Bizarre article claims genetic code is result of "design."

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Bizarre article claims genetic code is result of "design."

#1  Postby Shrunk » Mar 17, 2013 12:13 pm

The “Wow! signal” of the terrestrial genetic code
Vladimir I. shCherbaka, Maxim A. Makukovb

Abstract

It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but stronger in noise immunity is the genetic code. The code is a flexible mapping between codons and amino acids, and this flexibility allows modifying the code artificially. But once fixed, the code might stay unchanged over cosmological timescales; in fact, it is the most durable construct known. Therefore it represents an exceptionally reliable storage for an intelligent signature, if that conforms to biological and thermodynamic requirements. As the actual scenario for the origin of terrestrial life is far from being settled, the proposal that it might have been seeded intentionally cannot be ruled out. A statistically strong intelligent-like “signal” in the genetic code is then a testable consequence of such scenario. Here we show that the terrestrial code displays a thorough precision-type orderliness matching the criteria to be considered an informational signal. Simple arrangements of the code reveal an ensemble of arithmetical and ideographical patterns of the same symbolic language. Accurate and systematic, these underlying patterns appear as a product of precision logic and nontrivial computing rather than of stochastic processes (the null hypothesis that they are due to chance coupled with presumable evolutionary pathways is rejected with P-value < 10–13). The patterns display readily recognizable hallmarks of artificiality, among which are the symbol of zero, the privileged decimal syntax and semantical symmetries. Besides, extraction of the signal involves logically straightforward but abstract operations, making the patterns essentially irreducible to natural origin. Plausible ways of embedding the signal into the code and possible interpretation of its content are discussed. Overall, while the code is nearly optimized biologically, its limited capacity is used extremely efficiently to pass non-biological information.


It seems someone was asleep at the switch when this passed peer review. PZ Myers dismantles the paper here.

(NB: The authors are both mathematicians. And while it was published in a genuine peer-reviewed journal (once edited by Carl Sagan, no less!), that journal's focus is astronomy. A cursory glance by a biologist before publication might have prevented this fiasco.)
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Re: Bizarre article claims genetic code is result of "design."

#2  Postby kennyc » Mar 17, 2013 12:35 pm

OMG! How does shit like this get published in a peer-reviewed journal!
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Re: Bizarre article claims genetic code is result of "design."

#3  Postby theropod » Mar 17, 2013 2:25 pm

kennyc wrote:OMG! How does shit like this get published in a peer-reviewed journal!


If Joe (Atheistoclast) were still a member here he could crow about his submission(s) which have passed "peer review".

The big part of peer review that adds validity is how often such a publication is used in other papers as a reference. Initial publication is only the first step, and subsequent work based in whole, or part, on that work provides the follow-on confirmation of the original paper's validity.

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Re: Bizarre article claims genetic code is result of "design."

#4  Postby Calilasseia » Mar 17, 2013 8:58 pm

Though of course, you'll find that actual scientific papers still provide citations for professional liars for doctrine such as Dembski and Wells. Said citations, however, merely precede a thorough demolition of their canards.
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Re: Bizarre article claims genetic code is result of "design."

#5  Postby DarthHelmet86 » Mar 18, 2013 5:13 am

Seems it is a common tactic to aim at a journal that isn't really focused in the area that the paper is about in the hope that it will pass muster and can then be bragged about how they got a paper past peer review. The followers wont argue about what journal it got in, in fact I bet they wont even think to ask, and the liars get to keep spinning the yarn that they are fighting the good fight. Anything to keep the followers paying them the big bucks.
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Re: Bizarre article claims genetic code is result of "design."

#6  Postby kennyc » Mar 18, 2013 11:22 am

Yes. I notice this happening more often of late.
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Re: Bizarre article claims genetic code is result of "design."

#7  Postby salzberg » Nov 15, 2013 6:58 pm

I just happened to notice this post. Clearly Icarus should not have published this - however, you might be interested to know that the authors did submit this to at least one biology journal, from which it was rejected. I was one of the editors who received their submission, so I know this firsthand. I won't say which journal but my guess is that most (one would hope all) biologists would reject this bizarre article.
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Re: Bizarre article claims genetic code is result of "design."

#8  Postby Calilasseia » Nov 16, 2013 2:48 am

Well since I have 25 papers on the evolvability and evolution of the genetic code, I treat any claims about "design" thereof with entirely proper suspicion. Not least because the whole "design" apologetics peddled by professional liars for doctrine such as Luskin et al., is a grand exercise in discoursive duplicity, based upon two manifest baits and switches.
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Re: Bizarre article claims genetic code is result of "design."

#9  Postby james1v » Nov 16, 2013 2:52 am

How, bizarre.
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Re: Bizarre article claims genetic code is result of "design."

#10  Postby Greyman » Nov 16, 2013 3:57 am

DarthHelmet86 wrote:Seems it is a common tactic to aim at a journal that isn't really focused in the area that the paper is about in the hope that it will pass muster and can then be bragged about how they got a paper past peer review. The followers wont argue about what journal it got in, in fact I bet they wont even think to ask, and the liars get to keep spinning the yarn that they are fighting the good fight. Anything to keep the followers paying them the big bucks.

I'm unsure of how this is even working. What's happening? How do articles outside a journal's field of study even get published?

Are the reviewers unable to admit that an article is outside their area of expertise?

If no relevant expert is available to review it, is the job handed off to Bob, the janitor?

Or are they saying "we can't find anything wrong with this because it is ... (outside our expertise / blatant nonsense / whatever)," and the editors are just missing the qualifiers?

What?
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Re: Bizarre article claims genetic code is result of "design."

#11  Postby Calilasseia » Nov 16, 2013 4:50 am

Well one issue that I am aware of here, is that mathematicians sometimes have a habit of thinking that their pet hypotheses somehow magically dictate to reality. There's a lot of emphasis on pursuing elegance in mathematics, a concept I saw at work first hand in the mathematics classes I attended, courtesy of the fact that in many instances, a search for an elegant solution has proven to be of utility value repeatedly within that realm. for example, from my own classes, I can recall being taught how a number of proofs in the world of Cartesian coordinate geometry, which are tedious and long-winded when attacked within that system, become wonderfully elegant, and expressible with startlingly contrasting brevity, the moment you move on to vector analysis. Likewise, proving that certain results in the world of vector analysis are valid for all possible coordinate systems, is a tedious and long-winded affair, but the moment you move on to tensor analysis, the resulting proofs become simple, elegant, and expressible with an almost frightening brevity of notation. Indeed, it's impossible to do any serious work in General Relativity without recourse to tensors, and tensor analysis has proven time and again to be a wonderfully elegant vehicle within which to express some ferociously complex concepts in simple, elegant and succinct terms.

There's a dark side to this pursuit of elegance, though. Whilst pursuit of elegance in mathematical proof has, in numerous instances, led to entire new methods of analysis - indeed, the whole of modern analysis, involving groups, rings, fields, vector spaces, topologies, and more recently, category theory, arose from said pursuit of elegance, framed in terms of generalisation and unification of concepts - the temptation is ever-present for mathematicians to read into this something that may not necessarily be there. This temptation has led even world mathematicians to engage in dangerously fragile speculations, Kurt Gödel being a prime example. After having unleashed his Incompleteness Proof upon the world, a proof which ironically, from the standpoint of his later speculations, provided a proof that formal axiomatic systems had their limits, Gödel then went on to engage in some frankly worrisome speculations, centred upon the manner in which mathematics is so frequently a valuable tool for understanding the real world. It's a temptation that, as I learned in my classes, mathematicians have to be on their guard against. Constant vigilance is required, if a mathematician is to avoid making a leap from appreciating the utility value of elegance, to adopting seductive but unsupportable metaphysical assertions on the basis thereof.

Unfortunately, not every mathematician maintains that vigilance. Worse still, some fall into the trap of concluding that an elegant model they have constructed must somehow necessarily be right, simply because that model is so elegant and beautiful and sophisticated. Having seen the value of elegance elsewhere, some mathematicians fall into the trap of thinking that elegance constitutes some sort of soundness criterion for models of the real world, forgetting the lesson learned the hard way by empirical scientists, that no matter how exquisite one's theoretical constructions are, if those constructions don't agree with the data, then they're nothing more than academic curiosities.

Indeed, mathematicians have come a cropper in the past, with respect to trying to lecture biologists how biological systems behave. The infamous Wistar Conference in 1966 is a prime example, where mathematicians tried to tell biologists that evolution couldn't work, on the basis of their models, only for the biologists to point and laugh. Interested readers can find out a little more about this here. Needless to say, creationists routinely quote mine the findings of that conference in a duplicitous attempt to peddle their evidence-free, assertion-laden propaganda, laced with the usual lies about valid science. But I digress. This latest paper is, in effect, another instance of mathematicians thinking that they can dictate to other branches of science, just because they happen to have alighted upon something they regard as "elegant".

It's not surprising that a biology journal rejected this paper. Biologists have to put up with this sort of intrusion into their work all the time, which is why sensible biologists recruit their own mathematicians, and teach those mathematicians a few pertinent biological facts first. indeed, quite a few biologists have been sufficiently mathematically sophisticated in their own right, to make valuable contributions to mathematics as well, and I emphasise strongly at this point, that genuine cross-discipline contributions by appropriately gifted individuals are manifestly welcome, much as my caveats above might suggest otherwise to the naive reader (or, bearing in mind the likelihood thereof, the quote miner).

Funnily enough, Dembski began his career as a mathematician, though as others have observed, his actual output in that field of endeavour has been sparse to put it mildly. The idea that this individual, with few properly peer reviewed publications to his name even in mathematical journals, is some sort of genius ready to lead the way to a new creationist golden age, a notion that has been doing the rounds of the Discovery institute for some time, is another one of those fantasies creationists have a habit of entertaining, flagrantly disregarding the inconvenient facts whilst doing so. Dembski has not only allowed a preference for pretty models over ugly data to cloud his thinking, he's also allowed his religious ideology to cripple his intellect, to the point that many now regard him as a joke figure, one who wasted his time allowing the music of the spheres of his own verbal diarrhoea, to hypnotise him into adopting banal fantasies, and pretend that those banal fantasies somehow magically dictated to reality. Of course, he isn't alone amongst supernaturalists in this regard, supernaturalism by definition consists of pretending that the assertions of your favourite mythology dictate to reality, without bothering to ask whether or not reality actually agrees with this, but Dembski has added to the mix an unfortunate brand of hubris that any competent mathematician should be on guard against.
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Re: Bizarre article claims genetic code is result of "design."

#12  Postby Rumraket » Nov 17, 2013 12:43 pm

I love this claim of theirs:
Nutbag ID mathematicians wrote:To be considered unambiguously as an intelligent signal, any patterns in the code must satisfy the following two criteria: (1) they must be highly significant statistically and (2) not only must they possess intelligent-like features, but they should be inconsistent in principle with any natural process, be it Darwinian or Lamarckian evolution, driven by amino acid biosynthesis, genomic changes, affinities between (anti)codons and amino acids, selection for the increased diversity of proteins, energetics of codon-anticodon interactions, or various pre-translational mechanisms.

Good, then we can dismiss all their conclusions, because the genetic code is emphatically not inconsistent in princicple, with any natural process. Here's the simplest one: Chance.

QED.

How did this crap pass peer review? Astronomers reviewed it? Since when did astronomers lose the capacity for thought?
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Re: Bizarre article claims genetic code is result of "design."

#13  Postby Rumraket » Nov 17, 2013 12:46 pm

Hello salzberg, welcome to the forum. :cheers:

salzberg wrote:I just happened to notice this post. Clearly Icarus should not have published this - however, you might be interested to know that the authors did submit this to at least one biology journal, from which it was rejected. I was one of the editors who received their submission, so I know this firsthand. I won't say which journal but my guess is that most (one would hope all) biologists would reject this bizarre article.

Yes, no less because they supply their own criteria for falsification of their hypothesis by making a logically untenable absolutist claim.
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Re: Bizarre article claims genetic code is result of "design."

#14  Postby iamthereforeithink » Nov 17, 2013 2:49 pm

Here's the paper on arxiv: http://arxiv.org/ftp/arxiv/papers/1303/1303.6739.pdf

Holy shit! Maybe PZ Myers is on to something with this:

I don’t know how it got accepted for publication, other than by boring the reviewers with its incomprehensible digit fiddling.


I gave up after two pages, having failed to decipher the first thing about what the fuck the authors were talking about. Maybe the paper is hard to refute, because the refuter would need to be an expert in both mathematics as well as biology. Maybe susu.exp could comment?
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Re: Bizarre article claims genetic code is result of "design."

#15  Postby Rumraket » Nov 17, 2013 3:14 pm

I'm an expert in neither and I've refuted it above.
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Re: Bizarre article claims genetic code is result of "design."

#16  Postby iamthereforeithink » Nov 17, 2013 4:06 pm

Rumraket wrote:I'm an expert in neither and I've refuted it above.


Its possible that you might have. I didn't even understand what exactly their argument is, so I wouldn't know.
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Re: Bizarre article claims genetic code is result of "design."

#17  Postby Rumraket » Nov 17, 2013 5:34 pm

iamthereforeithink wrote:
Rumraket wrote:I'm an expert in neither and I've refuted it above.


Its possible that you might have. I didn't even understand what exactly their argument is, so I wouldn't know.

To be considered unambiguously as an intelligent signal, any patterns in the code must satisfy the following two criteria: (1) they must be highly significant statistically and (2) not only must they possess intelligent-like features, but they should be inconsistent in principle with any natural process, be it Darwinian or Lamarckian evolution, driven by amino acid biosynthesis, genomic changes, affinities between (anti)codons and amino acids, selection for the increased diversity of proteins, energetics of codon-anticodon interactions, or various pre-translational mechanisms.

Here they're claiming that if a statistically significant pattern can be found in the genetic code, and that pattern can't be explained by ANY naturalistic hypothesis even in principle, then that pattern can be "unambigously considered an intelligent signal".

It doesn't take much thought to realize that any kind of naturalistic rationalization thus, in their own words, would falsify their claim. So I just picked the simplest one I could think of: Chance.

We could postulate that the genetic code is a freak occurrence of mere statistical physics. Random brownian motion of all the requisite atoms happened to produce an organism with the modern genetic code. This is statistically a real physical possibility, (however unfathomably remote) - so we're done.
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Re: Bizarre article claims genetic code is result of "design."

#18  Postby Coroama » Dec 09, 2013 3:07 am

So I just picked the simplest one I could think of: Chance.


Hoyle and Wickramasinghe, p. 24.

“The trouble is that there are about two thousand enzymes, and the chance of obtaining them all in a random trial is only one part in (10^20)2,000 = 10^40,000, an outrageously small probability that could not be faced even if the whole universe consisted of organic soup. If one is not prejudiced either by social beliefs or by a scientific training into the conviction that life originated on the Earth [by chance or natural processes], this simple calculation wipes the idea entirely out of court.”
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Re: Bizarre article claims genetic code is result of "design."

#19  Postby Calilasseia » Dec 09, 2013 1:51 pm

Except of course, that this facile "calculation" of theirs not only involves the serial trials fallacy, but also ignores completely the effects of selection, ignores the fact that modern enzymes have a long history of being derived from simpler antecedents, and also invokes the "one true sequence" fallacy.
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Re: Bizarre article claims genetic code is result of "design."

#20  Postby Rumraket » Dec 09, 2013 2:16 pm

Coroama wrote:
So I just picked the simplest one I could think of: Chance.


Hoyle and Wickramasinghe, p. 24.

“The trouble is that there are about two thousand enzymes, and the chance of obtaining them all in a random trial is only one part in (10^20)2,000 = 10^40,000, an outrageously small probability that could not be faced even if the whole universe consisted of organic soup. If one is not prejudiced either by social beliefs or by a scientific training into the conviction that life originated on the Earth [by chance or natural processes], this simple calculation wipes the idea entirely out of court.”

Congratulations, you missed the point completely.
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