TT commenter chunkdz sparked this exchange about the genetic code, a subject which was recently cited at Telic Thoughts.
I have questions for those of you who believe that the genetic code evolved as a result of natural selection.
1. What was the biological context within which the evolution took place? Cellular? Extra-cellular? A combination of both? Explain what determined the answer you gave.
2. How does a code evolve incrementally?
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October 7th, 2008 at 1:10 am
Having read the PT exchanges, I agree with you that he was smoking, I'm just not sure what he was smoking. Something strong, though, if he thought he made good points.
Comment by steve — October 7, 2008 @ 1:10 am
October 7th, 2008 at 4:29 am
Yes, I too am amazed that anyone could be impressed by such a childish display of petulance. And that Bill Dembski actually blogs about it and I quote:
I rather think that Chunkdz's posts were eloquent on their own and needed no further response.
I do think he did an even better job of demonstrating the calibre of some pro-ID commenters than Guts did in an earlier foray to AtBC.
Keep it up, Chunkdz, you are doing a fine job.
Comment by Alan Fox — October 7, 2008 @ 4:29 am
October 7th, 2008 at 5:29 am
Steve, Alan:
Yeah right, like PT is the bastion of civility. Gimme a break, you guys are such hypocrites.
Comment by Jean — October 7, 2008 @ 5:29 am
October 7th, 2008 at 6:17 am
If you mean "et tu quoque", I doubt that any commenter could go to Uncommon Descent and post more than a comment or two adopting Chunkdz's language before being airbrushed out permanently. Besides, I was merely expressing amazement that Bill Dembski would apparently endorse such behaviour, considering the level of credibility he and his blog currently have. I fully endorse Chunkdz's right to demonstrate his intellectual capacity.
Comment by Alan Fox — October 7, 2008 @ 6:17 am
October 7th, 2008 at 6:51 am
Predictable witticism among nutrias.
Yeah, a gradual, step by step development of DNA codons, mRNA, varieties of tRNA and amino acyl tRNA synthetases, and all that on route to a genetic code- now that's something to stick in your weed pipe. Oh wait. Don't forget those enzymes had RNA precursors. It's canonical. Gotta be. But the genetic code optimal? Do swamp rats diet?
Comment by Bradford — October 7, 2008 @ 6:51 am
October 7th, 2008 at 6:54 am
From page two of the PT comments, these quotes from the original paper (emphasis from PT)
Chuckdz uses this to support his claim that the code is "optimal", but what does he mean by "optimal"? To me, that sounds like the single best solution, however later he says he does not mean that it is perfect.
If you have a system that you have incrementally improved, then that system is optmised. If you go though a thousand iterations, improving a system at each step, then that system is highly optimised. Highly optimised is a description of the process that produced the system, rather than a direct description of the system itself.
Optimal means something else. If a system is optimal, then it is the single best solution. It says nothing about how the system came to be; it could have been designed as the very best in one step, or it could have become that over several iterations.
chuckdz seems to be confusing these two.
Another post quotes this:
Clearly the authors do not think that the code is the single best solution, as they claim there are better solutions. To my mind that means the code is not optimal, at least as I understand the word.
Finally:
My reading of that conclusion is that these scientists made a hypothesis – a hypothesis based on a naturalistic abiogenesis/evolutionary scenario please note – drew a prediction from that hypothesis, tested the prediction and found it was right. I am somewhat confused how someone might think the paper therefore supports ID.
Comment by The Pixie Again — October 7, 2008 @ 6:54 am
October 7th, 2008 at 7:00 am
I followed that discussion from the begining. Initially chunkdz was quite civil and the PTers were predictably arrogant and juvenile. Eventually chunkdz returned the hospitality. It's amazing to me that the "pro-science" crowd is so insecure that they feel it necessary to resort to name calling because someone had the temerity to think the code was optimized. What a sinful thought!
When in Rome do as the Romans do. Incivility is a trademark of that forum.
Comment by Bradford — October 7, 2008 @ 7:00 am
October 7th, 2008 at 7:07 am
Exactly.
Then some of PT's finest would have been gone permanently. But we can't have that can we?
You ought to work for CNBC. Biased reporting of an event is your forte. Chunkdz is quite smart and has demonstrated that in this forum repeatedly.
Comment by Bradford — October 7, 2008 @ 7:07 am
October 7th, 2008 at 7:17 am
In one exchange a distinction was drawn between optimal and perfect. In a perfect world redundancy could be eliminated. But then again redundancy has its pupose too. How would you have designed a more optimal code Pixie? Pixie quoting authors:
The canonical code outperforms most theoretical alternatives if amino acid similarity is measured as polarity. A significant design property.
Comment by Bradford — October 7, 2008 @ 7:17 am
October 7th, 2008 at 7:18 am
How about some answers to the blog questions. It's easy enough to claim codes evolve. Where's the beef?
Comment by Bradford — October 7, 2008 @ 7:18 am
October 7th, 2008 at 7:22 am
Where am I doing any reporting, Bradford? All my comments are OPs, just like everyone else's. It's you and Dembski who are reporting Chunkdz's performance to your readers. I am merely expressing amazement at your chutzpah.
Pity he didn't give a similar demonstration at PT.
Comment by Alan Fox — October 7, 2008 @ 7:22 am
October 7th, 2008 at 7:23 am
Pixie:
Cool you are entitled to your opinion but understand Your argument is with the authors of the study. They said it was optimal. the paper was entitled Early Fixation of an Optimal Genetic Code.
Actually it does. Darwinists repeatedly point to structures that to them appear sub-optimal like the panda's thumb the vertebrate eye etc as evidence against design. By that criterion the code is evidence for design.
I have no problem with abandoning the criteria because of the difficulty of defining optimal but you can't have it both ways.
and your side has more to loose if we do so.
Peace
Comment by fifth monarchy man — October 7, 2008 @ 7:23 am
October 7th, 2008 at 7:34 am
No you're not. You're demonstrating your own. If chunkdz's behavior was notable then why was the boorish behavior of PTers ignored? CNBC style for sure.
Chunkdz is quite smart and has demonstrated that in this forum repeatedly.
I previously pointed out that chunkdz was initially very civil and his PT opponents not so from the outset. If the code is not optimal it is close to it.
Comment by Bradford — October 7, 2008 @ 7:34 am
October 7th, 2008 at 7:51 am
There's a more recent paper
The hard part is to find evidence to support a claim. In this case, no direct evidence remains and has to be inferred.
Comment by Alan Fox — October 7, 2008 @ 7:51 am
October 7th, 2008 at 8:00 am
Frankly, being a middle-aged European, I find the general lack of civility and off-colour language demonstrated by many American commenters rather unnecessary. But Chunkdz's indiscriminate insults achieved a new low for me. Perhaps I don't get out enough.
Comment by Alan Fox — October 7, 2008 @ 8:00 am
October 7th, 2008 at 8:05 am
I want to try and stay on topic. Is this a thread about what Chunkdz is smoking? Or the genetic code?
No one knows for sure at this time. Segregation of sensitive molecular structures is considered essential in most theories. Many researchers believe the genetic code evolved in primitive membranes and involved horizontal mechanisms. So the tentative answer is both.
There are a number of mechanisms. Treating the alphabet as a code, we have seen in other discussions how the letter j was added to the English alphabet by happenstance as a means to distinguish the second of two i's.
More particularly, we have plausible pathways for the evolution of singlet to doublet to triplet codes, of amino acids being added over deep time; for selection for error minimization; and for partial optimization of the code. These are just a few of the many papers that have explored the evolution hypothesis with regards to the genetic code:
Wu, Bagby and Van Den Elsen, Evolution of the genetic triplet code via two types of doublet codons, Journal of molecular evolution 2005.
Brooks et al., Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code, Molecular Biology and Evolution 2002.
Novozhilov, Wolf and Koonin, Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape, Biology Direct 2007.
Comment by Zachriel — October 7, 2008 @ 8:05 am
October 7th, 2008 at 9:12 am
Smokin as in a vigorous exchange generally used in refrence to boxing but befitting the exchanges typical of PT. What are the PTers smoking that puts them on edge when the code is claimed to be optimal? A child molester doing his thing would get a more tepid response from that crowd. But then again we all know the great threat posed to western civilization by ID.
Comment by Bradford — October 7, 2008 @ 9:12 am
October 7th, 2008 at 9:19 am
That kind of addition would work if a useable alphabet already existed and the letter j was a refinement. Much like a point mutation refining an existing genome. It does not explain how an alphabet or a code would arise from ground zero.
Context is critical to the evaluation of such claims which goes to the point of asking for the relevant biological environment.
Comment by Bradford — October 7, 2008 @ 9:19 am
October 7th, 2008 at 9:33 am
The evidence indicates the code is not optimal.
You asked how a code evolves, meaning changes over time. If you meant how does a code originate, it originates from simpler associations, in particular, the genetic code may have originated from stereochemical affinities.
We would always like to know more, but sometimes we can make discoveries even when lacking a complete picture. You would have to argue against the specifics of the cited research, not wave it away with a sweep of the hand.
Comment by Zachriel — October 7, 2008 @ 9:33 am
October 7th, 2008 at 9:39 am
You know, I have to admit, I am doubtful whether biologists can ever crack this nut. I don't know why Behe doesn't posit the universal genetic code as a candidate for IC, even allowing for the hypothesis of an earlier two codon code.
Comment by Alan Fox — October 7, 2008 @ 9:39 am
October 7th, 2008 at 9:43 am
I read the exchanges. The question was aimed at an answer that would explain the depth of hostility and emotion exhibited by the PTers. Once chunkdz got into the mud with them what ensued was predictable. But as I've pointed out chunkdz was greeted with the in your face tactics, so typical of ID critics, at the very outset when his tone was calm and his words civil.
Comment by Bradford — October 7, 2008 @ 9:43 am
October 7th, 2008 at 9:45 am
Though you are correct that it may be very difficult to unravel the actual pathway to the origin of the standard genetic code, Bradford's concern is more general. I think he rejects that it is possible—even in principle.
Comment by Zachriel — October 7, 2008 @ 9:45 am
October 7th, 2008 at 9:57 am
An analysis of the code could be the focus of an entire book.
Comment by Bradford — October 7, 2008 @ 9:57 am
October 7th, 2008 at 10:02 am
This is something else.
Read PvM's disclaimer after linking Chunk's posts:
Read his comments. The PT crowd seems more stunned and bothered by the fact that someone is simply disagreeing with them on their board.
But I wonder why PvM skips over this?
Wonder why Alan Fox states:
And Fox states:
Same with the PT posters, they seemed kind of put off by Chunk's tone.
But what about this bit of "tone" from a PT poster (wad of ID):
Fox's senses get put off by Chunk's tone?
Then wad suggests:
To which PvM replies:
So Pim was paying attention to the other posts. And certainly doesn't seem frazzled by wad's insults. PT is a joke. It's a closed-minded site for bigots and fundamentalists. Of a caliber I have not experienced on many other sites. Certainly not those claiming to be scientific in nature.
Comment by GringoRoyale — October 7, 2008 @ 10:02 am
October 7th, 2008 at 10:06 am
Here are my thoughts. The origin of the code is said to have a stereochemical basis by a good many contemporary analysts. An attempt at a chemically based origin explanation is obvious and understandable. What I do not see is a sound theoretical framework incorporating natural selection. If the claims are generally that such and such chemical affinities had selective advantages then I want to see the replicating entity envisioned by the theorist. It's absolutely critical to an accurate assessment of plausibility. How would the replicating entity be impacted, for example, by modifications of precursor tRNA molecules? What modifications would be favored and why and most importantly how is this system replicating?
Comment by Bradford — October 7, 2008 @ 10:06 am
October 7th, 2008 at 10:07 am
If Character had a silent "P" before it and Assassination had a silent "T" before it, we would know where the acronym "PT" comes from.
And if "PT" had a silent "Baseless rantings by enraged fools can be witnessed here at:" before it, then it would all make sense.
Comment by GringoRoyale — October 7, 2008 @ 10:07 am
October 7th, 2008 at 10:14 am
wad of ID ought to get together with Barney Frank if he wants dew on his putter.
Comment by Bradford — October 7, 2008 @ 10:14 am
October 7th, 2008 at 10:17 am
What would "in principle" mean in this context? How could a pathway be other than demonstrably possible or not?* I know I am suffering from the affliction of personal incredulity, but it does seem a completely different scale of event, or chain of events, that have to be in place before there is a self-replicating entity?
*maybe false dichotomy syndrome as well!
Comment by Alan Fox — October 7, 2008 @ 10:17 am
October 7th, 2008 at 10:26 am
There is a need for a specifiable determinstic outcome which must preceed a viable self-replicator. Something like, under these conditions reactions involving these compounds occur and the self-replicating product x results.
Comment by Bradford — October 7, 2008 @ 10:26 am
October 7th, 2008 at 10:30 am
Yes, and we would also like to "see" the formation of the Moon or the interior of the Sun. Meanwhile, we propose hypotheses and then test them. How did you think science was done?
It is quite possible to reach reasonable conclusions concerning the origin of the genetic code without knowing the entire biotic environment. For instance, the evidence indicates the following.
1. The standard genetic code can be placed on a error-minimizing fitness landscape of all possible codes.
2. The standard genetic code is not optimum.
3. The standard genetic code is found on the slope of the fitness function.
4. The standard genetic code has a non-random correlation with stereochemical affinities.
Comment by Zachriel — October 7, 2008 @ 10:30 am
October 7th, 2008 at 10:35 am
I would hope the one hypothesizing and incorporating a selection paradigm into theory, would have some specifiable concept as to what it is that is replicating.
Comment by Bradford — October 7, 2008 @ 10:35 am
October 7th, 2008 at 10:36 am
GringoRoyale asks
Because I thought it odd that Bill Dembski was impressed enough to blog about Chunkdz's stream of invective. For the record, I was disappointed that wad of id couldn't restrain himself; if I were moderating, his comments, along with Chunkdz's that contained insults would have been moved to the bathroom wall. I had a rule on my old blog that if I considered a comment unfit for my 88 year old mother to read, then it should be deleted.
That said, I suspect Chunkdz was deliberately provocative, as he either gets censored and can cry foul or he provokes retaliatory abuse and you can complain about that.
Comment by Alan Fox — October 7, 2008 @ 10:36 am
October 7th, 2008 at 10:54 am
That there are no selectable stepwise paths to the creation of any code. This is just a flavor of IC argument. Bradford sidestepped the issue, so perhaps that is not his position.
The evolution of the genetic code presumably occurs in living, competing organisms.
Comment by Zachriel — October 7, 2008 @ 10:54 am
October 7th, 2008 at 10:59 am
Why would this be the most reasonable thing to suspect?
Read the posts of Chunk prior to that. Tone wise they are pretty vanilla. But read the posts of those directed to him.
Let's see some of them:
**zero comprehension? Not to level-headed of a comment. But it gets better.
What was the 1st "insult" thrown by Chunk? Sarcastically calling someone a "genius".
Alan, do you think that the context that Chunk was responding in was conducive to civility? Why are you holding him to a standard so different than you seem to be holding the other posters to?
Was it because he wanted an out so that later he could cry "foul"?
Do you sincerely believe that, Alan?
I think it's more a matter of: when you're in a fist fight you use your fists.
I could scan back through the history of PT and find numerous examples of people dissenting with the general view of the site only to get blasted.
Comment by GringoRoyale — October 7, 2008 @ 10:59 am
October 7th, 2008 at 11:08 am
Most scientists believe it was a primitive cell, but that presumption isn't required for these results.
1. The standard genetic code can be placed on a error-minimizing fitness landscape of all possible codes.
2. The standard genetic code is not optimal.
3. The standard genetic code is found on the slope of the fitness function.
4. The standard genetic code has a non-random correlation with stereochemical affinities.
These non-trivial results are consistent with evolution of the genetic code.
Comment by Zachriel — October 7, 2008 @ 11:08 am
October 7th, 2008 at 11:29 am
With respects to what?
Also, this is probably one of the 1st times I have read someone claiming the code is not optimal.
This doesn't say much. On the slope relative to code with higher fitness. Where on the slope?
Tyson Gay is on the slope of fitness wrt running the 200 relative to Usain Bolt.
I don't get what you are saying. Why would the code not be related to its stereochemical structure in 3 dimensional space? The affinities acheived by virtue of its stereochemistry is not a given, because the stereochemistry of the nucleotide could have been different. And it could have been racemic. There is nothing barring l & d from linking…. throwing off the affinities.
Comment by GringoRoyale — October 7, 2008 @ 11:29 am
October 7th, 2008 at 11:33 am
Sorry if this is simplistic, but, as it is virtually universal with few though significant exceptions in some microorganisms, is it not fair to assume that the code has evolved and has been fixed for possibly a billion years or so?
Comment by Alan Fox — October 7, 2008 @ 11:33 am
October 7th, 2008 at 11:43 am
@ GringoRoyale
Yes I do believe what I write, when I write it, and I do try and acknowledge errors when they are pointed out.
Comment by Alan Fox — October 7, 2008 @ 11:43 am
October 7th, 2008 at 12:04 pm
A code that minimizes the phenotypic result of genetic error.
Novozhilov, Wolf and Koonin, Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape, Biology Direct 2007.
You might want to read the paper. It's open source.
"The fitness landscape of code evolution appears to be extremely rugged, containing numerous peaks with a broad distribution of heights, and the standard code is relatively unremarkable, being located on the slope of a moderate-height peak."
Because codons and amino acids are not (any longer) in direct contact, but mediated by transfer-RNA. If they were never in contact, then we would not predict a significant correlation between the genetic code and the affinity of codons for their associated amino acids.
Comment by Zachriel — October 7, 2008 @ 12:04 pm
October 7th, 2008 at 12:08 pm
Okay,
Then let's move the focus from you believing what you write to do you think your view, with respects to Chunkdz behavior, is reasonable.
I don't think it is. And I don't think it is because you appear to be taking his comments out of their context. By context I mean the site in general and PTs regular posts in particular.
If you were called some of the things that were directed at Chunk and his beliefs how do you think you would handle it? Let's not forget the very odd comment that I initially posted from wad of ID.
So, I don't think you have much of a foundation for maintaining what you suspected was the reasons behind Chunk's responses.
Comment by GringoRoyale — October 7, 2008 @ 12:08 pm
October 7th, 2008 at 12:12 pm
Absolutely. Because the standard genetic code is nearly ubiquitous, it is expected that it existed in the last universal common ancestor. It almost certainly evolved in a primitive cell.
Comment by Zachriel — October 7, 2008 @ 12:12 pm
October 7th, 2008 at 12:27 pm
A code that minimizes phenotypic expression of mutations? A code that minimizes mutations? I'm not trying to put these words in your mouth, but is this what you are aiming at?
I'm going to have to read the paper, because unremarkable to what? The one that we know, that maintained the biotic sphere from unicellular organisms to the diversity of the metazoans is unremarkable?
Life appeared shortly after the earth became mildly hospitable for it – and it has maintained on today – for billions of years. Seems to be doing the trick consistantly.
If they were never in contact or never in direct contact?
Unless of course the process was the result of intention of the behalf of an agent.
Comment by GringoRoyale — October 7, 2008 @ 12:27 pm
October 7th, 2008 at 12:46 pm
There's no if. I have been in receipt of plenty of abuse. I find responding to any substantive point there might be in the post, whilst ignoring the insults an effective strategy.
Comment by Alan Fox — October 7, 2008 @ 12:46 pm
October 7th, 2008 at 12:58 pm
GringoRoyale:
You should read the thread more carefully. This was a response to chunkdz' message right before:
chunkdz:
So chunkdz himself brought up the zero comprehension. He was also the first to use personal insults directly after the response to 0 comprehension: "smug prick". It went downhill from there. Chunkdz behaved like a child, as we have seen before. Why anyone would care to defend him besides for reasons of tribal loyalty is beyond me.
Regarding the (sub)optimality of the code. Several references have been provided with hypotheses concerning the evolutionary optimization of the code. How about some quid pro quo: a detailed step-by-step hypothesis about how the code was designed. How did the designer(s) do it?
Comment by Raevmo — October 7, 2008 @ 12:58 pm
October 7th, 2008 at 1:20 pm
Minimizes the phenotypic effect of translation error (roughly, codons to amino acids). Mutation refers to changes in the genetic sequence.
Note the word "relatively". I should think that the statement is self-explanatory. We are comparing the defined fitness of the standard genetic code to all other codes. The top of K2 (remarkable) compared to halfway up Pike's Peak (relatively unremarkable, but still much higher than the Great Plains below).
Apparently so could many other codes. They're not judged by some absolute standard, but by comparison with competitors.
Niels Bohr and Albert Einstein are walking in the woods discussing, as they often did, the fundamental nature of the universe. Suddenly, a great bear appears in their path. Bohr starts to lace on his running shoes. Einstein says, "Dear Niels, you can't outrun the bear!", to which Bohr replied, "But, dear Albert, I only have to outrun you."
That's a scientifically vacuous statement. Why is the sky blue? Because the agent likes blue.
Comment by Zachriel — October 7, 2008 @ 1:20 pm
October 7th, 2008 at 1:46 pm
Raevmo:
Raevmo, take your own advice and read the thread more carefully. Before chunkdz wrote: "600 words. 0 comprehension." wad of ID wrote:
Mike's crap… OK that's tame by PT standards but then there is this:
This guy loves the locker room sex stuff and here's the icing on the cake:
Not too original. This guy could use an upgrade on clever trash talking. Still, to borrow some of your own words:
So wad of ID himself brought up the IDiots. He was also the first to use personal insults even if not very effectively.
Comment by Bradford — October 7, 2008 @ 1:46 pm
October 7th, 2008 at 1:49 pm
From the guy that was asking what sexual positions my wife likes.
Yeah, beyond you indeed.
The last thing I wish to hear out of your mouth is you crying foul about any of this.
Comment by GringoRoyale — October 7, 2008 @ 1:49 pm
October 7th, 2008 at 1:52 pm
Except for some minor variations these competitors you mention are conceptual rather than actual.
Comment by Bradford — October 7, 2008 @ 1:52 pm
October 7th, 2008 at 1:59 pm
GringoRoyale:
What's wrong with asking what sexual positions your wife likes? You Americans are so prudish.
But if you don't want to discuss your wife, how about some more details about how the designer designed the genetic code?
Comment by Raevmo — October 7, 2008 @ 1:59 pm
October 7th, 2008 at 2:03 pm
Raevmo:
It was designed with the end goal in mind.
Comment by Bradford — October 7, 2008 @ 2:03 pm
October 7th, 2008 at 2:16 pm
Variations and translation errors demonstrate that alternative codes can be viable. Indeed, I seem to remember you making the point that arbitrariness of assignments is a characteristic feature of a code.
In any case, are you saying we can't reach some tentative conclusions about the genetic code?
1. The standard genetic code can be placed on a error-minimizing fitness landscape of all possible codes.
2. The standard genetic code is not optimal.
3. The standard genetic code is found on the slope of the fitness function.
4. The standard genetic code has a non-random correlation with stereochemical affinities.
Comment by Zachriel — October 7, 2008 @ 2:16 pm
October 7th, 2008 at 2:16 pm
That end goal being what, exactly?
Comment by Alan Fox — October 7, 2008 @ 2:16 pm
October 7th, 2008 at 2:25 pm
I don't doubt that alternative codes are viable. In fact I believe tRNA can be engineered so as to accomodate an entirely different set of assignments.
No. We can draw conclusions.
Comment by Bradford — October 7, 2008 @ 2:25 pm
October 7th, 2008 at 2:28 pm
Cellular viability or more specifically the capacity to replicate, synthesize proteins, adapt to an environment and evolve. In a nutshell the code enables life in all its diversity.
Comment by Bradford — October 7, 2008 @ 2:28 pm
October 7th, 2008 at 2:30 pm
Because it's my wife and I love her.
And I don't care to hear her brought up in conversations on these boards when she has nothing to do with them. And you're doing it to mock her.
You just got to me. Leave mention of her off of this fucking board.
Comment by GringoRoyale — October 7, 2008 @ 2:30 pm
October 7th, 2008 at 2:33 pm
In addition it's off-topic so leave it alone Raevmo.
Comment by Bradford — October 7, 2008 @ 2:33 pm
October 7th, 2008 at 2:44 pm
Then can you explain why the designer chose a suboptimal genetic code and why there is a stereochemical affinity between codons and amino acids? In other words, can you explain why it looks just as we would expect it to look if it evolved?
Comment by Zachriel — October 7, 2008 @ 2:44 pm
October 7th, 2008 at 3:00 pm
Mike had a couple of posts on this not too long ago.
I feel that they address the issue that you are raising, Zach:
1st there was An Interesting Pattern
And followed that up with A Life Code.
Looking at the TT comments when TT initially linked to IDthink regarding this there was only one post, by Bradford.
Nice to see the discussion finally get started.
Comment by GringoRoyale — October 7, 2008 @ 3:00 pm
October 7th, 2008 at 3:03 pm
Zachriel:
I'm not surprised that there would be stereochemical affinity. That could be expected with either paradigm. As for suboptimal, this is a very functional code. The difference between perfection and biological function could reflect intentions that are non-biological in nature.
Comment by Bradford — October 7, 2008 @ 3:03 pm
October 7th, 2008 at 4:21 pm
Bradford,
I always get a kick out of the 'suboptimal' arguments. Why would any designer create less-than-perfect (by our view) creations? As if the designer would certainly only want to create ubermensches or such. And then there's the rejoinder of since it doesn't look like, by their view, the stuff of perfect design.. it looks like 'it evolved'. Too bad we have no either-or view – something that looks like it evolved is akin to something that looks like it was machined. It's just one more tool in the mix.
Comment by nullasalus — October 7, 2008 @ 4:21 pm
October 7th, 2008 at 4:49 pm
How so? Oh, we can see your faulty reasoning below.
It could be that the unknown, unspecified designer likes blue skies. But the claim is scientifically vacuous.
Well, it is called *Intelligent* Design. But you're right, the Uber-Child might just like to dress up her dollies and hurl asteroids at planets. However, such a claim is scientifically vacuous.
Compare to a hypothesis that fish and land vertebrates share a common ancestor about 375 million years ago that predicts the discovery of an intermediate organism. As opposed to the 'hypothesis' that the Designer just likes to make fishes and things for whatever reason by whatever means.
Or compare to a hypothesis that the genetic code evolved from a simpler mechanism where codons directly created amino acids that predicts a stereochemical affinity between components of the modern system that no longer share a chemical interface. As opposed to the vacuous that the Designer just liked that particular combination out of a multitude. Or just likes blue skies instead of green.
Comment by Zachriel — October 7, 2008 @ 4:49 pm
October 7th, 2008 at 4:55 pm
Let's follow your reasoning process. If the code were optimal- the most perfect possible- you would then concede design correct?
Comment by Bradford — October 7, 2008 @ 4:55 pm
October 7th, 2008 at 4:59 pm
So a vehicle which sacrifices some fuel efficiency in the interest of a more artisitc design is not intelligently designed? Your one dimensional approach leaves something to be desired.
Comment by Bradford — October 7, 2008 @ 4:59 pm
October 7th, 2008 at 6:29 pm
Do the physicochemical distances between codons reflect the physicochemical distances between amino acids?
Simple test. Involving no mapping to 'fitness."
A test of both the "arbitrary" theory (of Bradford) and the stereochemical theory (of Zach).
Are the distances related purely and exactly in terms of the stereochemical hypothesis?Or are they "arbitrary."
If neither is true, and neither is true, then biologists are justified in calling the genetic code a code.
Comment by Rock — October 7, 2008 @ 6:29 pm
October 7th, 2008 at 6:40 pm
To support such a conjecture, you would have to have knowledge of the preferences of the designer. Sure, maybe the Designer made the sky blue because she likes that color. Maybe she picked the genetic code because it glistens in the Jovian twilight, or because the amino acids spell out her name in the local dialect,
Alaargasnaspcysgluglnglyhisile Leulysmetpheproserthrtrptyrval. But you have no evidence to support such a conjecture. The claim is scientifically vacuous.
Comment by Zachriel — October 7, 2008 @ 6:40 pm
October 7th, 2008 at 7:02 pm
We know the genetic code has much higher fitness than a random code, so it is not completely arbitrary. Indeed, we can say that it was 'selected' from among the many other possible codes.
Not "purely and exactly". However, there appears to be a statistically significant correlation.
The stereochemical correlation is largely irrelevant to the modern translation mechanism. It is only relevant to this discussion because it is a confirmed prediction of a hypothesis concerning the origin of the genetic code.
Comment by Zachriel — October 7, 2008 @ 7:02 pm
October 7th, 2008 at 9:32 pm
Zachriel:
Selected in the minds of some. This is not an observable natural selection process. Theories are so vague we don't even know the nature of the biological system that is replicating.
An origin which is almost totally speculative with respect to specifiable chemical reactions needed to yield a code.
Comment by Bradford — October 7, 2008 @ 9:32 pm
October 7th, 2008 at 10:08 pm
If you're saying it was naturally selected from among many possible codes, it's a scientifically vacuous statement. Or do you have a testable hypothesis that makes specific and distinguishing predictions about what led to The Code?
Comment by kornbelt888 — October 7, 2008 @ 10:08 pm
October 8th, 2008 at 7:41 am
Please note my use of the term 'selected' included scare-quotes. The standard genetic code is not a random code. It is significantly less error-prone. And there is that odd stereochemical affinity.
Are you saying we can't know anything about the origin of the genetic code unless we have a complete theory of abiogenesis.
These and many other results are consistent with the evolutionary model.
I keep citing scientific papers that propose and test hypotheses concerning the evolution of the genetic code. I can't make you read them.
Comment by Zachriel — October 8, 2008 @ 7:41 am
October 8th, 2008 at 1:39 pm
Zachriel,
You didn't read what I wrote closely.
"…do you have a testable hypothesis that makes specific and distinguishing predictions about what led to The Code?"
I'm talking about what led to the Code, not what somebody thinks may have led to it. With fossils, we can make a hypothesis and test real ancient historical evidence against the model and see if it confirms or not. What pre-Code historical evidence will you test your hypothesis against?
Comment by kornbelt888 — October 8, 2008 @ 1:39 pm
October 8th, 2008 at 2:40 pm
Yes, the evidence indicates that the standard code evolved. I have provided several cites, and would be happy to provide more. But you don't seem to be interested in the scientific evidence.
The most powerful evidence for common descent is not fossils, but extant genomes. Just as the evidence for the evolution of the genetic code is found in the extant code.
Perhaps angels move planets so they look just as they would under the influence of "gravity". But while positing gravity leads to testable predictions, positing angels adds nothing to our scientific understanding.
Perhaps angels handpicked the genetic code, but they happened to select one that looks just as it would if it evolved. But while positing evolution leads to testable predictions, positing angels adds nothing to our scientific understanding.
Comment by Zachriel — October 8, 2008 @ 2:40 pm
October 8th, 2008 at 3:13 pm
We have “statistically significant correlation” which is “largely irrelevant” but confirms a prediction.
This issue has come up before—of attributing data as confirming one theory, when it may be confirming another theory or theories, or may be properly attributed to a more fundamental theory, as in this case basic chemistry.
I will defer to Massimo di Giulio on the stereochemical theory (“totally absurd”).
“Error-minimization” involves a few key trade-offs, the most obvious being that variation (adaptation) is key to survival (reproduction, fitness). The idea of an adaptive genetic code leads naturally to a co-evolutionary theory.
This is why there was a little tussle going on between the authors and commentators over the difference between cost and fitness.
I think all evolution is co-evolution and so I think the co-evolutionary theory is certainly the correct one, and it is not contradicted by any “stereochemical” data (or theory) that I am aware of, other than the “extreme” (definitive?) statement that di Giulio was referring to.
I’m not much for angels moving planets.
Design is co-evolutionary.
Designers (that we know of) have limited poofing (pouncing, flouncing, vamping, voguing, etc.) abilities.
Comment by Rock — October 8, 2008 @ 3:13 pm
October 8th, 2008 at 3:20 pm
RT Journal A1 Jones, Susan A1 Daley, David T. A. A1 Luscombe, Nicholas M. A1 Berman, Helen M. A1 Thornton, Janet M. T1 Protein-RNA interactions: a structural analysis JF Nucleic Acids Research JO Nucl. Acids Res. YR 2001 FD February 15 VO 29 IS 4 SP 943 OP 954 DO 10.1093/nar/29.4.943 SN 1362-4962 UL http://nar.oxfordjournals.org/...
AB A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.
See Table 5 beginning on page 950.
Comment by Rock — October 8, 2008 @ 3:20 pm
October 8th, 2008 at 3:57 pm
Is that an argument? In point of fact, the context of di Giulio statement concerns an "extreme interpretation" (physicochemical determinism).
One of the reviewers took issue with the statement saying it "does not adequately address the mounting statistical evidence from several laboratories".
Moreover, the paper where de Giulio makes the statement doesn't even concern this issue. When de Giulio is questioned on the statement by the reviewer he defends by saying, "I do not discuss other theories on the genetic code because, paradoxically, this is not 'the right place'." We can therefore reject the statement as unsupported by the paper where the statement is made.
Yes, but they are not necessarily mutually exclusive. The total picture is still incomplete
Design (as regards biology) is poorly defined. The de Giulio paper concerns a non-telic theory.
De Giulio, An extension of the coevolution theory of the origin of the genetic code 2008: The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids.
Comment by Zachriel — October 8, 2008 @ 3:57 pm
October 8th, 2008 at 5:22 pm
I won’t argue about di Giulio’s statement anymore. I said I concurred and will provide the same reasons (and more) from my source (and others). The “stereochemical theory” is anunce.
“The stereochemical theory says that the code is universal
because each amino acid fits its own anticodon or codon in
some way [Emphasis added.].”
http://mmbr.asm.org/cgi/reprin...
LOL In some way.! A definitive prediction of the stereochemical theory.
Absurd.
(Anyone look at that table?)
Comment by Rock — October 8, 2008 @ 5:22 pm
October 8th, 2008 at 5:34 pm
Design (as regards biology) is poorly defined.
Not as I define "design" or "evolution."
Quite apart from these discussions, in the real world of applied science (design), it is generally recognized (as near as I can tell) that design and evolution are intimately related.
And that relation has nothing to do with "evilution vs. cretinism."
Comment by Rock — October 8, 2008 @ 5:34 pm
October 8th, 2008 at 6:46 pm
You forgot the definition, perhaps one with some scientific utility.
Comment by Zachriel — October 8, 2008 @ 6:46 pm
October 9th, 2008 at 11:28 am
"You forgot the definition…"
Go fish, buddy!
Ask Bradford. LOL
I don’t think anyone knows half of what they think they know about evolution, particularly human evolution, if they don’t know anything about design. You can’t design anything without variation and selection. So obviously design and evolution are related even in the most basic terms. In just as basic terms to design is to fit one thing to another. Which is just Darwin’s notion of fitness. Does everyone agree that design has something to do with planning? With plans? What is planning and what is a plan? If you don’t know anything about design (plan) then you shouldn’t be in the habit of referring to the genetic “code,” “program,” “blueprint,” etc. Those words refer to plans. Evolution occurs according to a plan. The genetic code is a plan for evolution. If you don’t know what plans and planning, designs and designing, are then what do you think you know about evolution? Why didn’t anyone answer Raevmo’s question? Because no one hear really knows anything about coding?
Design is part of our nature, and its fair to say its definitive of our nature, because virtually everything humans do is by design. Design is a very highly effective (optimal?) adaptive strategy that has evolved in us. We need to understand it, not just because evolution occurs over an adapted and adaptable substrate (such as our genes and our brains), but because it is an extremely risky adaptive strategy. We need to know what we are doing. I don’t think anyone can really understand evolutionary adaptation while pleading ignorance of design.
But how can you know anything about science if you don’t anything about design!
But this is all irrelevant! Isn’t it? Designs don’t evolve. They are created!
In the twinspeak of the IDers and their critics “design” means special or supernatural creation and that’s all these discussions are about. I didn’t have to ask you define design, as you use it Z, because you’ve made it quite plain. Design is table rocking, crossing yourself one way and not the other, astrology, whistling in the graveyard, Jesus in a taco, God playing craps with our fate.
All ever really do is add noise to these discussions, so you can fairly ignore anything I have to say, Z. (The stereochemica;l theory is safe, just strike out all those unpleasant things I had, or have, to say about it.)
Our perspectives on design are incommensurable, mutually incomprehensible. My perspective is informed by 25 years professional experience. Grounded in reality. What you guys are talking about is theology. Not reality. LOL
Comment by Rock — October 9, 2008 @ 11:28 am
October 9th, 2008 at 12:01 pm
I'd be happy to read whatever you've got. I haven't seen any cites. So, please post them again.
I agree.
I agree.
Comment by kornbelt888 — October 9, 2008 @ 12:01 pm
October 9th, 2008 at 12:09 pm
Not an answer.
That is the usual sense. The Theory of Evolution posits robust explanatory mechanisms devoid of planning.
That scientists coopt old words for new phenomena is not a valid argument. Any more than what scientists mean by "evolution" is to unroll a scroll.
I think many will read you that way. I do try to piece together some semblance of sense out of your comments. In this latest ramble, you seem to be conflating various definitions of "design".
Comment by Zachriel — October 9, 2008 @ 12:09 pm
October 9th, 2008 at 12:29 pm
I find it important to build on common ground, even if we have to travel far to get there.
See my first comment for a few relevant cites.
Comment by Zachriel — October 9, 2008 @ 12:29 pm
October 9th, 2008 at 1:28 pm
Zachriel,
Thanks. I'll read them, if I can get access.
Comment by kornbelt888 — October 9, 2008 @ 1:28 pm
October 9th, 2008 at 1:35 pm
Here's Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape. I'm not sure about the others. Most university libraries will have scientific journals, though.
Comment by Zachriel — October 9, 2008 @ 1:35 pm
October 9th, 2008 at 2:13 pm
In this latest ramble, you seem to be conflating various definitions of "design".—Zachriel
Pardon me! But you and the IDers argue endlessly about design w/o even knowing what the word means?! You have to ask me? Why me? But you do know what “design” means. It means supernatural creation! Sorry, but I don’t accept the meaning of design that you and the IDers share. I use the word “design” in the same way it is used by both evolutionary biologists and design engineers. I don’t need to “define” design any further. Go fish, buddy. Go find out what evolutionary biologists and engineers mean by design, because I’ve “conflated” nothing. My use of the term is perfectly consistent with how it is used in the scientific literature. And in that literature it is almost never used to mean “supernatural creation.” Which is the only way you guys use the term. You, not I, have to justify your peculiar usage of the term. Your conflations. Not mine. Because you guys share this tacit understanding of “design” (self-reinforcing by continuous rounds of self-involved “debate”) you never require each other to justify your “non-standard” usage of the term. I do not share your tacit understanding. As I said, what I know about design is derived from experience, from observations, and has been subject to experimental test.
And you might want to update your “Theory of Evolution” to circa 1950, when the genetic code was discovered. A code is a plan. Biologists did not “co-opt” the word, suggesting that they changed its meaning or usage. Evolutionary biologists use the word “code,” referring to the DNA molecule, in the same way coding theorists use the word “code.”
Of course, if you don’t really know anything about design you wouldn’t know that.
The Humpty-Dumpty argument.
All you told me was that your facile understanding of the “Theory of Evolution” is inconsistent with your facile understanding of design.
Comment by Rock — October 9, 2008 @ 2:13 pm
October 9th, 2008 at 2:26 pm
Here's a review that might be of interest.
The general stereochemical hypothesis is consistent with origin of the genetic code before or during RNA World. Interactive correlation with oligo-molecules rather than short sequences implies that these relationships were established during RNA World, then evolved from there. Other amino acids may have been added over time by different mechanisms. The extreme stereochemical hypothesis is an overstatement, but the evidence thus far seems to support a role for stereochemistry in the origin of the genetic code.
Comment by Zachriel — October 9, 2008 @ 2:26 pm
October 9th, 2008 at 2:48 pm
Rock, you said, "Not as I define 'design' or 'evolution'."
Because you said, "Not as I define 'design' or 'evolution'."
That's an odd definition.
Design engineering typically refers to human design. That would apparently exclude the historical origin of species. In biology, design is sometimes used to refer to a functional structure, but that usage doesn't have any telic connotations.
So it's a secret definition.
I don't typically use it in that fashion, but sometimes others do. I don't think the term "supernatural" is a particularly useful categorization in these discussions.
Comment by Zachriel — October 9, 2008 @ 2:48 pm
October 9th, 2008 at 3:08 pm
Michael Yarus, my alum! Don’t we belong to the same sorority? Oh, wait, that was my sole objective (adolescent fantasy) in going to college: joining a sorority. (Or the cheerleading squad.)
Women are such sexist-pigs! I didn’t know you had to be woman to join! How fair is that! It’s a lot like the sorority that the IDers and their critics have formed. Ya got to accept their rules.
As a designer I certainly appreciate the rules. But i also appreciate how the rules may be broken. I think that's what design is really all about: Breaking the rules.
A stereochemical theory of genetic code is, as I think you had already recognized, not in the least bit inconsistent with the idea that the genetic code is designed. (?) The “stereochemical” theory makes no distinguishing predictions. Designers, that we know of, select from amongst a natural given set of design elements (literally those elements in the periodic table of elements) those that seem most suited to their purposes.
How are the stereochemical rules broken in the design of the genetic code?
That they are is already recognized.
Comment by Rock — October 9, 2008 @ 3:08 pm
October 9th, 2008 at 3:28 pm
As I said, Not as I define either deisgn or evolution, but as those words are defined in the scientific literature, even if inly (and usally) implicitly. I said, which you ignored in your respnse, that i am using the term consistently with its usage in the literature. You want to make this peculiar to me. The Humpty Dumpty argument.
Ignoring what you have implied (only ever and never explicitly) what you mean by "design." Which I said you have repeatedly made clear–which is not how scientists generally use the word "design."
I had asked you and the IDers to warrant this peculiar usage of the term.
Just to repeat myself, even though you can't seem to "get it" no matter how many times I repeat it: I use the term the same way scientists use the term. You and the IDers do not.
It's an "odd" definition? It's what you implied by angels moving heavenly spheres!
Function has no "telic connotations." you can argue with the any number of evolutionary theorists (including Darwin) about that.
"Design engineering typically refers to human design. That would apparently exclude the historical origin of species."
Other than those species which we have, historically, designed ourselves.
"So it's a secret definition."
I don’t need to “define” design any further. Go fish, buddy. Go find out what evolutionary biologists and engineers mean by design, because I’ve “conflated” nothing. My use of the term is perfectly consistent with how it is used in the scientific literature. And in that literature it is almost never used to mean “supernatural creation.”
Yeh, its a big secret.
Comment by Rock — October 9, 2008 @ 3:28 pm
October 9th, 2008 at 3:34 pm
Zachriel,
So as I read the material you cite, what specific and distinguishing predictions have been made that you believe have been confirmed?
Comment by kornbelt888 — October 9, 2008 @ 3:34 pm
October 9th, 2008 at 5:13 pm
Looking at Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape.
There are several hypotheses of concern on the origin of the genetic code; frozen accident, stereochemistry, coevolution, and translation-error. The paper tests whether, starting from a random code, whether evolution could optimize the code for translation-fidelity to a degree found in nature, what characterizes that fitness landscape, and how does the standard code fit within that landscape. From the paper,
No single paper can be considered conclusive on the origin of the genetic code. This area of research is very tentative. But any research paper will propose and test a scientific hypothesis.
Comment by Zachriel — October 9, 2008 @ 5:13 pm
October 9th, 2008 at 8:53 pm
Zachriel,
What I want to know is what what specific and distinguishing predictions about the origin of life as it actually occurred, have been made that you believe have been confirmed? I.e, what do we know about what happened?
At any rate, if a gap-free hypothetical chain of events could be shown to lead to the Code or something similar to it, that would be enough for me. But the state of art doesn't seem to be anywhere near that yet. Full steam ahead!
I read the paper twice today and it was interesting for various reasons. I'll post some of my thoughts this weekend.
Comment by kornbelt888 — October 9, 2008 @ 8:53 pm
October 9th, 2008 at 9:22 pm
The hypothesis being tested was the transcription-error hypothesis. The hypothesis was generally supported by the result. This returns us to your original statement.
These are not vacuous claims because they have clear empirical implications. The evidence supports the hypothesis that the genetic code evolved. There is some support for stereochemistry in the code's early development, followed by optimization and expansion. These results are consistent with other research, including broader models having to do with RNA World and the proto-biotic cellular environment.
Comment by Zachriel — October 9, 2008 @ 9:22 pm
October 10th, 2008 at 10:01 pm
It's interesting to see that TT critics are not so different from PT critics. Entirely predictable.
Alan Fox begins by calling me childish and petulant, and then attacking Bill Dembski, and Guts. Unfortunately, none of his own teammates will ever be scrutinized in this way.
The Pixie tries to refute the results of a paper which he obviously only scavenged through for quotes.
Zachriel simply ignores the paper in favor of one that more readily suits his worldview.
And Raevmo basically says 'chunkdz started it'.
All of these types of responses were predicted by me at PT. Alan Fox is a culture warrior and will never in a million years criticize one of his own for their childish and petulant remarks. Hypocrisy is a safe place for him. No surprise there.
The Pixie will continue to say that it is I, not the researchers that are making some outlandish claim, or that the researchers never made this claim – ignoring what is directly in front of him.
Zachriel will continue to ignore the paper in question and follow Pim's marching orders.
And Raevmo – well… he'll always be the same childish and petulant Raevmo that we all adore.
As for the research, there's been dozens of related papers either directly or indirectly addressing the question of optimality over the last decade or so. As near as I can tell the issue is still far from consensus. There doesn't seem to be a methodology that everyone can agree upon, and there are many variables (such as codon usage) which alter the outcomes. Novozhilov, Wolf, and Koonin have used a very oversimplified algorithm (apparently with some faulty assumptions) to find the code perched on a fitness slope. But it seems that Woese is recently operating under the notion of the code being optimal. The Freeland et. al. paper is an admirable attempt to plausibly limit the search space, except that others (DiGiulio 2000) claim that THEIR methodology may have been flawed.
Personally, I have no idea whether the code is "the best of all possible codes" as Freeland et. al. said. I think all that IS agreed upon generally is that the code is not random, the code is very, very good at minimizing errors, and nobody knows how it came about.
But of course, the point of my Don Rickles routine at Panda's Thumb was never to make any bold claim about the code's origins. I find the research about the code to be truly fascinating, but what is really more fascinating to me is the phenomenon of political bias that inflames the more partisan fringes of the culture war. While Nozhilov, Koonin, Freeland, Knight, Goodarzi, etc. are busy exploring, the culture warriors are sharpening their knives and dulling their reason.
This is not just polemics on my part. Clinical study after clinical study has pointed out the connection between political partisanship and selective bias. The oversimplified version of the science is that if you are very politically invested in a belief, then you are selectively biased, you exhibit selective recall, and YOU WON'T EVEN KNOW YOU ARE DOING IT. In fact, you will actually believe that you are being completely rational and that your perceived enemies are irrational, even in the face of incontrovertable evidence.
So how can I, chunkdz, be sure that it is not me that is selectively biased and politically prejudiced? Well, probably no one can completely. But critical thinking can act as a mirror with which to examine ourselves and our surroundings. Another clue is to see whether we follow predictable patterns of avoidance when confrontation appears. First impulses are another clue. It's not always easy to critically analyze these in ourselves.
What does seem clear to me, however, is that when confronted by a scientific conclusion (maybe right, maybe wrong – who knows) that conflicts with our prejudices, the easiest and most rational response is curiosity. What we all too often find, however, is a biased response, and emotionally charged defense mechanisms take over. There is nothing "wrong" with this. Evolution has apparently fixed this stress response mechanism in our brains as a means of survival. It's a survival mechanism.
But as for me, and many of you, I don't want my brain to operate in survival mode when I am trying to think critically. It's hard, but it is worthwhile to retrain your brain to override these stress responses.
Mentioning the Freeland paper apparently is a source of stress for some people. They deal with this stress by lashing out at Bill Dembski. They deal with this stress by complaining about the Dover trial. They deal with the stress by ignoring the Freeland paper. They deal with the stress by attributing the paper's conclusions to a perceived enemy. They deal with the stress through stereotypes, bias, prejudice, vulgar hostility, and threats. These all provide a safe emotional cocoon from stress. Unfortunately, it also cocoons the critic from critical thinking, and possibly the truth.
Am I completely unbiased. Heck no. But having once been an anti-religion, anti-creationist critic myself, I am in a position to have some genuine insight into the mind of the critic. Consequently, I don't see the New Atheists and the ID critics as enemies, though I'm certain many of them see me as theirs. I look at every argument, every piece of the puzzle from my present angle, and the angle at which I used to view the world. This may not be a perfect prism, but it is an improvement over the raw political partisanship I once knew.
I'll end my screed now. I'd like to be able to say that I believe that anybody can break free from the instinct of partisan bias and prejudice to embrace critical thinking and someday we'll all live in rational bliss and bias free understanding. But unfortunately I actually don't believe this is true.
Comment by chunkdz — October 10, 2008 @ 10:01 pm
October 10th, 2008 at 10:28 pm
Hi chunkdz. I was hoping you would wade in.
Or if they think they know they cannot demonstrate how. Error minimization is a critical point in my view and fertile ground for future blogging. And the code was not the product of random events. Nor is it clear how selection would guide a process.
I enjoy watching both you and Rickles in action. But how you put up with the sliming is another matter. Imagine being in the same room with those smash mouths? Think they would slime someone sitting in front of them?
Well said. Welcome back to TT. There's some leftovers in the frig and some liquid refreshments if you're thirsty.
Comment by Bradford — October 10, 2008 @ 10:28 pm
October 10th, 2008 at 10:44 pm
Chunkdz complains about "childish and petulant remarks" then says,
We discussed that paper elsewhere. You clearly misinterpreted the results as they depend on the biosynthetic restrictions assumed in the test. I provided cites to more recent research above.
Yes, and the very papers you criticize are the very evidence which supports that statement.
Actually, what Freeland et al. said was the standard code was between 45% (Wong 1980) and 78% (DiGiulio 1994) of possible error minimization.
Nobody knows the details, but the evidence supports that a variety of mechanisms have come into play. Of note, no one has ever proposed a testable ID model.
The paper you say I should not ignore says,
{snip balance of chunkdz's screed}
Comment by Zachriel — October 10, 2008 @ 10:44 pm
October 11th, 2008 at 2:31 am
Two strongs don't make a right.
It almost seems as though there was some desperate attempt to make that statement.
Comment by computerist — October 11, 2008 @ 2:31 am
October 11th, 2008 at 8:32 am
It looks like they said what they meant. Strong evidence. Strong influence. More particularly, we have these basic findings:
* The standard genetic code can be placed on a translation error-minimizing fitness landscape of all possible codes.
* The landscape is rugged, but traversable by stepwise, evolutionary search.
* The standard genetic code is near the peak of a moderate-height peak.
* Comparable levels of optimization can be found by starting at a random location.
It didn't have to be this way. For instance, the landscape might have been chaotic, or the standard genetic code could have been isolated in the fitness landscape with no evolutionary approaches. The evidence looks just like it would if the genetic code evolved due to natural selection.
Comment by Zachriel — October 11, 2008 @ 8:32 am
October 11th, 2008 at 10:15 am
But aren't the chance worshipers always saying to us non-chance worshipers that evolution doesn't get into all that origin of genetic code, first cell and the rest of that OOL business?
I've had a note to self all this time that "I should never conflate the two, they are completely different and I'm a damn nut if I think Darwinian evolution applies to the OOL"
Although, everyone knows for a fact it had to happen that way via RM+NS. It's the default answer to all of lifes problems, literally!
So would you like to make the claim that the genetic code was optimized during the evolutionary process? Because I don't see whats stopping the magical powers of Darwinian Evolution from doing so.
Comment by computerist — October 11, 2008 @ 10:15 am
October 11th, 2008 at 10:56 am
"Chance worshippers"? Are we to take your comments seriously?
The Theory of Evolution doesn't encompass abiogenesis. The Theory of Evolution is a strongly supported theory of how life changes and has changed. On the other hand, there is no complete theory of abiogenesis. That doesn't mean we don't know anything about the origin of the genetic code. And it certainly doesn't mean we don't know anything about the evolutinary diversification of dinosaurs or hominids.
That's what the evidence supports. But there is still a lot unknown about that early epoch. A complete history of evolution reaching back that far is still not available.
No more magical than gravity. In any case, the evidence suggests that the standard genetic code probably evolved only once RNA-like oligomers came into existence.
Comment by Zachriel — October 11, 2008 @ 10:56 am
October 11th, 2008 at 12:01 pm
You flatter me. I have no vested interest in whether ID can promote itself into US public school curricula. My interest in the issue is mainly anthropological. That and my obsession with the doings of Assoc. Prof. (retd.) JAD. (BTW, did I mistake you for Sal?)
Just upthread, I wrote: "For the record, I was disappointed that wad of id couldn't restrain himself; if I were moderating, his comments, along with Chunkdz's that contained insults would have been moved to the bathroom wall." Furthermore, like Achilles, I am sulking in my tent at the moment over the erratic moderation at AtBC!
Comment by Alan Fox — October 11, 2008 @ 12:01 pm
October 11th, 2008 at 12:36 pm
Zach:
No, that would be Alan. I happen to love the childish and petulant remarks as they reveal the bias in those who only criticise their perceived enemies.
Interesting, since I didn't an interpretation of the results. I merely repeated the conclusion of the researchers.
Interesting, since I didn't criticize the paper. I merely repeated what the peer reviewers said.
Actually, Freeland et. al. said that if their plausible biological restrictions were accurate, then the code was "the best of all possible codes."
Yup. When you rule out "stereochemistry, biosynthetically mediated code expansion, or analytical methodology", there is only one a priori Darwinian alternative left. Of course,
Comment by chunkdz — October 11, 2008 @ 12:36 pm
October 11th, 2008 at 12:50 pm
Alan,
Who says you have to be vested to be a culture warrior?
LOL! I call them drooling monkeys and you call me "childish" and "petulant". Wad tells me to "s**k his c**k" and you are merely "disappointed".
Way to save face with your culture warrior buddies!
Actually, Alan, when you actually HAVE had an opportunity to moderate, your policy has been to delete obscenity and spam only. But it's nice to know that you are willing to alter your policy to accomodate your culture warrior buddies. LOL!
Hypocrite.
Comment by chunkdz — October 11, 2008 @ 12:50 pm
October 11th, 2008 at 1:50 pm
I retract my statement that you were complaining about "childish and petulant remarks".
No, you had cited the paper as evidence that the code was optimally designed. You repeatedly said "the code was optimal". The actual results depend upon certain assumptions of prebiotic chemistry. It's only optimal in the sense that evolution is constrained by its own history. (In the fitness landscape paradigm, we expect it to climb the local hill it finds itself on. A designer would presumably just plop it on top of the highest available peak.)
You reframed the conclusion, causing you to repeatedly misinterpret and misstate the results.
Scientists are writing for their peers. They expect that their papers will be read for their intended scientific content, not their quote-mining opportunities.
Comment by Zachriel — October 11, 2008 @ 1:50 pm
October 11th, 2008 at 3:26 pm
Zachriel,
Nope. I didn't say this was evidence that the code was designed. I said it would make monkeys fling their poo.
Actually, the research paper in question said the code is "a global optimum for error minimization" and "the best of all possible codes".
Yes, saying that it is "the best of all possible codes" is dependent upon certain "plausible biological parameters". Glad you agree.
So says Zachriel. The REAL scientists said it was a "global optimum", not a local optimum. And where does science say anything about where a putative designer would "plop" a code? There you go getting all metaphysical again…or are you simply conceding that design is actually detectable…???
Actually, I quoted the conclusion directly and I referenced the fact that their "plausible biological parameters" represented the best scientific knowledge at the time.
But if it upsets you so much to hear a scientist say that the canonical code is "the best of all possible codes", then simply reach down, grab some poo, and keep flinging.
Ummm, the title of the paper was "Early Fixation of an Optimal Code".
Do you really think I'm quote mining when I repeat that the code is optimal?
Man, where were you and your poo when I needed you at PT?
Comment by chunkdz — October 11, 2008 @ 3:26 pm
October 11th, 2008 at 3:41 pm
Hi Bradford,
I was wondering if someone was ever going to "get it". So far, it seems that only you and Bill Dembski "got" what happened at PT.
But that's the phenomenon, isn't it. They don't "get it" because they aren't wired to "get it". And they most likely will never "get it". It's really like two people looking at a green light, and one says it's green and the other says it's red. Even if you empirically measure the wavelength of the light, the critics will insist that you haven't properly defined "redness", or that the measurement is flawed in some way, or that Bill Dembski once ran a red light so it's all part of the vast ANTI-RED LIGHT conspiracy, etc. etc.. It will go on forever.
So to answer your question, I'd say that in a herd situation they'll follow the herd every single time.
Comment by chunkdz — October 11, 2008 @ 3:41 pm
October 11th, 2008 at 4:01 pm
You said, "ID’ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language – an optimal design." Then you *defended* the inaccurate claim by pointing to Early Fixation of an Optimal Genetic Code.
As I said, you are misinterpreting the paper. The standard genetic code is only a global optimum within the fitness space established by the *assumption of an evolutionary origin*. It is not a global optimum across all possible codes. You were citing the paper to support the ID claim; when in fact, it supports the evolutionary claim. And you did this repeatedly.
Comment by Zachriel — October 11, 2008 @ 4:01 pm
October 11th, 2008 at 4:05 pm
chunkdz:
This is timely. My daughter and I visited a large university in the northeastern section of the U.S. today which she is considering applying to. At one point we were treated to a dissertation on the values of feminism and multiculturalism by a dean who thought the message would impress us. Later an undergraduate student took my daughter aside after learning of her academic interests. She had studied some genetics and began explaining how the future held the promise that we would be able to identify genes that would explain various social behavior and presumably misbehavior as well. The atmosphere was charged with an unmistakable air of PC. It made my skin crawl. But some of it was amusing as well.
The so called God gene has been popularized and is mentioned in these types of bull sessions. I was surprised that the concept seems to be getting traction. Of course genetic make-up influences behavioral dispositions but oversimplification of the matter can be appalling particularly when given credence by academics. Behavior is better explained by the interaction of groups of expressed end products operating within systems. Emergence, which is over utilized in OOL explanations, is underused in behavioral explanations in my view.
Anyway I would have suggested that the genetics student consider a conformity gene.
The survival value of conformity hardly needs an explanation. Its genetic cousin could be a conceptual blindspot gene. 
The latter gene enhances the function of the former gene. Better to not think critically when conformity is valued.
Comment by Bradford — October 11, 2008 @ 4:05 pm
October 11th, 2008 at 4:05 pm
Off-topicI had written a similar comment earlier, but didn't post it because it was somewhat off-topic. However, as you brought it up again.
Sounds like you're a troll.
Dembski thinks you're a troll.
Ah, so you admit you're a troll.
Comment by Zachriel — October 11, 2008 @ 4:05 pm
October 11th, 2008 at 4:14 pm
A programming language need not be optimal to suggest design. It's not as if basic forces of physics encourage the expectation that symbolic codes arise in non-living systems.
Comment by Bradford — October 11, 2008 @ 4:14 pm
October 11th, 2008 at 4:23 pm
It sounded to me like he was interested in expressing his view on the code.
Dembski knows that any dissenting view on a major topic of interest will arouse the base passions of PTers. It matters not whether the proponent is civil or sincere or rational. The fact that one would have the temerity to swim against the tide infuriates PT types.
That needs explaining.
Comment by Bradford — October 11, 2008 @ 4:23 pm
October 11th, 2008 at 5:22 pm
Novozhilov, Wolf and Koonin, Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape, Biology Direct 2007.
Raevmo asked a question about how to design codes and the authors answered the question in the paper.
The stop codons bugged me. Not only are they frequently “reassigned,” but they score highest (in the “standard” code) on the polarity index, which is the test criteria.
Since polarity is such a function-critical variable, shifts in polarity could have dramatic effects on fitness (e.g., be lethal!). There is no reason to hold the block structure constant. Extant variants do not conserve block structure, or the “degree” of degeneracy that the “standard” code does.
However, as the authors note, not holding the block structure constant inflates an already analytically intractable designspace (“fitness landscape”), which was already beyond-astronomical in its dimensions!
I feel two points about the “fitness landscape” need to emphasized: 1) It is not constant and 2) It is highly degenerate. This means, extending the answer to Raevmo’s question, that there is no “optimal” solution to the problem of designing (evolving) an adaptive code.
What results reported by the authors conflicts with the idea that the code was designed?
None that I can see.
Comment by Rock — October 11, 2008 @ 5:22 pm
October 11th, 2008 at 6:11 pm
"…if you are very politically invested in a belief, then you are selectively biased, you exhibit selective recall, and YOU WON'T EVEN KNOW YOU ARE DOING IT. In fact, you will actually believe that you are being completely rational and that your perceived enemies are irrational, even in the face of incontrovertable evidence." – chunkdz
Clear now?
Comment by Alan Fox — October 11, 2008 @ 6:11 pm
October 11th, 2008 at 7:26 pm
Alan Fox:
Here is a definition of an internet troll that closely aligns with my understanding:
The term derives from "trolling", a style of fishing which involves trailing bait through a likely spot hoping for a bite. The troll posts a message, often in response to an honest question, that is intended to upset, disrupt or simply insult the group.
Chunkdz's initial messages were civil in tone and non-hostile in content. So did he intend to upset, disrupt or insult the group? Given the fact that the initial volley of insults was directed at him rather than coming from him, the intent to insult charge is dismissed. The insults were two ways only after PTers launched the initial assault. Disrupt? I thought PT was a discussion forum. Disagreements are allowed are they not? Disruption charge dismissed. There might be something to the upset charge. After all both chunkdz and I have indicated what many have repeatedly observed. IDists are met with hostility simply because they are IDists. They are hated for their beliefs. So anytime an IDist ventures into a mainstream forum and voices a dissenting view one can predict with great accuracy that he will upset people- even if he is civil and polite. But that is hard evidence to hang chunkdz on for you must acknowledge the intolerance of your own side to dissenting views in order to make your case.
Comment by Bradford — October 11, 2008 @ 7:26 pm
October 12th, 2008 at 1:18 pm
zach,
Are you saying ID'ers DON'T have this view?
When did I or the researchers ever say it was a global optimum across all possible codes?
Seriously, there's about a dozen pages of your kind of misrepresentation over at PT. You had your chance, I've had enough.
No, I cited a paper to expose how two contrasting worldviews look at scientific evidence. I drew no conclusions and made no claims, other than the claim that this particular research paper would cause a torrent of poo flinging. I am fairly vindicated in that.
What if I were a troll, Zach? Would that make your mischaracterizations any more relevant? Would it make your obfuscating ends justify your obfuscating means?
Or more importantly,
…would it make you feel better emotionally?
Comment by chunkdz — October 12, 2008 @ 1:18 pm
October 12th, 2008 at 1:45 pm
Bradford,
With research
like this, I think it's just a matter of time before the DNC and GOP start polling in the womb.
Comment by chunkdz — October 12, 2008 @ 1:45 pm
October 12th, 2008 at 1:54 pm
There is no doubt that many IDers claim that the standard genetic code is special in that it is optimal across all possible codes. You provided the cite to Early Fixation of an Optimal Genetic Code as support for this claim.
In fact, the paper says the standard genetic code is only optimal in the sense that evolution is constrained by its own history. The paper cannot fairly be read in any other way.
Comment by Zachriel — October 12, 2008 @ 1:54 pm
October 12th, 2008 at 2:04 pm
For the record.You provided the cite to support a broad claim of optimality, when the paper absolutely depends on evolutionary assumptions.
Comment by Zachriel — October 12, 2008 @ 2:04 pm
October 12th, 2008 at 2:42 pm
This paper (and related models and simulations), at least for me, didn’t answer any basic questions about how the “standard” genetic code fits, relative to hypothetical alternative designs, on some optimization scale.
The basis for the comparisons made in this simulation do not define any “global” extremum. Its an optimization problem in one variable!
We already know there are viable variants of the standard code, but how meaningful would it be, after all, to compare them by any “global” measure? Isn’t it safe to assume that the variants have evolved (been optimized) under any number of varying “local” conditions?
It’s still good. These kinds of toy models are often quite useful for testing assumptions, comparing methodologies, and may suggest further research. E.g., models including more factors in the code optimization problem and maybe relaxing certain requirements (e.g., the restriction upon block structure).
I don’t think it would be unreasonable for you, chunkdz, if you were to say that because the genetic code is (nearly) universal it may be inferred (and may even be testable) that it resides close to some global optimum. But it requires including more factors to determine the location of that optimum and the path to it, and there are true uncertainties involved.
The uncertainty here is the very existence of a global optimum! Are we getting all worked up over something we can’t even prove exists!
Oh, yeh! I forgot! That’s what all these arguments are about! LOL
This paper doesn’t provide much of a basis for discriminating between any number of theories of genetic code design, except, of course, the “stereochemical” theory. LOL
On what basis would I use this paper as an argument against the design of the genetic code?
Comment by Rock — October 12, 2008 @ 2:42 pm
October 13th, 2008 at 1:27 pm
Zachriel,
This is exactly the kind of misrepresentation I was talking about. I provided the cite to refute David Stanton's claim – not to support optimality of the code. As I said recently, I don't even know if the code is optimal or not.
But I do understand your need to somehow attribute Freeland's et. al. conclusion to me.
Comment by chunkdz — October 13, 2008 @ 1:27 pm
October 13th, 2008 at 1:37 pm
Zachriel,
Okay, I'll have to call your bluff on this.
The quote you snipped from me does not make the argument that the code is optimal "across all possible codes".
I don't recall ever saying that the code is optimal "across all possible codes".
I don't recall ever THINKING that the code is optimal "across all possible codes".
I don't recall the researchers ever saying that the code is optimal "across all possible codes".
I don't know a single person, ID'er or not, who thinks or says that the code is optimal "across all possible codes".
So prove to me that you are not some emotionally driven, win at all costs culture warrior who's brain is in survival mode. Simply show me unequivocally where I made the claim that the code is optimal "across all possible codes".
Comment by chunkdz — October 13, 2008 @ 1:37 pm
October 13th, 2008 at 2:01 pm
Rock,
I think it's even more interesting that the code has not been noticeably improved in the last 4 billion years.
Your point is taken well, though. It's kind of why I am agnostic on the optimality of the code. My point, of course, was that 4 respected scientists claiming that the code is "the best of all possible codes" would cause a torrent of poo flinging, drooling, and stupidity.
I think my hypothesis is panning out better than Freeland's.
Comment by chunkdz — October 13, 2008 @ 2:01 pm
October 13th, 2008 at 3:11 pm
The pretense surrounding your word-game does not constitute a valid argument. Stanton's claim and context was clear, as was your response. Your most previous comment continues your pattern of using quote-mining to deter clear understanding, and to provoke other commenters.
-
Comment by Zachriel — October 13, 2008 @ 3:11 pm
October 13th, 2008 at 3:25 pm
Just as I thought. You simply made up that part about "across all possible codes".
The question that fascinates me is "why?" Why would a professional scientist like Zachriel make up a false argument and attribute it to me?
The rational response would be to admit that you'd simply made an error, and to be more careful with your accusations in the future.
Yet time and time again we see this irrational pattern of denial, obfuscation, and mischaracterization.
Is it really all just to show some anonymous "troll" named chunkdz who's boss? I think there's something more fascinating at work in the mind of the critic.
Comment by chunkdz — October 13, 2008 @ 3:25 pm
October 13th, 2008 at 3:49 pm
This statement, made without caveats, was clearly intended to mislead and provoke.
It was just as clearly not intended to aid in communication or to advance the discussion. Your other comments are no better.
Comment by Zachriel — October 13, 2008 @ 3:49 pm
October 13th, 2008 at 4:06 pm
Zachriel,
No, my friend. Saying that "the genetic code is optimal" is not misleading (though it's obviously provocative). If it were misleading then you could launch the same accusation at Vetsigian, Woese, and Goldenfeld, since their entire 2006 paper is based upon the premise of an optimal universal code.
The only difference is that Woese recognizes the significance, and attempts to explain the optimality.
You, however, simply drool, fling poo, and complain.
Comment by chunkdz — October 13, 2008 @ 4:06 pm
October 13th, 2008 at 4:59 pm
Of course it was. By ignoring important caveats found in the paper, you were quote-mining. And you did this repeatedly, even after your error was pointed out to you. You clearly have no desire to communicate ideas or to advance the discussion.
Comment by Zachriel — October 13, 2008 @ 4:59 pm
October 13th, 2008 at 5:12 pm
Comment by Bradford — October 13, 2008 @ 5:12 pm
October 13th, 2008 at 5:21 pm
For the record, Chunkdz – bravo and well-played.
Comment by nullasalus — October 13, 2008 @ 5:21 pm
October 13th, 2008 at 5:40 pm
Zachriel,
Actually, the truth is that I mentioned the caveats several times. By page four of the PT thread I had already mentioned Freeland's caveat of plausible biological parameters around a half dozen times. I'm sure I mentioned it a lot more later in the discussion but I don't feel like taking more time to do a fact count just for your sake.
Your accusation is, once again, false.
My question, once again, is "why"?
I would love nothing more than to discuss the optimality of the code with professional scientists like yourself. Unfortunately, you can't seem to get beyond false accusations and poo flinging. Pity.
Comment by chunkdz — October 13, 2008 @ 5:40 pm
October 13th, 2008 at 5:52 pm
Vetsigian, Woese, and Goldenfeld refer to the same papers already discussed. The claim that the genetic code is maximally optimized depends on prior evolutionary assumptions. Furthermore, Bradford, they conclude that the genetic code reflects the evolution of the cell.
In the thread at issue, chunkdz invoked a constant stream of invective. He also repeatedly misrepresented the paper at issue, spurning every opportunity for a reasoned discussion.
Comment by Zachriel — October 13, 2008 @ 5:52 pm
October 13th, 2008 at 6:14 pm
I went back to PT and searched for the exchange which brought up the optimal code issue:
Do you find it credible Zachriel that the genetic code would qualify as incompetent and illogical design?
Chunkdz used the phrase "an optimal design." I could tag a number of Van Gogh paintings as such and think I'm accurate. That does not equate to the best that is possible. But let's acknowledge the real problem here. It is obvious at the outset that ID itself is the issue and hostility to the concept transfers to any individual willing to advocate an ID position.
Comment by Bradford — October 13, 2008 @ 6:14 pm
October 13th, 2008 at 6:35 pm
Thank you, Bradford.
Given its historical evolutionary constraints, the genetic code is highly optimized.
* The standard genetic code can be placed on a translation error-minimizing fitness landscape of all possible codes.
* The landscape is rugged, but traversable by stepwise, evolutionary search.
* The standard genetic code is near the peak of a moderate-height hill.
* Comparable levels of optimization can be found by starting at a random location.
Many structures in biology we might say are beautiful and elegant. Others, not so much. It was quite appropriate for chunkdz to point this out.
Yes, chunkdz could have easily clarified his remarks, but he misinterpreted the paper, and has consistently refused to acknowledge the error.
Comment by Zachriel — October 13, 2008 @ 6:35 pm
October 13th, 2008 at 10:36 pm
Pardon me for dropping in but I'd like to know how chunkdz misinterpreted the paper?
Wasn't his remark about ID and their belief in an 'optimal design' of the code simply to explain why PT get their knickers in a knot when evidence supports an optimal code?
Wasn't his actual position made clear twice up thread?
How much more clear can you get than that?
Comment by willo — October 13, 2008 @ 10:36 pm
October 14th, 2008 at 7:56 am
According to the cited study, the standard genetic code is only optimal in the sense that it was optimized by evolution (stepwise improvement from a posited prebiotic origin). Take away the evolutionary assumptions, and it's not optimal. Chunkdz did not understand the study (or misrepresented it), and continued to insist upon taking quotes from the study out of their valid context. He showed no desire or ability to engage in a constructive discussion, but laced nearly every comment with invective.
As Stanton's claim was that "the Intelligence that designed the systems in the first place is either incompetent, or, does not follow logic as we, humans, recognize it," chunkdz's cite does not properly refute it. For whatever reason, the Intelligence did not pick the best possible code. Chunkdz could have reworked his claim somewhat and made it more applicable, but he was more interested in his 'experiments'.
Yes, I agree. That was his apparent motive.
Comment by Zachriel — October 14, 2008 @ 7:56 am
October 14th, 2008 at 12:28 pm
Zachriel,
Actually, if the authors' "plausible biological parameters" are correct, it is the "best of all possible codes". Read the paper.
Comment by chunkdz — October 14, 2008 @ 12:28 pm
October 14th, 2008 at 12:47 pm
Stanton is wrong. If humans are the point of reference then Stanton should have pointed out that humans have just recently come to an understanding of the code and are still limited in their ability to manipulate it. Those humans engaged in work involving genetics tend to be at the optimal end of the human intelligence range so if Stanton thinks he is making a point by labeling the code as incompetent or illogical by human standards then I would suggest he further explore what medium human standards really are.
Comment by Bradford — October 14, 2008 @ 12:47 pm
October 14th, 2008 at 12:50 pm
“According to the cited study, the standard genetic code is only optimal in the sense that it was optimized by evolution (stepwise improvement from a posited prebiotic origin). Take away the evolutionary assumptions, and it's not optimal.”—Zachriel
Freeland, et al: Here, we show that if theoretically possible code structures are limited to reflect plausible
biological constraints, and amino acid similarity is quantified using empirical data of substitution frequencies, the
canonical code is at or very close to a global optimum for error minimization across plausible parameter space.
This result is robust to variation in the methods and assumptions of the analysis…
The observed variation in optimization estimates
for the canonical code thus indicates it to be highly optimized
under any set of assumptions, but ‘‘the best of
all possible codes’’ only if biosynthetic restrictions and
a moderate transition bias are assumed. [My emphases.]
Question begging assumptions ("It evolved. It was not designed.") aside,
What results reported by the authors conflicts with the idea that the code was designed?
Comment by Rock — October 14, 2008 @ 12:50 pm
October 14th, 2008 at 12:55 pm
Zachriel:
This is too much. I've observed these exchanges for years and have been involved in many myself. The types of individuals who comment at PT are for the most part uninterested in civil dialog. That is evident time and time again. They cannot even approach TT standards for civility and appear to be uninterested in trying.
Comment by Bradford — October 14, 2008 @ 12:55 pm
October 14th, 2008 at 1:12 pm
Zachriel, (to willo)
Actually, Zach, that's not the Stanton quote I was responding to. Your selectively biased recall seems to have blocked out the fact that you knew this two days ago, but conveniently forgot it when it was not of political value to you.
I tell you, this phenomenon of partisan bias stress response is really fascinating to watch in action.
Comment by chunkdz — October 14, 2008 @ 1:12 pm
October 14th, 2008 at 1:40 pm
The assumptions refer to the prebiotic environment. In other words, the conclusion "best of all possible codes" only makes sense if we assume the code evolved.
Stanton wasn't referring specifically to the genetic code. And there are ample examples that would support Stanton's general claim. It is presumed that a designer would be able to pick a code that was optimum. Once again,
The standard genetic code can be placed on a translation error-minimizing fitness landscape of all possible codes.
* The landscape is rugged, but traversable by stepwise, evolutionary search.
* The standard genetic code is near the peak of a moderate-height hill.
* Comparable levels of optimization can be evolved by starting at a random location.
It didn't have to be this way. For instance, the landscape might have been chaotic, or the standard genetic code could have been isolated in the fitness landscape with no evolutionary approaches. The evidence looks just like it would if the genetic code evolved due to natural selection.
The genetic code looks like it would if it evolved, just like the Solar System looks like it would if it had collapsed from a stellar nebula. Maybe God set the planetary orbits to mark the glory of His plan. Maybe angels could have picked any genetic code, yet they picked a code near the peak of a moderate-height hill for reasons beyond our kin. Maybe the view is better from there. But there is no scientific evidence to support such a claim.
Comment by Zachriel — October 14, 2008 @ 1:40 pm
October 14th, 2008 at 1:56 pm
Utilizing what biochemicals?
Comment by Bradford — October 14, 2008 @ 1:56 pm
October 14th, 2008 at 1:59 pm
Zachriel:
That's your subjective view. Why would nucleic acids form a code in a prebiotic setting? What forces of nature induced this?
Comment by Bradford — October 14, 2008 @ 1:59 pm
October 14th, 2008 at 2:01 pm
Gee whiz, chunkdz. Do I have to transcribe the entire conversation, then repeat it endlessly?
Stanton claimed that biology is not 'logical' as design. You pointed to the genetic code as an example of optimal design. For evidence you cited a paper that depends on the assumption that the genetic code *evolved* from prebiotic conditions.
It's not that big a deal to misread a paper. Take the opportunity to learn from the experience.
Comment by Zachriel — October 14, 2008 @ 2:01 pm
October 14th, 2008 at 2:30 pm
ID is not my 'theory'. Let me know when you work out the details.
Not at all. Let's start with this (fourth time):
* The standard genetic code can be placed on a translation error-minimizing fitness landscape of all possible codes.
* The landscape is rugged, but traversable by stepwise, evolutionary search.
* The standard genetic code is near the peak of a moderate-height hill.
* Comparable levels of optimization can be evolved by starting at a random location.
These studies do not consider the origin of nucleic acids, but provide supporting evidence that the genetic code evolved early in the history of life after the formation of RNA-like oligomolecules.
Comment by Zachriel — October 14, 2008 @ 2:30 pm
October 14th, 2008 at 4:21 pm
A more optimal code is an inherent part of your argument against chunkdz. So give us the code and what it is composed of.
Bradford: Why would nucleic acids form a code in a prebiotic setting? What forces of nature induced this?
How can you have supporting evidence when you are unable to specify any of the relevant details concerning this evolution?
Comment by Bradford — October 14, 2008 @ 4:21 pm
October 14th, 2008 at 4:41 pm
The paper presumes an evolutionary process without being able to substantiate the claim. But the unsubstantiated process allegation nevertheless points to the sophisticated programming language alluded to by chunkdz.
Comment by Bradford — October 14, 2008 @ 4:41 pm
October 14th, 2008 at 5:31 pm
A hypothesis *is* an assumption. The paper tests the implications of that assumption, and the results support an evolutionary origin.
hypothesis, a tentative assumption made in order to draw out and test its logical or empirical consequences.
Comment by Zachriel — October 14, 2008 @ 5:31 pm
October 14th, 2008 at 6:08 pm
Zachriel,
No. Simply being honest should be enough.
You told willo that I cited the paper so as to refute Stanton's claim that the designer is incompetent. That was dishonest.
You also said that I claimed that the code was optimal "across all possible codes". That was dishonest.
You also said that I ignored the restrictions mentioned in the paper. That was dishonest.
I'd love to have a real discussion about the optimality of the canonical code, but without honesty there's really no basis for dialog. Pity that you can't seem to stop.
Comment by chunkdz — October 14, 2008 @ 6:08 pm
October 14th, 2008 at 6:18 pm
Since when does evolution entail the "best of all possible" anything?
Comment by chunkdz — October 14, 2008 @ 6:18 pm
October 14th, 2008 at 7:40 pm
Zachriel:
How do you test for replication variation when you have no idea what it is that is replicating?
Comment by Bradford — October 14, 2008 @ 7:40 pm
October 15th, 2008 at 8:50 am
[...] J. Freeland, Robin D. Knight, Laura F. Landweber and Laurence D. Hurst was discussed in the thread Chunkdz Comes Out Smokin. From the paper: The evolutionary forces that produced the canonical genetic code before the last [...]
Pingback by Misusing Natural Selection - Telic Thoughts — October 15, 2008 @ 8:50 am
October 15th, 2008 at 10:10 am
Primitive cells. RNA-like sequences.
But that's the really amazing thing about the scientific method. We don't have to know the reason why the Earth spins, or have the ability to directly observe its motion, to hypothesis and test whether it does. We might hypothesize (assumption) that the Earth spins. If it does, then it should bulge somewhat near the equator. If it does, then the force of gravity should be slightly less near the equator. And if it is, then a pendulum should move slower near the equator. And that is what Edmund Halley showed.
(… he improved the sextant, collected a number of valuable facts relative to the ocean and atmosphere, noted the equatorial retardation of the pendulum, and made on St Helena, on 7 November 1677, the first complete observation of a transit of Mercury. Gowing; Halley, Cotes, and the nautical meridian, Historia Math. 1995.)
So, to the paper at issue, Early Fixation of an Optimal Genetic Code. One standing hypothesis is that the standard genetic code was optimized to minimize translation error. But it was already known that "significantly better code structures are possible". So, the proposed hypothesis concerns whether the evolution of the genetic code is *constrained* to "a set of theoretically possible codes from which the canonical code evolved." If so, then the standard genetic code "is at or very close to a global optimum for error minimization" and "provides strong evidence that the structure of the canonical code was strongly influenced by natural selection for error minimization."
This supports (but does not prove) that the genetic code evolved. This is just one of many such papers that supports genetic code evolution.
Comment by Zachriel — October 15, 2008 @ 10:10 am
October 15th, 2008 at 5:16 pm
Zachriel Says: The genetic code looks like it would if it evolved…
It “looks evolved” is not an answer to my question, Zachriel. It “looks evolved” to me too. I don’t accept it when IDers tell me it looks designed. But Yes. It looks designed to me too! But I expect objects that have evolved to look designed and I also expect designs to evolve. And I have scientific reasons for those expectations.
Telling me something “looks designed” or “looks evolved” (Or both!) isn’t telling me anything I don’t already know.
And I realize that it may be something that’s difficult to wrap one’s brain around, but not everyone thinks of those as mutually exclusive (or exhaustive) categories. After all, where does the exclusivist, that Either/Or, the whole Evilutionist vs Cretinist ethos take you? Feces-flinging contests. Is this as far as your science goes?
Evolution (that anything “looks evolved”) is not inconsistent with a design-theoretic perspective on the matter. Because we are designers doesn’t mean we are damn fools! (Some of us are.) We are evolutionists too! (Some of us are creationists.) Designers, that we know of (namely Us!), exploit their knowledge of evolution to suite their purposes. We know that’s true, because we’ve done it ourselves. We have demonstrated evolution for ourselves, largely independently of biologists, chemists, and physicists demonstrations of evolution (You might say we have independently re-discovered evolution!) and evolution is commonly accepted amongst design engineers as a matter of fact. It is not inaccurate to say that evolution is a fundamental design principle. I think a lot of designers would agree with me.
However, in these narrowly focused, philosophically dogmatic, discussions never the twain shall meet, design and evolution. Whereas in design science, design and evolution are quite commonly viewed as intimately related processes. So intimately related that they ma be indistinguishable in purely operational terms, i.e., in theory.
(This is particularly true in computer science. Because that’s my background, I tend think of codes as algorithms. The genetic code, from this perspective, is (literally?) a genetic algorithm. It is not an arbitrary and static, unevolved and unevolving, map. The genetic code is a program, an algorithm, a set of procedures for adapting and evolving.)
Obviously designers, that we know of, operate well within the bounds of the laws of chemistry, which hardly restrict or constrain their designing at all, actually! As you can see, from tossing around numbers like 10^18 and 10^84, the real problem for designers is the lack of constraints! (Not to mention the lack of any practical knowledge of such vast designscapes.) For that reason alone a physicochemical or “stereochemical” theory is not inconsistent with design. And since physicists assure us (designers) that everything forms a coevolving whole I can’t see how any co-evolutionary theory (that is true) could be inconsistent with design given the underlying physical reality. Designs are co-evolving entities just like life forms, quite literally their components quasi-independently evolve while maintaining functional integrity. A more elaborated biosynthetic theory is very interesting from design perspective, as implementing a basic design economy, and indeed seems necessitated by the adaptive demand for increasing precision, increasing reliability, increasing complexity—of adapting and evolving in increasingly more effective ways. This may (and does) involves some ingenious resource allocation and utilization strategies.
Other than the “extreme” form of the “stereochemical” theory, none of these theories is “antidesign.” I suspect its probably some combination of all these theories (and maybe more); making this a far more complicated optimization problem than has been considered heretofore.
Two things have long puzzled me. Why four bases? Why ~20 amino acids? Chemistry is an almost ideal design substrate, because of its enormous potential for diversity under natural conditions. There are far more than four bases and >>20 amino acids. (Its been a long time since college biochemistry, but I recall that there is a certain number of amino acids ~200 (?).) And more than four (five) bases. Amino acids and bases are highly evolved, quite diverse, classes of chemicals. (On a related note, protein design engineers have shown, at least theoretically, that common protein design motifs are reproducible using as few as 5-7 amino acids!)
Why four and twenty blackbirds baked in this pie?
Maybe there is a biochemical engineering rationale for these design elements and their relative proportions? Who knows? I sure don’t! I don’t think anyone else does either. Who knows?—Maybe it “just happened”? LOL
(You may have noticed that I am absolutely determined to immortalize the words of Richard Dawkins.) Doesn’t appear to be much of an evolutionary-theoretic “rationale” here either. I feel that I should remain somewhat open minded, not philosophically dogmatic, on the matter, nor do I feel in anyway compelled to any “scientific” assumptions about much of anything here, not prebiotic chemistry, or even how evolution is “supposed to work,” etc. (E.g.., mitocodes have evolved “symbiotically” with nuclear codes and these models don’t allow any number of such possible co-evolutionary scenarios.
Am I just being pigheaded about this? LOL
Error minimization is the subject; how good is the genetic code at minimizing some error function (cost, objective, or fitness function, or whatever ya wanna call it).
Obviously design and evolution are related in those terms, because there already exists an extant body of science covering that subject, search and optimization theory, and the theory of error-correcting codes, or algebraic coding theory. Shannon’s Mathematical Theory of Communication remains as good an introduction as any in print, but see also Vol. 1 (Part One, Chapter One!) of the Handbook of Coding Theory.
Coincidently (or not), DNA has been compared unfavorably, in terms of error minimization performance, to Huffman codes and Huffman is one of the editors of the Handbook.
But what kind of code is the genetic code, if its not obviously a Huffman code?
Plainly its block code (n=4, k=3, d=?), but inspection of the translation table reveals it to be a cyclical permutation block code. Interesting? Trivia? Irrelevant? Or is it even true?
Forty years ago, and what has been largely and unfortunately ignored, Rosemary Swanson said the standard genetic is a Gray code!
I think the fact that the genetic code is a Gray code is fascinating, not just in its own right (that the genetic code should in any way resemble any humanly devised coding system), but because Gray codes have certain intrinsically adaptive features. E.g., in translation from the domain of real valued function evaluations (as in any evaluation of optima or fitness, etc.), Gray codes introduce no artificial optima, and may indeed reduce the number of optima—thereby “smoothing” rugged optimization surfaces. Maybe that’s why Gray codes were selected over Huffman?
But, answering my own question, Who cares! It’s irrelevant in the context of these discussions. So, pardon the interruption, and let the shit fly!
Comment by Rock — October 15, 2008 @ 5:16 pm
October 15th, 2008 at 5:53 pm
Sure I did. My comment didn't refer to a trivial glance, but clearly referred to specific empirical patterns entailed in a hypothesis.
A simple example can be found in animal husbandry or plant domestication.
Comment by Zachriel — October 15, 2008 @ 5:53 pm
October 15th, 2008 at 6:35 pm
“Sure I did.”
Whatever it is that you did, you didn’t show how any of these hypotheses of the origin and evolution of the genetic code is inconsistent with design.
“A simple example can be found in animal husbandry or plant domestication.”
Of which you were previously unaware apparently:
"Design engineering typically refers to human design. That would apparently exclude the historical origin of species."
Other than those species which we have, historically, designed ourselves.
I count that as progress however. I mean, you may be progressing. I will return you to fold of progressive evolutionists, the warm embrace of Darwin and Fisher et al, Zachriel.
We have nothing to fear from creationists in exploring these matters. We shouldn’t allow creationists to determine for us how we think about evolution and design. They have no viable alternative.
Comment by Rock — October 15, 2008 @ 6:35 pm
October 15th, 2008 at 6:58 pm
Of course not. Darwin coined the term "Natural Selection" as a parallel to artificial selection.
Of course. Humans also alter genomes.
Comment by Zachriel — October 15, 2008 @ 6:58 pm
October 16th, 2008 at 10:12 am
Re:
Rock @ 5:16 pm.
Very well stated. In fact, if one looks close enough, evolution itself can be seen as a reliable indicator of previous intelligence. Conversely, there is to date no evidence that evolution of functionally specific information can even theoretically occur absent previous intelligence.
Comment by CJYman — October 16, 2008 @ 10:12 am
October 16th, 2008 at 1:34 pm
Rock,
This is mind blowing!
I do loves me some Rock!
Comment by chunkdz — October 16, 2008 @ 1:34 pm
October 16th, 2008 at 6:15 pm
CJYman:
That is really an astonishing claim. Are you saying that animal camouflage, which obviously reflects information about the animal's environment, cannot evolve, even in theory, absent previous intelligence? Intelligence made polar bears white?
Comment by Raevmo — October 16, 2008 @ 6:15 pm
October 17th, 2008 at 9:37 am
CJYman;
Raevmo:
Its really not that astonishing. Just show me any computational experiment which has produced complex functionally specific information starting from an arbitrary set of rules and without any type of foresight for future results.
What has to be in place in order to achieve animal camouflage? Trace it back and you'll find that previous intelligence is required in a complete causal chain. Yes, it is true that there are many instances of random variations that can occur from an informational node on a pre-programmed template so to speak. However, to even get to these positions where some random variations can occur with existing functionally specific information, intelligence is necessary and no one has ever shown otherwise. The information necessary for animals to evolve into their environments was most likely an intelligently pre-programmed target, based on the fine tuned laws of physics.
Furthermore, there is much empirical evidence in the form of experimenting with evolutionary algorithms and in the somewhat controversial mathematics behind COI that an evolutionary algorithm won't output more information, as a measure of probability, than the information content of the algorithm itself. Thus, if the algorithm produces intelligence, the best explanation is that it came from something with the same complexity and information content as intelligence — most probably previous intelligence. As well, so far, intelligence (foresight being one aspect) is a necessity to program the evolutionary development of complex, functionally specific information. Thus, there is also proof of concept for the ID position.
Here is an article, which discusses how evolution of complexity doesn't *just happen* via "natural selection" and a bunch of arbitrary initial conditions, that you may find interesting.
I especially would like to know how they came to the conclusion that "Unlike the real world, the outcome of computer evolution is built into its programming." First, yes, the experimental and mathematical work shows that the outcome of evolution is built into its programming (COI vindicated). But, how can they say that the real world is not like that, when it is basically uncontested physics that in order for life to evolve physical parameters have to be extremely fine tuned to extremely high improbability among all possible mathematical worlds, of which the vast majority wouldn't even be able to create compounds necessary for life much less last long enough for life to get started.
And if you want to go on about "well, then there would just be 'other' types of life" then go ahead and provide a definition of life, show that it has the same complex [beyond UPB improbability] functionally specific characteristics (which is really what needs explanation here) as life as we know it, and provide some evidence with computational simulation and physics that any arbitrary set of laws will produce this evolving life. Oh wait a minute, the aforementioned article cites exactly that scenario and shows that it doesn't work.
Comment by CJYman — October 17, 2008 @ 9:37 am
October 17th, 2008 at 10:59 am
CJYman:
That is a bizarre request. The non-arbitrary rules of mutation and selection are sufficient to transfer environmental information to gene pools. The frequency of an allele for white fur in bears tells me something about the environment the bears live in. The allele could originate by mutation of an allele for brown fur and the environment caused selection which caused a change in allele frequency.
Ah, so you admit that functional information can evolve, but now you're retreating to the deep past to claim that intelligence was required somewhere along the way. Please give me a step-by-step explanation of how this intelligence achieved what you think it achieved. Details please.
Let's say earth = environment + genomes. Even if the information content of the earth remains constant (which it doesn't since it is not a closed system), the information content of genomes can increase by applying an evolutionary algorithm which transfers information from the environment to genomes. It doesn't require fancy mathematics to see that.
Comment by Raevmo — October 17, 2008 @ 10:59 am
October 17th, 2008 at 11:19 am
CJYman:
You completely avoided the point of CJYman's question. Your answer illustrates how the coding system would function but avoids any explanation relevant to the origin of the system itself. The allele related to white fur exists within a system that is non-arbitrary. The coding function enabling the expression of the white fur allele already exists. The coding for the amino acids of the relevant protein already is there and so are the DNA repair functions securing the integrity of the genome. IOW, the rules have already been set for the white fur allele example you have introduced. As for foresight, that is inherent to the rules governing genomic function as well. A capacity for adaptation to environmental stress is evidence of foresight.
Comment by Bradford — October 17, 2008 @ 11:19 am
October 17th, 2008 at 12:22 pm
Bradford:
I refuted CJYman's claim that "evolution of functionally specific information can even theoretically occur absent previous intelligence." You seem to agree that genomes can accumulate functional information by the repeated application of an evolutionary algorithm. As usual, you crawl back into the gaps of knowledge regarding OOL and the genetic code.
Comment by Raevmo — October 17, 2008 @ 12:22 pm
October 17th, 2008 at 12:24 pm
Raevmo,
Eskimos are brown.
Comment by chunkdz — October 17, 2008 @ 12:24 pm
October 17th, 2008 at 12:38 pm
Raevmo:
No you didn't. You simply assumed that the coding system enabling the evolution of functionally specific information was formed in the absence of intelligence. You assumed the conclusion.
I'm pointing to the nature of the code itself. The gaps are expressions of your feeling that a materialist solution will be found to the origin of the code.
Comment by Bradford — October 17, 2008 @ 12:38 pm