Mark Pallen on Namba on the flagellum/ATPase homologies...and me

IDiots pwned! (again)

Congrats Nick! On a rekated note, what about the critique of the Liu and Ochman PNAS paper? Did you ever find someone willing to publish it, since PNAS doesn't publish letters?

Hi Dave -- a letter was attempted but didn't work so there will be stuff in the formal peer-reviewed literature eventually. But it will take awhile. Just kind of saying "they are wrong for simple reason X" isn't really enough to make a research article, whereas redoing the whole thing "right" is a nontrivial project.

The mysterious "Namba" is Keiichi Namba of Osaka University.

Who's not quite yet of single-name fame like Cher or Bono -- 'cept to PT flagella geeks.

He is also the Namba of the fantastic flagellum videos that the ID people like to use...

Am I the only one that keeps reading that as "Nambla", or the "North American Marlon Brando Look Alikes"?

We have a review of recent work on flagellar evolution with a gentle critique of Liu and Ochman in press at Trends in Microbiology. Should be available in the next week or two.

I wonder if the IDiots have Namba's permission to use his videos. Perhaps I could persuade him to sue for breach of copyright?! But I suspect he has more important things to do.

I waded through Mike's crap and had to laugh. He extols the "design reasons" for the construction of bacterial flagellum using an export system. But really what he's doing is saying nothing at all except to plead for suspension of thought. If you really play the think-like-a-designer game that Mike wants you to play, you'd quickly realize that the flagellum is a kluge.

Consider: you're building a submarine. You need a propulsion system. First thing you do. . . is build a waste disposal unit? But maybe that's not what you had in mind. At its most basic, a waste-disposal unit is a system that connects the outside world to the inside world. Now, a hole in the wall of a ship is not too terribly difficult to envision. But the key is propulsion. Propulsion can be generated vis-a-vis a hole in quite a number of ways. Really, what you want to do is manipulate the environment through the hole. You can construct a parachute and deploy it through the hole. Or design a pressurized jet system where water/gas/waste products/whatever-shit-you-have-on-board is ejected through the hole. Or design gunpowder. Or design a propeller. Or design paddles. But . . . rather than think like a human designer, you decide you much rather manipulate the environment with . . . wait-for-it . . . a whip. Yes, you are quite a hardcore bondage and S&M sort-a-guy. You bad boy you.

But how do you erect a whip so that it projects out the bloody hole in the wall? Well, you could build inside the submarine before hand. Unfortunately, the physics of this problem is that you need a whip as long as your propulsion-less-submarine. The ship would then have little left to do except carrying around a humongous flagellum. Here's an idea though: you could build your flagellum along the wall of your ship so that the flagellum covers the surface in a contiguous fashion, sorta like wrapping a string loosely around a spool. Then you bleb it off the surface of the ship, and then have it unfurl. Here's another idea: you could build your flagellum piecemeal by a ratchet-system. Put the most distal end of the whip into a hole, and then keep feeding it through as you build it up from the inside. Here's another idea: you could design the flagellum by having it polymerize particles from the outside, preferably from crap that you're already sending outside the waste disposal system. Here's another idea . . . but you get the idea.

Now why did the Designer do it the way he did? As evidence mounts, it looks like he really had no choice but to use what's he's got: a waste-disposal system. There was no evidence of ingenuity, no technical tour-de-force. Rather we found evidence of sloppy workarounds. The Designer outsourced the design of a propulsion system to the engineer working on the Port-a-john. But why did he do that? Here, Mike and the rest of the IDiots prefer you to stop thinking. No, they'll whine about designer-centrism, while they slip a couple of designer-worshiping commentary past you. But this is where the "science" of ID stops, folks. You explore the design space that Mother Nature's got to work with (and it is huge), and you wonder: why-in-the-world didn't it do it this way? Without the Designer, how else do you proceed with the analysis? You don't. And that's the point of this whole fucking controversy.

Pallen: We have a review of recent work on flagellar evolution with a gentle critique of Liu and Ochman in press at Trends in Microbiology.

wad of ID: I waded through Mike’s crap and had to laugh. He extols the “design reasons” for the construction of bacterial flagellum using an export system. But really what he’s doing is saying nothing at all except to plead for suspension of thought. If you really play the think-like-a-designer game that Mike wants you to play, you’d quickly realize that the flagellum is a kluge. Consider: you’re building a submarine. You need a propulsion system. First thing you do… is build a waste disposal unit? But maybe that’s not what you had in mind. At its most basic, a waste-disposal unit is a system that connects the outside world to the inside world. Now, a hole in the wall of a ship is not too terribly difficult to envision. But the key is propulsion. Propulsion can be generated vis-a-vis a hole in quite a number of ways. Really, what you want to do is manipulate the environment through the hole. You can construct a parachute and deploy it through the hole. Or design a pressurized jet system where water/gas/waste products/whatever-shit-you-have-on-board is ejected through the hole. Or design gunpowder. Or design a propeller. Or design paddles. But … rather than think like a human designer, you decide you much rather manipulate the environment with … wait-for-it … a whip. Yes, you are quite a hardcore bondage and S&M sort-a-guy. You bad boy you. But how do you erect a whip so that it projects out the bloody hole in the wall? Well, you could build inside the submarine before hand. Unfortunately, the physics of this problem is that you need a whip as long as your propulsion-less-submarine. The ship would then have little left to do except carrying around a humongous flagellum. Here’s an idea though: you could build your flagellum along the wall of your ship so that the flagellum covers the surface in a contiguous fashion, sorta like wrapping a string loosely around a spool. Then you bleb it off the surface of the ship, and then have it unfurl. Here’s another idea: you could build your flagellum piecemeal by a ratchet-system. Put the most distal end of the whip into a hole, and then keep feeding it through as you build it up from the inside. Here’s another idea: you could design the flagellum by having it polymerize particles from the outside, preferably from crap that you’re already sending outside the waste disposal system. Here’s another idea … but you get the idea. Now why did the Designer do it the way he did? As evidence mounts, it looks like he really had no choice but to use what’s he’s got: a waste-disposal system. There was no evidence of ingenuity, no technical tour-de-force. Rather we found evidence of sloppy workarounds. The Designer outsourced the design of a propulsion system to the engineer working on the Port-a-john. But why did he do that? Here, Mike and the rest of the IDiots prefer you to stop thinking. No, they’ll whine about designer-centrism, while they slip a couple of designer-worshiping commentary past you. But this is where the “science” of ID stops, folks. You explore the design space that Mother Nature’s got to work with (and it is huge), and you wonder: why-in-the-world didn’t it do it this way? Without the Designer, how else do you proceed with the analysis? You don’t. And that’s the point of this whole fucking controversy.

Cunkdz,

The fact that you have zero comprehension does not change the fact that wad hit the nail on the head. Perhaps you can describe for us what the future genetic data should reveal if the at least one of the thousands of types of flagella were designed by someone somewhere for some reason.

By the way, copying and pasting long sections of text without any substantive response is troll tactic number 3. You don't want to be labeled a troll now do you?

As for Nick, the genetic data has vindicated his position. He should be able to say I told you so.

David Stanton: Cunkdz, The fact that you have zero comprehension does not change the fact that wad hit the nail on the head.

By the way, copying and pasting long sections of text without any substantive response is troll tactic number 3. You don’t want to be labeled a troll now do you?

As for Nick, the genetic data has vindicated his position. He should be able to say I told you so.

chunkdz said:

David Stanton: Cunkdz, The fact that you have zero comprehension does not change the fact that wad hit the nail on the head.

The fact that you can't even spell my name doesn't change the fact that wad is engaged in strawman building. Mike never claimed ID was science, and his approach has never required independent knowledge of the designer.

By the way, copying and pasting long sections of text without any substantive response is troll tactic number 3. You don’t want to be labeled a troll now do you?

If exposing logical fallacy is considered trolling to you, then go ahead and break out your P-Touch and label me. Just try to spell my name right this time.

As for Nick, the genetic data has vindicated his position. He should be able to say I told you so.

I don't challenge Nick's acumen.He's a very smart fellow who's put in a lot of hours on this. But there's a difference between having a professional disagreement, and just being a smug prick.

[quote]Mike never claimed ID was science, and his approach has never required independent knowledge of the designer.[/quote]Where did I say Mike claimed ID was science?

The strawman is yours. What I assert is far stronger: ID cannot be science. Mike thinks it could be -- he is wrong.

I'll add another comment: Mike says he does not require independent knowledge of the designer. Actually what he does is imbue the designer with whatever characteristic he needs for his just-so story to make sense. It is as if he alone has a direct channel with the Designer. What I show above is that his Designer is completely unrecognizable from anything we know. In fact every once in a while Mike admits as much. So once again, where is the justification for his assumptions about the Designer? Nowhere. He just pulls it out of his ass and then labels it "proto-science". Let's all be honest and call it what it is: bullshit.

Chunkyz,

Thanks for responding to my comment, but conveniently not answering the question I asked. The point made by wad is still valid and you have written nothing to dispute it. By not answering the question you have again demonstrated the validity of the argument.

ID is not science and cannot ever be science. It did not successfully predict anything and it cannot explain any of the evidence. If the only thing you can do is make a posteriori "predictions" then you have failed miserably. Rerducing God to an incompetent boob is not something that most Christians would take kindly to.

wad of id said: [quote]Mike never claimed ID was science, and his approach has never required independent knowledge of the designer.[/quote]Where did I say Mike claimed ID was science? The strawman is yours. What I assert is far stronger: ID cannot be science. Mike thinks it could be -- he is wrong.

wad of id said: The Designer outsourced the design of a propulsion system to the engineer working on the Port-a-john.

Then, why do Intelligent Design proponents insist on being heard if they have no legitimate reason to challenge the Theory of Evolution?

Wad: Where did I say Mike claimed ID was science?

chunkdz said:

Then, why do Intelligent Design proponents insist on being heard if they have no legitimate reason to challenge the Theory of Evolution?

Wad was bashing Mike Gene who does not challenge the Theory of Evolution, nor does he insist on being heard. Prejudice is easy. Critical thinking is hard.

stanton: In fact, Wad highlights an important point, in that if Intelligent Design proponents actually bothered to look at all of the biological systems that they claim are “intelligently designed,” they would notice 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 said:

stanton: In fact, Wad highlights an important point, in that if Intelligent Design proponents actually bothered to look at all of the biological systems that they claim are “intelligently designed,” they would notice that the Intelligence that designed the systems in the first place is either incompetent, or, does not follow logic as we, humans, recognize it.

Good point. ID'ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design.

Critics like yourself think that it is flawed because it appears to them to be "incompetently" designed or "does not follow logic as we, humans, recognize it."

Of course, critics like yourself are just kidding yourself.

Of course, critics like yourself are just kidding yourself.

— Chunkdz

Now why did the Designer do it the way he did? As evidence mounts, it looks like he really had no choice but to use what’s he’s got: a waste-disposal system. There was no evidence of ingenuity, no technical tour-de-force. Rather we found evidence of sloppy workarounds. The Designer outsourced the design of a propulsion system to the engineer working on the Port-a-john. But why did he do that? Here, Mike and the rest of the IDiots prefer you to stop thinking. No, they’ll whine about designer-centrism, while they slip a couple of designer-worshiping commentary past you. But this is where the “science” of ID stops, folks. You explore the design space that Mother Nature’s got to work with (and it is huge), and you wonder: why-in-the-world didn’t it do it this way? Without the Designer, how else do you proceed with the analysis? You don’t. And that’s the point of this whole fucking controversy.

Chunkdz wrote:

"Good point. ID’ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design."

Once again you prove my point. The last twenty years of molecular genetics has shown us conclusively that the genome is anything but optimally designed. It is more of a hodge podge of useless repetitive sequences, harmful tandem repeats, mutation causing short and long interspersed transposable elements, nonfunctional pseudogenes, etc. etc. etc. Now who is fooling themselves?

Look, you just can't claim that the genome is optimally designed, you just can't. That ignores all of the evidence. Instead, the structure of the genome is exactly what one would expect if it were the product of billions of years of random mutation and natural selection. That is why ID fails miserably as science, No mater what the evidence, some idiot will be ignorant or stupid enough to claim that that is the way would have done it. Postdiction is not a valid test for a hypothesis.

So tell me again, exactly what sequence would one expect to find in this "optimal" code of life if some designer did something somewhere at sometime for some unknown reason?

David Stanton: Look, you just can’t claim that the genome is optimally designed, you just can’t. That ignores all of the evidence.

wad: The fucking arrogance is so damn hilarious. Hey chunkdz, suck my cock. Don’t cry as you do it please.

Mike Elzinga: That is a very strange accusation.

What I assert is far stronger: ID cannot be science. Mike thinks it could be – he is wrong.

Oh, if we're about positing fantasy worlds where we actually can sit down and speak with a putative "intelligent designer" and find out exactly how and when it operates in the world, THEN ID could be science.

since IDiots seem to love making up notions of the improbability of things, I'd have to add that such a scenario is so improbable as to make your strong assertion that ID cannot be science a relative certainty.

Of course, the likes of Dembski and Johnson already know this, but can readily rely on an army of wishful thinkers to keep the 'cause alive.

that said, hey, I'll be first in line to interview God as to mechanism whenever he manages to pop up from his infinitely long, self-imposed nonpresence.

I wonder if the above argument about genetic code is about the code, or about the genomes that make use of the code?

chunkdz said:

stanton: In fact, Wad highlights an important point, in that if Intelligent Design proponents actually bothered to look at all of the biological systems that they claim are “intelligently designed,” they would notice that the Intelligence that designed the systems in the first place is either incompetent, or, does not follow logic as we, humans, recognize it.

Good point. ID'ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design. Critics like yourself think that it is flawed because it appears to them to be "incompetently" designed or "does not follow logic as we, humans, recognize it." Of course, critics like yourself are just kidding yourself.

The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results from selection to minimize the effects of errors (e.g., mistranslation and mutation) on resulting proteins. If amino acid similarity is measured as polarity, the canonical code does indeed outperform most theoretical alternatives. However, this finding does not hold for other amino acid properties, ignores plausible restrictions on possible code structure, and does not address the naturally occurring nonstandard genetic codes. Finally, other analyses have shown that significantly better code structures are possible.

Conclusions We have presented comprehensive evidence that the standard genetic code is a product of natural selection to minimize the phenotypic impact of genetic error; the arrangement of codon assignments meets, to an extraordinarydegree, the predictions of the adaptive hypothesisand cannot be explained as an artifact of stereochemistry, biosynthetically mediated code expansion, or analytical methodology. However, the process by which an adaptive code evolved at present remains unclear, and yet its resolution may be of key importance to our understanding of the amino acid components universal to life.

D.P.Robin: "My,my, I can’t help but to conclude that you’ve engaged in wishful thinking here."

Results: The Adaptive Code Is No Artifact of Stereochemistry, Analytical Methodology, or Biosynthetic Restrictions Our analysis shows that when the canonical code is tested against a sample of one million random variants using PAM matrix data to measure amino acid dissimilarity, the code appears to be extremely highly optimized at all transition weightings and modular power functions. For the unrestricted set of codes, no better alternatives are found anywhere...This pattern is repeated for the restricted set of possible codes excepting the least plausible extremes of parameter space (no transition bias...and at a high-modularpower mapping function...where three and five better variants are found, respectively...Far from explaining reports of a highly adapted code structure as an artifact, high-modular-power scaling functions actually cause the code to appear less adaptive. This suggests that overall code optimality is not the result of careful arrangement of a few key outlier amino acids, but is indeed a reflection of a complex and intricate adaptive arrangement. When the analysis is repeated using Polar Requirement as a similarity measure, the results are remarkably similar: once again, no better alternatives are found in a sample of one million codes drawn from the unrestricted set ... and the only exceptions for the restricted set of codes are once again found in the absence of a transition bias (w 5 1)...It is noteworthy that where results differ, those based on PAM matrix data provide consistently higher estimates of code optimality (by around two orders of magnitude) than those based on Polar Requirement; the better the definition of amino acid similarity (in terms of selection), the better the canonical code appears. These observations vindicate previous adaptive evidence as a robust interpretation of code evolution rather than an artifact of, say, a stereochemically determined code. The Best of All Possible Codes? When the error value of the standard code is compared with the lowest error value of any code found in an extensive search of parameter space, results are somewhat more variable. Estimates based on PAM data for the restricted set of codes indicate that the canonical code achieves between 96% and 100% optimization relative to the best possible code configuration (fig. 2c). If our definition of biosynthetic restrictions are a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes.

D.P. Robin In other words, it seems that one particular genetic code (and not all, which you seem to claim above...

...is good at reducing the chances for genetic error having bad functional impacts. So, maybe it is “optimal” for one particular function; that cannot be equated with “perfection”, let alone good design.

If optimality is good design, then what does sub-optimality or lethality imply?

wad: If optimality is good design, then what does sub-optimality or lethality imply?

Chunkdz,

You should be more precise. The genetic code is not the "code of life". Also, the authors conclude that the code waas fixed, not designed. In any event my point still stands, the genome is not optimal in any way.

Oh and sub-optimal means incompetent design.

David Stanton: You should be more precise. The genetic code is not the “code of life”.

Also, the authors conclude that the code waas fixed, not designed.

In any event my point still stands, the genome is not optimal in any way.

Oh and sub-optimal means incompetent design.

Chunkdz,

Personal attacks do not address the substance of the argument. You did not use the proper terminology, so berating others for not understanding is counterproductive. You have not shown that the genetic code could not have evolved. Indeed there is much evidence that it has. You have also failed to refute the point that the genome is far from an optimal design and therefore implies an incompetent designer at best.

Well adapted systems give the illusion of design. What you need to do is devise a test that distinguishes between the two possibilities. Might I suggest the Explanatory Filter. Yea, that should yield a valid statistic that everyone can agree is biologically meaningful. I'm sure that everyone will be convinced by that.

David Stanton: "You have not shown that the genetic code could not have evolved."

"...Indeed there is much evidence that it has."

If life really is designed, how come you are extremely hesitant to explain how it is designed beyond making the blanket statement of it being "optimal"? Are we to assume that this is the very limit of your evidence, and that your constant personal attacks are to deflect scrutiny from your lack of evidence?

Stanton: "If life really is designed, how come you are extremely hesitant to explain how it is designed beyond making the blanket statement of it being “optimal”?"

"Are we to assume that this is the very limit of your evidence, and that your constant personal attacks are to deflect scrutiny from your lack of evidence?"

chunkdz said:

Stanton: "If life really is designed, how come you are extremely hesitant to explain how it is designed beyond making the blanket statement of it being “optimal”?"

Oh, shut up moron. You can't explain the origin of life any more than I can.

What I said was that you critics look at biological systems as kludgy hodge-podges and say that this is exactly what we expect to see with evolution. However, when confronted with scientific evidence that the canonical code upon which every biological system is based is optimal to an extremely high degree, you guys don't know whether to keep drooling or pick your nose or both.

"Are we to assume that this is the very limit of your evidence, and that your constant personal attacks are to deflect scrutiny from your lack of evidence?"

Spare me your false sanctimony, you mental midget. You are the one who broadly labeled ID'ers "smartmouthed, lazybrained vermin". Now you are whining because science didn't tell you what you wanted to hear.

Real bunch of freakin' Einsteins you've got here at PT.

Stanton: You keep saying that there is evidence that the “canonical code upon which every biological system is optimal to an extremely high degree,” yet, you refuse to show us this evidence. .

This coming from a person who instinctively resorts to personal attacks and insults in order to hide the fact that he can’t produce any evidence whatsoever to support his statements.

However, when confronted with scientific evidence that the canonical code upon which every biological system is based is optimal to an extremely high degree, you guys don’t know whether to keep drooling or pick your nose or both.

chunkdz said:

Stanton: You keep saying that there is evidence that the “canonical code upon which every biological system is optimal to an extremely high degree,” yet, you refuse to show us this evidence. .

So when I referenced a scientific report by Freeman, et. al. that says "the code appears to be extremely highly optimized" you didn't consider that to be evidence that the code is extremely highly optimized? You are stupider than I thought.

This coming from a person who instinctively resorts to personal attacks and insults in order to hide the fact that he can’t produce any evidence whatsoever to support his statements.

It seems that you are the only person who throws out insults while saying absolutely nothing of scientific merit. You ignore the published scientific report that I posted and proceed to whine about Big Bad Dembski, Medved and Johnson and all the "smartmouthed, lazybrained vermin".

Seriously, are you guys all this idiotic?

fnxtr: "Just a guess here… the optimal code is the one that replicated itself most successfully?"

"No wait, here’s another idea: POOF!"

chunkdz said:

fnxtr: "Just a guess here… the optimal code is the one that replicated itself most successfully?"

Since when does successful reproduction entail optimality? You apparently agree with the critics that nature is expected to produce kludgy hodge-podges except in the special case of the original canonical genetic code where it happened to produce the optimal "best of all possible codes"?

Optimality is not perfection. But chunky knew that. So optimality is not a problem for evolution because it is well known that evolution produces locally optimal solutions. In fact it is used for that specific purpose in artificial settings: look up genetic algorithms, for instance.

So the genetic code is "optimal." Unless you are chunky who wears blinders, you have to ask merely 2 questions:

1) Under what specific criteria is this system optimal.
2) Are these criteria necessary for life?

Chunky will fail both the answers to these questions because his teleological blinders prevents him from exploring the possibilities aside from what he has before him. It is is his failing. It need not be yours.

Stanton: "As David Stanton said, you misread the report. If the evidence of life being optimal is so earth-shakingly obvious, then how come you have to resort to insulting us, rather than restate your position more clearly? Like, how did they find out how to tell the difference between optimal and suboptimal, and how this is evidence for Intelligent Design?"

Furthermore, explain to me again how you intend to convince us of your claims and opinions by belittling and insulting us.

If you really think we are idiotic, then, why are you still coming here and posting your futile attempts to convince us of your claims by constantly insulting us?

So then can you demonstrate how optimality as evidence for Intelligent Design can explain things like Huntington's Disease, or do you simply wish to continue your stream of insults and ranting?

Well, chunkdz, how about the IDiotic alternative: we can out your IP address, find out your real life identity, and then send you in for an FBI background check because of your secret terrorist activities.

LOL

wad: So optimality is not a problem for evolution because it is well known that evolution produces locally optimal solutions.

So the genetic code is “optimal.” Unless you are chunky who wears blinders, you have to ask merely 2 questions: 1) Under what specific criteria is this system optimal.

2) Are these criteria necessary for life?

Exactly. It is optimal with respect to constraints. Read it again dipshit: CONSTRAINTS. Constraints = criteria. It is globally optimum with respect to these CONSTRAINTS.

Where do the authors say that the CONSTRAINTS are the only ones sufficient for life?

Read it and weep, dipshit.

Taken together, our results provide strong evidence that the structure of the canonical code was strongly influenced by natural selection for error minimization.

Stanton: So then can you demonstrate how optimality as evidence for Intelligent Design can explain things like Huntington’s Disease, or do you simply wish to continue your stream of insults and ranting?

The genetic code is globally optimal across all plausible search space.

wad: Exactly. It is optimal with respect to constraints. Read it again dipshit: CONSTRAINTS. Constraints = criteria. It is globally optimum with respect to these CONSTRAINTS.

So you didn't read the paper. They were very specific about the "plausible biological criteria." They didn't say "all." They didn't say "IM-plausible"

So burden is on you to show that these biological criteria are the ONLY criteria which sustain life. Not as we know it. Any life.

You can't.

wad: Now, I have the paper right before me. I searched for exactly the phrase “all plausible search space”. Guess how many hits I got? Let me help chunky in case he’s struggling with this: It’s an integer between -1 and 1.

Where was the word "all" in that phrase, dipshit?

wad: Where was the word “all” in that phrase, dipshit?

wad of id said: Clearly chunky forgot to read this pivotal conclusion of the authors:

Taken together, our results provide strong evidence that the structure of the canonical code was strongly influenced by natural selection for error minimization.

But oh wait, I bet someone already pointed this out to the dumbass.

LOL When faced with authoritative contradiction, caught in an outright lie, and shown to be embarrassingly uninformed, chunkydisease resorts to the last bastion of the simple-minded: close your mind and scream lalalalala. Let's not "simply" say anything, dumbass, because unlike you, I actually think about the matter and read.

While chunky is down for the count, let me kick him a coupla times more:

Evolution designs.

Oh my fucking god, the horror.

LOL

See, because we are blinkered by our limited perspective, we can never understand how what looks like contingency and accident is actually all part of the Perfect Master Plan. And one day someone will prove it. Scientifically. Maybe chunkdz will. Libraries and labs full of real work are no match for Aristotlean mind-wanking. You just wait.

Slightly OT, but I've been involved in a few disputes over randomness in gaming and gambling clubs, and I've noticed that the complaint is always that the low probability events are happening too often. Never once have I seen the complaint that the low probability events happen too seldom. I find that telling, since it is apparent that erring on the side of false positives would be evolutionarily advantageous for our psychology. The rabbit that bolts at the first sign of a coyote in the grass is going to pass on its genes far more frequently than the one that doesn't notice, or the one that does, but waits around to get more data before making a decision. It also is consistent with our tendency to remember outlying events more than routine ones, thus elevating their perceived frequency.

So it comes as no surprise to me that the dispute over the randomness in evolution would come from people claiming that the low probability events like bacterial flagellum and DNA were happening too often. It's the same mistake, just a different arena, but it helps explain what little secular appeal ID has for some people.

Well, I certainly won’t claim that this troll is entertaining.

So, as we already knew, according to ID/Creationists, optimum implies design.

But the argument that something being optimal implies design is old, seriously flawed, and is part of the repertoire of misconceptions of the ID/Creationist crowd.

Using these misconceptions, they could claim that a monkey, grabbing a length of rope or vine and flinging into the air and having it fall limply across two limbs, has just designed the catenary curve that minimizes the potential energy of the rope or vine. And also the parabolic arc that the center of mass of the rope followed before it landed on the limbs because that path also minimizes an action integral.

Similarly, if the monkey looked down at the reflections in a puddle of water, they could argue that the monkey positioned itself exactly at the point where the light rays from the reflected objects minimized their time of travel from the object, off the puddle, to the monkey. Therefore monkeys position themselves according to intelligent design.

Even more impressive; if the monkey is looking at an object lying at the bottom of a pond, the monkey again positioned itself exactly at the point where light from the object to the monkey took the path of least time but not the path of least distance. How did the monkey know to choose correctly between these alternatives?

And if the monkey tipped over a bucket of sand and the sand spilled down through a knothole and formed a cone-shaped pile on the ground below, they could say that the monkey designed the exact cone angle that minimized the potential energy of the sand pile.

Living systems that get sorted over time and are the ones that survive for a time might, in a very loose sense of the word, be “optimal”, but there is enough variability in what is able to survive that one would be mistaken to claim that it is the “best” of what came through a sequence of contingencies. The laws of physics and chemistry are always operating, and what falls out has to be consistent with those laws. But that doesn’t mean they are designed. Some pretty sloppy stuff gets through the sieve.

And there is still that issue which is never addressed by the ID/Creationists, namely, how does one infer design without having some notion of a designer? All we ever here from ID/Creationists is that they make inferences from what intelligent creatures do in the natural world.

Yet they can never show the “science” that permits them to attribute such qualities to a supernatural deity. How do they know what characteristics such a deity has? The bait-and-switch tactic to a “natural designer” simply puts the origins of life elsewhere and at another time, but now they have to worship a master race of fully natural space aliens. What comet did they hide their space ship behind?

Mike Elzinga said: So, as we already knew, according to ID/Creationists, optimum implies design.

wad: While chunky is down for the count, let me kick him a coupla times more: Evolution designs.

However, the process by which an adaptive code evolved at present remains unclear.

Mike Elzinga: Living systems that get sorted over time and are the ones that survive for a time might, in a very loose sense of the word, be “optimal”

iml8: The soap film is arranged in a neatly spherical configuration (how could a neat sphere just happen like that?) with the material in the bubble also neatly distributed in a highly uniform way over its surface. Seems pretty optimal to me.

iml8 said:

Mike Elzinga said: So, as we already knew, according to ID/Creationists, optimum implies design.

Hmm ... think of a soap bubble. The soap film is arranged in a neatly spherical configuration (how could a neat sphere just happen like that?) with the material in the bubble also neatly distributed in a highly uniform way over its surface. Seems pretty optimal to me. I have noticed that when Darwin-bashers raise arguments like this and are met with a simple counterexample, it's a sucker's bet they will denounce it as too simplistic, a "straw man" argument. "Ah, so there is no such thing as a free lunch -- but snacks are OK." White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Our rules permit 20! {approx} 2.43 x 1018 different codes (fig. 1a ), which we refer to as the "unrestricted" set. The incorporation of further restrictions to reflect the observation that biosynthetically related amino acids are often assigned codons with the same first base identity (fig. 1b ) produces a "restricted" set of (5!)4 {approx} 2 x 109 codes (fig. 1c )

Our analysis considers an optimal code as one in which the arrangement of amino acid assignments to synonymous codon blocks minimizes the average amino acid difference resulting from single-nucleotide changes within all codons.

Speaking of MG fan club representatives. It is quite interesting that they have ceased to discuss the actually topic of this blog: the fucking flagellum. Instead this one derailed the thread by going off on a deep tangent about optimal codes and monkeys. Why do you think they would do that? Because their idol actually fucked up regarding his ID analysis of the flagellum. In other words ID thinking couldn't have made him predict that the Designer cobbled the flagellum out of other parts. Here, he admits it himself: http://www.thedesignmatrix.com/content/evolution-of-bacterial-flagellum/

Oh well, it's only a matter of time before goal posts are shifted further back.

In other words ID thinking couldn’t have made him predict that the Designer cobbled the flagellum out of other parts.

— wad of id

Mike Elzinga: Looks like our troll has hit the wall. All he can do is name-call, sputter and fume about how stupid we are. This conversation has gone way over his head and he can’t even respond with anything intelligent. A pretty stupid design.

wad: Notice the significance of the numbers 20 and 5.

wad: Not even close to “all plausible biological” space, which is by definition infinite.

Error-minimizing codes are a kludge to fix a harsh reality of biological systems: they fucking evolve.

- what is the function of a soap bubble and how can you measure it’s optimality? What formula do you use?

Mike Elzinga: One of many possible functions is how long it can fascinate a child. The formula is time = the number of minutes the child plays with the soap bubble and makes more of them with a soap bubble solution.

So how does a bubble know to assume a spherical shape in order to minimize the potential energy of its surface?

chunkdz said: Anyhow, here's another research paper that shows that the code is also optimal for parallel coding. http://genome.cshlp.org/cgi/content/abstract/17/4/405

Are you guys serious or am I being punked by Casey Luskin? You idiots are just charicatures of your prejudiced sheep-like minds.

— chunckdz

I normally don't pay much mind to the ankle-biter visitors on PT,
since they have nothing interesting to say and answering them is
not a good use of breath. However, when told "you don't know
anything about optimization", I got to thinking and realized that,
actually, I do. My EE degree had a CS minor component, and I worked
a software development environment for the better part of two
decades -- not actually as a developer myself for the most part, in
a supporting role, but one that kept me intimately involved with
development life-cycles, to be occasionally called in to lend a
hand when needed.

So what does "optimization" mean in terms of software development?
It means either space optimization or speed optimization. It's
easy to measure space optimization, it's just the number of bytes of
the program. It's harder to measure speed optimization, one has to
come up with a set of benchmarks on the basis of observation and
judgement ... since much of what has to be optimized is obvious, that's
not TOO big a deal.

Note that space and speed optimization tend
to work at cross purposes: a bubble sort, for example, is easy to
implement but slow, while a shell sort is complicated but fast. There
is also the unfortunate and sometimes disastrous factor of
maintainability: it's all too easy to write tricky code that becomes
an intolerable burden to modify and update, particularly after the
slipshod programmer who wrote it goes elsewhere.

Anyway, so to achieve optimization the software development team
inspects the code and sees what changes can be made, either to
reduce its size or increase its speed or, inshallah, both. They
end up with an optimized program that is smaller or runs the
benchmarks faster. Is it now PERFECTLY optimized? How could
anyone tell? Can anyone rule out that better optimizations could
be found? It is simply more optimum in the desired characteristics
than the earlier version.

Now computer science people investigate efficiency of algorithms
and they can demonstrably prove, for example, that a fast Fourier
transform algoritm is much more efficient than a simple discrete
Fourier transform algorithm. Could such calculations be made for
a full applications program in all its actions? It's hard to see how,
nobody does, and nobody expects to.

It seems like the genome is being called "optimum" in the space
efficiency sense. Really? Can it be demonstrably proved that it
can't be reduced in size? Even I can think of how to do it --
cut out provirus and broken gene sequences, the DNA we actually
KNOW is junk. There is also the fact that some members of the
onion family have genomes five times as big as others, and that
there are plenty of organisms that we would judge as "simple"
that have much bigger genomes than we do. So are some genomes
optimized and others not? Why the selectiveness?

For us to understand the optimization of the genome, we'd have to
have a detailed knowledge of its operation to the point of being
able to design our own. Could we start cutting out chunks and
show they don't make a difference? Serious ethical problems here ...

Of course, comparing Windows OS with the size of the genome is
substantially more extreme than comparing apples (bad word here
for Windows!) and oranges. It's not even easy to compare different
computer languages -- I could write algorithms in one line in some
languages that would take pages in others (noted such one-liner
languages can be HIDEOUS to deal with). I could also implement
sophisticated algorithms to perform real-time differential equations
with a package of op amps, some resistors and capacitors ... does
that make a analog computer more optimum than a computer program?

An organism is not a digital computer.
It does have a digital-style storage system, but that's about the
sum of the resemblance. It does have analog-style systems, but
it's not an analog computer. There's no insight in making
comparisons between them, it's just the usual ID reasoning by
analogy. Even if we were to argue optimization
of biosystems versus human systems, there's nothing in the argument
that rules out billions of years of tuning by natural selection
as the cause. No human program has ever endured that kind of
tweaking.

This is useful information to the PT crowd. Our visitor? My
impression is that he has little or no familiarity with software
development.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Mike Elzinga: So there we have it; more name-calling and now paranoia, but not one bit of substance in any of its posts. The troll has no interest in the paper whatsoever, and it doesn’t know or care whether anyone here has read it or understood the substance of this thread.

iml8: It seems like the genome is being called “optimum” in the space efficiency sense. Really? Can it be demonstrably proved that it can’t be reduced in size?

Did you know you can find decaffeinated coffee that is
every bit as tasty as the real thing?

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

But you don’t have to wonder what the researchers are describing as optimal, you could just READ THE FREAKIN’ PAPER. They are pretty clear that the code is optimal for error minimization, NOT space efficiency.

— chunckdz

iml8: Did you know you can find decaffeinated coffee that is every bit as tasty as the real thing?

To the people who run PT: May I kindly suggest that
this thread now be consigned to the Bathroom Wall?
There is nothing of interest in it any longer and it
serves no useful purpose.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Mike Elzinga: If you have a point you are trying to make, other than venting your rage at what you claim to be a bunch of idiots, why don’t you make it?

I made my point several days ago. You geniuses just keep confirming it.

— chunckdz

Elzinga: The usual dodge. Never make a point, never clarify; just keep claiming you explained something before in order to continue the trolling.

"My point was, and remains, that you moron critics love to point out that nature is expected to make kludgy hodge-podges. Then when confronted with evidence that the basis for every single biological system is a non-hodge-podged, sophisticated, elegantly designed, optimal “best of all possible codes”, you monkeys simply wallow in your own feces, ignore the research, and complain about the evils of Big Bad Billy Dembski."

Chunky,

Every time you stoop to personal insults you reduce your credability. You are now in negative values. Despite all your insults, you have still not addressed even one of the germane issues. Here is a short list to help keep you focussed:

1) There is no way to define "optimal" function. That conclusion will always depend on the criteria, which will always be subjective.

2) Even if you could define "optimal" in a sufficiently rigorous way, you still need to distinguish between optimal function produced by evolution and that produced by "design". Until you do this, evidence of optimal function is irrelevant.

3) Even if you can demonstrate optimal design in some cases, you must also account for sub optimal design. In other words, if optimal design is interpreted as evidence of a perfect designer, then sub optimal design must be interpreted as evidence that no such designer exists.

In order to forestall any further personal attacks, let me respond proactively with the following:

I know you are but what am I?

David Stanton said: 2) Even if you could define "optimal" in a sufficiently rigorous way, you still need to distinguish between optimal function produced by evolution and that produced by "design".

Yes, it would be too much trouble for a moron like you to scroll up the page to see where I reiterate my point again. .

— chunckdz

Frankly, I don't give a fuck what chunky has to say. My responses were for the lurkers out there who have contempt for people like chunky and wish to learn some counter-IDiocy arguments. Chunky feeds off of Mike Gene's titties. And now he's a little fussy. I think it's time the little baby gets some more feeding from Mama Gene. LOL

My responses were for the lurkers out there who have contempt for people like chunky and wish to learn some counter-IDiocy arguments.

— wad of id

wad of id said: Frankly, I don't give a fuck what chunky has to say.

chunkdz said: The researcher's I cited RULED OUT stereochemistry as the sole cause of an optimal adaptive code, and concluded that the code must have been selected, not determined.

David Stanton: 1) There is no way to define “optimal” function. That conclusion will always depend on the criteria, which will always be subjective.

2) Even if you could define “optimal” in a sufficiently rigorous way, you still need to distinguish between optimal function produced by evolution and that produced by “design”. Until you do this, evidence of optimal function is irrelevant.

3) Even if you can demonstrate optimal design in some cases, you must also account for sub optimal design. In other words, if optimal design is interpreted as evidence of a perfect designer, then sub optimal design must be interpreted as evidence that no such designer exists.

tresmal: My emphasis and point.

wad: My responses were for the lurkers out there who have contempt for people like chunky and wish to learn some counter-IDiocy arguments.

Science Avenger said:

wad of id said: Frankly, I don't give a fuck what chunky has to say.

I certainly don't. They guy deserves the Dinesh D'Souza Award for the most words utterred to say very little. I'll bet he yells like D'Souza too.

Compare chunkydisease to another of Mama Gene's boys, Guts: http://helives.blogspot.com/2008/07/now-thats-just-ugly-by-design.html

Notice the difference? ;-)

chunkdz said:

tresmal: My emphasis and point.

What point is that? That the researchers have ruled out everything except an explanation that currently has no explanation? Imbecile.

Chunky,

You didn't address one of my points with a valid argument. And calling yourself all of those names is unfortunate.

1) The genetic code is not "optimal" for many different criteria. How do you know that those criteria are not more valid than the ones arbitrarily chosen? You don't and neither do the authors.

2) You still have not addressed the possibility that the code has evolved in any significant way. Why is that?

3) If the designer designed such a perfect code, why design such an inefficient and sub optimal genome to be decoded? The illusion of optimality is just as imaginary as the illusion of design.

4) If you claim the expertise and conclusions of the authors as authoratative then you are forced to accept thier conclusion that the genetic code evolved. You can't pick and choose and still use the argument from authority. Either they know what they are talking about and you are wrong, or they don't know what they are talking about and you have no evidence.

So now you are prejudiced, you are stupid, you are grasping at straws and you are a moron. There, does that make my argument any better?

Elzinga: Yup; he continues to rant without comprehension. His last post certainly suggests that he clearly doesn’t understand the sectarian preconceptions that go into seeing “optimal” design everywhere.

tresmal: Does this mean that the evidence of design that you have shoving into everybody’s face for the last couple of days is a paper written by imbeciles?

David Stanton: 1) The genetic code is not “optimal” for many different criteria.

2) You still have not addressed the possibility that the code has evolved in any significant way. Why is that?

3) If the designer designed such a perfect code, why design such an inefficient and sub optimal genome to be decoded? The illusion of optimality is just as imaginary as the illusion of design.

4) If you claim the expertise and conclusions of the authors as authoratative then you are forced to accept thier conclusion that the genetic code evolved. You can’t pick and choose and still use the argument from authority. Either they know what they are talking about and you are wrong, or they don’t know what they are talking about and you have no evidence.

I'm still wondering if the claimed optimization is referring to the code itself (which base combinations correspond to which amino acids) or implementations of it (the genomes of organisms).

I'm thinking that optimizing the code itself is something that would be considerably simpler before organisms had become dependent on it for day to day survival. After that, any change in the code would seem to require corresponding changes in the already established DNA sequences.

Henry

David Stanton: Every time you stoop to personal insults you reduce your credability.

Henry J: I’m still wondering if the claimed optimization is referring to the code itself (which base combinations correspond to which amino acids) or implementations of it (the genomes of organisms).

Chunky,

Way to address the issues man. Once again:

I know you are but what am I.

Juvenile, yes, but appropriate.

chunkdz said: You imbecilic troglodytes on the other hand are insisting that their research must be flawed somehow - yet you can't seem to bother actually reading their report.

Yup, I agree with tresmal above. I agree wholeheartedly with the author's conclusions based on their findings. Once again chunky lies to us.

It looks like chumpy is trying to do a Don Rickles impression.

He’s not very good at it.

chunkdz said: The researchers determined that the code is of the highest possible fidelity. This important knowledge has elicited a glassy eyed drooling "DUH" from you and your friends.

You imbecilic troglodytes on the other hand are insisting that their research must be flawed somehow

tresmal: Actually not everybody here is insisting that the research is flawed. Most here are arguing with your conclusion about the paper. A conclusion, I might add, not shared by the authors of that paper. P.S. I did read the paper, but like the authors, I don’t see it making even a down payment on evidence for design.

"And too bad you mush brained zombies couldn’t even fathom that I never claimed that an optimal code couldn’t evolve. My point was, and remains, that you moron critics love to point out that nature is expected to make kludgy hodge-podges. Then when confronted with evidence that the basis for every single biological system is a non-hodge-podged, sophisticated, elegantly designed, optimal “best of all possible codes”, you monkeys simply wallow in your own feces, ignore the research, and complain about the evils of Big Bad Billy Dembski. What a predictable bunch of pansies you are."

Chunky,

Perhaps I should clarify my position. I don't berate you just for using insults. I'm sure everyone just skips over those parts of your posts anyway. I berate you for substituting insults for arguiments. Others have not done that, so my condemnation of you is justified.

Second, I am not saying that the authors are wrong. I am saying that your interpretaion of their results is wrong. Quote mining and using the argument from authority won't work here. What you need is a better argument. Gratuitous use of insults isn't helping you to make any point here.

Eric: You’re wrong twice over. They found it was better than the vast majority of other genetic codes. “Better than the vast majority” is not optimal.

The research isn’t flawed. Its just your interpretation of it is blatantly wrong. Reading the first few sentences in the abstract is enough to determine that.

David Stanton: I am not saying that the authors are wrong. I am saying that your interpretaion of their results is wrong.

chunkdz said: The researchers determined that the code is of the highest possible fidelity. This important knowledge has elicited a glassy eyed drooling “DUH” from you and your friends.

chunkdz said:

Eric: You’re wrong twice over. They found it was better than the vast majority of other genetic codes. “Better than the vast majority” is not optimal.

Hello, stupid. What part of "The best of all possible codes" are you unable to comprehend? The code is optimal for error minimization, it is very nearly optimal for parallel coding. These scientific facts should make your eyes light up with wonder and amazement but instead it seems to only increase the flow of saliva from the corner of your gaping mouth.

What a pathetic, doughy, lipid brained bunch of mental midgets you all are.

Eric: The researchers didn’t even *check* to see if it was optimal compared to nongenetic systems. So your claim that its optimal is wrong again.

The evolutionary forces that produced the canonical genetic code before the last universal ancestor remain obscure. One hypothesis is that the arrangement of amino acid/codon assignments results from selection to minimize the effects of errors (e.g., mistranslation and mutation) on resulting proteins. If amino acid similarity is measured as polarity, the canonical code does indeed outperform most theoretical alternatives. However, this finding does not hold for other amino acid properties, ignores plausible restrictions on possible code structure, and does not address the naturally occurring nonstandard genetic codes. Finally, other analyses have shown that significantly better code structures are possible. 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.

Note that the work by Landweber, Knight and others has added significant understanding to the evolution of the genetic code, something which in ID has no equivalents.

So how does ID's 'explanation' compare to how science explains these findings?

chunkdz said:

Eric: The researchers didn’t even *check* to see if it was optimal compared to nongenetic systems. So your claim that its optimal is wrong again.

Will one of the other monkeys please explain to your half-brained cousin Eric that the claim of optimality was not mine, but rather it was the conclusion of Freeland, Knight, Landweber, and Hurst and was published in a journal in the year 2000? Is there anyone here who is not a complete dimwitted moron?

chunkdz said:

Mike Elzinga: That is a very strange accusation.

You mean my accusation that critics are fooling themselves into thinking that the genetic code is a kludgy "hodge podge" or "imcompetently designed"?

the correlation between amino acid biosynthetic pathways and amino acid assignments within the code reported by Taylor and Coates (1989)

Many of the 20 canonical amino acids are not plausible products of prebiotic chemistry (Wong and Bronskill 1979Citation ) and are only produced in extant organisms as biosynthetic modifications of their plausibly primordial counterparts.

Taken together, these observations have provoked the code coevolution hypothesis (Wong 1975Citation ), proposing that the canonical code evolved from a simpler ancestral form (encoding fewer amino acids with greater redundancy) by successively reassigning subsets of synonymous codons to incorporate novel amino acid biosynthetic derivatives.

PvM: It all depends on the meaning of “of”, it is not the highest possible fidelity but it is surely optimized for error minimization.

Namecalling makes you worse than those with whom you disagree, if that is your goal, you have succeeded.

PvM: Optimal when constrained by biological reality, not optimal in the sense of best in class, regardless of biological reality.

chunkdz said: PvM: It all depends on the meaning of “of”, it is not the highest possible fidelity but it is surely optimized for error minimization.

Namecalling makes you worse than those with whom you disagree, if that is your goal, you have succeeded.

PvM: Suggesting that the ‘designer’ was constrained by prebiotic chemistry, just as expected from a scientific perspective.

chunkdz said:

PvM: Optimal when constrained by biological reality, not optimal in the sense of best in class, regardless of biological reality.

If you want to do research outside of reality, be my guest, idiot. The lack of brain power here is just breathtaking.

chunkdz said:

PvM: Suggesting that the ‘designer’ was constrained by prebiotic chemistry, just as expected from a scientific perspective.

What I suggested is that this knowledge would cause you moron critics to become encrusted in your own saliva. Now you're making assumptions about a putative designer and saying that science predicts it. What a freakishly dumb frog-brained twit you are.

Of course, not only is the code 'optimal' when constrained by prebiotic chemistry, the redundancy of the code causes significant evolvability in the code through the existence of neutrality.
In other words, the success of evolution is explainable by observing that the code allows for significant redundancy (degeneracy) which leads to neutrality which leads to evolvability as Toussaint has shown how neutrality is a requirement for evolvability.

Fascinating how all these come to fit together nicely without the need for 'poof'.
So explain to us again, how does ID propose to explain these data?

PvM: It is not the best of all possible codes.

Taken together, our results provide strong evidence that the structure of the canonical code was strongly influenced by natural selection for error minimization. Analysis based on PAM matrix values demonstrates not only that results of previous analyses are unlikely to be an artifact of stereochemistry, but that if biosynthetic pathways limited codon assignments, then the code is very near to (and quite possibly at) a global optimum for error minimization. While our implementation of biosynthetic restrictions on possible code evolution may not be entirely accurate, it is the best available at present and is representative of general patterns within the code. Importantly, then, analysis of biosynthetically restricted codes indicates that code coevolution, far from explaining adaptive code structure as an artifact, actually precludes the few "better" alternative codon arrangements found in previous analyses.

chunkdz said:

PvM: It is not the best of all possible codes.

Well genius, you've single handedly refuted the Freeland paper. Congratulations, and you can go back scratching your butt and eating your own feces.

PvM: As to namecalling, if it were up to me, all sides would be sent to the bathroom wall when using these fallacies.

PvM: What I have done is single handedly refuted your ‘intepretation’ of the Freeland paper.

chunkdz said:

PvM: As to namecalling, if it were up to me, all sides would be sent to the bathroom wall when using these fallacies.

What a load of crap. You haven't criticized a single one of your own drooling sycophants. You only use your sanctimony as a culture warrior weapon. Please go back to the tree you were hanging from by your saliva encrusted prehensile tail.

chunkdz said:

PvM: What I have done is single handedly refuted your ‘intepretation’ of the Freeland paper.

Interesting, since I haven't even offered an interpretation - other than the fact that the study would elicit a strange mixture of bile and drool to seep from the corner of your unwashed, gaping hole of a mouth.

It was nice talking to you ChunkDZ, I have to run now for some errands, let me know if you have any further questions you believe I should address.

It's revealing and sad as an outsider to read who's throwing the ad hominems around.

My last contact with Scott Minnich suggests that the flagellar mechanism is still very much up and running as an example of irreducible complexity, the fact that one component can be removed and the whole system is not deactivated proves little, except a degree of redundancy - how does that invalidate Behe's central thesis? The challenge for materialists is to provide a feasible pathway to synthesis and a lineage - that remains exceedingly distant.

The new FliH/F-type ATPase homologies are interesting but of relatively little weight except as exactly that homologies.

As I see it, the TT3 mechanism is a rudimentary component, only present in species thought to be younger, and nothing like an assembly mechanism has yet been elucidated, far less a convincing evolutionary lineage.

It's unfortunate that PT's moderation has become so weak and useless that an aggressive ass like chunkdz is allowed to freely pollute the thread with vicious invective and it is allowed to stand as legitimate commentary, for meek fear of PT being seen as "censoring" anything, however idiotic and ill-intentioned. Is this supposed to be a science blog, or an opportunity to expose that a tiny fraction of the anti-evolution crowd (or any crowd) is composed of mindless, hateful morons? I think we already knew the latter, so what's the point?

Note that the work by Landweber, Knight and others has added significant understanding to the evolution of the genetic code, something which in ID has no equivalents.

— PvM

PvM: Oh yes, you did present your interpretation of the paper. You may not have recognized it as such but calling the code ““the best of all possible codes” based on the paper is an interpretation. While at odds with what the paper really showed, it is still an interpretation.

charles said: It's revealing and sad as an outsider to read who's throwing the ad hominems around. My last contact with Scott Minnich suggests that the flagellar mechanism is still very much up and running as an example of irreducible complexity, the fact that one component can be removed and the whole system is not deactivated proves little, except a degree of redundancy - how does that invalidate Behe's central thesis? The challenge for materialists is to provide a feasible pathway to synthesis and a lineage - that remains exceedingly distant.

Ben, It’s unfortunate that PT’s moderation has become so weak and useless that an aggressive ass like chunkdz is allowed to freely pollute the thread with vicious invective and it is allowed to stand as legitimate commentary, for meek fear of PT being seen as “censoring” anything, however idiotic and ill-intentioned.

Stanton said: You fail to realize that Behe said that all components of the flagellum were required for it to function, and missing even the most minor of components would destroy its ability to function, so, according to Behe, if even a redundant part is removed, the flagellum will stop working. Ergo, Behe's claims about irreducible complexity have been proven false, and you have no right or ability to say otherwise simply because you don't care for the example used to falsify irreducible complexity. You also fail to realize that people have already been working on elucidating an evolutionary pathway for both the eukaryotic and bacterial flagella, a fact that Behe either ignored or lied about in his books. In fact, if you actually read about the evolution of bacterial flagella, you would know that they are derived from bacterial proton pumps that have had accessory proteins added on. You also appear to fail to realize that people have been working on elucidating the evolutionary pathways of other proteins and metabolic pathways, including the vertebrate immune system, the blood-clotting cascade of vertebrates, and the antifreeze glycoprotein of Antarctic icefish.

Mike Elzinga said: My previous example of the catenary curve that minimizes the potential energy of a limp rope suspended between two points was intended as a simple illustration of something that appears to be optimum and, in the past, has provoked some to claim that their god made the best of all possible worlds (which, in turn, provoked Voltaire’s character Dr. Pangloss).

Take your pick here

Hmmm, heat but no light - uncharacteristically.

iml8: I have heard it is possible to squeeze an egg very hard and it won’t break as long as the forces are evenly distributed, but I won’t try that myself. They would be even more optimum from the respect of capacity and materials efficiency if they were spherical – but then they would be hard on the hen (or whatever) to lay. So the perfect spherical shape is compromised.

I feel slighted. Here I was expecting a torrent of
abuse, and all I got was the most perfunctory and
half-hearted insult. It was like I wasn't even worth
the effort!

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Well, come on, I'm waiting.

White Rabbit

Can you cite how the flagella have evolved from TTS pumps? Can you give an instance of a known lineage? Or to make things easier of a gene reduplication that has actually resulted in a small incremental step towards its evolution? Not hypothetically, but actually?

— charles

What's taking you? I haven't got all day.

White Rabbit (Greg Goebel)

Mike Elzinga said: The question also has behind it a veiled sneering challenge that “unless you can show me exactly step-by-step, molecule-by-molecule how this organism evolved from other organisms, evolution is in “dire trouble”.

Hmmm. Eggs, are optimum (sic), but they could be even more optimum (sic), “or whatever”.

iml8 said:

Mike Elzinga said: The question also has behind it a veiled sneering challenge that “unless you can show me exactly step-by-step, molecule-by-molecule how this organism evolved from other organisms, evolution is in “dire trouble”.

And of course the comeback is: show me details of how Design did this. With the answer: "I don't have to match your pathetic level of detail." Leading to the rejoinder: "You don't have to match it. Just provide something." White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Charles asks: Can you cite .... a small incremental step towards its evolution? Not hypothetically, but actually?

James F said: If they were honest, their answer would be "It's supernatural. We can't observe, measure, or analyze it in any way."

It's interesting that in contrast to the discussion up
to now, chatting with charles actually seems pleasant.

Still waiting to be given the consideration to be abused
properly, however.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

chunkdz said:

PvM: Oh yes, you did present your interpretation of the paper. You may not have recognized it as such but calling the code ““the best of all possible codes” based on the paper is an interpretation. While at odds with what the paper really showed, it is still an interpretation.

Wow. Moron, if you had actually read the paper you would have realized that the conclusion that the code is "the best of all possible codes" was not made by me - it was made by Freeland, Knight, Landweber, and Hurst.

Charles wrote:

"Can you cite .… a small incremental step towards its evolution? Not hypothetically, but actually?"

Yes I can, and thanks for asking. Now we are getting somewhere. Even though this is not the topic of this thread, the moderators have seen fit to let chunky spew forth for days now. It is about time that someone points out that the evolution of the genetic code has been well studied since the time of Watson and Crick. Here are a few references to get you started:

Alberti (1997) Journal of Molecular Evolution 45:352-258
Ardell and Sella (2002) Phil Trans. R. Soc. Lon. B 357:1625-1642
Brook et. al. (1998) Molecular Biology and Evolution 19(10):1645-1655
Wong (1075) PNAS 72:1090-1912

Perhaps the best example is the Brooks et. al. paper which describes the order in which amino acids were most lilkely added to the genetic code. The Wong paper is for real, no kidding.

And by the way, no one was around to observe the evolution of the genetic code, so no, none of these are eye witness acounts. I am sure that is not what you were asking for.

chunkdz said: Oh, how cute. Another trained rhesus monkey is trying to make a plea for civility at the Panda's Thumb. Of course, like all the other mind numbed lobotomized sheep around here, he is only willing to criticize those he sees as his enemy. This trained monkey Ben will never criticize the likes of wad "s**k my c**k" or Stanton "ID'ers are smartmouthed lazybrained vermin", or the rest of the herd like toe-jam and rev. lenny. No, that would mean actually going against the herd mentality and standing up for a principle.

Mike Elzinga said: The question also has behind it a veiled sneering challenge that “unless you can show me exactly step-by-step, molecule-by-molecule how this organism evolved from other organisms, evolution is in “dire trouble”.

Science Avenger said: First, it's like saying I won't believe you walked across town unless you show proof of every step.

stevaroni said: Well, Charles, can you cite an unambiguously designed feature?

Aww, it looks like chunky doesn't like cock. And he's clearly not getting any pussy either. So what the fuck is he doing here hanging around a bunch of monkeys for? Methinks this dumbass doth protest too much.

BTW, chunky, I have a simple challenge for ya. It's a science project, y'see. You can write the authors and see if they actually mean what you say they mean. Go ahead. I double dare ya.

LOL

First, it’s like saying I won’t believe you walked across town unless you show proof of every step. Second, the number of changes involved in such a long stochastic process would be enormous, and could easily exceed a human lifetime to map out.

— Science Avenger

Mike Elzinga said: Yet there are guys who manage to do it routinely.

That's it! ID = Inebriated Designer!

That’s it! ID = Inebriated Designer!

Science Avenger: When someone has shown over time that they are capable of rational discourse, and makes solid contributions to a forum, they are going to get a little more slack if they go all four-letter on someone. On the other hand, when someone who hasn’t demonstrated such traits barges in and starts ranting, especially when they make extremely basic errors (see any post by handjobby), they are going to get different treatment, and for good reason.

Chunky once again tries to make the discussion about insults rather that the issues. Why do you suppose that is?

chunkdz said:

Science Avenger: When someone has shown over time that they are capable of rational discourse, and makes solid contributions to a forum, they are going to get a little more slack if they go all four-letter on someone. On the other hand, when someone who hasn’t demonstrated such traits barges in and starts ranting, especially when they make extremely basic errors (see any post by handjobby), they are going to get different treatment, and for good reason.

You are a stupid hypocrite, science avenger. On page one, wad of id tore into an unprovoked rant attacking an ID essay, four letter words, ad hominems, insults, and a general misunderstanding of the basic argument. My response was terse, but not vulgar. I was then childishly told to s**k his c**k. Where were you then, you hypocritical moron? Where was your righteous indignation then you zombified sycophant? It's stupid culture warriors like yourself that perpetuate prejudice, bias, and bigotry. You being a petty bigot will never ever in a million years chastise one of your own culture war army because your only goal is to score points against your perceived enemies and you'll abandon science to do it. Thank you, moron, because by the criteria you just laid out, I am perfectly justified in insulting you brain dead idiots. Since not one of you guys is interested in reading or learning about science there seems to be not much else to do around here but point out what a bunch of brainless cretinous hypocrites you all are.

Science Avenger: I’ll also add that it’s no surprise to me that the defense of “everyone else is doing it too!” comes from people politically aligned with the Republicans.

PvM said: Wow, he surely has some buttons :-)

David Stanton: Chunky once again tries to make the discussion about insults rather that the issues. Why do you suppose that is?

Chunky,

Please refer to my previous post. Consider it a response to every post you have made.

wad: Aww, it looks like chunky doesn’t like cock. And he’s clearly not getting any pussy either. So what the fuck is he doing here hanging around a bunch of monkeys for? Methinks this dumbass doth protest too much.

PvM: Wow, he surely has some buttons :-)

chunkdz said:

PvM: Wow, he surely has some buttons :-)

Yes, one of them is troglodytes like you who criticize research without even reading it.

Of course, Freeland and Knight :-)

iml8 said:

PvM said: Wow, he surely has some buttons :-)

Little dogs like to bark. White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Whenever I debate about flagellar evolution, the argument always shifts to something like “Matzke disproved flagellar IC - just look it up.” To which I respond “Wrong. Matzke came up with several guesses at how he thinks it might have happened, but by his own admission it would have required something ‘radical’ to pull it off.” All he did was take a couple of guesses, all unsubstantiated, all unproven, all unobserved, all unprecedented. That’s not disproving IC. Don’t let anybody ever tell you that flagellar IC has been disproven.

— ChunkDZ

chunkdz: Bear with me here, I am just a troglodyte who has just figured out the whole opposable thumb thing but I would like to ask; why are you continuing with this farce? I am just a bucket of monkey pus, but do you have some sort of goal in mind with your comments? And a strategy for achieving that goal? Now I'll be the first to admit that I am a chancre on a rat's anus, but I struggle to see what outcome could occur, after you have posted your last comment on this thread, that would leave you satisfied that your time here was well spent. To show show you what a lobotomized, poo flinging monkey I am the best answer I could come up with is that you're persisting out of stubborn spite! I know what you're thinking, what a retard! But even that modest effort caused sweat to pool on my pronounced brow ridge. Could you explain to someone like me, who has a neural net for central nervous system, how you get a "win" or otherwise satisfactory outcome? Are you going to pursue Wad of Id, Ahab like, throughout the internet? Off topic, but have you run into a commenter by the nym fongooly on any of the Scienceblogs? Back on topic. You use the term culture warrior a lot, does this mean that this has all been a Godless-flagburnin-babykillin-treehuggin-homos vs. Real Americans debate and not an evolution vs. ID one? Because being the knuckle dragging, mouth breathing cretin that I am, I missed that! Lastly can you tell me how other commenters on this thread pull the old cut-and-paste-and-comment-on-a-paper-without-reading-it trick? That has this uppity monkey completely baffled.

chunkdz said: You are a stupid hypocrite, science avenger. On page one, wad of id tore into an unprovoked rant attacking an ID essay, four letter words, ad hominems, insults, and a general misunderstanding of the basic argument. My response was terse, but not vulgar. I was then childishly told to s**k his c**k. Where were you then, you hypocritical moron? Where was your righteous indignation then you zombified sycophant? It's stupid culture warriors like yourself that perpetuate prejudice, bias, and bigotry. You being a petty bigot will never ever in a million years chastise one of your own culture war army because your only goal is to score points against your perceived enemies and you'll abandon science to do it. Thank you, moron, because by the criteria you just laid out, I am perfectly justified in insulting you brain dead idiots. Since not one of you guys is interested in reading or learning about science there seems to be not much else to do around here but point out what a bunch of brainless cretinous hypocrites you all are.

Good point. ID’ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design. Critics like yourself think that it is flawed because it appears to them to be “incompetently” designed or “does not follow logic as we, humans, recognize it.” Of course, critics like yourself are just kidding yourself.

chunky: Since not one of you guys is interested in reading or learning about science there seems to be not much else to do around here but point out what a bunch of brainless cretinous hypocrites you all are.

wad of id said:

chunky: Since not one of you guys is interested in reading or learning about science there seems to be not much else to do around here but point out what a bunch of brainless cretinous hypocrites you all are.

In other words, chunky only wishes to vandalize this board. This seems like grounds for banning to me. Time to send the baby to juvy for some learnin'. LOL

PvM Even when I pointed out the flaws in his representation of the research did he persist in name calling.

Actually, I am quite familiar with the work of Freelander and Knight.

:PvM: Must hurt that Matzke’s guesses were validated by science. Not bad for science. Sour grapes I would say.

Science Avenger: You’d be amazed how little thought I give vulgar, fact-free, presumptive tirades from antiscience internet cranks.

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.

chunkdz said:

PvM Even when I pointed out the flaws in his representation of the research did he persist in name calling.

The flaw, you stupid simian, was that you thought that I was the one who said that the canonical genetic code was "the best of all possible codes". If you had actually read the paper like you pretended to, you would have known that it was THE RESEARCHERS who concluded that it was "the best of all possible codes". Or maybe, moron, it was difficult for you to find because it was under the sneaky and cryptically titled chapter: "The Best Of All Possible Codes?".

Actually, I am quite familiar with the work of Freelander and Knight.

Liar. You didn't even know what their conclusion was. You thought it was my conclusion so you argued against it. Now that you know that it was Freeland et. al. you are doing just as I predicted you would. Wallow in your own feces and drool. And now your just a pathetic liar to boot. What a sick little tribe you all are.

chunkdz said:

:PvM: Must hurt that Matzke’s guesses were validated by science. Not bad for science. Sour grapes I would say.

Nick is the only one of you lot that ever bothers to actually read a research paper. The rest of you idiots can't even be bothered to click on a link. You see "the best of all possible codes" and assume that since one of your perceived enemies is presenting this that it must be another creationist tactic. It never even occurs to your malformed brains that science could ever say such a thing because it doesn't fit your stereotypes. Blind, dumb monkeys all. One Matzke is worth a thousand of you diseased squirrel monkeys.

Or maybe, moron, it was difficult for you to find because it was under the sneaky and cryptically titled chapter: “The Best Of All Possible Codes?”.

— ChunkDZ

The Best of All Possible Codes? When the error value of the standard code is compared with the lowest error value of any code found in an extensive search of parameter space, results are somewhat more variable. Estimates based on PAM data for the restricted set of codes indicate that the canonical code achieves between 96% and 100% optimization relative to the best possible code configuration (fig. 2c ). If our definition of biosynthetic restrictions are a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes.

Equivalent calculations based on the unrestricted set of possible codes are much more variable over parameter space (fig. 2d ), placing code optimality between 76% and 97% relative to the global optimum arrangement of codon assignments.

You nailed it again, PvM. The problem is an absence of moderation. You also forgot another key offense: chunkdz is lashing out against everybody, every person who replies to him regardless of how civil the replies. So in the absence of moderation, in the presence of outlandish willful ignorance, what do you do? You treat it contemptuously. Until a moderator shows up and cleans up.

tresmal: You use the term culture warrior a lot, does this mean that this has all been a Godless-flagburnin-babykillin-treehuggin-homos vs. Real Americans debate and not an evolution vs. ID one?

wad of id said: You nailed it again, PvM. The problem is an absence of moderation. You also forgot another key offense: chunkdz is lashing out against everybody, every person who replies to him regardless of how civil the replies. So in the absence of moderation, in the presence of outlandish willful ignorance, what do you do? You treat it contemptuously. Until a moderator shows up and cleans up.

Morons one, morons all. And not one of you has even demonstrably understood the research.

— ChunkDZ

chunkdz said:

Science Avenger: You’d be amazed how little thought I give vulgar, fact-free, presumptive tirades from antiscience internet cranks.

Then you won't mind shutting up then, idiot. You are even more of an idiot for calling me "anti-science". I am the only one on this thread who has presented scientific evidence. So go ahead, Science Avenger, avenge me! What a stupid freakin name, by the way.

chunkdz said: Will one of the other monkeys please explain to your half-brained cousin Eric that the claim of optimality was not mine, but rather it was the conclusion of Freeland, Knight, Landweber, and Hurst and was published in a journal in the year 2000?

Chunk from September 23, 5:33pm: I said the code was optimal. Let’s see if the research agrees with me… [And later in the same post] ...Umm, optimality is a measurement of a code’s efficiency. I said the code was “optimal” not “perfection” as you erroneously quoted me.

Eric: Whether the claim for optimality original to you or whether you misinterpreted someone else’s research is beside the point. You DID make the claim.

Claiming the code is optimal is at least wrong.

chunkdz said: You can't be serious? You think that because I cite a scientific research paper that the claim then becomes mine?

You can’t be serious? You think that because I cite a scientific research paper that the claim then becomes mine?

PvM: Pwned…

PvM: Nope, when you cite research incorrectly, as you have done, then that claim becomes yours. Simple. Just read the paper. Or quote from it to support you claim. Simple, show us how a scientist supports its claims. Surprise us.

From the abstract of the paper:

"However, this finding does not hold for other amino acid properties..."

"Finally, other analyses have shown that significantly better code structures are possible."

"The arrangement of mino acid assignments to the codoins of the standard genetic code appears to be the direct product of natural selection..."

Your point was exactly what then?

Evolution by random mutation and natural selection is the equivalent of an approximation method in mathematics. Some approximation methods work better than others because they converge on a solution faster; but if a method converges at all, you expect it to produce optimal results if the n is big enough. Which is why it is hardly surprising that the genetic code is optimal: there were zillions of iterations of mutation and selection, umpteen more trials than what happens in the evolution of metazoan animals, for example, which is one of the reasons that pigs cannot fly.

The restrictions that the researchers speak of are restrictions to plausible biological parameters based on the best available data. In other words, based on our best knowledge of reality, the code is optimal.

A second weakness in previous adaptive analyses (Wong 1980; DiGiulio 1989, 1994; Haig and Hurst 1991; Goldman 1993; Ardell 1999; Freeland and Hurst 1998a) is that most have assumed that each synonymous codon block of the canonical code could have taken any amino acid assignment (fig. 1a ). A growing body of circumstantial evidence questions this assumption (Knight, Freeland, and Landweber 1999Citation ). Many of the 20 canonical amino acids are not plausible products of prebiotic chemistry (Wong and Bronskill 1979Citation ) and are only produced in extant organisms as biosynthetic modifications of their plausibly primordial counterparts. Furthermore, biosynthetically related amino acids are often assigned to similar codons within the canonical code (Wong 1975; Taylor and Coates 1989). Taken together, these observations have provoked the code coevolution hypothesis (Wong 1975), proposing that the canonical code evolved from a simpler ancestral form (encoding fewer amino acids with greater redundancy) by successively reassigning subsets of synonymous codons to incorporate novel amino acid biosynthetic derivatives.

If all or most amino acids show stereochemical affinities for their corresponding codons, this would suggest that natural selection worked in concert with stereochemical interactions and biosynthetic expansion to produce the canonical code de novo, "choosing" the current 20 amino acids as those that satisfied criteria for both stereochemical affinity and error minimization. This interpretation would thus offer a novel insight into the selection of the proteinaceous amino acids from the near-infinite possibilities of both prebiotic syntheses and biosynthetic modification.

PvM said: Funny. But in all seriousness, is ChunkDZ always so hypersensitive to criticism?

Here is where chunky's reasoning is bassackwards: he looks at the word "optimality" and goes ape-shit that optimality is in of itself a teleological end-point. What Freeland et al. looked at was the opposite conclusion: suppose optimality is the result of evolution (i.e. natural selection and random mutations) as it is known to optimize locally for many other selectable traits. Then ask the scientific question: What was the primary selective force for the evolution of the canonical code? It makes a key hypothesis: the selected trait produces a restricted set for which the canonical code is a global optimum.

This is the key question the paper attempts to address: is the code optimizing for some key property of amino acids, with the resulting code structure being an "accident"/"artifact"?? or is the code optimizing for structure, with the resulting optimality for certain amino acid properties an accident/artifact?? What they discovered was that code structure was selected with preservation of "amino acid similarity" as an artifact of a precanonical code. Again, the whole analysis fucking falls apart without an understanding of evolution.

chunkdz said:

PvM: Pwned…

Umm, you copied the very part of the paper where the researchers say that the code is "the best of all possible codes" and still you insist that they never said that the code is "the best of all possible codes."?

the canonical code is at or very close to a global optimum for error minimization across plausible parameter space

The Best of All Possible Codes? When the error value of the standard code is compared with the lowest error value of any code found in an extensive search of parameter space, results are somewhat more variable. Estimates based on PAM data for the restricted set of codes indicate that the canonical code achieves between 96% and 100% optimization relative to the best possible code configuration (fig. 2c). If our definition of biosynthetic restrictions are a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes.

eric said: On Septmeber 23 you said "I said the code was optimal." On September "the claim for optimality was not mine" Either my quotes or wrong or you lied the second time. Which is it?

chunkdz said: You can't be serious? You think that because I cite a scientific research paper that the claim then becomes mine?

PvM the genius: "...they did not state that the code was the best of all possible codes."

Real scientists with brains that work: "... it appears at or very close to a global optimum for error minimization: the best of all possible codes".

iml8: Eh, that ankle-biter will keep on barking until somebody yanks the thread. I’m outa here.

chunkdz said:

PvM the genius: "...they did not state that the code was the best of all possible codes."

Real scientists with brains that work: "... it appears at or very close to a global optimum for error minimization: the best of all possible codes".

What a drooling idiot you are.

Consequently, the globally optimal code might be unattainable, while the fittest code accessible by point mutations is still fitter than practically all alternatives. In fact, our results show that the canonical genetic code is more adaptive than practically all alternatives, and this conclusion is robust to differences in both measurement of fitness and distribution of possible codes (Freeland, Knight et al. 2000).

wad: Evolution optimizes. Fucking DUH.

heck even the original paper shows that it is close to but not necessarily the best code. Look at http://mbe.oxfordjournals.org/content/vol17/issue4/images/large/mbev-17-03-11-f02.jpeg

If the code were optimal then the boxes in a and b would all be at 0 and the boxes in c would be all at 100%. They are not, showing that better codes exist, although quite a few of them. Figure d shows the 'optimality' when instead of the restricted codes, all codes are considered and the optimality drops even further.

PvM: So again, in no way are your claims supported by the paper. You claimed that the code was the “best possible code”

...the paper shows that it is close to the best possible code...

... where the codes were limited to prebiotic relevant ones, in other words, a subset of the full code parameter space.

Ironically, even if we grant that the prior over the set of all cost functions is uniform, the NFL theorem does not say that optimization is very difficult. It actually says that, when the prior is uniform, optimization is child’s play! I mean that almost literally. Almost any strategy no matter how elaborate or crude will do.

After sampling 298 points the probability that at least one of them is among the best 1% is 0.95. After 916 sampled points the same probability is 0.9999. If instead we want a point among the best 0.1% we need to sample 2994 points to find one with probability 0.95, or approximately 9206 points to find one with probability 0.9999. That kind of performance may not be satisfactory when the optimization must be done very fast in real-time under critical conditions, but it is good for most purposes. Certainly our universe would seem to be able to spare the time necessary to sample 9206 points.

chunkdz said:

wad: Evolution optimizes. Fucking DUH.

You don't even understand the difference between local optima and global optima, moron. Evolution is known to produce local optima, it is not expected to produce global optima. You are embarrassing yourself more and more by the day, you sponge brained twerp. Oh and have you gone to wikipedia yet to look up what a "factorial" is? Once you master that I'll teach you long division. Won't your moron friends be impressed.

chunkdz said:

PvM: So again, in no way are your claims supported by the paper. You claimed that the code was the “best possible code”

No stupid, the researchers claimed that it was "the best of all possible codes".

...the paper shows that it is close to the best possible code...

Actually the paper said it is "the best of all possible codes".

... where the codes were limited to prebiotic relevant ones, in other words, a subset of the full code parameter space.

Yes moron, they limited their study to reality as we know it. Imagine that, huh? Science sticking to reality. You should try it sometime. What an embarrassing drooling mess you are.

Third, while previous analyses suggest that the canonical code outperforms most alternatives, a comprehensive search of possible code structures suggests that far better alternatives are possible (Wong 1980Citation ; DiGiulio 1989, 1994Citation ; Goldman 1993Citation ). Indeed, the canonical code achieves between 45.3% (Wong 1980Citation ) and 78% (DiGiulio 1994Citation ) of the possible error minimization, depending on precise assumptions.

Yes moron, they limited their study to reality as we know it.

Jim Harrison: Which is why it is hardly surprising that the genetic code is optimal: there were zillions of iterations of mutation and selection, umpteen more trials than what happens in the evolution of metazoan animals, for example, which is one of the reasons that pigs cannot fly.

PvM: What reality? It limits the codes to what would be expected to have arisen given our understanding of prebiotic chemistry, in that case the code is near optimal.

Reviewer 3: Rob Knight, University of Colorado, Boulder In this manuscript, Novozhilov et al. provide a more detailed exploration of the level of optimality of the genetic code and the evolutionary trajectory of optimization than has previously been available. Specifically, they use a standard approach to measuring the "cost" of a genetic code in terms of the weighted frequency of errors of different severity, and measure the trajectory of codes using a hill-climbing optimization algorithm. They recapture the uncontroversial result that the genetic code is much better at minimizing errors than a random genetic code (as has been shown by many authors), but is at neither a local nor global optimum (as has also been shown previously). However, the results go beyond what has previously been done by comparing the evolutionary trajectory of the standard genetic code to the trajectories of other, random codes to get an estimate of what the overall process should look like. I believe that the authors overstate their result that the standard genetic code is "not special". Their own results show that it is difficult to explain except as the result of an optimization process: the argument that the standard genetic code is a global optimum is not to my knowledge taken seriously in the field, so the results cannot be seen as overturning it (see discussion between Steve Freeland, Massimo Di Giulio and myself in TiBS in 2000, which is cited appropriately in the paper). Rather, they show that, like most other features of organisms, the genetic code is optimized but not optimal, and probably reflects a range of constraints beyond the specific feature being examined. The manuscript could also benefit from being shortened substantially, as it appears to be relatively long in relation to its news value.

1. The code fitness landscape is extremely rugged such that almost any random initial point (code) tends to its own local optimum (fitness peak). 2. The standard genetic code shows a level of optimization for robustness to errors of translation that can be achieved easily and exceeded by minimization procedure starting from almost any random code. 3. On average, optimization of random codes yielded evolutionary trajectories that converged at the same level of robustness as the optimization path of the standard code; however, the standard code required considerably fewer steps to reach that level than an average random code. 4. When evolutionary trajectories start from random codes whose fitness is comparable to the fitness of the standard code, they typically reach much higher level of optimization than that achieved by optimization of the standard code as an initial condition, and the same holds true for the minimization percentage. Thus, the standard code is much closer to its local minimum (fitness peak) than most of the random codes with similar levels of robustness (Fig. 9).

chunkdz said:

PvM: What reality? It limits the codes to what would be expected to have arisen given our understanding of prebiotic chemistry, in that case the code is near optimal.

No, moron, in that case it is at or near optimal, or in the words of actual scientists (not pretend Panda's Thumb scientists) "the best of all possible codes". You really are a stupid little dork, aren't you?

Chunky,

One last time, just to be fair:

The genetic code is optimal for an arbitrary criteria due to natural selection. That is what the authors conclude. That is what we can all agree on. If you have any other point to make, just make it and be done.

No one can claim that the code is the best possible code for all criteria. If you want to conclude this, you are wrong. If you say that the authors concluse this, you are wrong. Even if the authors did conclude this, they are wrong. Get over it.

There is absolutely no point to any of this. If you can't see that then I will just have to berate your intelligence until my sheer rudness forces you to admit that I am right.

then it appears at or very close to a global optimum for error minimization: the best of all possible codes.

David Stanton said: Chunky, One last time, just to be fair: The genetic code is optimal for an arbitrary criteria due to natural selection. That is what the authors conclude. That is what we can all agree on. If you have any other point to make, just make it and be done. No one can claim that the code is the best possible code for all criteria. If you want to conclude this, you are wrong. If you say that the authors concluse this, you are wrong. Even if the authors did conclude this, they are wrong. Get over it. There is absolutely no point to any of this. If you can't see that then I will just have to berate your intelligence until my sheer rudness forces you to admit that I am right.

PvM said: They do not even claim it is the best code for a single criterium but rather that it is at or very close to optimal.

David Stanton said: Chunky, One last time, just to be fair: The genetic code is optimal for an arbitrary criteria due to natural selection. That is what the authors conclude. That is what we can all agree on. If you have any other point to make, just make it and be done. No one can claim that the code is the best possible code for all criteria. If you want to conclude this, you are wrong. If you say that the authors concluse this, you are wrong. Even if the authors did conclude this, they are wrong. Get over it. There is absolutely no point to any of this. If you can't see that then I will just have to berate your intelligence until my sheer rudness forces you to admit that I am right.

You guys still at it? As I understand it the difference between the restricted and unrestricted sets is especially relevant for the design inference. A designer, unlike nature, would be able to take advantage of the unrestricted set which contains solutions that are at least a little bit better and maybe significantly better than the extant code. This means, if I understand correctly, that if the code is the result of purely undirected natural processes then - and only then - it is optimal or very nearly so for error minimization.
On the other hand if it is the result of design then it is more of a Microsoft product. (i.e. not so optimal) Apart from chunkdz does anyone here think that I have got it completely wrong?

PvM this guy's all yours buddy. Show me just how well your approach gets through with the dumbass.

wad of id said: PvM this guy's all yours buddy. Show me just how well your approach gets through with the dumbass.

tresmal said: You guys still at it? As I understand it the difference between the restricted and unrestricted sets is especially relevant for the design inference. A designer, unlike nature, would be able to take advantage of the unrestricted set which contains solutions that are at least a little bit better and maybe significantly better than the extant code. This means, if I understand correctly, that if the code is the result of purely undirected natural processes then - and only then - it is optimal or very nearly so for error minimization. On the other hand if it is the result of design then it is more of a Microsoft product. (i.e. not so optimal) Apart from chunkdz does anyone here think that I have got it completely wrong?

On the other hand if it is the result of design then it is more of a Microsoft product.

PvM said: There is always hope...

Where is chunkydisease? LOL Hats off to PvM for vanquishing another IDiot troll.

PvM: Chunky, One last time, just to be fair: The genetic code is optimal for an arbitrary criteria due to natural selection. That is what the authors conclude. That is what we can all agree on.

No one can claim that the code is the best possible code for all criteria.

PvM, Of course new findings have shown that the genetic code is hardly that optimal, and what is of particular interest is that Knight is one of the reviewers.

The mutation-selection balance/non-linear adaptation argument should be considered in the Conclusion where the authors ask, "Why did the code's evolution stop where it stopped?" An answer I glean from much of the error-minimization literature cited in the present work is that it might be wildly improbable for selection to push the level of error-minimization any higher, given countervailing pressure from mutation. If the genetic code is "one in a million" in the sense favored by Freeland and Hurst (JME 1998), that is a high level of optimization by most standards. (A demonstration that many mutations improve that one-in-a-million code would be compelling contrary evidence.) Algorithmic optimization of the sort carried out here is blind to such statistical features – in greedy minimization, the first optimization step is as easy as the last step, because all possible alternatives must be evaluated each time, whereas in a blind sampling-based process such as evolution, the farther uphill one climbs, the more improbable improvement becomes and the less likely it is to persist once attained. This is the essence of Freeland et al. TiBS (2000)'s criticism.

chunkdz said:

PvM, Of course new findings have shown that the genetic code is hardly that optimal, and what is of particular interest is that Knight is one of the reviewers.

And Knight is actually kind compared to the others, who roundly criticize their methodology. All three reviewers lambasted their "greedy algorithm". Consider:

The mutation-selection balance/non-linear adaptation argument should be considered in the Conclusion where the authors ask, "Why did the code's evolution stop where it stopped?" An answer I glean from much of the error-minimization literature cited in the present work is that it might be wildly improbable for selection to push the level of error-minimization any higher, given countervailing pressure from mutation. If the genetic code is "one in a million" in the sense favored by Freeland and Hurst (JME 1998), that is a high level of optimization by most standards. (A demonstration that many mutations improve that one-in-a-million code would be compelling contrary evidence.) Algorithmic optimization of the sort carried out here is blind to such statistical features – in greedy minimization, the first optimization step is as easy as the last step, because all possible alternatives must be evaluated each time, whereas in a blind sampling-based process such as evolution, the farther uphill one climbs, the more improbable improvement becomes and the less likely it is to persist once attained. This is the essence of Freeland et al. TiBS (2000)'s criticism.

But of course, since you were merely looking for any possible refutation of the Freeland paper, your pea brain must have simply ignored all this. What an idiot.

Actual scientists: "If our definition of biosynthetic restrictions are a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes."

PvM, drooling chimp: "The authors never claimed it was the best of all possible codes."

chunkdz said:

Actual scientists: "If our definition of biosynthetic restrictions are a good approximation of the possible variation from which the canonical code emerged, then it appears at or very close to a global optimum for error minimization: the best of all possible codes."

PvM, drooling chimp: "The authors never claimed it was the best of all possible codes."

There is really no further evidence necessary to demonstrate that PvM is a stupid obfusacating liar. The fact that you other idiot chimps howl and screech with approval says volumes about what a bunch of idiotic sycophants you all are.

They recapture the uncontroversial result that the genetic code is much better at minimizing errors than a random genetic code (as has been shown by many authors), but is at neither a local nor global optimum (as has also been shown previously).

Their own results show that it is difficult to explain except as the result of an optimization process: the argument that the standard genetic code is a global optimum is not to my knowledge taken seriously in the field, so the results cannot be seen as overturning it (see discussion between Steve Freeland, Massimo Di Giulio and myself in TiBS in 2000, which is cited appropriately in the paper). Rather, they show that, like most other features of organisms, the genetic code is optimized but not optimal, and probably reflects a range of constraints beyond the specific feature being examined. The manuscript could also benefit from being shortened substantially, as it appears to be relatively long in relation to its news value.

Chunky,

If the code is optimal for error minimization, it cannot be optimal for many other criteria. For example, the code could be much more efficient if there were six bases rather than four. Then each codon would only need to be two nucleotides in length instead of three and that would be much more efficient. Likewise, if only sixteen amino acids were used, even the four letter code would be much more efficient. So there are in fact many criteria for which the code is not optimal locally, globally or otherwise.

Anyway, you still haven't made any point at all. So what if the code is near optimal for one arbitrary criteria due to selection? You still have no point to make.

PvM Again, ChunkDZ shows how his inability to read leads him to unwarranted conclusions.

chunkdz said:

PvM Again, ChunkDZ shows how his inability to read leads him to unwarranted conclusions.

My only conclusion, moron, was that this research would cause you to sit in a puddle of your own diarrhea and that spittle would drip from the corner of your mouth as you stare glassy eyed. My prediction has been vindicated several dozen times over now. Especially now that you, in an effort to dismiss the scientific findings, are reduced to pathetically taking Knight out of context. No one, including Knight, ever said the code was optimal for all criteria, yet you idiots harp on this as if it's some kind of flaw in the research. The researchers have done an admirable job of examining the code against a plausible bilogical backdrop, and they have found that the code is an optimal code that was fixed before the LCA. "The best of all possible codes". Yet you drooling macaques screech and howl that they didn't compare the code to any implausible codes. What's the matter morons? Why does it make you monkeys mad that the research was limited to REAL PLAUSIBLE BIOLOGY? I'll tell you why - because you are a bunch of tadpole brained idiots, programmed to follow, not to think.

David Stanton: If the code is optimal for error minimization, it cannot be optimal for many other criteria.

For example, the code could be much more efficient if there were six bases rather than four. Then each codon would only need to be two nucleotides in length instead of three and that would be much more efficient. Likewise, if only sixteen amino acids were used, even the four letter code would be much more efficient.

So what if the code is near optimal for one arbitrary criteria due to selection?

PvM: So yes, given the prebiotic conditions and selection, the code is doing quite well, as would almost any other code, and many of them would do better.

Our analysis shows that when the canonical code is tested against a sample of one million random variants using PAM matrix data to measure amino acid dissimilarity, the code appears to be extremely highly optimized at all transition weightings and modular power functions. For the unrestricted set of codes, no better alternatives are found anywhere (data not shown). This pattern is repeated for the restricted set of possible codes excepting the least plausible extremes of parameter space (no transition bias [w = 1] and at a high-modular-power mapping function [4 p 5]), where three and five better variants are found, respectively (fig. 2a ).

PvM: Not real plausible biology but biology matching the prebiotic conditions...

An ‘intelligent designer’ would not have been constrained by such.

I can understand why you may have been misled about your conclusions but let's once again point out that

1. The authors claimed that the code was at or near its maximum, in other words, they did not claim that it was the best code but that it was close to optimum

2. The authors restricted the search to prebiotically relevant codes, and when expanded they showed how the code was not really that optimal. Note that pre-biotically relevance is no requirement unless you presume an evolutionary history, the code could have been totally arbitrary of pre-biotic chemistry and still work as well or better than the present code.

Just helping you understand how you may have come to your flawed interpretation of what the authors actually concluded and what the data showed

To no surprise thus, the more recent findings show indeed that most codes would reach the same 'optimality' or better from almost any initial condition.

Understanding is all that is needed.

PvM: I can understand why you may have been misled about your conclusions but let’s once again point out that 1. The authors claimed that the code was at or near its maximum, in other words, they did not claim that it was the best code but that it was close to optimum

2. The authors restricted the search to prebiotically relevant codes, and when expanded they showed how the code was not really that optimal. Note that pre-biotically relevance is no requirement unless you presume an evolutionary history, the code could have been totally arbitrary of pre-biotic chemistry and still work as well or better than the present code.

Just helping you understand how you may have come to your flawed interpretation of what the authors actually concluded and what the data showed.

To no surprise thus, the more recent findings show indeed that most codes would reach the same ‘optimality’ or better from almost any initial condition.

How's it going, PvM? You're getting through to the IDiot yet?

What part of “the best of all possible codes” don’t you understand?

Here: I'll dumb it down for ya. Explain to us what is the PAM. Go ahead, I double dare ya.

Chunky,

Why is error minimization a more valid criteria than efficiency? Sixty four codons for twenty amino acids seems pretty inefficient to me. It doesn't seem like a very intelligent design at all. Why is it a more valid criteria than reducing the number of amino acyl tRNA synthetases to a minimum or the number of tRNAs required? Why is it a more valid criteria than any other that anyone could come up with?

Of course natural selection will be stronger for some features than others. Obvioulsy error rate would be strongly selected on. Is that the point you were trying to make?

You have still provided no reason whatsoever why anyone should care if you think the code is optimal for anything or not. Until you do, learn some manners and go away, not necessarily in that order.

It is of no surprise to me that any code can become optimal, including those that are biologically implausible and tested using an irrelevant linear method and a severely flawed algorithm. What’s your point, (if you have one), imbecile?

— ChunkDZ

wad of id said: Here: I'll dumb it down for ya. Explain to us what is the PAM. Go ahead, I double dare ya.

chunkdz said:

My only conclusion, moron, was that this research would cause you to sit in a puddle of your own diarrhea and that spittle would drip from the corner of your mouth as you stare glassy eyed.

Question: why did you think that this research would have that effect on us?

What's the matter morons? Why does it make you monkeys mad that the research was limited to REAL PLAUSIBLE BIOLOGY?

Mad? It's us braindead poo flinging monkeys that brought it up as an important qualifier to the results.

Exactly, David.

He's like some fucking IDiot with a stutter: "op... op... optim ... optimal... It's op... op..."

Who cares about opimality outside of an evolutionary context?

The point of the article cannot be understood of this context. That's the point of the article, which he conveniently ignores.

Ban the fucker.

the argument that the standard genetic code is a global optimum is not to my knowledge taken seriously in the field, so the results cannot be seen as overturning it

David Stanton said: Chunky, Why is error minimization a more valid criteria than efficiency? Sixty four codons for twenty amino acids seems pretty inefficient to me. It doesn't seem like a very intelligent design at all. Why is it a more valid criteria than reducing the number of amino acyl tRNA synthetases to a minimum or the number of tRNAs required? Why is it a more valid criteria than any other that anyone could come up with? Of course natural selection will be stronger for some features than others. Obvioulsy error rate would be strongly selected on. Is that the point you were trying to make? You have still provided no reason whatsoever why anyone should care if you think the code is optimal for anything or not. Until you do, learn some manners and go away, not necessarily in that order.

I want to remind chunkydisease that there are hundreds of IDiotic websites where he can go play with other IDiots. This is a private server run by people who pay the bills for its service. Chunky is a guest here. He knows the rules. If he doesn't like the inhabitants, he has no reason to stay. Go along, you have lost the debate. Get a life.

Says the IDiot: Tell me moron - what do you think is the primary function of a code?

Compare the Huffman code vs. the genetic code. What do they have in common in terms of their primary purpose?

We decided to use the aforementioned, simple, and therefore, tractable, deterministic, greedy algorithm. In the revised manuscript, we clarified this point in the description of the search algorithm by making it explicit that the algorithm finds an optimization path in which each step involves the maximum possible increase of the code robustness, and added a statement on caveats in the Discussion

Again, this work is not an attempt to reconstruct a truly realistic scenario for the evolution of the code but rather to determine the status of the standard code in the code space, compared to various sets of random codes, and delineate possible evolutionary links between the standard code and different random codes. This is clarified in the revision.

wad: Tell me how they used the PAM to determine this optimality.

:David Stanton: Why is error minimization a more valid criteria than efficiency?

PvM: The unrestricted codes are not biologically implausible, as any code is equally possible unless one can hypothesize that prebiotic chemistry caused the origin of the genetic code.

chunkdz: Tell me moron - what do you think is the primary function of a code?

wad: Nobody knows.

PvM: In fact, the reason why the code may not be that optimal after all...

PvM: Of course, that still does not mean that the code was the best possible code...

chunkdz said:

PvM: The unrestricted codes are not biologically implausible, as any code is equally possible unless one can hypothesize that prebiotic chemistry caused the origin of the genetic code.

Like I said, moron, the research is only concerned with what scientists think plausibly could have happened given plausible biological parameters. If you want to explore the implausible, be my guest. I happen to think that it is plausible that you are a really dumb moron who can't think outside of his own prejudiced mind.

the argument that the standard genetic code is a global optimum is not to my knowledge taken seriously in the field, so the results cannot be seen as overturning it

chunkdz said:

PvM: Of course, that still does not mean that the code was the best possible code...

Only according to the pretend scientist from the University of Ediacara. According to Real Scientists from Real Universities, it is actually "the best of all possible codes". You may now go back to picking the lice off of your minions. Yes, you may eat them if you like.

chunkdz said:

wad: Tell me how they used the PAM to determine this optimality.

Why don't you read the paper, you thick craniumed imbecile?

chunkdz said:

PvM: In fact, the reason why the code may not be that optimal after all...

Umm, idiot, the title of the paper is "Early Fixation of an Optimal Code". What code do you think they're talking about? The stupidity is simply breathtaking, isn't it?

chunkdz said:

PvM: The unrestricted codes are not biologically implausible, as any code is equally possible unless one can hypothesize that prebiotic chemistry caused the origin of the genetic code.

Like I said, moron, the research is only concerned with what scientists think plausibly could have happened given plausible biological parameters. If you want to explore the implausible, be my guest. I happen to think that it is plausible that you are a really dumb moron who can't think outside of his own prejudiced mind.

wad of id said:

chunkdz said:

wad: Tell me how they used the PAM to determine this optimality.

Why don't you read the paper, you thick craniumed imbecile?

Well, that's funny, because the answer isn't in the paper, shitface. LOL You've just been examined and failed. Go back to school. So I just want to know on what authority you're speaking for the authors.

chunkdz said:

:David Stanton: Why is error minimization a more valid criteria than efficiency?

Who ever said that it was more "valid"? Are you this stupid?

However, when confronted with scientific evidence that the canonical code upon which every biological system is based is optimal to an extremely high degree, you guys don’t know whether to keep drooling or pick your nose or both.

chunkdz said:

David Stanton: Look, you just can’t claim that the genome is optimally designed, you just can’t. That ignores all atof the evidence.

What evidence? The evidence of your prejudiced preconceptions? Why don't you go examine some real evidence. Freeland, S.J.,Knight, R.D., Landwebber, L.F., Hurst, L.D., 2000. "Early Fixation of an Optimal Genetic Code." Molecular Biology and Evolution 17:511-518

chunkdz said: http://genome.cshlp.org/cgi/content/abstract/17/4/405 Not that you imbeciles care to actually read. Hey, maybe you could also ask the researchers to s**k your c**k too. Unfortunately, even if they did, you'd still be a colossal brainless moron just like the rest of your PT idiot friends.

PvM: I have been reading exchanges with chunkdz and his colleague, jobby, for some days now, and all I can say is that you make Job look like a pathetic whiner.

Arggh! your exchanges with etc.... (remember Preview is our friend)

tresmal said: PvM: I have been reading exchanges with chunkdz and his colleague, jobby, for some days now, and all I can say is that you make Job look like a pathetic whiner.

I meant the biblical Job.

tresmal said: I meant the biblical Job.

Who is this chunkdz and why is he providing so much entertainment to us with his childish insults and his total inability to understand basic concepts in biochemistry and genetics?

Yawn.

chunkydisease is a member of the Mama Gene fan club. His job as a peon is to disrupt all discussions about his Mama's screw ups by burying it with irrelevancies. He doesn't have to think, he just needs to type.

BTW, as I noted earlier in this thread, he was not the first of the fan club to employ this technique.

You can read about Guts here: http://helives.blogspot.com/2008/07/now-thats-just-ugly-by-design.html

Guts (aka 'Nelson Alonso') visited the AtBC forum recently and tried to sink a discussion about Mama Gene and her fascist moderation techniques. Except, as it is apparent, everybody noticed what a jackass he was. LOL

In reference to the error minimization criteria relative to other criteria chunky wrote:

"Who ever said that it was more “valid”?"

Your claim was that it was the "best of all possible codes" and that it represents a "global optimum". My point is that, even if that were true (which it isn't), it would only apply to one criteria. Evolutionary theory can easily account for the observation and indeed the authors do just that.

Now, if the criteria is not more valid than any other as yourself imply, then the code is demonstrably not the "best" and demonstrably not "optimum" with respect to other perhaps more valid criteria. Therefore, once again, you have no point to make whatsoever. Glad we cleared that up.

By the way, what does any of this mental masturbation have to do with flagella? That was the topic of the thread. Why do you seem intent on changing it?

It really hinges on what chunkydisease thinks the "primary function" of a code is. I bet he was about to go off on how codes function as error minimizing systems. In which case he'd be pretty fucking wrong.

PvM: Optimal perhaps, the best possible code of all codes, as you suggested, not really. Even Knight, the lead author of the paper you ‘quote’ seems to agree.

PvM: So in other words, it is only optimal in the sense that it is highly optimized given its evolutionary history but not globally optimized.

Actual scientists, including Knight: the canonical code is at or very close to a global optimum for error minimization across plausible parameter space.

PvM: well this moron can read and wonders what you believe near refers to as in ‘nearly optimal’

“at or very close to a global optimum for error minimization across plausible parameter space.”

David Stanton: Your claim was that it was the “best of all possible codes” and that it represents a “global optimum”.

Dale Husband: Who is this chunkdz and why is he providing so much entertainment to us with his childish insults and his total inability to understand basic concepts in biochemistry and genetics? Yawn.

wad: It really hinges on what chunkydisease thinks the “primary function” of a code is. I bet he was about to go off on how codes function as error minimizing systems. In which case he’d be pretty fucking wrong.

chunkdz said:

wad: It really hinges on what chunkydisease thinks the “primary function” of a code is. I bet he was about to go off on how codes function as error minimizing systems. In which case he’d be pretty fucking wrong.

Wow. You are really as dumb as a rock, and now you are reduced to arguing with yourself. What a pathetic cringing moron you are.

chunkdz said: PvM: Optimal perhaps, the best possible code of all codes, as you suggested, not really. Even Knight, the lead author of the paper you ‘quote’ seems to agree.

PvM: So in other words, it is only optimal in the sense that it is highly optimized given its evolutionary history but not globally optimized.

chunkdz said:

David Stanton: Your claim was that it was the “best of all possible codes” and that it represents a “global optimum”.

No, moron. It is the claim of some very respected scientists. I simply pointed it out to you monkeys so I could watch you screech, howl, drool, and fling poo. Don't stop now.

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.

Now, ChunkDZ can argue, as he has attempted, that of course the scientists constrained themselves to look at pathways which were plausible but that requires one to make assumptions about what defines plausible. In science, plausible is guided by a hypothesis about DNA origin and evolution which suggests that prebiotic chemistry guided early DNA code (stereochemistry) only to be later optimized by natural selection. Based on such a hypothesis, the code has reached or is close to optimal, a big win for science. However, ChunkDZ was arguing that this optimum is best explained by 'design' and yet, this would mean that he has to constrain the designer to use exactly the same pathways that evolution would have followed, and thus he has to explain why a designer is to be constrained by such. Since a designer is typically not constrained by historical contingencies, the claim that a local optimum is evidence of design is severely flawed by logic and evidence.

No wonder ChunkDZ is so abusive in his language. Not only has he argued in favor of the strength of evolutionary theory but he has also destroyed his design inference, all because of a misreading of what the paper actually argued.

Let me get this straight: Chunky didn't read the paper thoroughly. He doesn't even have the basic understanding of the techniques employed by the authors (e.g. he actually thought reading the specifics of PAM were in the paper ROFL). So what is he doing? Evangelizing over a few quote mines?

And for the last time, what does any of this have to do with the bacterial flagellum?

Ban the fucking troll.

wad of id said: Let me get this straight: Chunky didn't read the paper thoroughly. He doesn't even have the basic understanding of the techniques employed by the authors (e.g. he actually thought reading the specifics of PAM were in the paper ROFL). So what is he doing? Evangelizing over a few quote mines? And for the last time, what does any of this have to do with the bacterial flagellum? Ban the fucking troll.

PvM: Given the context, you miscontrued their statement as evidenced by Knight’s own admission that the concept that the code is a global optimum is not one maintained by science.

PvM, pretend scientist: science does not hold to a claim that the code is at a global optimum

Real scientists: "the canonical code is at or very close to a global optimum for error minimization across plausible parameter space."

PvM: However, ChunkDZ was arguing that this optimum is best explained by ‘design’ and yet, this would mean that he has to constrain the designer to use exactly the same pathways that evolution would have followed, and thus he has to explain why a designer is to be constrained by such.

“the canonical code is at or very close to a global optimum for error minimization across plausible parameter space.”

OK. We all agreed to this days ago. What is your point?

PvM: Since ChunkDZ was arguing that the code showed evidence of ‘design’ because of its global optimum...

chunkdz said:

PvM: Given the context, you miscontrued their statement as evidenced by Knight’s own admission that the concept that the code is a global optimum is not one maintained by science.

You are obfuscating. One paper dealt with plausible biological parameters, for which the code is optimal. One paper did not. How utterly dishonest of you to try to make it seem like Knight is contradicting himself. What a stupid dork you are to attempt such a ruse. Even your idiot sycophants can see right through this.

chunkydisease: Good point. ID’ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design.

Nope, didn’t make that argument either.

BTW, dipshit. Tell us what is the PAM and how the authors used it to determine optimality.

chunkdz said:

PvM, pretend scientist: science does not hold to a claim that the code is at a global optimum

Real scientists: "the canonical code is at or very close to a global optimum for error minimization across plausible parameter space."

Open your eyes, idiot.

hey recapture the uncontroversial result that the genetic code is much better at minimizing errors than a random genetic code (as has been shown by many authors), but is at neither a local nor global optimum (as has also been shown previously).

wad of id said: Yes, to get the point you have to return to page 1:

chunkydisease: Good point. ID’ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design.

Now he backtracks:

Nope, didn’t make that argument either.

So he flips-flops and drools fecal matter out of both sides of his mouth. What else does a cock-sucker do? ROFL

wad: Tell me how they used the PAM to determine this optimality.

chunkdz: Why don’t you read the paper, you thick craniumed imbecile?

wad: Well, that’s funny, because the answer isn’t in the paper, shitface.

Ban the fucking troll.

No you fuckface. The section describes "problems with PAM" but it doesn't actually describe what it is. What is it? How does it "measure amino acid similarity" and "overcome these potential problems"??

You're dodging the fucking question. That's why we should ban you.

PvM: Consistency is hard to achieve and indeed, it seems that now ChunkDZ had made a good claim that the hypothesis that the genetic code originated through stereochemistry and selection is well supported by the data.

All because of a confusion over the meaning of ‘global’

wad:No you fuckface. The section describes “problems with PAM” but it doesn’t actually describe what it is. What is it? How does it “measure amino acid similarity” and “overcome these potential problems”??

"We address this weakness by employing point accepted mutations (PAM) 74–100 matrix data (Benner, Cohen, and Gonnet 1994 ), which are derived from the pattern of amino acid substitution frequencies observed within naturally occurring pairs of homologous proteins and thus provide a direct measure of amino acid similarity in terms of protein biochemistry."

wad: You’re dodging the fucking question. That’s why we should ban you.

Well at least he isn't stupid enough to mix up the terms your and you're. Now that's stupid.

600 words. 0 comprehension. F

chunkdz said:

PvM: Consistency is hard to achieve and indeed, it seems that now ChunkDZ had made a good claim that the hypothesis that the genetic code originated through stereochemistry and selection is well supported by the data.

And where did I claim this?

And since we are supposed to be morons, chunkdz, perhaps you can help us monkey brains by making a long, coherent statement critiquing everyone else's positions in a proper scientific manner.

When you nitpick individual points like you've been doing, you waste your time. Clearly, you have never read a science journal, so you don't understand why we all have been laughing at your grade school theatrics.

You're still not answering the question. You have a sentence which describes what PAM does, but not what it is. Yes it is derived from substitution frequencies. But how?

That's like saying what is a cake? and then answering: "It's derived from flour". Or Q: "what is the first law of motion?" A: "It's derived by Newton." Q: "Who's Jesus?" A: "It's derived by God." LOL, 3rd graders know better than put an answer like that on a test. At least they've the know-how to make something else up.

So, once again dodged the fucking question.

I'll give you a hint where you might begin to find it. The authors helped you out right there. It involves you (*gasp*) reading a bit more.

Think you can handle that?

Here I'll dumb down the question even more: what does this "matrix" look like? Tell me what goes into each cell of the matrix.

PvM: Did you not claim that the code was the best possible code given the assumptions about the pre-biotic chemistry?

wad: You’re still not answering the question. You have a sentence which describes what PAM does, but not what it is. Yes it is derived from substitution frequencies. But how?

Dale Husband: And since we are supposed to be morons, chunkdz, perhaps you can help us monkey brains by making a long, coherent statement critiquing everyone else’s positions in a proper scientific manner.

Yea right. Quoting a paper means it must be true. I already explained to you that if the authors actually made this claim that they would be wrong. What part of that post did you not underrstand? You can repeat it all you want, but that won't make it ture.

Man, this is like saying I have the best possible mother. Of course you do - given certain arbitrary criteria. Other than that, even the concept is fundamentally flawed.

Of course you already know all this. You have just been too buzy making up lame insults to recognize it. Besides, you still have made no point at all. Even if your argumewnt is somehow correct - so what?

David Stanton: I already explained to you that if the authors actually made this claim that they would be wrong.

Man, this is like saying I have the best possible mother.

Of course you do - given certain arbitrary criteria. Other than that, even the concept is fundamentally flawed.

Even if your argumewnt is somehow correct - so what?

Ban the fucker.

But personally, I’ll take the opinion of 4 respected researchers over a bunch lice eating howler monkeys.

There’s nothing arbitrary about it. Error minimization optimality is a very distinct and meaningful measurement of code fidelity.

Take any modern programming language.

What do you look for:

Compile speed? Yup
Profile size? Yup
ByteCode optimization? Yup

Error minimization? Nope

Rather than try to explain a probability matrix for amino acid substitutions to a lobotomized rhesus such as yourself, I think you should just go to Monkeypedia and read about it yourself.

wad of id said: Ban the fucker.

It be just as fun to see him run back to his little groupie whining about his ass-whopping here.

But personally, I’ll take the opinion of 4 respected researchers over a bunch lice eating howler monkeys.

— ChunkDZ

Chunky: Good point. ID’ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design.

Or maybe he was distracted by how to make the flagellum using a poop-shoot?

wad of id said: Well it's a new page. Just in case we forget chunkydisease's original position on this IDiocy:

Chunky: Good point. ID’ers look at the basis of all biological systems, the code of life, as an elegant and sophisticated programming language - an optimal design.

Read it slowly: "the code of life . . an optimal design" So sophisticated a design, in fact that according to the authors, who ChunkyDisease repects, it has all the hallmarks of having been evolved from a prior precanonical code. Did the Designer not figure it out the first time? LOL

wad: He instead takes the intellectually lazy road and pawns the work off to real scientists.

Well, if reading their paper hasn’t taught you anything, then I surely won’t be able to.

wad: The Designer was a dumbass.

A moron like me schooling a shithole like you.

Y'know chunky I should be more grateful to you. Thanks to your hard-earned tax money, I get to spend it all day long on the Internet trying to teach something to people you.

Don't ya just wish you had the some privileges I do? LOL

Science rolls on while ID stays stuck in its non-productive rut! What we need more of is science!

PvM: However, ChunkDZ was arguing that this optimum is best explained by ‘design’ and yet, this would mean that he has to constrain the designer to use exactly the same pathways that evolution would have followed, and thus he has to explain why a designer is to be constrained by such.

chunkdz: One simple yes or no question: Do you believe that this paper provides at least a little bit of evidence in favor of ID?

Looking forward to your reply which will no doubt be laced with your famous arch Wildean wit.

wad: "Y’know chunky I should be more grateful to you. Thanks to your hard-earned tax money, I get to spend it all day long on the Internet trying to teach something to people you."

the designers (far from being constrained) chose the ones that they used for their own reasons.

The origin of the genetic code was constrained by pre-biotic chemistry (stereochemistry hypothesis) followed by a period of selection

The canonical optimal genetic code hasn’t been noticeably improved in 4,000,000,000 years. Of course, how much improvement would you expect from “the best of all possible codes”?

chunkdz said:

Dale Husband: And since we are supposed to be morons, chunkdz, perhaps you can help us monkey brains by making a long, coherent statement critiquing everyone else’s positions in a proper scientific manner.

You're not supposed to be morons, you just ARE morons. For example: PvM says "It is not the best of all possible codes." Then I quote a scientific study that says the code is "the best of all possible codes". See? Coherent. Scientific. Proper. Now go back to picking ticks off the backs of your monkey friends and eating them.

Dale Husband said:

chunkdz said:

Dale Husband: And since we are supposed to be morons, chunkdz, perhaps you can help us monkey brains by making a long, coherent statement critiquing everyone else’s positions in a proper scientific manner.

You're not supposed to be morons, you just ARE morons. For example: PvM says "It is not the best of all possible codes." Then I quote a scientific study that says the code is "the best of all possible codes". See? Coherent. Scientific. Proper. Now go back to picking ticks off the backs of your monkey friends and eating them.

In short, you will not even attempt to do what I asked. One scientific study does not prove anything. It can be debunked by peer review later. I assume PvM knows that and I certainly do. You didn't? Your idiocy is obvious.

PvM said: Remember that possible codes were from a set of restricted codes which reflected pre-biotic conditions.

Dale Husband said:

In short, you will not even attempt to do what I asked. One scientific study does not prove anything. It can be debunked by peer review later. I assume PvM knows that and I certainly do. You didn't? Your idiocy is obvious.

It’s like saying that because ascii is so historically ubiquitous in coding that the original designers must have been constrained to those english characters. This is complete monkey brained idiocy. The ubiquity of ascii means simply that ascii code was successfully selected and fixed at some point. Even though there were billions of other characters to choose from, the designers (far from being constrained) chose the ones that they used for their own reasons. The historical contingencies were a result of the design, not the other way around.

The X3.2 subcommittee designed ASCII based on earlier teleprinter encoding systems. Like other character encodings, ASCII specifies a correspondence between digital bit patterns and character symbols (i.e. graphemes and control characters). This allows digital devices to communicate with each other and to process, store, and communicate character-oriented information such as written language. The encodings in use before ASCII included 26 alphabetic characters, 10 numerical digits, and from 11 to 25 special graphic symbols.

The only difference is that while ascii has been modified and improved significantly over the past 50 years, the canonical optimal genetic code hasn’t been noticeably improved in 4,000,000,000 years. Of course, how much improvement would you expect from “the best of all possible codes”?

BTW, the bacterium E. coli. mutates everyday in your gut, far more frequently than the ASCII code. It improves itself to the local conditions of your gut flora by the hour as you subject it to toxins, antibiotics, changes in acidity, various nutritional media, etc...

So does that mean the E. coli wasn't an "optimal design" like the genetic code?

LOL. I love to Design-think. It's so easy, it's like masturbating.

Now, here's another aspect of the "error-minimizing" character of the genetic code that is quite unlike how Human Designers operate. Y'see the genome is still quite sensitive to mutations, despite the error-minimizing nature of the code. Take cystic fibrosis. It is a disease in a chloride channel that is most commonly caused by a mutation... a deletion in fact. Because of the deletion, patients with this disease are subjected to recurrent infections of their lungs, poor absorption of nutrients, long courses of antibiotic treatments that eventually select for a superbug, and overall poor quality of life and lower longetivity. Optimally designed to torture someone, wouldn't you say?

But why does an "error-minimizing" code not minimize errors like these? In English, we tolerate errors like this all the time. Watch:

Chnkydeas is qte the fkng mron.

You all know what I was trying to say. ROFL. But why? Because we have built in a system of contextual interpretation. We can extrapolate the closest sense of the word based on experience. This robust system is not in place in the genome. Why? Because it was really not intelligently designed. All proteins have motifs, yet it is extremely sensitive to the location of key amino acids in key positions, just like our recognition of English words are subject to recognizable letters in key positions. Yet the genome does not design to optimize robustness on the level of functional motifs. Go figure.

Here's another way in which the "optimal design" of the genetic code is not quite so optimal. Frame-shift mutations are known to be disastrous mutations. Here, you add or subtract less than a codon's length of base pairs. All of the sudden all the subsequent codons are whacked. Once again, suboptimal. But this problem could easily have been worked around. You could add "spacers" between the codons: unique nucleotides that are required to be present in a specific position to be read by the RNA machinery. Otherwise, it skips over it. In other words, you would make a 4-bp based code: XXXY, where XXX are your standard ACTG, and Y can be anything, but is fixed and the same throughout. Now consider the following DNA sequence based on this improved code:

AAGY TTTY CCTY CGTY ATCY ACGY GTCY

If you obtain a mutation that normally would cause a frameshift, say a deletion, you'd get something like:

AAGY TTTCCTY CGTY ATCY ACGY GTCY

Now the RNA machinery comes along and recognizes in the 2nd codon that there is a missing the Y. It skips reading this codon and moves on to the 3rd codon, resulting in either a missense or deletion mutation of codon 2. In the other scheme, all the other codons downstream of this one are fucked. You just have garbage instead of a less disastrous deletion/missense.

Look at that, in the span of 15 minutes, I've just "improved" on the genetic code. Says quite a bit about how much thought the Designer gave this coding scheme, eh?

Entertaining, but nothing much of substance in the comments.

Oh, science proves negatives all the time, contrary to what chunkdz said. E.g., Earth is not the center of the universe. There isn't a black hole in the center of the Earth.

We also like to use Modus Tollens to prove negatives.

It seems the new post on this thread has addressed all of chunkdz's concerns.