Chunkdz Comes Out Smokin
by BradfordTT 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?
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".