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Evolution and the Origin of Biological Information, Part 1: Intelligent Design

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March 10, 2011 Tags: Design

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Evolution and the Origin of Biological Information, Part 1: Intelligent Design

One prominent antievolutionary argument put forward by the Intelligent Design Movement (IDM) is that significant amounts of biological information cannot be created through evolutionary mechanisms – processes such as random mutation and natural selection. ID proponent and structural biologist Doug Axe frames the argument this way (his comments begin at approx. 15:19 in the video):

“Basically every gene, every new protein fold… there is nothing of significance that we can show [that] can be had in that gradualistic way. It’s all a mirage. None of it happens that way.”

The importance of this line of argumentation for the IDM can be seen clearly in Stephen Meyer’s book Signature in the Cell (published in 2009). In this book, Meyer claims that an intelligent agent is responsible for the information we observe in DNA because, in his words, natural mechanisms “will not suffice” to explain it:

Since the case for intelligent design as the best explanation for the origin of biological information necessary to build novel forms of life depends, in part, upon the claim that functional (information-rich) genes and proteins cannot be explained by random mutation and natural selection, this design hypothesis implies that selection and mutation will not suffice to produce genetic information … (p. 495)

It’s hard to overstate the importance of this argument for Meyer in Signature, and for the IDM as a whole. In the conclusion to a pivotal chapter entitled “The Best Explanation” Meyer presents the following summary of his case:

Since the intelligent-design hypothesis meets both the causal-adequacy and causal-existence criteria of a best explanation, and since no other competing explanation meets these conditions as well –or at all–it follows that the design hypothesis provides the best, most causally adequate explanation of the origin of the information necessary to produce the first life on earth. Indeed, our uniform experience affirms that specified information … always arises from an intelligent source, from a mind, and not a strictly material process. So the discovery of the specified digital information in the DNA molecule provides strong grounds for inferring that intelligence played a role in the origin of DNA. Indeed, whenever we find specified information and we know the causal story of how that information arose, we always find that it arose from an intelligent source. It follows that the best, most causally adequate explanation for the origin of the specified, digitally encoded information in DNA is that it too had an intelligent source. (p. 347)

Put more simply, Meyer claims that if we see specified information, we infer design, since we know of no mechanism that can produce specified information through an unintelligent, natural process. As a logical argument, Meyer’s position only works if (and this is a big if) – his premises are correct.

The issue is that Meyer’s case is open to refutation by counterexample, and even one counterexample would suffice. If any natural mechanism can be shown to produce “functional, information-rich genes and proteins”, then intelligent design is no longer the best explanation for the origin of information we observe in DNA, by Meyer’s own stated criteria. His entire (500+ page) argument would simply unravel.

The obvious problem for Meyer’s case is that biologists are well aware of a natural mechanism that does add functional, specified information to DNA sequences (and in some cases, creates new genes de novo): natural selection acting on genetic variation produced through random mutation. Not only are biologists aware of some examples of natural selection adding functional information to DNA, this effect has been observed time and again, and in some cases it has documented in exquisite detail. When I reviewed Signature for the American Scientific Affiliation journal Perspectives on Science and Christian Faith (PSCF) what struck me, repeatedly, was that Meyer made no mention of the evidence for natural selection as a mechanism to increase biological information. I fully expected him to dispute the evidence, certainly – but the surprise for me was that he simply denied it to be sufficient without addressing any evidence. The closest Meyer comes in addressing natural selection in Signature is in a section discussing evolutionary algorithms used to simulate evolution. As I said in my review:

Meyer’s denial of random mutation and natural selection as an information generator notwithstanding, in a discussion about evolutionary computer simulations, Meyer makes the following claim:

If computer simulations demonstrate anything, they subtly demonstrate the need for an intelligent agent to elect some options and exclude others- that is, to create information.

Employing this argument, Meyer claims that any mechanism that prefers one variant over another creates information. As such, the ample experimental evidence for natural selection as a mechanism to favor certain variants over others certainly qualifies as such a generator. Meyer, however, makes no mention of the evidence for natural selection in the book.(pp. 278-279)

In the PSCF review I went on to point out a few examples of known instances in biology where random mutation and natural selection have indeed led to substantial increases in biological information, but the limitations of space in that format precluded me from exploring those examples in more detail, or from presenting that information at a level readily accessible to non-specialists. In this series of posts I will attempt to remedy that shortcoming by exploring several examples in depth. The question of how new specified information arises in DNA, far from being an “enigma”, is one of great interest to biologists. While the IDM avoids this evidence to present a flawed argument for design, responding to this flawed argument provides an excellent opportunity to discuss some particularly elegant experiments in this area.

Of course, it should be noted that describing how specified information can arise through natural means does not in any way imply God’s absence from the process. After all, natural processes are equally a manifestation of God’s activity as what one would call supernatural events. So-called “natural” laws are what Christians understand to be a description of the ongoing, regular and repeatable activity of God. As such, the dichotomy presented in ID writings of “naturalism” versus theism is a false one: is not God the Author of nature, after all?

In the next post in this series, we will examine an ongoing experiment over twenty years in the making: the Long Term Evolution Experiment (LTEE) on E. Coli conducted in the laboratory of Richard Lenski at Michigan State University.


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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Dennis Venema - #54137

March 12th 2011

Rich,


It wasn’t a loaded question - I wanted to know because there are a few sections I wanted to point you to for consideration. 

Meyer repeatedly argues that information only comes from intelligence (some of the more succinct quotes are in the post above), hence we can be confident that the info we see in DNA is designed. Most of the chapter entitled “The Best Explanation” runs along these lines. 

So, natural mechanisms that add info to DNA are highly relevant to the discussion. Are
 you claiming they aren’t?

And yes, I read the whole thing - and yes, I read it carefully. 




Gregory - #54140

March 12th 2011

for the exchange between Dennis & Rich. I’d be glad to lightly officiate when questions aren’t answered or diversions raised, doing so as neutrally as possibe, as a mediator so to speak, if this would be welcome:

“Meyer’s book is not primarily *about* biological evolution, but about the origin of life.” - Rich

Can we agree on that Dennis?


Bilbo - #54141

March 12th 2011

  Hi Dennis, 

Meyer at least gives the appearance of evaluating all the current theories of how life got started by non-intelligent means, and concluding that they all fail.   I’ll let others determine how adequately he succeeded in that evaluation.   But given the premise that Meyer succeeded, his argument the ID is the best explanation for the origin of life is reasonable.   


Rich - #54151

March 12th 2011

Dennis:

Relevant to *which* discussion?  If the discussion is:  “Can natural mechanisms, without input from intelligence, ever result in a substantial increase in information?” then yes, if Meyer makes the claim that they cannot, empirical evidence that they can (in biological evolution) is relevant.  But if the discussion is:  “Can natural mechanisms, without input from intelligence, generate a living cell from molecules of carbon dioxide, ammonia, methane, and water?” then the capacity of biological evolution to generate information is irrelevant, because Meyer is talking about pre-biotic activity.  That’s what most of his book is about—how do you get from the prebiotic to the biological world?

If he mentions biological evolution from time to time, and you find flaws with his discussion of biological evolution, you’re free to point them out; but that’s not the main subject he’s addressing, so your focus strikes me as odd.  It’s like arguing that Darwin’s conclusion about natural selection is wrong because he misunderstood how continents move.  Darwin wouldn’t want his main thesis judged inadequate due to errors regarding something his main thesis doesn’t depend upon, and neither would Meyer.  I hope the rest of your articles will focus on what’s wrong with Meyer’s argument about the emergence of life from non-life, not what’s wrong with Meyer’s remarks about biological evolution.


Steve Ruble - #54185

March 13th 2011

Don Johnson,

There aren’t any programs, computers, or encoded messages  in cells. While it may be the case that some things that happen in cells are easier for us to understand and reason about when we think of them as running programs or decoding messages, it’s crucial to remember that intracellular processes are actually implemented at the scale of molecules.  The actual mechanisms of interaction between various moving parts within a cell are not remotely similar to the interactions between two computer systems, not least because the “messages” themselves may have physical effects on the structure and behavior of the “sender” and “receiver”. The behavior of structures at a molecular scales just isn’t like the behavior of things at the kind of scale we’re accustomed to, and it’s not like the behavior of computers and their programs, either. You can’t take two computers and squash them together to create a new computer that does something totally different, but that happens all the time at the level of proteins and enzymes. You can’t cut your hard drive in half and let your CPU physically reassemble it into two equivalent hard drives, but that’s how DNA is replicated. You can’t send an message to a computer that makes it physically reconfigure itself into a solar panel, or a garbage disposal, or twenty new messages, but such things are normal within a cell. You can’t… well, there’s an infinite number of ways that cellular machinery is dis-analogical to computers, so I’ll just leave it at that. 


Dennis Venema - #54195

March 13th 2011

Rich, the point is that Meyer ties the two together (chemical and biological evolution) and bases his argument on his assertion that an increase in information is impossible in both. If you don’t believe me, re-read pages 494 - 495. That’s the context for the first quote in the post above, and Meyer is explicitly talking about biological evolution first and foremost, and only secondarily chemical evolution - but he underscores that his argument stands or falls for both. 


Just read those pages, and you’ll see what I mean. 



Rich - #54202

March 13th 2011

Dennis (54195):

I agree that on the pages you mention, Meyer pulls together critiques of biological evolution with his critique of chemical evolution.  A few points, if I may:

1.  The passage you cite is in the Appendix, not in the main part of the book.  The Appendix is about predictions of Intelligent Design generally, and thus about questions of biological evolution as well as the origin of life. 

2.  Nonetheless, I agree with you that it is confusing, and in effect makes Meyer’s argument appear much more sweeping and hence much harder to defend.

3.  And at a few points even in the main text of the book, the subject wanders from the origin of life to biological evolution.  Had I been the editor of the book, I would have highlighted those passages and urged Meyer to dump them.  The book should have been exclusively about the origin of the cell and its DNA-protein apparatus, as Meyer indicated at the beginning (p. 8):  “... the mystery that has surrounded the discovery of the digital code in DNA and how that discovery has confounded repeated attempts to explain the origin of the first life on earth.”  A book should only have one thesis.

4.  I am not defending every line Meyer wrote in the book.  I’m not even claiming that he has established his thesis that intelligent design is “the best explanation” for the origin of life.  I’m just pointing out that the two claims, “Darwinian processes cannot yield significant increases in information” and “pre-cellular chemical processes cannot yield significant increases in information,” are distinct.  Pre-organic, simple molecules do not have the capacity for replication and variation that the DNA-protein system does.  The two arguments should be separated and dealt with in two different books.  If Meyer fails to do that consistently, that’s a legitimate criticism of the book.  But it doesn’t disprove his fundamental argument re the origin of life. 


sy - #54216

March 13th 2011

Rich

I am in total agreement with your comment. I too wished that Meyer had separated the two issues (and I wish everyone would) because they have little in common. I also join you in the hope that the bulk of Dennis’ remarks will be related to life origin (or chemical evolution) since that is clearly the issue that gives ID its strongest leverage.  


Alan Fox - #54217

March 13th 2011

Does information exist?


John Wilkins’ take (HT seversky) with a few interesting comments by Doug Theobald et al.

Troy - #54225

March 13th 2011

Don Johnson @ #54129

“I’m not talking about the size
of the genome or modifications of the message within the genome,
including the possibility of adding new symbols or replacing symbols
within the fundamental alphabet. I’m referring to the fundamental size
of the alphabet for coded message communication, which for a 3-codon,
2-base alphabet would be 8 (2^3), instead of 64 (4^3). Since coded
information transfer always requires agreement between sender and
receiver for the arbitrary encryption used, an error catastrophe would
result if the sender started using a larger aphabet than that understood
by the receiver.”

You are making a category error. You are trying to model the evolution of a population with genetic code A at time t1 to a population with genetic code B at time t2>t1 as a form of communication between sender with code A and a receiver with code B. That is simply a very bad model of evolution, bordering on absurdity. It is static, rather than dynamic. It treats a population as a probability distribution over an alphabet, rather than a collection of individuals that may have different alphabets. Etc, etc. I mean, come on.


Gregory - #54229

March 13th 2011

“I also join you in the hope that the bulk of Dennis’ remarks will be related to life origin (or chemical evolution) since that is clearly the issue that gives ID its strongest leverage.” - sy

Make that a third. (& Bilbo an obvious 4th.)

At this point there seem to be two opinions: 1) that Meyer’s book is mainly about the origins of life, 2) that Meyer’s book is mainly about biological evolution.

“Meyer’s book is not primarily *about* biological evolution, but about the origin of life.” - Rich

The basic question remains:
Can we agree on that Dennis? And if not, then why not?

Rich has made some significant clarifications & concessions re: Meyer’s argument. Will Dennis now follow suit? He does, after all, believe in a Creator/Designer too.

It is not like a BioLogos Foundation caucus meeting is needed in order to decide which way for Dennis to answer. The evidence is to be found in the book: what is the book *mainly* about? That’s one of the 1st questions in a book review.

From excerpts & the reviews I’ve read, I thought the book under consideration was mainly about origins of life (i.e. Meyer’s specialty). Thank goodness sy, Rich, Dennis (all PhD-level scholars) & others here have read the book cover to cover so that they can to tell those of us who haven’t.

So far there have been noted 2 pages of confusion, conflation or ‘tying the two together’ between biological & chemical evolution in Meyer’s book.


Alex - #54231

March 13th 2011

To answer Nick’s question,

What prevents information from adding up is that Darwinian selection implies that biological features tend to not persist unless they have function.  But Meyer’s book cites a lot of work (Axe is a good example) showing functional DNA sequences are like extremely isolated islands.  Neo-Darwinism requires a continuous evolutionary path, and can’t hop from one island to the next if there’s a big gap in between. 

Our buddy Darwin understood this problem when he wrote:

“If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”

Kinda seems like information won’t add up when it’s got to go across a wide valley to get to another adaptive peak.  Many successive slight modifications can’t always do the trick.


Alex - #54232

March 13th 2011

Anyone who reads Signature in the Cell (which I have) knows it’s about the origin information in the first life and does not claim to address the diversification of life under Darwinian selection.  Meyer wrote this in response to Francisco Ayala:

“Further, the topic that the book addresses is not the origin of the genomes of organisms or the human genome as the balance of Professor Ayala’s critique seems to imply, but instead the origin of the first life and the mystery surrounding the origin of the information necessary to produce it.” (Signature of Controversy, page 10)

I’m sure that Dennis Venema has read Signature in the Cell. But let’s not misunderstand Meyer’s argument, and let’s not make Dr. Ayala’s mistake again here on Biologos 


Alan Fox - #54235

March 13th 2011

Alex:


Anyone who reads Signature in the Cell (which I have) knows it’s about the origin information in the first life and does not claim to address the diversification of life under Darwinian selection.

What do you mean by “origin information”? Is this different from Dembski and Marks “active information”? Is someone going to have a go at trying to define what is meant by “information” with regard to living organisms?



Gregory - #54241

March 13th 2011

“Is someone going to have a go at trying to define what is meant by “information” with regard to living organisms?” - Alan Fox

Are you going to have a go then, Alan? You’re a biologist, is that right?

‘Living organisms’ is a pretty broad category. Would this ‘definition of information’ be best constructed in ‘life sciences’ then, since ‘living’ is involved? Or are you suggesting mathematical Shannon information applied to ‘living organisms’ or something ‘empirical’ in the sense of ‘countable information,’ i.e. how many ‘informations’? The variety of ways to speak about ‘information’ is of course considerable and as well all know, including Rich, Bilbo, sy and gingoro, Dembski is a far cry from being a ‘Newton of information’ or whatever it was someone called him in that vain+vein. So, you have my support, Alan, if you are asking for an open conversation, as well as defining your paramaters for ‘what might count’ as ‘information’ based on your foreground/background priorities.

Part of the challenge for all parties in this dialogue is that ‘information’ to some people implies ‘mind’ while to others it doesn’t. When social scientists speak about ‘information,’ e.g. they might associate it with Daniel Bell, Manuel Castells, Neil Postman or Marshall McLuhan, all of who focus specifically on ‘mind-embodied agents,’ i.e. on human beings. When biologists hear ‘information’ they look to very different ‘expert’ people for their collective guidance, and the masses of biologists (it not such a huge mass in the Academy) follw the leaders by accepting those views that are within their institutional scope of possibilities. *None* of the information-oriented biologists (tmk), however, are thinking ‘reflexively’ about ‘mind’ when they approach the topic of ‘information’.

We have entered (99% of those reading this) the electronic-information age (era/epoch), which is what allows us to communicate as we do here at BioLogos. There doesn’t yet *seem* to be a consensus on ‘information’ in biology or in most fields, so in this case the concept is not mature enough, such that people have constructed a ‘disciplined science’  around it, though some have tried to establish fields based mainly on ‘information’ (e.g. informatics, cybernetics) at the ideological core.

What makes me curious, in all the talk of ‘information’ & (pseudo-talk of) ‘information era’ by IDists, is why more of them are not schooled in cybernetics. This basically means the application of information to systems, including biological ones. ID should be rife with cyberneticians. Why isn’t it?

My hypothesis: The ideological associations of cybernetics with ‘the east’ is still a barrier in building shared understandings. In fact, this seems to me the path Roger and some others here ought to walk, eastwards, where the knowledge of ‘information’ via cybernetics is more mature (e.g. Journal Cybernetica: Ukrainian Academy of Sciences), with respect to symbiogenesis, mutual aid, and other ‘eastern’ terms in the creation/evolution, origins/processes, holistic/atomistic, etc. discourse, which paint a different picture than what is most often seen in ‘the west.’

This comes out of Alan Fox’s request in groping for peoples’ numerous definitions of ‘information’ (which apparently in his mind/heart can arise independently of mind/heart).


Gregory - #54244

March 13th 2011

“Neo-Darwinism requires a continuous evolutionary path, and can’t hop from one island to the next if there’s a big gap in between.” - Alex

Another way to say it, for the sports fans, is that “Neo-Darwinism ain’t got no hops.” & as everyone knows, one can’t dunk a basketball without hops!

This is like what I referred to here a few months back, that theistic neo-Darwinian evolutionists have a ‘whimper theology’ rather than a ‘bang theology.’

No hops :(


Lurker - #54249

March 13th 2011

Rich and Sy-

I’m curious: is it your position that the origins of the basic cell and the dna/protein apparatus have nothing to do with biological evolution? Is everything that happened prior to divergence from LUCA necessarily chemical evolution or design?

Alan Fox - #54255

March 13th 2011

Are you going to have a go then, Alan?


OK.

Information is an abstract descriptive like “beauty” or “intelligence”. It is not a property that can be quantified and thus is scientifically meaningless.

(IMHO)

nedbrek - #54263

March 13th 2011

Alan information is defined as entropy in the field of information theory:
http://en.wikipedia.org/wiki/Entropy_(information_theory)

“entropy is a measure of the uncertainty associated with a random variable…
The formula can be derived by calculating the mathematical expectation of the amount of information contained in a digit from the information source.” (emphasis in original)

Noise comes from the environment.  Noise always reduces the amount of information.  Noise can never generate information.


Don Johnson - #54275

March 14th 2011

Alan Fox - #54255

March 13th 2011

Are you going to have a go then, Alan?


OK.

Information is an abstract descriptive like “beauty” or “intelligence”. It is not a property that can be quantified and thus is scientifically meaningless.


THERE SEEMS TO BE MUCH MISUNDERSTANDING ABOUT INFORMATION, so I’ll point out the primary types of information I covered in my “Programming of Life” book (page 7-8). 

“Information” has three significant meanings that are important when considering the information of life: “functional” , “Shannon”, and “prescriptive”. Information always involves contingency that rules out other possibilities. Data and Shannon information (probabilistic complexity) may or may not be useful. Functional information (a subset of Shannon information), on the other hand, is useful or meaningful (about something). Prescriptive information is an algorithmic subset (recipe) of functional information.

As an example to illustrate the three information types, consider the data typed into a word-processing program. Most such data is functional in that it has a purpose of communicating information to the ultimate reader of that information. If a monkey typed random data into the program, that complex data would have no purpose, but would have a very high Shannon information content since Shannon information deals only with the probability of the data pattern, irrespective of any meaning. A computer program typed into the wordprocessor is more than just functional, but is prescriptive in that it contains instructions to accomplish objectives based on data to be supplied during the execution of the program being typed. Prescriptive information expresses the decisions to be made and the criteria for the different execution paths. A computer problem is formally solved before physically implementing it (a program doesn’t just appear on a disk).

The computers in life are as real as electronic computers or the purely mechanical computer build in 1910.  Technological platform isn’t what defines whether something is or isn’t a computer, but rather that the machine’s components reads an instantiated algorithm, processes input data, and produces meaningful output.  The computers in each cell meet those requirements, as verified by numerous information scientists, and even bileologists who are information savy, such as Craig Venter (see interview at http://www.guardian.co.uk/science/video/2010/may/20/craig-venter-new-life-form).  As I’ve pointed out to Troy, because cells are controlled by information, that information must follow the same information criteria as any non-biological system.  Those holding a chemical or biological evolutionary source of information need to show from information science that any proposed scenario is viable.  Information is a non-physical reality that can be instantiated into physicality.


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