ID in the United Kingdom

What is Intelligent Design?

2010-12-15T22:59:00.002Z

It is the area of science that studies the signs of intelligence.
Intelligent agents produce artifacts that other intelligent agents can recognize as the products of intelligence.
These artifacts may include:
1. Complex information

AND/OR

2. Multiple parts functioning together which have an irreducible core.

Shortcuts to new protein folds.

2010-10-17T22:30:00.000+01:00

There are some possible shortcuts.
1. The changes that are known to occur which change how specific an enzyme is for a particular reaction thus allowing it to use a slightly different chemical.
These are where a small change in the structure of an existing protein means that it can use a slightly altered substrate.
Examples of this kind of change are the oscillations in the antibiotics battle.
People discover an antibiotic --> microbes die
a microbe develops resistance by a small change in protein structure --> people die
People develop a slightly changed antibiotic --> microbes die.
Etc.
In these cases there is a shortcut to other similar functions by a relatively small number of mutations.
(Usually it is this kind of change that is presented as evidence for evolution.)
Why aren’t this kind of shortcuts sufficient to reassure us that evolution can solve the problem?
Not all proteins have this kind of relationship with each other. Protein databases have 1777 classes of structural domains These are the “superfamilies” of protein structures. There may be recognisable similarities between domains within a superfamily … but the superfamilies themselves are not related.
Even if all the proteins within a superfamily can be derived from one original sequence this does not explain the origin of all the 1777 plus classes of superfamily.
2. If a relatively few changes causes a change in function and this is followed by subsequent sequence divergence in the new protein. Axe considers an example of this from PA Alexander published in PNAS….. and argues that this will not get us very far.
3. If proteins are made up of a relatively small set of “chunks” rather like a lego kit. This would simplify the problem of building a new protein superfamily. Gene fusion events can be used to build a new structure.
But Axe states that…”The binding interfaces by which elements of secondary structure combine to become units of tertiary structure are predominantly sequence dependent, and therefore not generic.”
Thus enzymes with an identical function and 50% sequence similarity do not have chunks which are interchangeable. Even when this similarity is increased to 90% equivalent chunks are not interchangeable. Graziano and his co-workers constructed and tested a huge library of 10^8 variants of gene segments and found none that formed a folded structure.

Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends.

The Origin of Protein folds

2010-09-26T23:14:00.003+01:00

Just trying to simplify the arguments of Axe in his review paper...

If we take E.coli as our model then the average length of a functional protein is around 300 amino acids.

If the protein is longer or if a number of different proteins are required to act in concert then the problem is made worse.

The number of possible sequences to be sampled to find functional proteins of this moderate size is vast...

There are two ways of reducing the sparse sampling problem.

(a) The number of possible sequences with a particular function is very large. Sequence space is rich in function.

(b) The functional sequences are in some way linked- once you have one function it is easy to jump to the next.

Axe argues that experimental results indicate that (a) is not big enough to solve the sparse search problem....

I will look at what he says about (b) next week!

The Case Against a Darwinian Origin of Protein Folds

2010-08-17T09:00:00.003+01:00

One of the paragraphs from the conclusion of Douglas Axe's recent article:

Clearly, if this conclusion (A dawinian search is insufficient to find new protein folds) is correct it calls for a serious rethink of how we explain protein origins, and that means a rethink of biological origins as a whole. Drawing on some of the points developed here, I presented an earlier version of this case several years ago to two prominent experts in the field. Bothered by my conclusion, both felt that it must be in error. When the three of us met for a discussion, they had their own hunches about where my reasoning might have gone wrong. Interestingly, though, after perhaps two hours of heated discussion neither agreed with the other’s hunch, and we ended up at a polite but dissatisfying impasse. I left with the distinct impression that my conclusion was being rejected not because it was unfounded but because it was unwelcome.

Is intelligent design a possible cause of the origin of biological information?

2010-06-13T22:22:00.003+01:00

In his 7th chapter Meyer discusses the nature of “historical sciences” such as geology and paleontology and evolutionary biology and argues that they use different methods to “experimental sciences” such as physics and chemistry.

He states that Stephen Jay Gould accepted this distinction and argued that historical scientific theories were testable by analysing their “explanatory power” (Gould, “Evolution and the Triumph of Homology”) Gould describes the process of testing in historical sciences as seeking “consilience”. Consilience is the situation where many facts can be explained well by a single proposition or theory.
Gould argues that historical sciences depend upon the knowledge of the laws of nature to make inferences about the past.

Meyer then asks whether a design hypothesis can be formulated as a historical scientific theory about what happened in the past.

Historical scientists cite the occurrence of an event or series of events in the past as the explanation for some observable phenomenon in the present.

Historical scientists use a distinctive mode of reasoning. Using their knowledge of cause and effect relationships historical scientists “calculate backwards” and infer past conditions and causes from present conditions and causes.

This type of reasoning is called “abductive” reasoning as opposed to inductive (in which a universal law is established from repeated observations) or deductive (in which a particular fact is deduced by applying a general law to another particular case.

Abductive logic was first described by Charles Sanders Pierce.

Despite the tentative nature of abductive reasoning we do make conclusive inferences about the past.

A conclusion of abductive reasoning is certain if we cannot explain the currently observed facts without the past cause.

An abductive conclusion is established by showing that it is either the best or the only explanation of the effects in question.

To address this problem in geology Thomas Chamberlain proposed a method of “multiple working hypotheses. This is also known as “inference to the best explanation”

Peter Lipton is associated with this way of reasoning arguing that it is used both in science and ordinary life. Discovering certain particular marks in fresh snow we infer that a person with snow shoes has passed this way. Lipton argued that the ability to explain particular facts sometimes mattered more than predictive success in the evaluation of a particular hypothesis.

The problem with this method of assessing explanations is exactly how we judge which is the best explanation as opposed to the explanation we like the best.
What makes an explanation the best?
1. A good explanation is causal.
2. A good explanation for a particular event is something which provides a “causal difference” in the outcome.

Historical scientists use the principle of causal adequacy. Causes that are known to produce the effect in question are better explanations. Charles Lyell expressed this as – “explanation of the past by causes now in operation.” Michael Scriven described this method as “retrospective causal analysis.” The candidate cause must provide independent evidence showing itself able to produce this effect on other occasions.

When there is only one possible cause for a particular effect the solution to the problem of what really happened is easy. This situation is where historical scientists can infer a uniquely plausible cause. For example an archaeologist who knows that scribes are the only known cause of linguistic inscriptions will, when they find a tablet containing ancient writing infer scribal activity. Where a particular past cause is known to be necessary to produce a subsequent effect, the occurrence of the effect is taken as sufficient to establish the occurrence of the cause.

Where there is more than one possible cause the situation is more difficult. In this case scientists will look for additional evidence that can help distinguish the explanatory power of the remaining explanations. They will look for additional facts for which there is only one adequate causal explanation. In practice the process of determining the best explanation involves examining a list of possible hypotheses. These will be compared for their known causal powers against the relevant evidence and then, like a detective, the scientist will progressively eliminate inadequate explanations until only one is left.

A second way of addressing this problem is to ask which of the adequate causes was actually present at the time of the event in question. Thus two criteria are needed:
1. causal adequacy
2. causal existence
To meet the second criteria historical scientists must show that the proposed cause is not only able to produce the event in question but that it was actually present at the right time and in the right place.
There are two ways of doing this
1. Showing the presently acting course must have been present in the past because this cause is the only known cause of the effect in question.
2. By examining a wider class of facts to show that only one other possible cause explains the whole collection.

Michael Scriven summarises situation. To establish a causal claim a historical scientist
1. needs to show that his proposed cause was present
2. that his proposed cause able to produce the effect under study
3. there is an absence of evidence of other possible causes.

Many scholars think that Charles Darwin structured his argument in the Origin to show that natural selection was both causally adequate and had causal existence. His theory of universal common descent could not be tested by predicting future outcomes under controlled experimental conditions. It could be demonstrated to be right by showing that it could explain already known facts in a more adequate fashion.

The question is now whether a case for an intelligent cause can be formulated and justified in this way. Is intelligent design a possible historical scientific explanation for the origin of biological information? Is it possible to formulate a case for intelligent design as an inference to the best explanation for the origin of biological information?

It is possible to conceive of the purposeful acts of an intelligent agent is a causal event. This clearly represents a known and presently acting adequate cause for the origin of information.

Our uniform and repeated experience indicates that intelligent agents produce information rich systems.

What causes now in operation produce digital code or specified information? Is there a known cause of the origin of such information? What does our uniform experience tell us?

Intelligent design must qualify at least as a possible scientific explanation for the origin of biological information.
Is intelligent design the only known or adequate cause of the origin specified information? If so then the past action of designing intelligence will be established as the strongest and most logically compelling form of historical inference.

Is ID Science?

2010-05-23T21:44:00.004+01:00

This is not a simple or straight forward question. It is the question that Meyer addresses in his 7th chapter. I think I found this the most difficult chapter in the book.

Meyer discusses the nature of “historical sciences” such as geology and paleontology and evolutionary biology and argues that they use different methods to “experimental sciences” such as physics and chemistry. He states that Stephen Jay Gould accepted this distinction and argued that historical scientific theories were testable by analysing their “explanatory power” (Gould, “Evolution and the Triumph of Homology”) Gould describes the process of testing in historical sciences as seeking “consilience”. Consilience is the situation where many facts can be explained well by a single proposition or theory. Gould he says argues that historical sciences depend upon the knowledge of the laws of nature to make inferences about the past.
Meyer then asks whether a design hypothesis can be formulated as a historical scientific theory about what happened in the past.

Historical scientists cite the occurrence of an event or series of events in the past as the explanation for some observable phenomenon in the present. Historical scientists use a distinctive mode of reasoning. Using their knowledge of cause and effect relationships historical scientists “calculate backwards” and infer past conditions and causes from present conditions and causes.

This type of reasoning is called “abductive” reasoning as opposed to inductive(in which a universal law is established from repeated observations) or deductive (in which a particular fact is deduced by applying a general law to another particular case. Abductive logic was first described by Charles Sanders Pierce
Despite the tentative nature of abductive reasoning we do make conclusive inferences about the past.

A conclusion of abductive reasoning is certain if we cannot explain the currently observed facts without the past cause. An abductive conclusion is established by showing that it is either the best or the only explanation of the effects in question.

To address this problem in geology Thomas Chamberlain proposed a method of “multiple working hypotheses. This is also known as “inference to the best explanation”
Peter Lipton is associated with this way of reasoning arguing that it is used both in science and ordinary life. Discovering certain particular marks in fresh snow we infer that a person with snow shoes has passed this way. Lipton argued that the ability to explain particular facts sometimes mattered more than predictive success in the evaluation of a particular hypothesis.

The problem with this method of assessing explanations is exactly how we judge which is the best explanation as opposed to the explanation we like the best.

What is the relationship of ID to Science? Is it Science?

2010-05-23T21:37:00.002+01:00

Image from here

In his sixth chapter of “Signature in the Cell” Meyer presents the view that the scientific enterprise is much wider than “doing experiments.”
Kekule famously “discovered” the structure of benzene while having a daydream about snakes seizing their own tails.

I turned my chair to the fire [after having worked on the problem for some time] and dozed. Again the atoms were gamboling before my eyes. This time the smaller groups kept modestly to the background. My mental eye, rendered more acute by repeated vision of this kind, could not distinguish larger structures, of manifold conformation; long rows, sometimes more closely fitted together; all twining and twisting in snakelike motion. But look! What was that? One of the snakes had seized hold of its own tail, and the form whirled mockingly before my eyes. As if by a flash of lighting I awoke... Let us learn to dream, gentlemen.

Meyer uses the example of Watson and Crick who relied on other people’s experimental results and their own model building to present the structure of DNA. Once they had the idea…it was obviously right!
Copernicus, Newton and Einstein are among the most famous scientists but none of them were outstanding in terms of their laboratory experiments.
Darwin is not a famous scientist because of his experimental results on seed dispersal or worms or movement in plants.
Meyer reminds us that for the early days of science intelligent design was not a controversial or career breaking interest. A. N. Whitehead is quoted:
“There can be no living science unless there is a widespread conviction in the existence of an Order of Things, in particular, of an Order of Nature.”
This Whitehead argues was provided by the Christian belief in the rationality of God.
Steve Fuller has amplified Whitehead’s observation. Science began because theists believed that an intelligent God made the universe to be intelligible to human beings made in his image.
Why has intelligent design which was so important in the origin of science become so completely rejected from modern science?

The experiment that launched evolution.

2010-03-28T20:44:00.002+01:00

"Charles Darwin did little experimental science. He did make several descriptive studies of barnacles and worms and some experimental studies about how species spread through seed dispersal and other processes. Yet his masterpiece, On the Origin of Species by Means of Natural Selection, contains neither a single mathematical equation nor any report of original experimental research. Yet he formulated a great scientific theory."

Stephen Meyer - Signature in the Cell p139

The Axe-Meyer Axis.

2010-03-28T20:39:00.008+01:00

This is an attempt to state more clearly what I tried to say before...
How is Axe's published work relevant to ID?

Past posts for reference:
I was thinking...
J.Mol.Biol- 2000 -301-585-595
Controversial paper
Appearance of design

Making a functional protein from scratch is difficult. This is relevant in two situations(a) In a prebiotic soup making a protein to help stabilise or increase the function of a precellular replicon.
(b) after the origin of life the development of a brand new structural or functional protein which enhances the reproductive capacity of the organism.

The following argument is my version of what Stephen Meyer says on p206 and following in Signature in the Cell.

Most functional proteins are over 150 amino acids long. The average is estimated at around 300 amino acids long. With 20 different amino acids a protein 150 amino acids long gives a very large number of possible sequences - 10¹⁹⁵ (which is a pretty big number)

Firstly in a prebiotic soup with an abundance of amino acids there are a number of possible ways in which amino acids can link up- however to get a folding protein we need peptide bonds. The probability of forming a peptide link is about 1 in 2.

To get a 150 amino acid molecule with peptide bonds the whole way along will be a probability of 1 in 10⁴⁵.

Secondly in a prebiotic soup there will be 2 optical isomers of each amino acid. All the functional proteins in nature use only L isomers.

To get a 150 amino acid molecule with only L isomers the probability is also 1 in 10 ⁴⁵.

Thirdly there are constraints in terms of the exact order of amino acids that will produce a protein that can fold into a globular shape with the possibility of having a function.

Fourthly there are constraints in terms of the exact order of amino acids that will produce a protein that has a function.

The fourth issue was investigated by Robert Sauer in the late 1980's at MIT. Cassette mutagenesis was used to examine the tolerance to sequence change at a number of locations in a variety of proteins.

The results showed that the probability of acheiving a functional sequence in several small proteins was very low. In other words there are very few different combinations of amino acids that allow the function to be maintained.

The chance of hitting on one of these by chance was about 1 in 10⁶³.

Doug Axe was interested in Sauer's work and began to wonder if he had underestimated how much protein sequences can vary and still retain function.

He developed a more rigorous mechanism to test this. The results in a paper published in 2004 were particularly important. On the basis of these results Axe was able to demonstrate that the ratio of functional sequences to non functional sequences for the enzyme beta-lactamase was 1 functional sequence to every 1 x10^77.

Axe's work also allowed him to calculate the probabilities of finding any functional sequence amongst the possible sequences. This was done by looking at the probability of sequences being able to form stable folds (a necessary pre-requisite for stable 3D structure)

On the basis of his work he calculated the ratio of sequences able to form stable 3D structures to those which were not able to as 1 to 10 ⁷⁴.

A comparison of these odds:

The odds of finding a 150 amino acid sequence able to fold into a stable 3D shape is equivalent to finding a single marked atom out of all the atoms in a a billion Milky Ways (that is the galaxy[this is the star system rather than the chocolate bar] rather than the chocolate bar)

These are unpromising odds to say the least.

For a functional protein in a prebiotic soup the odds are considerably worsened.

For a complex of functional proteins occuring at the same time the odds are also considerable worsened.

The odds of a 150 amino acid protein with stable 3D shape in a prebiotic soup is 1 in 10 to 164 this is well below the entire probabalistic resources of the entire history of the entire universe.

The appearance of Design.

2010-03-18T10:00:00.002Z

The universe itself and living organisms in particular have the appearance of being designed. Human intelligence from very early times has concluded from this appearance of design that there must be a designer.
Darwin’s theory was an alternative seeking to explain the appearance of design without an actual designer.

In terms of biology ID writers suggest three key areas for investigation that interest me.
1. The origin of life itself.
2. The origin of new functional proteins
3. The origin of interdependent proteins where multiple proteins are fine tuned for a particular function and all are required simultaneously for minimal function.
With regards to area 1 I am interested in working through Stephen Meyers recent book – Signature in the Cell.
With regards to area 2 the key research is the investigation of the relative quantities of functional to non-functional proteins amongst all possible proteins. How easy is it to produce an entirely new functional protein? I am not talking about variants within a protein family but the production of an entirely new structure with a new function with no amino acid sequence homology to any other functional protein.
One way to investigate this is to ask how easily protein structure and function degrades when you change one or more amino acids around the active site of an enzyme or elsewhere in its structure.

This gives an increasingly clear picture of the size of the islands of protein functionality in the vast ocean of possible protein amino acid sequences.
It is this kind of experiment that Doug Axe did at Cambridge.

Some previous posts on this:

How big is the hole?
I was thinking..
Axe's paper
Axe's paper
Which Golf Course?

JBS Haldane on the origin of Life

2010-02-24T13:31:00.004Z

If the minimal organism involves not only the code for its proteins, but also twenty types of soluble RNA, one for each amino acid, and the equivalent of ribosomal RNA, our descendents may be able to make one, but we must give up the idea that such an organism could have been produced in the past, except by a similar pre-existing organism or by an agent, natural or supernatural, at least as intelligent as ourselves, and with a good deal more knowledge.

J. B. S. Haldane;
Data needed for a blueprint of the first organism, 1951.

Published posthumously in S. Fox (ed) The origins of prebiological systems and of their molecular matrices,
Proceedings of a conference at Wakulla Springs, Florida, 27-30 October 1963
Academic Press. New York 1965, p12.

Does anyone know anything about the context of this quote?

I have this page with some other quotes of JBS Haldane.

The proof of the Truth is in the citation index…

2009-12-01T16:11:00.001Z

A lost letter I came across in the historical archives dated November 30th 1871

Dear Gregor,

One of the hallmarks of science is that it is fruitful. A good scientific paper will usually lead to much work along the same lines, work that confirms and extends the results, and work that produces more new ideas inspired by the paper. Although citation counts are not completely reliable metrics for evaluating scientific papers, they do give some general information about what papers are considered important.

Pea factorization advocates like to point to lists of “peer-reviewed publications” advocating their position. Upon closer examination, their lists are misleading, packed with publications that are either not in scientific journals, or that appeared in venues of questionable quality, or papers whose relationship to pea factorization is tangential at best. Today, however, I’d like to look at a different issue: the fruitfulness pea factorization work. Let’s take a particular Pea factor publication, one that was trumpeted by a religious nutcase as a “breakthrough”, and see how much further scientific work it inspired.

The paper I have in mind is your paper Experiments on Plant Hybridization, which was published, amid some controversy, in the relatively obscure journal Proceedings of the Natural History Society of Brünn in 1865.

What I want to do here is look at every scientific publication that has cited your paper to determine whether your work can fairly said to be “fruitful”. I used the ISI Web of Science Database to do a “cited reference” search on your article. This database, which used to be called Science Citation Index, is generally acknowledged to be one of the most comprehensive available. The search I did included Science Citation Index Expanded, Social Sciences Citation Index, and Arts & Humanities Citation Index. Even such a search will miss some papers, of course, but it will still give a general idea of how much the scientific community has been inspired by your work.

I found exactly 0 citations to your paper in this database. Of these, counting generously, exactly 0 are scientific research papers that cite you approvingly!

I hope that you will see how foolish it is for religious nutcases to pretend to be involved in real science and that you will content yourself with simply growing peas and singing hymns in your monastery.

Yours scoffingly,

Jeff

The Lenski Experiments

2009-10-18T23:06:00.003+01:00

In the Lenski experiment the E.Coli cells grown in the presence of oxygen gained the ability to transport citrate across the membrane. The allowed them to utilize citrate as a carbon source and provided a selective advantage in the conditions of the experiment.

In the absence of oxygen with another suitable source of energy the E.coli cells are able to transport and use citrate.

The mutation(s) that occurred in the Lenski experiment therefore allowed (unusually) the transport of citrate across the membrane in the presence of oxygen.

As far as I am aware the detailed molecular story of what happened in this particular case has yet to be unravelled. It seems that at least two different mutations must occur for this ability to be conferred.

As far as I am aware no new proteins are involved. The most likely explanations are a loss of the usual control of the anaerobic citrate transport system or a mutation in a protein that transports a similar molecule

What is significant from these results is that even for this small modification in an existing protein 31,500 generations were required with a population size of about 5 million. This was in the presence of the heaviest selection pressure possible.

Behe argues that this work is consistent with his arguments regarding the limit of evolution.

Behe’s discussion of the Lenski work.

A recent Scientific American article on the Lenski experiment. (HT to Psilo)

How big is the hole?

2009-10-13T18:03:00.002+01:00

In an earlier post I likened the production of a protein with a new function to a blind man playing golf. One commenter wondered how large the hole was. I thought of this again while reading Stephen Meyer's recent book "Signature in the Cell". He presents the figure of 1 out of 10^74 as the number of possible proteins 150 amino acids long which have any function whatsoever. If this is correct then the hole is very small indeed...roughly equivalent to finding a single marked atom blindfold from all the atoms in the milky way. This figure also assumes that all the amino acids are left handed and only peptide bonds are formed.

Change in Comments Policy

2009-09-30T10:46:00.002+01:00

Visitors will have noticed that there has not been much activity here for some time. This was because I have been unable to devote sufficient time to dealing with hostile comments. As a result of the increasingly unpleasant nature of these comments I have (reluctantly) decided to have only moderated comments.

For a comment to be published it must:
-be directly relevant to the post
-contain no bad language
-be polite

The God Delusion

2009-04-29T14:27:00.002+01:00

I am reading Dawkin's book with the above title. A couple of thoughts occurred to me as I read the chapter entitled "Why there is almost certainly no God."

1. If Darwin was correct in highlighting the discovery of a complex organ which cannot be produced by numerous slight successive modifications as a real possible falsification of his theory then we cannot simply rule out any such proposed organ as a "God of the gaps" argument. If the God of he gaps protest is permitted then the possible falsification has gone. If the falsification is a genuine possible one then we must allow for the existence of real gaps.

2. Dawkins argues that an intelligent designer must be more complex than the evidence of his design and therefore requires a further explanation of an even higher level of complexity. He seems to indicate that this is a sort or killer punch as if the rule of the universe is that all complexity must necessarily come from simplicity. However the fact that he spends time on other arguments seems to indicate that he is not entirely happy that his killer blow has actually killed.

Self Organisation is the Answer

2008-08-06T07:42:00.001+01:00

From an interesting Telegraph article here.

"Evolution on its own doesn't look like it can make the creative leaps that have occurred in the history of life," says Dr Seth Bullock, another of the conference's organisers. "It's a great process for refining, tinkering, and so on. But self-organisation is the process that is needed alongside natural selection before you get the kind of creative power that we see around us.

Is Science atheistic?

2008-05-29T07:40:00.003+01:00

“Some say God is living there. I was looking around very attentively, but I did not see anyone there. I did not detect either angels or gods…. I don’t believe in God. I believe in man—his strength, his possibilities, his reason.” (Titov USSR)

The question that interests me is whether atheistic scientists are willing to acknowledge that a clear line can be drawn between science and atheism. Can one be just as committed to science and yet believe in the reality of God, spirits, miracles and special revelation or is an atheistic, materialistic world view the only real position that a true scientist can take.

1. Is science intrinsically atheistic? Atheistic science is the true un-encrusted form whereas theistic science is a primitive medieval form of science prior to its emancipation to full grown materialism.

2. Can the tools of science be seen as a valuable toolbox which can be used usefully within a variety of philosophical contexts and presuppositions but has limited value in actually testing those contexts and presuppositions.

3. Can the results and evidence produced by the toolbox of science be seen in different ways according to the presuppositions and philosophical contexts of the individual scientist? Do the presuppositions and philosophical context of the scientist affect the way in which the data is interpreted and put together? Do the presuppositions and philosophical context predispose individual scientists to particular interpretations of the evidence?

Institutionalised Idolatry

2008-05-22T07:29:00.002+01:00

One of the key blindspots of atheistic scientists it seems to me is their inability to distinguish between beliefs based on evidence and beliefs based on presupposition. There seems to be the assumption that any "religious" position is antagonistic to some kind of "normal" view of any civilised democracy. The "normal" view of any civilised democracy is of course secular humanism - atheism- the worship of man as the highest authority. What they seem to have missed and be apparently completely blind to is that this secular humanism is just as much a "religious" position and faith as any other "religious" position. Its assumed "normal" and superior status is just another kind of religious orthodoxy seeking to impose its dogmas upon a society. Many people including top scientists seem to be entirely blind to this.

I thought Geoffrey Lean's article very perceptive.

Tail on the Donkey

2008-05-01T01:27:00.002+01:00

I was thinking about Intelligent Design and I thought of the old children’s game that we used to play – Pin a tail on the donkey. The children competing would be blindfolded and each would be given a tail with a pin in it. They would have to guess the correct position of the donkey and pin the tail where it was supposed to go. Get the tail in the right place and you are a winner.

This is a bit like finding a protein that works by random mutation. The protein that works is the donkey with the tail in the right place.

The key variables are the size of the available space for your pin and the number of people trying to stick the pin in the right place.

Of course there is not just one right sequence that works and gives a selective advantage and there are of course many more players in protein building than children at a party. However the key question is - how realistic is it to think that random mutation and natural selection are sufficient tools to build all the proteins and protein combinations that are required to explain biology as we know it?

If we made our illustration realistic….

How big would the board space be for sticking the pins in?
How big would the area be that give a selective advantage?
How many tails need to be stuck on how many donkeys at once?
How many children do we need on the board to make life as we know it a realistic achievement for chance mutation and natural selection?

These are the big questions for ID research. One would have thought that biologists would agree that these are really exciting questions to be asking. This is the area where there is a real possibility for the main mechanism proposed for evolution to be falsified and shown to be unrealistic. That surely makes this research great science and exciting science.

That is the sort of research that Doug Axe is trying to do…. But it isn’t being funded by the usual biology funding pathways. He has developed a good method. He has published good work in the field. When you mention that he works in the Biologic Institute to the Darwin faithful at best you get a sneer at worst a snarl and curses!

You could put his decisions down to one big weird publicity stunt or say that the fellow has lost his marbles or you could say that there is more going on in modern molecular biology than a disinterested pursuit of the truth…wherever it leads.

I have a hunch that it isn’t just a publicity stunt and that his marbles are pretty much all present and correct and that he might be right and he might be able to demonstrate that he is right. I hope so and wish him well!

The Biologic Institute.

2008-04-24T07:54:00.005+01:00

I have been following Douglas Axe's work with interest (see here and here) so I was very keen to look at the website of the Biologic Institute. This is the research institute that is funded by the Centre for Science and Culture which Douglas Axe is in charge of.

On the research page there are reports of what they have been working on and descriptions of the research which has been or is shortly to be submitted for peer review. "The difficulty of interconverting the functions of structurally similar enzymes" is one of the areas in which I will be interested.

The sad part of the story is why such an institute is needed at all. The work that Douglas Axe has done and the systems that he has set up should be supported in the usual way without the need to set up a separately funded institute.

How do Scientists use the word “Theory”?

2008-03-28T22:59:00.000Z

I have heard many people who believe in Creation say “But evolution is only a theory.”
What they mean is that in denying the evolutionary view of life they are not denying proven facts.

The difficulty is that the statement includes two words which are used in very different ways and the statement is therefore open to serious misunderstanding.

I explained why I believe that distinguishing between micro and macro evolution here.

I want to set out a few thoughts about the word “theory” here.

It is a word with multiple senses from relatively loose to very tight and is therefore a source of confusion.

In ordinary speech it is used in the following ways:
Speculative suggestion which provides an explanation for one or more observations. The Shorter Oxford dictionary has this description: “An unsubstantiated hypothesis; a speculative (esp. fanciful) view.
Theory vs Practice – In theory how something should be done – Abstract knowledge and speculative thought. A scheme of how to do something including all the rules and principles to be followed- eg a theory about bringing up children.
A hypothesis that has been confirmed or established by experiments or observations and is accepted as accounting for known facts.
In science the word has a set of more specialised meanings.
There seem to be two dimensions of use of the word “Theory” in Science.

Its reach – how high in the hierarchy of scientific knowledge is it?
“a comprehensive explanation”
The oxidative stress theory of Ageing is of a much lower order in Biological Theories than the theory of evolution.

Its validity – how certain are we that it is correct?

There are five ways the word is used in science:

1. The NAS definition of scientific theory indicates that the use of the word theory should be reserved for the very highest level of validity:

“supported by many facts gathered over time” “so well established that no new evidence is likely to alter them”
Tests – Logical consistency, How throroughly it explains data and how broadly it can be applied.
The Panspermia theory of the origin of life on earth is of much lower validity than Theory of DNA being the coding molecule for the production of proteins in the cell.

The NAS has attempted to define the word theory as having a very wide reach and the highest possible standard of validity.

“In science, the word theory refers to a comprehensive explanation of an important feature of nature that is supported by many facts gathered over time.”
“Some scientific explanations are so well established that no new evidence is likely to alter them. The explanation becomes a scientific theory.”

However though the NAS clearly uses the word like this in some of its publications this is not a comprehensive definition covering all uses of the word in the current professional scientific literature. On its own this is actually a misleading definition and is therefore unhelpful. It does not relect the real usage of the word in science.

2. It is used for a confirmed hypothesis.
e.g. New theory confirms that genetic kin recognition is inherently unstable, explaining its rarity.
3. It is used for an unconfirmed hypothesis or for one of several competing hypotheses.
e.g. here
4. It is used for explanations which have been shown to be incomplete or even wrong.
e.g The Ether Theory for the propagation of light.
Newtons theory of motion ie it is not a complete theory and does not work well near the speed of light.
5. Theoretical speculation currently unverifiable- String Theory or Theories of Everything.

Now in what way is ID a scientific theory and in what way is it not?

I would answer
1. No
2. No
3. Yes
ID is one of several competing hypotheses for the origin of biological complexity.
4. No
5. No

Other references:
http://en.wikipedia.org/wiki/Theory

http://www2.ncseweb.org/kvd/experts/behe.pdf
(9.6MB includes large images)

Realistic Cooption.

2008-03-26T08:33:00.000Z

It seems clear to me that, at the very least, Behe’s book “Darwin’s black box” stimulated interest in, thinking about and probably research into - the origin of complex integrated biological systems.

As I understand it the current Miller/Matzke etal explanation for the origin of the rotary motor propulsion systems in bacteria is a series of cooption events.

Function 1 (1 or more proteins)

↓

← Function 2 (1 or more proteins)
↓

Function 3 (2 or more proteins)

There is an assumption that all the proteins which form the motor have all been collected and modified from other purposes in the bacterial cell. In the words of the New Scientist article- it was “cobbled together.” Some of the proteins in the motor have not been found to have any homologues elsewhere but let us assume that homologies for all the proteins will be found at some point.

My big question is whether this explanation is realistic. Obviously we can imagine it happening providing if we try hard enough. The big question that remains to me is whether this is just wishful thinking. Is it realistic to imagine this happening? How can we know when a series of imagined cooption events is realistic or not.

Obviously if we find compelling examples of intermediate stages this helps but is there a way in which we can test whether our evolutionary imaginations are being kept within realistic limits?

Outboard motors made without design.

2008-02-14T22:31:00.004Z

The New Scientist has a piece announcing the death of the flagellum as the great champion of the demonstrations of design in biology.

It is a well written piece and gives a useful summary of the response of Darwinists to Michael Behe's argument of Darwin's Black box.

The arguments can be summarised:

1. There are lots of different flagellum like systems. If there was a designer he would not design this more than once

[This makes the assumption that people who believe in design do not believe in any evolution at all. It is a theological argument which claims to be able to see into the mind of God and say what he would or would not do.]

2. There are strong homologies of the flagellum proteins with the proteins of the Type 3 secretory system(T3SS). (Workers acknowledge that the T3SS probably came from the flagellum rather than the other way around.)

3. There are homologies with many of the other proteins suggesting that many of the flagellum proteins may have been co-opted from other functioning structures.

The conclusion is...
"this abundance of homology provides incontrovertible evidence that bacterial flagella are cobbled together from recycled components of other systems - and vice versa - through gene duplication and diversification. In other words, they evolved."

To my mind that is just rubbish.
Most of the proteins showing some homology to other proteins does not prove that it is reasonable to think that the blind watchmaker made it without any help.

"Evolutionary biologists have put their house in order. It's time for their opponents to do the same." Doolittle

This is about as close as Darwinists go to saying that Behe made an important point in his book!

I am afraid that I still think that it is reasonable to conclude that the bacterial flagellum could not be assembled in the way that these champions of the fight against "unreason" maintain. [Unreason = any vestige of a conviction that intelligence is required for the origin or diversity of life]

It is a pretty cheap response to Behe's argument to present the whole problem as essentially concluded in favour of a blind watchmaker simply by showing that many of the proteins in the flagellum have sequence similarity to other bacterial proteins.

The big questions that still remain in my mind are these:

1. Is it reasonable to think that there is a pathway from these proteins doing something else to their specific function in the flagellum that we see today.

2. Is it reasonable to think that the proteins that are required but which have no known homologies could also arrive to allow the flagellum to function.
3. Is it possible to get to a clear answer for the above two questions. Is it possible to test whether Darwinists are simply excercising too much faith in the power of the blind watchmaker or not.

I am aware that Darwinists are good at imagining long pathways of functioning machines with gradually increasing complexity...but how do we know if they are reasonable or not? Should I believe them until someone demonstrates it is impossible or should I disbelieve them until someone demonstrates it is possible?

Maybe a simple thought experiment will clarify what I mean...

Let us imagine a machine which does something useful (but is not a motor)which contains all but 4 of the proteins needed to make a motor.

Let us imagine that those four proteins are busy doing something else in the boring but busy immobile bacterium.

Let us imagine that those four proteins have all duplicated and the duplicate of each is busy accumulating point mutations etc such that they can no longer perform the function the blind watchmaker made them for.

Let us imagine that the times are good- all the economic indicators for bacteria are favourable - it is a real baby boom and the population is rocketing!

My question is - How big are the targets that these four proteins are aiming for? (please excuse the teleological nature of the sentence!)

Is it reasonable to think of all four hitting the target at the same time?

Is that a reasonable scenario or do Darwinists imagine the co-option of one protein at once? With each addition providing selective advantage??

Who adjudicates fairly what is reasonable here? The champions of reason of course.

Freak spaghetti arrangement?

2007-09-10T18:18:00.000+01:00

Synthetic Life.

2007-09-08T15:25:00.000+01:00

Spontaneous living cells in a test tube from simple ingredients?
Well no …..not quite…. we supply the carefully made membranes….oh and the 36 enzymes…. Oh and also the ribosomes…..oh and also the genetic information! But we are nearly there!

At least this is the illusion that some origin of life researchers seek to indicate.

Dr. Giovanni Murtas from the Synthetic Biology and Supramolecular Chemistry group at RomaTre University says:

"We can prove at this point that we can have protein synthesis with a minimum set of enzymes - 36 at the moment."

The fluescent green colouring indicates that these "primitive cells" can synthesize a protein from the supplied genetic information.

According to the guardian account this result “will teach us about the earliest stirrings of life in Earth’s primeval slime some 3.5bn years ago.”

Yerrr sure!

I would have thought that to any unbiased observer this result simply reminds us all that there is no hope that the primeval slime…no matter how exotic and how many billion years you give it will ever produce a living organism with minimal information and functioning protein machinery.

The information to specify such elegant structures as these does not hang around in primeval slime waiting for 36 enzymes and a few ribosomes to arrive.

I am not against this kind of work at all... I applaud it! What I am against is giving the impression that the solution to the problem of the origin of life is nearly solved and it is just a matter of time before we crack it.

Melanie Phillips - Life in a random Universe?

2007-08-25T07:58:00.000+01:00

"Moreover, since science essentially takes us wherever the evidence leads, the findings of more than 50 years of DNA research — which have revealed the almost unbelievable complexity of the arrangements which are needed to produce life — have thrown into doubt the theory that life emerged spontaneously in a random universe."

See the whole piece here.

Science Vs Religion.

2007-08-23T14:09:00.000+01:00

Publication of Steve Fuller’s Dissent over Descent has been delayed until Spring 2008. However, in the meanwhile, he has just published another book relating to ID, Science vs Religion? Intelligent Design and the Problem of Evolution (Polity). You can peek inside the book by going to the Amazon website.

Fuller will be speaking at the Leeds University conference, ‘Darwinism after Darwin’, on 3-5 September. This includes an appearance on a panel discussing Richard Weikart’s controversial From Darwin to Hitler (Palgrave), with Weikart as respondent. For more information about this conference, which is open to the public, see the website: http://www.darwinismafterdarwin.com/

Darwin or Design.

2007-08-23T09:02:00.000+01:00

Jason Rennie, the young Australian producer of the on-line ‘thesciphishow’, has released ‘Darwin or Design’, 9.5 hours of interviews with various people on either side of this controversy.

The links to these interviews are here.

An overview of Evolution
Chapter 1 : PZ Myers, An overview of Evolution and ID 15:48
Chapter 2 : Sean Carroll, What is Evo Devo ? 20:17
Chapter 3 : Nick Matzke, Can the Flagella Evolve ? 29:27

Design in the ID advocates own words
Chapter 4 : Salvador Cordova, What is ID ? 20:20
Chapter 5 : Mike Behe, What is Irreducible Complexity ? 17:51
Chapter 6 : Angus Menuge, Agency and how to identify it 18:28
Chapter 7 : Guillermo Gonzalez, The Privileged Planet 17:26
Chapter 8 : Joey Campana, Does ID research actually exist ? 26:17
Chapter 9 : James Shapiro, Sentient Cells ? 33:50
Chapter 10 : Mike Gene, What is Front Loading ? 23:37

ID's critics
Chapter 11 : Elliot Sober, ID and the Philosophy of Science 10:46
Chapter 12 : Scott Turner, The problem of Design 24:02
Chapter 13 : Glenn Morton, Can ID work in Biology ? 15:19
Chapter 14 : Ryan Nichols, Are ID and Theology Inseperable ? 14:28
Chapter 15 : Georgia Purdon, Isn't ID just Creationism in Disguise ? 21:44

ID, The Philosophy of Science, History and The Law
Chapter 16 : David Livingstone, Evolution and Christianity, The History 32:37
Chapter 17 : Del Ratzsch, Can ID be Science ? 25:38
Chapter 18 : Massimo Pigliucci, Evolutionary Epistemology and ID 28:34
Chapter 19 : Henry Schaefer, Science and Religion 14:40
Chapter 20 : Donald McConnell, Intelligent Design, Creationism and The Law 34:42
Chapter 21 : Steve Fuller, ID & Social Epistemology 19:11

ID in the Wild
Chapter 22 : John Davison, The Price of Dissent 35:26
Chapter 23 : Denyse O'Leary, ID & The Media 22:51
Chapter 24 : Geoff Simmons, Darwinism, ID & Medicine 27:40
Chapter 25 : Rob Sawyer, Calculating God 25:27

Expelled!

2007-08-23T08:52:00.000+01:00

A trailer for this film due to be released on Darwins birthday (February 12th next year) is now available here.

Press release is here.

It looks interesting!

Separation of Science and Religion

2007-06-20T08:44:00.000+01:00

The separation of the religious and the scientific means in the end the separation of the religious and the true; and this means that religion dies among true men.

(James Denney - Studies in Theology 1894)

Teaching Intelligent Design is the perfect recipe for mass producing suicide bombers!

2007-05-23T14:38:00.000+01:00

This is apparently what Harry Kroto (an otherwise intelligent fellow) seriously believes!

The Education Guardian included this extract from Sir Harry Kroto’s (Francis Eppes professor in the department of chemistry and biochemistry at Florida State University) “Can the Prizes Still Glitter? The Future of British Universities in a Changing World” published by Agora.

Do I think there is any hope for UK? I am really not sure. It is beyond belief that in the 21st century, our prime minister and the Department for Education and Skills are diverting taxpayers' money to faith-based groups intent on propagating culturally divisive dogma that is antagonistic to the secular, enlightened philosophy that created the modern world.

It is a scandal that the present system is enabling a car salesman to divert significant government funds to propagate dogma such as "intelligent design" in our schools. State funds are also being used to support some schools that abuse impressionable young people by brainwashing them into believing that non-believers will burn for all eternity in the fires of hell. This policy is a perfect recipe for the creation of the next generation of homegrown and state-educated suicide bombers.

I think there is every likelihood that the lack of scientifically educated and aware young people in the UK will result in ever poorer performance on a global scale, and a takeover by the next generation of young Chinese and Indians, ravenous for the scientific knowledge that will free them from the shackles of present poverty levels. They are being actively encouraged by their governments, who understand that the future lies in a scientific education based on doubt and questioning, rather than on belief.

It is truly disturbing that a well-funded cohort of religious groups - aided, abetted and condoned by the Labour government - is undermining our science education. If they achieve any more success in their subversion of the intrinsic secular safeguards embodied in our democratic institutions and our educational system, there can be no doubt there is major trouble ahead. So my final message is: "Do Panic!"

Harry Kroto is a brilliant scientist. However as an example of what he describes as “the enquiring mindset” he leaves a great deal to be desired with regards to the influence of his own materialist mindset on his convictions about those who disagree with his philosophy.

It is scarcely credible that a well educated scientist feels that he can write such patently ridiculous, offensive, ill informed, vitriolic gibberish.

If he feels as strongly about this as he appears to from this extract then at the very least he ought to get his facts straight! Being passionate about something is one thing. Being passionate about and publishing your passionate rhetoric without checking your facts is the quickest way to make yourself and your cause appear ridiculous.

What evidence is there that a traditional Christian education produces a higher proportion of suicide bombers than an atheistic, materialistic, relativistic one or any other sort of education? Presumably Kroto lumps all religious education together as being equally destructive. If you are religious then you are a secret member of the Taleban. So much for a carefully nuanced and a meticulously researched piece of prose!
What evidence does he have that a particular car salesman is in favour of teaching any intelligent design or creationism in science lessons let alone that he is diverting government funds for this purpose?
What right has he got to claim all the improvements in the modern world as the natural children of “secular, enlightened philosophy” (which presumably means materialism)?
What evidence does he have that there is “brainwashing” taking place in any UK state school?
Since when did the UK become a secular materialist state?

I share Prof Kroto’s concern for improved science education at the university level in the UK. However I do not think that insisting upon an ideological commitment to materialism like the bad old days of the USSR is the way to catch up with the US where there is considerably more creationism and intelligent design than in the UK.

Evolution becomes fact.

2007-05-07T08:12:00.000+01:00

"For many years it was possible to doubt the validity of Darwin's theory, but skepticism is not a tenable position today."

Cynthia Russett, Darwin in America 1976, p210

When did this transition take place? What were the key discoveries that resulted in this transition?

Science and Materialism.

2007-04-17T09:44:00.000+01:00

I was interested in this quote from Martin Redfern's article.

"Everyone is entitled to their beliefs, but what annoys Eugenie Scott is the way in which the received wisdom of Genesis is given equal or higher status to scientific evidence; and the way in which the latter is used selectively.

'In the card game of creationism, the Bible trumps science every time,' she says.

But in her game, science is dealt a hand that is purely materialistic. Ideas of a supernatural being belong in a different game, be it philosophy or theology."

Fuller Dissent.

2007-04-17T09:02:00.000+01:00

Steve Fuller has a new book out:

I have pre-ordered a copy so I will be interested in his view of this controversy on this broad canvas. I wonder if his arguments will include things like this?

Methodological Naturalism

2007-04-11T20:41:00.000+01:00

Just over a year ago Paul Nelson posed this question here

"Ask oneself a simple question. Suppose life actually were designed by a nonhuman intelligence -- would methodological naturalism allow us to discover that? If the answer is no, then methodological naturalism hinders scientific discovery and dictates the shape of reality as thoroughly as philosophical naturalism. If the answer is yes, then methodological naturalism is superfluous and says nothing more than that science should be empirical and testable."

Do you agree?

Questions....

2007-03-17T09:33:00.000Z

1. Is Methodological naturalism (MN) an essential commitment for scientific progress?
2. Is MN falsifiable? Could MN be false? How would we know?
3. Is the origin of life without intelligence reasonable without a prior commitment to MN? Is it acceptable scientifically to think that the origin of life requires an intelligent agent?
4. Is MN significantly different from philosophical naturalism? Are MN and consistent Theism compatible?

Douglas Axe - J.Mol.Biol.(2000) 301, 585-595

2007-02-22T11:20:00.000Z

Thanks to "Smokey" for the paper.
Previous blog post here.
This paper examines the idea that there are many amino acid residues in an enzyme which almost act as non-specific spacer residues and the nature of their side groups is almost completely irrelevant to the enzyme function. The only requirement is that the external residues be polar and the internal ones be hydrophobic (the binary code hypothesis). The paper argues that this idea is erroneous. Axe’s arguments rely on data from two different, unrelated enzymes.

Firstly, several amino acids are exchanged with several other very similar amino acids on the surface of the molecule and away from the active site and the effects measured. When roughly 1 in 5 of these residues is changed this results in complete loss of function in both enzymes examined.

Secondly, hybrids are constructed between two different versions of B-lactamase enzymes using various combinations of their surface sections. All of these hybrids are inactive.

Axe concludes that homologues that share less than 2/3 sequence identity should be considered as distinct designs with their own set of optimising features.

These results were surprising as they followed similar experiments where the hydrophobic core or an enzyme was systematically replaced and the conclusion was that general hydrophobicity was the only requirement for these core residues.

It was expected that the surface residues distant from the active site would show an even greater degree of tolerance to change than the hydrophobic core residues.

Axe compares the two hybrid situations with two functionally equivalent linguistic messages where exchanges between the non-conserved letters is functionally disastrous.

Away for a few days.

2007-02-13T17:26:00.000Z

I will not be around for a few days so I will look at comments when I get back.

Inside the Cell.

2007-02-08T13:39:00.000Z

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.)

"Strong indications of design."

2007-02-08T13:28:00.000Z

Nick Jackson of the Independent interviews Stuart Burgess who argues that there are "strong indications of design" in the four bar linkage of the knee joint. The report is here.

The making of "The Root of All Evil."

2007-02-05T21:32:00.000Z

In response to this question:
Why have you not engaged in public debate with Alister McGrath, Mary Midgley, Michael Ruse, Keith Ward, or indeed anyone else who would present you with a serious challenge? JAMES RADFORD, By e-mail
Richard Dawkins replied:
The producers of my Channel 4 documentary [Root of All Evil?] invited the Archbishop of Canterbury, the Cardinal Archbishop of Westminster and the Chief Rabbi to be interviewed by me. All declined, doubtless for good reasons. I don't enjoy the debate format, but I once had a public debate with the then Archbishop of York, and The Observer quoted the verdict of one disconsolate clergyman as he left the hall: "That was easy to sum up - Lions 10, Christians nil."
(from here)

Alistair McGrath gives a somewhat different slant...
Dawkins and I both love the sciences; we both believe in evidence-based reasoning. So how do we make sense of our different ways of looking at the world? That is one of the issues about which I have often wished we might have a proper discussion. Our paths do cross on the television networks and we even managed to spar briefly across a BBC sofa a few months back. We were also filmed having a debate for Dawkins's recent Channel 4 programme, The Root Of All Evil? Dawkins outlined his main criticisms of God, and I offered answers to what were clearly exaggerations and misunderstandings. It was hardly rocket science.
For instance, Dawkins often compares belief in God to an infantile belief in Santa Claus or the Tooth Fairy, saying it is something we should all outgrow. But the analogy is flawed. How many people do you know who started to believe in Santa Claus in adulthood?
Many people discover God decades after they have ceased believing in the Tooth Fairy. Dawkins, of course, would just respond that people such as this are senile or mad, but that is not logical argument. Dawkins can no more 'prove' the non-existence of God than anyone else can prove He does exist.
Most of us are aware that we hold many beliefs we cannot prove to be true. It reminds us that we need to treat those who disagree with us with intellectual respect, rather than dismissing them - as Dawkins does - as liars, knaves and charlatans. But when I debated these points with him, Dawkins seemed uncomfortable. I was not surprised to be told that my contribution was to be cut. The Root Of All Evil? was subsequently panned for its blatant unfairness. Where, the critics asked, was a responsible, informed Christian response to Dawkins? The answer: on the cutting-room floor.
(from here)

Comments.

2007-02-03T12:31:00.000Z

The comments section at IDintheUK has been entirely uncensored up till now (apart from really foul comments and obvious advertising.) I would like it to remain like this. I have learned a lot from the very high quality of comments from people on both sides of this argument. This seems to me a great benefit of this kind of site.

In order for this to continue it does require some self discipline on the part of the commenters.

Generally you have responded well to previous pleas.

I would like people to feel free to comment under whatever name they like and to be able to comment annonymously if they so choose. I think that part of good blog behaviour is to respect that choice. Attacks on another commenter because of their background and percieved or actual bias are to be avoided- it is the arguments about the data and its interpretation that we should focus on.

Please try to avoid overly emotive language- I know that many commenters feel very very strongly about this area - It is good to feel strongly about truth and to expose what is not true ruthlessly and energetically. However resorting to the red card "LIAR" is rarely helpful in my experience. Even if you are convinced that someone is deliberately and knowingly lying it is better to suggest that they may be mistaken first and point to the evidence. If you must make an allegation of deliberate, knowing deception please make sure you have a cast iron case and please try to do it as little as you possibly can.

The Dawkins Delusion.

2007-02-02T10:23:00.000Z

I have noticed several pieces about this odd phenomenon. Bill Dembski seems to have got hold of a very strange interview with Dr Terry Tommyrot, available here. Another interesting report of a discussion on the same subject is here.

Possible Pathways for the evolution of intracellular transport.

2007-01-27T16:45:00.001Z

In his book “Darwin’s Black Box Behe made the claim with regards to the cellular transport systems that:
"A search of the professional literature and textbooks shows that no one has ever proposed a detailed route by which such a system could have come to be."

Some commenters here have argued that Behe is being intentionally deceptive they argue that there is an abundance of published material – shelf loads of it - that give a clear outline of how a pathway transporting a newly synthesized protein to an intracellular compartment could arise.

Some suggestions were given as to where I should start – (I acknowledge that they were probably hurriedly put together sources by scientists who are very busy doing more important work than arguing with me and I do appreciate the attempt to provide me with the references.)

http://www.mrc-lmb.cam.ac.uk/myosin/Review/Reviewframeset.html

This is sequence comparisons in the myosin superfamily looking at homologies between the different types of myosin molecules in different organisms.

http://www.pnas.org/cgi/content/full/103/10/3498
This is the attempted production of a phylogenetic tree comparing different types of myosin molecule.

The Richards and Cavalier Smith Nature paper is similar and suggests that the most primitive eukaryotes had three types of myosin from which all eukaryotic myosins come but that does not really help me.

This gives 111 delightful titles but not really what I am after. They are mainly phylogenetic trees and studies of sequence similarities. Behe accepts that there are an abundance of this kind of study.

What I am after is a simple step by step process whereby a single transport system from protein translation completion to function in a separate compartment can arise. It does not have to be a DVD of the process happening just a suggestion of some of the useful steps along the way.
I am thinking of the kind of thing that Matt Inlay produced in response to Behe’s Immunology chapter (here) or Nick Matzke’s response to the flagellum chapter ( here)

Tony’s scenario:
This problem concerns the way proteins are targeted to the mitochondria. These organelles (again, they’re shown in your diagram) are responsible for supplying a major fraction of the cell’s energy needs. They are distantly descended from free-living bacteria that began a symbiotic relationship with an early eukaryote. As part of that evolutionary history, mitochondria still retain a small genome which encodes a few of the proteins required by the organelle. However, over evolutionary time there has been a general drift towards more and more mitochondrial genes being transplanted to the nucleus. Mitochondrial proteins produced from such nuclear genes somehow have to get to their correct organelle. How do they do that? It turns out that such proteins contain, right at the start of their amino acid sequence, a so called ‘targeting signal’ made of about the first ten or so amino acids and which docks with import machinery in the mitochondrion. A mitochondrial gene newly transplanted into the nuclear genome must acquire this signal or it risks turning into a pseudogene. So how easy is it to acquire a functioning targeting signal? Some years ago a clever experiment was performed to find out. It’s a neat example of how our intuitive ‘gut feelings’ about these issues can lead us badly off-course. The scientists took a gene for a mitochondrial protein, then replaced its normal targeting signal with random DNA sequences sized to encode between about ten and thirty amino acids. They then determined what fraction of these random sequences acted as functioning mitochondrial targeting signals for the protein.What do you think the answer was? One in ten million? Or some other Dembski number perhaps? Actually, they got a remarkable 3 to 5%! Subsequent work with more truly random and uniformly-length sequences increased this estimate still further. Evidently, it’s almost ridiculously easy to evolve working targeting signals. One more point is worth making here. Because the results were so striking and the way the experiment was conducted was so elegant, this work is rather well known in the field. It was published in 1987 – almost ten years before Behe wrote his book. Yet he tells us with a straight face that no experiments have been done to address the evolutionary origins of protein traffic!

Tony’s point here is that the ID code for the mitondrial car park is pretty easy to forge. The fellow checking the ID’s is a pretty sloppy fellow and a great variety of ID sequences will do.

However let us imagine that this putative mitochondrial gene is the very first one to complete the journey into the cell’s genome. Let us also assume that the appropriate insertion of DNA occurs of the correct length and with the approximately correct sequence. Is this all that is required for the newly made protein to find its way into the mitochondrion? Is it just a single rough ID sequence that is needed or are other modifications required in the mitochondrial genome and elsewhere in the cell?

Molecular Meccano

2007-01-26T15:21:00.000Z

Described by some researchers as a strange form of molecular “lego” and by others as “molecular basket weaving” the beautifully shaped propeller like molecules of clathrin have a crucial role in the cell’s internal distribution network. Another description in the literature is “groovy” which I think is about right! A single clathrin complex is made up of 3 light chains together with 3 heavy chains

to form the propeller like structure called a “triskelion” meaning three-legged.
These 3 legged units can be attracted to a membrane by a variety of different molecular structures on the surface of the membrane. As they are attracted they begin to associate

and as they associate they begin to bend the membrane inwards. The structure grows to form a complete and beautiful basket or cage around a little blister of membrane which is eventually pinched off to form a separate bubble inside the membrane.

At this point the clathrin complexes can be removed and reused elsewhere.

The diagram below is adapted from here (thanks to Dr. Tony Jackson)

A Quicktime Movie is here showing the assembly of a clathrin coated vesicle. (You may have to wait a little time for it to load.)

A Flash animation of the budding off of a clathrin vesicle is available here.

Intracellular Transport systems

2007-01-24T22:50:00.000Z

There are two types of living cells that we know of on earth-
1. Prokaryotic cells:

2. Eukaryotic cells [from the greek word karyon meaning nut or kernel – prokaryotic meaning “before a kernel” and eukaryotic meaning “with a true kernel” – the kernel being the nucleus of the cell.]

Eukaryotic cells not only have a “kernel” the nucleus but they have a goodly number of other internal compartments inside the cell too.

There is the complex structure of the onion like “endoplasmic reticulum” around the nucleus, there is the “golgi apparatus” looking like a pile of plates ready for a feast, there are the mitochondia looking like sausages out of some crazy sausage machineand there are the lysozymes- the waste recycling plants of the cell.

These different compartments each have their special function inside the eukaryotic cell.

The problems of transport are therefore much more complicated in the eukaryotic cell than they are in the prokaryotic cell.

It is these traffic problems that Behe mentions in chapter 5 – (From here to there) of “Darwin’s black box”

He first uses two analogies to explain the problem he is seeking to elucidate.

1. The delivery of urgently needed vaccine to an area of the country where there is an outbreak of a highly infectious viral disease. If the correct vaccine arrives at the correct location then lives can be saved- if not lives will be lost. Behe then imagines a film director making a film called “epidemic” in which the vaccine labels get muddled – This situation is similar to the situation inside a cell he argues when the transport system breaks down- death is the result.
2. He then imagines a robotic space ship exploring space with its battery crusher compartment, its library, its master machines and so on- This imaginary space probe is then compared to a cell

He then asks…. Is this analogy real?

This is illustrated using a protein he calls “garbigase.” A temporary copy of the relevant section of data from the DNA library is made- the messenger molecule. This messenger molecule passes to a nuclear pore- a tiny little door in the wall of the kernel. Proteins in the pore recognise the molecule in a process analogous to a challenge of identity with a secret password being given and the pore opens. In the cytoplasm a master machine the “ribosome” begin the process of converting the linear coded data into a 3D machine- in a process which biochemists have aptly named “translation” to make part of a brand new gleaming machine.

Diagram of translation:

Diagrams of a ribosome:

The first part of the machine to be made is a special combination code which quickly and neatly sticks to a code “hood” (signal recognition particle) causing the translation process to pause. The hooded new machine then locates a docking site in the surface of the onion. The docking process un-pauses the translation process and the newly made full length machine – a baby garbigase molecule - is fed into the inside of the onion compartment. As it passes into this new compartment the special code sequence to gain its safe entry is clipped off and a large carbohydrate molecule is bolted onto it.

Special proteins then cause a bubble of the onion wall to form and this pinches off into a separate little bubble containing molecules of the new garbagase protein. This little package then moves to another compartment called the Golgi apparatus and joins with the wall of this new compartment.

This kind of process happens two more times as the enzyme passes through several compartments of the Golgi apparatus. Another carbohydrate group is added to the enzyme and this is then trimmed by another enzyme leaving an special code MI-6 molecule.

In the final compartment of the golgi apparatus 3 blade propellor proteins snap together in a patch forming a bubble making cage. Within this bubble there is a MI-6 checker protein that binds to MI-6 pulling it into the bubble before it buds off. On the outside of the bubble is a tiny rabbit-SNARE protein that binds only to a tiny rabbit- proteins on the surface of the final compartment to which this little bubble is journeying.

Once the final docking process has completed further special membrane fusing proteins join the bubble to the wall of the waste disposal compartment so that it becomes part of it emptying its contents into its final destination.

A very controversial paper!

2007-01-22T16:25:00.000Z

Doug Axes’ work was controversial even as he was carrying it out. It was funded by an Institute that never under any circumstances funds anything but misguided PR material- The Discovery Institute. When another researcher in his lab pointed to the Discovery Institute's agenda and suggested that Axe be asked to leave, Prof Fersht refused. (New Scientist article)

It was controversial when it had been published with Dembski hailing it as a peer reviewed publication which supported his arguments.

Axes’ work has continued to be controversial with the set up of the Biologic Institute and his announcement that he does consider his work as supportive of the ID view.

Ed Brayton (here and here) thinks that the Journal of Molecular Biology accepted a paper in which the author got the title of his paper to mean the opposite of what his results suggested!

“The 2000 JMB paper did not show "severe sequence constraints" at all. It showed quite the opposite, that you could make massive changes in the sequence of amino acids in an enzyme, knocking out 10, 20, even 30 amino acids at a time, without completely destroying the function of the enzyme. It showed that you could make 10 substitutions at a time with only a negligible effect on the enzyme's function. And this is "severe sequence constraints"? Not even close.”

The title according to Ed should not have been “Extreme functional sensitivity to….” But Extreme functional INsensitivity to…” I immediately thought that the fact that the paper’s author and the papers reviewers made such a monumental error and that Ed managed to come to the rescue and point this out was rather odd to say the least. That it managed to get through the JMB peer review process without anyone noticing that the title was saying the opposite of the results seems quite remarkable to say the least! Perhaps it was a simple printing error?

Matt Inlay critiques the early claims that Dembski made for this research. Interestingly Matt Inlay does not mention that Axe got his title wrong.

Arthur Hunt likewise does not mention that Axe got his title so completely wrong and argues that of all the values for enzyme functionality in possible sequence space the lower ones give easily attainable rates in bacterial populations. However the much smaller populations in larger animals still present difficulties for explaining the origin of their unique proteins.
(Interestingly Arthur Hunt mentions that Douglas axe helped him with early drafts of this essay.)

Hunt present the enzyme activity as hills with a wide or narrow base. The size of the base of the hill indicates the likelihood of finding a functional protein by random mutation.

Personally I like my golf course analogy better which turns the diagram upside down. (here and here)

Abstracts of Axes Papers: here and here

Heaven and Earth

2007-01-22T15:58:00.000Z

ID was one of the subjects under discussion on the Heaven and Earth programme.
Prof. Mark Walport (Director of the Wellcome Trust) spoke against ID maintaining that:

"Evolution is truth now... there is huge anounts of experiment evidence to back it up."

Dr Alistair Noble spoke in defence of ID:

"Intelligent design is a very ancient idea going back at least to the Greeks - It maintains that there is evidence for design in the universe. The constants of physics are finely tuned for life and this looks like design, complex systems are necessary for life and these look designed above all the coded information locked into DNA looks designed."

Former Education Secretary David Blunkett "helpfully" added that ID is “just a much more sophisticated version of creationism.”

Simon Barrow, of "Ekklesia" dismissed ID as a “mistaken religious ideas” and “a political and religious problem”.

Dr Noble responded by distingishing ID from creationism in the following way:

“the difference between intelligent design and creationism is that they have very difference starting points. I would want to insist that the starting point for intelligent design is scientific observation.”

Intelligent Design and Evolution have the same status as scientific theories.

2007-01-12T16:44:00.001Z

Royal Holoway University of London are hosting a debate on the above proposition on 21st February at 5.00pm.
Steve Fuller graduated as a sociologist and then studied the history and philosophy of science and has focused on the writings of Thomas Kuhn and Karl Popper. He describes himself as a secular humanist.

He has commented on the Dover judgement (in which he was a witness) here.
He has explained how he became involved in the ID debate here.
A brief outline of a previous debate with Jack Cohen is here.

Lewis Wolpert is a developmental biologist who was made a Fellow of the Royal Society in 1980 and was awarded the CBE in 1990. He was for 4 years Chairperson of the Committee for Public Understanding of Science. He is a well known rationalist.

Given that we have a rationalist debating a secular humanist this hardly looks like a standard religion versus science debate!

Abiogenesis and the 2nd Law of Thermodynamics.

2007-01-06T18:13:00.000Z

Previous related posts:
Andy MacIntosh and the 2nd Law.
The idea of unintelligent Abiogenesis.
Is Abiogenesis Falsifiable?

This post is based on Walter Bradley’s chapter on “Information, Entropy and the Origin of Life.” In “Debating Design” Edited by Ruse and Dembski and published by Cambridge University Press.

Walter L. Bradley was one of the authors of “The Mystery of Life’s Origin.” which remains as the best selling advanced level text on the Origin of Life.

Bradley states that the second law of thermodynamics (2lot) and the theory of evolution are two of the three major scientific discoveries of the nineteenth century with Maxwell’s field equations for electricity and magnetism being the third. He is intrigued that the theory of evolution and the 2lot appear to be in conflict. The 2lot suggests a progression to disorder from order, from complexity to simplicity. Evolution involves progression to increasingly more complex forms of living organisms.

Erwin Schroedinger noted that living systems are characterized by highly ordered, aperiodic structures that survive by drawing “negentropy” from their environment and feeding on it! Today we recognise Schroedinger’s ordered structures as the complex biopolymers of protein and nucleic acids.

Living organisms use information stored in these biopolymers to resist the pull of the 2lot towards equilibrium. They are able to store information, to replicate with minimal information loss and they are able to feed on “negentropy.”

The existence of these three abilities allow us to understand how living organisms can continue to exist without violating the 2lot but the difficulty is understanding how these three abilities came to exist without violating the 2lot. This is the greatest mystery in science. At the heart of this problem is the difficulty of explaining how the complex specified information within these biopolymers can originate.

Bradley discusses the significant quantities of Shannon information that are stored in cytochrome c and in the E.coli bacterial chromosome.

At best the 2lot gives a very small yield of unsequenced polymers that have no biological function. The sequencing required for function is not facilitated by the 2lot.

Bradley then goes on to discuss the various origin of life scenarios that have been proposed in the light of the problem of the need for information and the pressure of the 2lot towards disorder.

He concludes: The origin of life seems to be the ultimate example of irreducible complexity. I believe that cosmology and the origin of life provide the most compelling examples of Intelligent design in nature. I am compelled to agree with the eloquent affirmation of design by Harold Morowitz (1987):

“I find it hard not to see design in a universe that works so well. Each new scientific discovery seems to reinforce that vision of design. As I like to say to my friends, the universe works much better than we have any right to expect.”

The 2nd Law of Thermodymamics and Abiogenesis.

2007-01-04T01:32:00.000Z

I commented on William Crawley’s “Sunday Sequence” and its aftermath here.

William Crawley has put several posts up following this. “Finding Darwin’s God” a piece on Ken Miller. Richard Dawkin’s letter to the Guardian. A piece on Andy Macintosh. A piece on the letters defending Andy Macintosh. Andy Macintoshes reply. Since then William Crawley has chosen Richard Dawkins as his Blog’s Person of the year. He has linked to a Salon interview with Ron Number’s the author of “The Creationists” and blogged on the letter from senior academics defending TiS.

Clearly William Crawley has a more than passing interest in the brewing "Biological Origins War" in the UK.

I was very interested in the exchange between Richard Dawkins (RD) and Andy MacIntosh (AM) and its aftermath. RD clearly thought that he was on to a big hitting winner with AM mentioning that the 2^nd Law of thermodynamics rules out an unintelligent origin for biological information systems. RD seemed to be keen that Leed’s University should take action against one of its professors speaking in this way about a subject that is clearly within his own area of special competence- thermodynamics.

I got the impression RD really wanted AM to say something like “The 2^nd law of Thermodynamics means that evolution is impossible.” RD could then show watertight evidence for micro-evolution and initiate a national UK science day of laughter at the silly creationists. However this is not what AM actually said. He has further clarified his position with a comment which has been published on William Crawley’s blog.

This is what he said:

Now that the 2nd law has had time to work on the Turkey this Christmas . . . maybe a few words are in order on thermodynamics and living machinery which I spoke about on the Sunday Sequence program on Dec 10th. I don't usually enter lots of blog discussions, but I see that you are having quite a debate here, so perhaps a word is in order from me. I do not on principle enter into any ad hominem attacks or respond to such against me. They do not add weight to any arguments and it is the science which is important.

The reason of course why this subject of origins will not go away is that there is a scientific case, whether Dawkins likes it or not, which is a challenge to the neo-Darwinian attempts to explain life in terms of common descent. It is a straightforward case of testable science versus the modern evolutionary ‘just-so’ story telling. Scientists like myself who believe in Creation have no problem with natural selection. It is simply the natural equivalent of artificial selection. But natural selection has no power to create new functional structures. It does not increase information and does not build machines which are not there already (either fully developed or in embryonic form).

The principles of thermodynamics even in open systems do not allow a new function using raised free energy levels to be achieved without new machinery. And new machines are not made by simply adding energy to existing machines. This was the point at issue in the programme of Dec 10th. Intelligence is needed.

And this thesis is falsifiable. If anyone was to take an existing chemical machine and produce a different chemical machine which was not there before (either as a sub part or latently coded for in the DNA template) then this argument would have been falsified. No one has ever achieved this.

I suggest that all the listeners read again if they have not done already, the excellent book by Wilder Smith called 'The natural sciences know nothing of evolution'. It is available on Amazon.

Clearly this kind of argument has been bubbling around for some time since Wilder Smith raised it. I do not think that when scientists of the standing of AM and Granville Sewel (University of Texas El Paso) are willing to stick their necks out over this that it can simply be dismissed as "showmanship bluffing" to a willing audience.

It is a also a subject which has also been raised by Walter Bradley (2004) "Information, Entropy, and the Origin of Life" pp 331-251 in Dembski and Ruse (eds) "Debating Design" Cambridge University Press.

I became interested in the concept of entropy in my A-level Chemistry classes but I really have only a very basic understanding of the concept. It seemed to me however that the 2^nd Law of Thermodynamics ruled out the idea that matter is eternal.

Those who believe that life originates without intelligence argue that all that is needed to produce life is energy plus matter plus lots of time. They tend to argue that the demonstration that this is true is the fact that life is here on earth!

AM, Wilder Smith, Walter Bradley,Granville Sewell and others clearly have the conviction that this formula is flawed and something else is needed.

Energy + Matter + Time + ? = Life (with its computer like information system)

The needed ingredient they say is a plan, an idea…intelligent design.

Prominent Academics support Truth in Science.

2007-01-02T23:34:00.000Z

Previous posts on "Truth in Science":
http://idintheuk.blogspot.com/2006/09/launch-of-truth-in-science.html
http://idintheuk.blogspot.com/2006/11/truth-in-science-materials.html
http://idintheuk.blogspot.com/2006/10/truth-in-science.html

It has emerged that 12 prominent academics wrote to Tony Blair and Alan Johnson, the education secretary, last month arguing that ID should be taught as part of science on the national curriculum.

They included 1. Norman Nevin OBE, Professor Emeritus of Medical Genetics, Queen's University of Belfast, 2. Antony Flew, formerly professor of philosophy at Reading University; 3. Terry Hamblin, professor of immunohaemotology at Southampton University; 4. John Walton, professor of chemistry at St Andrews University, 5. David Back, Professor of Pharmacology at the University of Liverpool; 6. Steve Fuller, Professor of Sociology at Warwick University; 7. Mart de Groot, Director, Retired, Armagh Astronomical Observatory; and 8. Colin Reeves, Professor of Operational Research at Coventry University

http://www.timesonline.co.uk/article/0,,2087-2524442_1,00.html

http://www.truthinscience.org.uk/site/content/view/217/63

Introduction to the Controversy - Part 3.

2006-12-30T15:50:00.000Z

Contributed by Howard Taylor.

Part 1 is here.
Part 2 is here.

POSTSCRIPT – FURTHER CONSIDERATIONS.

The Argument from Design – Bertrand Russell and David Hume.

Russell.
Bertrand Russell greatly respected the argument from design especially as expounded by Leibniz. (He regarded Leibniz, in whom he specialised, as "one of the supreme intellects of all time") BR writes: "This argument contends that, on a survey of the known world, we find things which cannot plausibly be explained as the product of blind natural forces, but are much more reasonably to be regarded as evidences of a beneficent purpose."
He regards this familiar argument as having no "formal logical defect". He rightly points out that it does not prove the infinite or good God of normal religious belief but nevertheless says, that if true, (and BR does not give any argument against it) it demonstrates that God is "vastly wiser and more powerful than we are".
(See his chapter on Leibniz in his History Of Western Philosophy.)

Hume[1].
It is important to appreciate that, religious sceptic though he was, (but not one who ever characterised himself as an atheist), Hume shows no sympathy to the approach we calling “methodological materialism”. That is, in Hume there is no trace of the idea that teleological concepts such as “intelligence” and “design” are inappropriate on methodological grounds in the context of biological explanation. As was usually the case with thinkers prior to Darwin, the basic question for Hume was how much soundly based knowledge can the Argument from Design yield. In Hume’s view, in turns out, the answer to this most general of questions is “not as much as previous philosophers have hitherto imagined”, but this conclusion does not depend in any way on the notion that the concept of “design” itself is in some sense inadmissibility at the outset of an investigation into the features and origin of organic nature.

What is Hume’s most general verdict on natural theological reasoning? The third sentence of his earlier work The Natural History of Religion of 1751 will surprise those who, without properly studying him, hail Hume as a committed metaphysical atheist. Hume in fact writes as follows:

“The whole frame of nature bespeaks an intelligent author; and no
rational enquirer can, after serious reflection, suspend his belief a
moment with regard to the primary principles of genuine Theism
and Religion.”

ID – A threat to science?
Some allege that it is. But what do they mean? They are usually unconsciously using a definition of science which says it is that subject which only looks for physical causes for physical effects.
But what is the basis of that definition? It assumes that physical nature is a closed system of cause and effect. However we can’t assume that. There is no evidence for that belief. Some have argued from an interpretation of Godel’s theorem that the physical world is not a closed system. Why not define science as that discipline which seeks to explain physical effects by following the evidence wherever it leads rather than be bound by an unprovable metaphysics which denies that non-physical realities impinge upon the physical world?

One seamless whole?
It is often claimed by theistic evolutionists and atheists that nature is ‘one seamless whole’. That is to say it must be regarded as one without the need to postulate further creative acts. But what is the basis of this belief? It isn’t scientific because science has not shown it to be true. There is still no viable theory of how lifeless matter turned into living organisms. It is not philosophical because there is no convincing ontology to give basis for the belief. It is not theological because the Bible does not teach it. It is a prejudice.

God of the gaps.
It is often alleged that ID people are evoking the dreaded ‘god of the gaps’. This criticism is based on the assumption that all physical effects have physical causes. Just because many physical effects have been found to have physical causes, does not mean that we can assume that all will. That is an unwarranted assumption. Further the ‘god of the gaps’ gets less as science advances.
However with the biological understanding of life, the advance of science has revealed a world of marvels unthought-of before. The ‘gaps’ or mysteries are getting greater.

False dualisms in criticism of ID by some Christians.

I. Spiritual/Physical.
It is alleged that Genesis 1 and other Biblical passages are ‘spiritual’ or ‘theological’ and not ‘physical’. However Genesis 1 and other passages have as their subject God and the physical world. Theology is concerned, not only with the spiritual, but also with the physical. Hence, although the Resurrection of Christ had a spiritual dimension, it was nevertheless a Resurrection of the Body.

II. Creation/Redemption.
Many Christians accept the miracles of Redemption as seen in Jesus but reject the Divine creative input expounded in Genesis 1. The Incarnation holds together the Creation and Redemption and therefore they should not be treated as totally distinct.

ID makes no predictions as normal scientific theories do.
This is a common criticism of ID. However it should be remembered that the theory of evolution makes no predictions either. It is ‘immunised’ (Karl Popper’s phrase – see below) against such a test. Actually ID does make predictions. It predicts that there will always be a discontinuity between non living matter and living matter. The exclusively physical properties between non-living matter and living matter will never be found. The basis of this prediction is that the DNA and RNA (essential to life) are a form of code – see section above entitled: Messages, languages, and coded information ONLY come from minds.

Karl Popper.
He says Evolution is not a scientific theory because it cannot be tested. He regards theories as ‘immunised’ as those that are protected against all future discoveries because they can be reconciled with anything[2]. His theory of falsification says that for a theory to be counted as scientific, the proposer must be able to stipulate what new facts if found in the future would falsify his theory. Evolution in its modern form fails this test and is ‘immunised’ against all possible future discoveries. He regards this as a bad thing. He says ‘Evolution’ is at best a philosophical framework in which other scientific disciplines can find their home. He therefore reluctantly accepted it.
But can it provide such a framework? This leads us to the next topic.

Two opinions
Not being in the same scientific league as many geneticists I cannot argue with their biology. However it is often said that Darwinian evolution provides the paradigm within which all biological research is carried out. For example Denis Alexander who has made his case against ID, says in his otherwise very good book ‘Rebuilding the Matrix:
The theory gives coherence to an immense varied array of research fields, including and behavioural psychology, to name but a few [3].
Now compare that statement with the following statement from Professor Philip S. Skell, Member, National Academy of Sciences (a very prestigious body), Evan Pugh Professor of Chemistry, Emeritus Penn State University. He researched researchers. He asked them to consider a world where there was no theory of evolution. What difference would it have made to their research?
In 2005 he said:
I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin's theory was wrong. The responses were all the same: No.I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin's theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.
Many of the scientific criticisms of (neo-Darwinism) are well known by scientists in various disciplines, including the disciplines of chemistry and biochemistry, in which I have done my work. I have found that some of my scientific colleagues are very reluctant to acknowledge the existence of problems with evolutionary theory to the general public. They display an almost religious zeal for a strictly Darwinian view of biological origins.Darwinian evolution is an interesting theory about the remote history of life. Nonetheless, it has little practical impact on those branches of science that do not address questions of biological history (largely based on stones, the fossil evidence). Modern biology is engaged in the examination of tissues from living organisms with new methods and instruments. None of the great discoveries in biology and medicine over the past century depended on guidance from Darwinian evolution---it provided no support.

Dawkins and the Origin of Complexity.

So who made God? This question is the essence of Richard Dawkins' argument on page 141 of his ‘The Blind Watchmaker’[4].

He says a Creator, in order to make such a thing as the DNA would have to be at least as complex as the DNA. If we have to explain the origin of the DNA's complexity then we must explain the origin of the complexity of God. What is wrong with this argument? It assumes that the laws of nature (i.e. cause and effect) apply to that which is beyond nature - a patently false assumption. If God exists then He is, by definition, beyond nature. Dawkins goes on to say:
"You have to say something like 'God was always there', and if you allow yourself that sort of lazy way out, you might as well just say 'DNA was always there', or 'Life was always there'. and be done with it."

Although, no doubt Dawkins means this as a rhetorical sentence, its rhetoric can only be effective if the sentence makes any sense. But it doesn't. It is beyond dispute that DNA and life were not always there! No one pretends that they were. We do not know the laws that relate to the Eternal existence of God who is beyond nature, but what we do know is that life has not always existed. [5]
It is a common claim of Richard Dawkins and others that a cause for nature’s complexity must be more complex than nature itself. Thus that complex cause’s existence must call for explanation. However is this true? For example a war between nations maybe very complex, but the cause of the war maybe one man’s greed, jealousy or ambition. Just as we invoke non-complex but personal causes for complex situations, why not invoke a Personal cause for the existence of life?[6] Indeed Thomas Aquinas argues that God must be simple i.e. He must have no component parts.
[1] I owe this section on Hume to Dr. T. S. Torrance, senior lecturer in Economics and Philosophy at Heriot-Watt University.
[2] Unended Quest.
[3] Page 289.
[4] The Whole Book is reviewed in www.apologetics.fsnet.co.uk/dawkins.htm
[5] I give another response to this often asserted Dawkins argument at the end of the ‘philosophy’ section in the appendix on Intelligent Design.
[6] This is the essence of Keith Ward’s argument in a Tablet article in January 2006.

The Biologic Institute.

2006-12-19T16:50:00.000Z

A tantalising glimpse of some of the work going on in ID is here.

The Sunday Sequence

2006-12-19T16:45:00.000Z

This was an interesting (in parts) debate featuring Richard Dawkins and Andy McIntosh from Truth in Science.
The presenter (William Crawley) summary of the sequence is here
Listen again is here.

Things became interesting when AM challenged RD on whether abiogenesis requires intelligence or not. RD interpreted this to mean that AM was maintaining that evolution breaks the 2nd Law of Thermodynamics.

Is seems clear to me that they were talking past each other at this point. AM is talking about the problem of abiogenesis whereas RD is talking about things like gene duplications and subsequent mutation.

Richard Dawkin's reflects on the sequence here

This has been followed up by a letter in the Guardian really pushing for Leeds University to take further action with regard to AM.

“However, the claim that McIntosh's eccentric view of reality is unconnected
with his teaching or research as a professor of thermodynamics would appear to
be cast into some doubt by a conversation that I recently had with him on BBC
Belfast's Sunday Sequence. McIntosh publicly stated that evolution is
incompatible with the second law of thermodynamics.”

According to RD YEC beliefs should bar a person from any position anywhere in UK education or research. This includes areas entirely unrelated to science as well as to science itself.

“As to the general point about whether barmy views like McIntosh's should debar
somebody from teaching a subject which is not directly connected to that
particular nonsense, it is a difficult question. Would you like your child to be
taught, say, chemistry or German, by a teacher who believes in the Flat Earth
theory? It doesn't matter, you might say, because chemistry and German would be
the same on a flat Earth. But wouldn't you lose CONFIDENCE in that teacher's
qualification to teach ANYTHING? Would you entrust your child's education in any
subject to a man whose perception of reality was so demonstrably unreal?”

"Extremists" shaping the future.

2006-11-30T11:58:00.000Z

Lord Rees (Professor Martin Rees, Lord Rees of Ludlow Kt PRS) was interviewed by John Humphreys on the Today programme this morning.

http://www.bbc.co.uk/radio4/today/listenagain/

Lord Rees was speaking in advance of his 2006 Anniversary lecture celebrating 346 years of the Society’s existence and outlining the challenges facing science and society today and in the future.

He has warned that “we may be sleep walking into a future shaped by extremists.”
Asked by John Humphreys to name the extremists he refused to do so. Amongst his concerns however is the matter of “creationism” of any sort.

In the discussion he says:

“All I would say about this is that I'm a scientist...I feel that science is part of our culture and anyone is culturally deprived (my emphasis) who can't appreciate how our universe evolved from a mysterious beginning to creation of atoms, stars, planets, biospheres and eventually brains who could wonder about it all and share the wonder and the mystery, and I think that that is a marvellous story which is part of our culture and those who can't share it are impoverished.

JH: And those who argue otherwise are extremists?

MR: No, I would say they are impoverished (my emphasis). And the view that I am taking I think is shared not just by scientists but by most people including most mainstream religious people.

It is a small step between calling any kind of creationist education “cultural deprivation” and “cultural impoverishment” to calling it “child abuse” as Richard Dawkins maintains.

Truth In Science Materials.

2006-11-27T21:40:00.000Z

The "Truth in Science"

material is attraction considerable attention and discussion.

The Guardian- Revealed: rise of creationism in UK schools

The Nuffield Curriculum Centre.

The Guardian Seminar.

UPD8 Intelligent Design in Science.

BBC- Let's test Darwin.

It is also to be the subject of a discussion on Newsnight tonight between Lewis Wolpert and Andy MacIntish.

Peter Hitchen's piece in the Mail on Sunday...a rare journalist who can see the difference between ID and various forms of creationism.

Denyse O-Leary's analysis.

Lucy Sherrif writes a standard ID=creationism line at The Register.

Introduction to the Controversy - Part 2.

2006-11-27T15:24:00.000Z

Contributed by Howard Taylor.

(Part 1 is here.)

My exposition of the convictions of the ID movement[1].

ID maintains that the origin, nature and development of life (the subject of biology) needs non-material and intelligent Mind as its source.

However it holds that in the final analysis materialist explanations for any physical phenomenon are inadequate. The answers to the questions ‘What is matter?’ and ‘What is energy?’ raise fundamental mysteries about the nature and the origin of the intelligibility of all material existence. Biological complexity is just one particularly striking example of this.

We can summarise the convictions under the following four headings:

I. Science.

* Science has revealed a biological world in its simplest form, (before the alleged processes of evolution could get started) that is full of information and complexity - a complexity that exceeds the complexity of the most intricate of man made machines. Intelligent mind is needed to explain the origin of life.

* ID also casts strong doubt on the orthodox theories of neo-Darwinism, believing that they are completely inadequate to explain the development of life. Intelligent mind is needed to explain the development of life.

* Alleged evidence for natural selection from ‘beneficial’ mutations in bacteria or viruses is not evidence for evolution because the changes only involve the switching on or off or shuffling of parts of the already existing DNA or RNA molecules and do not produce any new organs or features to the existing life form, or add and extra level of complexity to the bacteria or virus. On the contrary they do the opposite. As every computer scientist knows the transfer of information cannot produce more information only a change (usually a detrimental change) in the original.

II. Philosophical
ID rejects Philosophical Naturalism, which makes the false assumption (in principle an improvable assumption) that the physical world's existence and properties are self-explanatory.

* Origin of the physical world. Either the origin of all things is eternal impersonal particles/energy and laws of physics or the origin is Eternal Mind. ID holds the latter view because the origin or matter cannot be matter itself!

* Mind and Matter Interact.
Everyday we see mind and matter interacting.

* Human thinking (which cannot be completely material) affects the physical world and vice versa.

* Therefore solely material explanations for the behaviour of material things must be inadequate.

* Therefore the existence of Divine agency in the material world should not present surprises.

III. Theological and Biblical.

* The Bible teaches that it is Uncreated Mind or Word, who seeks to know and be known, who is the origin and sustainer of all physical things.

* The Creation was not one event.
There were a small number of stages. Among these were: (1). Matter-Energy, (2). Non-conscious life (3). Conscious life and (4). Conscious life that is capable of abstract reasoning.

ID concentrates on (2). - The origin and development of living things studied by biology and genetics.

IV. Ethical

* In the long term the conviction that human life is valuable cannot be sustained unless there is a belief in an overall purpose

* Morality and Ethics would be bound to disintegrate in confusion.
We see the effects of this all around us.

============================
COMMENTARY.

ID maintains that the origin and nature and development of life (the subject of biology) needs non-material and intelligent Mind as its source.

However it holds that in the final analysis materialist explanations for any physical phenomenon are inadequate. The answers to the questions ‘What is matter?’ and ‘What is energy?’ raise fundamental mysteries about the nature and the origin of the intelligibility of all material existence. Biological complexity is just one particularly striking example of this.
I. Science.
ID proponents hold that all of nature points to Mind. However its main interest is in two things namely
1. The origin of life or self replicating molecules.
2. The development of life.

1. Science reveals the inner workings of the simplest forms of life to be composed of intricate circuits, miniaturised motors and enough digital code to fill an encyclopaedia. All these things exist in a cell without any brain, nervous system, liver, eyes, ears, blood, lungs, leaves, feathers, bark, roots, petals, etc. Digital code is a form of language and all languages arise from mind. Writing cannot be accounted for from the chemistry of the ink and paper (say) but must have its origin in mind.
2. All the above must have been present before the alleged processes of evolution could get started.
3. ID people also doubt evolution as an explanation for the whole history of life. Random mutation through the sieve of natural selection may be able to account for small changes in living organisms. However sustainable mutations have their limits.
4. Therefore these changes cannot account for the huge changes from a simple bacterium to all the life forms (including ourselves) that we see around us.
5. ID proponents believe there are mathematical tests for design in the origin and development of life. They show that the type of complexity found in biological systems cannot be the result of mindless algorithms or the properties of matter but must have intelligent mind as its source. For example language needs a mind and we find codes (types of language) in all living things.

The inference of Design is used and universally accepted in several sciences. For example if someone falls off a cliff, forensic science determines whether he/she was pushed or she fell by accident. Was there a purpose (intelligent design) or was it an accident? Forensic science tells us which.

6. The world famous atheist philosopher, Professor Anthony Flew, has given up atheism for theism. What is the basis for his change of mind? The extraordinary complexity of the supposed 'simple' form of life discovered by modern biology. In a Philosophy Journal which interviews him he says: "It seems to me that Richard Dawkins constantly overlooks the fact that Darwin himself, in the fourteenth chapter of The Origin of Species, pointed out that his whole argument began with a being which already possessed reproductive powers. This is the creature the evolution of which a truly comprehensive theory of evolution must give some account. Darwin himself was well aware that he had not produced such an account. It now seems to me that the findings of more than fifty years of DNA research have provided materials for a new and enormously powerful argument to design."
II. Philosophical
What exists? (Ontology)
Resistance to the ID view comes from (a). Those who deny that non-physical entities exist or (b) those who hold that non-physical entities may exist but do not affect the physical.
Since physical science examines physical things there could be no evidence to support the position (a).
Position (b) only could have support if it could be shown that the physical universe is a closed system of cause and effect - nothing non-physical affecting what goes on in it.
If physics provided us with a TOE (Theory of Everything) it would have gone along way to reaching that goal. However there are several problems:

1. The advance of science reveals more and more mystery.
2. Many have argued from Godel's theorem that it can be proved that the universe will never be understood from within itself alone.

Origins.
It makes no sense to say that the origin of matter and energy is matter or energy.
Since personal beings (with minds) certainly exist in the universe, it is reasonable to believe that the origin of all reality, at least, must be Personal Mind.

Mind and Matter.
ID holds the view that non-material minds have effects in the physical world. Therefore we should expect that the Eternal Mind also to affect the physical world.

Thinking (what minds do) cannot be simply the sum of material processes. If we discover a physical cause (say a virus in the brain) for a belief or a thought then that belief and thought would lose its value.
If all our thoughts were exclusively the movement of physical entities in our brains, then there would be no way, by thinking, of determining which 'thought' was correct and which was incorrect since that determining by thinking, itself would be a mere physical process.

One difference between physical events and thoughts of the mind.
Any physical process, unlike a thought, is neither true nor false, it just is.
However thoughts may have the additional property of being true or false.
So thoughts cannot be identical to physical processes or a combination of exclusively physical processes.

For example a river running through a valley is neither true nor false (though thoughts about the flow of the river may be true or false). Its running through the valley just exists.

Thus there is a fundamental distinction between physical processes (such as the flow of water), which merely exist, and thoughts, which not only exist but also may be true or false. Thus thoughts cannot be mere physical processes.

Bertrand Russell said:

If we imagine a world of mere matter, there would be no room for falsehood in such a world, and although it would contain what may be called ‘facts’, it would not contain any truths, in the sense in which truths are things of the same kind as falsehoods. In fact, truth and falsehood are properties of beliefs and statements: hence a world of mere matter, since it would contain no beliefs or statements, would also contain no truth or falsehood. [2]

Messages, languages, and coded information ONLY come from minds. (Minds are conscious.) - minds that have agreed on an alphabet and a meaning of words and sentences and that express both desire and intent.

The atheist Richard Dawkins writes:

What lies at the heart of every living thing is not a fire, warm breath, nor a 'spark of life'. It is information, words, instructions . . . Think of a billion discrete digital characters . . . If you want to understand life, think about information technology.[3]

If we analyze language with advanced mathematics and engineering communication theory, we can say:

Messages, languages and coded information never come from anything else besides a mind. No-one has ever produced a single example of a message that did not come from a mind.

Languages etc can be carried by matter or energy (eg sounds, ink, electronic and radio signals) but they are none of these things. Indeed they are not matter or energy at all. They are not ‘physical’.
The physical universe can create fascinating patterns - snowflakes, crystals, stalactites, tornados, turbulence and cloud formations etc. But non-living and non-conscious things cannot create language. They cannot create codes.

Drusilla Scott tells us of Michael Polanyi's reaction to the claim that the discovery of the DNA double helix is the final proof that living things are physically and chemically determined.

No said Polanyi it proves the opposite. No arrangement of physical units can be a code and convey information unless the order of its units is not fixed by its physical chemical make-up. His example is a railway station on the Welsh border where an arrangement of pebbles on a bank spelled the message - "Welcome to Wales by British Rail". This information content of pebbles clearly showed that their arrangement was not due to their physical chemical interaction but to a purpose on the part of the stationmaster ... The arrangement of the DNA could have come about chance, just as the pebbles on that station could have rolled down a hillside and arranged themselves in the worlds of the message, but it would be bizarre to maintain that this was so ... [4]

Of course many committed to materialism (without evidence) insist that the mind is no more than an aspect of the physical brain/nervous system. We should remember the words of Gödel: That the mind is the brain is the great prejudice of our age.

Mind and Matter interact.
My thoughts (non-physical) may affect the physical river if I decide to have go for a swim in it. I make a splash. So our everyday experience of thinking (and deciding) can affect the physical world - making us move our physical bodies and other things too. Thus minds can and do affect physical reality. This was Karl Popper's argument. How mind acts on matter remains a mystery.

ID believes that not only the origin of matter comes from non-material mind, but that that Mind continues to act in His creation.

John Polkinghorne believes that God’s action in the material world does not involve and extra “push” but and input of information.

This means that the physical sciences are bound to reach points in their research when they come up against a brick wall. They are right to search for physical explanations, but they must have in the back of their minds the fact that all materialist explanations are ultimately inadequate to account for the existence and properties of the physical world.

III. Theological and Biblical.
The Bible teaches that it is not uncreated impersonal particles/energies/laws of physics that are the eternal origin of all things, but an Uncreated Mind or Word who seeks to know and be known. This is how the New Testament which Christians at least accept puts it:

In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through him, and without him was not any thing made that was made. And the Word became flesh and dwelt among us, and we have seen his glory, glory as of the only Son from the Father, full of grace and truth.[5]

ID people may have different interpretations of Genesis 1, but they believe that the Creation was not one event. There were a small number of stages. Among these were (1). Matter-Energy, (2). Non-conscious life (3). Conscious life and (4). Conscious life that is capable of abstract reasoning.

This means that the sciences should expect to find discontinuities in their examination of nature.

1. The understanding of matter and energy cannot be reduced to 'nothing'.
2. The understanding of non-conscious life cannot be reduced to a complex form of matter and energy. (Biology cannot be wholly reduced to chemistry and physics).
3. The understanding of conscious life cannot be wholly reduced to a complex form of non-conscious life.
4. The understanding of abstract reasoning cannot be reduced to the consciousness of animals.

[1] This is my own summary of ID's beliefs and it does not necessarily represent other views from within people associated with ID.
[2] Bertrand Russell, The Problems of Philosophy, page 70
[3] The Blind Watchmaker, page 112.
[4] Scott Drusilla, 1995, Everyman Revived - the Common Sense of Michael Polanyi pages 116 and 117.
[5] John 1:3,14

Stunning Animations!

2006-11-16T22:31:00.000Z

Do take time to have a look at these amazing animations....

The Inner Life of the Cell

Michael Behe and Astrology- What did he mean?

2006-11-16T21:30:00.003Z

For those who are interested in what Michael Behe actually meant.
After the discussion resulting from the previous post on this subject I thought I would ask him....

Q1. At the deposition for the Dover trial when you were asked the question about astrology where you answered "It could be...Yes" were you thinking of "astrology" as it is practiced in terms of the present day...horoscopes etc or were you thinking in terms of astrology related to astronomy in the history of science... or something else?

(deposition statement)

17 Q. Using your definition of theory, is Creationism -- using
18 your definition of scientific theory, is Creationism a
19 scientific theory?
20 Behe. No.
21 Q. What about creation science?
22 Behe. No.
23 Q. Is astrology a theory under that definition?
24 Behe. Is astrology? It could be, yes.

Michael Behe:

I was not thinking of the modern superstition of astrology, but of the idea of astrology in the middle ages, when people were trying to discern what forces actually were in play in nature. After all, if planetary bodies such as the moon and sun could affect the tides on earth, perhaps they could affect other things as well, such as people's behavior. We now know that to be wrong, but at the time it was a reasonable idea, based on physical evidence. I am told by some historians of science that the educated classes of Europe thought astrology to be quite scientific.

Q2. At the time of your deposition statement did you believe that astrology (as it is understood and practiced today) was included within your broader definition of "scientific theory?"

Michael Behe:

No, not modern astrology, as practiced by card readers with bandanas on their heads and such. I had in mind astrology of centuries ago, when educated people thought it might really have explanatory power.

Q3. Do you currently believe that astrology (as it is understood and practiced today) is included now within your broader definition of "scientific theory?"

Michael Behe:

No, of course not. Best wishes. Mike Behe

This was what I had surmised from reading the transcript of Behe from the trial. It is good to know that I had understood his position correctly.

Introduction to the Controversy. Part 1

2006-11-15T21:22:00.000Z

Contributed by Howard Taylor

The present day argument, considered here, is between those who hold to so-called Intelligent Design and those who accept the prevailing opinion that natural processes alone can account for two things (a) biogenesis - the origin of life (before the alleged processes of evolution could get started) and (b) the subsequent development of life.

At the outset I should say that personally I prefer the term ‘Mind’ to ‘Intelligent Design’ because there is a history of thought going back thousands of years linking non-material mind with matter in various relationships. For example in our own time Roger Penrose FRS, formally professor of Maths at Oxford, believes that a non-material transcendent reality is the source of all truth, beauty and goodness. The term intelligent designer is probably included in this view of the transcendent world but the source of matter and life is much greater than this. However, for the purposes of this paper, I will be referring to the modern term ‘Intelligent Design’ (ID).

Opponents of ID includes many Jews and Christians - even evangelical Christians[1] - who believe that natural processes for the origin of life and evolution can be reconciled with Genesis 1. They usually hold that the matter of the universe including the natural laws of nature (such as gravity) were created by God and finally tuned to allow, stars, galaxies, planets like earth, and then life to form. In this view God endowed His creation with a 'fruitful potentiality' to produce all that we see around us today. (For short we refer to this view as TE meaning Theistic Evolution or Theistic Evolutionist.)The first group says that life is so so complex and information-rich, that an Intelligent Design is needed to explain it.
An important part of the argument is that the complexity of the simplest form of life contains information in the form of 'code' or 'words' or 'language' (DNA and RNA for example). It is contended that the origin of any code has to be Mind. If one is examining ancient markings on a rock, which are not just complex patterns but a language, one will conclude that they are the products of an intelligent mind. A detailed support for this view comes from the mathematician Bill Dembski who has written extensively on mathematics and information.Advocates of ID are not proposing a belief in a young earth or a particular religion, even though some of them may hold also to a young earth view that the earth is less than 10,000 years old. They simply are saying that life requires Mind for its origin and also its development as the amount of its information content increases. (There is more information in the DNA of an elephant than of a bacterium.)Against this view is the view of evolutionists and theistic evolutionists that the ID people are invoking the 'god of the gaps'. It is true, they say, that there in no viable theory of the origin of life - but one should not put any 'god' in that gap to explain it. Science is about finding physical causes for physical phenomena, not invoking God every time science is faced with a mystery.Those holding to TE say that to invoke God to explain part of creation is to attempt to introduce Him as part of the data of natural science and that is unacceptable. The Jewish/Christian doctrine of Creation says creation is separate from God and therefore one must not look for God in Creation.To summarise so far: whereas naturalistic science says science is defined as that study, which always looks for physical explanations, ID says 'no', science means 'follow the evidence' and the evidence leads to ID.

It might be wiser for ID to argue like this: As Einstein recognised science examines the rational structure of the material world but it can't explain why it is rational- or has the fundamental properties that it does. (He said: The only thing incomprehensible about the universe is that it is comprehensible.) The intelligent (Einstein's word) non-material source of matter's rational structure, he called The Old One or The Dear Lord.

It seems to me that ID is just taking this one step further. It is saying that the properties of the living world cannot be reduced to the properties (rational structure) of the non-living material world but it has a rational structure of its own.
[1] Written from a Christian Standpoint an impressive book criticising ID is Rebuilding the Matrix, by Denis Alexander, published 2005.

Michael Behe and Astrology.

2006-11-14T23:30:00.000Z

If you want to comment on Michael Behe’s desire to see Astrology in every science lesson please read the following before doing so.

Other links:
Behe believes in astrology
What's a Theory? Part II
Miller Misrepresents Behe Again
500 years ago

New Scientist reported the incident like this:

“Under cross examination, ID proponent Michael Behe, a biochemist at Lehigh
University in Bethlehem, Pennsylvania, admitted his definition of “theory” was
so broad it would also include astrology.”

Actually the truth is more interesting.

In Behe’s deposition he had made a careful argument using evidence from PubMed that the word “theory” is actually used in a variety of ways in scientific discourse.

He makes the point that if the NAS definition is used rigorously it would require quite a significant shift in the way the word is used by many scientists in their published work.

This was an important point in the whole debate and an important point relevant to the trial. When IDers argue that ID is a scientific theory in what sense are we using the relevant term “scientific theory”? When anti-IDers argue that ID is not a scientific theory in what sense are they using the term.

In his expert witness submission Behe argued that there are basically four different senses in which the word “theory” is used in modern peer reviewed scientific discourse.

He then went on to argue that the best sense for describing accurately ID as a scientific theory is “a proposed explanation for a set of facts.” He sets this as the alternative explanation to Ernst Mayr’s fifth claim of Evolution - natural selection as the cause of biological complexity.

The expert witness submission itself (as far as I can see- it is a set of images rather than searchable text) says nothing about astrology.
Link to expert witness

*The deposition does include the statement regarding astrology:

17 Q. Using your definition of theory, is Creationism -- using
18 your
definition of scientific theory, is Creationism a
19 scientific theory?
20
Behe. No.
21 Q. What about creation science?
22 Behe. No.
23 Q. Is astrology
a theory under that definition?
24 Behe. Is astrology? It could be, yes.

Link to deposition.

The astrology section comes up on Day 11 in the afternoon session
Link to court transcript

Q
But the way you are using it (“scientific theory”) is synonymous with the
definition of hypothesis?
Behe-
No, I would disagree. It can be used to cover hypotheses, but it can also
include ideas that are in fact well substantiated and so on. So while it does
include ideas that are synonymous or in fact are hypotheses, it also includes
stronger senses of that term.
Q
And using your definition, intelligent design is a scientific theory,
correct?
Behe
Yes.
Q
Under that same definition astrology is a scientific theory under your
definition, correct?
Behe Under my
definition, a scientific theory is a proposed explanation which focuses or
points to physical, observable data and logical inferences. There are many
things throughout the history of science which we now think to be incorrect
which nonetheless would fit that -- which would fit that definition. Yes,
astrology is in fact one, and so is the ether theory of the propagation of
light, and many other -- many other theories as well.
Q
The ether theory of light has been discarded, correct?
Behe
That is correct.
Q
But you are clear, under your definition, the definition that sweeps in
intelligent design, astrology is also a scientific theory, correct?
Behe
Yes, that's correct. And let me explain under my definition of the word
"theory," it is -- a sense of the word "theory" does not include the theory
being true, it means a proposition based on physical evidence to explain some
facts by logical inferences. There have been many theories throughout the
history of science which looked good at the time which further progress has
shown to be incorrect. Nonetheless, we can't go back and say that because they
were incorrect they were not theories. So many many things that we now realized
to be incorrect, incorrect theories, are nonetheless theories.
Q
Has there ever been a time when astrology has been accepted as a correct or
valid scientific theory, Professor Behe?
Behe
Well, I am not a historian of science. And certainly nobody -- well, not nobody,
but certainly the educated community has not accepted astrology as a science for
a long long time. But if you go back, you know, Middle Ages and before that,
when people were struggling to describe the natural world, some people might
indeed think that it is not a priori -- a priori ruled out that what we -- that
motions in the earth could affect things on the earth, or motions in the sky
could affect things on the earth.
Q
And just to be clear, why don't we pull up the definition of astrology from
Merriam-Webster.
MR.
ROTHSCHILD: If you would highlight that.
BY
MR. ROTHSCHILD:
Q
And archaically it was astronomy; right, that's what it says there?
Behe
Yes.
Q
And now the term is used, "The divination of the supposed influences of the
stars and planets on human affairs and terrestrial events by their positions and
aspects."
That's
the scientific theory of astrology?
Behe
That's what it says right there, but let me direct your attention to the archaic
definition, because the archaic definition is the one which was in effect when
astrology was actually thought to perhaps describe real events, at least by the
educated community.
Astrology
-- I think astronomy began in, and things like astrology, and the history of
science is replete with ideas that we now think to be wrong headed, nonetheless
giving way to better ways or more accurate ways of describing the world.
And
simply because an idea is old, and simply because in our time we see it to be
foolish, does not mean when it was being discussed as a live possibility, that
it was not actually a real scientific theory.

So this was the famous section of the court transcript that shows that Behe is a scientific illiterate who wants modern astrology in science lessons!
Note Behe is not arguing that Astrology as it is understood today is a scientific theory but that possibly when it was in a hopelessy tangled state with Astronomy there may have been justification for calling it a scientific theory. He argues that the ether theory of light propagation was also an example of this kind of theory from the history of science.

Note-I am not in the habit of praising the NCSE but I think that they have done an excellent job of making all the documents available online - Thankyou!
* Updated with the correct link to the deposition - thanks to Annonymous commenter.

Why is the bacterial flagellum so important for ID?

2006-11-03T17:38:00.000Z

The bacterial flagellum is a rotary motor. It needs fuel to drive its rotation. It needs a system for producing movement and a carefully crafted circular mechanism allowing smooth rotation. It also needs some kind of propeller outside the cell.

In all our observation of the material world a rotating engine visible to the human eye would be taken as proof of intelligent activity even if we knew nothing else about the object in question hence Paley’s reflections on a watch mechanism.

Also a rotary engine is an invention of genius. A great deal of our modern civilisation would be impossible without rotary engines of different kinds. Michael Faraday was a genius. To find a rotary engine produced by a mind that is not human would indicate that the mind that produced the rotary engine was in some respects similar to the human mind and consciousness. A mind that can design a rotary engine seems to be a mind that it would be interesting to know better.

The discovery of a clumsy inefficient electric motor in a physics lesson indicates that some GCSE pupils are trying to follow the thoughts of Michael Faraday.

The discovery of an electrical motor with 90% efficiency indicates civilisation at a comparable level to 20th century civilisation.

The discovery of a motor which is greater than 99% efficient and more than 10 times smaller than anything human beings have ever produced points to…

David Hume on Intelligent Design.

2006-10-26T21:40:00.001+01:00

The whole frame of nature bespeaks an intelligent author; and no rational enquirer can, after serious reflection, suspend his belief a moment with regard to the primary principles of genuine Theism and Religion.

(David Hume )

This is the third sentence of his “The Natural History of Religion” 1751

ID Optimism

2006-10-26T09:44:00.000+01:00

I think that the optimism of IDers is related to how they think about the following diagram:

1. represents the total of all possible proteins that could be coded for in DNA.

2. represents all possible proteins with a selectable function.

3. represents all actually existing functional proteins.

4. represents proteins essential for the simplest living membrane bound organism.

IDers tend to think that the huge size of 1 and the comparatively tiny size of 2,3 and 4 points clearly to some other solution to random testing of possibles until we get the working examples that are needed.

IDers tend to think that even our present knowledge of genomes indicates the need for some other mechanism than random testing to find the necessary tiny needles in this vast haystack. Do the genomes we know look like efficient testing machines to find rare useful proteins?

IDers tend to think that the little orange circle is too big to allow chance to be a realistic explanation for the origin of life. Chance is just the wrong sort of explanation for what we see. It is a little like thinking that random selection of notes in sequence can produce a great symphony.

With objects like the rotary motor function of the flagellum the contraints upon so many proteins at once for selectable function tends to breed scepticism that this object can occur without a designer. This problem is compounded many fold whenever we then begin to think about the origin of life. If it is a real snag that we are struggling to deal with in the flagellum then it is infinitely worse for the origin of life. To reject other explanations outright says more about the rules we impose on our bank of possible explanations than about the real origins of the objects we are examining.

Off Topic.

2006-10-25T15:44:00.000+01:00

If you live near Durham or are visiting near the area do take a trip to see a ridiculous sight in the cathedral. Close to the cloisters near the restaurant there is a bookshop with the title "Society for Promoting Christian Knowledge" on display you will find a book by Richard Dawkins entitled "The God Delusion." When asked about this the manager replied that it was done to "avoid discrimination."

Liar Liar!

2006-10-18T23:42:00.000+01:00

We were all told the story of the young lad who cried wolf too often as he ran down the hill from the sheep pen. I suggest that the anti-ID movement needs to recall the story and apply it carefully to the current debate. I think if we are to have productive debate we ought to bite our tongues on the temptation to use the “liar” word.

A liar is not someone who has made a mistake or repeated a false claim from someone else in good faith.

A liar is someone who tells a lie. A lie is an intentional false statement. In other words the liar knows that what he is saying is false but goes ahead and says it anyway seeking to give the impression that it is true.

Wesley Elsberry of the NCSE has suggested that using the “liar” label for ID supporters is a good strategy:

If you want to drive a wedge between an audience of evangelical Christians
and the professionals in the ID movement, you need a third approach: show that
the ID advocate on stage with you has been lying to his followers. Show misquote
after misquote; demonstrate error after checkable error, and make the audience
understand that if the ID advocate claims that the sky is blue, their next step
had better be to look out the window to see for themselves. Evangelicals do want
to take Christ’s message to the world, but they also have a deep loathing of
liars. (here)

I would entirely agree with him with one important condition. You had better be sure that the label fits... otherwise this strategy is going to seriously backfire!

One example of an attempt to attach the “liar" label to the writers and supporters of “Truth in Science” has been made on this blog.

The accusation was made with regard to the following quotation from this document:

“I ‘know’ that Tutt’s differential bird predation hypothesis is correct because
I ‘know’ about peppered moths… However, for those who do not ‘know’ the peppered moth, whether they are scientists, teachers or members of the public, this
should not, indeed it must not be enough."

(This quotation has apparently since been replaced by the following:

“I know the peppered moth, and I know that J.W. Tutt was essentially correct in
his explanation of the rise of carbonaria [the dark form]. However, for those
who do not ‘know’ the peppered moth, whether they are scientists, teachers or
members of the public, this should not, indeed, it must not be enough.”

[see here])

The purpose of the quote in its original context was to establish that there are real problems with the Kettlewell data which was originally presented in support of the differential predation hypothesis. The quote was to establish the point that Marjerus recognised that further data was needed to demonstrate unequivically that the differential predation hypothesis was correct.

The original quotation was made of two sections of text:

(P27)

"I ‘know’ that Tutt’s differential bird predation hypothesis is correct because
I ‘know’ about peppered moths…

The paragraphs in between deal with Marjerus’ love of moths and life time study of them. In other words they are a defence of his statement “I know about peppered moths.”

(p29)

However, for those who do not ‘know’ the peppered moth, whether they are
scientists, teachers or members of the public, this should not, indeed it must
not be enough."

The “However” of the beginning of the second part of the quotation is clearly linked to the stem of the argument which formed the first part of the quotation. It is entirely legitimate in my view to put these two parts of the argument together and indicate the deleted section with the ellipsis mark.

The quotation does not seek to mislead people it simply establishes the point that Marjerus recognises that the evidence for the differential predation hypothesis needs to be improved.

To seek to attach the label “liar” as a result of the use of this quotation is an example (in my view) of where the “liar, liar” strategy is backfiring badly.

[Apologies for the truncated appearance of the quotations... I can't seem to make the blogger do them nicely! Any free education on this would be gratefully recieved.]

The definition of “Irreducibly complex.”

2006-10-17T23:06:00.000+01:00

Definition 1. (From Darwin's Black Box)
A single system which is composed of several interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning

Definition 2. (Behe's "pathway definition")
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.

Definition 3. (Dembski's definition)
A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily 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.

I had put my definition here.

The Black Shadow.

2006-10-16T22:05:00.000+01:00

I had been aware of this organisation for quite some time but did not think that their website justified them being taken seriously. They have now taken the rather grand title of the "British Centre for Science Education" and are collaborating with their US friends from The NCSE. To be honest I would have thought that the NCSE would have wanted a rather drastic overhall of the whole set up before there was any public acknowledgement of a link.

MP Graham Stringer apparently has no concerns about the nature of this organisation or the contents of its website and has tabled the following early day motion:

"That this House shares the concerns of the British Centre for Science
Education that the literature being sent to every school in the United Kingdom
by the creationist religious group Truth in Science is full of scientific
mistakes and fails to disclose the group's creationist beliefs and objectives;
and urges all schools to treat this literature with extreme caution."

This motion it seems was tabled before the BCSE had actually seen the literature sent to the schools which is rather a back to front way of going about things in my view.

A new Blog has been established with the purpose of finding out a little more about the "Black Shadow"!

Questions on IC and ID.

2006-10-14T09:46:00.000+01:00

Matt Inlay posted these as a comment but I thought they were excellent questions so I will answer them here:

1. Do you feel that science has made progress understanding the origins of these systems since the publication of DBB?
Yes

2. Do you think science will continue to make progress understanding the origins of these systems? (Regardless of whether the final result of the research will ultimately satisfy Behe's requirement.)
Yes

3. Do you think that it is impossible (or implausible) for any IC system to have evolved?

Can I try and ask the question in a few different ways to explain my answers to different ways of understanding the question.

Do you think that there are complex systems in biology which unintelligent causes cannot produce?

Yes.

Do you still believe that there are such unevolvableIC systems within the immune system?

Yes. I would not use the complement example nor would I be confident in using any of the examples in DBB but I still have a hunch that ultimately there is need for intelligence to cause this system and that this will become clearer as more work is done.

Do you consider that it is more helpful in terms of the discussion for and against ID for IC to be used for systems which a person believes cannot be produced by unintelligent causes?

Yes. I think it confuses the debate to speak of IC systems evolving. If they can evolve by the usual processes then they are not IC. I think for the purposes of argument IC should be reserved for systems which a person believes cannot evolve.

4. Do you still consider it reasonable for Behe and company to conclude intelligent design based on the existence of IC systems in biology?

I consider that IC to ID is a fascinating argument. It is an interesting hypothesis well worthy of further investigation. I do not consider that it has been demonstrated that unintellegent causes can explain everything in biology. It is reasonable to infer design but it has not been clearly demonstrated in a rigorous way that I am aware of as yet. The terms of the calculations necessary need to be clarified in my view.

5. What do you see as to the future of the IC-to-ID argument? Do you think IDists will be able to further develop the concept, or will evidence against it continue to accumulate? In other words, will the IC-to-ID argument improve over time, remain the same, or decrease?

I am convinced that ultimately the IC to ID argument will prevail. I think ID will be developed and evidence for it will accumulate. I expect it to become a demonstrated fact at some point.

6. Do you think it is important for IDists to develop their own theory of origins, with "detailed, testable" models, or do you feel that the evidence against evolution is sufficient to take a pro-ID stance?

I do not consider that I am qualified to take a view on cosmological ID from fine tuning arguments because I have not got a clue about the physics and maths of them.
I think that in biology the argument has considerable appeal. A person's enthusiasm for it or antagonism against it is going to depend on their world view I think. I do not think that the argument is sufficiently well developed that all scientists should be convinced of it but I do not think that it should be dismissed from scientific discourse on the basis of the methodological naturalism argument.

I think a large number of ID supporters are pro-ID because of religious convictions. I think that there are however some people who are frustrated with "evolution only" explanations on the basis of the science alone but it is hard to distinguish between the two.

Unquestionably there is much work needing to be done if ID is to become convincing generally.

7. Do you think IDists will ever develop a "detailed, testable" model of ID?

Yes.

8. Do you think ID is science? If so, why?

Yes. ID is a mixture of lots of things but I am convinced that to exclude the possibility of a design inference is an unecessary restriction on possible explanations for what we see in the universe. I like the sort of work that Douglas Axe and Scot Minnich have done and think that this is the correct way forward.

Conclusion - IC in Immunology?

2006-10-04T01:09:00.000+01:00

My foray into immunology (here, here and here) was prompted by trying to work out who was bluffing when the large pile of books, essays and papers was used in the Dover trial. Behe maintained that there were no detailed explanations about the origin of the complex parts of the immune system. The anti-ID side maintained that there was plenty of evidence based research work sufficient to illustrate how the immune system originated.

Since the trial the argument degenerated into an argument over what constituted sufficient detail.

I looked at Matt Inlay's web essay responding to the immunology chapter of Behe Book and Matt Inlay and Ian Musgrove were kind enough to help me along through the maze of immunological complexity. (Thank you to you both.) My conclusion as a non-expert is that Matt's argument for the nonIC nature of these three systems is strongest for the complement system. (That is not to say that I think that his explanation is plausible but simply that the argument for its IC nature is not convincing.) I am less convinced by the arguments against the IC nature of the other two systems. I agree however that the arguments do need refining and that this needs to involve someone who is a professional immunologist.

I think that Behe’s points regarding the lack of detail in some of the explanations for the pathways to these complex systems are indeed valid.

Truth in Science.

2006-10-04T00:22:00.000+01:00

This organisation states that its area of initial focus is to be the origin of life and the origin of the diversity of life.
Their concerns seem to include the following:

1. Teaching on this subject has been “dogmatic and imbalanced.” Darwinian evolution is presented as uncontroversial and the only credible or scientific theory.

It is clear that evolution is controversial amongst the general population and amongst a substantial minority of parents. In this situation it is important for science teaching to go no further than the clear evidence warrants. It is clear that the overwhelming majority of scientists in the relevant fields believe that the evidence for common descent is convincing. However the history of the development of evolutionary thinking is on a backdrop of special creation thinking. Students cannot really grasp the complex nature of how science develops without appreciating the difficulties that Darwin faced. So from a historical perspective it is important to understand the alternative ways of thinking from a purely naturalistic view.

Where science becomes a simple platform for atheism as Richard Dawkins, P.Z. Myers and Daniel Dennett and others advocate this is clearly going to cause signficant difficulties for far more people than evangelical creationists.

We actually know very little about the origin of life and it is important to stress this in science lessons. We actually know very little about the origin of the data required to build different types of living organisms and this should be stressed. It is crucial that parents should be confident that science lessons are focusing on what we know rather than what we hope will turn out to be true.

2. Other explanations of origins are sometimes misrepresented. Children should be given fair and accurate representations of alternative views.

It is hard to understand anyone objecting to this concern. Any fair minded person should want the truth to be told even about people they strongly disagree with. If creationist views are misrepresented those misrepresentations should be corrected as soon as possible. Attacking straw men is a waste of everyones time.

3. The way origins are taught in science lessons fails to address the concerns of a large minority of parents about a purely naturalistic view.

I have commented on this in my remarks above. There is plainly a large minority of UK parents who are unconvinced by the entirely naturalistic explanations of life and the universe and who believe that alternative explanations should be presented to their children. Science education is always going to be a collaboration between scientists and parents. It behoves scientists to tread very carefully in this area unless they want to risk the situation of a confrontation with strongly held religious views of a large number of parents. Compulsory education demands great sensitivity to parental concerns.

4. Some evidences presented for evolution in some texts are flawed and inaccurate.

I understand that this is a very sensitive area but it is clear from my own experience that bad examples of teaching and textbook materials persist in this area far longer that they should have done and improvement of accuracy here should be welcomed by all.

Conclusion.
If I have understood the aims and objectives of "Truth in Science" then I am strongly in support of what they are seeking to do.

Launch of "Truth in Science."

2006-09-21T22:58:00.000+01:00

A new organisation has been launched to shine a spotlight on the origins issue in British Schools. The organisation is called "Truth in Science" and their website is here.

I hope to do a more detailed post on this new venture when I have read more on their site.

System 3

2006-09-06T12:21:00.000+01:00

The complement system.

For a biochemical switch to be useful you need

1. A mechanism to detect a change in the environment of a cell

2. An alternative action/pathway to switch to when the change is detected.

The switch on its own is no good if is doesn’t activate some kind of response to the change it detects.
The alternative "something to do" however is no use unless when it is needed you can switch it on. Usually the action to be switched on is a function which is needed only in certain conditions. Thus for it to work you need the switch and the function together. It is a logical "IF-THEN-ELSE" function. This is the central idea of Irreducible Complexity (IC) which Behe raised as a possible candidate for falsification of RMNS as the sole generator of biological complexity and as an indicator of intelligent design.

Switches (according to Behe) with their two alternative responses and some kind of detector system are therefore a good sign of intelligent design.

The complement system (as I understand it) is a system for blowing up cells. Blowing things to pieces is a dangerous job and needs to be handled by careful operators.

For an animal to obtain a system for blowing cells to pieces (bear in mind that an animal is made up of cells) is extraordinary.

To blow up a cell you only need to make a suitably sized hole in it. The rest happens as a matter of course.

Let us start from the position of having a fully functional cell blasting system which is triggered by molecules usually associated with bacteria detected by innate unchanging proteins sticking to carbohydrate molecules only found on the surface of bacteria. These are what I am calling the “dumb immigration officers.” The “dumb immigration officers” don’t do anything very clever they just look for sugar molecules with a foreign appearance and stick to them.

The switch in these systems is a switch between a “snipper” protein with a protective cover and a “snipper” protein that is going around snipping things.

The conversion to an active “snipper” is caused in the “dumb immigration officer” system by a protein complex sticking to certain sugar type molecules only found on bacteria surfaces.

See the molecules involved here.
The solution to the evolution of the “intelligence led immigration officer” system is that the same “snipper” switch (presumably by gene duplication and mutation) becomes activated by antibody which has stuck to a foreigner rather than by sticking to bits of the foreigner itself.

Behe asks whether it is reasonable to believe that this development of the cell blasting system together with the “intelligence led immigration officer” system can be explained by a gradual step by step process of incrementally increased function.

The problem with fiddling around with the binding site of one of these snippers is that you are fiddling around with explosives! The only binding sites that will be useful are those which are unique to foreigners….and if you get things wrong you have pressed the suicide button.

Is it reasonable to think of an organism experimenting with a duplicated "snipper" gene until it hits on a binding site that binds antibody stuck to a foreigner? My gut response is that this is not going to work but I suppose it depends on the frequency of useful binding sites as opposed to the lethal ones.

System 2

2006-08-25T19:06:00.000+01:00

Just a few thoughts after having read Matt Inlay’s response to Behe’s immunology chapter section 2.

The mechanism explaining the origin of a rearranging gene segment system to generate antibody diversity.

(CAUTION – I am a self confessed delusional crank with no immunology or evolutionary biology qualifications.)

As I understand it this is a summary of the best guess currently available for the origin of the gene rearranging system to generate variable antibodies.

1. A transposon became inserted either into a sperm cell, and egg cell or a very early embryo cell. Presumably at this stage it is a transposon that only becomes active in transcribed genes rather than having eukaryotic transcription control sequences. It must have initially integrated into an active gene in such a way that it could transpose when that gene was expressed. This is something that is presumably a selective disadvantage.

2. After jumping around the genome for x generations it happened to insert into an innate immune system receptor at the point where its eventual excision would cause variation in the antigen binding site and thus be an advantage to the cell. This is also presumably an exceedingly rare event.

At this point in the description the proposed pathway becomes very sketchy. By means of 4(or 5) genetic duplication events plus an incorrect recombination event we produce a set of variable antibody producing genes with heavy and light chains which fit together beautifully and a set of T-cell receptors using a similar process for a totally different function.

If this is the best that is currently available then I would agree with Behe that it is time someone got their act together or was ready to admit publically that at the moment we really have got lots of major problems explaining the origin of variable antibodies.

(Please note I am not intending to belittle Matt Inlay’s essay. I think he has done an excellent job explaining this to a non-specialist for the web. Thank you Matt!)

(Please note I am not intending to belittle the work of evolutionary immunologists comparing immune systems in different organisms and trying to put together a scheme for its evolution. I am very appreciative indeed of research immunologists. I am merely saying that this account is very sletchy indeed and for it to be convincing you need to already believe that it really did evolve without any intelligent input.)

(BTW are there different RSS sequences at the two join sites and different RAG proteins…what stops them getting muddled?)

System 1.

2006-08-23T23:18:00.000+01:00

I have read and thought about the first part of Matt Inlay’s response to Behe’s Immunology IC (irreducibly complex) argument. This section is written to rebut Behe’s claim that a simple Antibody receptor system is IC.

Behe claims that there are 3 components each of which is needed for the system to function.
1. A membrane bound form of the antibody
2. Messenger system
3. Secreted form of the antibody.

As far as I understand Matt Inlay’s response he is saying that the whole system came as a working variant of some other 3 component system.

He suggests macrophage scavenger receptor, CD14, and Beta2 or hemolin (which is described in more detail.)

Thus Matt Inlay’s answer to the origin of this simplified antibody system is to pick another such system from those available, duplicate the genetic information and modify the relevant parts.

The problem with this answer is that it simply takes the IC issue somewhere else. You have to develop an example of one of these systems in the first place.

It is a bit like the Panspermia idea of Anaxigorus, Arrhenius, Hoyle and Wickramasinghe the origin of life issue is just taken somewhere else in the universe only in this case somewhere else in the genome.

Having looked (very briefly) at some of the control pathways for some of the suggested origins explaining their origin is indeed a matter of some difficulty. It is especially in the messenger and control pathways that the IC argument is I believe strongest.

What does the quote mean...in context?

2006-08-23T22:32:00.000+01:00

I like to think that I am reasonably good at working out what someone meant when they wrote a particular piece of text. For those who think that I am defending the undefensible I include the preceding two paragraphs from the paragraph which Judge Jones and the Anti-ID-ers made so much of so that you can see for yourself the precise context in which it was made.

Another paper that gamely tries to account for a piece of the immune system is entitled "Evolution of the Complement System." Like the paper discussed above, it is very short and is a commentary article-in other words, not a research article. The authors make some imaginative guesses about what might come first and second, but inevitably they join Russell Doolittle in proposing unexplained proteins that are "unleashed" and "spring forth" ("At some point a critical gene fusion created a protease with a binding site for the primitive Cab"; "Evolution of the other alternative pathway components further improved the amplification and specificity"; and "C2, created by the duplication of the factor B gene, would then have allowed further divergence and specialization of the two pathways"). No quantitative calculations appear in the paper. Nor does an acknowledgment that gene duplications would not immediately make a new protein. Nor does any worry about a lack of controls to regulate the pathway. But then, it would be hard to fit those concerns in the four paragraphs of the paper that deal with molecular mechanisms.

There are other papers and books that discuss the evolution of the immune system. Most of them, however, are at the level of cell biology and thus unconcerned with detailed molecular mechanisms, or else they are concerned simply with comparison of DNA or protein sequences. Comparing sequences might be a good way to study relatedness, but the results can't tell us anything about the mechanism that first produced the systems.

We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.

Now you can decide for yourselves whether I have understood this particular piece of text when I say that the three things that Behe is looking for are:
1. Quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means.
2. Acknowledgement that gene duplication is different from new protein production.
3. Mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways.

Behe and the Literature – Who is bluffing?

2006-08-23T08:32:00.000+01:00

These series of Posts (here, here and here) started as a result of reading Behe’s response to the Dover legal opinion of Judge Jones.

As a result of the discussion one commenter pointed me in the direction of Matt Inlay’s essay responding to Behe’s immunology chapter in DBB.

In the paper he looks at three systems which Behe suggests exhibit IC (irreducible complexity) and provides suggestions as to how they could come about as a result of gradual step by step change (RMNS)

I had argued from the context of the much quoted claim “The scientific literature has no answers to the question of the origin of the immune system”

That Behe intended to be understood to be asking the following three questions:
1. Do any of these papers present quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means?
2. Do they acknowledge that gene duplication is different from new protein production?
3. Do they provide mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways?

With regard to Matt Inlays essay we must conclude that there is no attempt to address question 1. (Anti-IDers I think respond by stating that this is asking for unreasonable detail…or even impossible detail.)
Question 2 is satisfied I am sure.
With regard to question 3 there is an attempt at least partially to address this issue.

Matt Inlay divides his essay into three sections with each section dealing with one of the claims for IC in the immune system.

1. The production of a clonal selection system
2. A rearranging antigen receptor.
3. The origin of the complement system.
I would like to go through these three sections seperately in following posts.

Matt Inlay I assume did not write his essay for research immunologists. It was focused at people with a reasonable background in biology who were interested in the response of immunologists to Behe’s arguments…. In other words for people like me who are ceratinly not immunologists!

Forgive me therefore if I demonstrate publically that I am not an immunologist!

Unreasonable Detail?

2006-08-17T23:21:00.000+01:00

The argument over whether Behe is asking for unreasonable detail regarding the origin of the immune system will be determined either way by how one defines “unreasonable.” We should I think acknowledge that this will be affected by whether we have a basically materialist/naturalistic view of the universe or not.

A naturalist will tend to look at homologies between systems in different organisms and be happy to take this as proof that evolution has occurred.

A ID sympathiser will tend to say that we need a clear possible pathway to explain these interconnected complex systems.

The Immunology Chapter in DBB has three sections arguing that the system contains irreducibly complex mechanisms.

1. The production of Plasma Antibody.

The process by which the randomly produced antibodies become bound on the membrane of the B-cell. The process by which the binding of the antigen to the surface antibody triggers the ingestion of the antigen/antibody complex. The process by which a fragment of a foreign protein become attached to the MHC protein. The interaction of the B cell with the helper T cell producing interlekin. The interaction of the interleukin with the B cell to produce plasma cells and free antibody.
Behe concentrates upon the production of a clonal selection system. The need for there to be a genetic connection between the membrane bound antibody and the genetic information coding for that antibody. There needs to be a message system to transmit ON signal from the surface to the antibody gene in side the cell.
Behe imagines a system of data transfer involving only one other protein (thus missing out the T cell/MHC interaction problem) He argues that such a system therefore has three ingredients
(a) The membrane bound antibody
(b) The exported form of the antibody
(c) The messenger protein.
This would constitute an ICS
Behe argues that even this simplified system needs all of these items to produce a properly working system even without the issue of involving the T cell system.

2. The Complement System.
The problem that the complement system needs the antibody system and the anitobody system needs the complement system. This cascade system Behe argues suffers from the same problems as the gradual production of a blood clotting system.

3. The Antibody diversity generation system.
Behe argues that there is need for accurate developmental triggers to rearrange the DNA to form particular B cells.
There is need for carefully controlled somatic hypermutation. He argues that an ICS will be composed of:

The antibody coding fragments.
Signal identifying start and end of the coding fragments
Mechanism for cutting out the intervening sequences.

Behe argues that such a system must exhibit a selective advantage at each stage of its development.

Behe mentions the RAG protein as a function that could have come from a bacterium and been luckily transferred to an animal. It has the ability to rearrange DNA fragments.

But this is a very far cry from explaining the step by step process to a properly functioning immune system.

The question that needs to be asked is whether (in the face of the evidence currently available) it has been demonstrated beyond all reasonable doubt that the immune system was produced without any intelligent input.

Has it even been demonstrated beyond reasonable doubt that these kind of systems can be assembled without intelligent input.

Are Behe’s doubts reasonable?

Calling someone’s bluff…..

2006-08-17T11:41:00.000+01:00

I have attempted to discover precisely what Behe was saying when he made his statement about the literature concerning the origin of the immune system (here).

3 aspects.
1. Do any of these papers present quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means?
2. Do they acknowledge that gene duplication is different from new protein production?
3. Do they provide mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways?

My point here is that Behe cannot be both wrong and at the same time be making unreasonable demands.

If he is just plain wrong then the papers from the literature which refute the two remaining prongs need to be listed. A paper which provides evidence that the control system was coopted from somewhere else is not a satisfactory prong 3 refutation as it does not explain anything about the origin of the control system.

If he is making unreasonable demands for evidence then this is a different matter entirely and much more difficult to resolve. However if this is the Anti-ID response then I would say that presenting a large pile of papers etc and claiming that they have demonstrated that Behe is wrong is not a very helpful way of making their argument that he is making unreasonable demands. It does not deal with the precise point that Behe is making.

If Behe is making unreasonable demands for evidence then this is a tacit admission that at least technically he made a correct statement about the current origin of the immune system literature.

He cannot be both wrong – (the papers and evidence are there staring him in the face but he refuses to look at them poor fool!)
AND
Be making unreasonable demands for proof – (he is asking for a complete unedited DVD of the history of life on earth … doesn’t he realise that DVD recorders were not around in the Cambrian!)

So let me be clear are you arguing–
Behe is technically correct but asking for a DVD that Amazon do not sell or have the technology to make at present.
OR
Behe is wrong and here are the references.

I personally find a mixture of the two confusing.

Putting the Polls together…

2006-08-16T10:20:00.000+01:00

There have been three fairly recent polls regarding UK beliefs in origins.

1. Ipsos MORI for the BBC's Horizon series (see here).
22% chose creationism
A further 17% favoured intelligent design.
(39% combined)
48% chose evolution.
Uncommitted 13%

2. The UK section of the Science magazine article by J.Miller et.al. (See here and here and here)
67-68% Accept Evolution as true using it seems a combination measure of several questions about evolution.
15% unsure
17% rejecting.

3. The recent Opinion panel Research poll reported in the guardian. (See here)
(This is focused on students.)
In this poll 12% of students chose creationsism.
A further 19% favoured intelligent design.
(31% combined)
56% chose evolution.
Uncommitted 13%

What these results show it seems to me (as always) is that a great deal depends on the precise questions that are asked and perhaps the context of the questions. The Ipsos and the Opinion Panel results are comparable. If they are broadly correct then it appears that the Science survey seems to include some intelligent design supporters as those who believe evolution is true.

Behe and the Dover “Literature Bluff”

2006-08-12T08:35:00.000+01:00

So Who is Bluffing?

Useful links:

Barry A's original thoughts on the Literature Bluff here.
Barry A's further musings on the Literature Bluff here.
Wesley Elsberry's take on the Literature Bluff here.

"We can look high or we can look low, in books, or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system."

It was this proposition of Behe (Darwin’s Black Box p138, 2003 paperback ed) that the pile of books, articles and journals was intended to refute at the Dover trial and which Judge Jones mentioned in his opinion.

"However, Dr. Miller presented peer-reviewed studies refuting Professor Behe’s claim that the immune system was irreducibly complex. Between 1996 and 2002, various studies confirmed each element of the evolutionary hypothesis explaining the origin of the immune system."

What exactly did Behe mean?

The quote comes in the section of his book which examines the mechanism of the immune system looking at the complement pathway and the function and contruction of antibodies. (Chapter 6 – A Dangerous World)

In the concluding sections of this chapter Behe appears to be seeking to present the current understanding of the mechanism by which this system cam to exist. He maintains that the best efforts to do this are in two short papers:

1. David Baltimore’s 1994 article “Molecular Evolution of the Vertebrate Immune System.” PNAS 91, 10769-10770
Behe says that Baltimore suggests that the 3 sets of proteins are required for a functioning immune system (antigen receptors, antigen presentation molecules and the gene rearranging proteins.) They then argue that sharks have all three and note that immunoglobulin and TCR genes both require RAG proteins for rearrangement. On the other hand, RAG proteins (RAG is the component that rearranges the genes) require specific recombination signals to rearrange immunoglobulin and TCR genes. In this paper Behe notes that the authors speculate that a gene from a bacterium might have luckily been transferred to an animal. Luckily the protein coded by the gene could itself rearrange genes; and luckily in the animals DNA there were signals that were near antibody genes; and so on.

2. Farries, T.C., and Atkinson, J.P. (1991) Evolution of the Complement System. Immunology Today, 12, 295-300. In this paper the authors, says Behe, join Russel Doolittle in proposing unexplained proteins that are “unleashed” and “spring forth”

Behe acknowledges that there are other papers, articles and books on the subject but maintains that most of them are at the level of cell biology and are thus unconcerned about molecular mechanisms, or else they are concerned simply with comparison of DNA or protein sequences. He maintains that comparing sequences may be a good method to study relatedness, but the results can’t tell us anything about the mechanism that first produced the systems.

Behe complains that the papers fail to present quantitative calculations. He complains that they fail to acknowledge that gene duplications do not immediately make a new protein. He complains that none of them worry about the control mechanisms to regulate the pathway.

The “literature bluff” which was set up in the Dover trial presumably by Ken Miller presented a series of 8 articles in the pre trial documentation and a further "fifty- eight peer-reviewed publications, nine books, and several immunology textbook chapters" in the pile in the courtroom.

The question that I wish to ask is this… Who was right about the stack of papers. Behe mantains that these papers do not affect his proposition that the scientific literature has no answers to the origin of the immune system. Was Behe right when he made that proposition? Is he still correct?

So let us put this formally into what I will call the 3 pronged Behe test.

1. Do any of these papers present quantitative calculations showing a reasonable pathway for the origin of the immune system by non-intelligent means?
2. Do they acknowledge that gene duplication is different from new protein production?
3. Do they provide mechanisms for the origin of necessary control mechanisms to regulate the immune system pathways?

Dover- Behe's response to the Immunology document stack.

2006-08-07T13:49:00.000+01:00

Added insert(....10-8-06)
I just read BarryA's description here of Rule 803(18) which he says applies directly to this situation and demonstrates Judge Jones incompetence in his reliance upon this stunt.

Appenix A of the booklet is Behe’s response to the judgement which contains this little rather funny snippet:
(11) In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not “good enough.” (23:19 (Behe)).
Several points:
1) Although the opinion’s phrasing makes it seem to come from my mouth, the remark about the studies being “not good enough” was the cross-examining attorney’s, not mine.
2) I was given no chance to read them, and at the time considered the dumping of a stack of papers and books on the witness stand to be just a stunt, simply bad courtroom theater. Yet the Court treats it seriously.
3) The Court here speaks of “evidence for evolution”. Throughout the trial I carefully distinguished between the various meanings of the word “evolution”, and I made it abundantly clear that I was challenging Darwin’s proposed mechanism of random mutation coupled to natural selection. Unfortunately, the Court here, as in many other places in its opinion, ignores the distinction between evolution and Darwinism. I said in my testimony that the studies may have been fine as far as they went, but that they certainly did not present detailed, rigorous explanations for the evolution of the immune system by random mutation and natural selection — if they had, that knowledge would be reflected in more recent studies that I had had a chance to read (see below).
4) This is the most blatant example of the Court’s simply accepting the Plaintiffs’ say-so on the state of the science and disregarding the opinions of the defendants’ experts. I strongly suspect the Court did not itself read the “fifty eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system” and determine from its own expertise that they demonstrated Darwinian claims. How can the Court declare that a stack of publications shows anything at all if the defense expert disputes it and the Court has not itself read and understood them?
In my own direct testimony I went through the papers referenced by Professor Miller in his testimony and showed they didn’t even contain the phrase “random mutation”; that is, they assumed Darwinian evolution by random mutation and natural selection was true — they did not even try to demonstrate it. I further showed in particular that several very recent immunology papers cited by Miller were highly speculative, in other words, that there is no current rigorous Darwinian explanation for the immune system. The Court does not mention this testimony.

Dover - The History of ID

2006-08-07T13:00:00.000+01:00

The discussion of the history of the intelligent design movement in Judge Jones opinion comes in the section in which the Judge seeks to determine whether the Dover school Board were guilty of endorsing or disapproving a particular religious viewpoint.

Judge Jones seeks to establish the proposition that ID is a religious strategy that evolved from earlier forms of creationism. He concludes:

“the evidence at trial demonstrates that ID is nothing less than the progeny of creationism.”

(I understand that to mean- ID is nothing but the progeny of creationism.
I understand creationism to mean - the Fundamentalist effort to get God and the bible into state funded science lessons.)

This argument swallows the false idea that ID is nothing but creationism in a new box. It is exactly the same product with a new label.

There are at least 4 problems with this argument.

1. He argues that the strongest evidence supporting this finding is the history and pedigree of the book Pandas and People which is mentioned in the text that teachers were to read to pupils.

In coming to his conclusion Judge Jones places great weight upon the implied intentions of changes of language in the text of “Pandas and People” (the text that was mentioned in the paragraphs to be read to students) to establish the point that ID is a religious matter. Barbara Forest’s analysis and interpretation of the textual changes is swallowed hook line and sinker despite the fact that it conflicts with the explicit testimony of one of the authors Charles Thaxton included as part of his deposition:

“I wasn’t comfortable with the typical vocabulary that for most part creationists were using because it didn’t express what I was trying to do. They were wanting to bring God into the discussion, and I was wanting to stay within the empirical domain and do what you can do legitimately there.”

Why should Barbara Forest have a better insight into the intentions of the authors than one of the authors themselves? Why does the Judge describes Forest’s book “Creationism’s Trojan Horse” as a “thorough and exhaustive chronicle of the history of ID”? Why should we accept Forest’s description of ID as entirely objective and non-partisan?

2. It fails to recognise the ancient nature of the argument.
These arguments did not spring into Aquinas’s brain from nowhere. There are two more ancient streams of thought one of which is not of Judeo-Christian. Socrates, Plato and Aristotle argued that mind is a prerequisite for life, Heraclitus, Empedocles, Democritus and Anaximander argued the reverse. Cicero argued for design well before the Christain Era.

3. It fails to do just to the nature of the recent revival of the design argument stimulated by the discoveries of nano-technology and information systems in molecular biology. It was the significance of these discoveries that cause chemist and philosopher Michael Polanyi to argue in 1967 that “machines are not reducible to physics and chemistry” and that “likewise the mechanistic structures of living beings appear to be likewise irreducible.”

It was Michael Denton’s book “Evolution - a Theory in Crisis” that caused the radical change in direction for Micahel Behe. Denton’s book has no connection to Christianity or creationism and Denton himself was not a Christian.

Several other leading ID thinkers testify that it is the molecular biology that led them to ID not the bible.

4. It fails to recognise the importance of the design debate in physics and Cosmology going back to Fred Hoyles conviction that the carbon 12 resonance evidence pointed to “some superintellect has monkeyed with physics as well as chemistry and biology.”

Dover - Introduction

2006-08-07T12:58:00.000+01:00

Judge Jones’ opinion stretches to 139 pages. There are two main sections to his arguments after his legal background and introductory sections.

The first (Section E p14-90) deals with his application of the “Endorsement Test” to the case. The second (Section F p90-132)deals with his application of the Lemon test to the case.

It is the first of these two main sections with which I am concerned. It is in this section that he seeks to present the history of ID and to determine whether it is Science or not.

If the Judge had limited his judgement to section F then I probably would not be very interested in it… but when a Judge is presenting a verdict concerning the history of ID and coming to a final verdict on whether ID is science or not then I cannot help but be interested.

Dover - preliminary thoughts.

2006-08-07T12:40:00.000+01:00

1. I think the Dover policy was a clumsy misguided policy.
2. I do not think that ID should be a specified part of a national curriculum in science at present but I am in favour of a teachers freedom to discuss ideas about origins including intelligent design and to state their own views. Schools with a religious ethos may wish to explore the way in which science and religion interact in society with a more detailed look at the history of the conflict regarding evolution and the way in which developments in physics and cosmology and molecular biology have resulted in a revival of the design argument in the minds of some scientists.
3. I think that students need to be taught the theory of evolution and the evidence for it and should also be made aware of the areas in which the evidence is weak and where scientists do not have full and detailed explanations of how certain features arose. When we don’t know we should say we don’t know and not give the impression that evolution has a full and detailed explanation for everything in biology when it does not.

The Kitzmiller vs Dover Decision.

2006-08-05T10:18:00.000+01:00

I have decided to look at this decison by means of a review of the Discovery Insitute booklet entitled "Traipsing into Evolution" by DeWolf, West, Luskinand Witt. I had been reluctant to do this without the booklet and I was reluctant to pay the £9.78 necessary to get the booklet. I was hoping that the bulk of the arguments would come out clearly on the web and I could spend my gold on other books. I have finally succumbed to the pressure and purchased the booklet.

There has been a recent brief review of the book at the NRO here. Which resulted in an interesting back and forth between Casy Luskin (here, here and here) and Wesley Elsberry (here)

The criticism in the book is divided into 4 sections:
1. The partisam history of Intelligent Design.
2. The unpersuasive case against the scientific status of ID.
3. The failure to treat religion in a neutral manner
4. The limited value as precedent.

I intend to look at these 4 sections in separate posts. I trust that visitors who remember my promise to look at this decision at some point in the future will be satisfied with this as a fulfillment of my promise.

One sentence that stood out in my reading of the introduction was this...

"... he asserted (that is Judge Jones asserted) that scientists who support ID have published no peer-reviewed articles or research..."

(I wrote in the margin....Did he in fact assert this?)

Science Education

2006-07-28T12:50:00.000+01:00

1. Is Science education is not simply a matter for scientists alone? Do the parents of the children have a crucial place in the discussion?
2. Is the world view that is behind the approach to issues of origins a matter of great concern to many parents? Does the approach have huge implications well beyond the confines of the subject? Where there is a world view conflict between teachers and parents is this a recipe for a very uncomfortable parent/school relationship?
3. Is the tendency of strict methodological naturalism to become closely allied to philosophical naturalism and in some cases to become indistinguishable?
4. Do both philosophical naturalism and methodological naturalism tend to lead to an overly positive view of the evidence for abiogenesis and macro-evolution?
5. If scientists say that science education should be taught in an atmosphere of philosophical naturalism and parents say that they want science taught in an atmosphere of theism who should win?
6. If the majority of parents want a religious ethos and environment for their children during their formative years does the state have the right to deny them their desire? Is it right for the tax system to be used to provide an education which ends up being hostile to the worldview and ethos that the majority of parents desire? Is this a stable situation in the longterm?

The Case of Dean Kenyon

2006-07-25T08:10:00.000+01:00

Dean Kenyon was a distinguished senior biology professor at San Francisco State University and co-author of a standard work on the origin of life on earth, “Biochemical Predestination.” Kenyon eventually became disillusioned with efforts to explain life as a product of purposeless and unguided chemical reactions. He became a proponent of intelligent design.

When Kenyon taught the prevailing naturalistic theories of biological origins in his introductory course for non-majors he also explained his own scepticism about whether these theories are consistent with the evidence and argued that intelligent design is a legitimate alternative to naturalistic explanations of the origin of life.

A handful of students complained, and the department chairman immediately endorsed their complaints. He announced that he would not allow Kenyon to teach this course in the future, on the ground that Kenyon was improperly introducing his religious opinions into the science curriculum.

Was the department chairman right?

The idea of unintelligent abiogenesis.

2006-07-19T22:52:00.000+01:00

Comments on the previous post focused on the terminology usage which is frustrating though I am partly to blame for this. Apologies.

Allow me to concede the semantic point to commenter “Anonymous” regarding the usage of the phrase “the theory of abiogenesis.” at present this “field of research” should not apparently be dignified with this title. Apologies.

May I call it the “scientific idea of unintelligent abiogenesis.”

Now…
What are the criteria for determining whether an idea is a scientific idea or not?

Is it necessary for the idea of unintelligent abiogenesis to be falsifiable for it to be considered a scientific idea or is the idea of unintelligent abiogenesis a simple axiom of scientific thinking with no other options permissible within science.

In other words is the following proposition necessarily true:

Life exists in the universe therefore it must have had an unintelligent origin at some point in time.

Is Abiogenesis Falsifiable?

2006-07-18T08:43:00.000+01:00

(With acknowledgements to Commenter William Bradford)

The theory of Abiogenesis is closely related to the Theory of Evolution. In many text book treatments of evolution abiogenesis is included within the category of evolution in its broadest meaning.

Abiogenesis is the natural extension of the principle of common descent allowing a chance/time bridge to be built between inanimate and animate matter.

Abiogenesis is the hypothesis that it is possible to account for the origin of life either on the earth or somewhere else in the universe by chance without the intervention of pre-existing intelligence… in other words without design.

Materialists have two options (it seems to me.)

1. Abiogenesis is probable enough to have occurred in this universe… and in fact it has.
2. Abiogenesis is not probable enough to have occurred in this universe and so there must be multiple universes and we simply happen to be in one of the universes that spawned life.

Option 2 (it seems to me) should be excluded from science because by definition we cannot have any evidence of the existence of another universe. Which leaves only option 1.

What does a materialist do if 1 is actually falsified?

Can science in principle allow 1 to be falsified? If so how? If not is Abiogenesis really science?

Intelligent Design ....or not?

2006-07-15T08:55:00.000+01:00

Is this a collection of random boulders or have they been placed intelligently? How do we know?

Holiday Pictures

2006-07-15T08:46:00.000+01:00

The view from Slioch.

Eilean Donan Castle

Loch Maree

On Holiday

2006-06-16T08:31:00.000+01:00

We are off to the NW Highlands of Scotland for 3 weeks... I will post some pictures when I return I hope!

Reliable Recognition of Intelligent Agency.

2006-06-10T08:36:00.000+01:00

Which of the following propositions do you agree with?

1. Human intelligent agency is a distinct type of causation which can be recognised and is recognised successfully as an integral part of our normal lives. The evidence left from some human acts is indistinguishable from other animals. The evidence left from other human acts is distinguishable from all other known animal activity. eg writing books and using a complex language.

2. Human intelligent causation can be recognised as having occured even in situations where we know nothing about the individual agents concerned. We believe in their existence solely on the basis of the recognition of human like intelligent causation.

3. Human intelligent causation is currently our only physical model for the whole field of intelligent causation...we have no other material intelligent agents to study yet.

4. It is possible to concieve of other different intelligent agents from ourselves. It is not impossible that such beings may exist.

5. It is legitimate to use human intelligent causation as a model for the whole field of possible intelligent causation-
(a) from different time periods
(b) from different planets.
(c) from other non-material/hyper material intelligent agents.

6. It is possible to come to a correct conclusion of intelligent causation when examining
(a) the universe as a whole
(b) particular instances of intelligent design e.g. a living cell or a flagellum.

Quote (Part 2)

2006-06-10T08:32:00.000+01:00

"After figuring that out, it was the death of rationalism, as far as I was concerned. The problem with rationalism is that it isn’t rational. It fails to give sufficient importance to the development of the choice of the right premises; it tries to justify them by circular reasoning. Once I was alert to that distinction, I was able to critique the things that previously I felt I had to take for granted. "

Phillip Johnson

Quote

2006-06-09T16:52:00.000+01:00

When you speak of rationality, there are two very distinct components. One is logical reasoning, which is about going from premises to conclusions, conclusions that should be as good as your premises. Thus, logic will get you into insanity if you’ve got the wrong premises.

The other component of rationality is having the right premises. How do you get them and how do you determine that they are right? Not by logical reasoning, surely, because then you would be reasoning from other premises in order to justify them. There is an instinct, or revelation, or whatever you want to call it, that underlies your thinking, and the only interesting problem in philosophy is how you get that.

Phillip Johnson

Peacock Feather.

2006-06-09T10:48:00.000+01:00

I love peacock feathers!

"For myself, also, I rejoice profoundly; for, thinking of so many cases of men pursuing an illusion for years, often and often a cold shudder has run through me, and I have asked myself whether I may not have devoted my life to a phantasy. Now I look at it as morally impossible that investigators of truth, like you and Hooker, can be wholly wrong, and therefore I rest in peace."

He now discussed the arguments:

"About the weak points I agree. The eye to this day gives me a cold shudder, but when I think of the fine known gradations, my reason tells me I ought to conquer the cold shudder." "I remember well the time when the thought of the eye made me cold all over, but I have got over this stage of the complaint, and now small trifling particulars of structure often make me feel uncomfortable. The sight of a feather in a peacock's tail, whenever I gaze at it, makes me sick!"

Charles Darwin

(The life and Letters of Charles Darwin, John Murray, London, Vol.2, p296, 1887)

Can he really mean that? Why did he feel like that?

What is "Natural Regularity"?

2006-06-06T10:22:00.000+01:00

Pauls Nelson's view:
It is synonymous with "physical regularity" and the following are genuine physical regularities:
-- the principle of superposition in stratigraphy
-- Newton’s second law
-- the speed of light in a vacuum
-- Maxwell’s equations
And so on. Physical regularities can be described in equations or simple relations.

I found this quotation from Michael Ruse which seems to agree...
"Science is an attempt to understand the physical world, primarily through law, that is, through unbroken natural regularity." (Montagu, pg. 328)

Also from this page:
http://www.ucs.mun.ca/~alatus/phil1200/CT4Fallacies.html

In discussing the following argument:
As scientists have shown us, the world is a well regulated place. They have discovered many laws of physics (such as the law of mass conservation). But everyone knows that you cannot have laws without a lawmaker. There must therefore be a Supreme Lawmaker. In spite of their anti-religious tendencies, then, scientists have actually helped to prove the existence of God.

The author says:
This argument commits the fallacy of equivocation. In the second sentence, law means something like 'natural regularity'. In the third sentence, it means something like 'a command made by a governing body or person'

This fits with the above senses of the phrase.