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Topic: Peter Borger: Genetic Redundancy: The Ultimate Evidence of the Design of Life
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peter borger
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Member # 722
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posted 22. November 2006 08:16
John and REC,
FROM GUToB:
"Inspection of the distribution of codons demonstrated that the genetic code was designed to minimise the deleterious effects of mutations. If a mutation occurs that changes the first position of a codon, it will usually specify a similar, if not the same, amino acid. Furthermore, codons with a pyrimidine (C or T) in the second position usually specify hydrophobic, fat-soluble amino acids. Codons with a purine (A or G) in the second position correspond to hydrophilic, water-soluble amino acids. This is important since most occurring mutations are transitions mutations that replace a pyrimidine or a purine. Hence, if point mutations occur in the second position of a codon they will usually replace the amino acid with a very similar one. And when transition mutations occur in the third position of a codon the specified amino acid will almost certainly not change. Even when an error leads to the incorporation of the wrong amino acid, the code's arrangement ensures that the chemical character of the substitute is similar to that of the pre-programmed amino acid, making the alteration in the mutated protein relatively harmless. The redundancy of the genetic code may have been designed so as to coexist with some other kind of higher genomic code – a secondary code created by the first code – but of unknown character. In 2006, Eran Segal and coworkers described the discovery of a genomic code for nucleosomes positioning [3]. In an interview with the New York Times Segal said the secondary code could be the nucleosome code [4].
Another remarkable consistency of the code is that whenever G or C occupies the first two positions of a codon, each of the four nucleotides in the third position specifies the amino acid. This is observed for alanine, arginine, glycine, and proline. In contrast, if the first positions are both occupied by an A or U, the identity of the nucleotide on the third position is irrelevant. Because GC base pairs are stronger than AU pairs, mismatches in pairing in the third position are often tolerated if the first two positions in the codon make strong GC base pairs. Having all four nucleotides in the third position ensures the incorporation of the same amino acid in the protein and operates as a safety mechanism to minimise errors. Stability rules biology!
But there is more to the design of the code. Once it was known how the 64 codons related to the 20 amino acids, it had to be figured out how the codons were recognized and how the message was translated into functional protein. Scientists concerned with this task initially thought that every codon would be recognized by a specific complementary anticodon present in the transfer RNA that carried the corresponding amino acid. If perfect pairing occurred between the codon of the messenger and the anticodon of the transfer RNA, then 64 different codons would require an equal number of transfer RNA molecules – one specific transfer RNA for each codon. The translation system turned out to be more elegant. A single transfer RNA recognizes multiple codons because of non-standard base pairing between the third letter of the codon and its complementary partner – the first letter in the anticodon. This principle is known as wobble and allows that one transfer RNA recognizes more than one codon; and conversely, it allows a codon to be recognised by more than one kind of transfer RNA, which, off course, will bear the same amino acid. This elegant principle only works because of the special design of transfer RNA molecules – they have a modified G(uanine) in their in their anticodon: inosine. In the wobble position of the anticodon inosine forms pairs with either C, A or U and ensures that a single transfer RNA molecule is sufficient to decode three different codons. The ‘wobbly’ chemistry of inosine enables that a minimum of 32 anticodons are required to decode all 64 codons; the wobble mechanism witnesses a design for high speed and high fidelity protein synthesis."
REC, there are indeed a few dissonant codes, but these are so similar to the universal one that they must be secondary derived modifications of the one canonical code.
(GUToB continued)
"Four decades have passed since scientists cracked the code, and there have been extensive debates about its origins. Some claimed the code must be the result of a random accident, a freak event that established the code in the first primordial organism. Others – the Darwinians – believe it has been shaped gradually, and was step-wise improved through natural selection. Most of these debates were of philosophical character, with little data to back either side. Only in recent years have new discoveries revealed how sophisticated a piece of programming the code really is. In 1998, Science reported that powerful computer analysis showed that only one in a million other possible, randomly generated codes was better at producing a workable protein even when the DNA carried mistakes.
“For example, in 1991, evolutionary biologist Laurence Hurst of the University of Bath in England and David Craig of Harvard University showed that all the possible codes made from the four bases and the 20 amino acids, the natural code is among the best at minimizing the effects of mutations. They found that single-base changes in a codon are likely to substitute a chemically similar amino acid and therefore make only minimal changes to the final protein. […] Now Hurst's graduate student Stephen Freeland at Cambridge University in England has taken the analysis a step farther by taking into account the kinds of mistakes that are most likely to occur. […] When those mistake frequencies are factored in, the natural code looks even better: Only one in a million randomly generated codes was more error-proof”. [5]
One in million means, that, when compared to a million other three-letter codes that can be generated from four symbols, 999’999 would do a worse job as a buffer against deleterious mutations. One in a million is very good. Still, the data implied that there might be better codes. Two years later, in 2000, the same group of scientists showed that, when realistic biosynthetic restrictions were factored in their calculations and a more accurate measurement of amino acid similarity was employed, the code as we observe it in living organisms is the best code possible. The one code currently in use by all organisms is the best there is as a buffer against deleterious mutations:
“When the error value of the standard code is compared with the lowest error value of any code found in an extensive search of parameter space, results are somewhat more variable. Estimates based on PAM data for the restricted set of codes indicate that the canonical code achieves between 96% and 100% optimisation relative to the best possible code configuration. If our definition of biosynthetic restrictions is a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes.” [6]
Freeland and his colleagues reported that their new analysis showed that previous reports of a less optimised genetic code are based on a flawed measurement system. Their new analysis is more accurate and precise. If you were asked to design a genetic code from scratch, and you had all knowledge present of the new biology, you would end up with the one currently in use by all organisms. That is astounding! The universal genetic code appears a masterpiece of error-buffering design. Because the same code is used by all organisms there is no reason to assume the code has ever been different or that it has gradually evolved. If it would have been evolved gradually and was optimised by natural selection, we would certainly have found micro-organisms using distinctly different codes. We do not find them. The reported variants of the natural genetic code show that it may drift away a bit from the standard that, with its current perfection, was present from the start. The biological findings are what one might expect when the code is the product of intelligent design."
John, the one canonical code and the few minor variations indicate that all live is from a single source.
References:
[3] Segal E, et al. A genomic code for nucleosome positioning. Nature 2006, volume (online 19 july)
[4] Wade N. Scientists Say They’ve Found a Code Beyond Genetics in DNA. The New York Times 2006, July 25.
[5] Vogel G. Tracking the history of the genetic code. Science 1998, volume 281, pages 329-31.
[6] Freeland SJ, Knight RD, Landweber LF, Hurst LD. Early fixation of an optimal genetic code. Mol Biol Evol 2000, volume 17, pages 511-8.
[ 22. November 2006, 08:19: Message edited by: peter borger ]
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John A. Davison
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posted 22. November 2006 10:18
Peter
I realize the triplet code suggests a single source but I also recognize that a lot of other undisputable facts indicate multiple orgins. All I am doing is keeping an open mind. I hope others will do as much. If they don't that is fine too.
"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
[ 25. November 2006, 09:43: Message edited by: John A. Davison ]
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Daniel Smith
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posted 22. November 2006 17:52
John and Peter,
Perhaps the one genetic code and the evidence of multiple origins combine to show that there was a single designer with multiple creation events.
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John A. Davison
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posted 22. November 2006 18:23
Sure and why assume a single designer? The truth is nobody knows a thing about these matters.
"Men believe most what they least understand."
Montaigne
"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
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seer
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posted 25. November 2006 06:56
quote:
"Our actions should be based on the ever-present awareness that human beings in their THINKING, FEELING, AND ACTING are not free but are just as causally bound as the stars in their motion."
So John, if you ever were to take up theology again, I suppose that you would be a hyper-calvinist?
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John A. Davison
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posted 25. November 2006 07:52
Seer
I am not a theologian, never was, and don't plan on ever becoming one. I am a bench scientist or was until they took my laboratory away from me.
"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
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seer
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posted 25. November 2006 10:08
quote:
Seer
I am not a theologian, never was, and don't plan on ever becoming one. I am a bench scientist or was until they took my laboratory away from me.
"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
No you are not a theologian, but your beliefs do have some profound implications - especially when it comes to moral responsibility and justice...
[ 25. November 2006, 10:08: Message edited by: seer ]
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John A. Davison
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posted 26. November 2006 15:44
Seer
What we as individuals believe means nothing. People believe what they choose to believe, what they were predestined and subsequently conditioned to believe. The truth is all that matters and that is all I am really interested in. I am not very happy with some the conclusions I have been forced to reach. I recommend "Born That Way" by William Wright. I believe you will learn much about yourself as I did.
"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
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seer
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posted 26. November 2006 16:34
quote:
Seer
What we as individuals believe means nothing. People believe what they choose to believe, what they were predestined and subsequently conditioned to believe. The truth is all that matters and that is all I am really interested in. I am not very happy with some the conclusions I have been forced to reach. I recommend "Born That Way" by William Wright. I believe you will learn much about yourself as I did.
I have heard of that book before. But think about what you are saying. Perhaps we were predestined and conditioned to belief false things. Perhaps your conclusions are not true, how would you know?
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peter borger
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posted 27. November 2006 04:36
quote:
Perhaps we were predestined and conditioned to belief false things. Perhaps your conclusions are not true, how would you know
That the DNA molecule is rapidly degrading and subject to non-random changes does not mean everything we do and think has been predestined. Our bodies may be built of biological machines we have no control over, but our conscienceness may be able to choose. I believe we have a free will, as the result of the processing of a free-thinking, unrestricted, not-predetermined computing organ. We are not robots.
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John A. Davison
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posted 27. November 2006 05:32
Seer
Since you have "heard about that book before," I recommend that you now read it and consider its implications as I have. It is pretty scary stuff I must admit but to pretend that it does not exist is even worse.
I also recommend that all vist other forums and blogs to witness the degeneration that has come to characterize the methods employed by those who must ban rational discussion from their proceedings in order to preserve and protect their own selfish "prescribed" philosophical biases from exposure. It is an education in human behavior if nothing else.
One of the unique features of "Brainstorms" has been its capacity to remain receptive to opposing ideologies. It remains the only major forum from which I am not now banned and I think I can explain why. This forum is not dominated by an individual or a small group of individuals as is almost invariably the case in internet blogs and forums. It is also unique in that most of its participants actually use their given names which I take to be a sign of intellectual maturity and confidence in ones position. Compare the composition of this forum with the membership of Panda's Thumb for example which is littered with ludicrous pseudonyms so that it is virtually impossible to have any idea who these people are. They spend most of their time congratulating one another on their idiotic appraisals of others with whom they disagree. It is, as Martin has observed, a "madhouse." How Martin has escaped bannishent is a miracle and he is now being told that no one CARES what he says or thinks. That is why it is very important to visit these other "groupthinktanks," observe their shabby tactics, and comment on them here as I have done. Those who must practice such tactics as denigration, personal insult, isolation, disemvoweling, isolating their critics in "Boot Camp" and "The Bathroom Wall" and in "Davison's Soap Box" are nothing but animals and should be so identified. The final and ultimate cowardly act is bannishment, the mark of their total defeat which is why I can always say in response to such tactics no matter what forum or blog finds it necessary -
I love it so!
There are other ways in which one can prevent unsavory comments such as delaying their appearance. Those who ban participation by their presumed or imagined adversaries are intellectual cowards who are so insecure in their convictions that they sometimes even have to get others like David Springer (DaveScot) to do the banning and the denigrating for them. It is all very revealing and as I say once more -
I love it so!
We critcs of the Darwinian nightmare still do not exist either by the atheist worshippers of the Great God Chance or by those who try to slip Protestant Fundamentalism into the guise of real science. Ascertainable truth lies elsewhere and I remain confident that I know where that is. Otherwise I would never have published my convictions.
"Then there are the fanatical atheists whose intolerance is the same as that of the religious fanatics, and it springs form the same source... They are creatures who can't hear the music of the spheres."
Albert Einstein
Here's to "brainstorms," a "decent" forum, something one cannot say about most of them. Long may it live!
"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
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seer
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posted 27. November 2006 06:19
quote:
Seer
Since you have "heard about that book before," I recommend that you now read it and consider its implications as I have. It is pretty scary stuff I must admit but to pretend that it does not exist is even worse.
Well John, I'm certainly familar with determinism on the theological level. I'm not sure if it would change much on the biological level. But there is a real problem which I mentioned in my last post. One could never be sure that his beliefs or reasoning are true. There is no necessity for the biological process to produce truth.
As far as boards go, I hope you do make it to the TWEB. It is very active with a lot of give and take. I already started two threads based on your quotes. And I referenced Dee's e-mail in your other thread, she can help you get back on.
Some over there have really taken exception to some of your conclusions:
http://www.theologyweb.com/campus/showthread.php?t=87591
Peace, Jim
[ 27. November 2006, 06:34: Message edited by: seer ]
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seer
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posted 27. November 2006 06:24
quote:
That the DNA molecule is rapidly degrading and subject to non-random changes does not mean everything we do and think has been predestined. Our bodies may be built of biological machines we have no control over, but our conscienceness may be able to choose. I believe we have a free will, as the result of the processing of a free-thinking, unrestricted, not-predetermined computing organ. We are not robots.
Then conscienceness must be more than the biological process. Of course as I theist I believe this.
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John A. Davison
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posted 27. November 2006 07:08
*Attention, William Dembski*
I specifically recommend that William Dembski visit "After The Bar Closes" to witness the recently documented testimony of his personally appointed blogczar - David Springer. I hope Dembski will reconsider having this man in any way associated with Uncommon Descent or with any other venue associated with the promotion of Intelligent Design and civilized communication. I also hope that one day Dembski might see fit, at the very least, to mention my name as one of the pioneers in the Intelligent Design movement as every one of my published scientific papers so clearly testifies. To pretend that I do not exist, as he continues to do, does not bode well for one of ID's most prominent spokespersons. Neither does his inexplicable alliance with the most virulent and unprincipled bully in the history of internet communication - David Springer.
Of course those choices are Dembski's and his alone. I am only trying to offer some constructive advice wherever I am still able. That I will continue to do wherever and whenever I am permitted. Trust me.
A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
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