The Recurrent Problem of Chirality

You're not getting it. Aminoacyl tRNA synthetase cannot charge tRNAs with D-amino acids. This is due to the genetic code and it's exclusive use of L-amino acids. D-aminos just can't get in due to conformational differences. L-aminos fit.
Now, the fundamental proteins that mediate replication, transcription, translation, and expression are all coded for by DNA that directs L-amino acids. These proteins have conformations that only work with L-amino acids and so on through metabolic pathways.You would have to go back to step one for these fundamental differences to change. You should be getting the idea by now. In other words, you have no idea what you are talking about.
You babble on about things with absolutely no biological or chemical relevancy.

Ha Ha Ha! You are so full of shit! You have shown nothing but first class ignorance of the subject! You've never addressed the subject. You've only thrown out your thoughts or ideas that you can't support with any observable evidence or data. In fact, your responses show nothing but a complete ignorance of this subject.

Show me the evidence. Was that slow enough for you? I'll say it again in case you missed it, show me the evidence. Sure, you stick to observable, reproducible observations and not speculation and I'll be civil. If you keep speculating with no evidence to back it up, I'll keep telling you you're full of shit. Ha Ha Please! I've presented nothing but evidence in my posts to you. Evidently you lack even basic education in biology and chemistry to undestand it. Sucks to be you. I absolutely do not know it all. I have however dedicated the last five years of my life to this field. I don't claim to be an expert in any other field. I do know more than the layman (that includes you and Brad)about molecular biology. Exactly what I've been doing. See there, I would certainly acknowledge that you are more knowledgeable than me in posting to this group and in computers in general.
BTW, the evidence still does not fit your view.

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.

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?

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.

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.

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.

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.