Introduction to the Controversy - Part 3.

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.

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

The Sunday Sequence

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.

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.

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.

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!

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?

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

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.

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?

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.

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

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.

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!

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.”

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.

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.

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?

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.

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."

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

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

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.

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?

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?

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?

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…..

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…

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.