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Author
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Topic: Replication & Metabolism: What Is It We Are Trying to Explain?
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James A. Barham
Member
Member # 50
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posted 24. June 2002 11:43
I think one of the reasons why the discussion here at Brainstorms is sometimes difficult is that Darwinians and their opponents are operating with some very different fundamental assumptions about what it is we are trying to explain. Therefore, I would like to open a thread devoted to discussing these assumptions.
The Darwinian, I think, views replication as the essence of life, and all the rest as details. As long as the basic requirements for natural selection---good but not perfect replication and competition for limited resources---are met, then not much else matters. Whatever is found to exist that is consistent with these assumptions will naturally be able to be explained within this framework. The replicator (the gene) is the focus of attention, and everything else is just window dressing (the "vehicle"). We may call this the replication-centered view of life.
For the opponent of this way of thinking, what is central is the fantastic complexity and functional organization of life. This is what we are trying to understand, and we just don't buy the idea that natural selection is a sufficient explanation of it. Some of us believe this primarily because of information-theoretic and probabilistic considerations, and others because we feel that the logical structure of selection theory begs the very question at issue---how to rationalize the teleological organization of life. On this view, the gene is just one element among myriads that cooperate together to produce life. This may be called the metabolism-centered view of life.
What is the best way to proceed with a discussion of these two views? I think the origin of life literature is very instructive for this purpose. The case for the metabolism-centered view of life can be made in two steps, one negative, one positive.
On the negative side, Robert Shapiro has been arguing for years that the replication-first approach to the origin of life makes no sense from a physical-chemical perspective (see, e.g., "A Replicator Was Not Involved in the Origin of Life," IUBMB Life, 2000, 49: 173--176). The basic argument is very simple. One cannot expect to derive macromolecules (proteins, and even less so nucleic acids) that are currently produced using templates all at one go out of the "prebiotic soup." So, the RNA world, while it may be a way-station on the road to the full-fledged system as we know it now, is not the solution to the problem all by itself. (Many other people have made the same point---for a good introduction to the immense literature on the origin of life, see N. Lahav, Biogenesis, Oxford UP, 1999).
So, what is the positive argument? A number of authors have tried to show how self-sustaining autocatalytic networks might arise out of plausible prebiotic environments. One of the best discussions I have encountered is D. Segre and D. Lancet, "A Statistical Chemical Approach to the Origin of Life," Chemtracts---Biochemistry and Molecular Biology, 1999, 12: 382--397. To be sure, they make certain minimal assumptions that may still be disputed (they assume lipid membranes and specific monomer compositions), and their model is still too abstract to be easily tested in the laboratory. But they do seem to show that Dyson's, Kauffman's, Morowitz's, Bagley's, and other models all contain certain generic formal features that would lead one to believe that a self-organizing metabolic network could in fact exist. From my point of view, the most interesting feature of their work is that they show that replication derives directly from metabolism---or, as they say, "homeostasis." Here is a short quote from their paper cited above:
"An important principle incorporated in GARD [Graded Autocatalytic Replication Domain model] is the equivalence of homeostasis and replication. Simply formulated, if an enclosed, externally fed catalytic set undergoes expansion, and if its catalytic network is effective, then its idiosyncratic internal composition will tend to be homeostatically preserved, despite the continuous growth in volume. If the compartment subsequently undergoes splitting due to physical forces, the 'progeny' may constitute compositional similes of the original, and replication may ensue, subject to the Morowitz boundary conditions." (p. 391)
Now, Segre and Lancet may or may not be right in the details of their model. I cannot pronounce judgment on that. (If their approach is completely adequate to explain the origin of life, then I am wrong about the need for quantum coherence---on that point, time will tell.) But it does seem to me that their and Shapiro's arguments are much more persuasive than those of the replication-first school.
At any rate, what I do wish to claim is that IF metabolism-first is correct, in general terms, then evolution is explained by the underlying dynamics of life, and "natural selection" is just a short-hand description for that dynamics, not the other way around. Thus, the current emphasis on selection theory is acting as an intellectual blinder that is preventing us from seeing the real nature of the challenge facing us in understanding life.
[ 24 June 2002, 11:48: Message edited by: James A. Barham ]
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Leonid Andreev
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Member # 282
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posted 24. June 2002 21:48
It looks as if the Brainstorms members have teamed up to find the solution for the grand challenge of all the times – finding the answer to the question of what Life is. In the meantime, brainstorming of this problem can only be meaningful if there is a clear and common scientific platform, otherwise a discussion ceases to be scientific and turns into an art/literary activity. Although art needs an order, too much order in art is poor art. If there are any areas that cannot survive without good order and consistency, the problem of where the ray of life is coming from is one of them. When you are looking for the source of light, you do not scrutinize the objects in the light spot.
A hypothesis of emergence of life can only be treated seriously if it puts forth some key mechanism (or mechanisms?) that might have caused such a transformation of micelle of the primary broth that made them evolve to contributors of the Brainstorms forum. One cannot turn a unicellular organism into a multi-cellular one by means of smoothly worded scientific passages. “Self-organizing metabolic network” is a coinage that cannot become a discovery instrument and is as barren as the concept of creation of the world within one week..
Division into Darwinists and non-Darwinists is not correct. Old man Darwin has proffered a very sound idea. It does not have to provide a detailed explanation at a quantitative level for phylogenesis of living organisms, and demanding such an explanation from Darwin would be an insult to his legacy. After all, in his time, computer simulation was not yet available. It would be more appropriate to classify evolutionists into normal and cranky Darwinists. The latter of the two lead the good idea ad absurdum.
Assume that you are growing a bacterial strain that carries an antibiotic-resistant plasmid in a growth medium that does not contain the antibiotic. By decreasing the concentration of growth substrate you can cause the plasmid to abort, i.e. to stop replicating along with the cell replication. It is the starving population’s economy: better one small fish than an empty Petri dish. Now assume that in the same experiment the growth medium contains the antibiotic the resistance to which determines the said factor of extrachromosomal heredity. The bacterial population behavior will be much more complex in this case, and you may end up finding a new property in the bacteria under study: they will modify their genetic material (circular DNA) by throwing away all what is “excessive”. I can’t help being curious as to how one would go about separating metabolism from replication in this case: apples to apples, oranges to oranges?
[ 26 June 2002, 01:31: Message edited by: Leonid Andreev ]
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James A. Barham
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Member # 50
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posted 25. June 2002 19:41
Leonid:
I am sorry, but I don't quite grasp your example.
In the first example, there is starvation with no antibiotic and the plasmid is jettisoned because it is not needed. Is that right?
In the second case, there is also starvation (?), but this time in the presence of antibiotic, and the plasmid is what --- it sounds like you are saying it is also rejected?? I would assume it would be retained in the second case, or that what would happen would be determined by a competition between the starvation and the action of the antibiotic.
But in both cases, it is the tendency of the cells to react to circumstances in a goal-directed or functional way that explains what is going on, isn't it?
I realize that the standard Darwinian answer is that variations simply arise "by chance." That is in itself a complex issue, but let that pass. Let's say that's so. Some bacteria by chance lose the plasmid in the first scenario and so thrive (under those circumstances) at the expense of the others.
My point is that it is still the functional superiority of the plasmid-less types that is doing all the explanatory work here. It is always superior functioning that explains differential reproduction, not the other way around.
Even if mutations really were always truly random (which seems increasingly less likely), it is still the case that the new mutation must be integrated into a fully functional form before it can have any evolutionary impact (since otherwise it will be a non-viable teratology). So, the theory is simply assuming the functional integrity of the new form, no matter what the source of the mutation may have been.
In short, it is the fact that the bacteria are striving to maximize their efficiency that explains how they evolve. So, the theory of natural selection cannot pretend to explain why organisms strive to maximize their efficiency.
This is not just a problem that we encounter at the origin of life. It is a fundamental problem with the foundation of selection theory. The theory simply does not explain the source of the functional integrity of life.
Now, there are many scientific contexts in which that would not matter. But from my point of view, that is the main thing that needs explaining.
BTW: I like your distinction between cranky and non-cranky Darwinians a lot! (I guess you could make a parallel distinction between cranky and non-cranky self-organization theorists . . .)
[ 25 June 2002, 19:42: Message edited by: James A. Barham ]
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Frances
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Member # 169
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posted 26. June 2002 01:28
James wrote:
quote:
In short, it is the fact that the bacteria are striving to maximize their efficiency that explains how they evolve. So, the theory of natural selection cannot pretend to explain why organisms strive to maximize their efficiency.
I am not sure why it would even have to explain this, after all who is arguing that organisms 'strive' to maximize their efficiency? Before we continue on the road of teleology in nature we need to first establish how Darwin explained evolution. He used variation and natural selection, and although it is often poorly represented as "survival of the fittest" over time it's story seems to have varied.
I have posted Endler's description of a non-tautological formulation of natural selection. Or as Endler states "natural selection is a process resulting from the interaction between viable organisms and environment and not a mysterious "force" that "acts""
Natural selection cannot "generate" genetic changes within populations, there is no striving to maximize efficiency per se.
James continues
quote:
Even if mutations really were always truly random (which seems increasingly less likely), it is still the case that the new mutation must be integrated into a fully functional form before it can have any evolutionary impact (since otherwise it will be a non-viable teratology). So, the theory is simply assuming the functional integrity of the new form, no matter what the source of the mutation may have been.
I do not believe that the theory assumes functional integrity of the new form, in fact as genetics have shown us most point mutations tend to be neutral and few deliterious and few beneficial. But with the recent research it has become obvious that gene duplication may have played a big role. Not to mention Kaufmann's ideas. I am not sure if selection does not explain the functional integrity of life. In fact, IF life arose through RM&NS then it can explain the continuation of the integrity. Perhaps for the origin of the functional integrity, the origin of life, we need to include additional theories such as self organization. Fox protocells seem to provide some insight in what early 'life' may have looked like.
Let me ask you a question, is there any theory that can explain the functional integrity of life?
Also, is the emphasis on selection theory acting as a blinder? Perhaps, but given the interest in the many additional mechanisms that may have played a role in evolution, I would not say that it is preventing progress.
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James A. Barham
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Member # 50
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posted 27. June 2002 10:21
Frances:
The point about "maximizing efficiency" was simply that in Leonid's example, the new form without the plasmid was more efficient in a functional sense than the other forms, and that differential functional efficiency (or success, if you prefer) is the explanation for the subsequent differential reproduction, not the other way around.
That is one point. There is a separate point about how life finds new and better functional regimes, namely, whether variations arise purely by "chance," or whether they are "directed" in some sense. This is a difficult and highly contentious subject, and from what I have read it does not seem possible yet to say for sure one way or the other, but there does seem to be more and more evidence that genetic variability itself is under metabolic control, at least in prokaryotes (see the collection by Lynn H. Caporale and the work of Richard von Sternberg, for example).
Maybe "maximizing" efficiency was not the best choice of words. All I really meant was that the bacterium is actively striving to survive and this active striving must ultimately be explained if we are to have a deeper understanding of how transformation occurs. When a better form comes along, it is seized upon. If it is good enough, it proliferates. It is the "good" and the "better" that are doing all the explanatory work, here, and these normative concepts have not yet been integrated into the rest of science. The claim that natural selection does so is simply a mistake (so I say). But probably the process can be better described as "satisficing" than as "maximizing", since all adaptations are always to local extrema. But that is a secondary issue compared to the primary issue, which is the status of teleology itself in all of this.
I agree with you that we have no theory of the functional integrity, teleological (which just means "goal-directed," remember) striving, and intelligent agency (the ability to coordinate means with ends) that all living things exhibit. But that does not mean that we will not figure it out. The end of science is not yet at hand, despite rumors to the contrary.
I also agree that new ideas are coming along, but it is in spite of, not thanks to, the Darwinian mindset. Indeed, it is often in the teeth of their opposition. But now we are drifting off into taboo sociological considerations again, so I had better hold my tongue.
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Leonid Andreev
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Member # 282
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posted 01. July 2002 16:07
James:
This in reply to your June 25 posting. First, a brief comment on your comment:
You wrote, "BTW: I like your distinction between cranky and non-cranky Darwinians a lot! (I guess you could make a parallel distinction between cranky and non-cranky self-organization theorists . . .)"
I would not care if a self-organization theorist is cranky or not. Self-organization of life on Earth cannot be partial or conditional anymore than a pregnancy can partial or conditional. That is to say that a self-organization theorist is either a self-organization theorist or something else. As for cranky Darwinians, they are only good in technical writing – they compose manuals to the software designed and developed by Life and seem to forget that the software functionality does not depend on eloquence of a technical writer.
Speaking about bacterial growth in a starvation medium with antibiotic, I certainly did not imply that bacteria “knowingly” reduce a plasmid copy number and rid the plasmids of anything that is excessive, still keeping them able to neutralize the damaging effect of antibiotics. It all happens simply because any biosynthesis process always yields some products that display abnormality, and under extreme conditions, only those clones survive that incidentally appeared to be in a position to “spare efforts” due to a plasmid modification.
The question of relationship between replication and metabolism is indeed crucial in understanding of why eukaryotic cells happened to emerge. A nuclear membrane, hence endoplasmic reticulum was the solution for the problem of restricting the influence of metabolism (thus, the effect of environmental changes) on genome replication. However, as life rarely offers a free ride, the innovation resulted in some new complexities, which the evolution has eventually turned into advantages. The relative simplicity of gene expression which is inherent in prokaryotes with their circular DNA was lost for eukaryotes. In eukaryotes, expression of some genes is strictly bound with activation of certain non-specific (energetic, metabolic, and other) functions specifically set for supporting those particular genes. Setting up such “individual gene support groups” involves a major part of the genome, which explains a large percentage of repetitive DNA and the existence of so-called silent genes.
[ 01 July 2002, 18:29: Message edited by: Leonid Andreev ]
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