Flagellum evolution in New Scientist

| 485 Comments

PT readers may be interested to check out this great new article in New Scientist, which reviews recent developments in flagellum evolution. The thing I find interesting about all this is how the IDists have been intellectually unable to concede any tiny little mistake in anything they said, e.g. this standard ID argument from DI fellow Bruce Gordon as it was presented in 2006:

As the biochemist Michael Behe has pointed out, this flagellar motor depends on the coordinated function of 30 protein parts and it will not work if even one of them is removed – it is, in his terminology, “irreducibly complex.” Since natural selection works (in neo-Darwinian theory) by environmental “selection” of functional advantages manifested in the phenotype that have arisen through random genetic mutations, it can select the motor once it has arisen as a functional whole, but it cannot produce it in the step-by-step fashion required by neo-Darwinism because every stage of lesser complexity is completely nonfunctional.

Now, the best you will get from the ID guys are evasions like “oh, we never claimed that subsystems would be nonfunctional.” See above, guys.

485 Comments

I LOVE to read the article but it’s subscription-only! Why tease us like this?

Why tease us like this?

Seconded!

Rolf Aalberg:

Why tease us like this?

Seconded!

Thirded!

DJ and Rolf,

I don’t like to be teased either, but with a little money one can access the article. But in Behe’s case, all the money in the world can’t seem to get us to the good part - how, where and when that first designed flagellum came to be.

I’m registered! Here is the article in full. It’s a long one.

Uncovering the evolution of the bacterial flagellum

16 February 2008 From New Scientist Print Edition. Subscribe and get 4 free issues. Dan Jones

[snipping] The relevance to flagellum evolution? Variants of at least seven T3SS proteins are also found in the flagellum, within a subsystem called the protein export system. This sits within the basal body and funnels replacement flagellin subunits to the filament, using a mechanism remarkably similar to the T3SS. In fact, the two systems are so similar that the flagellar protein export system is now considered to be a subclass of the T3SS (Trends in Microbiology, vol 14, p 157).

Such similarities, or “homologies”, are strong evidence that the two systems evolved from a common ancestor - analogous to the way that the arrangement of bones in the limbs of horses, bats and whales reveal their common ancestry despite their very different outward appearance and function. Similar homologies can be seen in the DNA sequences of genes, and in the amino acid sequences and 3D structures of proteins - all are clear evidence of shared descent.

The evolutionary events linking flagella and T3SSs are not clear, but the homology between them is a devastating blow to the claim of irreducible complexity. This requires that a partial flagellum should be of no use whatsoever - but clearly it is. “The T3SS is a useful model of how a ‘partial flagellum’ could function in protein export,” says Nicholas Matzke of the University of California, Berkeley, a prominent defender of evolution and author of a number of academic articles on the flagellum. Miller adds: “The notion that these proteins can only be used in flagella simply falls apart.” This argument helped swing the outcome of the “ID trial” in Dover, Pennsylvania, in 2005, in which irreducible complexity formed a key plank of the ID movement’s failed bid to have ID taught in school science classes.

So how exactly is the flagellum’s protein export system related to the T3SS? One possibility is that the T3SS evolved first and was later co-opted as part of the flagellum. A second is that the flagellum evolved first and its protein-export system gave rise to the T3SS. It is also possible that both evolved in parallel from a common ancestor.

[snipping more – sorry, I don’t like copyright either but we don’t want to be sued – thanks for the thought though! Nick]

I wrote the above article, and while I’m not sure how the folks at New Scientist will feel if they see the text being pasted here, I’m glad PT readers have a chance to read the article - although you don’t get to see the nice pictures and graphics that the NS art team put together for the piece!

Cheers,

Dan. http://psom.blogspot.com/

Oooops…

It is a great article and I thought since no one was able to access it then I would do them a favour by reproducing it here. I do hope NS doesn’t mind, but no doubt the administrators will pull it if they do.

Hey Maxi, didn’t mean to admonish you for putting the peice up - that’s someone else’s job! ;-) I’m pleased it’s ‘out there’. And pleased you like it.

Cheers,

D.

Maxi, could you please edit your post. Posting the full article, rather than a short excerpt for scholarly purposes, is violation of copyright.If you could put in an excerpt and your own brief summary of the article that would be fine.

Dan Jones, thanks for writing the NewScientist article, it is a very nice summary of the recent work on flagella. The Panda’s crew does not condone copyright violation though.

AHHRGGG, of course Maxi can’t edit his/her post. My brain does not work at this hour of the night.

Hope the admins pull the full post, even if the author does not object. The copyright is owned by NS and it clearly wants to sell subscriptions. I subscribe to its newsletters even then it would not let me access the full article.

The author’s blog http://psom.blogspot.com/ and our old thread on this http://www.pandasthumb.org/archives[…]evolu_1.html have lots of interesting info without copyright encumbrances.

It is sad to see great news sources like New Scientist and NPR beg for a few dollars and operate on shoe string budgets while peddlers of ignorance seem to be awash in cash. They claim 10% of the income of the adherents, (even though the actual collection is much less).

Lurkers please subscribe to at least one of National Geographic, Scientific American or New Scientist or some such mag. And my fellow Americans, please pledge some money to your local NPR station. Today is, after all, the last full day of the pledge week.

To be honest, I wasn’t sure how NS would feel about a non-profit/educational-type site such as PT using the text, but Ravilyn’s advice above seems on the money. A subscription to NS isn’t that much (just $89), and you get 50-odd glossy issues a year (and, of course, acces to archived content)! Listen to me, I’m turning into a salesman (as the mantra from David Mamet’s superb ‘Gelngarry Glenross’ goes, “ABC: alwasy be closing, ALWAYS BE CLOSING!”).

D.

Hey, I subscribe to the print edition of NS, and I need to register separately to access the web articles. Since I invariably throw away the cover in which the print edition arrives before I remember that I need the code number from it to access the web articles, I’ve given up trying to access the subscription-only web articles of NS.

Hmm, reading back that looks rather clumsy, but I hope it is not too hard to parse out the intended meaning.

I would like to apologise for my thoughtless copyright infringement. I was trying to be helpful but I see now what damage I have caused.

I would glady erase it myself, but cannot.

I do subscribe to New Scientist, and would recommend it to everyone!

I expect maxi’s post to be changed as soon as someone* wakes up.

I subscribe to the print edition of NS, and I need to register separately to access the web articles.

That seems odd. Last night I took out a subscription to the print edition (Can$72 plus a few dollars for the mail) and was immediately able to access the article. While browsing I came across a good idea for a ketchup sachet submarine to show my basic science class (taken from a book with the title ‘How to fossilize your hamster’).

The sentence “The study of complex molecular systems has been given added impetus by the “intelligent design” (ID) movement - the intellectual heirs of Paley.” should more correctly end “…the anti-intellectual heirs of Paley.”

Richard Simons:

I subscribe to the print edition of NS, and I need to register separately to access the web articles.

That seems odd. Last night I took out a subscription to the print edition (Can$72 plus a few dollars for the mail) and was immediately able to access the article. While browsing I came across a good idea for a ketchup sachet submarine to show my basic science class (taken from a book with the title ‘How to fossilize your hamster’).

Hey, I think I’m being “done”. A UK subscription to this UK-based magazine seems to be more than the US or Canadian price (over £100 [=US$200 approx.] for a year’s supply)!

I think all I need to do to access the web-based content is to enter the code number that is on the cover in which my print edition arrives. So, I don’t need to pay any extra, I just need to remember to keep the cover of my hardcopy.

For all the ID proponents

This should save time and energy when reading and digesting the posted article from the New Scientist. All quote mined with 6 words added.

“In an oft-quoted passage from On the Origin of Species, Charles Darwin wrote: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.””

“Biologists have been interested in the bacterial flagellum for decades, not least because it is a prime example of a complex molecular system - an intricate nanomachine beyond the craft of any human engineer.” “With its intricate arrangement of interconnecting parts, the flagellum looks no less designed than a watch, and would surely have had Paley reaching for the existence of its “maker”.” “The bacterial flagellum is one of the most complex and elegant pieces of biological machinery known.” “It is the bacterial world’s outboard motor, rotating at high speeds to propel bacteria through their watery environments.”

““It’s very difficult to work out the evolution of a complex system when you don’t understand how the system works.” “In the absence of this knowledge, biologists all too often fell back on the assertion that “bacterial flagella evolved and that is that”, according to Mark Pallen, a microbiologist at the University of Birmingham in the UK.”

To counteract this “[t]he study of complex molecular systems has been given added impetus by the “intelligent design” (ID) movement - the intellectual heirs of Paley.” In the case of the flagellum, “each of its interacting components is essential for the system to function, and if you remove any one of them the whole thing grinds to a halt.” “[B]ecause of this irreducible complexity, such systems cannot be explained by the stepwise process of natural selection and therefore must be the handiwork of an “intelligent designer”.”

Delta Pi Gamma (Scientia et Fermentum)

I wrote the above article, and while I’m not sure how the folks at New Scientist will feel if they see the text being pasted here, I’m glad PT readers have a chance to read the article - although you don’t get to see the nice pictures and graphics that the NS art team put together for the piece!

Dan, find out the NS policy on self-archiving your publications. If they are one of the many scientific publishers that allow it, you can make the article downloadable from your blog and post the link here.

It is sad to see great news sources like New Scientist and NPR beg for a few dollars and operate on shoe string budgets while peddlers of ignorance seem to be awash in cash

NS isn’t a non-profit like NPR.

If they are one of the many scientific publishers that allow it, you can make the article downloadable from your blog and post the link here.

Nor are they a “scientific publisher” as I understand the term (i.e. a publisher of journals).

It’s a popsci weekly with a mix of science articles of interest to the layperson or non-specialist and science news coverage.

Anyway, the full copy of the article should be summarized or deleted, they’re entitled to the money they charge to access it.

Dan, Very nice article - thanks. I’d like to ask you a question about it. Behe’s flagship claim is of course that the flagellum was intelligently designed. I’d have expected to see a reaction from him about this latest research. Did you in fact approach him for a comment? If so, did he respond at all?

Good article, but sadly, even if creationists/idists read it closely, they will mine a few bits to COUNTER the article’s argument.

I’d see this being quote-mined:

“Most researchers think the best options are flagellum-first or parallel evolution. One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. “The most parsimonious explanation is that the T3SS arose later,” says biochemist Howard Ochman at the University of Arizona in Tucson.”

Right before this paragraph, you’re using the example of T3SS as flagellum-proteins being used in non-flagellum ways to show how an example of functioning “partial-flagellum”, but this paragraph shows scientists tend to favour the idea (in THIS case) of flagellum coming first. You know the IDiots would jump on it in this way: “scientists say there exists functioning partial-flagellum, but they also say the FULL functioning flagellum had to come first”. That’s what I’d expect from an IDiot who actually reads the article.

I’ve removed the comment that had the full article.

Great article Dan, but what I’d really like to see is how the IDists react to it. I love to read their squirming semantics. If anyone has any good links to ID ‘refutations’ please post! Here is my prediction - continued research will make it impossible for them to use the flagellum as an argument. A new, more covert, movement will be initiated in which the ID/creationist ‘scientists’ keep their theological motivation hidden. There will be no ‘Wedge’ document error next time. Look forward to a more devious and cunning breed disguised as atheists!

Reed A. Cartwright:

I’ve removed the comment that had the full article.

Some web sites bring up a Delete box, just for the poster. This way each person (or robot) can delete their own comments, if desired.

Drats! My library subscribes through some sort of service, but there is a one month delay for electronic access.

Hasn’t this whole T3SS thing been answered ages ago by the ID people? See:

http://www.discovery.org/scripts/vi[…]&id=1364

What would be said to that?

Such similarities…are strong evidence that the two systems evolved from a common ancestor.

I am setting a goal of studying more about how biologists go from noting coincidences to glibly asserting common descent.

Without knowing enough of the details, such assertions seem odd, and very much akin to the specious assertion that this program (wave.c) and this program (bubble sort) are obviously descendants of this program (hello world) simply because they all contain the same “extra operator error” in the sequences ‘/*’ and ‘*/’ instead of just a ‘/’ or a ‘*’.

@ PvM:

A sequence of nucleotides produced by random mutations will have zero shannon information,

No, it will maximize the information if it is the channel.

But Dawkins point is that it doesn’t need to be, it can be seen as the observer and it is moreover natural to do so. The sender is the environment, the channel becomes generational replication (pre- and post probabilities of alleles), and variation/selection is functions operating on the channel.

The information learned is how to survive, i.e. which alleles contribute to (most replicative) survival.

Other definitions of observer, channel, et cetera is possible, which I believe happens when explaining information increase in gene duplication.

@ Jim:

Empirical testing has been at the heart of my comments about the problem of induction.

It isn’t, as testing circumvents your imaginary problem by rejecting false theories. Your objection that falsification no longer applies is contradictory to your claim on Popper. Your back must hurt by this much goalpost moving.

“Reasonable doubt” is a legal concept, not a scientific concept.

It is a description of what the quantified certainty means in context. And you try to slip in absolute truth into science about facts. More goalpost moving, and to no avail - you aren’t describing science but dogmatic fantasy.

And we know how the immune system could have evolved, beyond reasonable doubt.

resort to condescension

I just stated what is obvious to us all, you don’t know first thing about what you are discussing. You discuss much apologetics but no science.

If you are through, fine. Too bad you don’t want to admit to your’s and Behe’s failures.

@ Jim:

that doesn’t make information a material phenomenon.

Don’t make the mistake of thinking that a relative measure (relative to the system, including which observer you use) isn’t measurable on an appropriate phenomenon.

Now, i would argue instead that evolution isn’t an appropriate phenomenon, as it is the traits allele frequencies that population genetics treats and their function that we are interested in. The information as measured by Shannon information overlaps completely so doesn’t confer any new knowledge on the system.

Big Bang theory is another theory with obvious theistic implications. If Judge Jones were asked to decide the scientific legitimacy of Big Bang theory, consistency in reasoning would require him to declare the theory to be religion, not science.

You are confusing the findings of objective science with the subjective dogma of your particular religion. Besides, the process and its current concordance theory are plenty verified (beyond reasonable doubt in fact), now latest with the WMAP 5 year data release.

it implies a cause of the Big Bang that is external to nature (or supernatural).

As evolution, the verification of the big bang expansion phenomena and its theories aren’t depending on deriving the initial state (abiogenesis vs quantum gravity). Remember, we rely on predictions and falsification, not assumptions.

Oh, and sorry about your headache. Your creationist indoctrination makes it impossible to learn science. My advice is, forget every falsehood you have picked up and go back to early school texts and learn science instead. Not intended as condescending, just an analysis on a science blog of what you need.

halo said: “At any rate, critics of the argument from irreducible complexity look to save Darwinism not by enlisting direct Darwinian pathways to bring about irreducibly complex systems but by enlisting indirect Darwinian pathways to bring them about. In indirect Darwinian pathways, a system evolves not by preserving and enhancing an existing function but by continually transforming its function… How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical. The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known. At best biologists have been able to isolate subsystems of such systems that perform other functions. But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system. [[What’s needed is a seamless Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.]] No such accounts are available or have so far been forthcoming. Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted.”

Behe Wrote (c) 1996, 2006, that,

halo said: “This little story teaches several lessons. First, the word jump can be offered as an explanation of how someone crossed a barrier, but the explanation can range from completely convincing to totally inadequate depending on the details (such as how wide the barrier is). Second, [[long journeys can be made much more plausible if they are explained as a series of smaller jumps rather than one great leap]]. And third, in the absence of smaller jumps, it is very difficult to prove right or wrong someone who asserts that stepping stones existed in the past but have disappeared.”

So Halo, in “[[What’s needed is a [[[seamless]]] Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.]]”, says that Behe is completely wrong in “[[long journeys can be made [[[much more plausible]]] if they are explained as [[[a series of smaller jumps]]] rather than [[[one great leap]]] ]]” because even filling in more gaps (with new potential DNA code flagellum subcomponents being found and used which makes them available for mutatable DNA material) doesn’t reconstruct the seamless mutation history of the now nonexistant past observation data. And even constructing a complete story from evidences and mechanisms in the future, with the best DNA simulation programs of the future, will not provably reconstruct time-history from millions of years ago.

So only a time machine is suitable for Halo, and Behe is plain wrong that smaller steps are “much more plausible”, as Halo only claims a seamless reconstruction of time and DNA history millions of years ago will suffice for the faithlessness of Creationists in all Science.

By the way, since you (Halo) like evidence and concrete things without any faith in an ultimate truth in Science, what do you think is the meaning of the nearly identical DNA chromosomes, architecture, and details between chimpanzees and humans shown in the video? It means something, but what? Mice, amoeba, plants, and bacteria, don’t have DNA chromsomes, architecture, and detail code ordering at all like each other or humans and primates, unlike the similarity found between humans and chimpanzees so well show. Or explanation of methods of complexity arising from complexity arising from simplicty naturally described in my blog, section 3?

http://www.youtube.com/watch?v=oI29OXqLB8M

BLOG: http://lonerubberdragon.blogspot.com/

Sean said:

halo said: “At any rate, critics of the argument from irreducible complexity look to save Darwinism not by enlisting direct Darwinian pathways to bring about irreducibly complex systems but by enlisting indirect Darwinian pathways to bring them about. In indirect Darwinian pathways, a system evolves not by preserving and enhancing an existing function but by continually transforming its function… How does the argument from irreducible complexity handle indirect Darwinian pathways? Here the point at issue is no longer logical but empirical. The fact is that for irreducibly complex biochemical systems, no indirect Darwinian pathways are known. At best biologists have been able to isolate subsystems of such systems that perform other functions. But any reasonably complicated machine always includes subsystems that perform functions distinct from the original machine. So the mere occurrence or identification of subsystems that could perform some function on their own is no evidence for an indirect Darwinian pathway leading to the system. [[What’s needed is a seamless Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.]] No such accounts are available or have so far been forthcoming. Indeed, if such accounts were available, critics of intelligent design would merely need to cite them, and intelligent design would be refuted.”

Behe Wrote (c) 1996, 2006, that,

“This little story teaches several lessons. First, the word jump can be offered as an explanation of how someone crossed a barrier, but the explanation can range from completely convincing to totally inadequate depending on the details (such as how wide the barrier is). Second, [[long journeys can be made much more plausible if they are explained as a series of smaller jumps rather than one great leap]]. And third, in the absence of smaller jumps, it is very difficult to prove right or wrong someone who asserts that stepping stones existed in the past but have disappeared.”

So Halo, in “[[What’s needed is a [[[seamless]]] Darwinian account that’s both detailed and testable of how subsystems undergoing coevolution could gradually transform into an irreducibly complex system.]]”, says that Behe is completely wrong in “[[long journeys can be made [[[much more plausible]]] if they are explained as [[[a series of smaller jumps]]] rather than [[[one great leap]]] ]]” because even filling in more gaps (with new potential DNA code flagellum subcomponents being found and used which makes them available for mutatable DNA material) doesn’t reconstruct the seamless mutation history of the now nonexistant past observation data. And even constructing a complete story from evidences and mechanisms in the future, with the best DNA simulation programs of the future, will not provably reconstruct time-history from millions of years ago.

So only a time machine is suitable for Halo, and Behe is plain wrong that smaller steps are “much more plausible”, as Halo only claims a seamless reconstruction of time and DNA history millions of years ago will suffice for the faithlessness of Creationists in all Science.

By the way, since you (Halo) like evidence and concrete things without any faith in an ultimate truth in Science, what do you think is the meaning of the nearly identical DNA chromosomes, architecture, and details between chimpanzees and humans shown in the video? It means something, but what? Mice, amoeba, plants, and bacteria, don’t have DNA chromsomes, architecture, and detail code ordering at all like each other or humans and primates, unlike the similarity found between humans and chimpanzees so well show. Or explanation of methods of complexity arising from complexity arising from simplicty naturally described in my blog, section 3?

http://www.youtube.com/watch?v=oI29OXqLB8M

BLOG: http://lonerubberdragon.blogspot.com/

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This page contains a single entry by Nick Matzke published on February 14, 2008 7:41 PM.

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