Peanut Gallery for the debate between mindspawn and RAZD

Genomicus writes: Do you have an example? My eyes are itchy and I need to focus better, but I am at a loss here. Examples must exist? Thanks in advance....

bluegenesBack to work on the basics for me before I can even start formulating relevant questions on these references. I know nothing about the subject.Anyway, your references inspired me to enroll in a basic course on genetics at my local University. I did some enquiries and it seems as if they do have a basic course starting next semester (July where I live).Thank you for those references, they made me realize again that I don't know anything about the subject; but expect some (hopefully) sensible questions from me in about a year's time. I know I do need much more than a year to get me up to scratch on the basics, though!Edited by Pressie, : Added the name of Bluegenes as I replied to the wrong message. Duh!Edited by Pressie, : No reason given.Edited by Pressie, : Spelling again.

The bulk of the arguments from mindspawn: Now intricacy is used instead of ‘complexity’. About as useful for the purposes of this threadnothing at all.Just arguments from incredubility and vagueness. Nothing to learn from mindspawn; lots to learn from RAZD. That’s about it.

Certainly not this evolutionist. It's stating the obvious. What you don't seem to know is that it's well established that new protein coding genes can be created by mutations. What the current research literature is about is not whether or not this happens, but the fine details of exactly how it happens, and the relative frequency of the various different ways in which it happens.Your equivalent would be if you had already established by observation that supernatural beings make things, including genes, and you were making observations about the details of the actual process of how they do it, step by step. But you haven't got to the first stage yet. Do you expect to get there soon? Edited by bluegenes, : No reason given.

Thank you RAZD and bluegenes for providing such a wonderful free education. That course on basic genetics at Uni is going to cost me a fortuneAnyway, from message 22 by mindspawn: Mindspawn is setting up a straw man here. That certainly is not what RAZD even implied. Nope.It is possible that life, as we know it, started off with long or short DNA chains (correct word?), or even without any DNA. There's no way to be sure (yet).An occurrence of isotopically light graphite microparticles within graded beds in the Isua supracrustal belt of southwestern Greenland (3.7 to 3.8 billion years old) may provide evidence of the earliest life? on Earth.Although there are examples of these splitting (budding in the way that yeast do), it is not clear whether they were living cells or nonliving microspheres.The oldest unchallenged fossils of prokaryotes found so far are around 3.5 billion years old, in Western Australia.So, yes, it is possible that DNA became highly ‘involved’ before life, as we know it, evolved.Department of Geosciences | Baylor UniversityRead some of the references provided there as well, especially
Lepland, A., van Zuilen, M.A., Arrhenius, G., Whitehouse, M.J., and Fedo, C.M., 2005, Questioning the evidence for Earth's earliest life -- Akilia revisited: Geology, v. 33, p. 77-79.Rosing, M.T., 1999, 13C-depleted carbon microparticles in ?3700-Ma sea-floor sedimentary rocks from West Greenland: Science, v. 283, p. 674-676.

The problem with this argument is that it is based on a universal negative which is very difficult to demonstrate. It usually boils down to an argument from ignorance/incredulity. For example, can anyone show us a bacteria a generation before and a generation after the flagellum appeared, and show how that transition could not have been produced by evolution?

Posting evidence that storms can blow down trees does not demonstrate that all storms blow down trees.The overwhelming majority of all mutations are near neutral or detrimental, including duplications. They happen in individuals, and the clear detrimentals will not go to fixation in a population group. Paralogs that have gone to fixation are easily found, and these are necessarily near neutral or advantageous. Highly conserved paralogs with different functions can easily be found, and that means that both functions are important to the organism.When a pair of paralogs retain the function of the ancestral gene and either enhance it or add a new function to the phenotype in a way that aids the organism in survival, that would "improve fitness". I gave a specific example in a post above, which involves an added new function with a clear advantage for the Douc Langur monkey. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf eating monkey.In addition to established examples like that, biologists can tell that a paralog is performing a significant fitness function for the organism without even finding out what it does to the phenotype. If you don't know how, the clue's in the italicized sentence up above.Enjoy the paper, and do tell us all what you disagree with in it, if anything.

So we can only conclude that the single celled ameoba is orders of magnitude more complex than humans given the difference in the size of our genomes. That seems problematic for mindspawn's argument. The original position was that none of the duplication events were beneficial. Citing cases of deleterious gene duplications does not support this claim at all. This is like citing deaths from penicillin caused anaphylactic shock as evidence that no one is made healthier by taking penicillin. Mindspawn needs to show why gene duplications can never result in beneficial traits in principle. From what I have read, nowhere has mindspawn shown a mechanism that would prevent gene duplications from being beneficial.One interesting article I found used random DNA recombination between two highly homologous genes and a selection process to find novel enzyme functions, and that is exactly what they found.

quote:

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The shuffled library contained enzymes with up to 150-fold greater transformation rates than either parent. It also contained enzymes that hydrolyzed five of eight triazines that were not substrates for either starting enzyme.
http://www.sciencedirect.com/...rticle/pii/S1074552101000618

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If DNA recombination does occur, it is most likely to occur between homologs that share a lot of sequence, and that is exactly what happened in this case. It demonstrates that novel function can and does evolve.Edited by Taq, : No reason given.

Really? Is it? (whatever he means with ‘gaining new novel coding genes’. He certainly hasn’t even tried to define what he means by it, yet). Really? Is it? (whatever he means with ‘gaining new novel coding genes’. He certainly hasn’t even tried to define what he means by it, yet).From mindspawn all we get are all these very long and vague word salads without any real substance to them.It would help if he starts defining what he means when writing those words he uses.

Sorry, I shouldn't do this, but it was to funny to ignore. Yes. Physics.

So leopards can become cheetah's without evolving, eh?This kind of argument likely includes its own demise and demolition.

Does he think the ever increasing speed of this population of lepcheetards comes from eating more wheaties? The incremental speed differences generation to generation occur because of changes in the alleles in the genome. Does he not count allele differences under "mutation" which means "change"? What mechanism changes the genome without making a change?Does he know the full scope of what "mutation" involves?

Just now jumping in with no background of either thread, but just judging from this one message.Selection works on the variation of traits within a population. If selection is tight enough so that only the most fit can survive, then the variability of those traits will diminish to near-zero; as I understand it, cheetahs are just about there. One of the ways in which the variability of traits can increase is changes in the genome, which we call mutation, though that is only one factor in genetic variability. So what we end up seeing in most populations is an increase in genetic variability trying to balance itself against the restriction of genetic variability through selection (my apologies for unnecessary anthropomorphizing).Lysenkoism keeps coming to mind. Soviet scientist Lysenko (of "folk scientist"; I forget all the details) rejected the bourgeois idea of genetics and proposed that effective crop management could be accomplished purely through planting methods rather than through breeding programs. His methods, which were far above the peasants' (excuse me please! ... the Proleteriats') traditional ineffective methods generate immediate and fantastic results, so the Soviet Union dropped the teaching of genetics. And as a result, suffered devastating crop failures a few decades later.

mindspawn has been making it clear all along that he does not think that the addition of new protein coding genes is necessary for "new traits/functions/features to evolve", so it's hard to see why so much time is being wasted in the debate on a general point on which the participants agree. "Gene addition" might have been a better phrase, as it doesn't necessarily require duplication to add them.The point that mindspawn is trying to make could be easily summed up as this: On the reasonable assumption that the earliest organisms would have had relatively few protein coding genes, and the observation that some modern organisms have tens of thousands, there has to be a process or processes by which additional protein coding genes are created.Well, that could be better expressed. For example, I think mindspawn meant instantaneous when he typed spontaneous.What he has identified could be described as a conditional prediction of evolutionary theory. "Conditional", because of the assumption that there were very few proteins in early organisms. Let's call that "assumption A". So: if "A", evolutionary theory predicts that there must be a mutational process or processes that add new protein coding genes.That is correct. But is assumption "A" reasonable? I agree with mindspawn that it is (assuming that he meant instantaneous, not spontaneous!). That's because our current knowledge of how the physical world operates would make the instantaneous assembly of a genome with, for example, 20,000 protein coding genes from scratch appear extremely unlikely, if not impossible. It would be hard (or impossible) to find evolutionary biologists who don't agree with mindspawn on this point. Evolutionary processes would be assumed to be necessary to get to the 20,000.So, we have a reasonable prediction. A prediction means that, if the theory is correct, something (in this case the existence of one or more gene adding processes) must be true. If we could demonstrate that that something is false, then the prediction is falsified, and the theory would either require serious modification, or would be discarded.A theory like evolutionary theory makes many predictions. These don't have to be immediately confirmed in order to make the theory a "best explanation", but the more that are confirmed the stronger the theory becomes. Mindspawn is misunderstanding science when he implies that the absence of confirmation of a specific prediction reduces a theory to "just a hypothesis". To damage the theory, we must establish that one of its predictions is false.So, can mindspawn demonstrate beyond all reasonable doubt that there are no processes that add protein coding genes to genomes and thus reasonably falsify an important prediction of evolutionary theory? Clearly not. Not just because that would be a very difficult (but theoretically possible) thing to do, but because the prediction has already been confirmed to be correct beyond all reasonable doubt by the evidence that supports the view that mutation, selection and drift (plus HGT if we don't include it under the broad definition of "mutation") do add new protein coding genes to genomes. Mindspawn may not know it, but he's actually brought up an area in which, far from throwing doubt on evolutionary theory, recent observations add to its support.As I said in an earlier post, the current discussion in the literature is about the fine details of the creative processes, not about whether or not they happen.Edited by bluegenes, : negative selection on a grammatical mutationEdited by bluegenes, : No reason given.

In message 36 of the debate mindspawn writes: Nope. mindspawn still hasn't even defined what exactly he means when he uses the phrase 'novel coding genes'. I mean, gene duplication, then just one little point mutation somewhere, can also be seen as an 'increase in the number of novel coding genes'. This debate will go nowhere unless the words used are properly defined. It certainly is not just semantics.Defining what is meant by a word used is essential for everyone else to able to understand what is said.For example, mindspawn refuses to define what he means by the word 'complex' when he uses it. It can mean anything and everything whatever he wants it to mean when it suits him.I've learned that creationists do tend to keep words very vague; it's their way of being able to move the goalposts every time it suits them. Words such as 'kind', 'complex', 'intricate', 'genetic information' are prime examples. These words are thrown around by creationists like kids throwing around their toys. Although they never want to define exactly what they mean when using them....In the meantime I'm learning a lot from RAZD and bluegenes. Thanks guys.Edited by Pressie, : Added last sentenceEdited by Pressie, : Fixed mistakes