Is There an Edge to Evolution? Part 3

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October 23, 2010 Tags: Design

Today's entry was written by David Ussery. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Is There an Edge to Evolution? Part 3

In his previous post, Dr. Ussery showed that Behe’s analysis of the probability of getting beneficial mutations is flawed at fundamental levels. Beneficial mutations do occur, new genes do evolve and he cited some research articles that demonstrate this and then showed the interested reader how to gain access to the vast scientific literature that exists. He expresses concern that Michael Behe has not chosen to make the general public aware of what is being done in this arena.

In today’s post he goes on to examine what Behe states is the limit of what Darwinian evolution can and cannot do.

Chapter 4 - What Darwinism Can Do

The title for this chapter is a bit deceptive, in that most of this chapter is not really about what evolution CAN do, but rather what the limits to evolution are (the topic for the next chapter). There is a short description of genome sequence analysis and the types of mutations observed in the laboratory, but in my opinion this chapter is really missing a thorough discussion of the astounding variety and diversity we find when we examine genomes.

Again, Behe emphasizes that he has no problem with evolution by common descent:

Over the next few sections I'll show some of the newest evidence from studies of DNA that convinces most scientists, including myself, that one leg of Darwin's theory - common descent - is correct. (page 65).

Once again, the problem is random mutations:

The bottom line is this. Common descent is true; yet the explanation of common descent – even the common descent of humans and chimps – although fascinating, is in a profound sense trivial. It says merely that commonalities were there from the start, present in a common ancestor. It does not even begin to explain where those commonalities come from, or how humans subsequently acquired remarkable differences. Something nonrandom must account for the common descent of life. (page 65, emphasis in the original).

I absolutely agree with Behe – there must be a ‘non-random’ account. But I’m a bit confused here, because natural selection is, by definition, definitely non-random. That’s the whole point! There is (random) variation, and then those variants that are better are selected. It is not at all random. But Behe’s claim here is that there are not enough random variants produced for evolution to occur. 150 years ago, at the time of Darwin’s writing, it was not known whether the variation was random or produced in some other manner – and in a sense this did not matter.

What was important for Darwin was that the variation was there, and that the method for non-random selection – also known as “natural selection” – could account for the non-random common descent of life. One of the analogies Darwin used was “artificial selection”, where, for example, dog breeders would breed certain traits, giving rise to a large variety of dogs within a short amount of time – merely by [non-randomly] selecting for desired traits. Darwin reasoned if this worked for breeders, why couldn’t it work in natural environments? And as far as “random variations” go, we have quite a bit of variance in dogs, from tiny toy poodles to St. Bernards.

More than half the chapter is devoted to species that have had duplications of their entire genome. Behe focuses especially on yeast, although he mentions in a footnote that other whole genome duplications have been documented. But again, the text written is more within the framework of the limits of evolution—what it can’t do, which should be the subject for the next chapter (I suspect a chapter strictly about what Behe thought evolution could do would be quite thin). The claim that “genome duplication…. has not given baker’s yeast any advantage it wouldn’t otherwise have had” (page 74) seems pretty harsh, especially now that more than two dozen different strains of yeast have been sequenced, and there are clear advantages in survival associated with duplication of many of these genes.

Perhaps, once again, Behe is not familiar with the literature and not willing to have a look at what has been published. I encourage the interested reader to go ahead and have a look at what is out there—go to PubMed, and type in the words “yeast genome duplication evolution” and have a look at the articles found. Today when I did this, I found 420 articles. The second one on the list has this statement in the concluding sentence of the abstract: “Our results provide a scenario for how evolution like a tinker exploits pre-existing materials of a conserved post-transcriptional regulon to regulate gene expression for novel functional roles.” Behe concludes the chapter by saying that “although Darwin hoped otherwise, random variation doesn't explain the most basic features of biology” (page 83).

For more on what evolution CAN do, I mention “The Edge of Evolution” in a footnote in the last chapter (Evolution of Microbial Communities) of my textbook on Comparative Genomics. It is in a section on “Where Does Diversity Come From?”, and I make the statement that some anti-evolutionists “claim that there is not enough diversity in bacterial populations for evolution to occur.” I encourage the interested reader to have a look at this section, as I think it is a nice culmination of a story I’ve slowly built up through the previous chapters on bacterial genomics.

I readily admit that this is something that takes time to understand and cannot easily be explained in a 10-second sound bite – this textbook came from a course I’ve taught at the Technical University of Denmark since 2000. Currently the course meets in the autumn semester, for 8 hours a week, for 13 weeks; this year I have 54 students. So this takes time to explain, but my point here is that the claim that nothing has changed over the past 10 years, in terms of evidence for evolution and documented diversity, is simply wrong.

Chapter 5 - What Darwinism Can't Do

The title of this chapter reminds me of a book by Lenny Moss, called What Gene’s Can’t Do. I think this is a wonderful book, kind of countering the “gene-centric” popular culture. It’s a well-written book, and in my opinion he makes some valid scientific points. Unfortunately, although Behe could have had a similar good discussion here, instead we are treated to poor quality left-overs. This chapter is kind of an update on “irreducible complexity” as outlined in Behe's previous book, Darwin's Black Box. In spite of strong protestations from many (including myself) in their reviews of that work, Behe still clings to the idea that no one has ever published anything about the evolution of these complex molecular machines. “Despite the amazing advance of molecular biology as a whole, despite the sequencing of hundreds of entire genomes and other leaps in knowledge, despite the provocation of Darwin's Black Box itself, in the more than ten years since I pointed out that a situation concerning missing Darwinian explanations for the evolution of the cilium is utterly unchanged” (page 95).

Again, the interested reader is invited to visit PubMed, type in “cilium evolution” and see for oneself: are we to believe that articles with titles like “The evolution of the cilium and the eukaryotic cell” and 'Origin of the cilium: novel approaches to examine a centriolar evolution hypothesis” simply don't exist? Perhaps if one closes their eyes, and clicks their heels three times, thinking, “They don't exist, they don't exist”, maybe these articles can simply vanish!

Last week I gave a lecture in my course about the 10th anniversary of sequencing the human genome. In the field of genomics, much has happened in the past 10 years. There has been an explosion in the amount of genomic data available, and also in the strong, clear evidence for evolution in exactly the manner Behe claims is impossible and will never happen. To put this in perspective – when I first came to the Center for Biological Sequence Analysis in 1997, there were four bacterial genomes sequenced. Last week, in my course I showed an update of the currently sequenced genomes: there are now more than four thousand genomes sequenced, and the number is growing on a daily basis. And the more genomes we sequence, the more we learn about how evolution works. When I was growing up, the preacher in our church used to say, “Did you hear about the guy who said ‘It can’t be done?’ Well he got run over by the guy doing it!” I think there is some truth in this – Behe says it can’t be done, and a decade later, despite this vast amount of data, he claims things remain “utterly unchanged”.

In my next post, I will examine Behe’s discussion of whether random mutation hitched to natural selection is a biological explanation for various molecular phenomena.


David Ussery is an associate professor of comparative microbial genomics at the Center for Biological Sequence Analysis at the Technical University of Denmark and on the faculty at the University in Oslo, Norway. Ussery is the co-author of Computing for Comparative Microbial Genomics and has authored or co-authored 130 articles for science and professional journals. He is also a frequent public speaker on the topic of bacterial genomics.

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sy - #37519

October 30th 2010

To John and Luther

First of all I should clarify that I do not agree with Meyer’s view of origin of life (sorry for the confusion with Behe, I also need an editor sometimes), and no, I do not base my knowledge of biology on his book. I also agree that an RNA world is quite possible. And I know that riboszymes are, at least theoretically, capable of catalysis of many reactions. That has been shown. It has also been shown that ribozyme replicators can evolve. So I don’t doubt (as Meyer does) that life could have spontaneously arisen from and RNA based world.

I think it is likely that modern life, which is DNA and code based, came somehow from that RNA world, so far I am with you guys. The problem I have, and here is where I think Meyer begins to make sense, is how do we get there. How do we get a code?  I am pretty familiar with the literature in this area, and that problem has not been solved.


sy - #37521

October 30th 2010

(Cont)

Direct specific interactions between amino acids and codons, or anti codons or tRNAs have been ruled out. If there was a designer, this is where He came in. But this is not science, so I stop there with mechanism. My point is that Meyer is trying to attack naturalistic origin of life from the wrong angle by dismissing RNA world. What he should be saying is that RNA world is fine, (but quite limited) but in order to get to modern life (which can further evolve) you need proteins, DNA and a translation code that can convert genotype to phenotype. Ribozymes just cant cut it.
As to whether Meyer is being deceptive or ignorant, I think Luther is right and it is more the latter. What he does that is annoying, is start from an assumed position, and then gathers evidence to support it, sometimes (but not always) ignoring contradictory evidence. While we know that this is not scientific, I forgive him for that, since I know a few real scientists who are also guilty of that behavior.


Arthur Hunt - #37529

October 30th 2010

sy:

Direct specific interactions between amino acids and codons, or anti codons or tRNAs have been ruled out.

I beg to differ.


John - #37566

October 30th 2010

Sy wrote:
“And I know that riboszymes are, at least theoretically, capable of catalysis of many reactions. That has been shown.”

But Meyer’s deception is in not showing their actual, not theoretical, importance in life as it exists today.

“I am pretty familiar with the literature in this area, and that problem has not been solved.”

Right. So what are the two major modern ribozymes that Meyer strategically omits?

“Direct specific interactions between amino acids and codons, or anti codons or tRNAs have been ruled out.”

Even without knowing the data, how could anyone rule them out?


Gregory - #37601

October 30th 2010

“How do we get a code?” - sy

Is your question the same as ‘intelligent design’ (in Rich’s non-IDM-sense), when it asks: “How do we get a code…with or without intelligence/Intelligence?”

I agree with Rich #37262. I don’t find it helpful to speak of ‘Meyer’s deception.’ Likewise, I don’t find Bilbo’s accusations of Ussery helpful. Where one sees ‘dection’ another sees ignorance or simply a different interpretation of the same thing.

When people want to divorce ‘motivations’ & ‘values’, among other non-purely physical things in the action of ‘doing science,’ we recognize that ‘science’ (often meant in a capitalised, neo-Euro-Enlightenment sense as Science) is not as ‘objective’ as it pretends to be. This is precisely when ideology comes into play.

I’m glad to read Lurker & sy address John’s arguments with Behe & his book in the realm of biology. Also, Rich’s & Tom’s back & forth on broader topic of ‘irreducible complexity’ operates at a higher level, which is helpful.

So please note, John, when you ask Bilbo or I to discuss biology at a technical level, you’ve hit a wall. We’re not ‘running away.’ We don’t have language to continue. & it was you who ‘ran away’ from me re: ‘Darwinism.’


sy - #37607

October 30th 2010

Arthur

Yes, i am aware of Yarus ideas and work on aptamers. However, his views do not represent the consensus in the field. I am traveling at the moment, but will try to get some links to the relevant papers as soon as I can.


sy - #37608

October 30th 2010

John

“Right. So what are the two major modern ribozymes that Meyer strategically omits?”

Thank you, its been many decades since the last time I was given a quiz. You are making feel young again. Of course these days it doesnt work so well thanks to Wikipedia. Their list of ribozymes dont look familiar to me except for RNAseP, which I did recognise. So why dont you enlighten us (and I will humbly accept a D for the test) and tell us what Meyer left out.

As for tRNA amino acid interactions, a great deal of work has been done on this. The sum total has been negative as reported in a review article which I will post a link to as soon as I can. Yarus paper, cited by Arthur Hunt, is one of the few that continues to pursue this idea of the origin of the genetic code.


sy - #37609

October 30th 2010

Gregory

Yes, I think that is a fair assesment of my views. And I pretty much agree with the rest of your comment.


sy - #37614

October 30th 2010

“On the whole, it appears that the aptamer experiments, although suggestive, fail to clinch the case for the stereochemical theory of the code. As noticed earlier, the affinities are rather weak, so that even the conclusions on their reality hinge on the adopted statistical models. Even more disturbing, for different amino acids, the aptamers show enrichment for either codon or anticodon sequence or even for both (76), a lack of coherence that is hard to reconcile with these interactions being the physical basis of the code.”

The above quote is trom the paper (sorry I cant get to a link right now).
Koonin EV and Novozhilov AS 2009 Origin and Evolution of the Genetic Code: The Universal Enigma.  Life, 6: 99–111.
The reference 76 is an earlier paper by Yarus, which is very similar to one cited by Arthur Hunt.


Lurker - #37658

October 30th 2010

In regards to Meyer-

Confirmation bias (together with a bit of the Dunning-Kruger effect, I’d add) is a better explanation for Meyer’s errors than deception. However, I’m much less willing to say this is insignificant. It’s true scientists are prone to the same behavior (though I’d argue the most successful scientists tend to be those able to resist this common error); but SitC is presented as a scientific treatise, not a popular science book, and, at least in Chapter 14, it is riddled with errors that would, as John points out, leave the naïve reader with a very inaccurate understanding of the evidence for the RNA world. That’s a rather serious flaw in a book about the origin of modern life.

In regards to coding-

You’d find very few people working on early life that would disagree that “in order to get to modern life (which can further evolve) you need proteins, DNA and a translation code that can convert genotype to phenotype. Ribozymes just cant cut it.” I presume you further claim at least one of the following:

1) There is no plausible selective pressure under which the RNA World could evolve coded protein translation. (i.e., which came first, encoded proteins or translation?)


Lurker - #37659

October 30th 2010

(continued)

2) A ribozymal peptide synthesis apparatus would never be sophisticated enough for coded translation of a protein enzyme. (i.e., any proto-ribosome needs its protein partners to be able to translate full proteins)

Meyer handles neither point well, demanding, without any good cause that I can see, that the entire modern translation system and a complement of modern encoded proteins are all necessary before a translation system pays off. He ignores the substantial evidence that the modern translation system evolved from something much simpler, and presents every artificial ribozyme as an example of the best RNA can do, rather than a very rudimentary test in the lab of the basic catalytic potential of RNA.

I think you are familiar with the various ways people are trying to address these issues; and I’d say a better characterization of the current state of knowledge is that we don’t know whether either statement is true or false. Given our general lack of knowledge of the space of functional peptides and RNA, and of life simpler than the modern cell, I don’t know of any good argument that either of the above should be true (nor for that matter that either is definitely false). What do you see differently?


John - #37664

October 30th 2010

sy: “I am pretty familiar with the literature in this area, and that problem has not been solved.”

me: “Right. So what are the two major modern ribozymes that Meyer strategically omits?”

sy: “Thank you, its been many decades since the last time I was given a quiz. You are making feel young again. Of course these days it doesnt work so well thanks to Wikipedia. Their list of ribozymes dont look familiar to me except for RNAseP, which I did recognise. So why dont you enlighten us (and I will humbly accept a D for the test) and tell us what Meyer left out.”

Well, you did claim to be pretty familiar with the literature. The Tetrahymena rDNA intron (there’s even a reference to it in the bibliography, so ignorance is not an excuse) and telomerase.

sy quoted:
“On the whole, it appears that the aptamer experiments, although suggestive, fail to clinch the case for the stereochemical theory of the code.”

The case is still open. Art and I were objecting to your claim that the case was closed in the opposite direction: “Direct specific interactions between amino acids and codons, or anti codons or tRNAs have been ruled out.”


John - #37667

October 30th 2010

Gregory:
“I agree with Rich #37262. I don’t find it helpful to speak of ‘Meyer’s deception.’”

The evidence is overwhelming that the false claim on p. 128 was not an isolated mistake. More examples from a single p.305:

“Presumably, these [primitive] RNA molecules would need to perform the functions of the 20 specific tRNA synthatases and fifty ribosomal proteins…[omitting the fact that enzymatically active site of the modern ribosome is RNA, with the proteins as scaffolding]”

“These mRNAs would need to be able to direct protein synthesis using, at first, the transitional ribozyme-based protein-synthesis machinery [completely false, as the MODERN protein-synthesis machinery is ribozyme-based] and then, later, the permanent and predominantly protein-based protein-synthesis machinery [false for the same reason]. In short, the evolving RNA world would need to develop a coding and translation system based entirely on RNA and also generate the information necessary to build the proteins that later would be needed to replace it [completely false, as most of the translation machinery right now is based on RNA].

Mendacity, utter incompetence, or both? These falsehoods can’t be explained by interpretation.


sy - #37683

October 31st 2010

Lurker

I think you stated both of those points quite well, and yes,  I think both are true. Am I certain that both are true? Of course not. We clearly have major knowledge gaps here. But I havent seen any very good hypothetical mechanisms to counter either of the two claims you list. I am utterly unconvinced by the aptamer experiments of Yarus, and I think some of his conclusions are not supported by the data.

Lets not forget that modern life can be defined in one sense as having the ability to evolve by natural se3letl selection, and that the process of natural selection requires a very tight conjunction between genotype and phenotype. While selection can occur in RNA world, cells can only evolve so far, and not to anything resembling the complexity of a even a modern prokaryote, withough a code based translation system. Some theories have been advanced regarding how this could have developed, but I think they are all deeply flawed.


sy - #37684

October 31st 2010

John

You are claiming mendacity on the part of Meyer because he didnt discuss the tetrahymena intron and telomerase? Are you serious? First of all, as you I am sure well know, but possibly some other readers don’t, telomerase is a protein enzyme with a small RNA component. It is certainly not a good model of a self sufficient ribozyme. And the tetrahymena intron, one of the first ribozymes to be discovered, is very interesting from a basic biochemical point of view (and helped Cech to win the Nobel) but its activity is not terribly important in cell function. So I feel a bit better about not being able to guess what “major” ribozymes Meyer was leaving out.

As for your statement that most of the machinery of translation is RNA based, that is just silly. The ribosome is of course a wondrous structure, and absolutely required for the process. But remember that the peptidyl transferase ribozyme cannot transfer enough energy to allow the peptide bond to form. The necessary energy is supplied by the activation of the amino acid in its binding to the protein amino acid tRNA synthetases. And it is also these protein enzymes that provide all of the specificity necessary to allow the coding system to work.


Lurker - #37687

October 31st 2010

Sy-
For point (1), things are uncertain. I agree with you, and Koonin, that the stereochemical hypothesis is not all that convincing, for the reasons Koonin mentions. The path that people like Koonin, Harry Noller, and Tom Cech have proposed goes from amino acid and peptide cofactors, to RNPs, to full blown proteins; and although quite vague, I don’t see anything there that is physically or chemically implausible, and there’s biological precedent for each of the stages. To conclude that specific design is the better explanation, one would need some positive evidence, and here I find Meyer’s and his other DI associates’ work utterly unconvincing.

In regards to point (2), I’d argue the weight of the evidence suggests that it’s false. Meyer’s claims that ribozymes can’t undergo conformational changes, nor concerted reactions, are not true (consider aptazymes for the former, and introns for the latter). The current state of research here is far from discouraging. What we do know is that all the major activities of the ribosome, from codon recognition to peptide synthesis to translocation, are primarily, if not only, RNA based. RNA can perform the basic chemistry of aminoacylation and amino acid recognition.


Lurker - #37688

October 31st 2010

(continued)

Then there are tantalizing clues that the tRNA/aaRS system evolved from something much simpler (I recommend Paul Schimmel’s work in this area), and even more recently both Ada Yonath and Bokov and Steinberg have shown that the ribosome may still bear traces in its structure of its origin from a very small ribozyme.

I don’t think I follow the argument in your latter paragraph. A ribozyme has as tight a connection between genotype and phenotype as a coded protein does, and quite a bit more direct. Evolution by natural selection is readily possible in all-RNA systems, and this has been demonstrated experimentally. Given what we know about RNA catalysis (and simple protocells), a ribo-organism would be able to catalyze most of the basic chemistries for replication, metabolism, and rudimentary cell division, and most importantly, peptide synthesis. So we’re back with can ribozymes catalyze coded protein synthesis (point 2), and would they evolve to do so (point 1). The former seems likely, the latter is unknown, though there is evidence that translation evolved from something much simpler, with much fewer protein components. We’re probably going to have to beg to differ on this.


Lurker - #37690

October 31st 2010

OK, one more point. The aaRS are crucial to translation, but let’s not forget that the ribosome is more strongly conserved, engages a huge fraction of cell mass, and is more central to the translational system. It’s kind of a big deal.

Is it implausible that RNA could perform as an aaRS? RNA can aminoacylate and can activate an amino acid with ATP, both with high specificity. That there isn’t a ribozyme that can do both in a concerted manner, nor a suite of them for each of the amino acids says more about the sophistication of in vitro evolution (or perhaps the priorities of agencies that fund biochemistry labs), than it does about the basic capacities of RNA. I know this isn’t a certainty, but it seems a surprising claim to make.

Is the issue that ribozymes couldn’t discriminate between closely related aa? Since there are already aptamers that discriminate between molecules differing by a single methyl group, this seems dubious. But even so, how many distinct amino acids are needed to make the first protein? Certainly not 20; as I recall, people have made structures with less than 5.

If all you’re saying is that none of this is proven, fair enough. But from a strictly chemical point of view, how unlikely is it?


sy - #37758

October 31st 2010

Lurker

Thanks for your answer. I certainly agree (and I think I said this somewhere above) that RNA world life can evolve, and that ribozymes can self replicate. I also agree that based on the ribosome activity that we know, ribozymes can produce peptides. My own guess as to the origin of life is that RNA replicators were selected for high replication efficiency, and that the catalytic function to include peptide catalytic sites also evolved. We can add metabolism and membranes and stuff (clearly I am a replication first guy).

So we have life starting and evolving quite nicely on it own, based on RNA. Cells grow, metabolism occurs with some simple ribozymes catalyzing reactions, the genotype (which is the composite sequence of all the ribozymes in the cell, right?) is inherited thanks to the high fidelity self replication of each ribozyme (?), and as you say we have a nice tight connection between genotype and phenotype.

Now here is my question for you. How far could such cells evolve? Second question. Assuming that these RNA cells were alive, what kind of selection pressure would have them go toward DNA world, and what steps could one imagine they could take to start on that road. In other words, how do we get DNA?


sy - #37760

October 31st 2010

Lurker

I should also say that I don’t at all agree with Meyer’s underlying philosophical approach. He and Behe, and DI folks are trying to find scientific evidence (or negative evidence) for the existence of design, which is their fundamental belief. I don’t.

I believe in God, the creator of the universe. I think it is possible that God also created the first modern DNA based evolvable cell (for teleological reasons, since RNA cells could never reach even the eukaroyote level, never mind us). I don’t think this can be proven, and if more data shows it is probably wrong, and a good mechanism for a natural selection based step wise progression from RNA world to DNA life is ever proposed, I would be happy to accept it, while I doubt that the DI folks would.

As you might have figured out, I am a biologist, and the fundamental principle of science is to go with the data, even if it goes against your ideas. I like the idea that God created life, but I can let it go, if it turns out to be wrong. That certainly wouldn’t shake my faith, since there is only one truth, and God wants us to find it. I believe that is why we are here.


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