Amino Acid Coding Question

Given that a codon has 3 nucleotides (A,C,T,G (U)), giving 64 possible combinations. As can be seen, most amino acids are coded for by more than one codon.My question is, are the codons chemically linked to the amino acid, or are they symbolic, in that it is ACTUALLY possible to have CCU (proline) code for methionine (AUG). If not, what chemical property prevents CCU, or any other triplet coding for anything else, other than indicated on the chart?Hope that was clear....Many Thanks,Mark------------------
Occam's razor is not for shaving with.

Hi, I think that I can help a little here. There is minimal data concerning a direct chemical link between the actual coding of the triplicate codon and the amino acid that it codes for. This would indicate that it was largely chance that caused a specific codon to code for a specific amino acid. That said, I seem to remember a paper dealing with biological applications of information theory that indicated a slight statistical correlation w.r.t. the tRNA and the amino acid, this could lend a slight bias to the codon and the amino acid bound to the tRNA that carries the amino acid to the translation site. I also remember that there was precious little physical evidence to back this up. I will try to find this paper and post a reference.

Dr T,Thanks for the reply, I answered my own question eventually (i think). Since the "universal" genetic code isn't actually universal. Some codons code for different amino acids in different species, so the answer would seem to be, as you have indicated, that the anti-codon/amino acid is "symbolic" rather than chemical. This, of course, assumes that the anti-codon is exactly the same chemically in those species. If it weren't, then the link could be chemical after all.I would be grateful for that extra info, however.Cheers,Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 03-19-2002]

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[This message has been edited by mark24, 03-19-2002]

If anyone's still interested...Each amino acid has a specific tRNA with a region of complementarity to the appropriate codon. The specificity of the amino acid for the right tRNA is ensured by the fact that each tRNA has a corresponding enzyme which charges it with the correct amino acid. These enzymes can distinguish between amino acids as close in structure as leucine
and isoleucine...
Link

Jimlad,Thanks for the link........Mark------------------
Occam's razor is not for shaving with.

Mark24You may already be aware of this information, judging from your comment "Since the "universal" genetic code isn't actually universal."But here is an interesting article by Kenneth Miller posted at the National Center (funny spelling) for Science Education which gives a references to some studies on the universality of the genetic code and a nice (but small) tree showing the evolutionary connections between the standard genetic code and the identified variants. Ken Miller answers Discovery Institute[Shortened too-long link. --Percy]Is this evidence of the degeneration resulting from the fall of man in Eden or an interesting twist to the complex story of evolution?!

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[This message has been edited by Percipient, 04-03-2002]

The Ken Miller link represents a good opportunity for highlighting another aspect of the debate. One might ask why Ken Miller bothers to respond to Discovery Institute (DI) at all. He's doing science, and they're not. Their opinions shouldn't matter to him because they don't contribute or participate in any of the same journals or conferences that he does. Why does he bother?The answer seems obvious to me. I believe he cares deeply about science and wants to combat misstatements and misrepresentations wherever they appear. But what really happens when scientists engage Creationists in debate? Does anyone believe, including Ken Miller, that his response to DI persuaded any Creationists? I would push even further and ask the deeper question, is a response actually counterproductive? Do responses from people like Ken Miller represent success for Creationism by conferring upon it a false legitimacy? Does it dignify their ideas merely to respond?Yup!As long as there is a vibrant and active debate, those inclined to accept a literal interpretation of Genesis will be comforted by the strong circumstantial evidence that the issue of evolution is not yet settled.--Percy

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Originally posted by Percipient:
Why does he bother?

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The answer seems obvious to me. I believe he cares deeply about science and wants to combat misstatements and misrepresentations wherever they appear. But what really happens when scientists engage Creationists in debate? Does anyone believe, including Ken Miller, that his response to DI persuaded any Creationists? I would push even further and ask the deeper question, is a response actually counterproductive? Do responses from people like Ken Miller represent success for Creationism by conferring upon it a false legitimacy? Does it dignify their ideas merely to respond?

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Yup!

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Hi Percy, I am afraid that I have to disagree with you in this. Back in the 80's when the Moral Majority came along most scientists did not want to be bothered with debating "scientific" creationists. They considered it a waste of time and believed that most of the public would come to the conclusion that the "scientific" creationists were
full of it. It did not work out that way and for over a decade people who support science fought what could only be described as an uphill battle with an enemy that, while scientifically erroneous, displayed a wonderful political understanding. Dr. Miller, like so many other scientists now, understand that what the "scientific" creationists actually want is to remake science in their own image (they are a little idolatrous that way IMO), they would essentially wreck science teaching for a generation or more. When scientists do not refute and point out the errors in the creationists statements the public seems to feel that the creationists have a valid point, even when they do not. It is a sad fact that the majority of thw public really has little knowledge of or understanding about science, either about the facts or the workings of the subject. Silence in the face of the challenge posed by the creationists, regardless of what they call themselves, really does mean defeat.

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As long as there is a vibrant and active debate, those inclined to accept a literal interpretation of Genesis will be comforted by the strong circumstantial evidence that the issue of evolution is not yet settled.

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Actually they would be just as comforted by silence from the science camp. The only way to defeat the destruction of knowledge by the creationists is to point out the errors made and distortions told by the creationists. Allowing the enemy to shape the battle field is a sure path to defeat (a little paraphrasing of Sun Tsu there ).------------------
"Chance favors the prepared mind." L. Pasteur
Taz

Opps, sorry about the double post.------------------
"Chance favors the prepared mind." L. Pasteur
Taz

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Dr_Tazimus_maximus writes:
Hi Percy, I am afraid that I have to disagree with you in this.

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Sorry, Doctor, I'm afraid I'm going to have to agree with you. Though I didn't mention the other side of the coin, I see both responding and not responding as problematic. To me it's a clear catch-22 situation. If scientists answer then it's construed that there's an active debate and that issues aren't settled. If they don't answer then it's construed that there is no answer and that Creationism must have a valid point. It's a lose-lose proposition.If it weren't for Creationist efforts in public education then treating the issue with silence would be effective, but unfortunately when Creationists bring their issues to school boards then science is forced to develop scientific answers to what is, in essense, mere nonsense. It's a frustrating exercise.Why is science so powerless in the face of this challenge? We tell ourselves that *we* understand why Creationism is wrong, that it's just very difficult to explain it to the non-scientist, but while this is true it isn't the whole story. When a layperson witnesses a debate between a scientist and a Creationist they usually can't tell who, if anyone, won. And even in one-on-one debate here and at similar venues, it's rare that one side or the other is forced to beat an embarassed retreat, and this isn't something that happens only to Creationists.It's one thing to be unable to make headway in debate with someone who not only doesn't understand what you're saying, but also doesn't even understand what they themselves are saying. Sometimes the ignorance seems insatiable. But Fred Williams, just for example, understands (some might say misunderstands) a ton of science, can follow rather intricate discussions, and is capable of researching a topic, yet he's a YEC who has never been bested in debate that I've ever heard of. Whether the topic is information or 2LOT or Biblical inconsistencies, he has an answer for every challenge.Now I don't mean to get off into the topic of Fred, I was just using him because he's well known. My point is that even with knowledgable and informed Creationists there is rarely if ever progress in expanding the area of common understanding. Just chalking it up to human nature (ours, too, since we're as unlikely to change our views as they are) is unsatisfying and explains too little, at least for me. Whether the Creationists are convinced or not is really irrelevant to the scientific issues, which are already decided and settled as far as any form of Creationism goes, including OEC and ID. I think there's something fundamental driving this debate, but that we don't yet know what it is.--Percy

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Originally posted by Percipient:
But Fred Williams, just for example, understands (some might say misunderstands) a ton of science, can follow rather intricate discussions, and is capable of researching a topic, yet he's a YEC who has never been bested in debate that I've ever heard of. Whether the topic is information or 2LOT or Biblical inconsistencies, he has an answer for every challenge.

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Yeah, of course sometimes his answer is to throw empirical evidence out of the window in favour of a mathematical model that predates the discovery of DNA (his ongoing "discussion" with SLP about Haldanes dilemma).....

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Originally posted by Percipient:
If scientists answer then it's construed that there's an active debate and that issues aren't settled. If they don't answer then it's construed that there is no answer and that Creationism must have a valid point. It's a lose-lose proposition.

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If it weren't for Creationist efforts in public education then treating the issue with silence would be effective, but unfortunately when Creationists bring their issues to school boards then science is forced to develop scientific answers to what is, in essense, mere nonsense. It's a frustrating exercise.

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I feel like a bit of an outsider on this issue as I have only recently been acutely aware of the extent of anti-evolution activity in the US. I knew it happened, but I had no idea it was either so widespread or so extreme.There is an answer to the dilemma - scientists should not answer except on their areas of speciality. Most of the issues are not issues of science but issues of theology, philosophy and public policy. I certainly do not mean that scientists should not be involved in the debate, but the scientific community could well do with extending the scope of the debate to bring in theologians, philosophers and politicians on their side.The problem to my mind stems from the tendency of some scientists to leap to the defence of their field almost too vigorously: find a lawyer to contend with Philip Johnson, real scientists have better things to do with their time. Let scientists ignore Behe and Dembski until they actually publish some peer-reviewed work on IC or ID: they can be dealt with by philosophers of science, logicians and popular science writers.Sadly, scientists enjoy a good old argument like the rest of us, and a public profile helps bring in the research dollars, so I fear the scientific community will continue to inadvertently bolster the egos of the anti-evolutionists.[b] [QUOTE]I think there's something fundamental driving this debate, but that we don't yet know what it is.[/b][/QUOTE]I don't think you have to look very far for what is driving the debate from the creationists' side - profound insecurity and a need for clarity: political, social and theological. One can see this clearly when a social agenda is explicitly attached to creatonism, as with the entryist "wedge" strategy. But it is also apparent in the approach to scientific knowledge: the more extreme creationists not only exploit grey areas to undermine knowledge, but tend to take an absolutist approach to fact, theory, hypothesis and inference that is quite unlike any other area of science.

I speak from the perspective of a complete outsider to the evolution / creationism debate in the US.I believe that ignoring the creationist political and propoganda effort would be a grievous mistake. I understand that taking on the creationists (in fundamentalist or intelligent designer guise) may give them some patina of credibility in the mind of the (generally scientifically illiterate) public. But, if there is no opposing view, it will give the appearance to that undecided and/or uninterested public the false view that conventional science is unable to counter the creationist arguments or evidence.One has to appreciate that this is not a battle of evidence and intellect. Creationists are not trying to win the intellectual argument by publishing in the scientific media. They publish for the general public in a way which is simple enough for the public to grasp without being overwhelmed by detail. How much easier to convince the general public that immunological cascades are reeeally complicated and we can't think of how trial and error could have produced it so it must have been made by the supernatural creator. This, coming from a writer like Behe who has the aura of a practicing scientist in the field would be compelling to a general public which has a strong christian pervasion anyway. Compare that with trying to explain how the cascade could have evolved and worked at each stage.I think that it must be appreciated that the creationist debaters are not there to win the intellectual debate, they are there to win the hearts of the audience. Therefore the science debaters need to also engage on that level, as well as on the intellectual level. And this is not easy or natural for many. The main creationist debaters have had many years to hone their skills to be effective presenters, even if the material they present falls apart on close examination. How many science debaters have had the inclination and opportunity to hone such skills? It's different to teaching a class where the audience is generally more interested in the content than the packaging.I think it important that science spokespeople take a high profile because that will have a strong trickle-down effect to areas where decisions are being made by school boards etc. How much easier and more effective on the general public for the interested science supporter to cite what Gould or Dawkins or Brown or whoever said on tv last week than what was written in the last issue of Nature? And most of your politicians at all levels appear to be sensitive to public opinion and what is happening in the media. If they perceive that ID or "equal time in science classes" is the band wagon, will they resist it?Damned if you do and damned if you don't. On balance, I think it better to engage in the battle rather than hope the enemy will lose interest if the opposition doesn't show up.