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Originally posted by ImaFungi
reply to post by rhinoceros
Before Genetic code existed and the associated codons and proteins and amino acids, was there another 'style' of genetic code or DNA which competed with the present 'style'? Like of completely different molecules and such, I know you mentioned that in different DNA the same molecule or codon can be used to perform different functions, or that 6 of one creates one thing, while 2 of that same one creates another thing, but im wondering if biology on earth was able to utilize any other format for containing the genetic code besides what we know all biologic life uses?
Originally posted by ImaFungi
Im also wondering if we hypothetically are able to code DNA ourselves? If we know all the building block codon pieces, and we know in sequence what means what, are we able to place things in certain order to come up with a viable outcome of a life form?
Originally posted by ImaFungi
Also if we know how many codons a certain life form has, can we create a million different sequences using random orders of codons, and create new creatures, or at least potentially novel mutations?
Originally posted by rhinoceros
It's difficult to avoid seeing terms like the "DNA code" being used in this forum. To me at least, this term wouWeld imply code similar to a computer program, with recursive algorithms and such. However, in real life, no such term exists. The correct term is the "genetic code", which is simply a collection of translation tables with minor differences. According to each translation table, a triplet of nucleotides (all together 64 unique ones), read from the messenger RNA molecule by the ribosomes, define either an amino acid that is to be added to the growing polypeptide, or signal termination of translation. Below is the "universal" translation table:
As we see, the code is not random. As an example, all the four codons that begin with CC, define the amino acid Proline. As such, these codons are called synonymous. Be it CCU, CCC, CCA, or CCG, in the messenger RNA molecule, the bit of information is always interpreted similarly, that is, a Proline is added to the growing polypeptide. As we see, all together, in the universal genetic code, 8 blocks of codons are 4-fold degenerate (Leu, Val, Ser, Pro, Thr, Ala, Arg and Gly). The rest of the sixteen 4-fold codon blocks are split between two or more alternatives. As an example, the amino acid Leucine is defined by CUU, CUC, CUA, CUG, and by UUA and UUG. The other two UU codons, that is, UUU and UUC, specify the amino acid Phenylalanine. So in total, 6 different codons specify Leucine, but only two codons specify Phenylalanine. Here I would also like to note, that with the exception of the AUN and UGN codon blocks, the split codon blocks are always split so that U and C ending codons define one amino acid, and G and A ending codons another. The chemical rationale for this is, that U and C are pyrimidines, and A and G are purines. Purines and pyrimidines have different kinds of carbon rings. To keep things simple, I just note that purines have two fused rings, whereas pyrimidines have a single ring, i.e. purines are much larger than pyrimidines.
There are 10 pre-biotic amino acids. That is, no biological pathways are needed to generate them, instead in experiments such as that of Miller, these amino acids can come to be through strictly abiotic chemical reactions. Interestingly, 8 of these 10 amino acids are specified by the 4-fold degenerate codon blocks (Leu, Val, Ser, Pro, Thr, Ala, Arg and Gly). The additional two pre-biotic amino acids share the GAN codon block, and are Aspartic acid (GAU, GAC) and Glutamic acid (GAA, GAG). All the other amino acids need to be synthesized by biological pathways which involve proteins. In this context, it appears that these amino acids were added to the genetic code only after pathways for their generation were in place. For example, many amino acids are byproducts of metabolic pathways, and prior to them being added to the code, they might have represented waste products, much like how alcohol is a waste product of fermentation.
In this context, the observation that 6 codons still define 3 amino acids (Arg, Leu, and Ser), makes sense. We can extrapolate, that for example the now split UUN codon block was reserved for Leucine entirely. That is, 8 codons in total, UUU, UUC, UUA, UUG, CUU, CUC, CUA, and CUA, all represented Leucine in the primordial genetic code. Likewise, e.g. UAN and UGN codons all signaled termination of translation. In the context of the evolving code, the present day distribution of codons makes sense. However, some people insist that genetic code was designed. Would it not be fair then for these people to explain, why exactly does the present day code for example have 6 codons for Argine, but only one or two for Tryptophan, depending which genetic code we infer (e.g. in human nuclear DNA UGA signals stop, but in many mitochondria, UGA encodes Tryptophan)?
I hope we can keep the discussion civil, and provide references for the claims made.
For reference and further information:
arxiv.org...
www.sciencedirect.com...
Originally posted by rhinoceros
It's difficult to avoid seeing terms like the "DNA code" being used in this forum. To me at least, this term would imply code similar to a computer program, with recursive algorithms and such. However, in real life, no such term exists. The correct term is the "genetic code", which is simply a collection of translation tables with minor differences. According to each translation table, a triplet of nucleotides (all together 64 unique ones), read from the messenger RNA molecule by the ribosomes, define either an amino acid that is to be added to the growing polypeptide, or signal termination of translation. Below is the "universal" translation table:
As we see, the code is not random. As an example, all the four codons that begin with CC, define the amino acid Proline. As such, these codons are called synonymous. Be it CCU, CCC, CCA, or CCG, in the messenger RNA molecule, the bit of information is always interpreted similarly, that is, a Proline is added to the growing polypeptide. As we see, all together, in the universal genetic code, 8 blocks of codons are 4-fold degenerate (Leu, Val, Ser, Pro, Thr, Ala, Arg and Gly). The rest of the sixteen 4-fold codon blocks are split between two or more alternatives. As an example, the amino acid Leucine is defined by CUU, CUC, CUA, CUG, and by UUA and UUG. The other two UU codons, that is, UUU and UUC, specify the amino acid Phenylalanine. So in total, 6 different codons specify Leucine, but only two codons specify Phenylalanine. Here I would also like to note, that with the exception of the AUN and UGN codon blocks, the split codon blocks are always split so that U and C ending codons define one amino acid, and G and A ending codons another. The chemical rationale for this is, that U and C are pyrimidines, and A and G are purines. Purines and pyrimidines have different kinds of carbon rings. To keep things simple, I just note that purines have two fused rings, whereas pyrimidines have a single ring, i.e. purines are much larger than pyrimidines.
There are 10 pre-biotic amino acids. That is, no biological pathways are needed to generate them, instead in experiments such as that of Miller, these amino acids can come to be through strictly abiotic chemical reactions. Interestingly, 8 of these 10 amino acids are specified by the 4-fold degenerate codon blocks (Leu, Val, Ser, Pro, Thr, Ala, Arg and Gly). The additional two pre-biotic amino acids share the GAN codon block, and are Aspartic acid (GAU, GAC) and Glutamic acid (GAA, GAG). All the other amino acids need to be synthesized by biological pathways which involve proteins. In this context, it appears that these amino acids were added to the genetic code only after pathways for their generation were in place. For example, many amino acids are byproducts of metabolic pathways, and prior to them being added to the code, they might have represented waste products, much like how alcohol is a waste product of fermentation.
In this context, the observation that 6 codons still define 3 amino acids (Arg, Leu, and Ser), makes sense. We can extrapolate, that for example the now split UUN codon block was reserved for Leucine entirely. That is, 8 codons in total, UUU, UUC, UUA, UUG, CUU, CUC, CUA, and CUA, all represented Leucine in the primordial genetic code. Likewise, e.g. UAN and UGN codons all signaled termination of translation. In the context of the evolving code, the present day distribution of codons makes sense. However, some people insist that genetic code was designed. Would it not be fair then for these people to explain, why exactly does the present day code for example have 6 codons for Argine, but only one or two for Tryptophan, depending which genetic code we infer (e.g. in human nuclear DNA UGA signals stop, but in many mitochondria, UGA encodes Tryptophan)?
I hope we can keep the discussion civil, and provide references for the claims made.
For reference and further information:
arxiv.org...
www.sciencedirect.com...
why exactly does the present day code for example have 6 codons for Argine, but only one or two for Tryptophan, depending which genetic code we infer (e.g. in human nuclear DNA UGA signals stop, but in many mitochondria, UGA encodes Tryptophan)?
It can't be dumped down much more.
Biologists must constantly keep in mind that what they see was not designed, but rather evolved.
An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to be satisfied to get it going.
A co-discoverer of the double helical structure of the DNA molecule, Crick found it impossible that the complexity of DNA could have evolved naturally.
Originally posted by helldiver
You seem confused as to why your OP hasn't attracted much attention so I have taken the liberty of reviewing for you.
Originally posted by helldiver
To be honest it reeks of arrogance and vanity. Your opening few sentences say it all. If anyone who is not a biologist chooses to talk about the DNA code and this annoys you then that's fine. But to infer that everyone should be familiar with scientific parlance is arrogant.
Originally posted by helldiver
You should have constructed your OP along the lines of a scientific press release where little or no prior knowledge of the topic is assumed by the author. This is a basic concept commonly seen in scientific fields, even down to undergraduate level.
Originally posted by helldiver
The OP is littered with assumptions of the reader. For example, when you refer to certain codon blocks you use the letter N but do not explain that it refers to any nucleobase. There are many other examples of such assumptions. Also you frequently touch on subjects that you could have left out, this only serves to confuse and patronise the reader. It should be noted that a codon table is text book stuff and is taught at high school level. Another point, you bring up the term "DNA code" but then go on to discuss the RNA translation table. It would have been more appropriate to refer to a DNA table throughout.
Originally posted by helldiver
What is absolutely astounding about this post is that you have basically taken the results from the paper you have linked as further reading (at the bottom of your OP) and taken credit for them as being your own observations. You have on many instances even copied directly from the text!! Nowhere have you referenced the paper either. Many universities and institutions take plagiarism very seriously and I guarantee you that if you had handed your OP in as a piece of course work then their plagiarism software would have detected this in a flash.
Originally posted by helldiver
What I don't get is why would you include the paper in the link in the first place?
Originally posted by helldiver
Anyway, i see you have a few followers on here and i'm sure i'll get flamed for this post but first i'd like to invite them to read the paper first and see for themselves. It's a fantastic read and is extremely easy to follow, unlike your condensed version of it.
Originally posted by helldiver
To summarise, your OP isn't accessible to many readers and is extremely patronising. However, the biggest issue with this post is the fact that you have taken credit for the work of others.
To be honest it reeks of arrogance and vanity. Your opening few sentences say it all. If anyone who is not a biologist chooses to talk about the DNA code and this annoys you then that's fine. But to infer that everyone should be familiar with scientific parlance is arrogant.
Without looking up that term I'd like to know what 'natural selection' etc means in the context of describing how the various amino acids and their components are made and how it is decided what should be 'kept' and what should be 'discarded'.
1. if i read it right, dna is made of nucleotides which are themselves composed of various atoms, i.e. carbon, nitrogen, phosphorous etc. At the core of the process by which dna is created, how do the atoms which make the nucleotides know how to order themselves in order to create the dna and then the amino acids?
2. If we can synthesize amino acids, which are the building blocks of life, (you mentioned that some aminos need biological pathways to be created?) and it seems like we understand the process pretty well....why arent we able to create life without the biological pathways? Or are we? Can we use completely chemical processes without biological pathways to create those biological pathways that are needed to create the other amino acids?
When i see 'natural' used as the basis of an explanation for how or why things happen it just seems like a very loaded 'cop out' kind of word thats sort of a stop gap for a lack of understanding about how or why these things 'just work'.
I remember once while studying animal evolution they were talking about how different animals get their traits. They spoke of how the giraffe got its long neck, for example, and i remember how 'they' said it was because over time there were leaves on taller and taller trees and that the giraffe had to reach higher and higher to get them. I remember thinking very clearly at the time, not being predisposed to religion etc, how nonsensical that explanation seemed. I thought to myself 'you mean somehow the giraffe stretching its neck as far as it could go, and somehow 'needing' to reach higher, told the dna, the cells, etc....to grow the neck longer?
ImaFungi
reply to post by rhinoceros
ok im editing because i realize you have a problem with the word design
edit on 8-8-2012 by ImaFungi because: (no reason given)