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A Code That Isn’t Universal
| May 18, 2010 | Posted by Cornelius Hunter under Intelligent Design |
The DNA code, which translates DNA sequences into protein sequences, has always been claimed as extremely compelling evidence for evolution. The code was first described in the mid twentieth century and, among other things, was found to be universal, or nearly so. The same DNA code is used in the cells in your brain and your big toe. The same DNA code is used in different species. The same DNA code is even used across the major kingdoms. All tissues, all species use the same code? Surely they were not independently created—they must have evolved. And if the code varied, on the other hand, evolution would surely be falsified. In one fell swoop, the DNA code not only is another compelling evidence for evolution, it also demonstrates that evolution is falsifiable, a badge that is crucial for evolutionists who seek to distinguish themselves from those religious rascals. But now a new code has been discovered and, believe it or not, it is not universal. Read more
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Mr. Nakashima;
“If you found a second or third instantiation of the genetic code in nature in which the same code was instantiated as magnetism vs polarisation of light beams, that would be a very strong evidence that it did not occur via the channels we now are investigating.”
I really hope you see the circular argument in this. You start by claiming that the genetic code is a “naturally occurring code” and then you use it to distinguish it from other code systems – which form the basis of your argument.
You first need to establish beyond reasonable doubt that it actually is “the only naturally occurring code”. You have not done so with your effort to simplify the interactions that the code baring medium has with nature. In fact your simplification should be applicable to all potential code baring media in nature, and yet we don’t see code baring patterns all over. Statistically there are media that can more easily be endowed with “randomly generated messages”. Yet we don’t see them around.
Your proposed mechanism is flawed and certainly not supported by observation.
KF-san,
3 –> And if the atmosphere is more reducing, you get UV disintegration of complex molecules. So, off to convenient caves and deep sea vents.
IOW, I’d prefer to be distractive than to admit there are solutions to this problem. Indeed, rather than a problem, high energy photons are an important source of the energy gradient necessary for life, even today.
4 –> next problem: chirality.
Next solution, late afternoon sunlight. Remember you were just saying how strong it was back then? Or some other process:
Imitating Prebiotic Homochirality on Earth
From the abstract:
The process can start with a miniscule excess and in one step generate water solutions with L/D ratios in the over 90% region. Kinetic processes can exceed the results from equilibria. We have also examined such amplifications with ribonucleosides, and have shown that initial modest excesses of the D-nucleosides can be amplified to afford water solutions with D to L ratios in the high 90’s.
Mr Mullerpr,
I’m sorry, you misunderstand the purpose of my example. Your initial objection was that a code can be instantiated in multiple ways. That is certainly true of codes in general, and we see that humans do instantiate codes in different ways. However, the genetic code is only found in nature instantiated in one way, as the association of RNA triplets and amino acids. Failing evidence of multiple independent instantiations, we have no warrant that the code exists as an abstraction prior to, or independent of, that particular instance in nature.
I did not argue that the genetic code was the only naturally occuring code. I agree that there are other naturally occuring media that can host coded information. For example, patterns of magnetic reversals – we use these on our hard drives, and they do occur in nature. There could be patterns of L vs D enantiomers, or open vs closed chromatin. The problem is that nature does not create a lasting association between any of these.
While the word ‘code’ is common and appropriate, it is also freighted with numerous associations that might not be appropriate when considering the origin of the code. If we just called it an association or bijection there might be less of that.
The stereochemical hypothesis is not a complete explanation, but it is supported by observation. I refer you to the paper already linked or the results of a Google search.
Granville:
In other words, despite decades of claims that evolution is a “fact, fact, fact…”, and that biological systems are replete with examples of evolution “in action” (ie, the peppered moths), New Scientist admits that its not until 2008 that we “finally” caught evolution in the act! And then…only after intervention on the part of an intelligent agent! Got it! Thanks for clearing that up!
“The Designer Who only uses found objects is indistinguishable from Nature.”
If I build a house out of stones and wood, then I am indistinguishable from nature. This is one of Nakashima’s stupider comments and he is not a stupid person but he was forced to do something. He may want to rethink this particular claim. This is a desperate attempt to get out of a hole he dug for himself.
Nakashima tries hard and it is rare when he admits a little support or understanding for the ID position but then he saw what he did and had to try and cover immediately. Anti ID people must be 100% anti and lack any sympathy or even understanding for an ID position. Thus, we have sympathy for the stupid comment. It was necessary to show he has not been corrupted.
Way to go, Nakashima. You make the ID case every time you come here because you are smart and try the hardest but then come up with nothing. What better support for our position could we ask for.
Follow up notes:
1: Above, I suggest a read through of the online book on he controversy over Signature in the cell, here. (It will also give you a pretty good idea of the level of critiques out there.)
2: I already corrected my error, on spotting it in JT;s cite [I really must be getting tired], and it is 7 bits per letter [I am using an assumption of basic ASCII, not extensions up to 8 or 16 bits.]
3: Nakashima-san, UV disintegrates complex, energetically unfavourable molecules, overwhelmingly. Indeed, I have seen it argued that this is what keeps the beaches on certain Caribbean islands bathe-able, by killing off bacteria in the clear water. And if R/DNA molecules in pre biotic environments were strong UV absorbers, then that would translate into they were rapidly broken up, not just that hey rotated, stretched and vibrated their bonds more intensely. The Ozone shield is vital to keeping life going on earth today. My point was, there is a double challenge: reducing atmosphere [which is not credible on other grounds] no Ozone shield. Oxygen, and required paths are poisoned by oxygen, an extremely reactive species. That is what sent OOL speculators to deep sea vents and to comets etc.
4: Similarly, I observe the chirality generation abstract to say in its first sentence: “We show how the amino acids needed on prebiotic earth in their homochiral L form can be produced by a reaction of L-alpha-methyl amino acids—that have been identified in the Murchison meteorite—with alpha-keto acids under credible prebiotic conditions.” First, the meteorite as I recall was recovered in a sheep farm, so its credibility for natural origin of L-form molecules is suspect. Since we are dealing with essentially geometry, abiotic chemical processes strongly tend to produce racemic forms, which are generally energetically equivalent. To get homo-chirality, you have to start with same, which can indeed in certain cases pick it out in a racemic context. So, the article’s premise of pre-exisitng presumably meteoric L-form amino acids to start the cascade, is suspect.
5: Further, I see that “With copper ion a square planar complex with two of the reaction intermediates is formed, and now there is the desired L to L transformation, producing small enantioexcesses of the normal L-amino acids. We also show how these can be amplified, not by making more of the L form but by increasing its concentration in water solution.” Le Chetalier and relief of constraints is the obvious explanation, but the question arises: how does one increase concentration sans Chemists and apparati, in a real world watery matrix which will have many other cross-interfering reagents and reaction paths that on concentration will most likely eat up the relevant reagents?
6: In short, we are back to the Shapiro-Orgel exchange on OOL scenarios, and implausible chemistry.
7: And, we have not yet got to the issue of the spontaneous origin of a von Neumann Replicator on such chemistry, complete with codes, algorithms, data structures and storage, code readers and algorithm effectors, plus either metabolic machines to build components or reservoirs of components; all in a compass of a few microns.
GEM of TKI
“Srsly? Which part of the peer reviewed scientific studies I referenced have been refuted? I look forward to reading the papers you reference.”
Exactly the sort of response one expects of persons unconcerned with reasoning properly.
“This is one of Nakashima’s stupider comments and he is not a stupid person but he was forced to do something.”
Exactly. DarwinDefenders aren’t stupid people … they just constantly make incredibly stupid assertions because that “logic” of attempting to protect Darwinism from critical and rational scrutiny requires it of them.
“That is, before the discovery of the 21st amino acid, the DNA code was believed to be a one-to-many encoding; now it is known to be a many-to-many encoding.”
Though, I did mean to write “many-to-one,” not “one-to-many.”
Mr Jerry,
If I build a house out of stones and wood, then I am indistinguishable from nature.
If your house looks like a pile of rocks or a tree, then yes. If you’ve pushed the rocks into a circle, you’re doing at least as well as a seagull. If you’ve piled sticks and branches up around and empty space, you’re doing at least as well as a beaver. The design of these houses is distinguishable from nature. If you point me at some boulders left over from an avalanche and say “I designed it.” then I have a hard time distinguishing your work from Nature.
Nakashima,
I think I did not misunderstand your argument, however you might have misunderstood my argument. To highlight the conclusion of my argument regarding the independence of a code from the medium that contains it was stated as follows:
@20 “The media does not “select” to be a code system on its own account. There is an intentional coder, message & decoder necessary.”
I considered the following article on your proposed mechanism:
Coding coenzyme handles: A hypothesis for the origin of the
genetic code
(ribozymes/RNA world/origin of life)
EORS SZATHMARY*
http://www.pnas.org/content/90/21/9916.full.pdf
Maybe someone can inform me why this is not a just so story. Dependent on the same question begging arguments presented here.
I still hold that there is no reason to accept the argument that the only natural occurring code is the DNA code, therefore the DNA code is a naturally occurring code. This is exactly the argument you use to distinguish between human generated code and the DNA code.
The ID argument sounds much better and is not begging the question. Intelligence at work is the only known code generating phenomenon.
KF-san,
Thank you for a direct questioning of the science involved. I appreciate that you are willing to question and challenge the facts and results as reported.
your 3 – What does UV do to RNA? From the above linked paper:
RNA/DNA strongly absorb ultraviolet radiation at around 260 nm at 1 atmosphere pressure
(Haggis, 1974; Chang, 2000) due to the 1 pi-pi * electronic excitation of the bases (Voet et al.,
1963; Callis, 1983). Most noteworthy, these molecules are ultra-fast at converting the
electronic excitation energy into heat through internal conversion; that is, into vibrational
motion of the atoms of the surrounding water molecules (Pecourt et al., 2000, 2001). This non-radiative process occurs on the sub-picosecond time scale, making RNA/DNA a very efficient absorber since the molecule promptly returns to the ground state, ready to absorb another photon.
So I agree that our intuition might be that absorbing UV would break the molecule. It seems that our intuition is wrong by not taking into account how rapidly this particular kind of chemical bond can convert a high energy photon into vibrational energy and dissipate it as heat into the surrounding water.
(The Zinc World hypothesis also assumes that RNA tethered to the surface of ZnS can share the energy with that bulk material faster than the RNA can break apart.)
your 4&5 – in part you say:
how does one increase concentration sans Chemists and apparati, in a real world watery matrix which will have many other cross-interfering reagents and reaction paths that on concentration will most likely eat up the relevant reagents?
As with the paper above, and many other OOL hypotheses, you work in the topmost microlayer, or in tidal pools (closer Moon, faster rotaton = more tidal action). There are plenty of places where evaporation can raise concentration.
7: And, we have not yet got to the issue of the spontaneous origin of a von Neumann Replicator …
Yes, there is so much exciting chemistry still to be discovered! It is wonderful to live in a time of such great advances.
Nakashima,
You might feel unfairly treated since your argument is actually: The DNA code is only instantiated in the living cell and therefore it is naturally occurring. Even so, it boils down to the same self-referential argument.
Explain to me how uniqueness of the code bearing can possibly convince anyone of its purely natural origin?
Sorry I missed a word, #42 should end with:
Explain to me how can the uniqueness of the code bearing MEDIUM possibly convince anyone of its purely natural origin?
Mr Mullerpr,
Thank you for being patient with me, if I have misunderstood you.
The article you reference is a discussion of a speculative hypothesis, as the first sentence of the abstract says. It presents no experimental results in favor of the hypothesis, only suggests that the hypothesis can be tested.
It is important to distinguish this kind of sharing of hypotheses from the publication of experimental results which do or do not support a particular hypothesis. The paper I have referenced is a report of experimental results, and it does support the stereochemical hypothesis for some amino acids while not supporting it for other amino acids. Both positive and negative results are published.
I’ve tried to make a distinction between a code and an instantiation of a code. I don’t think the genetic code is the only natural code possible, and I don’t think the media of amino acids and RNA triplets are the only natural media that can participate in a code.
I do think that the only instantiation in nature of the genetic code is the association of AA and RNA.
If I understand your position, you hold that there are at least two competing hypotheses:
H1 – An intelligent designer composed the genetic code in the abstract, and then implemented it in organic matter as a number of interacting chemicals.
H2 – A number of chemicals slowly assumed more and more definite associations over time, with more elaborate mechanisms to enforce that definiteness.
Is that correct?
Mr Mullerpr,
Explain to me how can the uniqueness of the code bearing MEDIUM possibly convince anyone of its purely natural origin?
It doesn’t. Whereas multiple independent instantiations might be a warrant that a code is an intelligent design, lack of evidence for one hypothesis is not positive evidence for another hypothesis.
Nakashima,
There is an old saying,
“It is a good thing to follow the first law of holes; if you are in one, stop digging.”
Quit digging and get out of the hole and move on. You are looking foolish and as I said, you are a smart person.
Well Jerry, I don’t think its possible for Nak to stop digging holes. I believe he lives in a self imposed box,
http://www.crystalinks.com/outsidebox.jpg
A self imposed box where it is impossible for him to even consider the possibility of not digging holes (to think outside the box):
Dig it – From the Disney Movie “Holes” – song
http://www.youtube.com/watch?v=ybjSSExktzI
Actually Nak, I think self imposed prison is a better analogy:
Creed – My Own Prison
http://www.youtube.com/watch?v=_YoUuwDZuW0
Mr Jerry,
You are very kind, thank you.
Actually this is a demonstration of quantum tunneling. By Heisenberg’s Uncertainty Principle, the more certain you are that I am in the hole, the faster I’ll be out of it!
Nakashima in #40
With respect to this response, one wonders exactly what features, then, would indicate intelligent design as opposed to the blind, purposeless forces of nature. Would, say, an irreducibly complex biological system also be “indistinguishable” from nature? You’ve practically tripped over one of the major foci of ID: distinguishing between undirected, natural causes and intelligent causes. From the example list you provided above, perhaps you might indicate precisely what characteristics would tell you that something is not the result of undirected, natural cause.
Mr DonaldM,
You’re quite right, this is the foci of ID. In the spirit of the Rev Paley, if I go walking through the forest and happen upon a log cabin, I will conclude design, while if I happen upon a deadfall, I will conclude nature acting by chance. Suddenly, a woodsmen appears out of the forest and claims to have designed the deadfall. What is the evidence he can bring that would convince me?
Would, say, an irreducibly complex biological system also be “indistinguishable” from nature? You’ve practically tripped over one of the major foci of ID: distinguishing between undirected, natural causes and intelligent causes.
As we can see from the fact that you dropped it from your second sentence, the phrase “irreducibly complex” adds nothing to the issue. As an attempt at problemizing complexity, it has failed.
From the example list you provided above, perhaps you might indicate precisely what characteristics would tell you that something is not the result of undirected, natural cause.
Even if I didn’t see a beaver make it, the marks of the beaver’s teeth on the sticks would be one strong clue. Craig Venter’s synthetic DNA strand also contains makers marks.
BTW, since we have been discussing the genetic code earlier, I see that according to Wikipedia there are 23 versions of the genetic code already documented!