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

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Mark Pallen, author of the Rough Guide to Evolution and expert on Type III Secretion Systems (and producer of the famed Darwin in Dub), has a new blog. He just put up two posts about the third UK Type III Secretion meeting:

Dispatches from the cutting edge of flagellar biology, part 1

Dispatches from the cutting edge of flagellar biology, part 2

The short version: In the 2003 Big Flagellum Essay I reviewed the known homology and similarity between the flagellar export apparatus and the F1Fo-ATPase. I made a general prediction that there were likely more homologies waiting to be discovered between the two systems.

Being brave (and having no reputation to lose), I also made some specific suggestions for what the homologies might be. The mostly likely match, I thought, was between the flagellum protein FliH and the F1Fo-ATPase protein Fo-b (this was not a completely novel idea, there were a few hints in the literature and online databases). Another, admittedly more speculative, suggestion was that FliJ was homologous to the protein F1-delta. At the time, prominent ID proponents who commented on the Big Flagellum Essay – notably William Dembski and Mike Gene – dismissed, based on irreducible complexity arguments, the idea of further homologies as mere evolutionary storytelling. Mike Gene even wrote a whole detailed essay about why I was wrong.

Here’s a nice quote from Mike Gene:

“Since the complete lack of F0F1 IC interactions are missing from the TTS machinery of the flagellum, it is unlikely that the F0F1 complex is homologous to the TTS machinery, and thus cooption of the F0F1 complex is not a plausible explanation.”

And Dembski:

Matzke makes an unconvincing argument for homologies between the type III system and an ATP synthetase system.

There the matter sat until 2005, when – literally on the last day of the Kitzmiller trial, if I recall correctly – Mark Pallen looked me up out of the blue and informed me that he had confirmed a homology between FliH and Fo-b. Additionally, one domain of FliH was homologous to F1-delta, which made it unlikely that FliJ was the match to F1-delta. This was published in 2006 in Protein Science. (Summarized in the 2006 update to the Big Flagellum Essay)

Various other discoveries have rolled in since then that have also strengthened the idea of extensive homology between the flagellum export system and the F1Fo-ATPase (and, I should add, the archaeal and eukaryote relatives of F1Fo-ATPase, really the whole group of them can be called the VFA-ATPases). For example, the structure of the flagellar ATPase FliI is dramatically similar to the F1Fo-ATPases (although this was known to be extremely likely already based on sequence similarity), and it turns out that T3SS protein export is powered directly by proton motive force (the F1Fo-ATPase is also powered by proton motive force).

All of this was interesting, but now comes Pallen’s report on the T3SS meeting:

Anyhow, to get back to what Namba said at the Bristol meeting last week.…

He provided a run through of all the work leading up to his recent Nature article on the dispensibility of FliI. I was then very proud to see him cite my paper on the FliH/F-type ATPase homology. But then he provided the final piece in the jigsaw (and Nick Matzke’s ears should prick up at this point)!

Namba and colleagues have now solved the structure of FliJ, another protein that interacts with FliI and FliH. And what they found was clear evidence of homology with yet another protein from the F-type ATPase–the gamma subunit!

So, now we have deep and broad homologies between the flagellum and the F-type ATPase, just as Nick predicted. This provides another nail in the coffin of the idea that flagellum was intelligently designed. If the flagellum were the product of intelligent design, particularly by an omniscient deity, the designer could have custom-built it from scratch, so it need not resemble anything else in nature. By contrast, the processes of evolution tends to cobble together and tweak already existing components (something Francois Jacob called bricolage)–and slowly but steadily it is become clear that the flagellum has been built this way.

There are now likely to be serious scientific payoffs–what all these homologies mean is going to occupy Namba et al for years to come, and it’s a fair bet that comparisons between the two protein complexes are likely to clarify the structures and functions of both systems.

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

See Pallen’s full post for the history. And buy his book (which will be very good, I have seen chunks of it!) and put him on your blogroll!

357 Comments

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.

By gentle you mean Nick will stop referring to their research paper as a “dog”?

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.

600 words. 0 comprehension.

F

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.

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.

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.

Then, why do Intelligent Design proponents insist on being heard if they have no legitimate reason to challenge the Theory of Evolution? You must realize that by admitting that Intelligent Design is not scientific, and was never meant to be scientific in the first place, all of the arguments, objections and proposals put forth by Intelligent Design proponents are deader than gefelte fish in vinegar brine.

Philip Johnson freely admits that he set up the Discovery Institute to help him and like-minded individuals insert God/Jesus into literally all aspects of American society.

William Dembski freely admits that, as an Intelligent Design proponent, he is not obligated to examine minutiae like his biologist counterparts are.

And then there’s Michael Medved freely admitting that Intelligent Design is neither a science or even an alternative explanation, but a “challenge” to Evolution, totally ignorant of the fact that no one can challenge an established science without science or an alternative explanation.

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.

Simply tallying the number of words Wad of ID used and then giving him an “F” does not highlight any logical fallacy, if any at all, in Wad’s essay. David Stanton accuses you of trolling because your dismissal of Wad’s essay is identical to the manner the sock-puppeteering troll bobby/jacob/hamstrung/balanced/jobby dismisses other people’s posts by copying them in their entirety, then typing in a one-line response.

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. Wad also points out that in order to claim that these systems are irreducibly complex, therefore “unexplainable by evolution,” Intelligent Design proponents must routinely ignore the facts that the components of allegedly irreducibly complex systems either have homologues in, or are also used in other systems, such as the case with proteases that are used in both the blood clotting cascade, and in protein digestion, or even that irreducibly complex systems have been demonstrated to have evolved de novo, such as the antifreeze glycoprotein in Antarctic icefish, or nylonase in bacteria, or the countless means of antibiotic resistance in bacteria.

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.

Such as the instances where William Dembski has needlessly insulted his opponents, or have reported them to Homeland Security out of sheer spite?

[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.

The problem is that not only has Intelligent Design been demonstrated to be scientifically sterile by its critics, but, those Intelligent Design proponents who know better don’t care about presenting (or not presenting) Intelligent Design as a science, as demonstrated by the malignant scientific apathy of the Discovery Institute, and those ID proponents who don’t know better are totally incapable of presenting Intelligent Design as a science, as demonstrated by Michael Medved’s confession that Intelligent Design is “not an alternative, but a challenge,” and by the way creationists, such as one Mr Freshwater, use “teach the controversy” and Intelligent Design as excuses to not teach science to school children.

I get the feeling that the flagellum is now a dead parrot for ID-ers. And the content free protests from trolls confirm this.

wad of id said:

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

That wasn’t the last time either. I’m reminded of Neil deGrasse’s example of “an entertainment complex built around a sewage system”.

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.

Wad:

Where did I say Mike claimed ID was science?

Where did I say you said Mike claimed ID was science?

You bash him for being unscientific in your last paragraph, even though you are aware that he never claimed to be.

That along with your polemics and weak reasoning is why I gave you an F.

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.

Then how come you did not point this out when you “flunked” Wad’s essay in the first place?

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.

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.

It’s been my experience with Intelligent Design proponents that they don’t care to study anything at all. All of the “evidence” they provide for “Design” are anything that they don’t (care to) understand. At best, all they offer is meaningless, useless platitudes that they use to camouflage their academic incompetence. And at worst, Intelligent Design proponents reveal that they are nothing more than smartmouthed, lazybrained vermin who never had any intentions about engaging in intelligent conversation in the first place.

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.”

Then please explain how Intelligent Design explains why it is that vertebrate eyes are inferior when compared to cephalopod eyes? Why would an Intelligent Designer bother to design a taxon of organisms like the placoderms, set them up to be poised to take over the earth in less than 60 million years, only to have them disappear like a mirage?

Please explain to me why it is only the critics of Intelligent Design who study and offer explanations about biological systems, and not proponents of Intelligent Design?

Of course, critics like yourself are just kidding yourself.

Oh?

Why would I kid myself concerning Intelligent Design? Please tell me why I should kid myself when Intelligent Design proponents demonstrate time and time again that they don’t care about explaining or even studying any of the “perfect” biological systems they claim to be in awe of?

Chunkdz Wrote:

Of course, critics like yourself are just kidding yourself.

That is a very strange accusation.

No one is kidding when we point out that the ID crowd mischaracterize science repeatedly and continues to do so in new venues even after their egregious errors have been pointed out to them.

They mischaracterize the systems they claim are “intelligently” designed and then proceed to apply inappropriate pseudo-mathematics using guesses about probabilities pulled out of the air. So their “analyses” are not only inappropriate, they are dead wrong.

They continue to spread misconceptions of fundamental scientific concepts, and these misconceptions have a well-known pedigree going back to the writings of Henry Morris and Duane Gish. These misconceptions have been morphed to apply to biological systems at the molecular level, yet they retain the same fundamental errors they have always had.

They continue to quote-mine members of the scientific community. They allow misconceptions and conflated concepts to run rampant among their followers without making any effort to correct them; instead leaving it to the members of the scientific community to clean up the messes ID/Creationist leaders make.

None of their behaviors fit the profile of real scientists submitting ideas and data for peer review. In fact, all the behaviors of the ID/Creationist crowd fit solidly and clearly into the behaviors of pseudo-scientists peddling their wares to naive audiences in venues where they cannot be effectively challenged to answer for their misinformation and misconceptions. And there is a well-financed grass-roots political campaign designed to bypass the proper vetting of ideas in the scientific community before they are introduced to young, inexperienced students in the public schools.

Nobody here is kidding themselves; many of us have been tracking this phenomenon since the 1970s. The crap remains crap wrapped in crap. That is what we are dealing with.

Lol, chunkdz acts as if his grading me bothered one bit… Being graded by an IDiot is like being called names by a 5 year old. The fucking arrogance is so damn hilarious. Hey chunkdz, suck my cock. Don’t cry as you do it please.

Speaking of reading comprehension, show me exactly where I “bash” Mike for being “unscientific”. Here, I’ll quote the last paragraph:

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.

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

wad:

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

So predictable. Meanwhile, still no comprehension.

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”?

If it seems strange to you then simply refute the paper I cited from Molecular Biology and Evolution”. The fact that the genetic code is optimal has been scientifically established for some time despite the bile dripping blabberings from the PT peanut gallery.

Just remember that published scientific evidence can’t be refuted by whining about Henry Morris and Duane Gish.

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.

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

LOL, these “respected researchers” have each denounced the tenets of IDiocy.

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

Yes it is arbitrary. Name another programming code where it is important to be robust against syntax errors. LOL

The Designer was a dumbass.

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.

In other words, chunkydisease lied to us about comprehending the paper. Just as we suspected. He instead takes the intellectually lazy road and pawns the work off to real scientists. LOL

Nah, this is too much fun.

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.

ChunkDZ Wrote:

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

But you did not present their opinion as much as your interpretation of such. That’s fine of course.

So remind us again, what was your original argument? Care to tell or do you not remember?

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

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

In that case, an optimal design should be seen as optimal within the capabilities of the designer. In other words, a truly globally optimal system, meaning not constrained to code subsets, would indeed count as evidence in favor of ID since given the improbabilities involved.

However, what the researcher found is that the optimality had been guided by prebiotic stereochemistry, just as science had expected. So evolution 1 - intelligent design 0

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.

Now go back to scratching your inflamed rectum.

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

Exactly. You’re in no position to be advocating anything scientific, much like being a poseur.

Leave the science to the scientists. You can run along now and play with your little fellow IDiots in your own sandbox.

wad:

The Designer was a dumbass.

Yeah, should have realized that the optimal code would someday lead to a moron like you.

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

Since chunkydisease respects scientists so much, he should respect some of these remarks about his peer:

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

Now that we know chunkydisease respects this assessment, maybe he can explain to us why ID science didn’t produce these results regarding the evolution of bacterial flagellum. Couldn’t a Front-loaded IDiot predict the design of the flagellum from a toilet?

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.

Your argument isn’t even logical, moron.

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 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”?

Can you smelly marmosets stop eating fleas off each other to understand this?

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.”

Wow. That was almost coherent.

So in other words, design means that natural processes can fully explain it such as the pre-biotic chemistry and selection.

Sounds a lot like how evolutionary science explains it.

I knew you would come around and show that ‘design’ cannot exclude natural processes as its designer, as various ID critics have so aptly observed.

Compare the design hypothesis

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

versus the scientific hypothesis

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

Now which one do you think is the better hypothesis and why?

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”?

What do you mean, not noticeably? Not at all, not that you noticed, not that science noticed? How do you define ‘improved’.

And you are still misrepresenting the code, it is not the best of all possible codes.

But you are making a good case for the scientific vacuity of ID, for that I could not thank you more. You know what, I am some appreciative that I will turn this into a posting on PT of its own, its well worth exposing this. Can we say ad hoc and circular?

Lovely display of scientific vacuity of ID.

And further

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.

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

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.

Right. There is the question of whether DNA is the best possible carrier of genetic information. There is also the question of whether amino acids are the best agents to translate that genetic information into structual forms. Finally, we have to agree on what “best” is. It should be noted that if there was such a system of life that allowed for no copying errors (mutations), evolution would not occur.

THEN intelligent design would have had to create any complex forms of life made up from that coding system.

Not bad for a moronic monkey brain flinging poo, eh?

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.

What reasons?

How does one explore this hypothesis that chunkydisease just shat out without resorting to Designer-think?

Y’see Designer-centrism reigns supreme once again, just as I noted on page 1. They don’t want to talk about it, but fact of the matter is, they really really want to ROFL

Herein lies the key difference between IDiocy and science. In one realm, you’re simply content at the fact that “design” is a good enough explanation as long as you have faith in the Designer’s “reasons”. You live off of an intellectually lazy path down towards seeing Design in clouds and being happy but stupid. IDiocy makes out design into impregnable fortress of ignorance. Design: the ultimatum answer to “I dunno.”

In the other realm, you are stuck with the hard work of figuring out what are the forces behind the design, the historical contingencies behind the historical contingencies. You give uncertainties their proper names: unknowns, and leave them for future research.

So what about ASCII? It turns out if you dig a little deeper, thanks to the availability of the Designers, you learn:

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.

Source: Monkeypedia, care of Charles E. Mackenzie’s book on character encodings.

Now, look at that. Historical contingencies based on more historical contingencies. Chunkydisease would have had you believe that ASCII was just POOFed into existence. As I noted: intellectual laziness.

Now, having just woken up from his intellectual slumber, chunkydisease then poses an interesting problem to IDiocy:

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”?

Where is the error-minimization property in ASCII that is seen in the genetic code? Look at the ASCII table. If I mutate bit 3 in some of those elements, do I get the same character set back? Is it arranged so that if I mutated bit 3 in the encoding, the majority of English words remain the same?

Take the encoding for A: 100 0001. If I mutated the 3rd bit it becomes E: 100 0101. Now suppose I have the word “sea” does it have a similar meaning to the word “see”?

Clearly, this Designer cannot be understood in terms of human Designers, because when we design encodings, robustness to errors is not a priority. Why? Because we place emphasis on fidelity of reproduction. We don’t want our data streams to evolve. So on what basis does one conclude that one can understand this “optimal design” based on the Designer’s “reasons”??? NONE AT ALL. It is for all intents and purposes a statement of faith.

Which we knew all along.

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.

About this Entry

This page contains a single entry by Nick Matzke published on September 19, 2008 6:24 PM.

Luskin and the ID movement on immunology: immune to evidence was the previous entry in this blog.

Clergy Letter Project Expands to Include Rabbi Letter is the next entry in this blog.

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