Flagellum evolution in Nature Reviews Microbiology

| 53 Comments | 4 TrackBacks

When I returned from vacation today, I was surprised to discover this new article pop up in my automated searches for flagellum stuff in the literature databases:

Pallen MJ, Matzke NJ. (2006). “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790. October 2006. Advanced Online Publication on September 5, 2006. [PubMed] [Journal] [DOI] [Google Scholar]

In the recent Dover trial, and elsewhere, the ‘Intelligent Design’ movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look.

Matzke NJ? Hey, I know that guy!

I thought that this article was not coming out until October, and I would therefore have a few weeks to prepare some suitable PT posts to update everyone on developments in flagellar evolution since my first effort in 2003 (read this for background), and on the litany of errors and pseudoscience that the ID movement has produced regarding their favorite “Icon of Intelligent Design.” But, the powers that be at Nature Reviews Microbiology have seen fit to release the article as an Advanced Online Publication – and put it on their front page, no less – so it remains a secret no longer. C’est la vie.

There are several large flagellum-related topics I still plan to blog in the near future, but for the moment I would just like to hit one topic: what is The Main Point that PT readers should get out of the article?

The Main Point

A number of issues are discussed in this paper. I won’t belabor most of them (read the paper!), but I do want to make sure one key point is well understood by everyone in the evolution vs. ID/creationism debate – or at least among us skeptics of ID, since the ID/creationists probably won’t listen.

Referring to the Kitzmiller case, we note in Box 2: Of forelimbs and flagella,

ID advocates say that their position is supported by discontinuities between the flagellum and the rest of the biological world, just as a designed entity like a watch differs from an undesigned entity, such as a stone. In support of this line of reasoning, Scott Minnich in his expert witness report claimed that “the other thirty proteins in the flagellar motor (that are not present in the type III secretion system) are unique to the motor and are not found in any other living system.” As our discussion shows, this is not true. Instead, we have detected sequence homologies linking flagellar components to the rest of the biological universe (Table 1).

(Pallen and Matzke 2006, “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology advance online publication 5 September 2006.)

Below, I will show that Minnich’s claim has been repeated by many other leading ID advocates, and that they have all got their basic facts badly wrong.

What ID advocates have claimed

First, let’s look at what the IDists have written while arguing against the evolution of the flagellum:

It follows that the TTSS does not explain the evolution of the flagellum (despite the handwaving of Aizawa 2001). Nor, for that matter, does the bacterial flagellum explain in any meaningful sense the evolution of the TTSS. The TTSS is after all much simpler than the flagellum. The TTSS contains ten or so proteins that are homologous to proteins in the flagellum. The flagellum requires an additional thirty or forty proteins, which are unique.

William A. Dembski (2003). “Still Spinning Just Fine: A Response to Ken Miller.” DesignInference.com. February 17, 2003.

With the bacterial flagellum, you’re talking about a machine that’s got 40 structural parts. Yes, we find 10 of them are involved in another molecular machine, but the other 30 are unique! So where are you going to borrow them from? Eventually you’re going to have to account for the function of every single part as originally having some other purpose. So you can only follow that argument so far until you run into the problem of you’re borrowing parts from nothing.

Scott Minnich (2003), in the video Unlocking the Mystery of Life, online at The Apologia Project.

Miller’s scenario faces at least key three difficulties. First, the other thirty or so proteins in the flagellar motor are unique to it and are not found in any other living system. From where,then, were these protein parts co-opted?

Stephen C. Meyer (2004). “Verdict on the Bacterial Flagellum Premature: A Response to Begley’s ‘Evolution Critics Come Under Fire…’ in the Wall Street Journal.” Discovery Institute website, February 19, 2004.

Additionally, the other thirty proteins in the flagellar motor (that are not present in the TTSS) are unique to the motor and are not found in any other living system. From whence, then, were these protein parts co-opted?

Minnich (2005) expert report, March 31, 2005 / Scott A. Minnich & Stephen C. Meyer (2004). “Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria.” Second International Conference on Design & Nature, Rhodes Greece. Wessex Institute of Technology, September 1, 2004.

With regards to the flagellum at least 2/3 of the parts are not known to be shared with any other structure therefore might not be even a sub-part of another system at all.

Casey Luskin (2006). “Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones’s Straw Tests of Irreducible Complexity for the Bacterial Flagellum.” Evolution News & Views. April 19, 2006.

Summary: All the IDists think that 3/4 of the flagellum proteins are “unique”, i.e. do not share homologies with other proteins. All they are aware of is the homologies to T3SS, which they usually mention while rebutting Kenneth Miller. Casey Luskin, a late example, cuts the number to 2/3, probably because he is dimly aware that there are some other homologous proteins out there, perhaps because several of us ID skeptics have been mentioning this point repeatedly for several years.

The facts

What’s the truth? Have a look at Table 1 of Pallen and Matzke 2006:

Table 1: Homologies of flagellar proteins
ProteinLocationFunctionIndispensable?Homologies*Refs

* Homologies (as evidenced by expected values <1e05) can be confirmed by retrieving the relevant flagellar protein sequences for Escherichia coli K-12 or Salmonella enterica Typhimurium LT2 and carrying out the following:

||performing a BLASTp search at the NCBI site under default conditions.

performing multiple PSI-BLAST iterations at the NCBI site under default conditions;

§performing multiple iterations of PSI–BLAST at the NCBI site under default conditions, except for adjusting the threshold for inclusion to 0.05 and restricting the taxonomic scope to Enterobacteriaceae, starting with the protein sequences for FlgB, FlgL;

These similarities fail to achieve unequivocal significance using BLAST/PSI–BLAST under any of the above conditions, but are supported by other structural or functional considerations. T3SS, type III secretion system.

FlgAP ringChaperone?Absent from Gram-positive bacteriaCpaB25, 29
FlgBCFGRodTransmission shaftYesFlgBCEFGK§25
FlgDHookHook capYesNone yet known25
FlgEHookUniversal jointYesFlgBCEFGK§25
FlgHL ringBushingAbsent from Gram-positive bacteriaNone yet known25
FlgIP ringBushingAbsent from Gram-positive bacteriaNone yet known25
FlgJRodRod cap; muramidaseFlgJ N-terminal domain absent from some systemsNone yet known25
FlgKHook–filament junctionHook-associated protein 1YesFlgBCEFGK§25
FlgLHook–filament junctionHook-associated protein 3YesFliC§25
FlgMCytoplasm and exteriorAnti-sigma factorAbsent from CaulobacterNone yet known25
FlgNCytoplasmChaperoneUndetectable in some systemsNone yet known25
FlhAT3SS apparatusProtein exportYesLcrD/YscV||25
FlhBT3SS apparatusProtein exportYesYscU||25
FlhDCCytoplasmTranscriptional regulatorAbsent from many systemsOther activators25
FlhEUnknownUnknownMutant retains full motilityNone yet known25
FliACytoplasmsigma factorAbsent from CaulobacterRpoD, RpoH, RpoS||25
FliBCytoplasmN-methylaseAbsent from Escherichia coliNone yet known25
FliCFilamentFlagellinYesFlgL§, EspA25, 78
FliDFilamentFilament cap; hook-associated protein 2Absent from CaulobacterNone yet known25
FliERod/basal bodyMS ring–rod junctionYesNone yet known25
FliFT3SS apparatusProtein exportYesYscJ§25
FliGPeripheralMotorYesMgtE25
FliHT3SS apparatusRegulates FliIMutant retains some motilityYscL*, AtpFH38, 79
FliIT3SS apparatusATPase for protein exportYesYscN||, AtpD||, Rho||38
FliJCytoplasmChaperoneUndetectable in some systemsYscO25
FliKHook/basal bodyControls hook lengthYesYscP25
FliLBasal bodyUnknownMutant retains full motilityNone yet known80
FliMT3SS apparatusProtein exportYesFliN, YscQ25
FliNT3SS apparatusProtein exportYesFliM, YscQ25
FliOT3SS apparatusProtein exportUndetectable in some systemsNone yet known25
FliPT3SS apparatusProtein exportYesYscR||25
FliQT3SS apparatusProtein exportYesYscS||25
FliRT3SS apparatusProtein exportYesYscT||25
FliSCytoplasmFliC chaperoneAbsent from CaulobacterNone yet known25
FliTCytoplasmFliD chaperoneAbsent from many systemsNone yet known25
FliZCytoplasmRegulatorAbsent from many systemsNone yet known25
MotAInner membraneMotorYesExbB, TolQ25
MotBInner membraneMotorYesExbD, TolR, OmpA25

OK, let’s do the math.*

Total number of proteins listed: 42

(this table excludes the chemotaxis proteins; there are ~10 chemotaxis proteins in standard E. coli, but the number can range from 0 to 10+ in various bacteria)

Total number thought to be indispensable in modern flagella: 23 (55%)

Total number “unique” (no known homologs): 15 (36%)

Total number of indispensable proteins that are also “unique”: 2 (5%)

The implications

Here are some of the various implications of these findings:

1. Scott Minnich, the leading flagellum expert in the ID camp, was severely wrong about the most basic data relevant to the origins of the flagellum, the flagship system of the ID movement.

2. Minnich promoted his mistaken view in the video Unlocking the Mystery of Life, which has been widely promoted by ID advocates across the country, viewed in countless church basements, IDEA club meetings, etc.

3. Stephen Meyer, the Program Director of the Center for the Renewal of Science and Culture at the Discovery Institute, was severely wrong about the most basic data relevant to the origins of the flagellum, the flagship system of the ID movement.

4. The paper by Minnich and Meyer repeated this error, and if the paper was “peer-reviewed” at all, it was not by people who knew anything about the most basic data relevant to the origins of the flagellum.

5. The error propagated further in Minnich’s expert report.

6. William Dembski, who put the flagellum on the cover of his book No Free Lunch, uses the flagellum in all his talks, and makes it the key example in his only wild attempt to actually “do the calculation” of the probability of the natural origin of a complex biological system, was severely wrong about the most basic data relevant to the origins of the flagellum, the flagship system of the ID movement.

7. Discovery Institute spokesman Casey Luskin, although slightly less wrong than everyone else, was severely wrong about the most basic data relevant to the origins of the flagellum, the flagship system of the ID movement, even in an essay where he criticized Kenneth Miller and Judge Jones for getting the flagellum stuff wrong in the Kitzmiller case.

(And, I personally observed Casey Luskin promulgating this exact mistaken talking point to a gaggle of press at the Kitzmiller trial. I corrected him publicly right then (I think I said, “Just so you know, everything he said just then is totally wrong”), but to no avail.)

8. Casey Luskin’s helpers, “Alex Binz, David Klinghoffer, and an un-named biochemist in the University of California system” were also unable to catch the basic error.

9. None of the above folks ever bothered to go to the library and check their basic facts.

10. Heck, none of these guys bothered to get on the web and check their basic facts.

11. No one else in the ID movement, either leaders or fans, ever bothered to check their facts and correct these guys publicly or privately.

12. Apparently, everyone in the ID movement just mindlessly copies everyone else’s talking points.

13. None of these folks have a friggin’ clue what they are blathering about when it comes to flagellum evolution.

That about covers it, I think. Comments are welcome, as are further examples of this error in the ID literature.

PS: Yes, I am aware that several of the above ID articles contain various Emergency Backup Arguments that say something like “Even if all of the flagellum proteins had homologs, the flagellum still couldn’t evolve because of X.” I will address these in more detail later, but all of these arguments are clearly weaker than the “unique parts” argument. E.g., the most common Emergency Backup Argument is that evolving the necessary regulation is impossible even if the structural proteins are available. However, Table 1 shows that none of the regulatory proteins are universally conserved across flagella (unless you count FliK – but FliK has a homolog in nonflagellar T3SS).

* Note: the math has been fixed in edit. That’s what I get for posting in the middle of the night.

** Note: This version of the table is slightly different than the published one, which has some blank cells that should read “None yet known.”

[updated the AOP links to permanent links]

4 TrackBacks

Nick Matzke at Panda’s Thumb, what evidence is there that the type III secretion system appeared in nature before the flagellum? If the flagellum coopted the ttss then the ttss must predate the flagellum. The ttss mediates elaborate interactions... Read More

Whipping the Flagellum in the Quote-Mine Read More

Over on the hopefully-named “ID the Future” podcast website run by the Discovery Institute, Casey Luskin has posted a short interview with Michael Behe – evidently recorded in-studio rather than over the phone, although, for some rea... Read More

This just in. Current Biology has published a short dispatch piece reviewing the flagellum evolution issue: W. Ford Doolittle and Olga Zhaxybayeva (2007). “Reducible Complexity - The Case for Bacterial Flagella.” Current Biology, 17(13), R... Read More

53 Comments

From the table, I count 15 proteins with no known homologies, 2 of which are indispensable. What’s with that?

Great job, Nick. I wonder whether the “30 unique proteins” canard is going to find its way in the new edition of “Of Pandas and People”, that Dembski & C are supposed to be putting out shortly. That would be sweet.

I’ve just had a quick scan of the paper. Looks like being a good read. In the meantime (and I thought this was as good a place as any to put it) the following paper in today’s Nature is well worth a glance:

Keightley, P.D. and Otto, S.P. (2006) Interference among deleterious mutations favours sex and recombination in finite populations. Nature, 443, 89-92.

Sex and recombination are widespread, but explaining these phenomena has been one of the most difficult problems in evolutionary biology. Recombination is advantageous when different individuals in a population carry different advantageous alleles. By bringing together advantageous alleles onto the same chromosome, recombination speeds up the process of adaptation and opposes the fixation of harmful mutations by means of Muller’s ratchet. Nevertheless, adaptive substitutions favour sex and recombination only if the rate of adaptive mutation is high, and Muller’s ratchet operates only in small or asexual populations. Here, by tracking the fate of modifier alleles that alter the frequency of sex and recombination, we show that background selection against deleterious mutant alleles provides a stochastic advantage to sex and recombination that increases with population size. The advantage arises because, with low levels of recombination, selection at other loci severely reduces the effective population size and genetic variance in fitness at a focal locus (the Hill—Robertson effect), making a population less able to respond to selection and to rid itself of deleterious mutations. Sex and recombination reveal the hidden genetic variance in fitness by combining chromosomes of intermediate fitness to create chromosomes that are relatively free of (or are loaded with) deleterious mutations. This increase in genetic variance within finite populations improves the response to selection and generates a substantial advantage to sex and recombination that is fairly insensitive to the form of epistatic interactions between deleterious alleles. The mechanism supported by our results offers a robust and broadly applicable explanation for the evolutionary advantage of recombination and can explain the spread of costly sex.

One thought (and it may be a nitpick) about the abstract. I’m not entirely convinced by this sentence:

“Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities”

It seems to me that this is a little generous towards the ID crowd, implicitly crediting them with having an actual working scientific hypothesis for the origin of the bacterial flagella.

Am I just being pedantic?

SteveF Wrote:

Am I just being pedantic?

Not as pedantic as I’m about to be.

Nick, did you mean you’re not going to labor most of the issues in the paper, or did you really mean you’re not going to belabor (or violently beat) them?

Oh, darn it. I just looked it up and it means both. Now I look like an idiot.

From one pedant to another, belabor is prefectly acceptable in this context:

“to explain, worry about, or work at (something) repeatedly or more than is necessary: He kept belaboring the point long after we had agreed.”

Nick,

Your table lists two proteins (FlgD and FliE) that are indispensible but have no known homologies, not one as you say below the table. This doesn’t affect your main points, of course.

By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.”

–Michael Behe, Darwin’s Black Box.

the editor must have cut off the rest: “unless the part is FlgA, FlgH, FlgI, FlgJ, FlgM, FlgN, FlhDC, FlhE, FliA, FliB, FliD, FliH, FliJ, FliL, FliO, FliS, FliT, or FliZ. They don’t count. Just because.”

If you want to wade through this stupidity, Mike Gene makes some of his own claims about the flagellum. for instance

The flagellar motor is composed of five proteins: MotA, MotB, FliG, FliN, and FliM. We’ll discuss this more below, but right now it is worth pointing out that the type III systems have no homologs for MotA, MotB, or FliM.

no homologs for FliM? Let’s go to the board! Survey saaayyyys–

*ding*

FliM T3SS apparatus Protein export Yes FliN‡, YscQ‡

Oooo, thanks for playing. Here’s a DVD copy of The Dover Affair, featuring Denzel Washington as Nick Matzke, and Steve Buscemi as William Dembski. They would have gone with Peter Lorre, but he’s dead.

I agree with Corkscrew, if you count “None” (FliO) as equal to “None Yet Known” then you’ve got 15, 2 (FlgB, FliE) that are indispensable.

What stands out more to my eye is the obvious correlation of “Absent” and “None”. Can anyone elucidate that?

Congratulations Nick, you worked long and hard on that paper.

Could it be that real scientists are doing the work of the ID crowd for them? Of course not, because we are actually, bit by bit, clawing away at the “we don’t know at the moment = we can never know (and don’t want to know)” hypothesis. I wonder, though, to what extent ID is useful (god I hated writing that) in that it provides fruitful new areas of investigation? Might this kind of thing lead to real breakthroughs of the cure for X variety? What do you think Nick? Presumably as a scientist you aren’t wasting your time proving them wrong. And where do you go from here? Great work. But you’re right, they won’t listen.

Not being an expert in these matters, I don’t know much you relaxed the defaults to arrive at some of the homologies. I’m sure a rebuttal of this data will observe that only using the defaults flips the ratios around completely.

Does the paper explain the extent and significance of the variation from the defaults and why using the defaults was inappropriate? If the same criteria were applied to the other proteins in the table what would be the results? Especially the homologies identified by paragraph marks - from the brief explanation it sounds like these homologies are identified with extremely subjective criteria.

With all the pounding on ID advocates to define their terms and stick to a consistent definition, I can’t say I’m happy about a table that conflates four different meaning of the word homology in order to make its point. I’m very open to hearing from Nick or any other expert on using BLAST that this conflation is acceptable and standard procedure when counting homologies. As a non-expert however, that doesn’t jump out at me as true.

Thanks for the comments – making various edits. Apologies for counting errors, that’s what I get for posting in the middle of the night.

Great job. I’ve cited your argument on flagellum evolution often. I’ll be sure to update my links to the peer article.

Scott Minnich, the leading flagellum expert in the ID camp, was severely wrong about the most basic data relevant to the origins of the flagellum, the flagship system of the ID movement.

I’d suggest that’s the smallest thing about which he is severely wrong.

Hmm, I thought the issue discussed in the Keightley and Otto paper had been resolved a while back. Long-term effects like deterioration aren’t enough to overcome the twofold reproductive advantage of asexual species - the sexual species would get overrun before the problems became apparent. However, parasitism and disease, adapting as they do to target individual organisms, are able to do substantially more damage to identical children than to children produced sexually.

That’s the version I heard anyway, obviously I bow to the superior experience of anyone with actual scientific qualifications.

Regarding BLASTing on non-default settings: not really. Of the four categories, the first three are completely standard techniques and the homologies are well-accepted. Of the 28 homologies I counted just now (including a dual homology), only five are based on “structural/other” criteria, and even so several of those are well-accepted.

Homology by technique:

BLASTP defaults: 7 PSI-BLAST defaults: 7 PSI-BLAST slightly relaxed: 9 Structural/other: 5

The PT server appears to be overloaded at the moment, so I am having trouble logging in to do edits. For the record, the correct counts are 15 and 2 for “unique” and “unique + inessential.”

PS: Yes, I am aware that several of the above ID articles contain various Emergency Backup Arguments that say something like “Even if all of the flagellum proteins had homologs, the flagellum still couldn’t evolve because of X.”

Didn’t take them long, according to the trackback below. Apparently the X for today is “Maybe the proteins weren’t around before the flagellum, huh, did you think of that?”

September 7, 2006 Flagellum Evolution

Nick Matzke at Panda’s Thumb, what evidence is there that the type III secretion system appeared in nature before the flagellum? If the flagellum coopted the ttss then the ttss must predate the flagellum. The ttss mediates elaborate interactions with plant and animal hosts of the bacteria. The flagellum on the other hand is for locomotion, not parasitic or pathogenic relationships with more complex cells. The flagellum is useful absent more complex organisms in the environment while the ttss is not. It seems to me quite likely that the flagellum appeared in nature before the ttss. Probably billions of years before as the following supports:

I guess that sounds a lot better than “We repeated a bunch of untruths about the homologies, and Nick nailed us.”

More than factual details of your study, what is important here is that you have shown what good science does - it takes an unknown and chips away at it looking for answers. Since IDers can’t prove that something is irreducibly complex in principle, their claims rely on the fact that we don’t know everything there is to know. ID depends on science not going forward.

Good job taking away one of their icons. Of course, they’ll just find another dozen things we don’t know everything about and claim they’re irreducibly complex…

One thought (and it may be a nitpick) about the abstract. I’m not entirely convinced by this sentence:

“Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities”

It seems to me that this is a little generous towards the ID crowd, implicitly crediting them with having an actual working scientific hypothesis for the origin of the bacterial flagella.

Am I just being pedantic?

I had minor qualms about this also, because I do think that “ID did it” is untestable, and therefore it is not really a scientific alternative to evolution that one can directly argue against. At most, one can show that ID is unparsimonious and unnecessary, but this is not a falsification. What can be tested is specific claims about evolution, because evolution is testable and empirical claims like “flagellum evolution is impossible because the parts have no nonflagellar homologs” are readily testable.

But I am neither the editor nor the senior author ;-). Correctly, I think, clarity for a general scientific audience won out over philosophical exactitude for creationism nerds.

So yes, you’re being pedantic, but I was too.

AnthonyK Wrote:

I wonder, though, to what extent ID is useful (god I hated writing that) in that it provides fruitful new areas of investigation? Might this kind of thing lead to real breakthroughs of the cure for X variety?

ID isn’t useful at all. I don’t believe for a second that anything discovered in rebuking ID wouldn’t have been discovered anyway. It’s not like scientists are motivated by a desire to debunk ID. They’re motivated by a desire to do science; ID simply serves as a distraction that must be repulsed. The only thing ID can be said to accomplish scientifically is changing the focus (very slightly, I expect) of ongoing research from areas likely to produce innovations to other areas. These other areas are, in my opinion, less likely to produce useful innovation because if they seemed useful, scientists would be pursuing them already and wouldn’t need ID to shift the focus.

At best, the areas distracted to aren’t going to be more fruitful than the ones distracted from, so it’s either a losing game or one that breaks even.

Didn’t take them long, according to the trackback below. Apparently the X for today is “Maybe the proteins weren’t around before the flagellum, huh, did you think of that?”

September 7, 2006 Flagellum Evolution Nick Matzke at Panda’s Thumb, what evidence is there that the type III secretion system appeared in nature before the flagellum? If the flagellum coopted the ttss then the ttss must predate the flagellum. The ttss mediates elaborate interactions with plant and animal hosts of the bacteria. The flagellum on the other hand is for locomotion, not parasitic or pathogenic relationships with more complex cells. The flagellum is useful absent more complex organisms in the environment while the ttss is not. It seems to me quite likely that the flagellum appeared in nature before the ttss. Probably billions of years before as the following supports:

I have a post planned on exactly this question. The gene trees in the Nguyen et al. 2000 paper quoted by DaveScot there actually support the “sister groups” hypothesis rather than the “flagellum first” hypothesis. Nguyen et al. 2000 concluded “flagellum first” based on other data.

Despite the fact that the ID guys almost always cite articles from only one side of this scientific debate (Nguyen et al. 2000 and Saier 2004 are the most common), the truth is that the question is unresolved and scientists go both ways. I will blog this in more detail at some point, but this paragraph in the Pallen and Matzke paper sums up the current situation:

At least nine core flagellar proteins share common ancestry with core components of NF T3SSs. However, the scientific community is divided on the nature of their common ancestor. Some have argued that the NF T3SS was derived from the flagellum, based on the eukaryote-specific function of known NF T3SS, and the apparently limited distribution of known NF T3SSs relative to the broad phylogenetic distribution of flagella [34]. We, and others, have argued that the two systems are sister groups, as indicated by gene phylogenies and arguments based on parsimony, diverging through ‘descent with modification’ from a common, but simpler, ancestral secretion system [35, 36]. Regardless of the conclusion of this debate, the existence of NF T3SSs is ‘proof of concept’ that a flagellar subsystem can function for purposes other than motility.

[…]

34. Nguyen, L. , Paulsen, I. T. , Tchieu, J. , Hueck, C. J. & Saier, M. H. Jr. Phylogenetic analyses of the constituents of Type III protein secretion systems. J. Mol. Microbiol. Biotechnol. 2, 125—144 (2000).

35. Pallen, M. J. , Beatson, S. A. & Bailey, C. M. Bioinformatics, genomics and evolution of non-flagellar type-III secretion systems: a Darwinian perspective. FEMS Microbiol. Rev. 29, 201—229 (2005).

36. Gophna, U. , Ron, E. Z. & Graur, D. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312, 151—163 (2003).

Back in 2003 I was about 55-45 for the idea that the flagellum came first, but Pallen’s parsimony argument and a few additional small points have moved me about 60-40 for the sister groups idea. There are several specific lines of investigation that could clear this up immensely.

If DaveScot had only read the paper first…but clearly he did not. Seems to be a pattern, I must say.

The SpringerBot is, in his own words, an “autodidact.” If he wants to know what’s in the paper, he’ll tell YOU what’s in the paper.

this is another example of how I.D. is actually anti-science. While they are certainly imaginative in their questions (a very good thing!!) They are imaginative for the purpose of trying to find a question so difficult and so complex that they feel it can’t be answered. To them, unanswered questions are the ultimate goal, since it creates a safe haven for their “supernatural” answers. Finding a good difficult question is the last step in their “research” and it closes the door for them. (ie “how could the flagellum have evolved step by step?)

Science on the other hand has another reason to be imaginative in finding difficult and hard questions. Science is more about finding the correct question than the correct answer, because in science questions aren’t used to shut doors, but to open new doors. In this regard, it’s good to have the I.Dists around because sometimes they can offer up some imaginative questions that might not have been asked otherwise. Someone already mentioned this, but it looks to me like a lot of flagellum research is being done these days and I think at least a small part of that was influenced by the ID throwing down the challenge. (of course that’s just a guess)

Fross:

They [IDers] are imaginative [only] for the purpose of trying to find a question so difficult and so complex that they feel it can’t be answered. To them, unanswered questions are the ultimate goal, since it creates a safe haven for their “supernatural” answers. Finding a good difficult question is the last step in their “research” and it closes the door for them.

A good point, well-articulated.

Great post Nick, and congrats on the publication.

I’m sure the IDists will complain that only one side of the story is being given “airtime” in peer-reviewed journals, and that somehow that isn’t “fair”. However, it’s important to note that journals are not required to publish both sides of an argument when one side is based on faulty logic and science. Both sides must maintain a level of scientific rigor to be taken seriously by a journal. It’s obvious that IDists argue by omitting important information or outright lying. They shouldn’t whine that journals are unimpressed by it.

Another thing that’s important to remember is that the bacterial flagellum was chosen as their biochemical mascot specifically because it’s so friggin complex. It’s not as though the flagellum is the cornerstone of all life on earth. I doubt it’s even required for the bacteria that have it. If they really wanted to look for evidence of design, they would focus on those systems that were actually critical to all organisms (DNA replication, transcription, translation, to name a few). It shouldn’t be surprising that the flagellum would give the most difficulty in explaining its origins, that’s why they chose it.

If IC were really a roadblock for evolution, then it would apply equally to the most simple IC systems as well as the most complex. It’s funny that reading Nick’s post, I can see where other IC systems, like the complement system, have already bypassed the major hurdles that the flagellum research is still in the process of passing. For example, the IDists argue that the TTSS evolved from the flagellum and not vice versa. However, in the case of the complement system, we can see the steady accumulation of parts from the most basic complement system in sea urchin to the most complex in mammals. With regards to ICness, there’s no qualitative difference between the complement system and the bacterial flagellum, only quantitative (i.e. number of parts). That the IDists focus so much attention on one system and ignore the others speaks volumes as to the vacuity of their ideas.

Great stuff– I don’t have access to Nature but am looking forward to your forthcoming posts here on the subject.

Something related to this subject which I find very interesting but don’t know all that much about is the existence of variations in the flagellum. I’m told there are variations in structure, and your post here discusses variations in even composition (absent proteins), between the flagella of different organisms. I don’t know the extent of these variations, but it seems to me the mere existence of variations belies the ID model of the flagellum as an ancient, divinely engineered gift likely to have been handed down by God himself; the flagellum apparently continues to mutate, just like any other normal part of a living thing.

It also makes me wonder what else we can conclude from those variations. You discuss here the question of the ancestry of the NF T3SS system (a funny question in itself; why would Intelligent Design lead us to conclude the flagellum came first and the NF T3SS came after? Why couldn’t the designer have bestowed some bacteria with a secretion system, and then it “degraded” into an outbound motor? Is it just because the one is more “useful”?) …but I’m somewhat curious whether anything is known (or can be detected) about the ancestry in whatever variations in the finished flagellum itself exist from organism to organism.

Do there exist any examples of an organism whose bacterial flagellum is “unusual” (mutated) in some way, and this variation is not just the result of random genetic drift but was actually clearly selected for for some reason?

Is there somewhere I could find out more about such things?

Another question, are the flagella found in bacteria the same as the flagella found in complex eukaryotes (for example, sperm cells)?

Thanks.

Coin

It also makes me wonder what else we can conclude from those variations. You discuss here the question of the ancestry of the NF T3SS system (a funny question in itself; why would Intelligent Design lead us to conclude the flagellum came first and the NF T3SS came after? Why couldn’t the designer have bestowed some bacteria with a secretion system, and then it “degraded” into an outbound motor? Is it just because the one is more “useful”?) …but I’m somewhat curious whether anything is known (or can be detected) about the ancestry in whatever variations in the finished flagellum itself exist from organism to organism.

The question about which came first is raised in the 2000 paper by Nguyen et al. that is quoted at the current PD thread. These authors base their conclusion on “phylogenetic clustering”. My interpretation of that term is that they looked at the similarity in the order of how several genes encoding flagellar proteins are arranged in the genomes of several different bacterial species. There is nothing that I know of that the ID folks have contributed to this issue.

Why couldn’t the designer have bestowed some bacteria with a secretion system, and then it “degraded” into an outbound motor?

And we’ll forgive you this time that you used the D-word in this manner in your posting.

It seems we can use the flagellum as a scourge.

“At most, one can show that ID is unparsimonious and unnecessary”

I think one can show more in the particular cases, IC for example.

As TLTB says, one can’t show IC in principle, due to scaffolding et cetera. In fact one can’t in general show which structure or algorithm is the simplest to solve a specific task. If the global simplest solution is an illdefined concept, so is the local simplest (IC) solution.

So IC is illdefined. This forces IDers to specially plead to look for specific examples, and use an argument from ignorance to motivate a doubt.

In particular cases, probably all of them, it seems one can show that ID is unparsimonious, unnecessary, illdefined, nonuniversal, and arguing from ignorance.

The question about which came first is raised in the 2000 paper by Nguyen et al. that is quoted at the current PD thread. These authors base their conclusion on “phylogenetic clustering”.

They think so, do they? Well, clearly that just means they’re elitist, groupthinking academics, out-of-touch with the American public and conspiring to suppress the theory of Intelligent Secretions.

Coin:

They think so, do they? Well, clearly that just means they’re elitist, groupthinking academics, out-of-touch with the American public and conspiring to suppress the theory of Intelligent Secretions.

Good joke, I almost fell for it.

Just in case you are really serious: This work, even if it does not fully agree with its conclusions of Matzke, is a serious analysis of the subject. The only way they are out of touch with the American Public is that they have to use experimental techniques and technical terms that non-scientists should try to learn and understand before forming an opinion. Besides, DaveScot used their conclusions as arguments against the conclusions drawn here.

I wonder, though, to what extent ID is useful (god I hated writing that) in that it provides fruitful new areas of investigation?

None at all.

Serious scientists don’t even KNOW what the ID claims are. Any more than they know what the flat-earther claims are. Serious scientists simply don’t pay any attention to the nutters.

Serious scientists don’t even KNOW what the ID claims are. Any more than they know what the flat-earther claims are. Serious scientists simply don’t pay any attention to the nutters.

Very true. This is why we had to spend some time explaining what the ID guys say.

Our piece is a review piece; essentially none of the original research we review was done with the intent of debunking ID, as far as I know. The review, of course, does have that intent (in part), by showing how the research contradicts the ID claims.

Nick

Anyway, though my halfhearted joke (about which really comes first in ID, the flagellum or the secretion system) was not really intended to garner response, I am legitimately curious about what the record has to say about the phylogeny of whatever variations on the standard bacterial flagellum exist.

Nothing like a little flagellation to start the working day.

Onya Nick.

Well, the folks at the DI Media Complaints Division haven’t gotten the point yet:

And at Uncommon Descent, Dave Scott challenges a forthcoming article by Nick Matzke et. al. on a supposed evolutionary pathway for the bacterial flagellum. Readers might also want to read Stephen Meyer and Scott Minnich’s related paper on the “co-option” argument, “Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria,” as presented to the Second International Conference on Design & Nature, Rhodes Greece.

If I were them, I would try to hide Minnich & Meyer 2004 away in some closet. Not sure if they have even looked at the PT post or the paper – it’s Pallen and Matzke, not Matzke et al. Sigh…

Hi Coin,

Is there somewhere I could find out more about such things?

Most of your questions are discussed pretty thoroughly in the article, particularly diversity in extant flagellar systems. We may be able to convince NRM to put it up for free for purposes of public education or some such. Or if you can get to a university library with a thumb drive they will typically have access to the subscription journals.

Another question, are the flagella found in bacteria the same as the flagella found in complex eukaryotes (for example, sperm cells)?

They are very different. They both stick out of the cell and wiggle in some fashion, that is about the only similarity. Kind of like bird wings and insect wings. See Table 3 of the Big Flagellum Essay for a summary of the differences.

“I doubt it’s even required for the bacteria that have it.”

In “Unlocking Life’s Mysteries” they show bacteria lounging around on the bottom of pond since they lack a flagellum.

I pointed out that this was pretty sneaky false propaganda to the ID’ist showing the video since anyone who has ever seen movies of bacteria know that they are pretty much neutrally buoyant. Brownian motion is enough to get them around pretty good.

Thanks, I’ll see about finding a copy of the article then.

They [bacterial vs eukaryote flagellae] are very different. They both stick out of the cell and wiggle in some fashion, that is about the only similarity. Kind of like bird wings and insect wings. See Table 3 of the Big Flagellum Essay for a summary of the differences.

Okay, thanks. One more dumb question: Is the non-homologousness of the bacterial, eukariotic, and archaeal flagellae sufficient to conclude that the three kinds of flagellae would have each developed after the prokaryote/achaea/eukariote split?

Nick Matzke at Panda’s Thumb, what evidence is there that the type III secretion system appeared in nature before the flagellum?

I guess the UD guys haven’t bothered to actually go looking for their own answers, because I found this one in about 30 seconds with Google:

Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events, U. Gophna et al. / Gene 312 (2003) 151—163

Abstract: Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems.

Clue for the IDers: The TTSS “appearing before the flagellum” is not the only scenario that shatters your flawed and oversimplified arguments about the “designed” origins of the flagellum.

A seriously confused comment from chunkdz at Uncommon Descent:

Matzke castigates Luskin for saying that 2/3 of the proteins have no definite homolog. But in his 2003 paper, Matzke claims that 26 out of 40 proteins lack definite homologs. That sounds like about 2/3 to me. From Matzke’s evolution in Brownian Space-

17 have no potential homolog - (Flif, FlhA, FlhB, FliN, and 12 axial proteins) 2 have “little current supporting evidence” of homology - (FlgA and FliG) 8 have suggestive homology (inconclusive) - (FliHJOPQR, FlgI, FlgH)

What’s more, his latest paper claims 15 unique (no homolog) proteins. But many of those are proteins that he previously claimed to have known homologs for. (FlgJMN, FlhE, FliELOSTZ) Has he lost the data, or changed his mind?

Matzke also uses several different levels of criteria for determining homology - from a BLASTP, to a “slightly relaxed” PSI-BLAST, to “structural/other”. “Other” presumably means that Matzke can postulate a homolog without any BLAST or structural data.

What gives? Spearing Luskin for coming to the same conclusion he did 3 years ago? Changing status of homology? Including postulated homology as evidence for actual homology?

I’m no molecular biologist, but something seems fishy here. Cant wait to hear from some actual molecular biologists on this.

Taking the points in order:

Matzke castigates Luskin for saying that 2/3 of the proteins have no definite homolog. But in his 2003 paper, Matzke claims that 26 out of 40 proteins lack definite homologs. That sounds like about 2/3 to me.

You can only get this number from the 2003 paper if you exclude the T3SS (whereas Luskin was including the T3SS to provide the 1/3 of homologous proteins), and count each of the axial proteins separately even though most of them have known common ancestry with each other.

Chunkdz, referring to this section of the Big Flagellum Essay (BFE), writes,

From Matzke’s evolution in Brownian Space-

17 have no potential homolog - (Flif, FlhA, FlhB, FliN, and 12 axial proteins)

Actually, what I was saying back in 2003 was that even if one excludes the 10 homologs provided by T3SS, only 5 flagellar proteins have no potential homolog – FliF, FlhA, FlhB, FliN, and the single common ancestral protein of the 12 axial proteins.

On the 2003 model, the 12 axial proteins were considered to all be descended from a common ancestor. The rod-hook subfamily and the FliC/FlgL subfamily were well-accepted back then. Inclusion of the others was based on weaker similarities and mild extrapolation. The 2006 paper is more conservative and limits itself to the well-accepted subfamilies. (But several of the other axial proteins are shown to be inessential in Table 1)

As discussed in Section 4.1 of the BFE, FliF, FlhA, FlhB, and FliN all do have homologs in T3SS, which I was setting aside in that passage. Pallen and Matzke 2006 notes that there is good evidence for homology between the flagellar axial proteins and the filament proteins of NF-T3SS.

2 have “little current supporting evidence” of homology - (FlgA and FliG)

The FlgA homology is now well-documented, see the 2006 table.

FliG was thought to have a T3SS homolog in 2003, but evidently this was spurious. However, in Table 1 of the 2006 paper Pallen suggests that FliG is homologous to the membrane protein MgtE. This is the only novel homology proposal of the 2006 paper (all of the others are published elsewhere), and the only one that could be considered speculative or unconfirmed. Pallen has assembled several lines of evidence in support of the idea but it has not been published yet.

8 have suggestive homology (inconclusive) - (FliHJOPQR, FlgI, FlgH)

Homology to the F1F0-ATPase has been confirmed for FliH (see ref 38 listed in the table). I am still quite optimistic about FliQ and FliR. My two most speculative suggestions for ATPase homology, FliO and FliP, I would consider wrong.

When you include T3SS homologies, you get FliHJPQR. When you look at inessential proteins, you can check off FliHJO.

FlgI and FlgH (P- and L-ring) are inessential and missing in gram-positive bacteria (and some spirochetes I think). I still think that FlgI and FlgH are related to a secretin and a secretin chaperone, but this is speculative and so left out of the 2006 paper.

What’s more, his latest paper claims 15 unique (no homolog) proteins. But many of those are proteins that he previously claimed to have known homologs for. (FlgJMN, FlhE, FliELOSTZ) Has he lost the data, or changed his mind?

I don’t know where this is coming from. I don’t think I suggested homologs for any of these except for FlgJ (to muramidase and speculatively to other axial cap proteins) and FliE (speculatively to other axial proteins).

FlgMN, FlhE, and FliLOSTZ are all apparently nonuniversal parts dispensable in some systems, so I did not discuss them much in the BFE.

Matzke also uses several different levels of criteria for determining homology - from a BLASTP, to a “slightly relaxed” PSI-BLAST, to “structural/other”. “Other” presumably means that Matzke can postulate a homolog without any BLAST or structural data.

“Other” means detailed functional similarities, as in FliK and YscP, which are doing very similar things in a very similar way, just with little conserved sequence. This homology is well-accepted or at least very commonly suggested. The other homologs in this category are based on structure (e.g. FliC/EspA) or persistent database similarity hits that are just not quite undoubtable yet.

The “structure/other” category is only 5 homologies anyway, 3 of which are overlapped by other homologies in stronger categories.

What gives? Spearing Luskin for coming to the same conclusion he did 3 years ago? Changing status of homology? Including postulated homology as evidence for actual homology?

I’m no molecular biologist, but something seems fishy here. Cant wait to hear from some actual molecular biologists on this.

Your confusion is resulting from inaccurately comparing two very different “counts”:

The relevant bit from Section 4.1 of the 2003 paper: * deliberately set aside T3SS homologies (but mentioned them later) * ignored many regulatory/chaperone proteins (some of which were known to be inessential at the time, and most of which are inessential under table 1 in the 2006 paper) * listed everything from highly speculative homologies (which were labeled as such) to well-confirmed homologies

Whereas, Table 1 in the 2006 paper: * includes the T3SS homologies * includes the inessential proteins * excludes all highly speculative homologies

So these are really two fairly different things that cannot be directly compared.

I admit things would be clearer if I had done a homology table in 2003, but like I said in the OP, it was a first effort.

[updated in edit to fix a mistake I made about FliJ due to poor memory]

One more dumb question: Is the non-homologousness of the bacterial, eukariotic, and archaeal flagellae sufficient to conclude that the three kinds of flagellae would have each developed after the prokaryote/achaea [archaea]/eukariote [eukaryote] split?

Sort of. They are sufficiently different to exclude a flagella-like common ancestor of the three systems. The archaeal and bacterial flagellum could share some very remote ancestry, if their ancestral secretion systems (Type IV and Type III Secretion, respectively) themselves were descended from a common primitive secretion system. This would not surprise me if true, but it is speculation.

The eukaryotic flagellum/cilium is totally different and probably derived from the mitotic apparatus of eukaryotes.

But…

What this implies about the relationships of whole organismal groups (bacteria, archaea, and eukaryotes), this is a complex question. Cladistically speaking, each of these flagella is a complex, apparently derived feature found in one group and not the two others. So this constitutes a data point in favor of the idea that the three groups independently evolved flagellar motility via different means.

However, one data point doesn’t mean much. An alternative scenario proposed by Tom Cavalier-Smith, a very serious fellow, is that:

1. Bacteria are the ancestral group and developed bacteria flagella early but perhaps not before the last common ancestor.

2. Archaea branched off from gram-positive bacteria, lost their bacterial flagella and rapidly modified many other features while adapting to extremophile environments like hyperthermophily. Lacking standard flagella, they evolved new ones from the Type IV secretion system.

3. Archaea, some of which developed simple cytoskeletons and complex membranes as part of the extremophile adaptations, produced eukaryotes when a branch of Archaea returned to mesophilic conditions and, via the ability to live without a rigid cell wall, was able to take up phagocytosis – eating other bacteria by membrane envelopment. Membrane envelopment and lack of a rigid cell wall set off a whole series of changes including increase in size, loss of archaeal flagella, and eukaryotic mitosis which uses the mitotic spindles instead of a cell wall to separate chromosomes. The spindle apparatus, based on microtubules, then served as the basal body for primitive eukaryotic cilia/flagella.

I am agnostic on the scenario, but Cavalier-Smith has been assembling this view for 20 years in a series of very long, very detailed papers. He pretty much was the guy that identified the phylogenetic root of eukaryotes a few years back so he cannot be ignored. Go read articles by Cavalier-Smith for all of this. His most recent synthesis paper is free at Biology Direct, and he gets in his own digs at the flagellum argument in that paper.

Very interesting, thanks.

Bravo! One can see the flagellum myth being nibbled away, or sometimes chomped back, as with this installment, and need only see how long it takes before the ID set simply drop it from their mystery list and jomp to some other antievolutionary icon.

That guy who looks like a Disney-anthropomorphized rat Casey Luskin has a comment about Mr. Matzke.

I just learned about this today—could somebody please remind me where did I say in a currently published essay that 2/3 of flagellar parts lack homologs and what does Nick say in response to Mike Gene’s critique of his homology arguments?

Comment by Casey Luskin — September 7, 2006 @ 7:42 pm

http://www.uncommondescent.com/inde[…]omment-59157

Huh. The quote is from his “lugnuts” article as I referenced in the OP.

Nick,

Does your paper assert this claim made by Mike Gene?

When we look at the type III system its genes are commonly clustered and found on large virulence plasmids. When they are in the chromosome, their GC content is typically lower than the GC content of the surrounding genome. In other words, there is good reason to invoke horizontal transfer to explain type III distribution. In contrast, flagellar genes are usually split into three or more operons, they are not found on plasmids, and their GC content is the same as the surrounding genome. There is no evidence that the flagellum has been spread about by horizontal transfer.

Does your paper assert this claim made by Mike Gene?

Pallen has discussed this in other papers I believe. It is true that T3SS are known to be laterally transferred between bacterial lineages in the proteobacteria phylum (E. coli etc.). However, if one is going to use the lateral gene transfer point to support the hypothesis that NF-T3SS are late and derived from flagella, the important counterpoint is that NF-T3SS are found not just in phylum proteobacteria, but in a whole different phylum, chlamydia. I am not aware of any evidence for lateral transfer of T3S between these two phyla, and without such evidence, then NF-T3SS is at least as old as the common ancestor of these two phyla, which is presumably quite old.

There is no scientific consensus about the phylogenetic relationships of the bacterial phyla, and most of the phyla outside proteobacteria are poorly explored anyway. Flagella much easier to detect than NF-T3SS (presence of flagella can be determined with a mere microscope examination; finding a NF-T3SS requires a genome sequencing project), so I am not even sure that the wider distribution of flagella is telling us much.

I posted this in reply to the Uncommon Descent thread. However, my posts there have generally show up days/weeks later or not at all. Therefore, I am cross-posting it here. Thank you for your indulgence.

Scott wrote… “C’mon folks, why are we even still discussing the rediculous [sic] notion that the flagellum could have come about via Darwinian mechanisms?”

The reason this subject is of interest because it is something scientifically tangible. It provides an opportunity to explore the predictive nature of both ID and evolution. More importantly, debating this topic helps inform and define what is meant by the term “Intelligent Design” by various proponents.

At its core, the flagellum embodies the concept that if it looks designed it probably is. It also presents the challenge/opportunity to evolution proponents to hypothesize how this came about naturally. Why should anyone be surprised when evolution proponents start making predictions about the origin of the flagellum and testing those predictions? In my opinion debating this is both very topical and constructive (as opposed to arguing about who is and isn’t a true Christian).

I read with interest Joseph’s comments (even checked out his blog). This is an example of the positive aspects in discussing this. I can understand the position that the existence of the flagellum isn’t “anti-evolution” but is designed the same way that the earth/moon system is designed. They both came about via natural processes but, if I understand correctly, Joseph and other ID proponents are arguing that it is unlikely, if not impossible, that either came about from “sheer-dumb-luck”.

Unless ID wants to remain a simple variant of a “God in the gaps” argument, its proponents need to encourage discovery and discussion. We should all be eager for “actual molecular biologist[s]” to study and discuss evidence of the natural process that lead to the flagellum. This, of course, might be problematic for those whose real agenda is the promotion of the supernatural.

UPDATE - My post showed up at Uncommon Descent. It looks like things are improving in that regard.

I also wanted to add my appreciation of Nick Matzke’s work. I honestly hope it will lead to positive and constructive discourse on this interesting subject.

I posted some replies to comments at Telic Thoughts.

I have posted a short update to my Big Flagellum Essay from 2003.

I have also added some of the more recent articles to the Flagellum Background page.

About this Entry

This page contains a single entry by Nick Matzke published on September 7, 2006 4:29 AM.

The Politically Incorrect Guide to Darwinism and Intelligent Design Review: ID’s Newspeak was the previous entry in this blog.

The Politically Incorrect Guide to Darwinism and Intelligent Design Review: Honesty Matters (Chapter 5, Part 1) is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.361

Site Meter