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The Finely Tuned Genetic Code
| November 19, 2011 | Posted by Jonathan M under Intelligent Design |
Francis Crick regarded the genetic code found in nature as a “frozen accident.” Yet more and more it is looking to be the case that this code is exquisitely finely tuned — with features suggesting it is indeed one in a million. Therefore ought not purposive or intelligent design be regarded as a legitimate inference, as the best explanation for how the code came into existence?
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33 Responses to The Finely Tuned Genetic Code
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I disagree with the “selection” hypothesis myself. This does not, however, mean that design is the only alternative. After all, the code is only “one in a million”. If there are 10^70 codes, that means there are 10^64 better codes than ours – why don’t we have one of them?
The degeneracy and chemical conservatism of the modern code is plausibly derivable from constraint upon expansion of a narrower code set, not from competition between random variants on the 20-acid code. This piece makes the common assumption that 20 amino acids is the minimum requirement for functional protein-based catalysis, and that codon assignments are considered to be just pulled out of a bag entirely at random. While everything alive today uses that 20-acid system, this only means that nothing using a smaller set has left descendants through to the present that continue to do so.
To illustrate by a reductio ad absurdum, imagine that there was just one amino acid. All you could make is poly-alanine, and you do it by passing RNA through a ribosome. Because you are polymerising amino acids, which have a certain distance between links, you are constrained in the width of code units. You are also constrained by the strength of bonding between the tRNA and mRNA, and by inevitable curvature of the tRNA anticodon. A one-base code would be too wobbly and short; a four-base code too tightly bound and difficult to keep linear in the tRNA. So the code is triplet, but not for coding reasons.
Now, if you start with such a system, where every codon means either “alanine” or STOP, it is obviously even more degenerate than the current system – 50- or 60-fold degenerate, depending how many bases are covered. If another amino acid is added to the system, that substitution is least disruptive if it is chemically related. This constraint means that subsequent errors that mistranslate one acid for another seem to be chemically conservative as if by magic – but really, they simply reflect the historic constraint on code expansion. Now you have divided your code set in two – and the obvious way to do that is to tighten up the specificity at one codon position. You don’t need precise specificity, as the requirement only demands a two-way choice – so base-blindness at that position becomes purine-pyrimidine specificity, not absolute base distinction in all 3 positions. That gives you transition-transversion bias protection, again as if by magic – the mechanism of tightening specificity is the stereochemical distinctness of the two classes, which happens to be the reason why there is a transition-transversion bias.
By a succession of such progressive additions, all subject to the same constraints on chemical conservatism and retention of codon blindness (-> 16-fold or 4-fold degeneracy depending on the number of bases involved) or purine-pyrimidine specificity only (-> 8-fold or 2-fold degeneracy) it is possible for an apparently optimised code to arise. Degeneracy actually goes down, but the reward is greater catalytic flexibility, and sufficent residual degeneracy remains to surprise the investigator.
I am aware that this is hypothetical. I am also aware that poly-alanine has no obvious functional value.
ChasD you state:
And, besides your blanket assertion that there are 10^64 better codes than the DNA code, what is your actual evidence to prove there is ANY conceivable DNA code better than the optimal one we find in life??
OT: New Video of William Dembski:
Of note: not only is DNA code found to be ‘optimal’, the programming of the cell exceeds what man has accomplished in computers. i.e. A cell apparently seems to be successfully programmed along the very stringent guidelines laid out by Landauer’s principle of ‘reversible computation’:
If you read Jonathan’s article really carefully, he will tell you that there are 10^70 possible codes, and will also quote you papers with Freeland as co-author that assess the variant codes by various error-tolerance metrics – the very assessments that persuade many in the Creationist/ID community that it must be designed. One of Freeland’s papers is entitled the genetic code is one in a million.
10^64 is not a blanket assertion, it is simply the result of dividing 10^70 (all possible codes) by 10^6 (the fraction that is better, on those metrics, than the one we have).
Do you have some evidence to back up your assumption that it is the best of all 10^70 possibilities?
Chas you ask:
Well Hubert Yockey
asserts on pages 180-83 in,,
That,,,
Thus Chas unless you have concrete evidence that Professor Hubert Yockey, who helped develop the atomic bomb, was wrong. I guess I’ll stick with his assessment that the DNA code is optimal out of 10^70 possible codes;
further notes:
Verse and music
Oh, for goodness’ sake! Yockey helped develop the atomic bomb? What an excellent grounding for a career in molecular biology! Yockey’s musings on the prebiotic soup have absolutely no relevance to the evolution of the genetic code. You may or may not realise that the origin of life and the crystallisation of the modern genetic code are two completely separate phenomena. That is the whole point. I am suggesting that the first cell with a 20 amino acid genetic code was not the first cell.
You really didn’t grasp what I was saying, did you? All your quote says is that there are > 10^70 codes, and selection would have to explore ‘em all to find the best. He does not say that the one we have is the best.
I too think that selective optimisation of the genetic code is impossible – but that is not the only means by which the apparent fault-tolerance can be achieved, as I argued in my first post. However, you are at odds with Jonathan M and his quoted sources if you think that the code is the best out of 10^70, rather than one in a million. With you and Yockey’s deep knowledge of molecular biology, no doubt you can pull up some basis for your assertion. That’s what Freeland et al have tried to do – compare codes by various metrics, and they come up with about 1 in a million. I don’t see it in your quotes – by what heuristic have Yockey, and you as his disciple, concluded that this code is the best? And where has this result been published?
Further notes:
Verse and Music
Chas you are extremely biased in your reading of this for Freeland et al:
Found that the genetic code is the best out of 1 million compared. Yet even though they found no superior code out of 1 million, you assume that the 10^64 they did not search are superior to the one code. Where in fact the best you could say is that for each million of the 10^64 codes there may be one code that is equal to or better than the one we find. But you don’t know that for sure and it is extremely biased of you, to put it mildly, for you to assume that all 10^64 codes not surveyed are superior to the ones they checked. As for this comment of yours,,,
Really???
Further notes:
Moreover besides such severe constraint on ‘evolvability’ of the ‘optimal’ code, the protein machinery that replicates DNA is found to be vastly different in even the most ancient of different single celled organisms, thus exacerbating the Darwinists insurmountable problems once over again:
There simply is no smooth ‘gradual transition’ to be found between these most ancient of life forms, bacteria and archaea, as this following articles and videos clearly point out:
As for your swipe at Yockey’s ‘atomic bomb’ credentials, Well considering your sheer lack of integrity thus far in being forthright with the math of the evidence, I will take his word over your word 24 hours a day 7 days a week, and then some!!!
Chas D:
You are certainly right that there are alternative codes. Indeed we see different codes at work in other areas of the cell.
I’m not sure the idea that the existing DNA code being better than other codes is a good argument. “One in a million” who know? That sounds more like just a rhetorical statement to me. As you point out, if it is one in a million, that still leaves a lot of potential codes on the table, and we may never know why this particular code was chosen.
That said, there are lots of interesting things we have learned about DNA. For example, why a 4-bit digital code? We can get come inkling, perhaps: Coding for 20 amino acids requires more than a 2-bit code. A 3-bit code would not permit a complementary strand, which is critical to DNA function (this is a structural requirement, not a “coding” requirement). Therefore, the 4-bit code appears to be the minimal or the “most efficient” code that could accomplish the basic objectives. Are there other things, say structural elements, beyond the code itself that make DNA more optimal than other approaches? I suspect we’ll find additional things as we gain more understanding of DNA and the interactions between the various components.
Nevertheless, I don’t think a “one-in-a-million” type argument is particularly persuasive from a standpoint of design. Rather, the focus needs to be on the fact that *any* rational and functional code exists in life. That is the distinguishing factor for design, much moreso than being able to argue that it is the “best code” or the “only possible code that could work”, etc.
From page 175; ‘The Cell’s Design’; Fazale Rana:
I’m unconvinced the genetic code is really optimal.
One of your major sources: “Freeland et al. (2000) show that the genetic code is highly optimized — indeed “the best of all possible codes” — taking into account two parameters: first, the relative likelihood of transitions and transversions; and second, the relative impact of mutation.”
Has been highly questioned in the literature. In particular, DiGullo finds “the origins of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analysis tautologous” which seems pretty self-explanatory.
http://www.sciencedirect.com/s.....9300922069
Other work has suggested the genetic code is stuck in a local, not global minimum, and that codes equally and more fit are easily obtained, calling into question the statistical approaches you cite.
“Simulated evolution applied to study the genetic code optimality using a model of codon reassignments”
http://www.biomedcentral.com/1471-2105/12/56
“Knight RD, Freeland SJ, Landweber LF: Adaptive evolution of the genetic code. In The Genetic Code and the Origin of Life. Volume 80. Edited by Lluís Ribas de Pouplana. Kluwer Academic/Plenum Publishers; 2004:175-184.”
DrREC, in your characteristic severe lack of skepticism towards anything of a atheistic neo-Darwinian persuasion, don’t you find it even a little bit suspicious that neo-Darwinists have NOT randomly evolved EVEN ONE CODE from scratch to begin with???
Nor even a single protein from scratch???
DrREC, perhaps your skepticism would carry much more weight if you had any foundation in science to argue from in the first place, rather than just you insisting that materialism is true?!?~!?!
Further note
“don’t you find it even a little bit suspicious that neo-Darwinists have NOT randomly evolved EVEN ONE CODE from scratch to begin with???”
Make life de novo you darn scientists!!! And do it without design or selection!
Actually, new codon functions (e.g. genetically incorporating artificial amino acids) and even a four base coding ribosome have been developed using directed evolution.
DrREC, please reference your claims DrREC! So that we may a little fun seeing how jerry-rigged your supposed ‘evidence’ is!(And by the way I don’t even consider atheistic materialists as true scientists in the first place since number 1, quantum mechanics has shown reductive materialism to be false, and 2, science is impossible without God guaranteeing our perceptions and reasoning in reality are trustworthy in the first place!)
But to further critique the sheer absurdity of the atheist’s foundationless materialistic conjectures, for the ability of purely undirected material processes to generate function information, as well as parallel integrated coding that far, far, outclasses anything man has ever devised, I want to point out that the highest level of information in the DNA is not even the information that is encoded on the DNA in the first place, but is the transcendent quantum information which is holding the DNA together, is directing the shape of the DNA to be in the form it is in, and is preforming very impressive ‘quantum computation” in/on the DNA:
Notes: First DNA does not control body plan morphogenesis:
Here are a few comments on ‘non-local’ epigenetic information being a very plausible solution to 3-D spatial organization of Body Plans,,, (as well as in quantum computation):
Although when many people speak of epigenetic information they are mainly focused on information flow in the cell that is not DNA centric in its basis, such as the many examples of epigenetic information flow Dr. Shapiro lists on page 22 of this following paper: ,,,
,,,There is a particular type of extra ‘epigenetic’ information in life, that is not listed in Dr. Shapiro’s paper, that is very important for people to consider. This information is transcendent quantum information. To build on the last two references of post 4.1:
Quantum Action confirmed in DNA by direct empirical research;
further note on non-local quantum computation within DNA:
I would like to reiterate just how ‘spooky’, to use Einstein’s infamous word, it is to find something that blatantly defies our concepts of time and space, on a massive scale, within our bodies;
At the 6:05 minute mark, of this following video, cells are photographed as they pull themselves together, from a distance, to form flawless blood vessels. The commentator on the video refers to the ‘at a distance’ action of the cells, to form flawless blood vessels, as a ‘miracle’;
we also find that non-local quantum information/entanglement is also necessary for dictating the final shape that proteins will take upon protein folding;
etc.. etc..
Another very interesting piece of evidence, that non-local’ quantum information/entanglement is dictating the shape of a organism, comes forth when we realize that the ‘shape’ of a organism fairly quickly disintegrates to thermodynamic equilibrium upon the death of the organism:
As well it is very interesting to note that this quantum information/entanglement, which will assuredly be ‘totally missing’ from the organism, once the organism disintegrates to complete thermodynamic equilibrium, is shown to be ‘conserved’. i.e. This transcendent non-local quantum information, though missing from the dead, and now disintegrated, organism must reside somewhere ‘in the universe’ (this provides a mechanism for the ‘eternal soul’ of man):
Music and verse:
“DrREC, please reference your claims DrREC!”
If you google either of the phrases genetically incorporating artificial amino acids or four base coding ribosome without quotes, and read the first article, you’ll be fine.
“Quantum Dots Spotlight….”
Wow. Do you just do a google search for quantum and biology? Your inability to grasp that realism in physics does not equate with metaphysical realism notwithstanding, this one is the most hilarious yet. Quantum dots are man-made semi-conductors (quantum confined semiconductors to be precise, hence the name) that are really bright fluorophores used in cell biology as “tags” to follow certain processes.
This highlights the depth to which you try to understand something before it becomes one of your links. Maybe stick to the youtube videos and Bible quotes.
DrREC, you state:
and yet it is your very own cherished atheistic philosophy of reductive materialism which is directly falsified by quantum entanglement. And yet quantum entanglement is found on a massive scale in molecular biology. Science at its best DrREC!!! Thus apparently it is you who ignores the scientific fact that you now have no materialistic basis in science in which to make any solid neo-darwinian conjectures that will bear fruit to the truth. Go figure?!? But then again it was never about the science, or truth, in the first place was it DrREC!?!
and just to drive another nail in the materialistic coffin that you have chosen to lay in:
A song for you DrREC:
Moreover DrREC, the ‘quantum dot’ link is quoted as to draw attention to the quantum computation of ‘It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.”,
“Moreover DrREC, the ‘quantum dot’ link is quoted as to draw attention to the quantum computation”
No, it isn’t a “quantum computation.” It is a method used by the researchers to image the process.
From your article:
“The researchers sought to unravel the mystery by tagging two repair proteins, called UvrA and UvrB, with quantum dots, which are semi-conductor nanocrystals that light up in different colors. They also stretched the usually clumped DNA into multiple “tightropes” to see the process more clearly.”
I really don’t have time to go over how bogus most of your links are–but you seem to have a almost willful misunderstanding of them.
DrREC, so apparently you can now read my mind as to my intent for posting the link? But reading minds would be another falsification of materialism wouldn’t it be??
,,, instead of honestly addressing the overwhelming evidence for quantum non-locality in the DNA, you belittle me! Should figure it is par for the course in dealing with a dogmatic neo-Darwinists to hurl insults instead of honestly addressing the evidence!!!. The DNA repair evidence I cited is solid for highlighting impressive quantum computation in the DNA no matter what you may say to the contrary, or how much you may proclaim yourself to be wiser than everybody else.
Article: “quantum dots, which are semi-conductor nanocrystals that light up in different colors” used to image DNA repair.
You: “DNA repair evidence I cited is solid for highlighting impressive quantum computation in the DNA no matter what you may say to the contrary”
Sorry, but you’re just making stuff up. The cited article is not about quantum computation in the DNA. Is is about using quantum dots (quantum confined semiconductors) as fluorescent tracers to image DNA repair.
DrREC, try to be honest just once, (it may just grow on you), and honestly answer this question. Since this
shows that you can’t have an interpretation of a quantum state as probabilistic, exactly what is your non-local materialistic cause for a quantum state since probabilities are now ruled out?
“How this system works is an important unanswered question in this field,”
I guarantee you the answer for how DNA is figuring out how to ‘fix potholes on every street corner in America” ain’t a materialistic one!!!!
“DrREC, try to be honest just once, (it may just grow on you), and honestly answer this question.”
My replies here are always honest.
You first-will you retract your interpretation of the quantum dots paper?
Your question here is a bit mangled. Are you asking about non-local realism? “Non-local materialistic cause” isn’t exactly a phrase with meaning, or one you’ll find in the scientific literature. Google it.
As it stands, this paper is a hypothetical, a Gedankenexperiment: “given only very mild assumptions, the statistical interpretation of the quantum state is inconsistent with the predictions of quantum theory. This result holds even in the presence of small amounts of experimental noise, and is therefore amenable to experimental test using present or near-future technology. amenable to experimental test are confirmed, ”
See the “mild assumptions…. amenable to experimental test…. if the predictions are confirmed.” Bit of a reading comprehension fail from “since probabilities are now ruled out.”
And the last line of the abstract answers your question: “distinct quantum states must correspond to physically distinct states of reality” in a direction I don’t think you like, given your interesting interpretation of QM.
DrREC, you state ( i mean pontificate as if you had a clue):
“distinct quantum states must correspond to physically distinct states of reality”
Now do you really think you know what this means DrREC? This is going to be real good!
DrREC this statement means that quantum waves are physically real instead of abstract. In case you did not know, the position of materialists was that the quantum wave state was abstract. In fact Everett developed his entire Many Worlds (infinite parallel universes) hypothesis off of that very premise!,,, Night!
Ok…well, thanks for answering your own question before I had a chance to reply. I’m not sure why you asked me to interpret a sentence in plain English in such insulting terms. I could do without “as if you had a clue” and “try to be honest just once.” Others have been banned for less-but the hypocrisy of the blog moderators is a discussion for another day.
This, especially on a thread where the vacuousness of your links was pointed out. You literally searched for “quantum + DNA” and came up with a experiment where DNA repair was experimentally observed using quantum dots (semi-conducting nanocrystals) and advertised it as quantum computing of DNA!
So instead of admitting you were wrong, you start insulting me about some other link you found.
Again, that paper is a thought experiment without experimental verification, despite your claim that “since probabilities are now ruled out.” I also don’t think their hypothesis is decisively anti-materialist.
DrREC, Oh goody more derision and false accusation as to my true intention for posting the ‘quantum dot/quantum comoputation’ paper. I believe they call this type of argumentation ‘straw man’. Once again this is par for the course in dealing with a neo-Darwinist who is dogmatically committed to atheism! Moreover you act as if quantum computation in the DNA repair paper is not readily apparent. OK DrREC, if this massive ‘traveling salesman’ computation is being done ‘materially’ in the DNA, as you hold that it is,;
The traveling salesman problem is an:
,,,so as to allow the DNA to ‘materially’ (locally) calculate how to fix ‘every pothole in America before next rush hour’, where exactly in the DNA’s A, T, C, and Gs is this calculation being done??? Please point me to the CPU in the DNA so that I may see the DNA busily, materially, carrying this calculation out in a local (within space-time), material, fashion.
I’m all ears DrREC! Please show me where the ‘material’ calculation is being done!
corrected link:
DrREC, as to this comment:
Yet, although you, and the authors of the paper, are not aware of it yet, there actually is experimental verification that quantum waves are in fact ‘physically real’;
It is also interesting to note that materialists/atheists, instead of dealing forthrightly with the Theistic implications of quantum wave collapse, postulated quasi-infinite parallel universes, i.e. Many-Worlds, in which any absurdity would not be prevented from happening in the infinite parallel universes i.e. Elvis could be president, pink elephants, etc.. etc.. in the Many-Worlds model;
A closer look at the ‘physically real’ quantum wave state, reveals some very interesting things:
Moreover, quantum wave collapse is found to be instantaneous, and universal, to each unique point of observation in the universe:
Now, I find all of the preceding, that we have briefly gone over, to be absolutely fascinating! A photon, in its quantum wave state, is found to be mathematically defined as a ‘infinite-dimensional’ state, which ‘requires an infinite amount of information’ to describe it properly , which can be encoded with information in its ‘infinite dimensional’ state, and this ‘infinite dimensional’ photon is found to collapse to each individual point of observation in the universe, instantaneously, and thus ‘non-locally’, to just a 1 or 0 state, out of a infinite number of possibilities that the photon could have collapsed to instead!!!,,, Now my question to the materialistic atheists is this, “Exactly what ’final cause’ has been postulated throughout history to be completely independent of any space-time constraints, as well as possessing infinite knowledge and power, so as to be the ‘sufficient cause’ to explain what we see in the ‘effect’ of quantum wave collapse of a photons to each unique observer in the universe???
As to ‘thought experiments’:
Moving away from the face of a clock at the speed of light happens to be the ‘thought experiment’ that gave Einstein his breakthrough insight into e=mc2 and opened up a new era in physics.
As well, Einstein used a thought experiment of falling in a elevator to gain his breakthrough insight into general relativity:
As well a thought experiment was used to verify that the beginning of the universe must be absolute:
Thus DrREC, thought experiments, though poisonous, and very unfruitful when in the hands of neo-Darwinists, are actually very fruitful, in the field of physics, for discerning the Theistic foundation of reality
=
Further note on how Atheists have twisted the preceding proof:
Thanks, bornagain77, for the thoughts on error-minimization.
Like I said, I think we’ll find even additional things as we gain more understanding of DNA. Given that DNA is designed and the code was selected from among possible codes, it is very likely that the code (and related DNA structure) will turn out to be a remarkably efficient and capable code that performs its task beautifully from an engineering standpoint.
My point is simply that, by definition, the code is arbitrary. Therefore, to support design it does not have to be better than other codes or the best possible. There may be design constraints, as with any design process, that impose limitations and make the code less than perfect, or even less than other hypothetical possible codes.
Stated another way, the idea that the DNA code is “the best” or is “perfect” (I’m not saying this is your position) is really another example of the “perfect design” requirement that design critics try to impose. Then the argument is opened up to all kinds of attack, based on some alleged design shortcoming or some other possible “better” design. We shouldn’t get caught in that rhetorical trap.
I agree that the DNA code is impressive. I am also confident that the more we learn we will find that it is extremely finely tuned to the task at hand and that it will turn out to be another example of exquisite design, like so many things we see in biology.
My point is more narrow: (1) by definition the code is arbitrary, and therefore, there are other possible codes, including some that could turn out to be quite close in terms of function and capability; (2) the code can be functional and fill its task beautifully without meeting some arbitrary definition of “best” or “perfect” (in other words, the code can be imperfect and still be exquisitely functional); (3) the very existence of a complex functional code is the key evidence for design, not the particular code selected.