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Author Topic:   The Recurrent Problem of Chirality
Bradcap1
Inactive Member


Message 76 of 81 (336741)
07-30-2006 8:17 PM
Reply to: Message 75 by Belfry
07-30-2006 5:06 PM


Re: abiogenesis versus common descent, materials, etc
Absolutely not. Razd and I agree on this. However, he/she bristled when I suggested in my first response that there was no evidence to support the claim.
The point that is at issue now is that I have pointed out that the preference of living organisms for L-aminos is in fact due to the genomes of said organisms. Razd then stated that the use of DNA as genetic material could be due to common materials and not common descent (at least, this is my understanding of his post). I understood that the position of Razd is that homology between genomes is not evidence of common descent. My examples of assays based on complementary base pairing properties of DNA and homologous genes based on DNA sequencing are meant to support the position that conservation of sequence is evidence of common descent.
I was not trying to be combative to Razd or to misinterpret his/her post. If I did, Razd please accept my apologies.
Anyway, my vacation is over and its time to get back to work.
I tried to convey to Razd that I respect the effort that is being made to understand the subject.

This message is a reply to:
 Message 75 by Belfry, posted 07-30-2006 5:06 PM Belfry has not replied

  
Bradcap1
Inactive Member


Message 77 of 81 (336744)
07-30-2006 8:28 PM
Reply to: Message 75 by Belfry
07-30-2006 5:06 PM


Re: abiogenesis versus common descent, materials, etc
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.
Controversial claim #1:
There could have been any number of lines previous to the one that exists now.
See the scientific method in my previous post and the problems associated with this claim.
Controversial Claim #2:
Homology between genomes is not evidence of common descent.
See assays based on complimentary base pairing and the discipline of bioinformatics (comparative genomics), as well as any of the thousands of published research papers reporting on homologous genes.

This message is a reply to:
 Message 75 by Belfry, posted 07-30-2006 5:06 PM Belfry has replied

Replies to this message:
 Message 78 by nwr, posted 07-30-2006 8:52 PM Bradcap1 has not replied
 Message 79 by Belfry, posted 07-30-2006 9:00 PM Bradcap1 has not replied

  
nwr
Member
Posts: 6421
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 4.1


Message 78 of 81 (336751)
07-30-2006 8:52 PM
Reply to: Message 77 by Bradcap1
07-30-2006 8:28 PM


Re: abiogenesis versus common descent, materials, etc
Controversial claim #1:
There could have been any number of lines previous to the one that exists now.
You are perhaps the only person in the world who sees anything controversial there.
See the scientific method in my previous post and the problems associated with this claim.
In my opinion, that a simplistic view of the scientific method. But I won't press that point, since it is off topic for this thread. Even given that version of the scientific method, there is nothing controvsial in the listed claim. I'll suggest that you are misapplying those rules.
Controversial Claim #2:
Homology between genomes is not evidence of common descent.
I can't comment on that one. I haven't been following this thread closely enough to have noticed that RAZD made such a claim. If you can provide a reference to the particular message, I'll look more closely.

This message is a reply to:
 Message 77 by Bradcap1, posted 07-30-2006 8:28 PM Bradcap1 has not replied

  
Belfry
Member (Idle past 5169 days)
Posts: 177
From: Ocala, FL
Joined: 11-05-2005


Message 79 of 81 (336756)
07-30-2006 9:00 PM
Reply to: Message 77 by Bradcap1
07-30-2006 8:28 PM


Re: abiogenesis versus common descent, materials, etc
Bradcap1 writes:
Controversial claim #1:
There could have been any number of lines previous to the one that exists now.
See the scientific method in my previous post and the problems associated with this claim.
You yourself have agreed that there could have been more, but there is no evidence to support this view. So, you agree with RAZD - how then is it controversial? Would you say that it's impossible? In that case, the burden of proof would fall upon you.
Bradcap1 writes:
Controversial Claim #2:
Homology between genomes is not evidence of common descent.
See assays based on complimentary base pairing and the discipline of bioinformatics (comparative genomics), as well as any of the thousands of published research papers reporting on homologous genes.
Please show where RAZD made the claim that homology between genomes is not evidence of common descent. It is customary in requests like this to both quote and link to the message you're quoting (or at least tell us the message number).
The only related point I can find of RAZD's is where he said (with respect to chirality as evidence of common descent in Message 34):
RAZD writes:
I concur, common descent does\is not need to be a necessary result -- it can be a matter of common resources.
That's a far cry from the claim you're crediting to him.
Edited by Belfry, : typo

This message is a reply to:
 Message 77 by Bradcap1, posted 07-30-2006 8:28 PM Bradcap1 has not replied

  
RAZD
Member (Idle past 1489 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 80 of 81 (336795)
07-30-2006 11:07 PM
Reply to: Message 70 by Bradcap1
07-29-2006 9:30 AM


please.
At any rate, I am only interested in evolution and not abiogenesis.
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 & Comment
Arguing that viruses should be a 4th domain ...
But that is not the issue I have been discussing.
One more question: How would one be able to falsify your claim of organisms capable of incorporation of D-amino acids into peptides?
Not my claim.
Message 72
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.
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? ):
Evopeach writes:
Message 1
Life as we know it, uses twenty amino acids to form the molecules that enable life to operate biologically, whether plant or animal, macroscopic or microscopic.
These forms are except for one extant in nature in two, three-dimensional forms called levo and dextro, left and right handed as in a glove analogy.
Now when these two forms make their way into biological molecules used in life they appear in completely separated form and not in mixed forms of both types.
Life cannnot begin or proceed using racemic mixtures of the two forms for life molecules.
But of course never not ever nanda did such a possibility exist in the pre-rna rna world so how did the separation occur which is absolutly required for 3-d data storage on the DNA molecule... not one feasable theory or experiemnt has ever been been proposed much less performed and demonstrated.
Another demonstration of intelligent design.. inexplicable by evolutionary theory.
Your response was:
BradCap1 writes:
Message 19
Life could have began using D-amino acids. It did not. The fact that all living organisms use L-amino acids is very strong evidence of common descent.
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.
Absolutely not. Razd and I agree on this. However, he/she bristled ...
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).
Razd then stated that the use of DNA as genetic material could be due to common materials and not common descent (at least, this is my understanding of his post).
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).
Message 77
Controversial claim #1:
There could have been any number of lines previous to the one that exists now.
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
quote:
Westall remains concerned about the problem of misidentifying microfossils.
"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.
"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."
http://scienceweek.com/2005/sw050513-1.htm
quote:
... 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.
... 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).
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.
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.
Controversial Claim #2:
Homology between genomes is not evidence of common descent.
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.
in msg 76 again writes:
If I did, Razd please accept my apologies. Anyway, my vacation is over and its time to get back to work.
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 readability
Edited by RAZD, : went to quote format

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RAZD
Member (Idle past 1489 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 81 of 81 (423650)
09-23-2007 1:52 PM
Reply to: Message 10 by sidelined
02-11-2006 9:21 AM


Some new information
Regardless, this is simply not the case.There are models which are capable of giving clues to the origin though none fully developed simce the standards required by science are, unlike the intelligent design hypothesis,subject to rigorous investigation and experimental verification.
There is also another factor to consider in this whole discussion,
Is the origin of biological chirality a no-brainer?
quote:
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.
(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.)
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.
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.
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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we are limited in our ability to understand
by our ability to understand
RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
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