The Recurrent Problem of Chirality

welcome to the fraytype [qs]quote boxes are easy[/qs] and it becomes: It also could have started with both, just found that it works better with one - at this point we don't know.Enjoy.

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RebelAAmericanOZen[Deist
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This is why I think it is possible for early {proto-life\animate} systems to have started with a general mix and then selected for one chirality. It didn't have to start with only one.Consider early proto-life using both, and needing mechanisms to use both, then selection for simpler systems that only use one, eventually requiring that all are one-handed for the simplest system.There also seems to be a slight bias to L- vs D- if I recall, that may have been crucial to it being selected.Nice links. You have one I used in in my essay RAZD - Building Blocks of Life (sweet meteorites)Enjoy.

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RebelAAmericanOZen[Deist
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hey Brad (McFall v cap1). bradcap1 was refering to his manner of quoting evopeach, rather than any specific content of my message I believe, and that I showed him how to use quoteboxes. I agree that this is the common argument, that amino acids come in ambidextrous ambiguity, and that {selection} for {one v other v both} handedness shows a {hand} in the matter of an external source or function.It amuses me that the choice is so sinister in appearance (when it could just be accidental, a flip of the cosmic coin). And it may not have been "common" descent but a mixed metaphor descent in the early (flat) stages before the hills. Unfortunately belief has no effect on (a) evidence or (2) the past, so we may never know.It also has not been shown that a opposite hand life cannot form, nor one with mixed ratios (the question becoming then, is one more fit than others? ... if one keeps to evo-principles, or is one blessed versus sinned? ... if one keeps to {largess handed oblige} principles ...)Enjoy.

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RebelAAmericanOZen[Deist
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You've only posted 2 times on this whole forum, once to Evopeach and once to Brad McFall.Just curious.and Evopeach has not posted since february ...Edited by RAZD, : added last line

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RebelAAmericanOZen[Deist
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so he's a stalker?LOL.welcome to the fray ... lurker?

I concur, common descent does\is not need to be a necessary result -- it can be a matter of common resources.We see concentration of toxins in predators in similar manner than would apply to concentrations of raw materials for building cell materials -- it may come down to the ultimate prey - some herb or other - having preferred their sugar spun one way at the candy fair, and each organism consuming the salad of choice or in turn consuming the consumer, would also concentrate on the one sugar.There is too much we don't know about how much of which spin can be accomodated. We {as the sum of organisms} may also have lost any previous ability as supply was lost.So why do {plants\bacteria\algae} that ostensibly take raw materials from the environment direct rather than from some other organic source choose one side of the equations? Habit?

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RebelAAmericanOZen[Deist
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I'll say this slowely for you: we do not know how life started, nor how many different forms it had, all your evidence is based on what is alive today. You even admit this: That is inconclusive: we also do not really have evidence of L-forms from 3.5+ billion years ago. All we have is fairly recent, IIRC.Do we know what forms were specifically and exclusively used by a certain time, say the Cambrian "explosion" or the Cambrian\Ordovician Extinction event? That's only 488 million years ago eh? (1/7th of the 'history' of life on this planet?)Further comments:
Message 36, Message 38, Message 39, Message 41 and Message 43 are all responses to the same message, these could have been combined into one post (you can always edit to add material) - they could have been combined with Message 35 as well. Personally I find Brad McFalls posts intriguing and thought provoking, even when I thoroughly disagree with him.Likewise posts Message 37, Message 40, Message 42 could have been combined into one post.Of the 17 posts since my last post 12 are from you -- you could have written two or three and been more concise. Note (seeing as you are new here and don't know the ropes) that threads are generally cut off at 300, so "pile posting" is frowned on.The part you quoted in Message 41 and then said Was a quote of mine: Brad (McFall) was responding to my post not yours, you were just part of the discussion.This forum also has guidelines for gentlemanly debate ... You don't need to say this kind of thing. It adds nothing to the debate, and reflects more on you than anyone else.I'm not saying no-one here (least of all me) is immune to this, but we should all make the attempt at being civil. The last person to brag about his background did so to his dismay. Personally I find anyone that needs to say this has lost the argument -- the argument is based on the evidence you present, not who or what you are (that is, after all, the logicall fallacy of the appeal to authority with the added ego-centrism of claiming to be the authority). There are many kinds of arrogance. Another kind is thinking that you know it all. If I'm looking for a teacher I'll look for one who doesn't insult my intelligence first, and claim to be an expert second. In other words you are stalking him here? You seem awfully intent.Maybe you need to learn to enjoy the debate more?This thread, evopeach or no, is about the abiogenesis question, one that is as yet unanswered, about {why}{how} did only L-forms become the ones used in life as we know it.If you can demonstrate why they {had} to be L-forms, I am interested.Thanks.one final word, just to make your ... posts more interesting to read, you may have noted that indenting is nor preserved in the posts, nor is there any natural paragraph formating (note to percy ...), so the only way to really identify paragraphs is to double enter line breaks.Edited by RAZD, : typoEdited by RAZD, : typzs

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RebelAAmericanOZen[Deist
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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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RebelAAmericanOZen[Deist
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(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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RebelAAmericanOZen[Deist
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What I have been discussing is abiogenesis. Any - and all - evolution since some 3 to 3.5 billion years ago is therefore irrelevant to what I have been discussing. This is a point I have been trying to make clear for the last several posts, as clearly you are not understanding that little detail.As far as common ancestry of all known life is involved, I don't need your evidence, there is even more pursuasive (to me) evidence in articles like The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life.Also see (accessable Discover Mag article)
Discover Financial Services
(Nature article - need sign in to access)
Nature News & CommentArguing that viruses should be a 4th domain ...But that is not the issue I have been discussing. Not my claim. Actually what I see is that all your evidence supports Evopeach's assertion that only L-amino acides are used in all forms of life and that evolution cannot explain the choice of L-amino acids.Of course he assigns the choice to "intelligent design" (because that's what we normally do for anything we don't know eh? ): Your response was: This does not refute the assertion that this "choice" of L-amino over D-amino was due to some supernatural hand in the matter, it just agrees that all life as we know it is L-amino.And every post since has been about how completely life today is L-amino acid dependent.To refute the position stated by Evopeach means abiogenesis must be discussed and that such discussion must involve what was possible, what was NOT possible and what mechanisms MAY have been involved in dividing L-amino acids from D-amino acids.This -- irrespective of education, intelligence and whatever degree whoever has -- is logic as I know and use it.And because you have not attempted to refute the assertion of {divine choice}, all your evidence of the preponderance of L-amino life is apparantly actually supporting it. he. My avatar actually looks a fair bit like me (Message 91).What I "bristled" at was the implication that this HAD to be so at the beginning -- for abiogenesis (which is what I was discussing at the time). If you look at ALL my posts as being concerned with abiogenesis rather than {evolution since then} you may see what I was driving at there (and every other point). It would appear that you do not know much about abiogenesis (poke), as this is a fairly common concept, posed by any number of well respected scientists in the field.If the possibilities for life forming were high, then any number could have been in the mix at the begining, fighting for top dog. If they were all L-amino acid types (or predominantly so) they could have combined by horizontal gene transfer to combine the best of the different elements. There is a lot of evidence for combination of genetic material in this manner -- and the evidence cited above that shows that viruses have been around at least as long as all known domains of life, to insert viral genes into all these different actors (perhaps the role of viruses in the formation of life?)If the possibilities for life forming were low, with many obstacles to overcome, then life could have formed and gone extinct a number of times before it finally "caught on". Previous life forms could have been D-amino as easily as L-amino, and that may be why L-amino was chosen ... the D-aminos were used up.Or are you going to argue that the process was so "fine-tuned" that it only had to start once ... (joking).The earliest life forms we know (for sure) are the stromatolites in australia and south africa -- because they look like {life we know} we can recognize them as {life} (a rather circular argument).http://nai.nasa.gov/news_stories/news_detail.cfm?ID=186

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Westall remains concerned about the problem of misidentifying microfossils.

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"I am working with some colleagues in the hopes of establishing some biochemical technique to determine if there is any signal still from the degradation products of microbes in the very old rocks from South Africa and Australia," she states.

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"But the search for ancient life and its distribution is a painstaking slow process requiring much methodical examination of the ancient rocks," she adds. "It will take years before we have a reasonable overview of what early life was like on Earth."

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http://scienceweek.com/2005/sw050513-1.htm

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... There are only three known locations that host exposures of ancient sediments: Isua and Akilia in southwest Greenland, which are 3.8 to 3.7 billion years old (Ga), the Pilbara in northwestern Australia (3.5 to 3.3 Ga), and Barberton in eastern South Africa (3.5 to 3.3 Ga). These sediments, however, formed almost 1 billion years after the formation of the Earth (4.56 Ga). Any older sedimentary deposits, and with them any potential information on the origin of life and its initial evolution, have been destroyed by tectonic activity. Of the existing three exposures of ancient sediments, the Isua and Akilia rocks have been so altered by metamorphic changes over the past 3.8 billion years that they are no longer useful for microfossil studies. In contrast, large parts of the Pilbara and Barberton ancient terrains are exquisitely preserved, representing veritable goldmines for microfossil hunters.

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... The attention lavished on these microorganisms stems from early discoveries of fossil cyanobacteria [1], but since then the study of early life has moved into a more contentious, if more realistic, sphere. New questions are being raised: (i) What characteristics of life (structural and biogeochemical) also are produced by abiogenic processes and, consequently, how can we distinguish between signatures of past life and signatures of nonlife? (ii) What is the nature of the earliest preserved microorganisms, and (iii) what environments did they inhabit? The first question is a particularly thorny one -- and is especially pertinent to the search for life on other planets -- because we have no examples of the transition from nonlife to life. The life forms preserved in the oldest terrestrial sediments were already highly evolved compared with the earliest cell and with LUCA (last universal common ancestor).

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Owing to the difficulties in distinguishing between life and nonlife, no one signature of life -- for example, the fractionated isotopic ratio, the molecular carbon composition, or an isolated microfossil -- should be considered unequivocal evidence for traces of past life.

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If the common materials available for the formation of life only included L-amino acids in sufficient quantity and variety and concentration, then that would be a valid reason for life beginning with L-amino acids and being addicted to them ever since. The problem is that we just don't know ...We also do not know for sure that the bacteria fossils that were observed are L-amino or D-amino -- we can accept that some are L-amino tentatively based on their apparent similarity to modern cyano-bacteria, but there are other forms as well with no modern counterparts.There is also the issue of things we just don't recognize as being evidence of life because it is foreign to what we know as life.I reserve judgement.As noted, there are no (and not much hope of finding) fossil beds that show the origins of life, the oldest sedimentary rocks we can find that have not been hopelessly transformed by metamorphic processes (that destroy fossils) already show abundant life.What older rocks could show is anyones guess.I reserve judgement. Not claimed. You seem to have formed some idea of what I was talking about and can not let go of your misconception. Abiogenesis preceeds common descent. Oh I understand, and that is why I have tried to clarify the issues (and thanks to everyone else who also tried to clarify this).Enjoy.Edited by RAZD, : tan to silver for readabilityEdited by RAZD, : went to quote format

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RebelAAmericanOZen[Deist
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There is also another factor to consider in this whole discussion, Is the origin of biological chirality a no-brainer?

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I think people have fallen into the error of assuming that, at the molecular level, enantiomers are much more similar to each other than to other related molecules. But I don't think it's really any harder for an asymmetric reactant or catalyst to distinguish D-glucose from L-glucose than from either enantiomer of fructose or galactose. Or to distinguish L-leucine from D-leucine than from D- or L-isoleucine. They may contain the same atoms but they all have entirely different shapes, and so they are all entirely different molecules.

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(Here's the same point made about words. The words pacer and recap are palindromes, but most readers have no more trouble telling them apart than telling either from caper.)

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But chemists are late arrivals on the evolutionary scene, and the first self-replicating entities would usually have interacted with individual molecules in complex mixtures. Because all but the simplest of biologically relevant molecules are asymmetric, most inter-molecular interactions would always have been between asymmetric participants, each no more likely to confuse their partner with its enantiomer than with any other molecule. The fact that crystals of D-glucose and L-glucose have the same bulk properties (solubility, melting temperature) would have been irrelevant.

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We don't need to fuss with defining 'life', but can simply think about the origin of entities capable of evolving by natural selection (having heritable variation causing differential reproduction). Any molecule complex enough to have heritable variation would certainly have been complex enough to be asymmetric. To such molecules, discrimination between enantiomers wouldn't have been any more of a problem than discriminating between other possible reactants.

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In other words they wouldn't be mixed up using one for the other.Of course this could just explain why sorting mechanisms would have worked. Or why the first\last successful life happened to use L-acids and D-sugars.Enjoy.

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RebelAAmericanOZen[Deist
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