Intelligent Design and Transitional Fossils - by Calilasseia.
Let's start with so-called "irreducible complexity", shall we?
First of all, let's dismiss the canard that this was alighted upon by Michael Behe. It wasn't. He simply stole the concept, and tried to present it as a purported "problem" for evolutionary biology. Which becomes hilarious when you realise that the evolutionary biologist Hermann Joseph Müller alighted upon the idea of "irreducibly complex" structures not as a "problem" for evolutionary biology, but as a natural outcome of evolutionary processes. Here's how it works: it's called the Müllerian Two Step.
Step 1: Add a component;
Step 2: Make it necessary.
Indeed, Müller introduced this concept way back in 1918, and did so in the following scientific paper:
Genetic Variability, Twin Hybrids and Constant Hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918)
Here's the relevant quote from pages 465 and 466 of this paper, with the apposite part highlighted in boldface:
This was placed upon a rigorous footing by the 1930s, and evolutionary biologists refer to this in modern parlance using the term bricolage. Thus, Behe's canards were known to be canards by evolutionary biologists since before Behe was born.
Meanwhile, structures such as the eye and the bacterial flagellum didn't come into existence through random mutation alone - indeed, the omission of selection is another familiar creationist canard. Nick Matzke has not only published a paper in which he predicted that specific homologies would be found between flagellar proteins and those of antecedent systems, but also published a paper in which he presented a model for the selection of the relevant components. Indeed, I think it's worth reviewing the literature on the bacterial flagellum in detail, just to establish how much scientists actually do know about this structure, knowledge which would never have been acquired if they had followed Behe's lead and said "Magic Man did it, don't bother asking questions". So, sit down, and prepare for a long read, because I'm going to take you through about a dozen papers on the subject. Sitting comfortably? Good, I'll begin.
Those nice people over at TalkRational pointed me to a very interesting blog. Namely the blog of Mark Pallen, who was co-author with Nick Matzke of at least one peer reviewed paper in Nature] on the bacterial flagellum (and indeed probably wrote more - I just happen to be aware of the one I have saved to my hard drive). That paper is the following one:
From The Origin Of Species To The Origin Of Bacterial Flagella by Mark J. Pallen & Nicholas J. Matzke, Nature Reviews Microbiology, 4(10): 784-790 (October 2006).
I shall return to this paper shortly, but first, a little preamble is needed.
For those unfamiliar with the background, Nick Matzke was the author of an interesting article, namely this one, which hypothesised that the various proteins that are found in the bacterial flagellum would be found to be homologous with other proteins belonging to other metabolic systems, and that as a consequence, the bacterial flagellum would eventually be found to be the result of co-opting existing, earlier systems and re-using them for another purpose - a classic evolutionary process. Needless to say, a lot of noise was emitted by the ID brigade to the effect that Matzke's ideas were "speculation", and the rest of it, but, the point here is that Matzke made testable predictions in his article, and in doing so provided evolutionary biologists with real substance that they could pursue in the laboratory. The following quote from the abstract of Matzke's original paper is apposite:
Now, note that specific predictions were made with respect to the homologies involved, namely that homologies would be found between flagellar proteins and those of the Type 3 Secretory System, plus an enzyme called F1F0-ATP synthetase. I'll leave the latter enzyme aside for a moment, but return to it because this one turns out to play an important role. Stay tuned for the fun revelations!
Now, first of all, the paper from Nature Reviews Microbiology I cited above by Matzke & Pallen itself dispenses wholesale with the idea of the bacterial flagellum being "irreducibly complex", because, lo and behold, there are bacteria with flagella that are missing numerous components. From that paper, I copy the following details with respect to the presence or absence of specific flagellar proteins in various bacteria possessing flagella:
FlgA (P ring) - Absent from Gram-Positive bacteria
FlgBCFG (Rod) - universal
FlgD (Hook) - universal
FlgE (Hook) - universal
FlgH (L Ring) - Absent from Gram-Positive bacteria
FlgI (P Ring) - Absent from Gram-Positive bacteria
FlgJ (Rod) - FlgJ Rod N-terminal domain absent from some systems
FlgK (Hook-Filament Junction) - universal
FlgL (Hook-Filament Junction) - universal
FlgM (Cytoplasm & Exterior) - Absent from Caulobacter
FlgN (Cytoplasm) - Undetectable in some systems
FlhA (T3SS apparatus) - universal
FlhB (T3SS apparatus) - universal
FlhDC (Cytoplasm) - Absent from many systems
FlhE (Unknown) - Mutant retains full motility
FliA (Cytoplasm) - Absent from Caulobacter
FliB (Cytoplasm) - Absent from Escherichia coli
FliC (Filament) - universal
FliD (Filament) - Absent from Caulobacter
FliE (Rod/Basal Body) - universal
FliF (T3SS apparatus) - universal
FliG (Peripheral) - universal
FliH (T3SS apparatus) - Mutant retains some motility
FliI (T3SS apparatus) - universal
FliJ (Cytoplasm) - Undetectable in some systems
FliK (Hook/Basal Body) - universal
FliL (Basal body) - Mutant retains full motility
FliM (T3SS apparatus) - universal
FliN (T3SS apparatus) - universal
FliO (T3SS apparatus) - Undetectable in some systems
FliP (T3SS apparatus) - universal
FliQ (T3SS apparatus) - universal
FliR (T3SS apparatus) - universal
FliS (Cytoplasm) - Absent from Caulobacter
FliT (Cytoplasm) - Absent from many systems
FliZ (Cytoplasm) - Absent from many systems
MotA (Inner membrane) - universal
MotB (Inner membrane) - universal
So, the mere fact that there are in existence bacteria with missing proteins from the above list whose flagella still function rather makes a mockery of the "irreducible complexity" assertion to begin with. But, this is only part of the story. The same paper continues with the following:
Now, as a slight tangential diversion, which along the way provides yet more evidence for evolutionary hypotheses, one avenue of attack being considered with respect to the development of the bacterial flagellum is the reconstruction of earlier, more ancient versions of the proteins responsible for the construction of this structure. Precedents already exist with respect to the reconstruction of ancient genes, and the following four papers are examples thereof:
Crystal Structure Of An Ancient Protein: Evolution By Conformational Epistasis by Eric A. Ortlund, Jamie T. Bridgham, Matthew R. Redinbo and Joseph W. Thornton, Science, 317: 1544-1548 (14 September 2007)
Resurrecting Ancient Genes: Experimental Analysis Of Extinct Molecules by Joseph W. Thornton, Nature Reviews: Genetics, 5: 366-375 (5 May 2004)
Resurrection Of DNA Function In Vivo From An Extinct Genome by Andrew J. Pask, Richard R. Behringer and Marilyn B. Renfree, PLoS One, 3(5): e2240 (online version, May 2008)
The Past As The Key To The Present: Resurrection Of Ancient Proteins From Eosinophils by Steven A. Benner, Proc. Natl. Acad. Sci. USA., 99(8): 4760-4761 (16 April 2002)
From the paper by Pask et al above, we have:
So scientists are already resurrecting ancient proteins and testing their functionality in model organisms. Indeed, one of the results in the scientific literature comes courtesy of this paper:
Resurrecting The Ancestral Steroid Receptor: Ancient Origin Of Oestrogen Signalling by J.W. Thornton, E. Need and D. Crews, Science, 301: 1714-1717 (2003)
in which the scientists determined that the modern receptors for steroid hormones in modern organisms are traceable to an ancestral receptor dating back 600 million years, and reconstructed the ancestral steroid receptor in the laboratory to determine that it worked.
So, given that precedents already exist for the successful reconstruction of ancient proteins and the genes coding for them, this avenue of attack is likely to prove highly instructive with respect to the bacterial flagellum. Indeed, Pallen & Matzke make this very observation in their paper:
Now, back in 2006, Pallen & Matzke listed some known homologies, and once again, I reproduce their results from the table in the paper:
FlgA (P ring) - CpaB
FlgBCFG (Rod) - FlgBCEFGK
FlgD (Hook) - none specified
FlgE (Hook) - FlgBCEFGK
FlgH (L Ring) - none yet known
FlgI (P Ring) - none yet known
FlgJ (Rod) - none yet known
FlgK (Hook-Filament Junction) - FlgBCEFGK
FlgL (Hook-Filament Junction) - FliC
FlgM (Cytoplasm & Exterior) - none yet known
FlgN (Cytoplasm) - none yet known
FlhA (T3SS apparatus) - LcrD/YscV
FlhB (T3SS apparatus) - YscU
FlhDC (Cytoplasm) - Other activators
FlhE (Unknown) - none specified
FliA (Cytoplasm) - RpoD, RpoH, RpoS
FliB (Cytoplasm) - none specified
FliC (Filament) - FlgL, EspA
FliD (Filament) - none yet known
FliE (Rod/Basal Body) - none yet known
FliF (T3SS apparatus) - YscJ
FliG (Peripheral) - MgtE
FliH (T3SS apparatus) - YscL, AtpFH
FliI (T3SS apparatus) - YscN, AtpD, Rho
FliJ (Cytoplasm) - YscO
FliK (Hook/Basal Body) - YscI
FliL (Basal body) - none yet known
FliM (T3SS apparatus) - FliN, YscQ
FliN (T3SS apparatus) - FliM, YscQ
FliO (T3SS apparatus) - none
FliP (T3SS apparatus) - YscR
FliQ (T3SS apparatus) - YscS
FliR (T3SS apparatus) - YscT
FliS (Cytoplasm) - none yet known
FliT (Cytoplasm) - none yet known
FliZ (Cytoplasm) - none yet known
MotA (Inner membrane) - ExbB, TolQ
MotB (Inner membrane) - ExbD, TolR, OmpA
Now, as Pallen states in his blog entry as linked above, out of this list of proteins, only two were listed as being both essential to all bacterial flagella AND possessing no known homologues in 2006. Those proteins were FliE and FlgD. From the 2006 update of Matzke's original 2003 paper, we read:
At least, this was the situation back in 2006. However, science moves on!
First, take a look at atpsynthase.info, which is the site devoted to ATP synthase. Now, one of the homologies that Matzke originally hypothesised was that at least one of the flagellar proteins would prove to be homologous to proteins in the ATP synthase group, in particular the awkwardly named F1F0-ATP synthetase. Now it turns out that ATP synthases are themselves complex entities, and indeed F1-ATPase rotates on an axis as it performs its synthesis! However, as this paper:
Axle-Less F1-ATPase Rotates In The Correct Direction by Shou Furuike, Mohammad Delawar Hossain, Yasushi Maki, Kengo Adachi, Toshiharu Suzuki, Ayako Kohori, Hiroyasu Itoh, Masasuke Yoshida and Kazuhiko Kinosita, Jr., Science, 319: 955-958 (No. 5865, 15 February 2008)
reveals very succinctly, dismantling this structure so that it no longer has an axle to rotate about does not stop it from functioning! Here's the abstract:
Another blow to "irreducible complexity" sensu Behe (Hermann Müller would doubtless have smiled wryly over this!), but this isn't all. Returning to Pallen's blog, we find this:
So, the FliI protein appeared on the face of it to be essential, because knocking out the gene for FliI synthesis destroyed flagellar biosynthesis. But, and here's the part that really throws the spanner into "irreducible complexity" as espoused by Behe, if you knock out the gene coding for FliI, but in addition knock out the gene for FliH, flagellar biosynthesis returns! This rather buggers up Behe's version of "irreducible complexity" in a spectacular manner.
Yet even this is not the whole story. Believe it or not, there is more! Returning to Pallen's blog, we read:
Incidentally, the paper covering the homology between FliI and the alpha and beta subunits of the F-type ATPase is this paper:
Salmonella typhimurium Mutants Defective In Flagellar Filament Regrowth And Sequence Similarity Of FliI to F0F1, Vacuolar, And Archaebacterial ATPase Subunits by Alfried P. Vogler, Michio Homma, Vera M. Irikura and Robert M. McNab, Journal of Bacteriology, 173(11): 3564-3572 (June 1991) [Full paper downloadable]
so this homology had actually been known even before Behe made his assertions about "irreducible complexity", something he would have known if he had bothered to perform a basic literature search. After all, he has institutional access, whereas I don't currently, yet I was able to find this paper once pointed in the right direction. This paper also covers the knocking out of the gene for FliI and the effect on flagellar biosynthesis.
More pertinently, the following paper:
Evolutionary Links Between FliH/YscL-Like Proteins From Bacterial Type III Secretion Systems And Second-Stalk Components Of The F0F1 And Vacuolar ATPases by Mark J. Pallen, Christopher M. Bailey and Scott A. Beatson, Protein Science, 15: 935-941 (2006) [Full paper downloadable]
is the one containing the confirmation by Pallen of one of Matzke's predictions as cited above. Another homology was confirmed courtesy of this paper:
Structural Similarity Between The Flagellar Type III ATPase FliI And F1-ATPase Subunits by Katsumi Imada, Tohru Minamino, Aiko Tahara and Keiichi Namba, Proceedings of the National Academy of Sciences of the USA, 104(2): 485-490 [Full paper downloadable]
This paper:
Distinct Roles Of The FliI ATPase And Proton Motive Force In Bacterial Flagellar Protein Export by Tohru Minamino and Keiichi Namba, Nature, 451: 485-489 (24th January 2008) [Full paper downloadable]
is the paper that covers the knocking out of FliH and FliI resulting in restoration of flagellar biosynthesis.
So, now the only two proteins remaining to find homologies for are FliE and FlgD, and you can bet that this is being worked upon as I type this.
What was that about "evolution couldn't produce the bacterial flagellum" again? Looks like someone needs to spend time reading some real science instead of creationist websites.
Oh, and as for the "no transitional fossils" canard, allow me to present:
Here's a sequence of fossils covering the tetrapod lineage, namely:
Eusthenopteron ... 385 million years ago
Panderichthys ... 380 million years ago
Tiktaalik ... 375 million years ago
Acanthostega ... 365 million years ago
Ichthyostega ... 362.5 milllion years ago
Hypnerpeton] ... 360 million years ago
Several other taxa have been added since I compiled that list.
Indeed, Tiktaalik was predicted to exist before it was found. Not only was it predicted to exist, but it was predicted to possess specific features and to exist in a particular geological stratum before it was found. Moreover, the fossil was found where it was predicted to exist, and upon detailed examination, was found to possess the precise anatomical features that were predicted in advance by evolutionary biologists and palaeontologists. Here are some nice illustrations of anatomical comparisons (click on links to view):
Comparative anatomy of tetrapods
So, since scientists knew what to look for in advance, found the fossil of Tiktaalik where it was predicted it would exist, and found that Tiktaalik possessed the anatomical features it was predicted to possess on the basis of it being an intermediate step between earlier creatures and later creatures in the sequence, we can consider this confirmed set of predictions validated by real world evidence to be yet more support for the existence of a sequence of organisms in various stages of development between Rhipidistian fishes and land-dwelling tetrapods, as if, of course, all the other fossils cited above weren't enough to begin with.
Moving on to the theropods, here's a nice list of relevant fossils which exhibit a brace of features that any trained comparative anatomist would regard as "transitional":
Shuvuuia ... 81 million years ago
Protarchaeopteryx ... 122 million years ago
Sinosauropteryx ... 122 million years ago
Sinornithosaurus ... 122 million years ago
Caudipteryx ... 125 million years ago
Beipiaosaurus ... 125 million years ago
Yixianosaurus ... 125 million years ago
Jinfengopteryx ... 125 million years ago
Sinocalliopteryx ... 125 million years ago
Cryptovolans ... 130 million years ago
Dilong ... 130 million years ago
Microraptor ... 130 million years ago
Archaeopteryx ... 155 million years ago
Pedopenna ... 160 million years ago
Epidendrosaurus ... 170-120 million years ago (date yet to be more precisely determined)
Scansoriopteryx ... 170-120 million years ago (date yet to be more precisely determined)
An interesting scientific paper is this one which contains an extensive family tree of theropods and pre-Avian dinosaurs, namely:
A Basal Dromaeosaurid And Size Evolution Preceding Avian Flight by Alan H. Turner, Diego Pol, Julia A. Clarke, Gregroy M. Erickson and Mark A. Noreli, Science, 317: 1378-1381 (7th September 2007)
This paper includes a good number of illustrations of the fossils of a recent discovery among the Dromaeosaurids, namely Mahakala omnogovae - indeed, the paper describes the holotype.
What was that about "no transitional fossils" again?