The Talk.Origins Archive Post of the Month: December 1999

[Note: The following is actually four posts on the same subject by Sherilyn during the month of December 1999. --Ed.]

Article 1

In article <38531ECB.348142B7@no.hlk.spam.hj.se>, Sverker Johansson <lsj@no.hlk.spam.hj.se> wrote:
> Sherilyn wrote:
[Cited papers from JME that appear to contradict Behe's claim
that "zero papers" have appeared in the JME discussing detailed
models of the evolution of molecular machines]
> >
> > Just to make sure this is correct, is there a possibility that these
> > papers model structures which would not be regarded as complex by a
> > biochemist, or that the models discussed lack significant detail?
>
> All these are clearly complex. What a Beheite may object is that
> some of the evolutionary models may be lacking in detail.
>
> But it would be difficult to argue that Melendez-H et al is
> insufficiently detailed, with its wealth of chemical details, and
> its discussion of intermediate stages.
>
> Musser et al is likewise worth a closer look. The others do
> contain evolutionary models, but less detailed.
>
> > I can see how a paper with a title like 'Phylogenetic analysis of
> > components of the eukaryotic vesicle transport system reveals a common
> > origin of adaptor protein complexes 1, 2 and 3 and the F subcomplex of
> > the coatomer COPI' would tend to be classified as just another paper on
> > sequencing, are you sure it discusses a detailed evolutionary model?
>
> The bulk of the paper is about sequencing, but it did discuss also an
> evolutionary model.
>
> > For instance, would it be correct to state that the paper only infers a
> > common evolution, but does not discuss a feasible evolvable mechanism
> > for that origin?
>
> No. It did go one small step further than just discussing a common
> evolution. There are zillions of papers just inferring common
> evolution, without taking the next step, but this is not one of them.
>
> > I don't want to accuse anyone of misleading people on
> > the actual contents of the JME, unless it is quite clear that he has
> > done so.
>
> My take on that is that Behe intentionally includes weasel words
> like "detailed", so that he can always twist around and claim
> that whatever model is presented isn't sufficiently
> detailed. He sets up movable goalposts.
>
> But he'll have to move them far and fast to get the
> Melendez paper on the "right" side if them.

I visited the Springer Science Online website

http://link.springer.de/power.htm

and pulled up the abstract from Melendez (1996), which reads in full:

BEGIN QUOTE

The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one - taking the available material to build new pathways - demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.

END QUOTE

If the paper contains the analysis described, this certainly answers Behe's 1994 claim, which he has repeated at Temple and elsewhere more recently (1998?).

The Behe paper I quoted at the top of this thread is at:

http://www.arn.org/docs/behe/mb_mm92496.htm

It was originally delivered by Behe to the meeting of the C.S. Lewis Society, Cambridge University in 1994, so Behe might have been able to argue at that time that JME had published no papers containing a reasonable amount of detail. But Behe was still retailing that same statement when he visited Temple University and, according to Peter Nyikos' transcript of the speech said:

BEGIN QUOTE

==========

[begin transcript of relevant part of audiotape, notes added in in brackets]

But if these things can't be explained by Darwinian evolution, as I assert, then what have other scientists said about how they were produced? Well, a good place to look for an answer to that question is in a place called the Journal of Molecular Evolution.

Here is a recent table of contents from the journal.

[THE FIRST OF THE TWO TRANSPARENCIES WAS PUT UP ABOUT NOW]

As its name implies, the journal was set up specifically to look at questions of how life arose at the molecular level and how it might have evolved. It's a good journal. It's got maybe 40 scientists on its editorial board. Of those, maybe 15 are members of the National Academy of Sciences. It's had the odd Nobel Prize winner or two on its editorial board. And every month it publishes about a dozen papers. And here is a typical month. And from where you are sitting, some of you can't read the titles of the papers; and some of the non-scientists here would not be able to understand what they are about anyway if they could see the titles.

But briefly, in this issue, all 12 papers are concerned with something called sequence analysis. Briefly, sequence analysis is involved with protein and DNA sequences. Now proteins, as you know, are composed of subunits called amino acids. Now an interesting thing you can do is to take a protein from one species and compare it to a similar protein from another protein, er, from another species.

Suppose you took the hemoglobin from dog and the hemoglobin from horse, and you sequenced, or you determined the sequence of amino acids in both of those proteins. Now what you can do is say to yourself, well, with these two sequences, what can we say about the first amino acid position? Is it the same in dog and horse, or is it different? How about in the second position, and in the third position, or in the 50th position? And that would be an interesting thing to do; and from the results, you might be able to determine how related these organisms are. And that would be an interesting question to address.

But for our purposes right now, I want to say that although this is an interesting thing to do, it does not address the question of how you could put together complicated molecular machines, step by Darwinian step.

Let me try to give you an analogy to make that clear. Suppose you looked at the forelimb of a dog and the forelimb of a horse, and you saw that there were the same number of bones there, and they were in similar places. That would be very interesting, and it might give you an indication of how related those two organisms are. But comparing the bones in the forelimb of a dog with those of a horse can't tell you where bones came from in the first place. In order to do that, you've got to do experiments, you've got to build models and other laboratory type work. Well, it turns out that nobody in this issue of the Journal of Molecular Evolution did that. Nobody addressed the question of where these irreducibly complex molecular machines might have come from.

[At this point there was a 6-7 second silence on the tape due to technical difficulties. Clearly, there was a comment about the other issues of JME here.]

Of those, about 700 were about sequence analyses. And they are interesting, but they don't address the question we're thinking about today. Another 150 or so have to do with chemicals thought necessary for the origin of life. And again, that's another interesting subject, but, again, does not impinge on what we are doing. A few dozen were mathematical studies in order to determine methods to improve sequence analyses.

Of those thousand papers, how many addressed the Darwinian step-by-step evolution of complex molecular machines, such as cilia and flagella?

It's a round number. There aren't any.

[THE SECOND TRANSPARENCY WAS PUT UP RIGHT ABOUT HERE]

Zero. Zip. None.

It's really rather surprising. And there's a lot of biochemical journals. The JME is not the only one. There's the Proceedings of the National Academy and the Journal of Molecular Biology and a number of others. But if you look in them the story is pretty much the same. Occasionally, people speculate about how things like this could have arisen, but never in great detail and never in a testable way. People compare sequences and sequences, but nobody is much interested in the production of these molecular machines.

========================= end of JME-related portion of talk

END QUOTE

If my memory serves me correctly, PZ Myers of Temple U. told me about Behe's impending visit to Temple during an IRC conversation or email exchange in November/December 1998, so it appears if I am correct in this that Behe was still retailing the same, by now incorrect, tale four years after he had first told it.

In the 1994 paper I cited at the start of the thread, Behe mentions having looked at "868 papers" in the previous ten years. Now in the section Peter quoted, he says "of those thousand papers...", indicating that he has updated his work, but not brought it up to date (because we could expect about twelve papers per issue and in the four years between 1994 and 1998 the total would have been somewhat closer to 1200 papers).

Unfortunately, quite which particular "thousand papers" Behe was talking about is obscure, because Peter's transcript Behe does not contain an explanation of how this figure was counted, although there is the following note halfway through the JME section:

"[At this point there was a 6-7 second silence on the tape due to technical difficulties. Clearly, there was a comment about the other issues of JME here.]"

This ellipsis is most unfortunate. Presumably the person making the recording had to turn over the tape at just that point.

Article 2

In Melendez (1996) the mystery of the evolution of the Krebs Cycle (aka Citric Acid Cycle, aka Tricarboxylic Acid (TCA) Cycle) is finally reduced to a problem in chemical engineering and reverse engineered to produce a system for aerobic respiration. Previous studies had speculated that the cycle might have evolved from previously available pathways involved in the synthesis of amino acids, but there existed no detailed elaboration of how this could have happened. The Krebs Cycle is the basis of aerobic metabolism; its product, ATP, is known as "the energy currency of the cell". Melendez et al show the evolution of the cycle as an exercise in opportunism in evolution--coopting of existing components with entirely different functions and assembling them to perform a new function.

Key to the analysis of the evolution of the Krebs Cycle was Melendez' derivation of a set of rules for metabolic evolution, as follows:

1. Any enzymatic reaction is also chemically possible without the enzyme, although it would occur much more slowly and without a well-defined specificity.

2. All the intermediates of a chain of reactions to be used ultimately in a metabolic sequence must be stable towards rapid decomposition. The strongest reason for this assumption is evolutionary; at the beginning of the pathway design every rudimentary enzymatic reaction occurs very slowly, so unstable intermediates could not have been used.

3. Any material to be used by the new pathway has to exist in another metabolic process which was previously built for a different purpose. Design of this new pathway must involve continuity in the function of the previous one whose material has been used. A successive backward-in-time application of this rule would lead eventually to the origin of metabolism; on the primordial Earth the first available compounds had to be made through spontaneous chemical processes.

4. The new pathway cannot involve a reaction with any thermodynamic or kinetic incompatibility with a previous one that has to operate simultaneously in the same space.

A computer program called Chaos was used to generate candidate solutions to the problem of producing ATP from the condensation of acetyl with a feeder. Then the feasibility of each possible candidate was analysed. For instance a possible pathway with phosphomalate as a feeder was discarded (or rather set to one side in the absence of evidence that the feeder was available) by rule 3. Other pathways have chemical limitations covered by other rules. The Krebs cycle has no such limitations.

"In the evolution of the metabolism, the achievement of the fundamental steps of the Krebs cycle was not difficult at all. Almost all of its structure previously existed for very different purposes (anabolic), and cells had to add just one enzyme (succinyl-CoA synthetase for the transformation of succynol CoA into succinate) to convert a collection of different pathways into the central cyclic pathway of the metabolism. This is one of the most clear cases of opportunism we can find in evolution."

Of the phosphomalate pathway, which they had eliminated, they write: "...it could be argued, however, that [the feeder P-malate] could have played some role in earlier metabolism; and thus it could have been available. It is, in fact, highly unlikely that some ancient metabolic pathway involving such a compound has vanished without trace (although the original pathway has been lost, such an intermediate could have been kept to other purposes); however, it cannot be strictly discarded and thus, although unlikely, phosphomalate and the [alternative] Krebs cycle structure...might be found in some paleospecies as a case of paleometabolism."

Melendez et al conclude: "The Krebs cycle has been frequently quoted as a key problem in the evolution of living cells, hard to explain by Darwin's natural selection: How could natural selection explain the building of a complicated structure in toto, when the intermediate stages have no obvious fitness functionality? This looks, in principle, similar to the eye problem, as in 'What is the use of half an eye?' (see Dawkins 1986, 1994). However, our analysis demonstrates that this case is quite different. The eye evolved because the intermediary stages were also functional as eyes, and, thus the same target of fitness was operating during the complete evolution. In the Krebs cycle problem the intermediary stages were also useful, but for different purposes, and, therefore, its complete design was a very clear case of opportunism. The building of the eye was really a creative process in order to make a new thing specifically, but the Krebs cycle was built through the process that Jacob (1977) called 'evolution by molecular tinkering,' stating that evolution does not produce novelties from scratch: It works on what already exists. The most novel result of our analysis is seeing how, with minimal new material, evolution created the most important pathway of metabolism, achieving the best chemically possible design. In this case, a chemical engineer who was looking for the best design of the process could not have found a better design than the cycle which works in living cells."

The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution

Article 3

In a recent posting on this newsgroup I presented Melendez (1996) on the Krebs Cycle as an example of opportunism at work in the evolution of complex systems.

The significance of the paper is that it shows that, when the conditions are right, complex highly tuned systems can evolve by "molecular tinkering" rather than inching over a fitness landscape through step-by-step natural selection. The individual pathways of the cycle do have a fitness function--they are mostly used for amino acid synthesis--but they play no part in aerobic respiration until they are assembled in the basic form of the whole cycle.

So what is the minimum ruleset necessary for the evolution of a complex, highly tuned system? I'll put forth some ideas in the hope that someone can take them up.

1) the system must be capable of being assembled with a minimum of new parts from precursor systems

2) the assemblage must not result in a loss of function of the precursor systems

3) the precursor systems must be brought into close contact, and any change in their existing linkages must be accountable as an enhancement of their fitness at some level

4) loss-of-function mutations (cf: arch supports for a bridge) are permissible as long as the resulting construction has a fitness function

Article 4

Darwin's Black Box (Touchstone, New York, 1996) by Michael Behe, ISBN 0-684-83493-6 (Pbk).

What type of biological system could not be formed by "numerous successive, slight modifications?"

Well, for starters, a system that is irreducibly complex. By irreducibly complex, I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional.

Behe uses this concept as a plank in his argument for conscious design in nature.

(1) Behe states that an irreducibly complex system cannot be created by "numerous successive, slight modifications".

(2) Behe then tries to hedge his statement by playing with the definition of the word functional (functional as what? evolution is rife with examples of systems developed for one purpose and coopted for another).

(3) Behe's statement is incorrect. The Krebs Cycle (*) is a system that developed largely by opportunism, without a hint of design--Behe may technically be correct that it didn't evolve by small enough steps, but it's a rather thin complaint since the steps were evidently small enough to form biochemical systems. The essential parts were already available in the cell, and were simply coopted for the purposes of aerobic respiration. But it fits Behe's definition of an irreducibly complex system, though he may wish to deny it. It's "a single system compose of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning", using Behe's own definition of the term "functioning".

(*) See Melendez (1996) for a detailed description of the role of opportunism in the evolution of the Krebs Cycle.

The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution

I would like the following to be considered as a highly speculative addendum: It may well be that as we examine more biochemical systems, as we learn more about how the machinery of nature works, more expectations will be confounded. We already know that physics starts to work differently on the scale of the molecule. It is possible that the stepwise nature of natural selection may also be more granular at that level.

Behe, the Krebs Cycle, and Models of Origins of Complex Biochemical Structures

Post of the Month: December 1999

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