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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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Lurker - #37815

October 31st 2010

Sy (continued)-

The modern cell is highly optimized, and all those thousands of highly optimized proteins need an optimized translation system and large energy sources. The ribocyte would be functioning well below that, but the first translation system needs only produce a protein, or even a peptide, that can work better than what was there before.

How do we get DNA? I The consensus is that DNA replaced RNA after the invention of translation (because (1) RNA would have a hard time converting NTPs to dNTPs and (2) DNA replication was invented multiple times, whereas translation was invented only once). The long term pressure to switch to DNA is obvious: it’s more stable, and thus genomes could be larger and less prone to mutation. Patrick Forterre has some interesting theories about how viruses may have invented the earliest DNA genomes as a resistance adaptation. And if the conversion happened after translation, genetic information could be transferred from RNA to DNA easily. Translation strikes me as a much harder problem-it had to be invented without proteins, is a more complex process, and requires the invention of the genetic code as well.


Lurker - #37817

October 31st 2010

Sy (continued)-

If you’ll permit me, I think I’d summarize your views as follows: “The modern cell is complex, and though probably descended from an RNA organism, we still know very little about what happened in between. Absent that understanding, my religious beliefs cause me to suspect that God intervened directly to affect the transition, subject to future evidence to the contrary” Though I don’t agree with the latter part, I have no strong objection to that view. I only wish to emphasize that (a) although little is known in detail, the current state of evidence has if anything shown that the invention of translation by RNA is more likely than we previously thought, and (b) Meyer’s arguments have very little in common with that view, and rely on very flawed interpretations of the evidence I refer to in (a).


sy - #37818

October 31st 2010

@Rich - #37763

“Does that work both ways?  For example, if it turns out that a much deeper knowledge of macromolecules acquired in the future leads to the conclusion that the probability of the formation of the DNA-protein system without guidance is extremely low, on the order of, say, 1 in 10^100, would it be incumbent upon biologists to acknowledge a role for design in the origin of that system as “the best explanation”?”

Absolutely. But dont count on it.

The problem is, (as John might say, only with a different tone) that such evidence would be entirely negative, and while absence of an alternative explanation might POINT to design, it will never be thought of as evidence for design by biologists. What is needed to get that far would be some form of evidence or even a mechanistic theory that would be consistent with design.

I cannot think of such an experiment or theory, but that is just me. Maybe someone will. If not, as Mike Gene has stated on another thread here, it might not matter. I believe in design, as part of my religious views, even without any “hard evidence”. Science, as many have said, is not the only path to truth.


sy - #37822

October 31st 2010

Lurker

Your summary of my views is perfect, and I would ask your permission to copy and use that when pressed. I think you know more about RNA based translation than I do, and I certainly agree with all of your comments, including those pertaining to the ID argument, which is a bit simplistic, error prone, and ideology driven.

For me the real issue is code evolution. Here I think the ID folks have a strong point. I am curious as to what you think about the concept that the genetic code represents the first real symbolic informational system. I cannot conceive how this could evolve from even a fairly sophisticated RNA world ribocite. Thoughts?


Arthur Hunt - #37828

October 31st 2010

Lurker:

For me the real issue is code evolution. Here I think the ID folks have a strong point.

I wonder why.  Tenuous as Yarus’ studies may be (and I disagree with some of the criticisms raised by Koonin - but that’s perhaps for another venue), they still constitute an infinite amount more positive experimental evidence for one hypothesis of the origin of the genetic code than the whole entire sum of all positive experimental evidence for the ID hypothesis (whatever that may be).  For there is no positive evidence for any ID hypothesis pertaining to the origins of the genetic code.

But I won’t belabor these points in this already too-long discussion.  Instead, I thought I would toss out a couple of ideas that are much more fun to play around with.  (continued ...)


Arthur Hunt - #37829

October 31st 2010

First idea:  I see that people have a tendency to speak of the RNA World in the past tense.  I believe this is not only wrong, it is rather misleading.  The fact of the matter is that life as we know it is still firmly ensconced in the RNA World.  RNA lies at the heart of virtually every important process that goes on in the cell, and the cell devotes the lion’s share of its resources to the workings and replication of the core RNA machine in the cell - that would be the ribosome.  Heck, it is just as useful (and accurate) to view DNA as just an intermediate in the replication of ribosomes (think retroviruses here, in a convoluted and metaphorical sort of way) than as the raison d’etre of the cell.

Look at it this way - if some advanced alien species did a one day drive-by of earth and sampled the biota, their main observation would be “interesting - (rRNA) sure has found a lot of interesting ways to propagate itself on this world”.


Arthur Hunt - #37830

October 31st 2010

Second idea:  There is some speculation as to what the ribocyte - that mythical being from long-distant ages that seem inaccessible to us - may have looked like.  I will admit that I also wonder about this.  But I also wonder - what if the ribocyte is not extinct?

This is where eyes start to a-rolling.  The reflexive retort is - if they are not extinct, then where the heck are they?  Where indeed.  How would one actually identify a ribocyte?  If such an organism were microbial and lived amongst the microorganisms (mostly unculturable, but constituting the vast, overwhelming majority of biological diversity on the planet) that we have not yet discovered, let alone characterized, how would we find it?

It’s not an easy question.


Arthur Hunt - #37831

October 31st 2010

Oops, that would have been sy, not lurker, who said For me the real issue is code evolution. Here I think the ID folks have a strong point.   Sorry about that.


John - #37836

October 31st 2010

sy wrote:
“For me the real issue is code evolution. Here I think the ID folks have a strong point.”

Why? The term “code” is used metaphorically, as there is nothing symbolic about the system.

Moreover, while there are aspects of the system that seem intelligently designed, there are other very similar aspects that are very stupidly designed. There’s no way an intelligent designer would cover one and not the other, but there obvious reasons why evolution can do one and not the other.

Would you like an example?

Art wrote:
“The reflexive retort is - if they are not extinct, then where the heck are they?”

What if they continue to arise, but the fact that we are awash in nonlabile RNase prevents them from being detected or evolving further?


sy - #37843

November 1st 2010

John and Arthur

Listen guys, don’t get me wrong. I love RNA. I think RNA is the greatest stuff. I even used to do Northern blots (that will tell you something about my age). And I now know that Arthur is an RNA researcher, so I will refuse to say another word about the superiority of DNA as a replicator and information molecule, and proteins as catalysts. Not another word.

But really, are you serious about living ribocites? Isnt that going just a tad too far?  And frankly, the idea of ribosomes being the real center of everything just doesn’t quite fly outside of an RNA conference. But, I promised, not another word. Well, maybe just one more. I think it is dangerous for a scientist to fall too deeply in love with his/her subject. We all think our field is the center of everything. It aint. And that includes RNA,


Lurker - #37847

November 1st 2010

Well, a few things to respond to.
Sy-
First, I’m glad I captured your views so accurately, of course feel free to use it.

Second, in regards to the code. This has the potential to keep me rambling on for far too long, so I’m going to try to restrain myself. Obviously the origin of the code is one of the most interesting events in the origin of life, second only, in my view, to the origin of Darwinian evolution. Nevertheless, it is easy to exaggerate what the code is. If by “symbolic information” you mean something analogous to human language, or computer code, the genetic code has one huge difference: it lacks semantics. I think I first saw this mentioned by Randy Isaacs, but a sentence means the same thing written or spoken, in English or Esperanto, because it always is about the same concepts. But what is a gene about? The information in a gene doesn’t catalyze a reaction as either nucleic acid or protein, only one; and it isn’t about transition states or 3D structures. It’s just the determinant of a particular functional protein, but that’s as much true for an RNA gene encoding its ribozyme complement.


Lurker - #37848

November 1st 2010

Sy (continued)-

So, you ask how a coding system can evolve. I’ve said before, we don’t know how it did happen, and I don’t want to suggest that the issue is trivial. But is it that far a step from a modular peptide synthesis machine, say the ribozyme equivalent of the non-ribosomal peptide synthesis enzymes, to one which dynamically swaps out modules to synthesize different peptides. Then you already have a machine (maybe a protoribosome working with self-aminoacylating proto-tRNAs) that essentially follows a set of rules of the form “under condition x, add amino acid y”. That’s already a code of sorts, and one which, generalizing for x and y, is essentially the genetic code; and both before and after the generalization, the ribozyme is doing the same thing: making functional peptides. Plus x and y don’t have to be large initially, we know even binary peptides can have function, and Paul Schimmel’s work, as I mentioned above, suggests there may have originally been as few as 6 tRNA-amino acid pairs.


Lurker - #37849

November 1st 2010

Art-

I know you caught your error, but to emphasize, I don’t think you’ll ever hear me saying “the ID folks have a strong point”. As you say, no need to belabor the particular debate about Mike Yarus’ work, and that’s one of the very few things where I’d disagree with you at all.

On rRNA- I agree, to the extent that very few people grasp how intricately RNA is involved in the most basic functions of life, and how surprising that is from any perspective other than our origin as RNA machines. But it’s probably better to consider life as a collaboration between a number of molecular entities, than as one “master” molecule sinisterly manipulating all the others for its nefarious goals.


Lurker - #37851

November 1st 2010

Art (continued)-

On extant ribocytes-not so eye-rolling at all. Steve Benner had a program to look for them in nanoporous rock (because maybe ribocytes, not needing a ribosome, could be much smaller than bacteria), though no success. There are of course good reasons why ribocytes wouldn’t be able to hold their own against bacteria, but the payoff would be so huge I’m surprised so few are looking. A metagenomics screen is pretty easy to envision, though I worry that the non-canonical bases (found in rRNA and tRNA, and thus probably in the ribocyte) would cause trouble in PCR. I still think a better approach may be to mimic Benner, and try to imagine niches where ribo-organisms are actually at an advantage relative to modern life.


Arthur Hunt - #37893

November 1st 2010

Lurker:

But it’s probably better to consider life as a collaboration between a number of molecular entities, than as one “master” molecule sinisterly manipulating all the others for its nefarious goals.

LOL.  I feel like I’m Steven Colbert, playing to your Jon Stewart.


Argon - #37976

November 1st 2010

sy - #37843: “I even used to do Northern blots (that will tell you something about my age…”

What an old fart!. Then again, I used to do Maxim-Glibert sequencing and recrystallize phenol for DNA extraction. And back then we’d walk five miles to lab every day, uphill both ways!


Rich - #40920

November 20th 2010

For those interested, Behe has posted a reply to this column (and to Part IV as well) at:

http://www.evolutionnews.org/2010/11/the_edge_of_evolution_as_seen_040681.html#more


glsi - #64076

August 17th 2011

    **   “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.” **

br>
It’s been a while since I read Behe’s book, but I’m pretty sure he talks directly about this 19th century idea.   Dog breeding is a perfect example of (artificial or natural) selection producing adaptations.   Observation will tell you that they’re all dogs.  They remain dogs.  St. Bernard breeders cannot select for larger and larger St. Bernards which become Clydesdales.  Poodle breeders cannot breed 8 inch poodles which burrow and live underground.  There is a limit and an apparent “edge of evolution” which can’t be breeched by selection.   
br>
This is common sense that you don’t need a PhD to understand.  If there were factual examples of selective breeding producing novel, non-dog species then that would be the common sense favoring Darwinism.  But there are none.  Darwin’s finches are still finches.  The poor guy just made an honest  mistake and the world believed it. 

 


John - #64094

August 18th 2011

gisi,


This gross misrepresentation of Darwinian evolution that you’re pushing is a craven lie.

Note that I’m not saying that you are lying, but you’re regurgitating a filthy lie that has been refuted time and time again.

There is nothing about Darwinian theory that would EVER suggest that a dog would evolve into a horse. NOTHING. Therefore you aren’t addressing Darwinian evolution when you misrepresent it in such a way.

If you had enough common sense to actually attempt to understand Darwinian theory before desperately attacking it with laughable straw men, you’d know that dogs and horses share a common ancestor. You’d also know that single species split into two or more species, like branches on a tree. Maybe if you had common sense, you’d connect that with the metaphorical “tree of life.”

Now, on to your case. Are you claiming that St. Bernards and Chihuahuas aren’t reproductively isolated from each other? What Darwinian theory predicts is that they are on their way to becoming separate species if we no longer intervene.

Also, the name trope is old, boring, and yet another lie. Whether we call both “dogs” is irrelevant to whether they are becoming separate species.

So please keep in mind that when you parrot the lie that Darwinian theory predicts that one extant species morphs into another, you’re flushing your credibility.

Now, are you making an honest mistake, or did you already know that you were misrepresenting Darwinian theory, gisi?

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