Peanut Gallery for the debate between mindspawn and RAZD

As is normal for these Great Debates, I thought I would start a peanut gallery for general commentary on the points made in the debate between mindspawn and RAZD which can be found here:EvC Forum: Evolution Theory Issue - Great Debate -mindspawn and RAZD only

Thread copied here from the Peanut Gallery for the debate between mindspawn and RAZD thread in the Proposed New Topics forum.

Same old discredited argument. Only direct evidence counts. No inferences allowed. Of course we can cite the citrate eating modifications to E. Coli, but having done so, expect the goal posts to move again.Probably should anticipate a bogus 2nd law of thermodynamics complexity based argument. Ignoring the fact that evolution does explain exactly that. Perhaps this statement should be rephrased to indicate that mindspawn does not accept the explanation.Edited by NoNukes, : No reason given.

RAZD in message 10 writes:

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Complexity is, imho, a red herring. It is an emergent property of evolution, but is sometimes gained and sometimes lost as species evolve over time.

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I wouldn't really call it a red herring, but it comes close. The problem is two fold.First, selection is blind to complexity. Selection only sees reproductive success. If a less complex adaptation is better in a given environment then it is selected for. So we have a mechanism that is not entirely driven by complexity.Second, the complexity of the genome does not necessarily correlate with the complexity of the organism itself. One species of lowly amoeba has a genome with 670 billion bases. The puffer fish has a genome of only 400 million bases which is just 0.05% the size of the amoeba genome. Onions come in at 100 billion bases, if memory serves. Would anyone claim that the puffer fish has just 0.05% of the complexity found in an amoeba?Obviously, increasing complexity in animals has to come from somewhere other than adding new genes to already existing genes. Changing the interaction between existing genes could be the ticket.

Taq points out: In fact, according to the current Theory of Evolution, we would expect to see such things like the amoeba versus the puffer, according to the simple law of random mutations. Complexity is completely free to exist without any utility at all, unless the extra complexity is a disutility in the environment. Then it goes bye-bye. This is another feather in the cap of the current theory. These ID people will have a lot of explaining to do if they want to deal with this.

Complexity in itself is not what would amount to a challenge to Darwinian evolution. The problem comes in when we find complex traits that could not have been arrived at by a stepwise evolutionary pathway.

mindspawn seems to be interested in evidence for the evolution of "additional novel coding genes with novel functions that add fitness to the population of an organism" in Message 7 Here's an old favourite.That example involves gene duplication, which mindspawn has mentioned, but there are other known ways in which new genes can form. Here's an interesting more recent paper in which the authors claim that "de novo" genes are formed more often than generally thought. "De novo" meaning new protein coding genes forming from non-coding DNA. De Novo Origin of Human Protein-Coding Genes.That's debatable. But anyway, there is "evidence of this process".As Wu et al. point out in the second paper I linked to, gene duplication, exon shuffling, retroposition, mobile elements, lateral gene transfer, gene fusion/fission, and de novo origination are all mechanisms known to contribute to the formation of new genes.

I'm not too sure what the argument Mindspawn puts forward is here. Maybe someone who knows something about this could explain. I don't understand this. Nothing says that for new functions to evolve in populations, they have to come from new, additional novel genes. Some of the examples shown in the debate already indicate this. Number of genes don't indicate 'new functions'. I mean, doesn't evolution 'build' on existing phenonema? So, I don't really understand why mindspawn hammers on this. Maybe someone can illuminate why he does it? Again the word 'complexity'. Maybe he should actually explain what he means by complexity.Number of chromosomes? Then a Chimp is 'more complex' than a human.
Number of base pairs? Then some unicellular organisms are 'more complex' than humans.
Size of the genome? Then some rice varieties are 'more complex' than humans.It all indicates that additional, new, novel genes don't necessarily relates to 'complexity'. This indicates that it's what the genes do that count.(I'me here to learn, not to criticise).Edited by Pressie, : Added sentenceEdited by Pressie, : No reason given.

I see that mindspawn is trying to change the subject of the debate by, for example, presenting a false dichotomy: What about the overwhelming numbers of religious specialists on the subject of the theory of evolution who believe that their respective God or Gods created every living organism through (the theory of) evolution?Or those very small number of specialists on the subject who think that it was placed on earth by organisms from another planet?The possibilities are endless. Can't he just stick to the subject and the evidence?

Yes. What he's trying to say is that the earliest organisms to form would not have had the large numbers of functional genes that we see in modern organisms, which is a perfectly reasonable assumption that we can all agree on. Therefore, if naturalistic evolution is the story of the origin of modern species, there must be a mutational process or processes by which additional genes (not just variant alleles) with new functions arrive over time. So far, he's entirely right. He then wants to see the evidence for such a process or processes (one wonders if we'll ever be offered the equivalent observation based level of detail for alternative hypotheses on the building of complex organisms; "the angels took one molecule, then......").So, let's look at what he's saying now in relation to gene duplication, which is considered the best known source of such new additional genes (I gave an example of this in the Douc Langur monkey in my post above). That's not how neo-functional paralogs and ohnologs are identified. Mindspawn's description fits non-functional paralogs or ohnologs that are in the process of being removed from the population by negative selection or drift, which will be the fate of most. In the rarer cases when useful neofunctionalization and subfunctionalization (the things mindspawn professes interest in, whether he knows it or not!) have taken place, we are more likely to find the new genes at fixation across the population, and they are identified by the similarity of the pairs and other factors, not by whether or not all the population have them.For mindspawn and anyone else interested in the evidence for neofunctionalization and subfunctionalization of duplicates, there's an obvious route to go! neofunctionalization in paralogssubfunctionalization in paralogsneofunctionalization in ohnologssubfunctionalization in ohnologsPlenty to read on the subject, but as it's very much an area of current research, I'd recommend sticking mainly to papers from this century, especially those of the last few years. I find some of the stuff on "ohnologs" (pairs that are products of whole genome duplications) particularly interesting, especially concerning the two duplications that are thought to have taken place early in vertebrate evolution.So, get reading, mindspawn! It's fascinating stuff. And BTW, are you a pawn of minds, or the spawn of just one?

Thank you bluegenes.Such a lot to learn. I still have to find out what paralogs and ohnologs are! (I wonder whether mindspawn does?). Not to even mention neofunctionalization and subfunctionalization. Complete Greek to me.I do realise that it would take me lots and lots of years to understand it.Thank you (whether I would understand what those mean is a different story). OMG, I wish I took the basics on genetics when I went to Uni!Edited by Pressie, : No reason given.Edited by Pressie, : Added a sentence

Sorry, bluegenes, can you make it easier for me ( a complete novice). Isn't all DNA (and RNA) just made up of variants of ACGT put down in different combinations, lenghts of chains and combinations, etc?

Sorry, I meant to say what they are. Paralogs (or paralogues on this side of the pond) are pairs of genes formed by the duplication of single genes or small sections of the genome, and ohnologs are the same thing, but formed by whole genome duplications (every gene would have a partner immediately after these events, before deletion of useless stuff set in). Ohnologs is a bit of a joke name, as Ohno was the biologist who first came up with a duplication theory. His was fairly simple, and things have moved on since then, but it was a good idea, and proved to be partially correct.It's pretty sure now that there were two Whole Genome Duplication events that went to fixation early in the evolution of vertebrates, and it appears that nearly a third of human genes may be result of these "WGD"s.This is over simplification, but neofunctionalization is when one of the pair mutates to perform a new function while the other continues to perform the old function, and subfunctionalization is when both mutate in a way that neither perform the entire original function, but each performs different parts of it, so both are required for the function. It's one of the ways that you can get "irreducibly complex" systems. It looks (to creationists) as if the function couldn't evolve step by step, because both genes are, in the present, essential for the function.

So far as I know, yes, except that RNA uses uracil instead of thymine, so it's ACGU rather than T.

bluegenes writes: Oh no! Here and I thought Yoko had something to do with it....