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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R Hampton - #54472

March 15th 2011

nedbrek,
In the case of DNA, the solution is the computation (the formulation of the DNA) so I don’t think length of time is a genuine factor.


Bilbo - #54475

March 15th 2011

Hi John,

Do you think Robert Shapiro misrepresented the RNA world hypothesis, also?

<a href=“http://www.scientificamerican.com/article.cfm?id=a-simpler-origin-for-life&offset=7”>A Simpler Origin of Life</a>


nedbrek - #54476

March 15th 2011

If you can simulate it (which is what the genetic algorithm does), then you should be able to solve NP hard problems in polynomial time.  The fact that no one in industry does it, and no one has collected the $1e6 makes me skeptical.

The problem is that their topology is not complex enough.  It is effectively a hill (no local minima).  So hill climbing does just fine.  Once you give up on straight hill climbing (where back tracking is allowed), your time complexity is going to shoot up.


Bilbo - #54477

March 15th 2011

OK, let’s try it the old fashioned way:

http://www.scientificamerican.com/article.cfm?id=a-simpler-origin-for-life&offset=7


Christine S. - #54480

March 15th 2011

Bilbo, from what you linked to:

“DNA replication cannot proceed without the assistance of a number of
proteins—members of a family of large molecules that are chemically
very different from DNA. Proteins, like DNA, are constructed by linking
subunits, amino acids in this case, together to form a long chain.”

The confusion here stemms from the analogy of DNA needs proteins to link the monomeres and therefore proteins need proteins to link the monomeres. The last is not true. The peptide-link beteween aminoacids is catalysed by RNA and not a protein. Shapiro says both are linking reactions but only for the former does he identify proteins as the catalyst. Meyer is making the mistake to identify the linking molecule as a protein and even emphesises this in the quote given by John. This is not a minor oversight.
But to be precise, Shapiro does not make this mistake - he is just vage about it and leaves room for interpretation.


John - #54487

March 15th 2011

Bilbo:

“Do you think Robert Shapiro misrepresented the RNA world hypothesis, also?”

Not at all. Do you even realize how Meyer is misrepresenting it, Bilbo?

Christine S:
Meyer is making the mistake to identify the linking molecule as a protein and even emphesises this in the quote given by John. This is not a minor oversight.”

Moreover, there’s zero evidence that it was a mistake or oversight, and a lot of evidence, given the way he fudges the point elsewhere, that Meyer’s intent is to conceal the truth from his readers. It sure worked on Rich!

sy - #54505

March 15th 2011

Lurker - #54249

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?

I dont know that. I do know that the mechanism of evolution must have been different before the modern DNA/protein system came about. I dont know how such a system came about. Part of that system was the development of a genetic code, which contrary to the assertions of some, certainly seems to me to be informational. In fact it is a symbolic system, not because the letters we use are symbols, but because there is nothing about the chemistry of any codon that is in any way connected to the chemistry of any amino acid, just as the word tree has no relation to the big woody plant that grows outside my window. Information is found when something means something other than itself. The sequence of DNA means something other than itself.

For those who think life is not the first instance of information on our world, please provide us with a non living example of something that means something other than itself, that signifies, that provides information other than its own existence.

I dont know how life evolved before LUCA. I dont know if it did. I do think that RNA world is an interesting hypothesis, and that Meyer erred when he called peptidyl transferase a protein. (We have been over this before, John) but I dont think that RNA world yet answers two critical questions. What came before it, and how did it turn into DNA world, specifically how did a code arise.


Rich - #54536

March 16th 2011

Dennis:

Yoo-hoo!  Are you out there, Dennis? 

It seems to me that you invited my careful reply #54202, so I’m looking forward to your response.  I want to know if we have come any closer, given my concessions and clarifications.


John - #54549

March 16th 2011

sy:
“I do know that the mechanism of evolution must have been different before the modern DNA/protein system came about.”

Your label is missing a key component.

”...a genetic code, which contrary to the assertions of some, certainly seems to me to be informational.”

It is informational. It is not symbolic.

“In fact it is a symbolic system, not because the letters we use are symbols, but because there is nothing about the chemistry of any codon that is in any way connected to the chemistry of any amino acid…”

But even if that were true (and it’s not), that wouldn’t make it symbolic, Sy.

”... just as the word tree has no relation to the big woody plant that grows outside my window.”

They are very different, because the word “tree” fails to symbolize the object in communication unless we both are aware of the abstraction. No such symbolism or abstraction is involved in transcription or translation.

“I do think that RNA world is an interesting hypothesis, and that Meyer erred when he called peptidyl transferase a protein. (We have been over this before, John)…”

Yes, and there remains zero evidence suggesting that Meyer erred, while all the extant evidence points toward deception. Does the RNA World hypothesis simply predict that ribozymes are replaced by proteins?

”...but I dont think that RNA world yet answers two critical questions. What came before it, and how did it turn into DNA world, specifically how did a code arise.”

I agree with the former, but note that Meyer is withholding the truth from his readers. For the latter, the term “code” is used metaphorically, and the evidence for the origin of the (metaphorical) code points to evolutionary mechanisms. For example, you can’t coherently claim that the differences between translation initiation and termination flow from ID.


John - #54562

March 16th 2011

sy wrote:
“To be more specific RNA world contained a limited set of information, but was inefficient at the production of new proteins.”

Sy, I don’t understand the point you’re trying to make here. Why would inefficiency matter? We know that modern organisms tolerate massive inefficiencies, but more importantly, as long as there’s some sort of replication, inefficiency would be irrelevant at the origin of life.


Don Johnson - #54564

March 16th 2011

Responding to John - #54549 March 16th 2011

sy:
“I do know that the mechanism of evolution must have been different before the modern DNA/protein system came about.”
Your label is missing a key component.
”...a genetic code, which contrary to the assertions of some, certainly seems to me to be informational.”
It is informational. It is not symbolic.
“In fact it is a symbolic system, not because the letters we use are symbols, but because there is nothing about the chemistry of any codon that is in any way connected to the chemistry of any amino acid…”
But even if that were true (and it’s not), that wouldn’t make it symbolic, Sy.


The codon codes are indeed verifiable simiotic codes.  Outside human-produced codes, life is unique in the existence of semiosis.  There have been over 20 verifiable semiotic codes discovered in life over the past 10 years.  As Barbieri says in, “Life is Semiosis – The Biosemiotic View of Nature,” Cosmos and History: The Journal of Natural and Social Philosophy (4), 2008S, p29-51:

“The genes and proteins of the first cells had to have biological specificity, and specific molecules cannot be formed spontaneously. They can only be manufactured by molecular machines, and their production requires entities like sequences and codes that simply do not exist in spontaneous processes. That is what really divides matter from life. All components of matter arise by spontaneous processes that do not require sequences and codes, whereas all components of life arise by manufacturing processes that do require these entities. It is sequences and codes that make the difference between life and matter. It is semiosis that does not exist in the inanimate world, and that is why biology is not a complex form of chemistry”

Even beyond semiosis are the prescriptive algorithms instantiated into the DNA memory (DNA is not the genome, but merely a storage medium that HOLDs the genomic programs.  This has been verified, for example by Venter’s group; if you doubt this, see http://www.guardian.co.uk/science/video/2010/may/20/craig-venter-new-life-form.

My “Programming of Life” book states 16 specific scientific problems requiring scientific answers before propagating unsubstantiated origin of life or species scenarios as science.  It also highlights 11 hypotheses in peer-reviewed literature that require falsification before granting naturalistic scenarios scientific credibility.

BTW: Meyer’s CSI (this thread’s topic) seems to include both functional and prescriptive information, as focuses on the origin of information, not its modification.

Naturalists really have no choice but to believe in chemical and biological evolution since the cybernetic complexity of life eludes any verifiable explanation.  It should also be noted that every OOL scenario proposed thus far would be ruled “operationally falsified” by failing to exceed the Universal Plausibility Metric’s cut-off (http://www.tbiomed.com/content/pdf/1742-4682-6-27.pdf).



Gregory - #54569

March 16th 2011

Not sure if anyone else read G. Chaitin’s paper, from R Hampton’s link - thanks! - but I was surprised to see him applying the concept ‘intelligent design’ (11 times) in the mathematics & philosophy interface, in a contemporary way.

In a way, I suppose it relates to this thread: I’ve no doubt that if Venema and Meyer were ever to sit down & speak openly, Venema as genomicist would agree with much, if not *all* of Meyer’s philosophy of ‘origins,’ his ‘cosmogony.’ Venema & Meyer probably do, virtually if not literally, share the same cosmogony. It may likewise be that Meyer would agree with much of Venema’s genomics, though he places more focus on information, mind, intelligence & formal cause than does Venema (while I as sociologist am more ‘reflexive’ than both). Why not invite them into (‘intelligent’) dialogue with each other here and in a parallel comments thread at CSC to see? 

Here is a link to a few articles from Chaitin, though I’ve yet to discover his source or initial usage of ‘intelligent design’ in his writings:
http://www.umcs.maine.edu/~chaitin/midas.html

If anyone can trace Chaitin’s connection with this particular concept duo ‘intelligent design,’ which includes references to IDM texts in his papers, please do make that available.

Here is where ‘BioLogos’ must break free from ‘evolutionary creation’ to make any gain.

The notion that there has not been up until now ‘evolutionary mathematics’ is a bit misleading. There are mathematicians who apply evolutionary language in the mainstay of their works. To me, these are ‘evolutionary mathematicians’ (e.g. J.M. Smith), even if they may not be using an ‘evolutionary theory of mathematics’. Some say that language is not important, & dance away with a shrug & mention of ‘semantics;’ to them I say ‘great, then just be mute.’

For example, where I work there are at least two people who specialise in evolutionary systems & evolutionary computation. They are both of course using mathematics in their works. There are complex systems theorists who believe ‘everything evolves’ & that ‘non-evolution’ only depends on ‘scale,’ the boundaries of which cannot be clearly identified. One cannot see the signification ‘intelligent design mathematician’ making any sense at all, in this framework, unless it means simply applying mathematical specifications & pattern recognition to societies or to human-made things.

Yet the pertinent question for both ‘intelligent design mathematics’ & ‘evolutionary mathematics’ is how to save/seek/strike/etc. the right balance between elements, levels or systems of thought & knowledge, which is an extremely difficult thing to find. The socially responsible capitalist. Sustainable development. Static dynamics & vice versa.

And if we’re not careful on the blinking platform with our balance, then poof, it was gone…disequilibrium.


Gregory - #54571

March 16th 2011

p.s. not J.M. Smith, meant to include someone in ‘evolutionary computation’


John - #54572

March 16th 2011

Don Johnson:
“My “Programming of Life” book states 16 specific scientific problems requiring scientific answers…It also highlights 11 hypotheses in peer-reviewed literature that require falsification…”

If you believe that why are you selling books instead of testing hypotheses, Don?


sy - #54577

March 16th 2011

I said

“In fact it is a symbolic system, not because the letters we use are symbols, but because there is nothing about the chemistry of any codon that is in any way connected to the chemistry of any amino acid…”

John said
But even if that were true (and it’s not), that wouldn’t make it symbolic, Sy.

John. Leaving aside the definition of symbolic, I would like to question your assertion that my statement regarding chemical (inludling stereochemical) connections between codons and amino acids is not true.  I know this has become a renewed controversy. Can you point me to a reference that shows good evidence for aptamer recognition as the basis for a genetic code origin. The only evidence I have seen is not very convincing.


Lurker - #54578

March 16th 2011

Sy-
John has already made a few points I agree with for the most part (besides the stereochemical hypothesis, which we’ve been over before). I offer an additional response in a few separate points:

1. “the mechanism of evolution must have been different before the modern DNA/protein system”
How? In a trivial sense this must be true, in so far as a different life forms will behave differently. I presume you mean something more than this, something that would cripple RNA life, but it’s not clear to me what that is. RNA genes making ribozymes still obey the replicator-mutator equation and RNA space is as diverse and complex as protein space. What is it lacking? What threshold does RNA life fail to clear?

This is where the claim that Meyer’s argument isn’t centrally concerned with biological evolution fails. He’s trying to show that the central dogma was designed; the views of most biologists are not that this architecture arose abiotically, but that it evolved from simpler life; that’s true for Robert Shapiro as much as it was for Leslie Orgel.

2. “nothing about the chemistry of any codon that is in any way connected to the chemistry of any amino acid”
Sure- but that’s true for pretty much any signaling pathway found in modern biology. The phosphorylation of serine is chemically unrelated to any of the upstream chemical events that triggered it, or the downstream events it triggers. The differences between estrogen and testosterone don’t have any intrinsic relevance to the differences between women and men. These are symbols, as you define them, but we understand pretty well how they evolved de novo. Heck, any allosteric effector is ultimately a “symbol”; and there are allosteric ribozymes, evolved in nature and in the lab.

Here’s a separate way to look at it: how is the mechanism that converts a dna sequence to a protein sequence (translation) much different from the mechanism that converts a protein sequence into a 3D structure (folding)? Both seem informational and can be modeled by simple algorithms. The mechanism of the former is arbitrary? OK, but how is “DNA to Protein, when in the context of a living cell” arbitrary, but “Folded protein, when in aqueous solution in a narrow band of temperature, pH and salt, and sometimes chaperonins” not? But if you let in protein folding, you have to let in RNA folding- a linear RNA “gene” symbolizes a 3-D RNA “enzyme” in the same sense: under a specific set of conditions, one can be converted into the other.

3. “For those who think life is not the first instance of information on our world”
I’m sorry, this really doesn’t seem coherent to me. By any formal definition of information, there was information in this universe since the big bang.

As for symbolism,  something x signifies something y when x can reliably be taken to indicate y, even though x doesn’t have any necessary physical relation to y, correct? If so, then it seems to me examples in the non living world are abundant. Polaris reliably indicates the direction of the north pole, for reasons that are entirely coincidental. Now, you could say that non-living examples are less sophisticated, but that’s a feature of biological evolution- it can optimize.

4. “What came before it, and how did it turn into DNA world”
I agree with you, as John does, that the RNA world hypothesis doesn’t answer the former question. One can choose to believe some explanation for non-scientific reasons, and that’s fine; I choose to reserve judgement until we have a better understanding of the phenomena involved and early earth history.

As to the latter- there is a difference between a paradox and ignorance. The DNA/protein dichotomy is a paradox, in that there did not seem to be any way for an organism to function without both. That paradox can be resolved by the RNA world, and though I don’t consider the evidence conclusive, I would say that the preponderance of evidence favors it.

How RNA life evolved into a DNA/RNA/protein life is not well understood, due primarily to ignorance of events that happened long ago. I don’t, however, see a paradox, and if you think I’m wrong, please point out why. Modular synthesis is something life has evolved multiple times, including with peptides; we know RNA is capable of modular synthesis, and we know peptides, and even amino acids, would be useful as catalytic or structural cofactors for RNA- voila! coded peptide synthesis by RNA. I’m not saying this IS how it happened, but it is an example of how it could happen that doesn’t seem to be chemically implausible.

John - #54583

March 16th 2011

sy (emphasis mine):
”...there is nothing about the chemistry of any codon that is in any way connected to the chemistry of any amino acid…”

That’s about as absolute as you can get—nothing that is in any way connected to the chemistry of any amino acid! To me, you’re claiming that there’s no evidence whatsoever. Would you write something like that in a manuscript or grant application on the subject?

Then you became more realistic: 
“I know this has become a renewed controversy. Can you point me to a reference that shows good evidence for aptamer recognition as the basis for a genetic code origin. The only evidence I have seen is not very convincing.”

Sy, there’s a vast gulf between those two statements of yours on the continuum of scientific certainty, don’t you think? From my perspective, your first is simply false while your second is perfectly reasonable.


So, I’d like to know what evidence supports your conclusion that Meyer’s false claim about peptidyl transferase was a mere error in light of his concealment of the relevant evidence elsewhere. I’d also like to know why you think inefficiency counts for anything near the origin of life.

R Hampton - #54584

March 16th 2011

Gregory,

Chaitin used an intelligent search (intelligent design) to determine the maximum rate of evolution, and an exhaustive search to detemine the minimum rate. But these were only to establish boundaries. The rate of evolution he actually found within his random walk model did not match either the exhaustive or intelligent searches (he then goes on to explain how evolution can be natural, random, and limited). In other words, his paper finds no evidence for an intelligent search (intelligent design) operating within evolution.

Chaitin would like to see a rigorous (mathematical) proof of “Darwin-style biological evolution” (mutation and natural selection produce very highly complex systems), or a rigorous proof of the contrary, neither of which currently exist. His paper is the beginning of such a project.

Dennis Venema - #54595

March 17th 2011

Hi Rich,


Thanks for your patience - it’s been a very busy week so far. 

In general I agree with your comments, and I agree that Signature needed better editing and more careful argumentation. Where is disagree is that I think Meyer is intentionally arguing that natural mechanisms cannot produce new protein functions. The reason for this is because Meyer is using Douglas Axe’s work in that section - and Axe’s work is not about abiogenesis at all, it’s about protein evolution. I also feel that Meyer weaves this thread into his entire argument (that information only ever arises from intelligence). I agree it’s a poor argument (and easily refuted) - but that’s not obvious to everyone who reads Meyer. 

Meyer is not alone in making this argument within the ID movement either - Axe (obviously), Dembski, and Behe have all put forward variants of this basic idea. 



Rich - #54611

March 17th 2011

Dennis (54595):

Thanks for getting back to me.

The fact that ID proponents, in their writings, sometimes run together subjects and arguments that should be kept distinct, does not invalidate everything that they argue.  A responsible critique of Meyer may of course include objections that he has improperly blurred together origin-of-life questions and questions of Darwinian evolution, and that he has made very questionable claims about Darwinian evolution and the rise of new biological information.  But a responsible critique also requires the critic to address the main argument that Meyer claims to be making.

The main argument that Meyer promises to make at the beginning of his book, distilled from any side-excursions, is about the origin of life, not Darwinian evolution.  About the origin-of-life, he has three main points to make:  (1) current scientific explanations of the origin of life are not even close to adequate; (2) information theory suggests that current scientific explanations of the origin of life are barking up the wrong tree; (3) intelligent design is properly understood as a scientific alternative to current hypotheses on the origin of life, given the difference in method between historical and experimental sciences.

I am not here defending any of these arguments of Meyer’s book.  I am not even sure that I agree with all of them.  But I think that these are the points that should occupy a serious critic.  So, having made your point about Meyer’s confusion of two separate questions, and having made your point that new information can be generated by biological evolution, I think you are now obligated to focus your critique on the heart and soul of Meyer’s argument *regarding the origin of life*.

That’s all I’ll say on the subject.


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