with only 20 amino acids, but actually contain more than 20 amino acids. You see, some of the 20 are chemically modified by whole enzymatic pathways, a very, very stupid design, but exactly what we expect from evolution. Any intelligent designer would simply use one of the available codons to code for those other aas.

"... based on 3-letter DNA codons [64 possible states per codon, most of which code for varios amino acids . . . but include start/stop]..."

Wrong again, and your error reveals your inability to look for evidence of intelligent design vs. (variation + selection) x time.

Think about this (I know that you are incapable of doing so). Despite having 64 codons and only 20 amino acids, only one (AUG) starts translation (there are very rare exceptions) and at the same time, codes for methionine. AN INTELLIGENT DESIGNER WOULD NEVER DO SOMETHING SO OBVIOUSLY STUPID. Instead, evolution's fix for proteins that start with something other than methionine is to cleave it off after sythesizing a protein with it as the first aa residue.

Totally unintelligent, but you choose to ignore anything that doesn't fit your political view. Any intelligent designer would use one of the available codons as a start WITHOUT encoding an amino acid. That would allow the production of proteins without the Rube Goldberg mechanism of cleavage after translation.

" the flagellum or the blood clotting cascade, et c etc arguably contain similar IC cores [and note the point on CORE TJ, before rushing off to is it the Dolphin's blood clotting system. Onlookers, guess why he is introducing a new example not the flagellum . . . no prizes]"

Whales (not just dolphins) are missing one of the proteins that Behe regards as part of the core (the core bit is just a fallback because Behe, since embracing ID, is too lazy to produce any real data). If you'd like to do a little bit of learning, what about human hemopheliacs homozygous (or hemizygous) for NULL alleles at the loci encoding "core" clotting factors? Do they all have zero clotting activity, or is Behe full of it? Remember, only zero clotting activity will fulfill Behe's definition.

8:04 pm  
Anonymous merkur said...

Kairofocus: "First, you have again used my personal name without permission, Kindly desist."

This is just bizarre. Kairofocus, you continually link to your website - which has your personal name all over it. What grounds do you have for asking him to desist?

10:31 pm  
Anonymous kairosfocus said...

Andrew (and others):

Some round-up remarks are in order, as it is plain that the main point of this thread is over.

For, it is plain that the nanotechnology of life -- as Shpairo pointed out (in part inadvertently) is a major conundrum for the NDT-evolutionary materialist camp, but absent the imposition of their agenda it would have a very obvious explanation: agent action. And, that opens up a new vista for science, reverse engineering nature. Indeed, on the testimony of several clips and links above, that has already begun.

1] TJ: I’m not being harder on Behe that I would be on any other scientist.

This is of course a diversion of the thread, on a point where TJ thinks he can score points -- by attacking the man rather than addressing the issue. Behe is a qualified and practising biochemist who uses IC and thus FSCI in his work. Similarly, the Trevors and Abel papers are riddled with the issues of the biochemistry of life. Shapiro, of course, is a chemist and a metabilism first theorist (onlookers observe the want of an apology for an improper insinuation by TJ on this . . .), but in his discussion he adverts to essentially the same chemical and biochemical consisderations in the concept of complex specified, functional information. [And, in so doing he inadvertently exposes his own position to the same objection.]

The underlying issue, that the nanotechnolgy of the cell and a lot of other things in biology evince FSCI and/or IC a subset thereof, has not been seriously countered.

2] S: [on Galileo's Jovian moons] In what way is that an analogy?

Galileo observed Jupiter through a telescope and saw a main planetary body with four moons [the ones he could see] orbiting it. By analogy, he extended it to the solar system as a whole, with the sun in the centre and the planets including earth orbiting, as this was the model Copernicus had proposed.

Jupiter is not exactly a star, and moons are not exactly planets, but the fact of observing a Copernican-like system in the heavens had significant impact on the credibility of the Copernican view. It thus became one of the most famous arguments by analogy in science.

3] Proteins are SYNTHESIZED with only 20 amino acids, but actually contain more than 20 amino acids.

This is an irrelevancy, and in fact it adds to the complexity involved. (As do things like the oddball proteins that incorporate opposite chirality elements.)

That is, S, if the number of states in any one position of the amino acid chain of length N is greater than twenty as the base in the expression I used above, 20^N, becomes larger -- for illustration, say 25^N -- then that makes the configuration space much larger, given that N is of order 100 - 500 or so. 20^300 ~ 2.04*10^390, 21^300 ~ 4.63*10^396, That is, the latter configuration space is over 2 million times bigger than the former. I have been counting the space conservatively.

In short your rhetoric of dismissal backfires. For, that would make biofunctional states MORE sparse in the state-space of possible molecular chains.

4] Despite having 64 codons and only 20 amino acids, only one (AUG) starts translation (there are very rare exceptions) and at the same time, codes for methionine.

And, how does this contradict my statement: "based on 3-letter DNA codons [64 possible states per codon, most of which code for vario[u]s amino acids . . . but include start/stop"?

5] AN INTELLIGENT DESIGNER WOULD NEVER DO SOMETHING SO OBVIOUSLY STUPID . . . . Totally unintelligent, but you choose to ignore anything that doesn't fit your political view

Here we see the agenda: "I" wouldn't do it that way so it must be unintelligent. This is a classic non-sequitur. (FYI, designers usually face multiple constraints, some of which are not obvious and there is a classic problem of sub-optimisation whereby optimising on every feature in isolation creates an overall system that is sub optimal or even non-functional.)

It also utterly fails to address the basic point of the observed specified biofunctionality based on algorithmic processes and codes, which control the behaviour of the molecular machinery of the cell. In short,this is also a red herring distraction leading out to a strawman to be pummelled fallacy.

As to the notion that my view is a political one, that is simply a slander. My view is relative to what I know about functionally specified, complex information based on the common experience of humanity: it is in all cases where we observe the causal process directly, the signature of intelligent action. Absent imposition of a worldview of evolutionary materialism, it would be readily acknowledged that the far more complex cases in biosystems and in the finetuning of the cosmos too, point to similar intelligent action as their best explanation relative to what we do know and routinely use in common sense and in science. In short, S here indulges in a turnabout accusation, relative to the known institutional politics of science.

6] Whales (not just dolphins) are missing one of the proteins that Behe regards as part of the core (the core bit is just a fallback because Behe, since embracing ID, is too lazy to produce any real data)

Dolphins of course are generally regarded as a part of the wider whale family [e.g what are commonly called killer whales are dolphins], but that is even more besides the point.

The basic fact is that there is a question: multi-component multi step mechanisms in which the removal of certain steps, in isolation from the others, stops the process. That there are other steps that in other cases may be substituted or additional does not undercut this basic point.

In short, the real "politics" is being played by S, who knows full well that there are many biological systems which fit Behe's criterion, whether or not they or other similar cases have additional or alternate steps. The IC issue is, that there is a core to a given, i.e specific, process in which take one part or step out -- any one out -- and you stop the process. This is a fairly common feature of technologies, and biosystems are no exception.

Calling Behe lazy is simply a personal attack which only shows the underlying hostility; it does nothing to address the case on the merits. (It does of course help to further polarise the situation, through adding to the charged climate of contempt. As Aristotle warned, our judgements when we are pained and hostile are very different from those we make when we are pleased and friendly. But that hostility does not make our judgements any more likely to be sound; cf. above for cases in point!)

7] M: What grounds do you have for asking him to desist?

Have you considered that there is a basic and obvious difference between a relatively high traffic debate in a blog and a relatively low traffic reference site?

In the latter I have put enough that one may make contact for appropriate discussion.

FYI, I have learned through experience that putting up a layer of having to look up information makes a significant difference to spamming and even malware sending attempts. (FYFI, Just the stopping of the use of my name by H has made a significant difference, namely the wave of new "Creationist" spam observed once he started to maliciously use my name has now ceased. Due to past observation of the sending of malware and the situation with worm technology I of course took advantage of Yahoo's antispam features, so I cannot report on whether actual malware was involved this time. "Your" side of these debates has in it some really warped people, M. And on that you need to reflect on your own lack of seriously reflecting on the misbehaviour that is evident all over this thread from your side. Have a look in the comments here to see what that does to thoughtful people who get turned off by the ad hominems and worse.)

The effect I noted on probably has something to do with the old observation by newsmen that a jump line in a story costs you something like 25% of the readers of the first part of the story. It is most certainly not "bizarre," once you factor in human nature.

___________

It seems plain to me that this thread has long passed the point of diminishing returns. The above overnight comments, especially those by S, abundantly illustrate just why.

Cheerio

TKI

7:36 am  
Anonymous merkur said...

""Your" side of these debates has in it some really warped people, M."

With all due respect, you have no idea what "my" side of the debate is.

"And on that you need to reflect on your own lack of seriously reflecting on the misbehaviour that is evident all over this thread from your side."

I participate in a lot of online discussions, including acting as moderator for a number of online forums, and there is no evidence of misbehaviour on the part of the people you are calling "warped".

You also seem to have missed my main point. Since you have shown yourself to be fond of Aristotle, I will direct you to his Rhetoric, Book1, Chapter 2. You are generating neither the necessary ethos or pathos to convince the onlooker, and consequently your logos will go unheard, no matter how persuasive your arguments might be.

9:46 am  
Blogger Tony Jackson said...

In a previous post, we saw how new promoters for chloroplast genes freshly transplanted into the plant nuclear genome could evolve.

Well, bacterial genes also have promoters. In this case, the promoters have two features: a distinct sequence 10 or so bases from the start of the mRNA (so called -10 element) and another distinct sequence 35 or so bases from the mRNA start (so called -35 element). Both these elements have to be at approximately the right distance from each other for the whole promoter to work.

How likely is it do you think that we can evolve a new functional bacterial promoter starting just from DNA of random sequence? To find out, see:

Shumo Liu and Albert Libchaber

Some Aspects of E. coli Promoter Evolution Observed in a Molecular Evolution Experiment

Journal of Molecular Evolution, vol 62, pp536-550 (2006)

“Abstract: We devised a molecular evolution procedure to evolve E. coli promoter sequences and applied it to observe an arbitrary, nonfunctional sequence evolving into functional promoters. In the experiments, DNA sequence variations were generated with error-prone PCR and were inserted in the promoter region of the cat (chloramphenicol acetyl transferase) gene on a plasmid. Upon transforming the cells, functional promoters on the plasmid were selected according to the chloramphenicol resistance. Within a few cycles of mutation and selection, promoters emerged, and the sequences converged into a small number of groups. In the process, the extended minus 10 type of promoters emerged quickly, and small deletions were often involved in adjusting the length between the −35 and the −10 elements. Our results also suggest a possible selection for promoter stability against mutation.”

One experiment is worth a thousand words, wouldn't you say Gordon?

3:28 pm  
Blogger Smokey said...

Tony,

I'd have to disagree. Gordon's ratio of words to experiments is an order of magnitude or three higher than 1000.

In fact, the order of words to experiments (that involve the testing of ID hypotheses) in the ID movement is infinite. I've done more to test basic hypotheses (falsely presented as facts) underlying the ID movement than Behe, Dembski, and Minnich combined, just in the process of a completely different goal.

4:04 pm  
Blogger Tony Jackson said...

Ha! Agreed!

4:10 pm  
Anonymous paul said...

Tony .. thanks for your post. Cards on the table ...I'm a Christian and believe in a Creator. I hold this position by faith but I also believe that all scientific observations are in harmony with this view. I enjoy reading blogs such as this and delight in testing things (within my VERY limited knowledge). I believe that God originaly created living "kinds" (not sure what they all were !) and I have absolutey no problem in accepting mutation and natural selection whether it occurs in a laboratory and has an "intelligent" start or whether it occurs "on its own" in nature. However I do not believe the observable changes cross the boundaries of a "kind."... I am sure you disagree. And now to my question : Would the E-Coli cells -after the described changes - still have been regarded as E-Coli cells by experts in the field. This is not a trick question - it might be a stupid question because I am right out of my depth - but I am genuinely curious. Thanks in advance for taking the trouble to answer me. Paul

6:50 pm  
Blogger Tony Jackson said...

Hi Paul,

The neat thing about Liu and Libchaber’s paper (and similar work – there are other examples) is that the experimental set-up allows the researchers to record and track in molecular detail the step-by-step emergence of a new functional promoter from an initially random sequence of DNA (and if you think about it, you can’t get more detailed than that).

To put it another way, it shows how ‘new information’ appears in the genome as a result of the cumulative process of variation and selection. Of course, this is precisely the thing that Andy McIntosh and kairosfocus et al., so confidently assert is impossible. But then real scientists just quietly and methodically get on with their experiments, leaving the likes of McIntosh to blow hot air.

“Would the E-Coli cells -after the described changes - still have been regarded as E-Coli cells by experts in the field.”

Yes. Why is that a problem? It’s still an example of evolution.

“I believe that God originally created living "kinds" (not sure what they all were !) and I have absolutely no problem in accepting mutation and natural selection whether it occurs in a laboratory and has an "intelligent" start or whether it occurs "on its own" in nature. However I do not believe the observable changes cross the boundaries of a "kind."...

What is a “kind”? This concept is not mentioned in any evolutionary biology textbook, or in any of the course work on evolution we teach to undergraduates at my university.

I'm afraid that “Kind” is a made-up word that has no biological meaning. And what are these "boundaries"? By what mechanism do they work?

9:48 pm  
Blogger Smokey said...

Gordon wrote:
"For, that [the fact that proteins contain far more than 20 aa residues, unknown to Gordon] would make biofunctional states MORE sparse in the state-space of possible molecular chains."

Gordon, my point has absolutely nothing to do with state-space. It has everything to do with the intelligence of the assumed design in the mechanisms by which these extra residues end up in their positions.

"And, how does this contradict my statement: "based on 3-letter DNA codons [64 possible states per codon, most of which code for vario[u]s amino acids . . . but include start/stop"?"

Because the start is in the same category as the amino acids, not in the same category as the stop codons as you claimed. This is junior high-level molecular biology. And again, there is no intelligent basis for the start signal to be methionine, as many proteins are nonfunctional when the amino-terminal residue is methionine.

"Here we see the agenda: "I" wouldn't do it that way so it must be unintelligent."

No, we ALL agree that these ways are unintelligent. If the leaders of the ID movement sincerely believed that these could be explained by intelligence, you wouldn't be so laughably ignorant of them--they would be featured prominently in ID religious dogma.

"This is a classic non-sequitur. (FYI, designers usually face multiple constraints, some of which are not obvious and there is a classic problem of sub-optimisation whereby optimising on every feature in isolation creates an overall system that is sub optimal or even non-functional.)"

None of that gobbledygook applies in either of the two cases I presented. The intelligent modification to the existing system is obvious. Evolution ignores the obvious.

"It also utterly fails to address the basic point of the observed specified biofunctionality based on algorithmic processes and codes, which control the behaviour of the molecular machinery of the cell."

On the contrary--these are cases in which the "observed specified biofunctionality based on algorithmic processes and codes" would obviously be the intelligent, readily available choice, but the intelligent choice wasn't made.

This is why ID proponents lack the courage to make and test predictions from their hypotheses. Instead, they lie and claim that hypotheses that they are afraid to test have the status of theories.

"In short,this is also a red herring distraction leading out to a strawman to be pummelled fallacy."

It is neither. If you claim to see intelligent design in biology, your challenge is to demonstrate why not coding for a bunch of aas makes sense, given the large number of slots available in the code. You also have no intelligent explanation for why every protein should start with a methionine (given that many amino-termini are cleaved off by baroque enzymatic mechanisms), when having a start signal that allows any amino-terminal residue would be so easy to do.

"As to the notion that my view is a political one, that is simply a slander. My view is relative to what I know about functionally specified, complex information based on the common experience of humanity: it is in all cases where we observe the causal process directly, the signature of intelligent action."

Then why don't you explain why the two cases that I brought up represent intelligent choices, while explaining why you grossly misrepresented them?

"Dolphins of course are generally regarded as a part of the wider whale family [e.g what are commonly called killer whales are dolphins],..."

Your ignorance of systematics is as huge as your ignorance of the very molecular biology that you claim to know was intelligently designed.

"The basic fact is that there is a question: multi-component multi step mechanisms in which the removal of certain steps, in isolation from the others, stops the process."

But blood clotting is not one of those, because removal of most of the components does NOT stop the process. You don't know this because you are lazy, and Behe knows this.

"That there are other steps that in other cases may be substituted or additional does not undercut this basic point."

I didn't say anything about substituted or additional steps, Gordon. I wrote only about missing steps that did not result in stopping the process.

That you would choose to misrepresent what I wrote speaks volumes about your character.

"The IC issue is, that there is a core to a given, i.e specific, process in which take one part or step out -- any one out -- and you stop the process."

And blood clotting is not one of those processes. It's as simple as that.

"This is a fairly common feature of technologies, and biosystems are no exception."

It's the exception, not the rule, in biology.

"Calling Behe lazy is simply a personal attack which only shows the underlying hostility; it does nothing to address the case on the merits."

The merits of a scientific case boil down to conducting tests of one's hypotheses. Behe has failed to do that in more than a decade; therefore, he is either lazy or has renounced science itself.

3:53 am  
Anonymous Paul said...

Tony,

Many thanks for taking the trouble to respond. Much appreciated and I do want to try and get my head round the “new information” point in your post. You asked me whether I thought that the fact that the E-Coli cells were still E-Coli cells after the described changes. Absolutely no problem at all. It is an example of evolution within E-Coli cells. I simplistically view it as a laboratory equivalent of , say dog breeding where scientists have tinkered – used in the engineering sense and not the meddling sense – with the cells and got some new characteristics .. except it’s more obvious when it’s done by dog breeders !

You also asked what is a “kind” and pointed out that the word is not defined in any evolutionary biology textbook. I think you’ll generally find uncertainty amongst sources that would be sympatheic to a Christian viewpoint as well. Indeed Tony, I bet if you were to play “devil’s advocate” you would arrive at a better definition than I could ! Useful website I found on biblical kinds was : http://creationwiki.org/Created_kinds

Again thanks for replying and I shall continue to read these blogs and think through the issues raised. Paul.

8:49 am  
Anonymous kairosfocus said...

Hi Andrew and others . . .

This thread looks like anything but winding down to a close; though it seems that the substantial issue is plain: OOL and related microbiology within the chance + necessity only frame is in deep trouble.

I therefore, again, draw our attention to Shapiro's recent remarks on the state of OOL research and the core issues it faces [noting that I think, for good reason, his own metabolism first proposal is subject to he same strictures]:

>>A boundary is needed to separate life from non-life . . . . An energy source is needed to drive the organization process . . . . A coupling mechanism must link the release of energy to the organization process that produces and sustains life . . . . A chemical network must be formed, to permit adaptation and evolution . . . . The network must grow and reproduce . . . .

The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.>>

Observe too, on tone that to date, TJ has yet to apologise for his attempt to insinuate that I had claimed that Shapiro was an intentional ID supporter. Par for this track, I am afraid . . . S's remarks just above make that lapse look trivial.

Now, on points worth a note, and welcoming Paul to the back-forth, and his point that the case being headlined is all within E coli is of course quite relevant:

1] M: you have no idea what "my" side of the debate is.

M, when you jump all over me for an alleged attitude, claim that I have "lost on points" without substantiation and fail to address the issues with the other side on tone and the merits, it is fairly clear that you are not a neutral and balanced onlooker – until evidence emerges that plainly shows otherwise.

FYI, slander is misbehaviour, especially when one repeatedly calls people liars or worse, without warrant. Not to mention seeking to violate privacy of commenters, inviting spam attacks or worse. This has happened in the threads that lie behind this one. Just follow the links given earlier, especially to the one where the blog owner had to remark on the problems with comments.

As to "Warped." I am particularly referring to the pattern of behaviour of NCSE and several other advocacy groups who insistently misrepresent the truth and slander those who question Darwinian orthodoxy, now up to the level of career busting, as already linked and discussed.

Finally, the cluster of debaters int his forum hardly represents an audience amenable to ethos or pathos from the other side, given the perception that such are inevitably ignorant, stupid, insane or wicked. I am presenting the logos as that is what will in the end tell.

2] TJ: How likely is it do you think that we can evolve a new functional bacterial promoter starting just from DNA of random sequence?

Observe, again, the shift in subject to a more convenient topic. (It is not irrelevant to first of all note that the specific claimed case in point of apparent IC is of course the flagellum, not the protein chain described in the cited research. Is this a strawman being pummelled? Nah, couldn't be!)

Next, as the abstract describes, this is of course, a cherry-picked, intelligently manipulated case -- "We devised a molecular evolution procedure" [intelligently directed evolution, anyone? . . . h'mm, where does that point?]. So, coming our the starting gate, this does not address the fundamental issues starting from OOL and embracing the issues of Macro-level, body-plan shaping biodiversity -- WITHOUT intelligent intervention.

For, the sites were picked,the inserted "arbitrary" [not quite the same as random] sequences were picked and then the selecting environment was picked. All, by highly intelligent investigators, using highly sophisticated machinery, also designed by intelligent agents.

We are also long since at the case of E coli, i.e. in the regime of life forms with error correcting mechanisms. This may well be reflected in their onward observations: the extended minus 10 type of promoters emerged quickly, and small deletions were often involved in adjusting the length between the −35 and the −10 elements. Our results also suggest a possible selection for promoter stability against mutation.

Then, also, are we in the threshold of complexity beyond the range of say a configuration space of 10^150 or so, i.e the Dembski type limit? [That would require, on a crude calculation, about 250 4-state monomers in the GCAT chain, about an order of magnitude more than the numbers being cited in the abstract and by TJ. 4^35 ~ 1.2*10^21, a vastly smaller configuration space than that for just 250 elements.)

Notice, finally, that once life forms exist, we are long since in rather sparse and concentrated regions of the configuration space, i.e we have long since passed into FSCI.

Repeat: how do you get to such FSCI, starting from in effect chemical noise in prebiotic environments?

Then, how do you get the further major FSCI increments to create new, core-level body plans for tightly integrated systems?

To that, we will find no answer, apart from the honest reflections of Mr Shapiro or the like.

3] S: the order of words to experiments (that involve the testing of ID hypotheses) in the ID movement is infinite

Yet another repetition of an already disproved slander, cf above on the Behe--> Miller -> Minnich case. (For, infinity is the ultimate trend of a/b as b --> 0.)

Further to this, the issue is that we are now in the field of information, S. In that field we know a lot and have a vast body of experinece on information and noise. Sufficiently complex signals have never been observed to emerge out of noise. That is why I have put up the basic challenge: get a million PCs, rig their floppies to spew Zener noise across the disks and test for a properly formatted signal once every 30 seconds, for a year. That would give 10^12 tests. [This is of course an updated form of the million monkeys test.]

The ID prediction: no cases of properly formatted functional signals would emerge. The proof: this is the way we would expect to deformat the disks, not program them. Indeed, Uncle Bill over in Redmond does not write software that way – contrary to t he persistent rumours; i.e he and his works are living proof that suboptimal design is still design and is intelligently arrived at – let us not equivocate the term intelligence.

That is, once we see that this is an information problem, there is no shortage of empirical data/tests on point.

4] my point has absolutely nothing to do with state-space. It has everything to do with the intelligence of the assumed design in the mechanisms by which these extra residues end up in their positions.

On the contrary, if you are asserting that the amino acids have more than 20 possible states [even more if chirality is brought in] then you explode the configuration space. That is, you make the biofunctional states that much more sparse.

In the case of a 300 monomer chain, moving from 20 to 21 state elements, causes the space to expand by a factor of about 2 millions, comparable to t6he ration of the length of a mile and quarter race to the thickness of an old fashioned sixpence.

In both cases,the configuration states are so vastly beyond 10^150, that we can comfortably assert that on the gamut of the observed cosmos, they would never be likely to be arrived at by chance. That its the basic OOL problem, and it is the basic problem of body plan level evolution. Neither has been solved on the basis of chance plus necessity alone, and the case being shown as illustrative above is --as ever since Darwin -- a case of ARTIFICIAL selection.

5] Start/stop sequences in DNA chains.

I simply noted that DNA uses three letter codons which by and large encode for the 20 amino acids [mostly] used in life forms, and include some procedural ones too i.e. start/stop. Since I am accused in effect of being utterly ignorant even at high school level, let us use some basic reference materials, commonly used at high school level or the like to see what is going on there:

Last time I checked WIkipedia on this, DNAsequences were recorded as having three-letter start codons:

>>ATG and AUG denote sequences of DNA and RNA respectively that are the start codon or initiation codon encoding the amino acid methionine (Met) in eukaryotes and a modified Met (fMet) in prokaryotes . . . . Three nucleotide bases code for one amino acid in the genetic code. Usually the first three bases of the coding sequence(CDS) of mRNA to be translated into protein are AUG (or ATG in DNA). AUG encodes for methionine, and therefore the first amino acid of many proteins is methionine. The start codon is almost always preceded by an untranslated region 5' UTR.

Very rarely in higher organisms (eukaryotes) non AUG start codons are used.

In addition to AUG, alternative start codons, mainly GUG and UUG are used in prokaryotes. For example E. coli uses 77% ATG (AUG), 14% GTG (GUG), 8% TTG (UUG) and a few others. >>

On stop codons:

>>DNA sequence indicating gene end: a sequence of three chemical units base pairs linking complementary strands of DNA or RNA that indicates the end of a protein synthesis. The three stop codons are thymine-adenine-guanine, thymine-adenine-adenine, and thymine-guanine-adenine.
>>

This attempt to misrepresent the facts and distort what I said to attack me shows precisely the kind of "warped" mentality and "abusive" commentary I discussed above.

6] No, we ALL agree that these ways are unintelligent . . . . If you claim to see intelligent design in biology, your challenge is to demonstrate why not coding for a bunch of aas makes sense, given the large number of slots available in the code.

Okay, let's see . . .

We have an algorithmic coding system, which is rated by many as pretty optimal, and we have a sophisticated nanotechnology that uses that algorithmic information to implement a class of systems we cannot even design yet, and hope to reverse engineer, and that system is unintelligent, because you do not like how start/stop is coded for?

7] ID proponents lack the courage to make and test predictions from their hypotheses. Instead, they lie and claim that hypotheses that they are afraid to test have the status of theories.

All of this is repeated in the teeth of a specific case documented above, with Behe --> Miller --> Minnich, involving something like two phases of testing in Minnich's lab out of by my count five stages of lab work, and that under of course the ID frame.

This is insistent slander in the face of patent facts, pure and simple.

8] why don't you explain why the two cases that I brought up represent intelligent choices

There is a term for this sort of rhetoric, given the already brought out and unaddressed issues on FSCI and IC: straining at gnats while swallowing camels.

As Shapiro pointed out, there IS a major get-to-biofunctional information from molecular noise problem, starting from the prebiotic situation. It is further complicated by the issue of body plan level macroevolution. That, as onlookers can easily enough see for themselves, is utterly unanswered.

But, the misrepresented issue of the start and stop codons is raised as if it were a rebuttal on the merits! [The codons exist and they function algorithmically.)

Onlookers may find Behe's comments on the blood clotting cascade here interesting, e.g. his introductory point:

>>Since my book came out, as far as I am aware there have been no papers published in the scientific literature giving a detailed scenario or experiments to show how natural selection could have built the system . . . . Professor Doolittle argued that new laboratory work showed two components of the blood clotting cascade could be eliminated ("knocked-out") from mice and the mice got along fine without them. However, Doolittle misread the laboratory work: the double knock-out mice have severe problems and have no functioning blood clotting system. They are not models of evolutionary intermediates . . . .

Although embedded in a lengthy description of how blood clotting and other systems work, Professor Miller's actual explanation for how the vertebrate clotting cascade evolved consists of one paragraph. It is a just-so story that doesn't deal with any of the difficulties the evolution of such an intricate system would face. Even so, in the one paragraph Miller proposes what looks like a detrimental or fatal situation, akin to the knock-out mice (above) that lack critical components . . . .

Keith Robison proposed that a cascade might begin with a single enzyme with three different properties. Upon duplication of the gene for the enzyme, the duplicate loses several of the properties, resulting in a two-component cascade. Repetition of the scenario builds cascades with more components. Although intriguing, the scenario starts with a complex, unjustified situation (the enzyme with multiple abilities) that already has all necessary activities. What's more, the proposed gene duplication and several steps needed to lose function are "neutral," unselected mutations. Stringing together several very specific neutral mutations to build a complex system is vastly improbable and amounts to intelligent design.>>

In short, we see that there is typically a strawman misrepresentation of the issue IC raises: lack of a credible step by step detailed Darwinian pathway to the specific system in question, a want of addressing he effect of knocking out specific steps and an associated selective citation of the evidence alleged to counter the example. {Not to mention, the fact that we are dealing with a large number of cases so even if Behe were wrong in one or two or even several instances, that does not obviate his claim in the main. Just one instance of IC that stands the test is enough to shred the claims of NDT.]

More specifically, on blood clotting

9]Blood clotting and the challenge of IC:

Behe observes:

>>Why does blood clot when you cut yourself, but not at other times when a clot would cause a stroke or heart attack? Here's a diagram of what's called the blood clotting cascade. Let's go through just some of the reactions of clotting.

When an animal is cut a protein called Hageman factor sticks to the surface of cells near the wound. Bound Hageman factor is then cleaved by a protein called HMK to yield activated Hageman factor. Immediately the activated Hageman factor converts another protein, called prekallikrein, to its active form, kallikrein. Kallikrein helps HMK speed up the conversion of more Hageman factor to its active form. Activated Hageman factor and HMK then together transform another protein, called PTA, to its active form. Activated PTA in turn, together with the activated form of another protein (discussed below) called convertin, switch a protein called Christmas factor to its active form. Activated Christmas factor, together with antihemophilic factor (which is itself activated by thrombin in a manner similar to that of proaccelerin) changes Stuart factor to its active form. Stuart factor,working with accelerin, converts prothrombin to thrombin. Finally thrombin cuts fibrinogen to give fibrin, which aggregates with other fibrin molecules to form the meshwork clot you saw in the last picture.

Blood clotting requires extreme precision. When a pressurized blood circulation system is punctured, a clot must form quickly or the animal will bleed to death. On the other hand, if blood congeals at the wrong time or place, then the clot may block circulation as it does in heart attacks and strokes. Furthermore, a clot has to stop bleeding all along the length of the cut, sealing it completely. Yet blood clotting must be confined to the cut or the entire blood system of the animal might solidify, killing it. Consequently, clotting requires this enormously complex system so that the clot forms only when and only where it is required.>>

To disestablish the claim that this is and IC system, one would need to show in details (not in a just so story), that the BCC can be arrived at through probabilistically plausible steps, each of which leads to a functional system that can be stabilised in a population, then onwards to the ultimate situation.

Alternatively, one needs to show that for each specific cascade -- I accept that there are some alternative sub-paths in the various animals out there [it makes the problem in aggregate harder not easier for NDT, i..e you have to do this several times over] -- the knocking out of CORE elements/stages does not issue in breakdown of functionality, like Behe summarised with the mice example.

And, while we are at it, blood is part of a wider system: the circulatory system, integrated with the metabolic system, the waste elimination system, the hormones circulation system, etc. As a liquid tissue in the context that animals are subject to cutting, ALL of these have to evolve step by step in a coordinated integrated way that at each stage issues in an animal that can have reproductive advantages to dominate the relevant population, even in isolated sub-populations. This gets us into Haldane's dilemma, usually discussed in the context of human origins, but obviously of far wider applicability, including the BCC:

>>. . . let us make a small genetic calculation whether it was really possible for us human beings to evolve from a common ancestor.

A famous geneticist, Haldane (1957), calculated that given what he considered a “reasonable” mixture of recessive and dominant mutations, it would take (on average) 300 generations (at least 6,000 years) to select a single new mutation to fixation. Selection at this rate is so very slow, it is essentially the same as no selection at all. This problem has classically been called “Haldane’s dilemma”. At this rate of selection, one could only fix 1,000 beneficial nucleotide mutations within the whole genome, in the time since we supposedly evolved from chimps (6 million years). This simple fact has been confirmed independently by Crow and Kimura (1970), and ReMine (1993, 2005).

Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to have been fixed by random drift - creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors - it would surely have killed us. (Stanford, 2005) >>

All of the solutions to these challenges must on evo mat assumptions be rooted in undirected, random changes in DNA; which gives the parts list and some at least of the assembly instructions.

The probabilistic resources of the observed cosmos would be exhausted long before we get to that level of coordination in random changes. THAT is the core IC question.

But there is an alternative: the integrated functional system is an artifact of intelligence in action. Intelligence routinely produces FSCI rich systems. So, on an inference to best explanation basis, I conclude that the BCC and its cognate systems is an artifact of design.

10] Dolphins and "ignorance":

Wiki again:

>>Dolphins are aquatic mammals which are closely related to whales and porpoises . . . They vary in size from 1.2 m (4 ft) and 40 kg (88 lb) (Maui's Dolphin), up to 9.5 m (30 ft) and ten tonnes (the Orca) . . . The family Delphinidae is the largest in the Cetacea>>

Whales:

>>The term whale is ambiguous; it can refer to all cetaceans, to just the larger ones, or only to members of particular families within the order Cetacea. The last definition is the one followed here. Whales are those cetaceans which are neither dolphins (i.e. members of the families Delphinidae or Platanistoidea) nor porpoises. This can lead to some confusion because Orcas ("Killer Whales") and Pilot whales have "whale" in their name, but they are dolphins for the purpose of classification.>>

It should be plain from my earlier remarks that killer whales are actually dolphins that I was speaking of the common usage not the specifics of taxonomy. This example of quote mining wand casting out of obvious context is again an illustration of the Darwinist tactic of debating in bad faith through systematic misrepresentation that I and others have pointed out, a persistent pattern for DECADES, to my certain knowledge.

11] IC and blood clotting:

To my: "The IC issue is, that there is a core to a given, i.e specific, process in which take one part or step out -- any one out -- and you stop the process."

S: And blood clotting is not one of those processes. It's as simple as that.

Have you shown that there is not a CORE to the BCC that when one step is knocked out, then the cascade fails? Not at all.

To do what is needed, you will need to take it down step by step in functional ways, using whatever co-opted parts you please, and you have to integrate the resulting system in a viable animal that has enough reproductive success to get the new element integrated into a population, while you are at it. Or, going the other way, you need to show a reasonable path to the BCC relevant to the fossil world and/or to the known biochemistry of living or plausible ancestral organisms, etc.

Seems to me NDT paradigm defenders have not even begun that task properly, judging by the case with the mice.

12} On Behe again: The merits of a scientific case boil down to conducting tests of one's hypotheses. Behe has failed to do that in more than a decade; therefore, he is either lazy or has renounced science itself.

H'mm, was Einstein “lazy” when he did not himself empirically test his relativity theories? [He was a theoretical physicist, who worked out hypotheses and elaborated frameworks relative to known empirical findings and thought experiments, often in a quite acrimonious climate of debate.]

As long since highlighted in this very thread, Behe's proposal on the flagellum has been subjected to serious experimental work on the order of a decade and as of the last report from Minnich; has stood up well, thank you.

__________

I think that there is no need to resort to personal abuse in a context where there is a serious issue that can be addressed in a civil fashion. The insistent resort to abuse, contempt and misrepresentation on the part of evo mat advocates here and elsewhere is therefore, sadly, diagnostic. And the obvious diagnosis is not a good one, nor is its prognosis.

I think it is, unfortunately, plain that this thread has now obviously long since too often gone far beyond the pale of civil discourse on the evo mat side, and that is telling.

Issues are settled on the merits not on attacking the man or the straw man.

Onlookers, please take note.

Cheerio

TKI

1:35 pm  
Anonymous merkur said...

"Onlookers, please take note."

These two statements taken together do raise the interesting question of who these "onlookers" are, if you believe that they believe that you're "ignorant, stupid, insane or wicked." As far as I know, I don't believe I've used those words, or implied that I feel that way.

I was one of those onlookers. I've pointed out the problems I have with your style of presentation, that it doesn't seem to present a sympathetic argument, and your response is to dismiss me as biased and unbalanced, while treating me as a buffoon.

Do you ever wonder why you're not winning anybody over with your arguments?

2:54 pm  
Blogger Smokey said...

Gordon babbled:
"Yet another repetition of an already disproved slander, cf above on the Behe--> Miller -> Minnich case. (For, infinity is the ultimate trend of a/b as b --> 0.)"

No, because the only data in Minnich's paper had nothing whatsoever with testing an ID hypothesis. Your pathetic refusal to discuss the data in Fig. 2 demonstrates that you agree.

"Sufficiently complex signals have never been observed to emerge out of noise."

Yet Tony cited precisely such a case.

"That is, once we see that this is an information problem, there is no shortage of empirical data/tests on point."

Yet when Tony confronts you with such a "problem" that is easily solved by variation + selection, you bail.

"On the contrary, if you are asserting that the amino acids have more than 20 possible states [even more if chirality is brought in] then you explode the configuration space. That is, you make the biofunctional states that much more sparse."

My challenge to you, which you are clearly too cowardly to address, has only to do with mechanism. Let's stipulate that the genetic code is intelligently designed; now, simply explain the intelligent basis for NOT using the genetic code, which has 64 available codes but only has 22 signals (leaving 42 codes available to an intelligent designer), for:

1) other amino acids, and
2) synthesizing proteins with something other than methionine at the N-terminus.

You will receive no help from reading apologetics, as no one in the ID movement has the integrity to address these questions. IOW, the lack of intelligence in these mechanisms is painfully obvious.

Note that any attempt by you to divert attention from your intellectual cowardice in failing to document the intelligence in the "design" of these mechanisms will demonstrate to the observers that you agree that there is no evidence suggesting intelligence as an origin in these two mechanisms.

"I simply noted that DNA uses three letter codons which by and large encode for the 20 amino acids [mostly] used in life forms, and include some procedural ones too i.e. start/stop."

And I simply note that your claim that the code includes start/stop "too" is patently ignorant and/or dishonest, as the start codon IS NOT IN ADDIDTION to the aa codes, unlike the stop codons. IOW, it is a profoundly stupid design, and you have no intelligent explanation for it.

"AUG encodes for methionine, and therefore the first amino acid of many proteins is methionine."

And since the first amino acid RESIDUE (not amino acid, illustrating the intellectual poverty of using WIkipedia as a source) of many proteins is NOT methionine, my challenge to you is to explain why the mechanisms for doing this are intelligently designed. I'm allowing you to assume that the genetic code is intelligently designed, but even given that assumption, you are intellectually incapable of explaining them as products of intelligent design.

"This attempt to misrepresent the facts and distort what I said to attack me shows precisely the kind of "warped" mentality and "abusive" commentary I discussed above."

I made no attempt to misrepresent the facts. Claiming that start codons are in addition to codons encoding amino acids is a lie, as the two are combined. Your task, which you will desperately try to avoid, is to explain the intelligence behind combining the start with methionine, given the fact that many proteins in their final form lack methionine at the N-terminal position.

Nothing in ID or creationist apologetics will help you. You'll have to think for yourself, a prospect that frightens you.

"We have an algorithmic coding system, which is rated by many as pretty optimal,..."

I'm pointing out how, in these two cases, it is anything but optimal. Your task is to explain the intelligent design behind these obvious departures from obviously more optimal mechanisms.

Citing the opinions of others only emphasizes your inability to think independently.

"... and we have a sophisticated nanotechnology that uses that algorithmic information to implement a class of systems we cannot even design yet, and hope to reverse engineer, and that system is unintelligent, because you do not like how start/stop is coded for?"

I am challenging you to explain why the start signal is combined with a single amino acid. Every time you write "start/stop," you are misrepresenting my challenge to you. I am challenging you to explain WHY the start signal IS NOT ANYTHING LIKE the stop signals.

"Have you shown that there is not a CORE to the BCC that when one step is knocked out, then the cascade fails? Not at all."

Yes, I have. I pointed you to human hemophiliacs, and challenged you to show that null mutants have ZERO clotting activity. Unlike you, I already know the answer (you won't find it in Wikipedia), and you and Behe are simply wrong.

"To do what is needed, you will need to take it down step by step in functional ways..."

*I* don't need to. Nature has already done this, in the form of viable human animals known as hemophiliacs. Do they ALL have ZERO blood clotting activity?

Do you realize how obvious it is to the observers that you have ZERO ability for independent thought, that you can do nothing but regurgitate propaganda?

4:09 pm  
Blogger Tony Jackson said...

Gordon: you keep quoting Shapiro with the explicit intention of advancing your ID agenda, but as I pointed out, Shapiro does not accept that the origin of life needs such an explanation. At the very least, you're being a tad disingenuous.

With respect to the Liu and Libchaber paper: They started out with no promoters and, after several rounds of variation and selection they ended up with brand-spanking-new functional promoters. I think that's a neat example of how molecular evolution can be studied experimentally - that's science for you!

Moreover, each time they repeated the experiment, the exact promoter sequences they evolved were different in detail. We’ve seen this sort of thing before in the evolution of new mitochondrial targeting signals, where many different sequences will work. This is an important biological principle and Behe (being a biochemist) really ought to know about it. The fact that he chooses not to mention it in any of his writings is I think significant.

However, if you want to talk about the origin of life and how incredibly unlikely that was, then you should at least listen to the views of other mathematicians: eg here from mathematician Mark C. Chu-Carroll:

http://scienceblogs.com/goodmath/2006/08/bad_math_from_david_berlinksi.php

He’s discussing some similar stuff to yours by someone called David Berlinski, and Mark patiently explains the fallacies that Berlinski is making.

Incidentally, I couldn’t help noticing this comment from Mark about Berlinski’s writing style:

“It's very wordy. It rambles, it wanders off on tangents, it mixes quotes from various people into its argument in superfluous ways. The point of this seems to be to keep you, the reader, somewhat off balance; it's harder to analyze an argument when the argument is so scattered around, and it's easier to miss errors when the steps of the argument are separated by large quantities of cutesy writing”.

Does anyone else spot a similar pattern here?

4:34 pm  
Blogger Andrew Rowell said...

Tony,

I wasn't going to join in on this thread as I was suffering email overload but I do not see that this (selection for new promoters) is a good example of the generation of new information in the cell.

1. The promoter sequence is short compared to the information needed for a new protein. This was also true for your target signal example.

2. The promoter sequence itself is already defined by the binding affinity of the RNA polymerase. Thus this expt is selection towards an already known goal.

What happens if the experiment is reversed and you give a promoter and look for a functional antibiotic resistance enzyme?

9:08 am  
Anonymous kairosfocus said...

Andrew (and Others):

I think the time has come for a summing up, for current and future onlookers/readers. [It is quite plain that no real progress towards actual dialogue is possible so long as the evolutionary materialist secularists insist on attacks to the man and to the straw man, but the pattern thereby exposed reveals inadvertently the true state of the House of Darwin as the C21 dawns.)

Plainly, the central and unmet challenge to the evolutionary materialist view is the explanation, not of mere order, but of the finely tuned, specified complexity of the cosmos and of life within it. That is, we have learned over the past century, that we live in a literally meaningful, i.e. information-rich world; one that is only finitely old and invites scientific explanation in terms of a credible source of such a world order.

The conundrum for the inheritors of the traditions of the C19 materialists, is that the only directly known source of such functional, fine tuned, specific, complex information and organisation, is intelligent agency.

In the case of life, it could be within or beyond the cosmos. In the case of the cosmos, obviously, such an agency must be beyond the observed cosmos and interested in the synthesis of a life-habitable universe, given the delicacy of the required fine tuning.

That in turn puts major worldview issues and alternatives back on the table, many of which evolutionary materialists are at minimum reluctant to face, and in many cases are positively enraged over having to confront.

Thus, the continual resort to attacking the man and/or the strawman. Such tactics may well succeed in the short run, but in the long run, they presage the collapse of the secularist system.

Now, on points worth a note overnight:

1] M: your response is to dismiss me as biased and unbalanced, while treating me as a buffoon.

Really, now!

What I actually did was to call on you to provide cogent facts and reasoning instead of simply asserting one-sided assertions and conclusions in absence of material facts and the reasoning that they sustain. To date, this, you have not done.

2] S: name . . .

Again, S, you have asserted and use the privilege of anonymity.

Why is it that you cannot respect my privacy? Is this civil conduct?

3] the only data in Minnich's paper had nothing whatsoever with testing an ID hypothesis.

Demonstrably false. Onlookers, simply scroll up to where I actually went through the presented empirical data and the issues of inference to best explanation. Follow the links.

This is the fallacy of the closed mind, in a context of the Dawkins-style attitude that those who disagree are ignorant, stupid, insane or wicked. [And, M, that is my context, as I have long since noted repeatedly.]

4] Yet Tony cited precisely such a case

Note, onlookers, I spoke of sufficiently complex signals emerging from noise. That raises a question of both the available probabilistic resources and the noise as root.

As already noted TJ's remarks evidently meet neither criterion -- including not only the issues of short sequences and arbitrary as opposed to random strings being intelligently inserted but also the question of error correction, which is integral to the operation of current cells.

5] My challenge to you, which you are clearly too cowardly to address, has only to do with mechanism.

Again, observe that I have taken up key points, step by step now across the span of weeks. The resort to "coward" is of course classically Dawkinsian rhetoric and is abusive, ill-bred and slanderous.

Second, on the material point subsequently raised, as long since discussed in this blog and elsewhere, 4^2 = 16, 4^3 = 64.

That is, to accommodate 20 or so base elements requires at least three and not more than three four-state elements. The provision of further, duplicate codes, allows for redundancy, an important element in real-world codes; including of course natural languages. (It functions to help with error detection and correction, also in the case in view, some of the codes are such that they provide graceful degradation.)

As we may further observe, obviously a protein system based on 20 or so amino acids has proved quite effective in the real world thank you. In short, "I would not do it that way" is not a proper objection to the inference that a coding system is evidence of intelligent agency at work.

6] your claim that the code includes start/stop "too" is patently ignorant and/or dishonest

Again, a resort to slander. Observe again that even the Wiki article notes that start and stop codons are in the RNA/RNA code.

(You will note that I excerpted the Wiki as being of HS level explicitly, since you had made a statement about that level. Onlookers can go to this page for a College level summary, observe the RNA code for A -> U -> G, as Start, and that for U - > G - > A as stop, similar to UAA and UAG (NB: None of the last three codes for a protein). The page notes: DNA codes for protein synthesis by first coding for RNA. First, the DNA code is transcribed to RNA code, which is still in the “language” of nitrogenous bases, except that adenine on the DNA pairs with uracil (in place of thymine) on the RNA. The RNA code is then translated to protein code, which is a different “language.” This process involves ribosomes and two kinds of RNA: mRNA and tRNA. The mRNA codes for the gene in question and is copied off the DNA, while tRNA matches a specific group of nucleotides with a specific amino acid. A “unit” of three nucleotides on the tRNA codes for one amino acid. Each of these “units” is called an anticodon. These match up with corresponding three-nucleotide sequences on the mRNA called codons, and in this manner the amino acids are organized into the correct sequence to build a protein. The ribosome works with the mRNA and tRNA to hook the amino acids together to form a protein.]

7] Claiming that start codons are in addition to codons encoding amino acids is a lie

Note again the resort to slander and strawman misrepresentations through quote mining.

This is what I actually stated, from the beginning of this exchange [as S himself excerpted several days ago], and the context should be plain enough (like on the whales/dolphins case; also not apologised for, as usual – just, rush on to the next misrepresentation/slander/objection):

"... based on 3-letter DNA codons [64 possible states per codon, most of which code for vario[u]s amino acids . . . but include start/stop]..."

That is, the material descriptive point I noted [en passant] is that there is procedural language in the 64-state codon code, as well as a listing of amino acids. As I noted above, when we look at the stop codes, specifically, we have three codes that do not code for a protein at all, and simply code for a procedure. (Start, as S has made much ado over, also codes for a protein. At most, I would have made a minor error or ambiguity, but have plainly captured the material point correctly.)

Onlookers, given that the cited phrase is in fact materially accurate, how is what I said relative to the 64 codes, an intentional attempt to deceive, which is what "lie" denotes?

In short, we see the attack the man and/or the strawman agenda again.

8] Every time you write "start/stop," you are misrepresenting my challenge to you. I am challenging you to explain WHY the start signal IS NOT ANYTHING LIKE the stop signals.

Notice carefully, that the slander just noted is plainly intentional: I have consistently used start/stop to denote the procedures embedded in the code right from the beginning, as S himself cited. Second, S knows that the stop codons in particular are exactly as I described, both non-coding for proteins and denoting a procedure. So to state that most of the 64 codes link to a protein monomer [and I am but little impressed with the further side-issue over "residues" vs my use of “monomers” or “amino acids” and the like, as my context is plain] but some code for start/stop is correct relative to my own purpose in making the point.

Now, on the further rabbit trail, I have no need to answer as it is immaterial; nor do I have at this point a specific hypothesis or explanation for the difference; nor, do I need one. For,the rabbit-trail is immaterial to the point in the main. For, once we see a code -- and indeed one with procedural as well as data elements -- we already directly know through vast experience and observation that codes are in general inherently intelligent artifacts, the products of minds. It is those who claim a highly significant "exception" who have a case to prove.

9] BCC:

Again, an irrelevancy. Haemophiliacs are obviously less than functional in their blood clotting, and show that the breakdown of the BCC is problematic -- here, a life-threatening complaint results from even a partial breakdown based on loss of genetic information. Excerpting (and BTW, S, 99+% of real world and scientific arguments rely in part at least on authorities of one kind or another, so your complaint on this point is selectively hyperskeptical):

>>Haemophilia is a blood condition in which an essential clotting factor is either partly or completely missing. This causes a person with haemophilia to bleed for longer than normal . . . The main problem is internal bleeding into joints, muscles and soft tissues. Haemophilia is a lifelong inherited genetic condition, which affects females as carriers and males who inherit the condition . . . . There are two types of haemophilia, the most common being haemophilia A, in which Factor VIII is lacking. In haemophilia B, Factor IX is lacking. People with severe haemophilia can experience spontaneous bleeding usually into the joints. If left untreated these bleeds cause acute pain and severe joint damage leading to disability. Bleeding episodes have in the past caused difficulties with education and employment, as well as mobility problems for many who have been crippled by the effects of regular bleeding into joints.

Treatment for haemophilia is usually by replacement of the missing clotting factor.>>

H'mm: take away factor VIII or IX and the cascade breaks down, doing serious damage to the organism; and in the case of the last Czar's son, potentially helping trigger a revolution . Looks like IC in action to me.

10]"Propaganda"

H'mm, based on the above, I think S needs to do some serious rethinking here.

11] TJ: you keep quoting Shapiro with the explicit intention of advancing your ID agenda, but as I pointed out, Shapiro does not accept that the origin of life needs such an explanation.

First, TJ, kindly respect my privacy.

Second, I keep on stating that Shapiro is a metabolism first proponent in OOL, and that his objection to the majority RNA model is inadvertently also relevant to his own case, with reasons a mere link away.

In short, I am pointing out that he has highlighted a real problem, noting his own view/school of thought. I then go on to my own point that the problem is wider than he recognises and raises the issue that yet another alternative is credible. This is fair use, not disingenuous use.

12] Liu and Libchaber paper

Cf again my points above: they began with intelligently inserted "arbitrary" [as opposed to random] sequences, which from your silence on the point were plainly fairly short. Further to this, they were working with long since biofunctional cells, with error-correcting mechanisms long since in place. (Such mechanisms include of course the redundancy in which multiple codes and monomers can more or less substitute for one another. Indeed, part of my earlier remark on optimalisation is in the context of the effect of typical errors often being to push the code into a relatively good substitute monomer, e.g. on folding.)

None of these factors lends credence to the claim that this is a serious test of the issue in the main at stake: the origin of FSCI and in particular IC.

13} http://scienceblogs.com/goodmath/2006/08/bad_math_

Page does not link. Search leads to the blogger's summary of an exchange with Mr Berlinski, here and here mostly.

The tone and substance are in the main dismissive and rhetorical (warning, at at least one early point, using vulgar language) rather than substantial, as with the previous case chosen. (David Berlinski, BTW is a Mathematician and Jewish Agnostic who is a fellow of DI. He has a fairly literary style, and loves to make distant connexions in the world of ideas. My own “style” here for want of a better term, is just the opposite of literary. “pedantic” might be a more apt critique, but I am not aiming for stylistic points.)

I note briefly:

* "Big numbers arguments." The basic problem this Computer Scientist has is that he is probably unaware that the probabilistic resources of a relevant system is a core concept in say statistical thermodynamics, e.g. it grounds the credibility of the 2nd law of thermodynamics, through the implications of s = k ln w, w being the statistical weight of the relevant macrostate [usually OMEGA]. (This leads him to dismiss the significance of the issue of sparseness in configuration spaces for getting to functionality by chance + necessity only. Maybe, he would want to read Shapiro and even Denton.)

* Well we have more than one self-replicating etc state in the space. Irrelevant to the issue that we know that biofunctionality or pre-bio functionality in particular would be quite sparse relative to the outcomes of random combinations in monomer chains, much less in racemic, complex prebiotic mixes, and is subject to destructive perturbation. Shapiro makes this point highly plain. That's also why cells have serious error-correcting mechanisms and why there is a problem of progressive destruction through loss of genetic information as discussed under Haldane's dilemma.

* Simple self replicators: he neglects to mention that there is no credible model for the Dawkins replicator to emerge in the prebiotic world, as Shapiro just so eloquently pointed out.

* "If you've got a soup of nucleotides and polymers, and you get a self-replicating polymer, it's in an environment where the "target template" is quite likely to occur." This neglects the relevant equilibria and reaction kinetics especially the overwhelming energetic balance in favour of SIMPLE, often exothermically formed molecules. This, TMLO discussed 20+ years ago. You don't get TO a plausible prebiotic soup in the credible real world environment, and if you grant one for the sake of argument, the equilibria are hopelessly against forming even a 101 element protein, cf the calc that gives a conc of 10^-338 molar, in an observed cosmos that has maybe 10^80 atoms.

* And the like . . .

In short, the critique may well persuade those who already buy into the Evo Mat system, and may well confuse those who do not know enough to spot the holes in the critique [ let's face it, stat mech is not a popular undergrad course, for excellent reasons] but the critiques, again are fatally flawed -- starting with thermodynamics considerations.

As to the attempt to critique me on style and insinuate that I am resorting to cutesy writing to hide issues and conceal fallacies, that is laughable in itself! (One who does not shun to lay out thermodynamics and related information theory, even at basic level, can hardly be accused of trying to appeal to the popular audience on emotions and authority! And, responding on points step by step in more or less notes form is hardly an attempt at clever writing.)

________

Andrew, it is plain that this thread has long since passed the stage of diminishing returns. But it does show up the facts on the true state of the matter – as summed up above, complete with exposing the Dawkinsinan rhetorical agenda for what it is.

As at now, S in particular has obviously forfeited the right to be recognised as a participant in a civil dialogue. M needs to address matters onteh merits. Tj needs to look alittel closed athe arguments thosewho take his side are making as they impinge on information, probability and thermodynamics issues.

All the best

TKI

9:08 am  
Anonymous kairosfocus said...

Andrrew:

Welcome back, and thanks for the point.

TKI

9:22 am  
Blogger Tony Jackson said...

Liu and Libchaber aren’t trying to provide the answer to life the universe and everything. Their paper asked a simple, precise, very limited but nonetheless important question: "how easy is it to evolve new promoters?" The answer apparently is: "very easy indeed".

Even so, Liu and Libchaber didn’t just leave it at that. Another nice thing about their experimental design is that it allows them to manipulate variables like mutation rate and selection pressure and see how these factors affect promoter evolution.

Scientists appreciate that sort of thing – we say it’s an ‘elegant’ experiment that gives real quantitative insights into this important process. It certainly beats the spurious off-the-top-of-his-head armchair pontifications from kairosfocus.

Welcome back Andrew.

Look Andrew, the Liu and Libchaber paper describe in exquisite step-by-step molecular detail how new information appears in the genome. In all honesty, you can’t say “oh that doesn’t really count”. It bloody well does count!

“What happens if the experiment is reversed and you give a promoter and look for a functional antibiotic resistance enzyme?”

Er Andrew, unfortunately for us, that experiment is carried out in every hospital in the world every day. Don’t you know the answer?

Want some more enzyme evolution stuff?

Here, try these. Some (like the evolution of nylonase) refer just to the evolution of a new enzyme. Others document the recent evolution both of new enzymes, and also the evolution of whole new metabolic pathways in which newly evolved enzymes are embedded.

S Ohno ‘Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence’ PNAS (1984) 81: 2421–2425.

(Smokey’s already mentioned this paper in a previous thread, but it’s worth repeating to emphasize Leslie Orgel’s famous quip that “evolution is smarter than you are”).

Copley, SD ‘Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends in Biochem. Sci. (2000) 25 261-265.

Meynial Salles I, Forchhammer N, Croux C, Girbal L, Soucaille P. ‘Evolution of a Saccharomyces cerevisiae metabolic pathway in E coli’ Metab. Eng. (2007) 9 152-159.

Tawfik, DS. ‘Loop-grafting and the origins of enzyme species’. Science (2006) 27. 475-476.

Actually, you should probably read Dan Tawfik’s article first. Here’s the bottom-line from the introduction to his article:

“New enzymes have emerged throughout the natural history of this planet. These did not simply turn up, nor were they the subject of "intelligent design." They evolved through Darwinian processes of mutation and selection. In fact, new functions can evolve in a matter of a few decades or even months, as with enzymes that degrade synthetic chemicals (nonexistent on this planet until the 20th century) and the alarming evolution of drug resistance (in which an enzyme evolves to avoid a drug designed to block it).

1:40 pm  
Blogger Smokey said...

KF wrote:
"Again, S, you have asserted and use the privilege of anonymity."

And by choosing a name that connects to your real one, you have forfeited any such privilege.

"Demonstrably false. Onlookers, simply scroll up to where I actually went through the presented empirical data and the issues of inference to best explanation. Follow the links."

At no time in your rant did you state:
1) The specific DESIGN hypothesis being tested (IC is a definition, not a hypothesis);
2) The predictions of that hypothesis that distinguish it from other hypotheses;
3) The meaning of the Western blot presented.

Try again. See if you are intellectually capable of addressing my points with a single sentence each.

"As already noted TJ's remarks evidently meet neither criterion -- including not only the issues of short sequences and arbitrary as opposed to random strings being intelligently inserted but also the question of error correction, which is integral to the operation of current cells."

Pure hooey.

"Again, observe that I have taken up key points, step by step now across the span of weeks."

No, you have evaded.

"The resort to "coward" is of course classically Dawkinsian rhetoric and is abusive, ill-bred and slanderous."

Since you are afraid to offer an intelligent reason as to why your Designer chose to combine "start" with a particular codon that also codes for an amino acid residue, as opposed to designing a separate "start" signal that could be followed by ANY amino acid residue (a far more intelligent design), there is nothing slanderous about calling you a coward.

In addition to being cowardly, you are lazy because answering my challenge in the way you would like entails a basic understanding of the mechanism by which living things remove initiating methionines from many proteins to allow them to function.

Since this is not covered in any of the propaganda you have (because the leaders of the ID movement can't explain it either), you are lost. My hypothesis is that you are afraid of what you will find, and you should be.

"As we may further observe, obviously a protein system based on 20 or so amino acids has proved quite effective in the real world thank you."

Really? Then tell all of us the proportion of human proteins that have NO modifications to the R groups of their amino acid residues.

You won't. You are afraid to learn.

"In short, "I would not do it that way" is not a proper objection to the inference that a coding system is evidence of intelligent agency at work."

Sorry, but your evasion doesn't work. YOU have already cited the genetic code as an example of intelligent design. YOU now have the task of explaining the intelligence behind NOT using a system you already claim is intelligent for a system that you don't understand at all.

You are afraid, so you try and misrepresent my challenge.

"Observe again that even the Wiki article notes that start and stop codons are in the RNA/RNA code."

They are, but that's not the point. The only valid bifucation of the codons is "aa, of which one doubles as a start" vs. "stop codons that don't involve any particular aa." The nature (and mechanism) is completely different, so your attempt to lump start together with stop is a lie that evades the whole point of my challenge to you.

"...observe the RNA code for A -> U -> G, as Start, ..."

Now, you're using a lie of omission. AUG doesn't ONLY code for "start." It also codes for methionine. In addition, AUG codes for internal methionines as well, an extremely unintelligent design creates problems that aren't explained in any of the propaganda you limit yourself to reading.

"...and that for U - > G - > A as stop, similar to UAA and UAG (NB: None of the last three codes for a protein)."

Yes, and because none of them does, IT IS DISHONEST TO CATEGORIZE THEM WITH A SIGNAL THAT DOES DOUBLE/TRIPLE DUTY.

Your task is to explain the fundamental difference between the start/stop mechanisms in terms of intelligent design. IF THEY ARE DESIGNED, the stop mechanism is orders of magnitude more intelligent than the start one.

Why wasn't the start mechanism designed like the stop mechanism, Gordon? Anything other than a direct answer to this question is an evasion that supports the hypothesis of intellectual cowardice.

"That is, the material descriptive point I noted [en passant] is that there is procedural language in the 64-state codon code, as well as a listing of amino acids."

And the challenge that you lack the courage to answer is to explain the lack of intelligence in the "design" of the start procedure (the overlap with the "keep going" procedure) relative to the apparent presence of intelligence in the stop procedure.

You will blather, try to insult me, etc., but we both know that you are afraid to meet this challenge. We both know that you have no idea how to do it without guidance from ID leaders. They don't address it because they are dishonest, and know that they can't explain it.

"As I noted above, when we look at the stop codes, specifically, we have three codes that do not code for a protein at all, and simply code for a procedure. (Start, as S has made much ado over, also codes for a protein."

And my challenge to you is to explain why the start mechanism is "designed" differently (i.e., stupidly) from the stop mechanism.

"At most, I would have made a minor error or ambiguity, but have plainly captured the material point correctly.)"

You keep regurgitating, but you haven't explained the difference in terms of intelligent design.

Smokey: "I am challenging you to explain WHY the start signal IS NOT ANYTHING LIKE the stop signals."

"Notice carefully, that the slander just noted is plainly intentional: I have consistently used start/stop to denote the procedures embedded in the code right from the beginning, as S himself cited."

Your challenge is to explain the intelligence behind the differences in the start vs. stop mechanisms.

"Now, on the further rabbit trail, I have no need to answer as it is immaterial; nor do I have at this point a specific hypothesis or explanation for the difference; nor, do I need one."

Yes, you do, because MET explains the relative stupidity of the start mechanism easily.

"For,the rabbit-trail is immaterial to the point in the main. For, once we see a code -- and indeed one with procedural as well as data elements -- we already directly know through vast experience and observation that codes are in general inherently intelligent artifacts, the products of minds. It is those who claim a highly significant "exception" who have a case to prove."

For the sake of argument, I am allowing you to stipulate that the code and the protein synthetic machinery were designed. Your task, that you are too cowardly to accept, is to explain the differences in "design" between the start and stop mechanisms in a way that accounts for the problems (which you are too lazy to learn about) caused by the RELATIVE stupidity of the start mechanism.

"Again, an irrelevancy. Haemophiliacs are obviously less than functional in their blood clotting,..."

They are, but "less than functional" does not meet Behe's criterion, which is no function.

"H'mm: take away factor VIII or IX and the cascade breaks down, doing serious damage to the organism; and in the case of the last Czar's son, potentially helping trigger a revolution . Looks like IC in action to me."

Nope. IC requires NO function, not reduced function.

Evade away...

9:39 pm  
Anonymous kairosfocus said...

Andrew

I came by to see how things have got on. I see S insists on disrespecting my privacy, par for the course of his utter incivility.

As to his statement: by choosing a name that connects to your real one, you have forfeited any such privilege.

Not at all: I have here used the handle that I wish to be known by in this forum. To obtain my personal name you have to go elsewhere to a relatively obscure part of the Internet, and use information that is explicitly set in the context of contacting me responsibly for e.g. for corrective reference, or to use the “work” of those who have done so. To then come back to an open forum to trumpet my name -- and in the teeth of protests that it has [and is again doing so over the past couple of days -- notice the fact of the two waves corresponding to H and your usages] led to spam surges, is disrespectful to say the least, perhaps even malicious.

I have not set out to digup your personal information and use it int his forum because I know the potential consequences. Why is it that you cannot accord me the same basic degree of respect? Does my name make any difference to the issues, or is the trumpeting of my name not just done in the hope that it causes me the sort of problems that I noted? [And, in a context where I have documented, with cases in point, how people suffer workplace harassment and career busting for standing up for ID or simply entertaining a fair discussion on the merits, the breach of confidentiality is serious. It so happens that I am not in a context where I can be Sternberged, but that does not excuse such misbehaviour.]

Further, I do not find that there is now any real progress in the thread [especially because the NDT etc advocates are insisting that there is no problem, thought here obviously is . . ., compounded by debate tactics that are themselves a testimony to the underlying weakness of the evo mat case], but will note on some relevant points for the sake of onlookers who may want to hear that there is more than one side to the story:

1] TJ: Their paper asked a simple, precise, very limited but nonetheless important question: "how easy is it to evolve new promoters?" The answer apparently is: "very easy indeed" . . . . Another nice thing about their experimental design is that it allows them to manipulate variables like mutation rate and selection pressure and see how these factors affect promoter evolution.

That is, on the evidence, they are well within the bounds of COMPLEXITY that would be relevant, as pointed out above.

No-one argues that random searches are utterly ineffective, just that beyond a certain degree of complexity, the available probabilistic resources are exhausted.

Further to this, the experiment is in a context of intelligent action, with small changes in view, and in a context known to have redundancy and error correcting mechanisms that use that redundancy.

Dismissive rhetoric does not address the materiality of these points.

2] Re Minnich's work, excerpting from above in this very thread, as I pointed out . . .

S here resorts to the fact that few will actually follow up what Minnich did in details, to infer that he did not do what he in fact did and publicly reported to an audience of his peers.

A look above will show that S is bluffing. Sorry Andrew on bandwidth. Excerpting from earlier, responding to TJ:

[[* . . . this is what Mr Minnich claims to have done in his lab and in analysis based on that lab work, in outline:

>>Abstract: . . . Our interest in the Yersinia centers on the coordinate genetic regulation between flagellum biosynthesis and virulence TTSS expression. Y. enterocolitica, for example operates three TTSSs (motility, Ysa, and Yop), but each is expressed under defined mutually exclusive conditions. Y. pestis has lost the ability to assemble flagella (the genes are present on the chromosome) and expresses only the Yop system at 37oC, mammalian temperature. Using a combination of microarray analysis, genetic fusions, and behaviors of specific engineered mutants, we demonstrate how environmental factors influence gene expression of these multigene families, where the influence is exerted within each system, and propose why segregating these systems is critical for the organism. Our model [NB: synonymous with specific hypothesis] further offers an explanation as to why an important subset of human pathogens has lost motility during their histories >>

* On the flagellum and the algorithmic processes, he reports:

>>The rotary engine comprising the bacterial flagellum has been studied as a model for organelle development and assembly. Approximately 30 genes are involved in coding for its individual parts with another 10 genes regulating expression and assembly and 10 more for sensory perception or chemotaxis. These 50 genes constitute roughly one percent of the Escherichia coli or Salmonella typhimurium genome, a modest but significant information investment. . . . . Viewed as a whole, the flagellum is a true nanomachine of remarkable complexity in structure and assembly control. This macromolecular machine self-assembles [which is relevant to the issue on the TTSS as seen below] and repairs, displays assembly control and processing, operates with two gears, is fueled by proton motive force, and the apparatus is ‘hardwired’ to a sensory apparatus that functions on short term memory (chemotaxis). [The complexity involved is high, beyond our current technology] Rotor speeds for E. coli are estimated at 17,000 rpm but motors of some marine vibrios have been clocked upwards of 100,000 rpms [2]."

* on the TTSS:

>>In the early 1990s, several observations intimated the reciprocal temperature requirements of flagellar biosynthesis and Yop expression were more than coincidental effects. In the dissection of the mechanism of temperature regulation, Rohde et al. [4] isolated several spontaneous mutants that showed loss of motility and Yop synthesis suggesting regulatory coordination of these two disparate systems. Ramakrishnan et .al. [5], and Sanders et. al. [6] also found that the sequence of the Caulobacter crescentus flhA flagellar gene showed predicted sequence similarity to pYV-encoded LcrD. Soon thereafter another set of Caulobacter flagellar genes showed sequence similarity to additional ysc and lcr genes [7]. The common denominator for this association identified both sets of genes as required for protein secretion in each process, flagellar assembly or Yop secretion. It was this association that led to the recognition that virulence protein secretion and flagellar protein assembly involved similar mechanisms now classed as type III secretion systems>>

* On the hyp to be tested in his lab:

.. Before the separate parallel nature of the flagellar and Yop systems was dissected, our laboratory proposed that the simplest explanation for temperature regulation of these systems was a direct overlap in function. Thus, the flagellum in our view could be used not only as a propulsion machine, but a dedicated highly efficient protein secretory machine for the Yops . . . . This hypothesis was testable by the following predictions. [this is a testable hyp] First, nonmotile Y. pestis would also have to contain a set of flagellar genes, some of which would be expressed. Second, it predicted that both Y. enterocolitica and Y. pseudotuberculosis would maintain expression of a subset of flagellar genes even at the nonpermissive temperature (37oC) for motility. Finally, it suggested that a subclass of mutants should be defective in both Yop secretion and motility. Using genetic fusion with a reporter gene (lacZ) and northern blot assays, it was determined that at 37oC Y. enterocolitica continues to synthesize Class I and Class II flagellar genes. The loss of motility appears to be due to the immediate transcriptional arrest of Class III genes (25-30 fold repression) on exposure to 37oC [9]. A subset set of flagellar gene transposon insertionally inactivated genes were mapped to flagellar genes and also fail to secrete Yops. Finally, Y. pestis does contain a complete set of flagellar genes, and using RT PCR, some are transcribed [10] [Lab work stage 1] . . . . [After some back-forth on further issues and questions] Schneewind and co-workers [13] showed that TTSS proteins of plant pathogens were recognized and secreted by Y. enterocolitica and vice versa. This suggested that the secretory signal of TTS proteins was conserved across genera. Based on this observation, we came full circle back to our original hypothesis [i.e it had been in abeyance for a time, pending resolution of issues] of dual function of the flagellar basal body structure. Expression of multiple TTSSs in the same organism by mutually exclusive environmental conditions prevents cross contamination of secreted proteins. That is to say, if flagellum biosynthesis were expressed simultaneously with the Yop TTSS, flagellin monomers may be exported out the ‘needle-like’ structure as well as the flagellar basal body and vice versa in regard to Yops. Efficiency of both systems would suffer as a consequence.>>

* Further testing, lab work stage II in Minnich's lab, stage V overall if the work leading to the issues an then to the circling back are reckoned with :

>>To test the above hypothesis, a flagellin and two Yop genes (fleB and, yopD and yopM respectively) were cloned and fused to the inducible ptac promoter. By placing these plasmid constructs in various mutant strains lacking either a flagellum TTSS (flhD-, flhB-) or Yop TTSS (yscE-, pYV-), expression and secretion of FleB, YopM, and YopD could be examined under conditions when these proteins are not normally expressed . . . . As can be seen in Figure 2, it was found that FleB is indeed secreted by the Yop TTSS and even the Ysa TTSS (low temperature, high salt). Conversely, it has been shown that YopM is recognized by both the Ysa and flagellar TTSSs. The overall view of Y. enterocolitica type III segregation is illustrated in Figure 3.>>

* Thus, Minnich has done at least two relevant stages of lab work and is only reporting his latest findings in Fig 2 [which was dismissively referred to by TJ earlier], all in a context that rationalises why this is all relevant to the issues outlined above on the IC nature of the flagellum. In particular, we can see the ebb and flow of hypothesising, prediction, and testing across something like five stages of lab work, two in Minnich's lab, leading to the conclusions summarised in the abstract as cited.]]

In short, “elegant” lab work [even including he promoters . . .], and it supports the design-based hypotheses that were tested, including that famous Fig 2. Once we look in the actual context,the misrepresentations of he work and the significance of the work in its context both become plain. Observe, too, that here we see an information system that has in it a subset that is capable of generating a second, related system, a very high art form indeed in design.

3] As to the notions that I have been evasive . . .

Kindly simply look at the just above, and the earlier materials. It will be seen easily that this is an instance of accusing the man instead of addressing seriously the underlying issue.

4] Start/stop codons

Here we see the repeated resort to attacking the man and the strawman.

I have specifically said that I do not have a particular explanation of why the start codon should be different from the three stop codons (of course apart from the obvious one that brakes -- notice how we haveTWO brakes in a car!] are more important than the accelerator pedal, because of the consequences of failing to stop].

I have also pointed out that this limitation on my current state of knowledge is immaterial to the core issue, which my summary addressed: we have a complex, functional code, which on IBE is an artifact of mind. The insistence that absent “elegant” explanation of any and every thing that can be thrown out, we can ignore material points is of course straining at the gnat while swallowing the camel, joined to the attack to the man instead of addressing the issue on the merits.

Indeed, I have long since pointed out the relevant principle of sub-optimisation in design. Physical designs are subject to constraints and trade-offs, so that the attempt to optimise every feature leads as a rule to overall underperformance, and/or to failure. As a result, clever designers prioritise design objectives and make trade-offs in favour of the overall objective of the design. Further to this, it often makes better sense to get something good enough rather than optimal relative to some objective function or other, i.e. satisficing through application of useful rules of thumb etc, is often more sensible than attempted optimisation; in the overall context of the design. [Well do I recall my puzzlement when I first saw a potential divider transistor bias circuit and how the actual R, C etc numbers were generated, and worse, how the overall performance was modelled using h-parameters: satisfactory performance rather than optimal.].

As to the accusations of “laziness” and looking at “propaganda,” let the very insistent failure to answer to the obvious and central issue -- there is a CODE at the core of life that functions in a sophisticated information system based on molecular scale nanotechnology -- while rushing off to personal attacks speak for itself.

That is, resort to name-calling is the mark of one who has a weak case on the merits, but who thinks that by throwing down a chain of objections and accusations, can make an escape behind the resulting cloud of obfuscation of the core issues left unanswered. Further to this, it is S who properly has the burden of proof to demonstrate that the difference between the precise status of the start and the stop codons entails that the code as a whole and its use are best explained as the result of lucky noise in plausible prebiotic environments. That he has not done so but resorts to the tactic of attempting to shift the burden of proof is eloquent testimony that he cannot answer to the case in the main so wishes to decide it by default, inserting his preferred answer as the default. Then he clouds this over by making personal attacks.

Okay, then, let my brakes/accelerator analogy serve for now. [In other words, once we start, however we do so, the critical thing for survival given the length of the DNA chain and the finite resources of the cell and the possibility for clogging it with useless eternally lengthening polypeptide chains, we need to have a cluster of unambiguous STOPs to keep the system from runaway polymerisation. I gather that a random “frame” choice for DNA will run into frequent STOPS, too.]

5] The effectiveness of a life technology based on 20 amino acids

It has plainly succeeded in creating the biological world in which we live. That is, it has the very considerable justification of success, astonishing success.

After recognising that and its implications [in light of the empirically known source of FSCI], we can debate relatively minor points as we please, in their proper place.

5] "Dishonesty":

Again, accuse, don't address.

I simply set out to provide a summary of the fact that we have a three-letter, 64 state DNA code, which has in it redundant forms for the 20 monomers used, and also gives procedural items: start and stop. These are plain facts. That one of these procedural elements also codes for a monomer is irrelevant to the core point made -- absent specific demonstration by S of this assertion he implies. [He is also trying to shift the burden of proof on a relatively minor point, thus evading the force of the existence of a code, the material issue.]

It is very simply and obviously not dishonest to point out that such a fact as a code with parts list, sequencing and start/stop procedural items exists, then ask what do we know about the origin of codes, based on our experience. That is a plain and empirically anchored issue.

6] And so forth . . ..


___________

OBSERVED GENERAL EVOLUTIONARY MATERIALIST RHETORICAL PATTERN IN ID IN THE UK BLOG (and in a lot of other places):

Attack the man. If he objects to evo mat, he "must" be ignorant, stupid, insane or wicked. [That is spelled B-I-G-O-T-R-Y, FYI.)

Distort the issue. Attack the strawman. (This is misrepresentation.)

Never apoloigise when corrected, never acknowledge or heed correction. (Closed mindedness and incivility.)

Make such corrections the occasion for further accusation and attack.

When an objection or attack is cogently answered, ignore it and go on to the next attack and distortion. [Observe what has happened with the original issue: thermodynamics and OOL, as well as information out of lucky noise. Observe how men like Bradley etc. have been trashed without proper grounds, and without apology when the slanders were exposed for what they are. Observe what happened to those who stood up to say something is wrong here. Then, look at what ahas happened with other issues, along the same line. Then understand why this exchange joins my vault on exposing evolutionary materialist debate tactics. You will of course be properly cited and “credited” . . .]

When enough time has passed, circle back to the original attacks and distortions. [Cf the case of Minnich just above.)

Eventually, the public will recognise what is going on, and the backlash will be terrible and broadscale, without pausing to identify the guilty/innocent. [Just check how the case of Galileo is often used.]

Those who hold science dear should stand up now against such abusive tactics, before science finds itself utterly discredited in the public mind.

Enough has been said, and enough bits have been spilled to make the point absolutely clear. I will look back to see if there is any serious and civil onward dialogue, but will not hold my breath waiting for it.

IF such a dialogue ensues, I will respond.

Absent such, I reserve the right of comment on utterly outrageous accusations etc, but the summary just presented will be more than enough to show just what is really going on.

Cheerio, Andrew [with thanks] and others

TKI

11:27 am  
Anonymous kairosfocus said...

PS; Two follow up points:

1] Using a random model, 3/64 ~ .047, i.e about one in 20 times on a "random" frame assumption, we would run into a stop code. That will help to amplify the relative importance of stop over start.

2] Stop codes, are not entirely non-coding:

Professor John Kimball of Harvard etc, retired, has kindly provided the following:

>>. . . Nonstandard Amino Acids

The vast majority of proteins are assembled from the 20 amino acids listed above even though some of these may be chemically altered, e.g. by phosphorylation, at a later time.

However, two cases have been found where an amino acid that is not one of the standard 20 is inserted by a tRNA into the growing polypeptide.

* selenocysteine. This amino acid is encoded by UGA. UGA is still used as a chain terminator, but the translation machinery is able to discriminate when a UGA codon should be used for selenocysteine rather than STOP. This codon usage has been found in certain Archaea, eubacteria, and animals (humans synthesize 25 different proteins containing selenium).

* pyrrolysine. In one gene found in a member of the Archaea, this amino acid is encoded by UAG. How the translation machinery knows when it encounters UAG whether to insert a tRNA with pyrrolysine or to stop translation is not yet known. >>

This immediately tells us that the multiple use of codes for procedures is not strictly unique to start but also applies to stop. So any argument that the "difference" makes a big difference is not in accordance witht he global facts.

Second, it tells us that there is a partly unknown mechanism which disambiguates data from procedure. THis fits in with the point that we know enougto know there is a code and there are algorithmic protocols, but we have nor fully understood them. And, the material issue is ad always that algorithms, the codes and the information systems that physically instantiate same, are all known products of agency.

TKI

12:16 pm  
Blogger Tony Jackson said...

I'm not going to go over the promoter evolution paper yet again. It's obvious kairosfocus just doesn't 'get it'.

However, I encourage those genuinely interested in real biology to at least have a look at it and also at the other papers I mentioned. It's the only way to see how real science is done.

I hesitate to bring up yet again the Minnich and Meyer conference presentation. But thinking about it, there is something I missed last time and which also serves to illustrate the difference between a good paper and a sloppy one. It's found here in the abstract from their report:

"Using a combination of microarray analysis, genetic fusions, and behaviors of specific engineered mutants, we demonstrate how environmental factors influence gene expression of these multigene families,"

Now, by accepted convention, if, in a scientific paper, you say something like "here we demonstrate...." then er.. you really do have to show the data. This isn't some evil scientist plot. Surely everyone can see it's just good common sense honesty.

So, my questions for kairosfocus are this:

1) where in the Minnich and Meyer paper do they actually show the microarray data?

2) Do you in fact know what such data would actually look like?

5:40 pm  
Blogger Andrew Rowell said...

Tony,
I said:
“What happens if the experiment is reversed and you give a promoter and look for a functional antibiotic resistance enzyme?”

You said:
Er Andrew, unfortunately for us, that experiment is carried out in every hospital in the world every day.

What exactly are you saying here Tony? That brand new antibiotic resistance enzymes are produced from scratch every day in every hospital?

My point was that making an enzyme from scratch is a very different proposition from making a promoter. You agree with that point surely?

10:25 pm  
Blogger Andrew Rowell said...

Tony,

I can only look at the Ohno paper here unfortunately. I did read that some time ago. I did not think the Nylonase papers were terribly well written and felt I needed a good review. The http://www.nmsr.org/nylon.htm site I found more helpful.

11:04 pm  
Blogger Smokey said...

Gordon wrote:
"To obtain my personal name you have to go elsewhere to a relatively obscure part of the Internet..."

Google is the least obscure site of the Internet. The name you use here is the title of your blog.

"... and use information that is explicitly set in the context of contacting me responsibly for e.g. for corrective reference, or to use the “work” of those who have done so."

Baloney. Your blog simply says:
About Me
Name: Gordon

"I have not set out to digup your personal information and use it int his forum because I know the potential consequences."

Given your inability to dig up the most basic information on translation, I don't think that you have the capability.

"That is, on the evidence, they are well within the bounds of COMPLEXITY that would be relevant, as pointed out above. "

So, if we consider the TIME required to achieve that COMPLEXITY, how much TIME would be required to attain a COMPLEXITY that you claim is unattainable?

"No-one argues that random searches are utterly ineffective, just that beyond a certain degree of complexity, the available probabilistic resources are exhausted."

Straw man based on a creationist lie. Selection makes it a decidedly nonrandom search. Only the starting point and the variation were random.

"Further to this, the experiment is in a context of intelligent action,..."

The only intelligent action was in the selection. No intelligent DESIGN was involved.

"Using a combination of microarray analysis, genetic fusions, and behaviors of specific engineered mutants, we demonstrate how environmental factors influence gene expression of these multigene families, where the influence is exerted within each system, and propose why segregating these systems is critical for the organism."

Not a speck of ID there.

"Our model [NB: synonymous with specific hypothesis] further offers an explanation as to why an important subset of human pathogens has lost motility during their histories..."

[delete filler]

* On the hyp to be tested in his lab:

".. Before the separate parallel nature of the flagellar and Yop systems was dissected, our laboratory proposed that the simplest explanation for temperature regulation of these systems was a direct overlap in function. Thus, the flagellum in our view could be used not only as a propulsion machine, but a dedicated highly efficient protein secretory machine for the Yops . . . . This hypothesis was testable by the following predictions. [this is a testable hyp]..."

Indeed it is, but it has nothing whatsoever to do with intelligent design. Partially-overlapping functions are predicted by evolutionary mechanisms, not intelligent design.

">>To test the above hypothesis, a flagellin and two Yop genes (fleB and, yopD and yopM respectively) were cloned and fused to the inducible ptac promoter. By placing these plasmid constructs in various mutant strains lacking either a flagellum TTSS (flhD-, flhB-) or Yop TTSS (yscE-, pYV-), expression and secretion of FleB, YopM, and YopD could be examined under conditions when these proteins are not normally expressed . . . . As can be seen in Figure 2, it was found that FleB is indeed secreted by the Yop TTSS and even the Ysa TTSS (low temperature, high salt). Conversely, it has been shown that YopM is recognized by both the Ysa and flagellar TTSSs. The overall view of Y. enterocolitica type III segregation is illustrated in Figure 3.>>"

Nothing about intelligent design.

"* Thus, Minnich has done at least two relevant stages of lab work and is only reporting his latest findings in Fig 2 [which was dismissively referred to by TJ earlier], all in a context..."

Context? You're now admitting that you are being dishonest in claiming that an intelligent design hypothesis was being tested.

"... that rationalises why this is all relevant to the issues outlined above on the IC nature of the flagellum."

Gordon, if a subset of flagellar proteins mediates secretion, the definition of IC has not been met.

IC isn't ID. Behe HYPOTHESIZES that IC implies ID, but neither he nor Minnich has lifted a finger to test that hypothesis.

"In short, “elegant” lab work [even including he promoters . . .],..."

No expert would call it elegant. I call it "bashing," which is not a term of admiration.

"... and it supports the design-based hypotheses that were tested, including that famous Fig 2."

Not a single design-based hypothesis was tested. I'm trying to get you to test one below, and your fear prevents you from doing so.

"Observe, too, that here we see an information system that has in it a subset that is capable of generating a second, related system, a very high art form indeed in design."

Which fails to meet an essential criterion of Behe's definition of IC.

"4] Start/stop codons

"Here we see the repeated resort to attacking the man and the strawman."

No, I'm attacking your failure to address a prediction of ID.

"I have specifically said that I do not have a particular explanation of why the start codon should be different from the three stop codons..."

But if it was intelligently designed, there MUST be an intelligent explanation, correct?

"... (of course apart from the obvious one that brakes -- notice how we haveTWO brakes in a car!] are more important than the accelerator pedal, because of the consequences of failing to stop]."

The difference I have challenged you to explain has nothing to do with importance or the number of start vs. stop codons. You are evading.

"I have also pointed out that this limitation on my current state of knowledge is immaterial to the core issue, which my summary addressed: we have a complex, functional code, which on IBE is an artifact of mind."

Then there MUST be an artifact of mind to explain this glaring difference. That's called a prediction!

"The insistence that absent “elegant” explanation of any and every thing that can be thrown out, we can ignore material points is of course straining at the gnat while swallowing the camel, joined to the attack to the man instead of addressing the issue on the merits."

You are being dishonest again. I'm not the one ignoring material points, you are. If intelligent design is evident to you in the nature of the genetic code, you also should have evidence for the intelligent design combining the start signal with one for a single amino acid residue that does not work at the N-terminus of many, many proteins, which in turn requires a vast number of proteins to snip off those ends.

If you have none, that is fine; however, there still has to be one out there, and if you had a scientific bone in your body, you would be intrigued instead of evasive.

"Indeed, I have long since pointed out the relevant principle of sub-optimisation in design. Physical designs are subject to constraints and trade-offs, so that the attempt to optimise every feature leads as a rule to overall underperformance, and/or to failure."

Then explain, using evidence, why separating the start signal from the met signal would lead to failure.

"As a result, clever designers prioritise design objectives and make trade-offs in favour of the overall objective of the design."

Yes. Then it is your task to explain why this is an effective design, given all the inefficiencies it causes.

"Further to this, it often makes better sense to get something good enough rather than optimal relative to some objective function or other, i.e. satisficing through application of useful rules of thumb etc, is often more sensible than attempted optimisation; in the overall context of the design."

That's how evolution is predicted to "design" things.

"As to the accusations of “laziness” and looking at “propaganda,” let the very insistent failure to answer to the obvious and central issue -- there is a CODE at the core of life that functions in a sophisticated information system based on molecular scale nanotechnology ..."

I am challenging you to explain an obvious LACK of sophistication in start signals that is already present in the stop signals.

"...Further to this, it is S who properly has the burden of proof to demonstrate that the difference between the precise status of the start and the stop codons entails that the code as a whole and its use are best explained as the result of lucky noise in plausible prebiotic environments."

Not really. If you propose an intelligent design hypothesis, it's up to you to try and falsify it. If you had even a smidgen of relevant knowledge, you'd know that current ideas on the origin of the genetic code don't have its origination in prebiotic environments, but then, we both know that you have no real interest in biology.

"Okay, then, let my brakes/accelerator analogy serve for now. [In other words, once we start, however we do so, the critical thing for survival given the length of the DNA chain and the finite resources of the cell and the possibility for clogging it with useless eternally lengthening polypeptide chains, we need to have a cluster of unambiguous STOPs to keep the system from runaway polymerisation."

But useless polypeptide chains are CAUSED by the "design choice" of combining start with met. These are the chains that are initiated at internal AUG codons. You just admitted that the "design" is unintelligent!

"I gather that a random “frame” choice for DNA will run into frequent STOPS, too.]"

Yes, and the internal AUGs whose recognition you claim was intelligently designed cause precisely this problem!

"It [only 20 aas] has plainly succeeded in creating the biological world in which we live."

No, it has not. It has required baroque systems that modify some of the 20 for function.

You didn't answer my question: what proportion of functional proteins have 0 modified aa residues?

"I simply set out to provide a summary of the fact that we have a three-letter, 64 state DNA code, which has in it redundant forms for the 20 monomers used, and also gives procedural items: start and stop."

Your use of "also" is evasive. One of the codons codes for both an aa residue and start. SInce this methionine has to be cleaved off of many proteins before they are functional, an intelligent design would have two separate codes for met and start, or...HERE'S THE PREDICTION...there must be a detectable intelligent reason for them to be combined. Otherwise, intelligent design is not being detected in the genetic code.

The failure of any ID proponent to address this shows their lack of faith.

"These are plain facts. That one of these procedural elements also codes for a monomer is irrelevant to the core point made -- absent specific demonstration by S of this assertion he implies."

I have demonstrated it by pointing you to the inefficiencies, which you just admitted were inefficiencies above!

"1] Using a random model, 3/64 ~ .047, i.e about one in 20 times on a "random" frame assumption, we would run into a stop code. That will help to amplify the relative importance of stop over start."

That's irrelevant, because you have failed to address initiation at internal AUGs.

"2] Stop codes, are not entirely non-coding:..."

Which completely contradicts the hypothesis of intelligent design.

"The vast majority of proteins are assembled from the 20 amino acids listed above even though some of these may be chemically altered, e.g. by phosphorylation, at a later time."

Yes, I've pointed this out many times. Your challenge is to EXPLAIN why this, instead of using some of the 42 available codons, is an intelligent design.

Regurgitating this from another source instead of explaining it in terms of intelligent design only makes you look intellectually incompetent.

"However, two cases have been found where an amino acid that is not one of the standard 20 is inserted by a tRNA into the growing polypeptide."

And since they also double up, there is no intelligent explanation for this. There are evolutionary explanations for this lack of intelligence, too.

"This immediately tells us that the multiple use of codes for procedures is not strictly unique to start but also applies to stop."

Then, in those rare cases, you need to explain the intelligence you detect in those choices.

"So any argument that the "difference" makes a big difference is not in accordance witht he global facts."

The use of AUG as both start and methionine is global. The exceptions don't help you explain the intelligence you allegedly see in the design.

"Second, it tells us that there is a partly unknown mechanism which disambiguates data from procedure."

You claim to know and detect the mechanism--intelligent design. Yet you can't offer a single reason why these are intelligent choices, given the obviously more intelligent ones available to any intelligent designer.

"THis fits in with the point that we know enougto know there is a code and there are algorithmic protocols, but we have nor fully understood them."

WE understand them and can explain them with reference to the data. YOU claim to detect intelligence in them, but you clearly are lying. You don't even want to investigate or make a prediction. That's pure cowardice, not to mention lack of faith.

"And, the material issue is ad always that algorithms, the codes and the information systems that physically instantiate same, are all known products of agency."

And the challenge that you are too cowardly to accept is to explain these choices as intelligent ones. You have to if you claim to detect intelligence, but you never will. It's about the most dishonest sort of cherry-picking and ignoring any data you can't explain, in addition to cowering from making predictions.

2:13 am  
Blogger Andrew Rowell said...

Tony,

I hope you did not mind my editing that for you

8:16 am  
Anonymous Anonymous said...

Tony Jackson said...

Andrew

Come on...

New genes evolve all the time by selection acting on DNA duplications, DNA fusions, DNA deletions, exon shufflings and so on. Examples are given in the references I gave.

8:17 am  
Anonymous kairosfocus said...

Andrew (and others):

I have long since said enough to fulfill reasonable objectives in commenting in this blog: showing that there is another side to the story, and exposing the basic rhetorical problems that come from the evo mat side; having long since given up hopes that there would be any serious, civil responsiveness.

Those who wish to see what a basic introduction to the design argument looks like can always link through my name as it has always appeared in this blog to a summary introduction on the major topics. There, they will also find the onward links for reasonable dialogue abused by H and by S especially. [I must note that "outing" tactics in a context of say the Sternberg case, not only invite spamming waves as I have experienced, but retaliatory efforts. Andrew, that again raises issues on the discipline on comments in this blog.]

I have no wish to further prolong back-forths with those whose habitual resort is to attacking the man and/or the strawman, as I have already summarised. Therefore the following are closing remarks, addressing such points as developed over the past couple of days as I think can be productive for reasonable onlookers:

1] TJ: the promoter evolution paper yet again

Andrew and I have both raised a so-far unanswered question -- does the evolution in question pass the the reasonable threshold of complexity for the issue of FSCI to kick in? That level is for a four-state code such as DNA, about 250 monomers, equivalent to ~ 500 bits of information, or a configuration state space of ~ 10^150. [Cf discussion below.]

Further to this, what steps have been taken to eliminate the known existence of error correcting mechanisms in the relevant nanotechnology? [For, we are not speaking of the creation of a novel feature but of substituting a short length of erroneous code in a mechanism known to have an only partly understood error correction capacity. In short there are basic questions on the test-case that have not been cogently answered by those who advocate it.]

Underlying all of this, is the implicit assumption that lucky noise can credibly account for the origin of not only the particular codes, but the coding system and the associated nanotechnology-based information processing system, within the probabilistic resources of the observed universe. That, methinks is most incredible, and Trevors and Abel give reasons why here and here in two peer-reviewed papers.

(Observe how their reasoning has never been seriously taken up in the rush to strain at a gnat. Or the earlier reasoning relative to thermodynamics and information-generation from lucky noise. These are the elephants in the middle of the room that are being tiptoed around, so as we look at minor issues, let us never forget what is central – we should not be distracted by red herrings leading out to strawmen that are set up top be pummelled. Especially, since, intelligent agency is known to routinely produce FSCI, and in ALL cases of FSCI where we do independently know the causal story, this is the known source..)

2] Minnich-Meyer paper:

Onlookers, kindly read here.

On p. 6 next to the blot they give a simple summary table of experimental results, and discuss same in the main text [NB: journals and proceedings of course face space constraints so the appearance of summarised results in such a context is not surprising]. Minnich is accessible for detailed inquiry as a corresponding author; his address is given, and appears here in the proceedings Abstract. Were I in TJ's showes, I would take time to check the author before casting aspertions.

3] Oh, yes, I forgot: on haemophilia and loss of clotting factors:

I suppose, we are invited by S to think, above, that haemophilia was so named as it is an apt description of a properly functioning BCC.

4] Smokey tries to defend his insistence on using my personal name . . . while continuing to do so in the teeth of my telling him [with reasons] that he has no permission to do so

Thus, he demonstrates his want of civility, as is also abundantly shown above. Note the context in which both spam attacks and the like as well as potential for retaliation are on the table with given examples. Further to this, while pretending that a blog search is enough, he omits to mention the first attempt to abuse my name by H, which gives my surname as well. This is the context for my remarks.

In short, his abuse is in the context of other abuse of my name which actually led in part to a whole thread on abusive commentary – look back here, This he clearly knows or should know; since he was a participant. [BTW, to point out accurately, with examples, that certain conduct is beyond the pale of civility, in specific ways, is not insult, it is invitation to correction.]

5] Minnich again:

Onlookers, I actually excerpted and highlighted the pattern of experimental work and the hypotheses being tested. Those who are serious can simply read the paper, then if necessary correspond with Mr Minnich.

In any case, the underlying issue is the elephant in the middle of the room as noted.

6] On complexity and probabilistic resources

Had S bothered to look at my online discussion here -- linked in my table of contents, he would have seen that I gave a context for the reason why the Fisher-Dembski type credible but of course empirically defeatable probabilistic elimination of chance hypotheses as null makes sense.

Namely, that with an observed cosmos of ~ 10^80 atoms, a lifetime of maybe 10^25 seconds, and a minimum quantum state time of 10^- 45 seconds, we are looking at a maximum of ~ 10^150 quantum states in the observable universe across its entire estimated lifetime,which is about half gone. So, viewing the above as the number of times the deck can be shuffled, if an event is significantly more improbable than that, then it is unlikely to have ever occurred by chance in the lifetime of the observed universe. I think, that this is a lot less arbitrary than the .05 or .01 confidence levels commonly used in statistical inference.

Further to this there is an issue of selective hyperskepticism, once worldview level issues and associated agendas are at stake. Namely, we routinely infer to agency when we see sufficiently complex strings of digital characters e.g. this post. (The relevant probabilities and contexts are quite similar, as is also discussed by me as the first step in my analysis here.]

I also take time to discuss the usual escape, to posit that the observed cosmos is an arbitrary limit, as it is possible that the universe as a whole is a quasi-infinite array of sub-cosmi with randomly distributed laws and parameter values so that the improbabilities are swamped by the available resources. The problem -- as I pointed out a year ago -- is that this is of course an often unannounced passing from observationally anchored science to speculative worldview assertions. So the proper method changes and it should be analysed through comparative difficulties across worldview options. [Cf objection no 4.]

7] Start and stop codons

I pointed out that contrary to the earlier objection, both start and stop codons are in fact used for other purposes, as well as noting that stop codons have a good reason for being more abundant than start ones.

Next, given that the code in question exists in a context where there is evident disambiguation software, the code reuse is reasonable. [Note, in some cases in microcontroller design, high-end practitioners use the general purpose nature of digital symbols and codes as contexts of interpretation so that under one interpretation certain strings of memory locations are interpreted as code to be executed, and under other contexts,a s data to be read for use in processing. In short, we see here a parallel between the codes of life and known practices of designers of microcontrollers for algorithmic control of processes. Onlookers, I have already had occasion to point this out explicitly in an earlier thread, it was of course simply ignored.]

8] Minnich paper and inference to design:

Note, onlookers: the inference to design does not simply rest on the data found by Minnich, but also on other data from other researchers in the field. What emerges on a closer look at the situation in context is what Peterson aptly summarised -- and again this has already been adverted to, including in my remarks on the sequence Behe --> Miller --> Minnich [which is where the relevsant lab work comes in]:

>> Behe's most famous example is the bacterial flagellum described above. If you take away the driveshaft from the flagellar motor, you do not end up with a motor that functions less well. You have a motor that does not function at all. All of the essential parts must be there, all at once, for the motor to perform its function of propelling the bacterium through liquid . . . . that is precisely what Darwinian evolution cannot accomplish. Darwinian evolution is by definition "blind." It cannot plan ahead and create parts that might be useful to assemble a biological machine in the future. For the machine to be assembled, all or nearly all the parts must already be there and be performing a function. Why must they already be performing a function? Because if a part does not confer a real, present advantage for the organism's survival or reproduction, Darwinian natural selection will not preserve the gene responsible for that part. In fact, according to Darwinian theory, that gene will actually be selected against. An organism that expends resources on building a part that is useless handicaps itself compared to other organisms that are not wasting resources, and will tend to get outcompeted . . . .

Behe the biochemist . . . search[ed] the relevant scientific journals, books, and proceedings of meetings to find out what the Darwinists had really proven about the origin of complex biochemical systems . . . . "There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems" . . . Behe, recalling the "fierce resistance" he encountered after the publication of Darwin's Black Box, remarks that much of it came from "internet fans of Darwinism who claimed that, why, there were hundreds or thousands of research papers describing Darwinian evolution of irreducibly complex biochemical systems." Except that there aren't.

Well, this sent the Darwinians scrambling. Kenneth Miller, a biologist at Brown University who argues in favor of Darwinian evolution, made a splash when he announced (and he bolded the language in his article) that "the bacterial flagellum is not irreducibly complex." Miller cited a cellular structure known as the type III secretory system (TTSS) that allows certain bacteria to inject toxins through the cell walls of their hosts . . . .

But . . . the bubonic plague bacterium already has the full set of genes necessary to make a flagellum. [Cf here, e.g. Minnich's Abstract]Rather than making a flagellum, Y. pestis uses only part of the genes that are present to manufacture that . . . injector instead. As pointed out in a recent article by design theorist Stephen Meyer and microbiologist Scott Minnich (an expert on the flagellar system), the gene sequences suggest that "flagellar proteins arose first and those of the pump came later." If evolution was involved, the pump came from the motor, not the motor from the pump. Also, "the other thirty proteins in the flagellar motor (that are not present in the [pump]), are unique to the motor and are not found in any other living system." . . . In short, the proteins in the TTSS do not provide a "gradualist" Darwinian pathway to explain the step-by-step evolution of the irreducibly complex flagellar motor.>>

That should be plain enough on the relevance of the cited work to the matter; as the work in question precisely showed based on empirical data that it was credible that the secretory system uses a subset of the genes to create the injector, instead of using the same basic information to self-assemble the flagellum. So, the Miller claim that the flagellum has a functional precursor which has been used to try to discredit the concept of ID, has been refuted by empirically based facts, including the work by Mr Minnich presented in the conference paper.

9] Are Start/stop codons the proper test for whether FSCI exists in the DNA?

Here we see that I am highlighting the strawman nature of the issue D raised, by adverting to the elephant in the middle of the room: the sophisticated information system beyond the probabilistic resources of the observed cosmos. In short, the proper context for the discussion is OOL through plausible prebiotic chemistry that created FSCI-rich biofunctional nanotech information systems, which I have addressed in details uncivil ad hominems notwithstanding.

[And,S, FYI, I have some little knowledge of and experience in what it takes to design such low-level digitally based ISes and the associated coding schemes; the problem is far beyond the credible threshold of chance plus necessity; indeed, the very fact that we are looking at a complex, code-based nanotech system is decisive for me on the subject of whether or not agency was involved. It will be for a lot of others, too, as they begin to appreciate the complexity and specific functionality [rooted in the DNA's digital information expressed in that code you seem to so despise] that we can see e.g. through this Harvard University animation. Guess why it is linked through an ID supportive blog . . .]

Note, I have never adverted to start/stop codons as evidence for IC, nor to my best knowledge has anyone else. So this is a double strawman. S has either not troubled to try to understand what his interlocutor has been saying, or had calculatedly misrepresented me. On either horn of that dilemma, it does not look good for him.

His onward challenges on the Start/Stop codons as IC elements are therefore simply attempts to pummel the strawman he has set up. This is utterly irrelevant to the case at stake.

I repeat: the core design inference relative to DNA and its code, is that we have here an algorithmically based information system that implements a self-replicating, self-maintaining automaton. This is maximally unlikely to have emerged by chance plus necessity alone across the gamut of the observed cosmos, as discussed in brief and linked. But, we know that intelligent agents routinely create FSCI, and human intelligent agents have in the persons of Mr Turing, Mr Von Neumann, etc, starting in the 1930s analysed the criteria for setting up information systems, the onwards, self-replicating automata; the class of systems to which cells belong – even, as I recall, predicting that the cell would bean information system of this class. That design-oriented prediction has been abundantly confirmed.

_________

In short, the rhetorical games of attacking he man and attacking the strawman continue unabated. I have responded sufficiently to show that this is unwarranted and constitutes straining at a gnat while swallowing a camel.

As a contrast, onlookers might wish to look at what has emerged at UD here [contrasting the linked Time Magazine piece with its comments] as the moderation for civility has taken hold in at least the linked thread.

Andrew, Farewell:

GEM of TKI

11:49 am  
Anonymous kairosfocus said...

To the others:

I will close with a prayer for your blessing: Grace, open your eyes.

GEM of TKI

11:53 am  
Blogger Smokey said...

Gordon wrote:
"Underlying all of this, is the implicit assumption that lucky noise can credibly account for the origin of not only the particular codes, but the coding system and the associated nanotechnology-based information processing system, within the probabilistic resources of the observed universe."

THIS IS A LIE. Natural selection is neither luck nor noise.

"That, methinks is most incredible, and Trevors and Abel give reasons why here and here in two peer-reviewed papers."

Where is your evidence that they were peer-reviewed, Gordon? None of the reviews I've written have been peer-reviewed.

"2] Minnich-Meyer paper:..."

Has no data from a test of an ID hypothesis.

"3] Oh, yes, I forgot: on haemophilia and loss of clotting factors:

"I suppose, we are invited by S to think, above, that haemophilia was so named as it is an apt description of a properly functioning BCC."

You've got nothing but dishonesty. I'm going by Behe's definition, in which the absence (not relative absence) of function is required. You're moving the goalposts.

"Thus, he demonstrates his want of civility,..."

This from a guy complaining about ad hominem attacks!

"Further to this, while pretending that a blog search is enough,..."

A blog search? No, a Google search is enough. Your blog, with your name--Gordon--at the top, is the first hit.

"... he omits to mention the first attempt to abuse my name by H, which gives my surname as well."

I never used your surname.

"Onlookers, I actually excerpted and highlighted the pattern of experimental work and the hypotheses being tested."

None of those were ID hypotheses.

"Those who are serious can simply read the paper, then if necessary correspond with Mr Minnich."

It's Dr. Minnich.

"7] Start and stop codons

"I pointed out that contrary to the earlier objection, both start and stop codons are in fact used for other purposes,..."

I'm well aware of that. The rare (unintelligent) use of stop codons to code for aa residues has no effect on my pointing out that the stop codons clearly are a more intelligent design than combining start with methionine universally.

"... as well as noting that stop codons have a good reason for being more abundant than start ones."

Relative abundance is irrelevant. It's about the relative intelligence of the alleged designs.

"...[Note, in some cases in microcontroller design, high-end practitioners use the general purpose nature of digital symbols and codes as contexts of interpretation so that under one interpretation certain strings of memory locations are interpreted as code to be executed, and under other contexts,a s data to be read for use in processing."

Yes, that clearly is an intelligent design. However, the genetic code is not "designed" this way, because the data "AUG" is often read as "start with a methionine" in INTERNAL locations, resulting in huge amounts of nonfunctional proteins.

It's stupid.

"In short, we see here a parallel between the codes of life and known practices of designers of microcontrollers for algorithmic control of processes."

No, we see a huge difference, but only if we open our eyes to what our opponent is actually saying, something you'll never do.

"8] Minnich paper and inference to design:"

Straw man. You claimed the Minnich paper includes data from a test of an ID hypothesis. That's not the same thing as an "inference to design," and you know it.

Don't you feel better now that you've admitted your evasiveness and dishonesty?

">> Behe's most famous example is the bacterial flagellum described above. If you take away the driveshaft from the flagellar motor, you do not end up with a motor that functions less well."

You still have a secretory system, which means that it isn't IC.

"...In short, the rhetorical games of attacking he man and attacking the strawman continue unabated."

You'll never stop with those games.

9:10 am  
Blogger Tony Jackson said...

kairosfocus again: “On p. 6 next to the blot they give a simple summary table of experimental results, and discuss same in the main text"

Ha, ha, ha. Gordon, you complete idiot!

That ‘simple summary’ on page 6 refers to the western blot, (read the legend to the figure – “lane designations are in the table to the right showing strain genotypes”). This small table has nothing whatsoever to do with microarray data!

Anyone who knows anything about microarrays would laugh out loud at your mistake. But thank you for answering my second question: as I suspected, you don't know what microaray data should look like.

"[NB: journals and proceedings of course face space constraints so the appearance of summarised results in such a context is not surprising]."

It’s a bit desperate to blame ‘space constraints’ on the absence of any presented microarray data. On the web, such constraints are no longer a problem (which is precisely why many legitimate journals do indeed prefer to publish full and extensive microarray data as on-line supplementary material).

1:53 pm  
Blogger Tony Jackson said...

Seriously Gordon,what is a microarray?

Why is this technology important?

What sort of things does it tell us?

By all means use Google to fnd out if you need to. But at the end of your searching, perhaps you will finally appreciate why it's not cool for Minnich and Meyer to say:

"Using a combination of microarray analysis, genetic fusions, and behaviors of specific engineered mutants, we demonstrate how environmental factors influence gene expression of these multigene families,"

when they very clearly do no such thing.

2:28 pm  
Anonymous kairosfocus said...

Andrew, and others:

I decided to come by after a bit to see how this thread has got on.

The first thing that leaps out at me is the continued Dawkins et al style disrespect and manipulative rhetorical tactics:

1] Continued insistence on using my personal name, instead of respecting my request and concerns.

2] Continued resort to attacks to the man and to the strawman, including the insistent use of insulting language and ill-founded accusations or direct implications of deceit.

3] Continued straining at gnats while swallowing camels. In particular, note that here is a serious issue on the origin of information and information processing systems in the cell [the implicit issue for the thread] by lucky noise, and the related thermodynamics and probability issues. You would not realise that if you were to focus on the points being made on relatively minor issues, mostly attacks to the man and to the strawman.

4] Contrast, onlookers, the substance and tone of discussion here, to see what happens in the end when a discussion is properly regulated to focus on issues rather than tired, atmosphere-poisoning rhetoric. (The case in point also shows just how widespread such tactics are.)

5] Further to this, one should note that those who insistently resort to straining at gnats while swallowing camels, and seek to distract attention though atmosphere poisoning rhetoric via attacks to the man and the strawman, plainly have a poor case on the merits and are motivated by agendas that we should beware of.

Now, I will pick up a few select points, simply to show that the above rebuke is, sadly, well-warranted:

1] S: LIE. Natural selection is neither luck nor noise.

I daresay, we see here both a strawman mischaracterisation of what I have noted at length, and an unjust and now plainly spiteful personal attack -- the insistent demonstrably false accusation that I am a liar. When there is easily accessed always linked information that would tell the truth, then it is plain that such misrepresentation is both intentional and intended to deceive those who would not think to check the facts for themselves.

I cite here, first, Enc Brit online's brief excerpt on NS:

>>process that results in the adaptation of an organism to its environment by means of selectively reproducing changes in its genotype, or genetic constitution.

In natural selection, those variations in the genotype that increase an organism's chances of survival and procreation are preserved and multiplied from generation to generation at the expense of less . . . >>

Wikipedia (not exactly a YEC hangout):

>>Natural selection acts on the phenotype, or the observable characteristics of an organism, such that individuals with favorable phenotypes are more likely to survive and reproduce than those with less favorable phenotypes. If these phenotypes have a genetic basis, then the genotype associated with the favorable phenotype will increase in frequency in the next generation. Over time, this passive process can result in adaptations that enable organisms to be highly specialized for life in a particular ecological niche, and in speciation events in which new species emerge.>>

Professor Kimball:

>>* Living things produce more offspring than the finite resources available to them can support.
* Thus living things face a constant struggle for existence.
* The individuals in a population vary in their phenotypes.
* Some of this variation is inheritable; that is, it is a reflection of variations in genotype.
* Those variants best adapted to the conditions of their life are most likely to survive and reproduce themselves ("survival of the fittest").
* To the extent that their adaptations are inheritable, they will be passed on to their offspring. >>

And, the much maligned YECs at Answers in Genesis:

>>An organism may possess some inheritable trait or character which, in a given environment, gives that organism a greater chance of passing on all of its genes to the next generation (compared with those of its fellows which don’t have it). Over succeeding generations that trait or character has a good chance of becoming more widespread in that population. Such an improved chance of reproductive success (i.e. having offspring) might be obtained in several ways . . . . A greater chance of survival . . . . A greater chance of finding a mate . . . . Any other way of enhancing reproductive success >>

But of course NS is the FILTER part of the mechanism: odds of survival etc improved/lessened.

The root issue I raised by adverting to "lucky noise" is the need to first generate the biofunctionally specific, complex information and associated molecular nanotechnology, first to get to life, then to create the body plan level biodiversity we observe in the current and fossil biospheres. In BOTH cases, I have pointed out and explained, as have many others, why chance + necessity alone [As Nobel Prize winner Monod famously used] cannot credibly get to such systems as are observed, across the gamut of the observed universe. So, the claim that I am misrepresenting NS is false and misrepresent what I have argued in details with links.

In short, S makes a strawman attack joined to a slanderous accusation.

This pattern of misbehaviour is shameful; or, is it shameless?

2] a guy complaining about ad hominem attacks!

As onlookers can see yet again from the above, I am pointing out, and have detailed that there is a campaign of slanders and misrepresentations, sustained not only here but all across the Internet. [Cf the linked discussion in UD and the onward cases in point.]

3] TJ [having called me an idiot]: That ‘simple summary’ on page 6 refers to the western blot

In other words, what I pointed to, is exactly as I described, "a simple summary table of experimental results." [I never set out to claim anything in details about micro-arrays or western blots etc. I will pause to note that micro-array analysis inter alia has to do with assessing expression/non expression of DNA segments, so the table as reported on eemperature controlled expression or non-expression in the bacteria is credibly traceable to micro-array techniques, not just analysis of resulting proteins expressed based on separation by mass and antibody activity in gels etc. In short, there is a question here as to whether TJ set out to exploit assumed ignorance, or was careless and jaundiced in his reading of the paper. How, apart from the micro-array analysis they claimed, would Minnich credibly have obtained the data for the table, or are we being invited to infer on the strength of TJ's dismissal of a table that credibly can be so derived from micro-array analysis, that Minnich lied?]

Now, my main intent was to point out that Minnich and Meyer have presented relevant findings based on experimental work, theirs and that of others. Further to this, the now plainly quyestionable claims on absence of micro-array analysis results being made by TJ are:

[i] irrelevant to the main issue in the thread [i.e. Is yet another distraction by changing the focus of attention improperly];

[ii] irrelevant to the point that Minnich et al cited specific experimental results – theirs and others -- credible to rebut Miller's assertion that the TTSS is a darwinian intermediary tot he flagellum [if the full set of genes for the flagellum are present but are not expressed, then we see the use of a subset of information to generate a related but derivative system];

[iii] intended to undermine the credibility of Mr Minnich by implying that absent demonstrative proof otherwisehe is a liar in reporting as he reported in a peer-reviewed context;

[iv] intended to attack me on a technicality on a distraction rather than address the information-generation and nanotechnology generation issues in the main.]

Further discussion in the text amplified just what Minnich et al report that they did and what others did and how it is relevant to the issue at stake in the discussion from Behe to Miller to Minnich et al -- all as I have previously discussed.

The net result is that they have provided good reason to conclude that Mr Miller's dismissal of the IC nature of the flagellum is premature. [And, BTW, S, in case you do not know, it is proper to refer to a Doctorate-holding person as Mr etc., in a context where it is not intentionally disrespectful.]

I observe on rhetoric, that in a peer-reviewed context, Minnich -- a known researcher working in a known lab publishing in the scientific literature -- reports that he undertook certain experimental investigations. Thus, the burden of proof on showing the fact otherwise, rests on his detractors.

Sorry, it is not enough to imply that a man is a liar to assume that this is shown to be so absent proof to an arbitrarily high standard that he spoke the truth. [And, BTW, S, in the context of the Sternberg case, do you seriously believe that two articles in peer-reviewed journals that argue to ID supportive points will not be seriously peer reviewed before publication, i.e the papers of Trevors and Abel. Again, onlookers, note the unwarranted inference to lying.]

Further to this, observe carefully the rhetorical strategy: the actual focus of the thread is on the information systems of life and the associated nanotechnology. TJ is here distracting through attacking Mr Minnich, then me. And, in a context that there is reason to believe that the table I adverted to is based on micro-array analysis, which is precisely a way to get such data and is reported as the basis for the tabulated results.

Finally, TJ has yet to answer cogently to the issue of the credible origin of observed complex, biologically functional information on the gamut of the observed cosmos, in a context that does not refer to the known source of FSCI, agency. As a biochemist by his own admission, he should be able to address the thermodynamics and associated functionally complex information generation issues I and others have raised. That he has chosen instead to resort to tactics as above, is telling on the case in the main.

___________

I have again done sufficient to show that the onward pattern in the thread is just as unproductive as what obtained before, and that it is rooted in atmosphere poisoning rhetoric by evolutionary materialism advocated based on attacks to the man and the strawman.

Enough has again been said.

May Grace open eyes

GEM of TKI

12:08 pm  
Blogger Tony Jackson said...

Kairosfocus: I regretted calling you an idiot after my last post. But just when I’m beginning to feel contrite, what do you do? You send your latest pile of rambling rubbish and that makes me think I was right after all.

You say: “I will pause to note that micro-array analysis inter alia has to do with assessing expression/non expression of DNA segments, so the table as reported on temperature controlled expression or non-expression in the bacteria is credibly traceable to micro-array techniques, not just analysis of resulting proteins expressed based on separation by mass and antibody activity in gels etc.”

Excuse me while I pick my jaw up from the floor. This statement is pure double-distilled nonsense and confirms yet again that you simply don’t have the faintest idea what you’re talking about. Don’t try and bullshit your way out of this – my last published paper included a microarray analysis, so I think I can recognise such data when I see it and I absolutely, positively assure you that the table you quote in the Minnich and Meyer conference presentation has nothing whatsoever to do with microarrays!

“Finally, TJ has yet to answer cogently to the issue of the credible origin of observed complex, biologically functional information on the gamut of the observed cosmos, in a context that does not refer to the known source of FSCI, agency. As a biochemist by his own admission, he should be able to address the thermodynamics and associated functionally complex information generation issues I and others have raised. That he has chosen instead to resort to tactics as above, is telling on the case in the main.”

I have previously addressed the issue of FCSI and explained why serious scientists do not take it seriously. Similarly, I have previously explained why your invocation of thermodynamic equations in this particular context is misdirection. I have also candidly pointed out that at the moment, we don’t know how life got started on this planet. The origin of life is indeed a fascinating mystery, arguably one of the biggest unsolved problems in the whole of science. I don’t know what the detailed answer would look like – but then neither do you.

9:52 pm  

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