Let's discuss the genetic code

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...

Or simply put, atoms like to play with each other in the playground while being forced to play and interact with each-other through their differences and their governing faculty of the four forces with the head dean electromagnetism.

This is a bit technical, not sure what sort of feedback you expect here to be honest. Maybe you should post on a specialist scientific website with this kind of thing, or dumb it down to some points/questions that a layman can understand and resond to.....

reply to post by Atzil321

I think rhinoceros is saying that the genetic code shows considerable redundancy, and also seems to have evolved to work with pre-existing, abiogenetically produced amino acids. In other words, that it shows signs of being itself a product of natural selection; an intelligently designed code would be more elegant and all of a piece.

Well, at least that's what I got out of it. Open to correction.

Originally posted by Atzil321
This is a bit technical, not sure what sort of feedback you expect here to be honest. Maybe you should post on a specialist scientific website with this kind of thing, or dumb it down to some points/questions that a layman can understand and resond to.....

It can't be dumped down much more. I guess the general point here is to give people the basic understanding of what the genetic code is, and to engage the mysterious "DNA code" crowd and information theory "experts". For example, in the abiogenesis thread we see claims being made that all codes we know were intelligently designed. Well, in this thread, I have articulated a few observations that strongly point to the genetic code having evolved naturally..

Originally posted by Astyanax
reply to post by Atzil321

 

I think rhinoceros is saying that the genetic code shows considerable redundancy, and also seems to have evolved to work with pre-existing, abiogenetically produced amino acids. In other words, that it shows signs of being itself a product of natural selection; an intelligently designed code would be more elegant and all of a piece.

Well, at least that's what I got out of it. Open to correction.

That captures the essence of it rather well.

Hi Rhino, glad I could inspire a thread.

It's a good question. The answer is actually already in the literature, the synonymous codons may actually affect the timing of translation and in turn affect protein folding in subtle ways and then effect what chemical tags get attatched post translation.

I haven't time to hunt down papers, but you can simple try searching for "synonymous codons" and you should find a several studies. In other words yes they have been found to have a purpose.

There are 64 codons but only 20 amino acids, which lead to the belief that DNA is degenerate however...

www.ncbi.nlm.nih.gov...

I don't expect I'll be participating in this thread. Although I find the subject fascinating, I find the argument quite nauseating when dealing with these issues. It never turns out to be about actual science in the end.

Originally posted by squiz
Hi Rhino, glad I could inspire a thread.

It's a good question. The answer is actually already in the literature, the synonymous codons may actually affect the timing of translation and in turn affect protein folding in subtle ways and then effect what chemical tags get attatched post translation.

Are you implying that e.g. the fact that there are 6 codons encoding Argine and only 2 encoding e.g. Cysteine somehow implies design because specific synonymous codons might be read more efficiently/inefficiently in specific organisms? Why not only 4 synonymous codons for Argine as is the case with Proline? The fact that only pre-biotic amino acids have entire codon blocks dedicated to them doesn't indicate anything? The hypothetical designer just happened to make it that way, perhaps to confuse the scientists about the origins of the code?

Good thread, Rhino. Star and flag. I think that much misunderstanding comes from DNA code, it's nice to see a bunch of it being cleared up.

So, that's it? Not a single argument for the genetic code having been designed? What happened to all the "DNA code" experts of ATS?

reply to post by rhinoceros

Yes, I was afraid it would be. If you don't mind me saying so, one reason was the way you chose to present the issue; you would probably have got more of a response if you had front-ended your post by describing the salient, controversial issues in simple language and laying back a little on the technical stuff. You could always have gone into the details in a following post, or in a reply to someone, if you needed to.

The other reason, of course, is that real science is way, way above the heads of creationists – even the ones who come over all pseudoscientific in this forum, quoting from creationist papers and blogs. What they want to talk about is dinosaurs and Noah's Ark, why carbon dating is 'inaccurate' and how come there are no 'crocoducks' in the fossil record.

Still, good try.

reply to post by Astyanax

The problem is, that it just can't be dumped down more. Even now many crucial parts are missing. For example, I did not even get started with initiation of translation, which is completely different in bacteria and eukarya, i.e. eukaryotic mRNAs must be capped from their 5'-ends with certain proteins, without which translation usually cannot start. In bacterial translation systems, 5'-caps do not exist. This of course poses yet another question for those who insist that the systems were designed, i.e. why invent the wheel twice? It's also a good argument against irreducible complexity, i.e. at first hand the eukaryotic system appears as such, however, studying the bacterial system goes to show from what kind of state it almost certainly evolved. I understand my posts are meaningless for our resident creationists who really don't care about the truth. Blissful ignorance and all that..

reply to post by rhinoceros

The problem is, that it just can't be dumbed down more. Even now many crucial parts are missing. For example, I did not even get started with initiation of translation, which is completely different in bacteria and eukarya, i.e. eukaryotic mRNAs must be capped from their 5'-ends...

As someone who has worked in advertising and communications all my life, the phrase 'dumbing down' never fails to annoy me. It suggests the author thinks he is more intelligent than his readers, something that is fatal to effective communication. Having something important to say, yet not troubling to make oneself clear and comprehensible, is about as dumb a thing as anyone can do. Why, in that case, bother to write at all?

Your opening post should have done what I had to do for you instead: state your premises clearly and in simple language. They were so deeply secreted within those thickets of biochemical jargon that they could scarcely be found.

They should also have been highlighted in your thread title; something like 'Genetic Code Disproves Creationism', or, if that sounds too sensationalistic for you, how about 'What Does the Genetic Code Teach Us about Intelligent Design'? There are dozens of titles that you could have chosen. The one you did choose is almost calculated to put people off the thread. 'Let's discuss the genetic code' – gosh, that really sounds like an exciting topic, doesn't it?

The legendary advertising guru David Ogilvy advised copywriters to spend eighty percent of their time crafting the headline of an ad, and only twenty percent on the 'body copy'. This, he said, reflected the relative importance of each in terms of effective communications. Something to think about for your next thread.

I understand my posts are meaningless for our resident creationists who really don't care about the truth. Blissful ignorance and all that.

Yes – and frankly, to Hades with them. The trouble is, you missed a really great opportunity to educate the uncommitted and help them see through the lies of creationists.

As you know, we share the same views on this subject, and I consider you one of the more important contributors to this forum because of your extensive subject knowledge. I hope you will take what I have written in the right spirit; my intention is to be helpful, not to put you down. I have spent most of my life learning how to communicate with the general public, in advertising, public relations and corporate communications. This post is my attempt to share some basic lessons, learned in that arena, with you and other ATS members. The creationists, incidentally, don't need my advice; they understand all this very well indeed.

Originally posted by rhinoceros

Originally posted by Astyanax
reply to post by Atzil321

 

I think rhinoceros is saying that the genetic code shows considerable redundancy, and also seems to have evolved to work with pre-existing, abiogenetically produced amino acids. In other words, that it shows signs of being itself a product of natural selection; an intelligently designed code would be more elegant and all of a piece.

Well, at least that's what I got out of it. Open to correction.

That captures the essence of it rather well.

so instead of ID you believe in SD ( stupid design)?

Originally posted by ImaFungi

Originally posted by rhinoceros

Originally posted by Astyanax
reply to post by Atzil321

 

I think rhinoceros is saying that the genetic code shows considerable redundancy, and also seems to have evolved to work with pre-existing, abiogenetically produced amino acids. In other words, that it shows signs of being itself a product of natural selection; an intelligently designed code would be more elegant and all of a piece.

Well, at least that's what I got out of it. Open to correction.

That captures the essence of it rather well.

so instead of ID you believe in SD ( stupid design)?

More like I observe absence of design (AOD).

reply to post by rhinoceros


but we admit there is design in the universe, ( ok im editing because i realize you have a problem with the word design, its implications and connotations,.,.,when i say there is design in the universe,, in that above statement, i am only saying,, physical items have a design,, im not nessecarily implying a designer,,, " but we admit there is design in the universe" how things actually are is what their design is..,,.) ,, complex systems and structures,, information,, and intelligence,,.,

everything that we know exists that was not created by humans,,,, exists because of the lack of intelligence,,,,, or stupidity,,, or blind chance...... thats what you are saying,,.,., if you dont believe that intelligence was responsible for organization of the universe,, then you believe that the absence of intelligence was responsible,,,,,, there for blind chance was "intelligent" enough to create the order, complex systems, structures, information, and intelligence we observe in and as the universe.

Mendel's Genetic Law presents that change, inherent is nature cannot be reconciled with the diversity required in Evolutionary Theory. Alternatively, suggesting that God created reality, which resulted in the creation of the Universe and the development of life on Earth, is also form for creationism. In that vane DNA is a bit character in a process that potentially transcends human experience to date.

What We Actually Observe in Nature
We observe microevolution both in nature and through purposeful domestication within species. We do not observe macroevolution. Purposeful domestication (selective breeding) has been used to produce changes or desired variations within many species for more than 2000 years. Examples include cats, dogs, beef and milk cattle, race and plow horses, roses, wheat and corn. All have been changed through microevolution which follows Mendel’s law of inheritance, not the concept of blending traits envisioned by Darwin. Scientists admit macroevolution cannot be observed under natural conditions. If it happened, it occurred in the distant past and would be too slow to observe now.

However, in laboratory experiments, fruit flies have been altered to grow legs from there heads, one of many freakish major mutations possible. These changes were produced by large doses of radiation to greatly increase the mutation rate and alter genes. These changes neither created a new structure (just altering existed ones) nor changing the fly into a new kind of insect. These flies may breed under laboratory conditions, but cannot survive in nature because of this harmful mutation.

Davis writes, “Mutation does not introduce new levels of complexity, and it cannot be shown that it is a step in the right direction. Most observed mutations are harmful, and there is no experimental evidence to show that a new animal organism or even a novel structural feature has ever been produced from the raw material produced by mutations.

www.pilgrimtours.com...

Mendel’s laws of genetics
According to Mendel’s first law (the law of segregation), in each generation, two alleles of any gene present in the parent individual segregate into independent sex cells (e.g. into individual sperm) without undergoing any change and without affecting one another. The second law (the law of independent assortment of characters) states that the individual pairs of alleles of various genes segregate into sex cells independently of one another and that the manner of segregation of one pair of alleles in no way affects the segregation of another pair. In the first decades of the 20th century, geneticists demonstrated that Mendel’s second law applies only to pairs of genes, each of which belongs to a different chromosome

That is not the way it is Mr. Darwin


Any thoughts?

Just so we are clear to apply Punctuated Equalibria as an explanation is applicable generically, even to humans...

Any thoughts?

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...

Could you explain why 6 codons for Argine, and only 1 or 2 for Tryptophan causes one to infer no design?

Originally posted by addygrace
Could you explain why 6 codons for Argine, and only 1 or 2 for Tryptophan causes one to infer no design?

Argine is a pre-biotic amino acid whereas Tryptophan is not (in fact it's made from another amino acid). In the context of the evolving genetic code, the observed 6 codons for Argine and 1-2 codons for Tryptophan make sense - in the primitive genetic code the pre-biotic amino acid Argine was defined by 8 codons (2 codon blocks) and Tryptophan was not part of the code at all, in fact the whole UGN codon block most likely signaled termination, as nowadays the block is divided between two "late" amino acids (Tryptophan and Cysteine) and a termination signal (in the 'standard genetic code'). These observations (what codon encodes what) do not make sense in the context of ID, but are easily explained in the context of the evolving code (the pre-biotic amino acids are mostly defined by entire codon blocks, whereas the biotic amino acids are not, as is expected in the context of the evolving code). This also indicates that in the primordial code, only the first two nucleotides of the codon triplets were meaningful, which is an arrangement that has made a comeback in the genetic codes of many mitochondria, where there is often only one transfer RNA for 4-codon defined amino acids, and the wobble nucleotide of the anticodon of the transfer RNA (the nucleotide that corresponds to the last nucleotide of the codon) is U, which pairs with all four bases (A,U,G, and C).

The fact that the UGA codon signals termination of translation in the 'standard genetic code' and specifies Tryptophan in the genetic codes of many mitochondria, also makes sense in the context of the evolving code, but not in the context of ID. You see, these mitochondria lack a release factor that is specific to the UGA codon (in the same way as transfer RNAs are specific to their codons), and causes the disassociation of the messenger RNA from the ribosome upon encountering the codon. Now after these organelles lost this release factor, the UGA codon became "free", and in many cases was later "captured" by the transfer RNA that reads the UGG Tryptophan codons. Mitochondria often have a huge mutation pressure to have as many as possible A and T nucleotides, and as few as possible G and C nucleotides in their genomes. In cases where the Tryptophan transfer RNA has become able to read the UGA codons, basically all Tryptophans in that mitochondrial genome are encoded by UGA codons instead of UGG codons. However, in cases where a mutation has not enabled the reading of UGA codons by the Tryptophan transfer RNA, all the Tryptophans of that mitochondrial genome are encoded by UGG.