Wowbagger Responds to John Hewitt's Prebiotic Evolution Paper – PART B
Continuing my commentary from my last post in this thread:
Part 7: http://www.sexandphilosophy.co.uk/pe07_theories_of_prebiosis.htm
Whew boy! Lots to say here! He starts off very nicely, describing the sorts of criteria one ought to use for judging theories of prebiosis (although they are good for other lines of science, as well.) But, then things break down a bit, when he begins to criticize the competition.
In principle, irreducible complexity could provide a criterion to distinguish evolution from design but, although Darwin devised this test, he identified no clear way to determine whether any particular structure is, or is not, irreducibly complex. As a result, one cannot say, beyond all possible doubt whether any one structure is, or is not, evidence of intelligent design and these debates tend to be moot.
Well, how about studying each example of "irreducible complexity", until you find a plausible way for it to have evolved?! ID is nothing more than personal incredulity.
In fairness, I should say that, overall, Mr. Hewitt does seem to understand that ID is not a scientifically testable or useable in any way. So, his brain is in the right place. He just gives ID too much credit as a "debate-worthy" idea.
For Silicate Surfaces and "RNA World" theories:
The theory offers no a priori basis for defining the fitness of a defect structure. Rather, fitness is defined, a posteriori, as that structure that will catalyze the formation of a self-replicating RNA molecule.
I believe this because this was a theory born out of experimental results. Controlled experiments show hints that such a thing could happen. Whether this is likely to occur in an uncontrolled environment would be the real question.
Offers no indication of how high energy precursors for RNA synthesis might be produced and selected from the primordial soup or the nature of the energy source that produces these precursors.
Does not indicate why other molecules from the soup do not adsorb onto the bare catalytic surface of this defect structure and poison its catalytic activity.
These are things that are not impossible. They merely have yet to be worked out completely, and may have already been worked out, to some partial degree.
(Although, most of the "working out" has been done in computer simulations, as far as I can tell. So, who knows if reality is like that?)
Fails in one of its main claims of explaining how the reagents might be kept together, why the small molecular weight components in the prebiotic mixture do not simply diffuse apart. If surface binding were really so tight as to prevent this diffusion then, by the same token, it is likely that lateral diffusion would also slow down and slow the reaction.
"Fails" is a strong word. Plausible explanations have been thought out. Though, no one is sure which one is the right one. From your wording, it makes it sound as if no one has any idea how these things could possibly work!
Finally, since the products of RNA synthesis are postulated to be large molecules, they should be held to the surface by multiple bonds which, in their totality, would be stronger than those which hold small molecules onto the surface. Hence, it is hard to see how a large RNA molecule could ever emerge from the rocky surface, let alone become an independent replicator floating free in solution.
I don't think the theory postulates this. I think it postulates a "scaffolding" that would bring smaller bits together into large bits, but all in a process of cumulative evolution. To think that RNA molecules could emerge from a rocky surface, in one sudden get-go is no better than ID, and thankfully, that is not what the RNA-World theorists think!
It is very hard to see how the silicate component of such an organism, with the correct defect structure, would have been replicated. Moreover, if small pieces of silicate were really part of some protocellular genetic apparatus, then those small pieces might be expected to have survived fossilization and be observable in the fossil record. There is no reported evidence for them. No archaic silico-organic organism has ever been found and many species are known that do not seem to need silicon at all, even as a trace element. (Though humans may require silicon in that role.)
Some of this is valid criticism. There is no observable evidence in the fossil record, and no "silico-organic organisms" exist, today. All we have are some hints found in some controlled experiments.
Finally, one notes that many of the above arguments can be applied not just to RNA but to the formation of any large biopolymer at a silicate surface. Hence, this author finds it hard to justify the silicate surface theory. It is undeniable arguable that any reactions catalyzed at such surfaces would have been factors in producing the primordial soup but it seems unlikely that early cells were made there.
Maybe they moved. You have early-part-silicon-RNA-ancestors falling off, into puddles of other stuff, or something, where some of them developed membranes around themselves. And the ones that could form membranes were selected for survival.
... interprets its own data content but one should note that proteins also do this.
Ah, but the difference is that RNA happened to take on a higher role in becoming the inheritable target of selection pressures.
First, RNA is chemically labile and, unless protected by a protein coat, it breaks down much more easily than does either DNA or protein. It is hard to see how an RNA world would have survived the depredations of random chemical events and yet been stable enough for the process of evolution to be maintained.
So, here is another opportunity for examining ways to combine various theories. Perhaps the experimental data that supports both RNA-World and Prebiotic-Oscillations could both happen in an uncontrolled environment, and sometimes occurred together, in some form or order. Early RNA that did not form membranes did have these problems, and were not selected for survival. Perhaps the enzymes that catalyzed or otherwise induced the formation of lipid membranes are, themselves, that early form of RNA.
Second, at the heart of the RNA world theory, there is a special entity, an extraordinary RNA molecule or replicator ribozyme complex that is stable enough to survive in a hostile environment, able to catalyze its own replication and able to catalytically copy other RNA molecules. This special RNA molecule cannot have emerged by selective adaptation but still needs to have some remarkable properties. The whole theory hinges on the idea that this specially "fit" RNA will emerge by chance synthesis, possibly on a silicate template. It must be synthesized de novo and immediately possess all the catalytic activities needed to copy both itself and other RNA molecules. Subsequently, it must have lost this capacity because, even under laboratory conditions, no current RNA molecule is able to do these things.
This
would be a valid criticism,
if scientists actually believed this! If, they did, the whole RNA-world would be no better than ID. Thankfully, they speculate otherwise! They would say that
many variations arose, at various times, in various different cumulative ways. The "winner" happened to be the one to copy most effectively, and also offer a good opportunity for variation, at the same time.
Remember: Variation opportunity has to be "balanced" to a certain degree: Too little, and the unit can not adapt to changing environments. Too much, and you lose copy-fidelity and other such things.
This balance
only needs to be "perfect" in comparison to the competition. It need not be optimal to any mathematical law we favor.
I would even say that RNA world provides a better opportunity for this balance to emerge, than a pure oscillation theory. So, again, maybe elements from both are needed.
Fourth, the RNA world theory does not address, let alone solve, the bounding problem...
it is very hard to see how this special RNA molecule could marshal all these small molecular weight substrates and energy sources needed for its catalytic role.
First of all, that is a lack of imagination. Second of all, it is a non-problem: Evolving systems do not necessarily need physical boundaries built around them. Evolution could begin without them. But, those that do form them, are more likely to be selected for continued survival. There is no reason to think evolving systems can not begin within a mish-mash of mixed-up chemical bits.
In fact, some experiments demonstrate how organic compounds could "spontaneously*" generate, and even begin alter themselves, in a vat of inorganic compounds.
(*I use the word "spontaneously" a little facetiously here. In reality, scientists have a solid understanding of what is going on in the flask, to cause these chemicals to form.)
The idea of a replicator is closely related to the RNA world and to the special ribozyme described in the previous section but the idea of a primordial replicator has roots in general evolutionary theorizing rather than in discussions of prebiosis. In fact, the idea of a replicator arises from a basic error in modern evolutionary theory and from the need to merge two different but closely related strands of biological science - Darwinism and genetics.
In Darwin's original conception, the theory of natural selection depends upon the ability of whole organisms to reproduce or replicate. The theory considers the degree of success, the fitness, of a whole organism in replicating or reproducing itself. Fitness is simply a measure of the ability to produce succeeding generations.
Emphasis added.
The need for a replicator arises from the basic fact that life replicates!!! What kind of silly nonsense is this, about an "error" in the need to merge to ideas?!
Perhaps you are missing a key point.
Selection (natural or otherwise) need something to select from! That something could be considered a replicator, if that something happens to replicate!!!
Genes are the driving force of replication, and also the source of inherited traits, and therefore the principal target of selection. No one came up with the idea for a replicator, after realizing Darwin's concept of organisms as the smallest reproducer was flawed, in light of genetics. That is fiction. What we realized is that genes could be thought of as a replicator, themselves, after demonstrating the necessary properties.
Genes do not self-replicate, they are copied, along with the rest of the cell or the organism as it replicates.
Yes, they do. Transposons are one example: Some genes express the necessary phenotypes to get themselves copied into multiple places at once.
For example, Dawkins' well-known work, The Selfish Gene, explicitly sets out to reduce all evolutionary theorizing to its fundamental unit which is, supposedly, the gene. The error in this argument is that genes are not fundamental to evolution, only to biology, and this error becomes significant whenever the evolutionary process under study does not primarily involve genetic data.
I already discussed this, a bit. But, to reiterate:
Selection pressures
are fundamental to evolution. And, it has been worked out quite conclusively, that genes are the fundamental target of selection pressures in reproducing life forms. Therefore, the gene has every right to be fundamental to biological evolution, and not necessarily other forms of evolution. Other forms of evolution have other ways selection selects from them.
Prebiosis is one of the places where these errors become manifest, with the widely known claim that all evolution must involves replicators, which is incorrect, and that genes somehow emerged from primordial replicators, which they almost certainly did not.
Maybe some systems, such as prebiotic evolution, do not need replicators: they can evolve "in place". But, once a replicator of some sort (you know, defined as something that simply replicates itself!) emerges, it is almost impossible for such systems to not evolve. In fact, the evolution becomes only more apparent over successive generations.
If you disagree that genes are replicators, you have to explain why they can copy themselves faster than their cell can copy itself? In other words, you have to explain the existence of "junk" DNA and transposons, using an idea where the gene is not actually creating more copies of itself. Good luck with that.
There is no more evidence for the notion of genes as replicators than there is for the idea that God created the heavens and the earth.
Now, this line I find particularly insulting.
Here are several good reasons why Genes-as-Replicators is a better idea than God-Created-Heaven-And Earth:
1. Genes demonstrate the 3 important properties all replicators must show well: Longevity, Fecundity, and Copy-Fidelity.
2. Transposons. You may think the cell is making them. But, look again: it is the genes directing what is going on.
3. Other forms of "junk" DNA seems to copy faster, inside a cell, than the cell itself.
4. You are the replication of your parents: Your genes replicated from your parents' genes.
5. It is easier to see how genes can be selected for forming cells, than it is for dividable cell membranes to evolve genes. (Although, this is debatable, I guess.)
6. Cells will not induce their own replication after its DNA is removed. However, if you remove almost anything else from a cell, it can still induce its own replication (with varying degrees of success).
7. Mitochondria: They can reproduce independently inside a cell. And, guess what: They have their own DNA to that with! (This DNA may be vestigial: left over from when the mitochondria was, itself, an independent life form. It may have stayed in the cell, as an act of mutually beneficial symbiosis.)
8. At least we know genes exist. We can not test for the existence of God.
So, it is possible for in-place transformations to be considered evolution. But, generally speaking, in Biological Evolution,
something needs to replicate (produce offspring). Whether that replicator is a gene, a cell, or whatever, is debatable. But, to say that the idea of a replicator is flawed, is nuts!! And, it demonstrates your misunderstanding of basic biological concepts. Saying replicators are not necessary for evolution, is like saying you can do math without numbers. Replicators are favored by selection, because they open opportunities for variation and fecundity. If a life form does not replicate, it stagnates, and may not survive changes in the environment.
By the way, even if genes were not the original replicators, even if membranes came first, and somehow generated genes, then that would only invalidate the "origins" portion of Selfish Gene theory, not the whole thing. Once genes arrived on the scene, they became the fundamental unit of selection, and they do seem quite "selfish", today.
So, this whole section is really just a change in location. Not a new theory. So, there is nothing more to say, here.
For example, Copley, Smith and Morowitz (2005) have argued that the early code was based on a two base pair codon, basing their arguments on the pattern of amino acid biosynthesis. This whole discussion is a major topic that cannot be pursued within the bounds of this study.
Actually, other numbers of base pairs, from 2 to many numbers higher, may have emerged. But, four was selected as "optimal" at some very early stage. And, now we seem to be stuck with it.
The arguments for DNA arising before RNA are, first, DNA is chemically more stable than RNA, which would give it survival value in the prebiotic soup, second, DNA makes use of only four bases whereas RNA adds several minor bases and, third, under unusual conditions, single stranded DNA can serve as a template for protein synthesis, giving it potential to both self-copy and to direct protein synthesis.
Weak arguments. The fact that DNA is more stable means it is less likely to emerge from uncontrolled chemistry, first. The fact that RNA has several minor bases could also mean it is more primitive (although, this does not prove the point). And, finally, who says early RNA could not also direct protein synthesis, in a similar manner than DNA?
The next stage in the development of this discussion would be to address the origin of the genetic code that converts the data of nucleic acid sequence to that of protein sequence. Such a study would be of value but this would be a large undertaking and it seems most natural to stop this discussion here.
I recommend you develop some ways to go about producing these studies. If you want your theory to compete with the ones all ready well-developed, you are going to need all the details you can get!
Continued in my next post:
