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

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

#241  Postby hackenslash » Aug 02, 2014 12:29 am

Well, if you'd read my post, mate...

The simple fact is that the data support no conclusions as yet. We have some good models, and little else.
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Re: Bizarre article claims genetic code is result of "design."

#242  Postby Darwinsbulldog » Aug 02, 2014 2:04 am

hackenslash wrote:Well, if you'd read my post, mate...

The simple fact is that the data support no conclusions as yet. We have some good models, and little else.


Yet! :grin:

I think we should remain agnostic, for now. There is reasonable hope that the models will become testable. Not all good models seem to be implemented in nature, but many are. Metaphysically speaking, biological evolution works, and chemical evolution works, perusing the idea of physical evolution of universe[s] is not a retarded idea. We should not expect evidence to come flowing like a strongly flowing tap all the time. Getting evidence for multiverses may be tricky, but it may be crucial. Multiverses are implied by inflation, after all. :thumbup:
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Re: Bizarre article claims genetic code is result of "design."

#243  Postby Max » Aug 02, 2014 7:16 am

Shrunk wrote:And the imprint in the clay is not the square object itself. But if we hypothesized the square object had fallen into the clay, then we know what kind of evidence would have to be there, right? If no imprint, then object did not fall into the clay. Wherease, if the clay happens to show no imprint, but also happens to be in a shape that we find "interesting" for some reason, what does that tell us? Not a lot, really, does it?

False analogy. Particularly because there is no any definite a priori hypothesis here.

The logic fail lies in your useless definition of "message", such that almost anything can meet it if you look hard enough. Really, the main problem is demonstrated in this earlier post of yours

If you really think that would be evidence that some intelligence was arranging the candies to create a message, you need to straighten out your thinking. (Hint: What is your rigorous, objective definition of "special"?)


Wait a minute. I have never in this topic offered any definitions of a message. Why are you constantly speaking up for me? I have already learnt from you that I am a mathematician and a creationist, and now I am learning that somewhere in this topic I had provided definitions of a message. It's really hard to have a normal discussion with you :(

The thought experiment was not an example of a message (at least, this would be a completely irrelevant analogy to the message in the genetic code). Neither it was intended to examine statistical issues. You're messing everything up. It was solely implied to demonstrate that notations (symbolic representations of quantities) are alien to natural processes. That's all.

Rumraket wrote:Now that's a failure of basic logic if I ever saw one. You made a statement, I'm asking you to back it up. Your response is to demand that I disprove your statement first.

Well, it is you who made an extraordinary claim ("natural processes might distinguish between notation systems"), therefore it is your business to prove/disprove it, not mine. But do not bother to disprove - I do admit that there might exist natural processes which do distinguish between notation systems. But I bet that if such a process is discovered, that would have much more implications than receiving a signal from ETI :lol:

It looks to me like you're trying to say that the mapping of the code cannot have evolved because it's not subject to natural selection, so it must have been designed.

The mapping of the code is subject to the strongest purifying (a.k.a negative) selection - this obvious fact is clearly stated in both our papers. This is exactly what makes the mapping "frozen". If it were not the case, the whole approach of a message in the code would have no sense.

I'm not claiming there cannot possibly be a message hidden in the genetic code, I'm saying your reasoning for ruling out the extant mapping being the inadvertent result of a natural process (which could have selected for many other things, of which the extant code's mapping simply resulted) is flawed.

We do not rule that out (would you ever peek into the paper?). In statistical testing we do take into account the constraints which reflect evolutionary pathways most widely believed to shape the mapping of the code. I guess you'll say - but no one knows exactly how the code emerged and evolved, so it is impossible to take into account any plausible pathway. I would certainly agree and will add that while there is no better option, directed panspermia is the most parsimonious explanation to those patterns (you don't have to appeal to unknown mysterious processes - good old Occam's razor). The rather that this is not an ad hoc explanation - the patterns themselves were found on the basis of this hypothesis.

Heck, you're the one interpreting the mapping of the genetic code through notations. Why does the result surprise you?

I do not interpret the mapping of the code through notations - false statement. But I see that every time an exact nucleon equality is observed in logical arrangements of the code, the sums that make up those equalities systematically happen to have distinctive notation in one and the same system (decimal, to be concrete) - no matter how any one interprets anything.

It didn't, you did. For fucks sake.

Appearance of profanities is a sign that a rational discussion turns into emotional wrangle. (By the way - that's why normally I abstain from discussions on forums - you never know the person you are talking with, and this anonymity allows that person to feel less responsibility for his statements, use personal affront, etc.).

You should be old enough to appreciate that what you like or don't doesn't magically alter reality.

Attacking a straw man. I said that I am not sympathetic to the idea, but I didn't say that it is wrong.

and so in none of them a being like Santa Clause is possible - because it would violate the laws in all those universes.

Which laws poor Santa Claus violates? Conservation of energy? momentum? Pauli principle? Lorentz invariance?


Sorry, guys, but you stubbornly refuse to look into the papers for concrete results and arguments. As a consequence, we are now not discussing what's in the paper. We are discussing raisins, red cars, clay pottery, and Santa Claus. Let's dance! :dance:

I have neither time nor wish to have discussion in this fashion, so I say bye-bye. You are welcome to accept this as my utter defeat. Thanks for discussion though. :smoke:
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Re: Bizarre article claims genetic code is result of "design."

#244  Postby Rumraket » Aug 02, 2014 12:22 pm

Max wrote:
Rumraket wrote:and so in none of them a being like Santa Clause is possible - because it would violate the laws in all those universes.

Which laws poor Santa Claus violates? Conservation of energy? momentum? Pauli principle? Lorentz invariance?

For Santa to be able to deliver presents to everyone on a single night, he'd have to be traveling some absurd velocity several thousand times the speed of sound. Friction with air molecules would disintegrate Santa's body. The g-forces associated with his acceleration and deceleration would also totally annihilate him, his carriage, everything in it and his mysterious flying Reindeer. His sleigh can only carry enough presents for a few households, meaning he'd have to restock somewhere every few visits. Reindeer also can't fly.
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Re: Bizarre article claims genetic code is result of "design."

#245  Postby hackenslash » Aug 02, 2014 12:46 pm

Had a scan of the paper. Lots of technical detail concerning items of interest to the authors of the paper in that they allegedly demonstrate instances that fulfil the author's criteria for message, but the underlying logic is just a beautiful commission of the Sherlock Holmes fallacy.
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Re: Bizarre article claims genetic code is result of "design."

#246  Postby surreptitious57 » Aug 02, 2014 1:43 pm

Would that be a perfectly logical deduction which is actually false

Or a completely true one that has not been subject to falsification
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Re: Bizarre article claims genetic code is result of "design."

#247  Postby hackenslash » Aug 02, 2014 2:07 pm

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

#248  Postby hackenslash » Aug 02, 2014 2:10 pm

Actually, I'd love to see an example of a true statement that has been subjected to falsification...
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Re: Bizarre article claims genetic code is result of "design."

#249  Postby surreptitious57 » Aug 02, 2014 2:24 pm

But how would you know if something is true unless you subject it to falsification

Specifically scientific truth not mathematical truth because they are not the same
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Re: Bizarre article claims genetic code is result of "design."

#250  Postby hackenslash » Aug 02, 2014 3:24 pm

If something's been subjected to falsification, it's wrong. That's the point.

I still think you haven't grasped falsifiability correctly.
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Re: Bizarre article claims genetic code is result of "design."

#251  Postby Scar » Aug 02, 2014 4:35 pm

surreptitious57 wrote:But how would you know if something is true unless you subject it to falsification

Specifically scientific truth not mathematical truth because they are not the same


Falsification is the process of determining wether something is false. Falsifiability means that this can be done, in principle.
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Re: Bizarre article claims genetic code is result of "design."

#252  Postby Rumraket » Aug 09, 2014 7:29 pm

@Max

http://arxiv.org/ftp/arxiv/papers/1303/1303.6739.pdf
I'm sorry but I maintain that your paper is crap. For example the fact that you use a non-standard genetic code (from some obscure ciliate), which is just one of dozens of variants, arbitrarily manipulate the numbers by considering non or rare physiological tautomers of the amino acid in question when the nucleon sums isn't what you need it to be.

The message you're "seeing" doesn't exist, you worked very hard indeed to create it. You're now surprised that you've found an intelligent signal of your own making. It doesn't get any more ridiculous than this. This is bible code numerology.

There are many questions I asked of you in my previous post you have neglected to answer.
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Re: Bizarre article claims genetic code is result of "design."

#253  Postby hackenslash » Aug 09, 2014 10:03 pm

Come back Michael Drosnin, all is forgiven. :thumbup:
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Re: Bizarre article claims genetic code is result of "design."

#254  Postby Jan_Thomas » Aug 10, 2015 11:34 am

Hi there!

I have joined this forum with the intention of resurrecting this year old thread, hoping to still reach some of the original commenters. Forgive me for doing so, but I am really curious about your reasoning. Many of the commenters here are still active according to their forum profiles, so I hope to still reach you. This was of course long ago, so I understand a lack of replies. Thanks in advance for any answers you care to give!

I have just finished working through the article that user "shrunk" quoted in the original post. It can be found in its entirety here (click "download pdf only" on the upper right.)
http://arxiv.org/abs/1303.6739
As a physician I have just enough professional knowledge of genetics to find it highly intriguing. I am however no expert. Be it true or false, I find the reasoning inside the article makes for a compelling read.

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


Kenny, did you read the abstract or the entire article? On what did you base your categorizing the article as shit? I found the abstract to sound like science fiction. After reading the whole thing, I'm not so sure.

I just saw that the OP is also still active. Shrunk, at which point did you think of the article as a fiasko?

Calilasseia wrote: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.


Calilasseia: You seem to me an expert in the field, having published papers like you say. I looked for a Luskin and found a "Casey Luskin" working for https://en.wikipedia.org/wiki/Center_fo ... ture#Staff ... This entity seems to promote Intelligent Design by a higher being or similar. Did you mean this guy? Your criticism seems to be directed at a similar agenda in the article by shCherbaka. I can asure you that I found not a single hint at some higher being or ID in the entire article. shCherbaka seems to be a man of science with a bold hypothesis. The hypothesis seems to be about finding signs for directed panspermia, not finding God Almighty's signature in the code.

I am honestly interested in your opinion: Do you with 100% certainty know that directed panspermia is impossible? If not, can you dismiss for certain that a signal could be embedded in a artificially modified genetic code? If I understand correctly, it is already possible to alter the code in, for example, E. coli, switching codons for two amino-acids or introducing new ones. Is this incorrect?

Rumraket wrote: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?


Rumraket: Your argument is interesting. Have you read the appendices? There the authors describe their efforts of creating - by chance - other genetic codesets that yield the same amount of symmetries and ideograms, while still remaining biologically viable. They generated large volumes of codesets and searched for symmetries in every one, to rule out the effect of "look long enough, and you will find patterns everywhere". It seemed a plausible way to dismiss their findings as random, however the actual genetic code seems to contain the highest amount of regularities among all candidates. How do you think of this? Did they cheat?

The authors argue that our genetic code seems to be coincidentally the one with the highest amount of nucleotide balances amond a billion others they generated by chance (which are still biologically valid... or near enough). Where did they go wrong?

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.


This is a valid response. I found the paper to be hard to understand in many places. I have a basic understanding of genetics, and it took me four days of spare time to get through it. I am of the opinion that they COULD be on to something. Or maybe I just don't see where they go wrong. That's why I am here.

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.


You argue that the authors are liars. On what do you base this?



I want to once more emphasize my earnest wish for discussing this matter. Any responses are very welcome!

Regards

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

#255  Postby Shrunk » Aug 10, 2015 12:42 pm

Hi, Jan_Thomas. Welcome to the group.

I think you'll find the flaws in the paper quite thoroughly dealt with in PZ Myers' article I linked in the OP. Here's the link again:

http://freethoughtblogs.com/pharyngula/ ... /#comments

If there's anything there you're not understanding, I'm sure some of the members here can help clear up your confusion.
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Re: Bizarre article claims genetic code is result of "design."

#256  Postby Rumraket » Aug 10, 2015 1:49 pm

Jan_Thomas wrote:Hi there!

Rumraket wrote: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?


Rumraket: Your argument is interesting. Have you read the appendices?

I have read the entire paper. I also, here in this very thread, discussed it with one of the authors. (You will note that I do not receive answers to my questions).

Jan_Thomas wrote:There the authors describe their efforts of creating - by chance - other genetic codesets that yield the same amount of symmetries and ideograms, while still remaining biologically viable.

Yes and as you well know, chance is remarkably unreliable. Look, read the sentence I highlight in red and notice how completely unjustified their claim is. They claim to rule out everything, even the unknown. You can't do that in a scientific paper, it is absurd.

Also, how the hell would the authors know what is biologically viable? The extant genetic code might be highly optimized for error minimization due to mistranslation, and robustness against non-silent mutations in coding regions, but who the fuck says a less optimized and less robust code is not biologically viable? It might be worse than the extant genetic code, but still a workable and functional code for some hypothetical organism.

The authors simply does not establish, anywhere, that less optimized and "more random" codes aren't "biologically viable".

You can't rule out chance in principle, you can only argue that it is more less likely depending on what the chances are.

But the authors claim to have ruled out chance even in principle. I'm sorry but this is simply not possible. Because guess what, it's a matter of chance. You can only make statements of probabilities. For example, "it is highly unlikely" that the genetic code is the result of chance. I agree, I don't believe the genetic code is the result of chance either. That doesn't mean it was designed (by aliens or supernatural agents).

Jan_Thomas wrote:It seemed a plausible way to dismiss their findings as random, however the actual genetic code seems to contain the highest amount of regularities among all candidates. How do you think of this?

They make up arbitrary criteria for what chemical states the amino acids they search for are supposed to exist in in order to get the result they want. Try reading the actual paper. A lot of time is spent retrofitting biosynthetic intermediate forms of amino acids to their "nucleon sum" and then picking that as "the one" because it fits.

Jan_Thomas wrote: Did they cheat?

Depends on what you mean by cheat. They did not, as far as I know, make up or falsify data. What they did was ad-hoc rationalization for why specific chemical manipulations of certain amino acids should be the ones "that count", instead of other precursors or derivatives also found in vivo.
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Re: Bizarre article claims genetic code is result of "design."

#257  Postby Shrunk » Aug 10, 2015 1:55 pm

One further point, if I may:

Jan_Thomas wrote:
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.


You argue that the authors are liars. On what do you base this?


In context, DarthHelmet86 was referring to creationists in general, not to the authors.
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Re: Bizarre article claims genetic code is result of "design."

#258  Postby Jan_Thomas » Aug 10, 2015 8:57 pm

Shrunk and Rumraket, thank you for your answers, I will consider them. I further need to stop posting after coming home from 4 consecutive night shifts - I actually believed I was resurrecting a thread from 2013 but didn't notice I was just looking at page one of thirteen... Sorry for that blunder. I will proceed to read the entire thing, then come back into the discussion.

Regarding this:

"They make up arbitrary criteria for what chemical states the amino acids they search for are supposed to exist in in order to get the result they want. Try reading the actual paper. A lot of time is spent retrofitting biosynthetic intermediate forms of amino acids to their "nucleon sum" and then picking that as "the one" because it fits."

I did read the entire thing. I needed four days to fully understand it. Are you referring to the hydrogen transfer in proline and the use of "idealized" amino acids? That struck me as a nice way for a postulated code designer to make the regularities emerge only when viewed in an abstract way by intelligent observers. The "misplaced" proline hydrogen really stands out among the amino acid structure, does it not?

Anyway, let me read the entire thread first. I'll be back.
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Re: Bizarre article claims genetic code is result of "design."

#259  Postby Shrunk » Aug 10, 2015 9:14 pm

If I may ask, why are you spending so much time trying to grok this worthless article? Aren't there any more worthwhile publications you could be reading? You really think these guys have found scientific proof of God, and no one has noticed?
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Re: Bizarre article claims genetic code is result of "design."

#260  Postby Calilasseia » Aug 10, 2015 9:51 pm

Jan_Thomas wrote:Calilasseia: You seem to me an expert in the field


Correction, I merely claim to have paid attention to the experts in the field, by reading their papers. People such as Szostak, Sutherland, Joyce, Wächtershaüser, Dworkin and Orgel. All of whom have numerous peer reviewed papers to their credit. It also helps that I passed my chemistry exams, so I know some of what these people are telling me.

Jan_Thomas wrote:having published papers like you say.


Collected from authors such as those cited above.

Jan_Thomas wrote:I looked for a Luskin and found a "Casey Luskin" working for https://en.wikipedia.org/wiki/Center_fo ... ture#Staff ... This entity seems to promote Intelligent Design by a higher being or similar. Did you mean this guy?


Bingo.

Jan_Thomas wrote:Your criticism seems to be directed at a similar agenda in the article by shCherbaka.


I've learned to be suspicious of assertions about "design". Not least because many of those peddling this assertion manifestly don't know what it takes to convert this assertion into a proper, evidentially supported postulate. Let's see if you do, shall we?

Jan_Thomas wrote:I can asure you that I found not a single hint at some higher being or ID in the entire article. shCherbaka seems to be a man of science with a bold hypothesis. The hypothesis seems to be about finding signs for directed panspermia, not finding God Almighty's signature in the code.


Well first of all, this merely pushes back the question. If a previous life form was purportedly responsible for "directing" the course of life on Earth, this leads immediately to two questions, namely [1] where's the evidence that this previous life form existed, and [2] how did that previous life form come into being. At some point in the chain, there has to be a starting life form, that wasn't the product of manipulations by an antecedent. How did that life form arise? The best answer to date for the second of those questions, one that is considered by just about every competent scientist in the field to apply to life here on Earth, is that life arose via testable natural processes, in our case, chemistry. Courtesy of the fact that life on Earth is chemistry writ large. Millions of chemical reactions are taking place in your body right now, and if some of those chemical reactions stop, you die. It therefore makes eminent sense to postulate a chemical origin for life that is manifestly based upon chemistry. There is currently zero evidence either for tinkering by little green men in flying saucers, or tinkering by mythological magic entities.

Jan_Thomas wrote:I am honestly interested in your opinion: Do you with 100% certainty know that directed panspermia is impossible?


No, but this is a red herring. Because no one is obliged to treat an assertion about this as true, in the complete absence of any supporting evidence for that assertion. This is one of the central operating principles of proper discourse. On the other hand, those papers I've mentioned provide empirical demonstrations that specific postulated mechanisms for the origin of life work, and on that basis, are far more likely to provide an account for the origin of life than unsupported assertions.

Jan_Thomas wrote:If not, can you dismiss for certain that a signal could be embedded in a artificially modified genetic code?


Please explain why no one has actually found any purported "signal" of this sort, in any of the vast body of genome transcription data currently available?

As an example of the sort of challenge that has been issued in the past to people pushing "design" assertions, go and take a look at this past article in the archives of The Panda's Thumb. Not one "design" assertionist stepped up to the plate to take on that challenge. You'll find the results covered in detail here.

Oh, while you're at it, you can take my own little challenge, that I keep tossing in the direction of people who think they have some sort of privileged handle on "detecting design". One of the rocks in the photo below is "designed", in the sense that it was shaped by a Palaeolithic human. Can you work out which one?

Which Of These Rocks Is Designed.jpg
Which Of These Rocks Is Designed.jpg (114.59 KiB) Viewed 2138 times


Jan_Thomas wrote:If I understand correctly, it is already possible to alter the code in, for example, E. coli, switching codons for two amino-acids or introducing new ones. Is this incorrect?


I'm conversant with the literature on genetic code modification, which, if you actually read it, set out to demonstrate that the genetic code is indeed an evolvable entity. In other words, the genetic code extant in living organisms today wasn't the product of tinkering by sentience, rather it arose the same way that other evolvable entities arose.
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