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 Fellow of Biology for The BioLogos Foundation and associate professor of biology at Trinity Western University in Langley, British Columbia. His research is focused on the genetics of pattern formation and signalling.

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Roger A. Sawtelle - #54616

March 17th 2011

I know you scientists do not want a philosopher/theologian messing with your arguments, but I am going to offer a thought any way.

It seems to me that the primary question is, “Is the universe relational or not?” 

Materialists/physicalists/scientismers seem to say that the universe is simply an unordered collection of molecules.  The structure or order provided by natural laws is not physical, but relational.  If the universe is relational as E = mc2 indicates, then it seems to follow that life and intelligence could reasonable evolve from a “dead” universe, because these are also relational.  Thus we have similar but different evolving from similar but different, rather than life evolving from radically different dead matter.  It is the order or design that makes things different, not the substance of things.

Also if Einstein was right that all things are relational, then it is not unreasonable to think that the universe has meaning and a purpose.  Order and rationality are built into nature, which is the reason why the universe is comprehensible and science is possible.

The genetic code is relational, that is it transmits information or instructions by the relationships found within and between the codons.       


Dennis Venema - #54633

March 17th 2011

Hi Rich, 


As I see it, Meyer and I agree that the ability of natural selection to act as a generator of information during biological evolution is highly relevant to assessing if “specified information” only comes into existence via intelligence. If you want to argue differently, that’s fine - I’m responding to Meyer and his claims. This claim is a common one in ID circles, so it’s well worth responding to. 

Also, if you look at my review of Signature in the ASA journal you’ll see that I spend a lot of time going through Meyer’s critique of origin-of-life hypotheses. That part of the book doesn’t hold up either - see the review for the full treatment. 

Best,

Dennis

sy - #54642

March 17th 2011

John

This might not be the best place to continue this discussion, so I will be brief. (relatively). I really dont know what was in Meyer’s head re peptidyl transferase, and I dont think it is as important an issue as you do. Yes, my first statement was too sweeping regarding aptamers, so I agree there could be some evidence for a stereochemical basis of code origin, but I still think it is very weak, and hasnt gotten much stronger with time.

As for efficiency, I am not talking about energy consumption, I agree that is irrelevant. Efficiency is probably not the right word. My point is that an RNA based replication/transcription system is severely limited in relation to the palette of catalysts (protein or RNA) that can be made. In order to work, each ribozyme must self replicate. While a few ribzymes might be just great at catalysis, the suite of available catalytic ribosymes is severely limited compared to the very large number of potential protein catalysts that can be coded for by a sinlge informational DNA molecule. 

So, I can imagine a very primitive RNA world cell, with a hundred or so vital ribozymes, each of which self replicates. But I cant imagine that this system could work for any modern  cell, (even a modern bacterium) that needs a thousand or more diverse enzymatic catalysts. 

So my view is that RNA world could very well have existed, (once we deal with the cytosine problem), but I dont see how it evolved into DNA world. Even theoretically. 

I dont agree with Meyer here, who is much more negative about RNA in general, and I agree with you, that that is an error, based on either deliberate or unknowing false statements related to the power of some ribozymes.


Bilbo - #54645

March 17th 2011

John:  “<i>For example, you
can’t coherently claim that the differences between translation
initiation and termination flow from ID.</i>”

Hi John, I tried asking you about this before, but for some reason my comment was closed.  I’ll try again.  I think that’s a very interesting statement that you make.  I wonder if you would mind presenting your argument for it.


John - #54650

March 17th 2011

Sy:

”... the suite of available catalytic ribosymes is severely limited compared to the very large number of potential protein catalysts that can be coded for by a sinlge informational DNA molecule.”

I agree completely! But an RNA-based cell, protocell, or puddle didn’t have to compete against cells/protocells/puddles with DNA and larger suites. The bar for survival and reproduction in the absence of competition is very, very low!

“So, I can imagine a very primitive RNA world cell, with a hundred or so vital ribozymes, each of which self replicates. But I cant imagine that this system could work for any modern  cell, (even a modern bacterium) that needs a thousand or more diverse enzymatic catalysts.”

I agree, except that I only see a requirement for a boundary, not for cellularity. What I find intriguing about this is that the earliest stages of the origin of life could be occurring all the time, but we’d miss them for two reasons: first, those replicators would quickly lose any competition with modern life; and second, as you probably know, ribonuclease is incredibly stable, secreted, and everywhere. 

“So my view is that RNA world could very well have existed, (once we deal with the cytosine problem), but I dont see how it evolved into DNA world. Even theoretically.”

But there’s a lot we don’t know yet! In 1990, would you have predicted that ribosomal proteins don’t contribute to peptidyl transferase activity, or that tRNA does? I thought that rRNA would just be scaffolding.

 


John - #54652

March 17th 2011

Bilbo:
“I think that’s a very interesting statement that you make.  I wonder if you would mind presenting your argument for it.”

Sure, but it’s more an observation than an argument. We know that proteins can end with any amino acid residue because we have 3 stop codons that end translation without coding for for any residue. Do you perceive intelligence in that design?


Gregory - #54658

March 17th 2011

To both Rich & Dennis: Is the so-called ‘intelligence’ in question considered to be ‘natural,’ ´unnatural,´ or a mixture of both?

 

Now that he is turning to address S. Meyer’s cosmogony, whose ‘origins of life’ perspective does Venema prefer to Meyer’s? Is that written in his PSCF article?

It certainly can’t be anyone ‘in’ BioLogos because they are not educated in ‘origins of life’ as is Meyer. Cambridge PhD degree on that particular topic isn’t something that can be fudged & no one in BioLogos is trained in cosmogony (or even philosophy of science, other than perhaps Giberson). Venema would seem to be going over his head to speak cosmogony with Meyer, though Venema of course doesn’t think so.

 

Why can Dennis not answer the questions that sy, Rich, Bilbo & I are asking him, about Meyers’ views on the ‘origins of life’ & how they relate to his own? Making a review in PSCF is not the same as making it here. Why not make it here Dennis?


Or would you invite Rich to review your review here?


The main point is this: By fiat, no ‘intelligence’ is allowed in biology, right? Iow, Venema is simply saying that ‘intelligence’ is a non-biological concept. ‘Intelligence’ is a concept that is improper to use in biological sciences, it doesn’t ‘belong’ in studies of the biosphere, including genomics, which he charges Meyer with doing.

What Venema is thus doing is protecting the borders & boundaries of ‘what counts as biological science,’ in which he claims Meyer’s views don’t (or shouldn’t) count. He is also suggesting that neither Meyer nor anyone else in the world today or tomorrow can-should ‘insert intelligence’ into biology. 


& most people would notice &/or accept those terms.


Otoh, we can say to Venema: ‘rightfully defend your turf.’ Otoh, we can say to Venema: ‘learn your place young genomicist.’


Venema seems to be trying something more than just defending biology, however. As a geneticist, what Venema is asking for (i.e. still promoting in 21
stc!) is absolute lack of reflexivity in ‘doing science.’ He thus makes his own personal definition of science = unreflexive. Iow, one cannot include one’s own ‘human intelligence’ in the ‘doing of genetics’ because one is trying to be (as) ‘objectivistic’ (as possible). Personal = problematic in ‘doing’ Natural-Physical Sciences (NPSs), including biology. Get rid of the personal as much as possible, just don’t you tip the beakers.

& so it goes in NPSs…


Gregory - #54661

March 17th 2011

Such is called a ‘modernist’ approach to science. Often its practitioners are simply unaware of the influence of post-modern critiques, sociology & psychology of science & scientists (e.g. many NPSs react with fear at being ‘uncovered’), the hermeneutic turn, phenomenology, cognitive studies, media ecology, etc. The modernist, unaware of the recent advances or perspectives available, attempts to construct a genetics that mimics the empiricism in modern physics, & regularly jokes that physicists envy the ‘rigour’ of mathematics. The end of the road for such a perspective: counting.

 

It is as Nietzsche saw in Victorian evolutionism: “<?xml:namespace prefix = st1 ns = “urn:schemas-microsoft-com:office:smarttags” />Darwin forgot the spirit.”

 

There are newer perspectives however, such as B. Smocovitis with her ‘unifying biology.’ I don’t hear a broader approach that integrates cosmogony with genomics in Venema’s ´evolutionary creationism.´. The íntelligence that Venema assumes in his worldview disappears when he enters the laboratory.


As a non-biologist who focuses on ideas, Rich knows how to call Dennis’ bluff about ‘origins of life.’ The irony is Dennis actually believes in ‘intelligence,’ in pretty much the same sense as Rich, myself & other monotheists in the Abrahamic tradition. What Dennis thinks he cannot afford to do is allow ‘intelligence’ into his modernist view of science. But he doesn´t have to. 

What Rich, I & others *can* do is entertain ‘hallmarks of intelligence’ or whatever one chooses to call them, e.g. Mike Gene, even argues as a legitimate topic in biology. Personally, I don’t go so far as to speak of ‘intelligence in biology.’ But I don´t have the time or calling to further investigate the issue in biology. It is obvious that discarding ‘real, historical A&E’ on the basis of (the science of) ‘genomics’ is unnecessary.


Well, anyway, so it seemeth from here.

- Gr.


John - #54669

March 17th 2011

Gregory:
“It certainly can’t be anyone ‘in’ BioLogos because they are not educated in ‘origins of life’ as is Meyer.”

Please spare us your snobbery. 

If you’re going to argue expertise (and expertise in biology is derived by doing, which Meyer hasn’t done), then you need to explain why Meyer never tells his readers about the most important evidence supporting the RNA World hypothesis. This evidence was published with great fanfare at the turn of the century and won the Nobel Prize in 2009, yet Rich, who has studied Meyer’s every word, claims that it has nothing whatsoever to do with the hypothesis. 

What Rich and Sy are claiming is an error on Meyer’s part is covered in undergraduate biology, Gregory. Therefore, we can throw your attempt to protect Meyer by arguing that he has superior training right out the window. 

Then you can explain why Meyer flatly claims that the RNA World hypothesis predicts that ribozymes will be replaced, given that he cites the original Nature blurb by Wally Gilbert that discusses on the ribozymes that have not been replaced and that might not be replaced. Meyer has to account for those by design, but he can’t.

“Cambridge PhD degree on that particular topic isn’t something that can be fudged & no one in BioLogos is trained in cosmogony (or even philosophy of science, other than perhaps Giberson).”

Meyer’s false claim that peptidyl transferase is a protein has zero to do with cosmogony or philosophy of science, but it has everything to do with the RNA World hypothesis. Meyer is making false claims about the facts, just as Rich is so fond of doing, and no amount of pomo, pseudoacademic babble can change or account for that.

“Venema would seem to be going over his head to speak cosmogony with Meyer, though Venema of course doesn’t think so.”

Gregory, the whole point of ID is that its promoters go way over their heads to trick the public while avoiding working in the lab or the field, and Meyer is a perfect example of that. 

Children can figure out how to do science intuitively with minimal guidance. Meyer is afraid to do science.

Arthur Hunt - #54676

March 17th 2011

Don Johnson,

A serious problem with your arguments is that you view the “code” - the strings of A’s, G’s, C’s and U’s - as the be all and end all of the informational system here.  In order for your arguments to have any biological relevance, they need to incorporate a rather different “language”, one that consists of amino acids and their chemical properties (things that do not reduce to informational notions such as you are describing in this discussion).

Among other things, once you understand this nuance, you will see that your assertions about error catastrophe and hypothetical transitions from a two-base to four-base alphabet are not very pertinent.


Bilbo - #54683

March 17th 2011

John:  “Sure, but it’s more an observation than an argument. We know that proteins can end with any amino acid residue because we have 3 stop codons that end translation without coding for for any residue. Do you perceive intelligence in that design?”

Mike Gene did:

http://designmatrix.wordpress.com/2009/02/27/special-stop-codons/

http://designmatrix.wordpress.com/2009/03/02/special-stop-codons-in-the-exceptional-code/


John - #54684

March 17th 2011

Me:

“Do you perceive intelligence in that design?”

Bilbo:
“Mike Gene did:”

That’s nice, but I was asking you. Courage, Bilbo!

Lurker - #54688

March 18th 2011

Sy-
I found your response to John slightly perplexing. Particularly the claim that “In order to work, each ribozyme must self replicate”.

Why do you think that each ribozyme must be self-replicating? Why could there not be a single replicase ribozyme that replicated itself and all other ribozymes in each ribo-organism? In that format ribozymes wouldn’t be constrained to maintain any function other than catalysis.

I understand why you wouldn’t want to spend your time explaining this point in more detail in the tail ends of a blog comments section, but is there an online reference for this argument? Is it published anywhere? I don’t think Meyer discusses the point at all. Again, it seems odd to me; the specialization of one ribozyme for replication would be a straight-forward solution.

2 other points:
1) most studies I know of peg the minimal genome at low hundreds, not thousands, of genes. And most of those genes are involved in translation.

2) Re: the cytosine problem - you don’t fine John Sutherland’s research promising in this regard?

Don Johnson - #54728

March 18th 2011

Responding to 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?

I point out the hypotheses that have been proposed in peer-reviewed literature over the past 10 years that REQUIRE FALSIFICATION before accepting a scenario as science.
Unfortunately for science, the scenarios ARE accepted on the basis of presuppositional beliefs, as opposed to evidence.  I doubt if the hypotheses will EVER be falsified, since such falsification would also demonstrate that much of information science is wrong (biosemiosis and biocybernetics are verified as reality).
I placed a 52-second exercept of Venter’s interview on http://scienceintegrity.net/SynthesizedGenome.aspx in case anyone doubts the reality of life’s hardware and software.

In response to Arthur Hunt - #54676 March 17th

2011
Don Johnson,
A serious problem with your arguments is that you view the “code” - the strings of A’s, G’s, C’s and U’s - as the be all and end all of the informational system here.  In order for your arguments to have any biological relevance, they need to incorporate a rather different “language”, one that consists of amino acids and their chemical properties (things that do not reduce to informational notions such as you are describing in this discussion).
Among other things, once you understand this nuance, you will see that your assertions about error catastrophe and hypothetical transitions from a two-base to four-base alphabet are not very pertinent

My assertion is that anyone who claims that digital information can be transmitted between systems with the source having a lower alphabet capacity than the destination, would have to provide proof that Shannon’s Capacity Theorem has been falsified.  While Shannon information requires no functionality, the transmission of a coded message is limited by Shannon Chanel Capacity.

Once again, those committed to “matter and energy is all there is” have no choice but to attempt to explain away any science that conflicts with their beliefs.  Keep your metaphysical beliefs private, and show me the science!


John - #54735

March 18th 2011

Don, you evaded my question. If those hypotheses REQUIRE FALSIFICATION, why aren’t YOU working to falsify or confirm them empirically?


Don Johnson - #54752

March 18th 2011

To John - #54735 March 18th 2011
Don, you evaded my question. If those hypotheses REQUIRE FALSIFICATION, why aren’t YOU working to falsify or confirm them empirically?

Your question indicates you misunderstand what falsification means.  A falsifiable scientific hypothesis is proposed, and if it is falsified, the hypothesis is either rejected or modified into a new falsifiable hypothesis.  If the proposer of a hypothesis falsifies it, the hypothesis would obviously be false. Those hypotheses REQUIRE FALSIFICATION BEFORE promoting speculations for the origin of life or species as SCIENCE.


John - #54758

March 18th 2011

Don:

“Your question indicates you misunderstand what falsification means.”

Please, Don, I’m an actual scientist who actually tests actual hypotheses and if my data falsify them, I still publish my data.

 “A falsifiable scientific hypothesis is proposed,…”

No, Don, while this CAN happen, no one has to propose anything anywhere. Hypotheses are tools, and the vast majority of them are conceived and tested without proposing them to others.

”... and if it is falsified, the hypothesis is either rejected or modified into a new falsifiable hypothesis.”

And if it is supported, what happens in your mind?

“If the proposer of a hypothesis falsifies it, the hypothesis would obviously be false.”

The proposer is irrelevant, Don.

“Those hypotheses REQUIRE FALSIFICATION BEFORE promoting speculations for the origin of life or species as SCIENCE.”

So you say, but you’re still not explaining why YOU can’t get it together and test them yourself. Moreover, there are testable hypotheses regarding the origin of life, and they are being tested. You don’t get to dictate from your keyboard.

 


Don Johnson - #54780

March 18th 2011

To John - #54758
Don, I’m an actual scientist who actually tests actual hypotheses and if my data falsify them, I still publish my data.

Don: Amazing—you publish data you know is false!


From Wikipedia: Falsifiability, particularly testability, is an important concept in science and the philosophy of science. The concept was made popular by Karl Popper in his philosophical analysis of the scientific method. Popper concluded that a hypothesis, proposition, or theory is “scientific” only if it is, among other things, falsifiable. That is, falsifiability is a necessary (but not sufficient) criterion for scientific ideas. Popper asserted that unfalsifiable statements are non-scientific, although not without relevance.

John: So you say, but you’re still not explaining why YOU can’t get it together and test them yourself. Moreover, there are testable hypotheses regarding the origin of life, and they are being tested. You don’t get to dictate from your keyboard.

Don: I have tested scenarios using information science and found them operationally falsified (http://www.tbiomed.com/content/pdf/1742-4682-6-27.pdf), which evidently you dismiss.

Please inform us of  the “testable hypotheses regarding the origin of life, and they are being tested” that you claim.  Show how the scenarios are falsifiable, using specific hypotheses proposed for falsification.


Don Johnson - #54784

March 18th 2011

To John - #54758
Don, I’m an actual scientist who actually tests actual hypotheses and if my data falsify them, I still publish my data.

Don: Amazing—you publish data you know is false!
I should add that I approve of publishing method and results (not necessarily the data) that shows a hypothesis to be false, since the scientific community needn’t waste time, money, and other resources testing a scenario that someone has already proven false.
Unfortunately, many scientists don’t publish “failures,” because they desire to have ideas that may be productive.  I believe it’s as important to rule something out.


John - #54818

March 19th 2011

Don:


 “Amazing—you publish data you know is false!”

Don, try reading it again. I publish data that falsify a hypothesis. You have falsely accused me of behaving unethically.

“I should add that I approve of publishing method and results (not necessarily the data)…”

You’re not making any sense. Results = data in this context.

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