Thursday, January 19, 2006

ID Falsification - Stage 1

ID is rejected as science both because it cannot be falsified and because it has been falsified (Ken Miller) which seems rather odd to me. I tend to agree with Ken Miller... that ID is falsifiable but that the Type 3 secretory system is insufficient for a really good hit below the water line!

The suggestion of co-option as one of the means by which biological complexity is generated is used to explain apparent irreducible complexity and the Type 3 Secretory system is suggested as a clear candidate for a functional intermediate along the way to a fully functional motor.

Behe and other ID theorists respond by saying that the Type 3 system is a broken flagellum rather than a stepping stone on the way there and if if it was a stepping stone on the way there it does not allow macro-evolutionists to cross the river.

Can this impasse be resolved?

I suggest that it could. Matzke proposes 6 stages along the way to a functional flagellum.
If it could be shown that these six stages provide a selectively advantageous function and that the steps in between are "mutationally plausible" as Matzke claims then for me the argument over the flagellum is over.

If we take as an example the two putative structures from Matzke’s series either side of the acquisition of the mutation which gives a selectable motility trait:

It surely cannot be beyond the limits of modern mathematics, computer science and molecular biology to work out the probability of the necessary changes occurring independently in the relevant proteins to get a primitive flagellum can it?

Given the mutation rate and an estimate for the time and approximate number ofrelevant bacteria....is this a reasonable step?

I have no idea...but If it is and if the Protoflagellum works and provides a selective advantage then as far as I am concerned the argument over the flagellum is over. Those "if's" are very big however!

Show me 6 selectable intermediates and show me that the above step is indeed mutationally possible and I will stop shouting....Look at this motor .....Look at this motor!

Is that a reasonable challenge? Is it falsifiable?

18 Comments:

Blogger Lifewish said...

I'd agree with the premise that if evolution is the correct explanation it should be eventually possible to show that all the steps required to get to that point are fairly probable. So yes, your hypothesis (that there will never be a demonstrably plausible approach to flagellum evolution) is broadly speaking falsifiable. However, there's a couple of caveats.

First is the phrase "fairly probable". Any given combination of mutations will be horribly improbable, and that includes ones that have demonstrably occurred (for example, the recently-evolved nylon eating bacterium). I speak as someone who's actually doing a bioinformatics project on this very subject. The question then arises: "probable compared to what?"

Secondly, and on a similar note, it's not entirely fair to point at an existing feature and say "see that? That couldn't possibly have occurred naturally"*. If you threw a bunch of coins and came up with some random combination of heads and tails, you could probably eventually figure out a way in which that sequence appeared non-random ("it's a ROT-13 encrypted version of the Unicode encoding of a mistranslation of some random Bible phrase from the ancient Hebrew into Sanskrit. See, that could never have occurred naturally"). Without knowledge of the number of different objects that would have garnered a response of "that doesn't look natural" it's impossible to objectively determine how likely it is for said claim to be correct.

So yes, the flagellum may be implausible (I currently don't know), but if there are 5000000 other structures that are effectively interchangeable with it then it starts to look less unlikely that one of them occurred.

Thirdly, an inability to present a detailed explanation here and now of how this thing might have evolved does not in any way imply that it couldn't have evolved. You'd have to have a positive argument for why it couldn't have evolved, otherwise any attempt to infer Divine Intervention would be a classic God of the Gaps argument. The problem being that this means you're biased against any legitimate reduction in the size of the gaps, which isn't a very scientific attitude. "I can't see how it could have happened, so it didn't" wasn't a valid argument when it was being used to deny the existence of plate tectonics, and it's not very convincing now.

So yes, it's falsifiable, but you'd have to subject it to scrutiny for at least a few years before claiming that the fact that it hadn't been falsified was a big thing.

Fourthly, I should point out (probably unnecessarily) that although the hypothesis you state is falsifiable, this doesn't mean that ID as a whole is, because you're still able to say "OK, maybe that feature can evolve naturally, but I'm sure this one can't".

Having said that, I will keep an eye out for a detailed explanation.

* I'm aware that's not exactly what you're saying - apologies for paraphrasing.

10:58 pm  
Blogger Andrew Rowell said...

Lifewish,

Thank you for your helpful comment. Do you believe in some kind of "upper probability boundary"?

8:53 am  
Blogger Paul (probably - maybe Liz) said...

Hi, Andrew. As you know (but lifewish seems not to) the issue of probability boundaries is being addressed in threads on ARN, and on my blogsite I have talked about it in several stages. If the number of possible working structures is 10^6, but the total number of structures is 10^150. then frankly, the fact that there are multiple solutions is irrelevant. But the discussion is (at last! - I have been pushing for more formalism in this debate for over a year) possibly moving past there to some hard numbers.

The nylon-eating bacterium is not that improbable, actually - neither was the mutation that may have led to anti-freeze glycoproteins being present in some fish. These examples are on their way to becoming icons of evolution.

9:09 am  
Blogger Stephen E. Jones said...

Andrew

Congratulations on a fine blog.

There is a simple answer to how improbable the assembling of the bacterial flagellum rotary motor is, and that is it arose only *once* in the entire ~2.5 billion-year history of bacteria (the oldest, most numerous, shortest generation, form of life).

Darwinists were once fond of quoting that the eye arose independently 40+ times (it turned out the basic pax-6 gene eye machinery, and therefore the eye, arose only *once*!) and that showed that it was relatively easy for the natural selection of random mutations to produce something as complex as the eye.

So by the Darwinists own logic, if something arose only *once* in the entire history of life (especially in the form of life that had had the most random mutations), then it must be as close to impossible as one could imagine.

Which means that it actually *could* be impossible - by the natural selection of random mutations!

Stephen E. Jones
http://creationevolutiondesign.blogspot.com/

3:41 pm  
Blogger Lifewish said...

Thank you for your helpful comment. Do you believe in some kind of "upper probability boundary"?

Not really. Things that in and of themselves are staggeringly improbable happen every day of the week. As an example, throw a handful of coins in the air. Miraculously, all of them end up lying flat and stationary on the ground, rather than hovering in midair! What are the chances of that? On the face of it, the probability of this occurring would seem to be incredibly small - consider the number of speeds, positions and orientations the coins could take.

The appearance of biological structures that are on the face of it incredibly improbable is only unlikely if you live in a world with no evolution. Likewise, a lot of coins all flat on the floor is only unlikely if you live on a (non-rotating) space station. In both cases, raw computation of probabilities is likely to be unhelpful.

Incidentally, Paul: I'm perfectly aware of the discussion at ARN - I post there under the name of Corkscrew (sadly it was taken when I signed up to Blogspot). I assume you're referring to the "ID challenge" thread? I've been avoiding responding to it because term just started and I need to work but, to summarise, evolution doesn't work by brute force and any attempt to model it as brute force is likely to be just as effective as the infamous model of kangaroos that "proved" they can't jump.

I'm kinda losing respect for the ARN forums after my attempt to actually propose an experiment for EAM vs. RMNS was met with what I can only describe as a sulky reaction from mturner to the very idea of *gasp* testing stuff. The fact that this didn't seem to bother anyone else (apart from Gary) in the slightest was rather off-putting, especially after the time I put into figuring out how to make the experiment bias-free.

There is a simple answer to how improbable the assembling of the bacterial flagellum rotary motor is, and that is it arose only *once* in the entire ~2.5 billion-year history of bacteria (the oldest, most numerous, shortest generation, form of life).

(I'll assume you meant that the flagellum only evolved twice overall - the eukaryotic flagellum is fundamentally different from the bacterial flagellum)

How do you know that? It could have evolved a thousand times in various species of bacterium and we wouldn't know because the less effective versions would tend to die out. History is written by the winner, and the same goes for the natural world we see today.

So by the Darwinists own logic, if something arose only *once* in the entire history of life (especially in the form of life that had had the most random mutations), then it must be as close to impossible as one could imagine.

Things that arise only once are a dime a dozen in biology - you're an example, so am I, so is Andrew etc. And the probability of any one of us having arisen is indeed practically zero. This does not mean that we were cloned by aliens (or equivalent "unnatural" approach of your choice).

This is precisely the point I made in the first and second caveats of my original post. The question therefore remains: unlikely compared to what? Additionally, as I pointed out, we have no idea how many billions of different structures there are out there that could be substituted for a bacterial flagellum.

Incidentally, if you're interested in probability in genetics, you might be interested in this computer project that I'm working on at uni. It's obviously no substitute for training in biology, but it gives an excellent feel for how improbability is actually calculated on a genetic level. The answer being: they generally don't bother, for the aforementioned reasons. Instead they calculate a "distance" function, to see how easy it is to flow from one to the other.

Sadly, I'm not sure how this could be calculated for historical examples like the eye - we don't actually have copies of the genome for the last few hundred million years of our ancestry :(

7:46 pm  
Blogger Lifewish said...

Uh... apologies for length of post :-/

7:46 pm  
Anonymous Anonymous said...

Lifewish said,

"Things that arise only once are a dime a dozen in biology - you're an example, so am I, so is Andrew etc. "

I somehow cannot seperate this functionality of today's baby births apart from our overall existence. While it may seem simple to biology, the problem seems to be one of reductionism.

"And the probability of any one of us having arisen is indeed practically zero. "

OK, this I can relate to as to the universe itself we seem to be quite extraordinary.

This does not mean that we were cloned by aliens (or equivalent "unnatural" approach of your choice)."

Truth is we don't know do we? I mean, not by any scientific standards? Its possible outside our 'known' universe exist intelligent beings which have had a billion years to play and create worlds? We're playing with new forms of life today, Green pigs? And I think it rather remarkable we are doing so as far as educated man is here for how long? 4000 years ago were first symbolic written words? Where will we be 4000 years from now?

Are there any scientific estimates and stats upon which the community of scientist agree of our unique self-aware existence?

I remember past 'scientific' estimates that we were not unique at all. Is the current trend any different today?

Why is nylon eating bacteria 'horribly improbable'?

Eventually everything breaks down into component parts. Bacteria is one of the mechanisms to enhance the cycle. I would expect bacteria to not only eat nylon, but many other 'man-made' objects as well.

heres a quote from microbe.org.
"They "eat" everything from sugar and starch to sunlight, sulfur and iron. There's even a species of bacteria—Deinococcus radiodurans—that can withstand blasts of radiation 1,000 times greater than would kill a human being."

I'm just a lay person, 20 years since I picked up a calculus book, but it seems apples and oranges are being mixed about here.

We must take a starting point. Flagellum seems a good point in comparison to the eye. It is one of the simplest structures to look at and determine steps. I think science should be able to answer these questions eventually utilizing evolutionary theory or it will be less and less defensible in the future.

And I think the reason why is science is starting to morph its own genetic renditions of life and we will be able to track each new slice of morphology. Green pigs today, Polka Dotted green tomorrow, and with less fat the next year.

Green Eggs and Ham indeed He said with a sly grin around the table, Green Eggs and Ham bobbing his head with the gleeful sound of his fable.

Michael

1:34 am  
Blogger Paul (probably - maybe Liz) said...

Hi, Lifewish. Nice to know that the CompSci tripos hasn't got substantially lighter since I was there.

See also my comments on Avida, however.

10:32 pm  
Blogger Lifewish said...

'This does not mean that we were cloned by aliens (or equivalent "unnatural" approach of your choice)."'

Truth is we don't know do we?


Well, personally I'm fairly sure I was the product of natural reproduction. I was talking about individual humans, not the human race. Every single one of us is a unique, and vastly improbable, event.

The point being, of course, that the fact that something only arose once in no way means that it couldn't have occurred. The calculation of whether something could plausibly have occurred is vastly more complex than you suggest.

Its possible outside our 'known' universe exist intelligent beings which have had a billion years to play and create worlds?

Oh, entirely possible. Probably not necessary though. And if it's not necessary then positing undetectable entities is not considered scientifically helpful. Heck, it's not always considered helpful even if it is considered necessary - consider the rows that erupted over dark matter.

Why is nylon eating bacteria 'horribly improbable'?

Because nylon wasn't around til 1935. That means that the bacteria have had a maximum of 71 years to evolve the ability to eat the stuff, an ability that they did not have before.

And no, nylon does not easily break down into its component parts. Consider the contents of pretty much any landfill site.

We must take a starting point. Flagellum seems a good point in comparison to the eye. It is one of the simplest structures to look at and determine steps. I think science should be able to answer these questions eventually utilizing evolutionary theory or it will be less and less defensible in the future.

I thought the point was that it wasn't simple :P

Nonetheless, fair point. I'm trying and failing to come up with an approach to determining whether the step Andrew originally mentioned was implausible. The simplest plausibility test would be just to compare some sort of minimal genome in the case of a "before" species and an "after" species to figure out how different they were, then estimate from that how many generations it would have taken to make the change.

The problem is that this doesn't take into account the plausibility of intermediate steps - both species are on the same golf course, and the "after" species is closer to the hole than the "before" species, but for all we know there's a ridge between them. The only way this approach would be valid would be if the answer turned out to be only a few generations, in which case the obstacle would be small enough for the golf ball to bounce over.

Anyway, given the reproduction rate of bacteria, pretty much any change in their genome would probably pass this test. Make of that what you will.

The next simplest plausibility test would involve testing bacteria modified to have some of the DNA from one species and some from the other. This would then give us a vague idea of the terrain between the two species.

The problem here is that a lot of Irreducibly Complex structures were believed to have had "scaffolding" at one point - extra structures which made the evolutionary process more trivial and which have since evolved away. In golf terms, the fairway would zigzag - any attempt to go straight from the tee to the hole would land you in the rough. Without knowing the shape of the zigzags it would be very difficult to generate an appropriate set of modified bacteria, and if we know the shape then the experiment would be redundant anyway.

I can't think of any better plausibility test. In an ideal world, we'd be able to plot the fitness of a genome as a direct function of its code without having to actually implant it in a bacterium and watch it breed for a few generations. If we could do this, it would then be mathematically plausible to figure out the chance of any one genome evolving into another. Sadly, such a function does not exist and quite possibly never will.

All we can do is keep an eye open for possible intermediate forms. We'll either get lucky or we won't. Problem is, even if we do get very lucky and manage to map out the flagellum evolution even more thoroughly than we already have, it still won't convince everybody - the infamous "every transitional fossil just creates two new gaps" fallacy can be brought into play with demands for the next level of detail.

12:00 am  
Blogger Lifewish said...

Incidentally, I've just noticed that this discussion is slightly irrelevant. The statement of Behe et al is that the flagellum couldn't have evolved because IC structures break without all their parts present. This claim is falsified by the existence of the type 3 secretory system, regardless of whether it's a protoflagellum or a broken flagellum. The counter-rebuttal employed by Behe et al is thus irrelevant.

It'd still be nice to figure out an exact route by which the flagellum could have evolved, of course. I'll read up on it when I have spare time (ah, the joys of having a copyright library just down the road :P)

12:07 am  
Anonymous Farshad said...


Stephen Said:
There is a simple answer to how improbable the assembling of the bacterial flagellum rotary motor is, and that is it arose only *once* in the entire ~2.5 billion-year history of bacteria (the oldest, most numerous, shortest generation, form of life).


Very good point indeed. If nature own a flagellum design factory it should have worked only for a very short period of time in whole history of life and then bankrupted.

The question here is if the nature has the capability to evolve the flagellum, why the e-coli remains unchanged for past billions of years. If evolution is so dynamic as we expect it to be as we understand from its darwinian definiton, then I can expect to grow cultures of bacteria in my kitchen and after millions of generation -which I can easily obtain in a few weeks or days I don't know- they turn out to be something else lets say a bacteria equipped with a Type-V bacterial secretion system enhanced with some form of afterburner!

You can go forward and build a bacteria farm to produce billions of generations of it for your whole life but at the end what you will have is still the same species of bacteria.

I'm not sure how much time will it take for biologists to convince themselves that antibiotic resistance in bacteria is not caused as a result of random mutations but it is some form of adaption of bacterial immunity system which is a built-in capability of bacteria that is there by design.

10:22 pm  
Blogger Lifewish said...

The question here is if the nature has the capability to evolve the flagellum, why the e-coli remains unchanged for past billions of years.

Because E Coli is perfectly happy where it is. It has optimised itself to fit its environment to a tee. That means that any variations from the norm tend not to do as well.

Now, if you put it in a different environment, that it's not optimised for, then you'd expect to see it evolve, to re-optimise itself for this new environment.

Want to try an experiment to demonstrate this? Build your bacteria farm. Figure out the minimal proportion of bleach in water that'll kill the bacteria outright. Then put the bacteria in water that contains, say, a tenth of that proportion. Some will die; some will limp along; some will take it in their stride.

Wait a few weeks then up the proportion - use two-tenths of the lethal dose. Again, some bacteria will die or be hobbled and some will keep going. Wait a few more weeks then up the dose again.

Repeat the process for about 10 iterations. Or maybe more - you may need to reduce the rate at which the dosage increases if it starts to kill all the bacteria outright). You may also need to wait slightly longer between iterations for the bacteria to get themselves back up to speed. But eventually, you should have a population of bacteria that can thrive in what should be a lethal dose of bleach.

Now to check that it's genetic not developmental. Place the bacteria back in uncontaminated water (this'll probably kill a few of them outright, but hey) and wait til they've divided a couple of times. The new bacteria won't have been exposed to bleach while forming. Now put them back in the bleach-tainted water. If the change is genetic, they should survive.

I actually have no idea what the outcome of this experiment would be cos I haven't done it myself but, if it produces the results I predicted, that would constitute strong evidence that E Coli are perfectly capable of evolving when necessary.

---------------

Now, consider the consequences for bacteria like this if a large amount of bleach got released into the world's oceans. Suddenly, they're top dog. They've got an entire ocean that's almost completely free of competition to live in, plus they have plenty of food (what did you think happened to the dolphins...). Their population will explode, and almost all of them will survive, regardless of what dumb mistakes get made in the DNA copying process.

So what if a secretory system starts growing a pilus? That's not gonna get the bacterium killed off instantly and, by the time the ocean's full up of bacteria again (and thus the selective pressure reappears), the mutated bacterium will have found itself in a position to occupy a new evolutionary niche - that of sticky bacterium.

So what if an ion pump accidentally gets wired up to the base of a bacterium with a pilus? The new variant will survive long enough to "discover" that the resultant structure, if properly fine-tuned, is excellent for moving it around, even in the direction of food. The bacterium has found yet another new niche - that of speedy bacterium.

And so on and so forth.

4:59 pm  
Anonymous Farshad said...

I was away from this Blog for a while. Lately in my free time was busy reading the Dover trial and what Behe said on behalf of Intelligent Design. In trial transcripts the flagellum part took my interest and from those insigths I can say the following:

lifewish said:
Because E Coli is perfectly happy where it is. It has optimised itself to fit its environment to a tee. That means that any variations from the norm tend not to do as well.


The above statement looks interesting. The first question that arises here is that if E Coli or in general bacteria family was happy when they reach to some certain point of saturation in their evolution, why a line of them evolved further and transorfmed into more complex life forms? At this point one may speculate that because one line of them went under a different selective pressure that directed them to evolve.

However if we assume this speculation is true then I need to ask another question:

Evolution theory claims that at some moment in the past there was an species of E-Coli without a flagellum that gradually evolved into ones equipped with a flagellum.

If one line of bacteria evolved into complex life forms and the rest decided not to evolve because of different selective pressures on them, why in same way we don't see ancestors of E Coli that are not equipped with flagellum?

There must have been an environment that those ancestors of "E Coli without a flagellum" could perfectly be happy where they are. However we don't see any of those transitional forms of bacteria: staring with a flagellum-less bacteria to one equipped with a completed flagellum-

There must be thousands of those transitional forms that could have isolate themselves somewhere on this planet,lived happily and optimised themself to fit their particular environment which doesn't necessarily require a flagellum to survive.

If E coli could remain intact for billions of years why not even one of its original ancestors couldn't remain intact also?

Isn't lack of these ancestors an evidence for the fact that E-Coli was always E-Coli and will always remain as E-coli?

The same must be true for other transitional forms of all life forms too. Why we don't see any of them around? Natural selection deosn't mean that all of those T/F must have been extincted.

The problem here with N/S is that the definition for N/S is too vague to enable us decide on the above matters. But again I can say N/S shouldn't necessarily mean that all ancestors of an evolved life form must be doomed to death. According to darwinism if descendants of Bacteria could evolve into mamals and human(a big wow here!) but the bacteria itself could be preserved over billions of years then we could expect that ancestors of bacteria also must have been preserved in sameway.

Am I correct or missing something?

When we say E coli is happy here and it stopped evolving does it mean if somehow we make it unhappy, will it start to develop different mechanisms and micro-motors to adapt himself and be happy again?
If it is so then it must be somehow easy to test because an e-coli can reproduce in 20 minutes and it opens a door to empiricaly test it as Behe states:

"In fact, intelligent design is open to direct experimental rebuttal. Here is a thought experiment that makes the point clear. In Darwin's Black Box, I claimed that the bacterial flagellum was irreducibly complex and so required deliberate intelligent design. The flip side of this claim is that the flagellum can't be produced by natural selection acting on random mutation, or any other unintelligent process.

To falsify such a claim, a scientist could go into the laboratory, place a bacterial species lacking a flagellum under some selective pressure, for mobility, say, grow it for 10,000 generations, and see if a flagellum, or any equally complex system, was produced. If that happened, my claims would be neatly disproven

So let me summarize that slide. It says that if, in fact, by experiment, by growing something or seeing that in some organism such as a bacterium grown under laboratory conditions, grown for and examined before and afterwards, if it were seen that random mutation and natural selection could indeed produce the purposeful arrangement of parts of sufficient complexity to mimic things that we find in the cell, then, in fact, my claim that intelligent design was necessary to explain such things would be neatly falsified."


Now I want to ask. Can we take a group of E-coli with flagellum code removed from their genes and then reproduce them in a lab under a selective pressure for motion for thousands of generations and then gradually observe them producing a sectretory system leading to a flagellum?

---------------------------------

...and for resistance of E-coli to different chemicals it seems to be its built-in immunity system that can adapt itself to different hazardous environments rather than an evolutionary process.

I can speculate that E coli knows by design how to develope resistance under different conditions so it can survive.i.e. it is one of the E coli's internal capabilties to resist chemicals.

However it's open to discussion.

Also if it is evolution then according to me it is MicroEvolution process and must not be confused with macro changes like appearance of a complex flagellum which is quiet a diffent subject.

6:12 pm  
Anonymous Farshad said...

lifewish said:
Because E Coli is perfectly happy where it is


another thing that I forgot to mention is:

I don't think being happy is an criterion for the evolution process to stop. Evolution is about random trial and error until the best is found and this process is done continously regardless of the current state of the fitness of that species. Being happy is a subjective point of view. There can always be a more efficient and more fit(happy) species of the E-Coli so if Evolution is true then E-Coli must undergo this process even if it seems to be quite happy, otherwise evolution must have been stopped billions of years ago.

6:42 pm  
Blogger beervolcano said...

Why the bacterial flagellum? Why not photosystem I or photosystem II?

Those are WAY more complicated and intricate than the bacterial flagellum.

1:45 am  
Blogger Andrew Rowell said...

Beer,

You have got to start somewhere. If it works for the flagellum then it will work for more complex structures like the photosystems or a ribosome etc.

1:58 pm  
Blogger beervolcano said...

So you consider the ribosome irreducibly complex?

Both kinds? 80S and 70S? What about all the different subunits? Are they irreducibly complex too?

What about the whole process of translation? Take away t-RNAs and the whole thing breaks down. Take away m-RNA the whole thing breaks down. Take away start and stop codons, the whole thing breaks down. Take away any of the ribosomal subunits and the whole thing breaks down. Take away the proteins that catalyze most of this process and the whole thing breaks down. Uh oh, where did those proteins come from? You can't have them without ribosomes, right? Whew, they came from the parent who, in turn, got something slightly different from its parent and so on. Thank God, life is one long chain of being and everything is interconnected and interdependent. Wow, it's so interconnected and interdependent that if you take out one small bit here and maybe a bit from over there the whole thing breaks down and reaches equilibrium (death). I guess that's what IC means? Take out my heart and I die, or my brain perhaps.

Or maybe IC is a flawed concept.

I'm not saying that there are many things in this world and many processes of living things that can withstand removal of one of the chain of events and survive equilibrium (death). I'm saying that just because some process or structure is interconnected and interdependent, it does not mean that there is no way for that process or structure to have evolved.

1:46 am  
Blogger Andrew Rowell said...

Beervolcano,

The macro-evolutionist says that it is reasonable to believe that all this complexity happened without any intelligence being involved. I simply want to know if it is so....

I suspect that it aint so...

Is there a way in which we can answer that question once for all?

Can we really develop a reliable design detection apparatus or not?

10:55 am  

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