The Recurrent Problem of Chirality

Really? And reachng a conclusion, then going out and looking for evidence to support it does not?
This perversion of the scientific method hardly seems worthy of these "first class theoretical biologists."
Where does one get a degree in theoretical biology anyway? You see, at the University I attended, we were unjustly required to take lab courses where we had to set up experiments, accumulate data, analyze the data, then reach conclusions.
It's nice that there is someone out there to protect scam artists like the two I've been conversing with from mean old scientists like me who demand that they back up their claims with physical evidence.

You are still mistaking evidence of {life today} for evidence of {all life at the beginning}. You have not demonstrated any evidence that is more than 50 years old. We can extrapolate that {life today} back to common ancestors of {all current life}, but that is a very small fraction of {all life that ever existed}.The evidence of life today does not exclude the possibility that some forms of early life were otherwise. The evidence is lacking that all life was one form v any other at the early stages of development.Curiously, this is what the topic is about, not what is present today, but what was present at the beginning. You haven't shown any from 488 million years ago to say nothing of earlier. Other life forms that could have had different modus operandi could have been wiped out by that extinction event resulting in the genetic 'cleansing' that has been passed down since then. Again you are talking about {life today} and not {life at the beginning} as Brad McFall was. Apples and Oranges. Again, curiously, that is what the topic is about -- going back to step one, and then one more. You have just made all your 'evidence' non-applicable. Thanks.Website chosen at random:
THE Medical Biochemistry Page Are you willing to bet that no bacteria will ever take advantage of the resources available when compounds like D-amino acids are used in antibiotics? Given the many surprises that bacteria have foisted on us uninformed people over the years, I wouldn't make such a bet.I repeat: And no, you have not demonstrated why the first forms of life {HAD} to use L-forms, all you have demonstrated is that current life {HAS} L-forms. To claim that this is evidence that it {HAD} to be is begging the question -- another logical fallacy, btw.Now if you were a specialist in abiogenesis and had actually shown why it {HAD} to be, then I might be impressed with your appeal to authority, but apparently you aren't, and you haven't, so your field of experteze (and your grasp of it, while extensive no doubt) is not necessarily indicative of knowledge applicable to the topic ... the initial formation of life (such as what preceeded the current DNA replication systems).EnjoyRAZD - "scam artist"

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If you were able to get that impression from his posts then you're already a lot smarter than I am.Seriously, though. I don't even see the intent to make sense in BMF's posts. I don't think its there. And I'd rather see you address people who know how to make some sense, because you're clearly intelligent and informed, rather than get banned for trying to provoke Brad McFall into making sense, because that's not going to happen. My deepest condolences.

Some bacteria already make use of D form amino acids. Incoporation of D-Alanine into the bacterial cell wall can confer a degree of Vancomycin resistance to some bacteria (May, et al., 2005). This is not part of the process of protein synthesis at the ribosomal level however but a subsequent biochemical incorporation with the structural elements of the cell wall, specifically teichoic acid.TTFN,WKEdited by Wounded King, : No reason given.

A 24 hour suspension for violation of rules 1 and 10.

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Cum on frogert,Razd got it.Common ancestry is not common descent.If there were determinative information that modern taxas' useof "lefts" CONSTRAINS Gould's third leg where Gould insists on constraints from the INSIDE, then a mathematical demonstration of handedness *might* foil the analogy to Kant's "glove" positionining (in general)INTERNALLY and thus BECOME an argument against say Evopeach's placement of the concepts revolved (thus getting "god" out of it as you would probably like to see occurr) but to do so one would need to ARGUE that the common ancestry indicated by modern use of L forms is not just "evidence for common descent"(inter thread alia) but common descent in any decent use of the word.I would be more than happy, as you are probably fully and painfully aware, to discuss my own ideas in the appropriate places on EVC. Sure, one could even laminate me with less than superlatives in the ALL ABOUT BM thread as it is still under 300, but there IS still something more that should be obvious.Since Gould restricts his use of geography to the third leg and as there is some non-Brad science on the effect of the rotation of the Earth causal with chirality (I have posted info from Gladyshev many times here at EvC)a simple lingo to discuss the issue about the mathematical aspect of the handedness in an origin of life (getting by with a defintion, to be agreed on, as to what "life" is, (not Mayr's view that biology need not use the difference of "life and death" anymore, etc.)) seems definately tied to the existence of the triplet code linguistically(to me), but some BIOLOGICAL affect must also be present. Bradcap1 simply seems to discount this possibility.
He responded for instance not realizing or avoiding that I was ANSWERING his question TO ME, elaborating a bit on how the symbol for such a thought might be dividing the physical pace of form-making and translation in space.That is fine if he is simply at odds with my view but again it should at any time be obvious that common ancestry is not common descent.I have no issue with Lforms indicating some kind of common lineage relations. It is ALWAYS the similarites between forms that first leads the taxonomist to a hierarchic proposal. You know this, I know.
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"Geographic distribution is the last but not the least thing the taxanomist considers"- Leon Croizat.

Exactly. This is a post-translational modification. Different proteins are required to do this job. The L-amino acids incorporated into peptides required for protein synthesis have different conformations than those that modify the peptides of the cell wall.

You got it. It does pain me though to watch someone make claims that are completely contrary to everything my professors taught me as well as to my experience in the lab.

You might have missed this, but the way we understand the past is by studying the present.
You and Brad evidently do not feel that the exclusive use of L-amino acids by living organisms is not evidence of common descent. I have demonstrated that the use of L-aminos is due to the proteome, which is in turn due to the transcriptome, which is ultimately due to the genome. Even if you want to point to a primordial RNA world, your opinion is not supported. If you feel that common use of amino acids is not evidence of common descent, then I am forced to conclude that you feel that homology within genomes is not evidence of common descent. Is this correct?
You have also expressed an opinion that the preference for L-aminos could be due to predator-prey relationships. The point at which l-aminos were exclusively being used would presumably have been far earlier than these relationships would have existed.
So, from a scientific standpoint, there is no evidence to support your opinion. This is what I said earlier. Until you find an organism that is/was capable of incorporating D-aminos into nascent peptides, you are merely speculating. A line of organisms capable of incorporating D-aminos would be so fundamentally different from the rest of the tree of life that it would warrant its own domain. Have you ever seen ANY fossil record suggesting that this is the case?
If you are talking about looking at this from a philosophical standpoint, yes a lineage of D-amino using organisms could have existed. But, the problem with this perspective is that there could have been an infinite amount of other possibilities such as the seeding by aliens that an earlier post jokingly referred to. The possibilities of little green men have just as much evidence to support them as does your conjecture.
Fortunately, the scientific method overcomes this obstacle by requiring observable, reproducible evidence on which opinions are based.
There is simply no evidence to support what you say. I was not addressing abiogenesis in my first posts. In fact, the issue that started this was that I stated that the exclusive use of L-amino acids was evidence of common descent. Common descent is not abiogenesis. You have evidently created a strawman of my statement. It appears you are the party guilty of the logical fallacy.

An example of a non-chiral molecule (glycine) is a poor example on which to base a claim of the usage of D-amino chiral aminos.
I am surprised that you would use antibiotics to support your views for a couple of reasons:
1) The use of D-aminos in these molecules are due to post-translational modifications of peptides. This is a completely different pathway from protein synthesis. As you prefer to say, "apples and oranges."
2) The mechanism by which antibiotics act supports my position, not yours. The post-translational inclusion of D-aminos acts on the protein synthesis machinery of bacteria. In effect, it jams up the ribosomes prohibiting protein synthesis. So, inclusion of D-aminos appear to have a deleterious effect on bacteria. Again, this hardly supports your position.
3) This particular ability to modify translated proteins into antibiotics developed in eukaryotic fungi, far later in evolutionary time than you propose.At any rate, I am only interested in evolution and not abiogenesis. My iniitial comment that universal use of L-amino acids is evidence of common descent is supported by observation and experiment. Any claims of the exclusive use of D-aminos is mere speculation and is not based on any observation of reality. You stated this in your previous reply to my first post. I don't understand why you are arguing this point now.
It appears that you are intelligent and possess some common sense. I recommend that you enroll in biology and chemistry courses at your local University so that you can see through the misinformation that Brad McPhall has thus far provided.One more question: How would one be able to falsify your claim of organisms capable of incorporation of D-amino acids into peptides?

(bold and underline mine for emPHAsis)We obviously were discussing abiogenesis. No, I was pointing out that your comments were not relevant to the discussion (abiogenesis) when you thought they were (common descent).When it comes to abiogenesis I am content to say "we don't know" and include in that "we don't know" that there could have been multiple starts on life, multiple answers to the riddle of replication, etc, before life {settled} on the solution we see about us today.The evidence we have today for genetic etc universal use of L-amino acids is a very small subset of all the evidence of use by all organisms since life on earth began. Thus {L-aminos} are evidence that does not refute {common descent} but it also does not prove {common descent}. Even if you could show that NO forms of life could use {D-aminos} this would not be evidence that would prove {common descent}. It - alone - is not conclusive evidence of {ultimate common descent}, just of common materials. You could have common descent with {D-amino} and {both amino} and you would still have common descent. You could have two or more different lines of {recent common descent} that (all) happen to use {L-amino} at their start, and you would not have evidence for {ultimate common descent}. Even if "recent" was every thing since 488 million years ago (ie since Cambrian\Ordovician Extinction event}.Many species today derive their {raw materials} from other life -- ie {L-amino} are pre-selected for use with {D-amino} absent from the possible choices (except at the base level). It could be that {base level} users of {D-amino} went extinct in any one of the numerous extinction events since life began, and that all {D-amino} dependent life forms that derived their {raw materials} solely from {D-amino} life followed, but that {some} users of {both-amino} were able to survive on {L-amino} life supply and now have only {L-amino} due to supply rather than {ultimate common descent}.The {base level} forms of life match raw materials to their templates for replication - as you noted, I believe - and thus can only use {L-amino} materials unless (and until} some mutation changes this fact. But there could have been hundreds or thousands of different {initial replication systems} using {L-amino} that {became\developed into\evolved to} life and that would have had a similar but NOT {ultimate common descent} template for {L-amino} only raw materials.What we can infer from the past is an extrapolation from the present combined with hypotheses of what could have been, and can not be taken as any kind of final word. In this case the extrapolation is of {recent common descent} to {ultimate common descent} - whether that is warranted or not.Evidence that {hypothesis A} {CAN} be correct does not invalidate {hypothesis B} from also being correct unless it also shows that {hypothsis B} {CAN'T} be correct. The tree of life you are talking about is one based on the assumption of {common descent} so it is not evidence for common descent, just of the logical conclusions based on it. Using a conclusion from {common descent} as evidence for {common descent} is either {begging the question} or {circular reasoning} -- logical fallacies again.Again, you have not demonstrated how {D-amino} life {CAN'T} have occurred.There are whole branches on that {assumed common descent} tree of life that are (a) now totally extinct (b) have been extinct for millions of years (c) life where there is no evidence of their being conclusively {L-amino} or {D-amino} or {both-amino} or {whatever} and (d) that are connected by dashed lines (== an assumption of {common descent}) to the rest of the tree -- those life forms which do have {recent genetic {L-amino} evidence}: ie - we don't have evidence that they were NO {D-amino} life forms.Yes, it would be a new {domain} - or an even higher division {D-life?} - so? Has this never happened in the last ... say, 50 years?
Introduction to the Archaea (website chosen at random).Note that this domain shift occurred due to {recent} genetic information of {currently living} forms of Archaea -- and would NOT have occurred without it.Personally I believe that there was a bias towards {L-amino} use (by concentration systems) and that life as we know it was the result of that - however slight - bias due to economies of production outperforming any competing systems. What I cannot do is rule out the possibility of other life systems at the start, that is not speculating, but saying "we don't know" ... (yet).If you can provide evidence that does rule out the possibility of other life systems at the start, I am interested: it's an important question, and not one to be taken lightly. The evidence is that RNA and DNA could have different {chemical descent} and thus be evidence for {common materials} used in their formation before {life}came into existence (which gets us into the Definition of Life issue).It may well be that chemical bias towards the formation of replication systems from {L-amino} building blocks existed and that these {L-amino} activated replication systems then developed into life as we know it (on earth anyway). This too, would be evidence for {common materials} rather than {ultimate common descent}, as you could then have any number of independent formations of {life} from the same {L-amino} building blocks. Forms that could pirate from other forms, as in horizontal gene transfer and as in inclusion (mtDNA).It could be that {life} required a couple of systems to come together to form a self concentrating self replicating self developing system, but "we don't know" ... (yet).At best {biology\evolution\common descent} can only take us back to an initial interactive population, but it cannot force that population to be homogeneous nor can it force it to be unique, just be the one that survived (so far). Anything else is a post hoc ergo propter hoc logical fallacy.btw - Brad McFall is a creationist, with an extensive eclectic education, who just marches to his own drummer. He is working on a usable definition of "kind" among other things, which could be interesting. I reserve judgment.I also would like your input on Will mutations become less freqent?, as your expertize in this area exceeds my knowledge, and I am always happy to learn more.Enjoy.ps - thanks for coming back.

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My initial response to you was that the evidence does not support your position. You have confirmed that this is the case twice. You then take issue with this statement. This does not make sense. My initial post was in response to Evopeach. His post implies that chirality poses a problem for evolutionary theory. My response explained that it does not support his position, it in fact supports evolutionary theory.
Nowhere in the provided quotebox is abiogenesis obvious or implied. I will state again that the evidence does not support this position. Unless you can provide it, you must concede this point. It appears the you've been ignoring my explanations of how gene expression works. DNA and RNA are both directional molecules. They produce proteins that incorporate L-amino acids into nascent peptides. Thus 5'-3' right handed helical DNA will always result in the incorporation of L-aminos. Without modifying the genetic code in a drastic way, so drastic that vestiges of it would remain today, D-aminos cannot be incorporated into peptides. Organisms that evolved mechanisms to make post-translational modifications of petides by adding d-aminos and/or polysaccharides are also evidence of common descent. I have also demonstrated that there are 41 codon sequences that are redundant for L-aminos. Not one of them code for D-aminos.
Now, the complementary base-pairing properties of DNA are the ultimate evidence of common descent. Before DNA sequencing became routine, genes that were characterized in model organisms like Drosophila and C. elegans were used to find homologous genes in other organisms including man. In an assay called a zoo blot, a fragment of a gene from the model organism is labeled with a radioactive label and hybridized to the DNA of the organisms whose gene you are trying to find. For example, the sequence 5'-GACT-3' would hybridize only to the sequence 3'-CTGA-5'. In reality the probe is going to be a longer sequence. The longer the sequence, the more specific the probe becomes. At each position on the DNA stand there are 4 posible bases (1 in 4). The odds of a 40 base sequence is 1 in 4^40. As you can see, these probes are very specific.
Today, DNA sequencing is routinely done and complete genomes of numerous organisms have been sequenced. The average size of the coding region of a gene is 2500 bases. The possibilty of thes genes arising from an independent event is 1 in 4^2500. Yet we find these genes time and time again. Examples of this are hox genes, globin genes, distalless, pax6, and thousands more. The gene for pax6 has even been removed from Drosophila and replaced with the Pax6 gene from mice and restored eye formation that was lost when the gene was removed.
Pseudogenes that exist across genomes reinforce the concept of common descent as does high conservation of sequence in exons and low conservation in introns. You can't be serious. Please go take some courses and learn the fundamentals of science before trying to take on advanced subjects like this. You have curiousity, that is good. Now do something with it.
The scientific method follows (from http://physics.ucr.edu/~wudka/Physics7/Notes_www/node6.html):
1. Observe some aspect of the universe.
2. Invent a tentative description, called a hypothesis, that is consistent with what you have observed.
3. Use the hypothesis to make predictions.
4. Test those predictions by experiments or further observations and modify the hypothesis in the light of your results.
5. Repeat steps 3 and 4 until there are no discrepancies between theory and experiment and/or observation.Are you stating that this is logical fallacy?
The problem with ideas you propose is step 1. The phenomena you propose hasn't been observed. You also can't test any predictions you might be able to make (step 4).
The bottom line here is that both you and Mr. Mcphall are capable of intelligent thought, but you lack the education and training in this field to put forth speculation like this. Your ideas are easily dismissed by OBSERVED evidence that is published in hundreds of professional journals.
Please, go get educated in this area, your curiousity and energy would make you a good scientist. I'm not trying to be a smart-aleck here, but I've been in Atlantic City on a well-deserved vacation and had no idea that I had been banned for a day.

I'm at a loss to understand what is being argued here.In Message 71, RAZD wrote: You responded, in Message 72, with: A statement, such as you made, does not refute anything. As best I can tell, you have not refuted RAZD's statement anywhere in this thread. So I don't see that RAZD has to concede anything. I'm quite sure that RAZD knows very well how gene expression works. But it seems not relevant to the point he was making.I'm wondering if you have understood what RAZD is arguing.

Razd proposes that more than one line could have existed prior to the line that exists now. I stated that there is no evidence to support this view. He has supported my statement by twice admitting that there is no evidence to support his claim. He apparently does not. You apparently do not either. The structure of DNA and RNA results in the incorporation of L-amino acids in peptide synthesis. This is apparently escaping the notice of all of you.
Why don't any of you write up a grant proposal on this and submit it to the NIH or the NSF? How about preparing a doctoral thesis on this ? I'd love to see the response you get.
You might try actually looking up the research that has been done in this area.
As for me, I am quite surprised at the level of scientific illiteracy that is present in this thread.

Bradcap, I've been lurking here, adn your posts are confusing, as they seem to be ascribing a "position" to RAZD and others that they have not expressed and do not appear to hold.For example: It appears that RAZD agrees with you on this - he says that there is no evidence for nor against the idea, just that it is a possibility that hasn't been (and perhaps can't be) falsified. It also appears that you agree that it can't be ruled out nor supported based on the evidence.RAZD and NWR don't appear to be disagreeing with you on anything. So, sarcastic suggestions that they submit a "claim" for publication are rather out of the blue, as they are making no controversial claim, as far as I can see.I wonder if you think they're creationists, and that's why you're being so combative?Edited by Belfry, : No reason given.