Specified Information

Many ID proponents argue that life is chock full of ‘complex specified information’ and thus must have been designed.  For example, if you take a particular protein, its function is dependent on its conformation and its conformation is dependent on its amino acid sequence.  It would seem that to elicit a particular function, a particular amino acid sequence would be required.

The problem is that many of these ID arguments assume that there are only a small number of amino acid sequences that can specify a particular function.  But what if the opposite is true?  What if a large number of amino acid sequences could specify a particular function?

Let’s consider the hook protein from the bacterial flagellum as shown in the figure below.


As you can see, the hook protein is FlgE. I retrieved the amino acid sequence of this protein from Escherichia coli, Ralstonia solanacearum, Treponema pallidum, Bacillus licheniformis, Aquifex aeolicus, Acidimicrobium ferrooxidans. These are all very distantly related bacteria, meaning that the amino acid sequence of this protein has undergone mutations for billions of years since the last common ancestral version of the hook.

The first thing to note about the amino acid sequence is that the size of the protein has varied from 263 to 482 amino acids.   So let’s say that 263 amino acids is the minimal size for a functioning hook protein.

But now let’s line up the proteins to determine which positions have resisted change after billions of years of mutation:


FlgE_[Bacillus_licheniformis      MLRSLYSGISGMKNFQTKLDVVANNISNINTAGYKKSRVTFKDIVSQQLS
FlgE_[Treponema_pallidum]         MMRSLFSGVSGMQNHQTRMDVIGNNVANVNTTGFKRGRVNFQDLISQQLS
FlgE_[Acidimicrobium_ferroox      MTKSLSSAISGIEANQEWLDNIANNIANANTTGYQSTQTEFADLLYQQQS
FlgE_[Ralstonia_solanacearum      --MGFQQGLSGLDAASKNLDVIGSNVANANTVGYKKSTAEFGDVYARSLV
FlgE_[Escherichia_coli_O157_      --MAFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAG---
FlgE_[Aquifex_aeolicus_VF5]       MLRSFYNAITGMDVSRFALDVTSDNLANANTVGFKKSRPIFQDMVSQVVV
                                     .: ..::*:.     :*  ..*::*  * *::     * *:      

FlgE_[Bacillus_licheniformis      GASSSTA-NRGSVNGQQVGLGATIGSIDIIHTNAAPSTTGRQLDMTITGD
FlgE_[Treponema_pallidum]         AAARPNE-EVGGVNPKEVGLGVLIASIDTVHTQGALQTTGINTDVSIQGS
FlgE_[Acidimicrobium_ferroox      AAGGPVPGQTGGTNPLVVGSGVRVSATPTDFSQGTIVQTGTSTDVAIQGQ
FlgE_[Ralstonia_solanacearum      GASDN-----------QIGQGVDVTKVSQSFTQGNVTVTGNPLDIAINGT
FlgE_[Escherichia_coli_O157_      ----S-----------KVGLGVKVAGITQDFTDGTTTNTGRGLDVAISQN
FlgE_[Aquifex_aeolicus_VF5]       GLNTTTG----TVKTTTFGAGAVVDSTQKVWTIGSFKQTEITTDLAIEGK
                                                   .* *. :       : .    *    *::*   

FlgE_[Bacillus_licheniformis      GYFRVGS--GDEVYYTRSGNFYRSDEGDLVT-------------------
FlgE_[Treponema_pallidum]         GFFVLKS--GEKTFFTRAGAFGVDNAGTLVNPANGMRVQGWMAQDVAGER
FlgE_[Acidimicrobium_ferroox      GFLVVNQ--GGQNYYTRDGALQLDGAGQLVT-ASGALVMGWVPNAAG---
FlgE_[Ralstonia_solanacearum      GFYRMVDTSSGQVSYTRNGQFQTDKNGYIIS-ATGQNLTGYAADATG---
FlgE_[Escherichia_coli_O157_      GFFRLVD-SNGSVFYSRNGQFKLDENRNLVN-MQGLQLTGYPATGTP--P
FlgE_[Aquifex_aeolicus_VF5]       ALFILRDVLTNQTYYTRDGRFRINREGYLIN-PNGLYVQGFKVNPVTGEV
                                  .   : .    .  ::* * :  .    ::.                   

FlgE_[Bacillus_licheniformis      --------------------------------------------------
FlgE_[Treponema_pallidum]         LINSSAQTQDLVIPIGQKIDAQQTSTVHYACNLDKRLPELAADANEADVR
FlgE_[Acidimicrobium_ferroox      QVNQNAPLAALTIPQGQVAQPVATSTITLGGNLPAGSSNPVVVTTTG---
FlgE_[Ralstonia_solanacearum      KINT-AVLTNLQIPVNDLAPLATTNTAFTINLDAAGTVPTTTPFSATN--
FlgE_[Escherichia_coli_O157_      TIQQGANPTNISIPNTLMAAKTTTTASMQINLNSSDPLPSVNAFDASN--
FlgE_[Aquifex_aeolicus_VF5]       TGTQLEDIRVETQIPPKATGEIYFNPPTNLDERAPIIDQTTTPFNPLDSF

FlgE_[Bacillus_licheniformis      --------------------------------------------------
FlgE_[Treponema_pallidum]         KSTWTTDFQVYDSFGQQHTLQINFSRV------------PGTNNQWQATV
FlgE_[Acidimicrobium_ferroox      ----------YDDLGNPVPIQLTFTPS------------TTANQWTLTAE
FlgE_[Ralstonia_solanacearum      ---------------------------------------SATYNHSVSEQ
FlgE_[Escherichia_coli_O157_      ---------------------------------------ADSYNKKGSVT
FlgE_[Aquifex_aeolicus_VF5]       TYNYRYTLTIYDSLGREVPADIYFVKTGTNQWKVYFLASLKERYINVDWN

FlgE_[Bacillus_licheniformis      -VDG-------------------------------LFVLTANNGRIN---
FlgE_[Treponema_pallidum]         AVDPGTEVDTQTRVGVGTSDGAANTFIVNFDNFGHLASVTDTAGNVTGPT
FlgE_[Acidimicrobium_ferroox      TTPPGATSPVALTVGGASS---------------QTVTFDPATGQISAIS
FlgE_[Ralstonia_solanacearum      VYDGTGTSHMLTNYYVRTAAG-----------WDVYSTVDGAAPTG-GNP
FlgE_[Escherichia_coli_O157_      VFDSQGNAHDMSVYFVKTGDN----------NWQVY-TQDSSDPTGTAEP
FlgE_[Aquifex_aeolicus_VF5]       GDDDKTDIVFLDLFNDQVHIADNGTFSTLPTFASKTLEFDPSTGKLVYIP

FlgE_[Bacillus_licheniformis      --------------IPQDA-------------------------------
FlgE_[Treponema_pallidum]         GQVLLEASYDVVGANPDDAGQVTRHAFTLNLGEIGTARNTITQFAERST-
FlgE_[Acidimicrobium_ferroox      GTSTANPDQLALGGFPTSYDLPAGYAMNLDFPTPGTAQAVTQFAASSPT-
FlgE_[Ralstonia_solanacearum      VTSLTFNSSGVLTSSPSK--VAVAFTGMSIA--SMDFTGTTQYGGGFN--
FlgE_[Escherichia_coli_O157_      AMKLVFNANGVLTSNPTENITTGAINGAEPATFSLSFLNSMQQNTGANN-
FlgE_[Aquifex_aeolicus_VF5]       GGDIVQDTANQKFYLEVDLTPESGPSEINDPNDTESYLNKLGAKLGSETN
                                                   .                                

FlgE_[Bacillus_licheniformis      ------------------------------------------QS-FSIAP
FlgE_[Treponema_pallidum]         ----------------------------TKAYRQDGYAMGYLEN-FKIDQ
FlgE_[Acidimicrobium_ferroox      ----------------------------AQVTNQNGYPSGALAG-FTIGS
FlgE_[Ralstonia_solanacearum      ----------------------------DTSVTQDGYATGRLAS-YSVGN
FlgE_[Escherichia_coli_O157_      ----------------------------IVATTQNGYKPGDLVS-YQIND
FlgE_[Aquifex_aeolicus_VF5]       KIKIYVGEGILQNNVIQNSYITQHAADFVVTMDQDGYARGELIDLYVLSE
                                                                             . : :  

FlgE_[Bacillus_licheniformis      DGTVSYVDQNNENQTAGQISLATFSNTSGLSKAGDNLYRETLSSGDPQVV
FlgE_[Treponema_pallidum]         SGVITGVYSNGVSQDIGQLALAGFANQGGLEKAGENTYVQSNNSGIANIS
FlgE_[Acidimicrobium_ferroox      DGVIEGTYANGRTQVLGQIALAQFANAQGLSKQGNLLYAATTNSGAPQLG
FlgE_[Ralstonia_solanacearum      DGTITGRYSNGRTSTLGQIAMTNFKAPDGLQNIGGNQWVETAESGSPQMG
FlgE_[Escherichia_coli_O157_      DGTVVGNYSNEQTQLLGQIVLANFANNEGLASEGDNVWSATQSSGVALLG
FlgE_[Aquifex_aeolicus_VF5]       DGVVVGVYSNGETLPTYRLALAQFTDPEELVKKGSNLYASVKTPTILLPG
                                  .*.:     *  .    :: :: *     * . *   :     .      

FlgE_[Bacillus_licheniformis      VPGEGGSGKIQTSALEMSNVDLSEEFSEMIIAQRGFQSNAKIITTSDEIL
FlgE_[Treponema_pallidum]         TSGVMGKGKLIAGTLEMSNVDLTDQFTDMIITQKGFQAGAKTIQTSDTML
FlgE_[Acidimicrobium_ferroox      SPGAAGLGQLVGGALESSNVSIGSELTNLVVAQTDYQANTKVVQTTATVL
FlgE_[Ralstonia_solanacearum      TPGMGSFGLLQSSAVEQSNVDLSAELVNMIVAQRSYQANAQTIKTEDQLL
FlgE_[Escherichia_coli_O157_      TAGTGNFGTLTNGALEASNVDLSKELVNMIVAQRNYQSNAQTIKTQDQIL
FlgE_[Aquifex_aeolicus_VF5]       -----GSNKIRSAVVEMSNVDIAKEFINLITAQRTYQVTQGR--------
                                       . . :  ..:* ***.:  :: ::: :*  :*             

FlgE_[Bacillus_licheniformis      QELVNLKR
FlgE_[Treponema_pallidum]         DTVLSLKR
FlgE_[Acidimicrobium_ferroox      QSLVQMA-
FlgE_[Ralstonia_solanacearum      QTLVSMR-
FlgE_[Escherichia_coli_O157_      NTLVNLR-
FlgE_[Aquifex_aeolicus_VF5]       --------

The perfectly conserved positions are marked with an *.  And as you can see for yourself, there are only 26 such positions.  In other words, only 10% of the positions must be “specified” to elicit this function.  Let’s be charitable and  increase this somewhat by factoring in the highly conserved sites [indicated by :].  If we went ahead and assumed they were also perfectly conserved, that would amount to only 36 more positions, for a total of 62. That gets us to about 24% of the positions.

It would thus seem that in order to elicit flagellar hook function in a protein of about 250 amino acids, anywhere from 75-90% of the positions do not need to be “specified.”

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25 responses to “Specified Information

  1. If I understand your point, Mike, you are saying that any amino acids can be in the other 224-234 positions, and it will still yield the FlgE protein. Is that correct?

  2. Assuming that all that is needed to yield the FlgE protein are 26 amino acids in the exact positions of the 260 possible, we still have what looks like a very specific, complex requirement. If we needed to spell a 26 letter word exactly, and were picking randomly from all 26 letters of the alphabet, I think that would mean that the chances of getting it right would be 1 in 26^26. For a protein that needed the right 26 amino acids, that would be (I think) 1 in 26^20, not including the fact that they apparently need to be in the right places along the 260 length chain. Would that make it 1 in (26^20)^260? Perhaps my math is wrong, but it still seems it would be quite a bit higher.
    Of course, it is at least logically possible that every single 260 length sequence yields a functional protein. In that case, a random search will be successful every time.
    So in order to determine how much specific information there is in FlgE, we need to know more than how many of its own amino acids need to be in the right order. We need to know how many other similar length proteins can be formed.
    Over at Telicthoughts, Zachriel cited a paper that said the chances of finding an 80 amino acid chain that yielded any protein, using a random search was 1 in 10^12. Stephen Meyer cites Douglas Axe, who says that it is 1 in 10^74, for a 150 length sequence. Either way, the specific information of proteins, in general, seems rather high.
    When we factor in the low probability of a natural environment offering conditions where left-handed amino acids will form the right kind of bonds with each other, and not with other subtances, it still looks like the protein-first scenario for the origin of life has no realistic chance of happening.
    Of course, once we have life, the question still remains, how improbable is it to randomly evolve other proteins from the ones we start out with?

  3. Hi Mike,

    Can you point me to any useful websites that have as detailed graphical diagrams for any of the bacteria you listed?

    I looked and found only micro images with very little detail, no where near the sophistication as this flagellum.

    thanks

  4. flagella, flagellum… just don’t flag me if I dissent bro… 😉

  5. Hi Bilbo,

    Sorry for the late reply, but as usual, I’m always busy in the real world.

    No, I do not think you can place any amino acid at any of those 75-90% of varying positions. Consider an extreme example – fill all of the varying positions with a bulky, hydrophobic amino acid like phenylalanine. I would guess that such a protein would not fold properly to position those 26 invariant positions and would thus not function. What’s more, if you look at the varying positions, the variation is being constrained by the genetic code (it’s not truly random). So there probably is indeed some level of “information” that is being supplied by the varying positions. Yet the constraint from the code also means that there could be many other proteins that don’t have the same 26 invariant positions yet still have FlgE function. There could be other sets of amino acids which themselves might be “invariant” yet also different from what we actually see. We can’t see them simply because evolution has been constrained by the sequence of the ancestral FlgE.

    The reason I’m not impressed by these specified information arguments is that they are all built on our superficial understanding of protein function and too many unknowns. Perhaps sometime in the distant future, as scientist get a much better handle on proteins, the specificity arguments might become more powerful. But as they stand now, they vastly over-reach in regard to any design inference. That’s why I would consider them, at best, as one of the clues that could be fed into the Discontinuity score of the Matrix.

    Personally, I think any case for design here would be much more subtle, but also more mind-blowing. Recall that I think the flagellum likely evolved. For example, if you look at that figure above, the rod, hook, and filament proteins appear to be homologous. Thus, the function of this conserved sequence is not merely the mechanical function of the flagellum (the reason the invariant position are at both ends is that these proteins interact end-to-end), but the assembly function of the flagellum across time. In other words, the sequence was meant to unfold into the flagellar filament and that may be why this particular sequence, among all possible sequences, exists.

  6. Datcg,

    Sorry, but I don’t know of any such sites.

  7. Mike,

    Wow, that surprises me a little. Not that you don’t know, but that graphic information seems so limited. Any books you might recommend? I get quite busy too, so a quick look on the web didn’t turn up anything.

    Except for petri dish type images, though interesting, nothing that shows this level of detail for each protein.

    I would like to visually see the protein you are discussing in other bacteria.

    Besides BLAST and comparisons, have you seen the FlgE protein in detail like this in other bacteria? Without any other visualization it makes me curious about sequence differentiation and possible stress induced changes. And I’m curious if in other bacteria do we see actual physical differences as well as similarities?

    Do you know?

  8. See the problems I’m running into on the web…

    The Pox

    ;-)… scary, huh?

  9. Here is an actual image of T. Pallidum cross-section, it appears… they have the other standard wormy looking fella, but it is impossible to tell where one protein begins and another one ends.

    Where is the FlgE protein in this image? Certainly, microbiologist, disease and other scientific researchers have better to work with? If they can image the flagella parts so good with electron microscopy.

    Hmmmm… now I’m real curious to find more detailed images. OK… search on electon images, turned up Wiki of course:

    http://commons.wikimedia.org/wiki/index.html?curid=2256695

    So where is the hook FlgE in this image? It is a little better.

    Wait… ok, tracked the wiki image back to CDC Image Library!

    http://phil.cdc.gov/phil/details.asp

    You can use this for future references, cool. This is better. It is interesting to see the categories.

    They should categorize by functional parts as well. Hmmm… maybe they do, don’t have enough time to look around.

  10. Sigh, well… not so much luck on other bacteria at CDC. Interesting, so only two detailed pics by the CDC. Sorry for multiple post, but I find this all very enlightening at times. I jus assumed I could find similar images to the famous flagellum and am somewhat surprised.

    The illustration of the hook in T Pallidum is cool, but it still is not the image I’m looking for.

    OK, have a great weekend if I don’t check back in.

  11. Mike, you write: “The reason I’m not impressed by these specified information arguments is that they are all built on our superficial understanding of protein function and too many unknowns. Perhaps sometime in the distant future, as scientist get a much better handle on proteins, the specificity arguments might become more powerful. But as they stand now, they vastly over-reach in regard to any design inference. That’s why I would consider them, at best, as one of the clues that could be fed into the Discontinuity score of the Matrix.

    So you would say that the estimate made in the paper that Zachriel cites and Douglas Axe’s estimate are based on too little information?

  12. Hi Bilbo,

    1 in 10^12 to 1 in 10^74 is quite a spread. If I claimed to have an economic theory which, if implemented, would result in predicted unemployment rates from 3-20%, I doubt anyone would think much of the theory. And 3-20% is a much smaller spread than 1 in 10^12 to 1 in 10^74.

    BTW, 1 in 10^12 is not that big, given the fact that at any moment, there are 10^30 bacteria on this planet.

  13. I hate to repeat my question, but I will: So you would say that the estimate made in the paper that Zachriel cites and Douglas Axe’s estimate are based on too little information?

    You write: “BTW, 1 in 10^12 is not that big, given the fact that at any moment, there are 10^30 bacteria on this planet.

    Yes, I think that 1 in 10^12 is probably too improbable for the origin of life by protein-first scenarios, given that the random combinations of amino acids also would need to overcome only left-handed amino acids, in the right kind of bonds with each other, and not with other substances. And if I remember correctly, it has to be in a non-aquaeous (sp?) solution. But once we had living cells, 1 in 10^12 might not be a problem.

  14. Pingback: Troublemaker - Telic Thoughts

  15. Mike, I am disappointed that you would not recognize the restraints on amino acid interchange.

    I am looking at a graph I found by googling “amino acid properties”. It shows that if an amino acid is offering the protein the role of hydrophobia there are about ten aminos that will do. If, however, the amino is offering to the protein both the property of hydrophobia and +ve, then there are only two aminos that qualify — H&K. Ultimately the amino pairs A&G I&L W&Y are almost always interchangeable. (It would be interesting to reanalyse your results assuming that A=G I=L and W=Y.)

    This model, where each amino has properties that overlap with other aminos seems designed for flexibility, designed to welcome evolution. However, the fact that depending on the role an amino is playing in the protein, there is a limited list of substitutes, significantly constrains the ability of an amino to be randomly changed.

    Proteins do not by any means allow for a willy nilly changing of the aminos. It still solidly remains that most mutations will be deleterious. Further, the mutations that simply replace one amino with a particular property set with another negligably changes the function of the gene.

  16. Is that true that a protein’s conformation is dependent on its amino acid sequence?

    What about HSPs and other chaperones?

    I think the sequence aids in the folding but doesn’t determine it.

    But that’s just me…

  17. Hi Bilbo,

    I have not read those papers, so I can not make any judgment about your specific question (can you get the refs?). But what I do question is any attempt to extrapolate those numbers to make some general point (whether it be really easy or very hard for random processes to stumble upon a functional protein). Can we really say, with strong confidence, that the chance of finding FlgE function is 1 in 10^12? 1 in 10^74?

    I followed the trackback to TT and over there, Alan Fox makes the point very succinctly:

    ID critics have been pointing out the fallacy in the assumption that, for instance oxytocin’s 9 residue chain is a 1 in 20^9 probability. We don’t know how many of those 20^9 sequences could have some useful biological function in some context. Ditto for any other number of amino acids in a sequence.

    It’s not just a problem of nailing down the probability of finding a particular function (ie., hook function in bacterial flagellum), but the probability of finding ANY function (something, anything, that would serve the cell). If one’s argument is premised on the claim that some (or ANY) function could not possibly arise by non-telic means, then one has positioned themselves such that they need to know this information to make that argument.

    As for the OOL distinction, I am sympathetic with what you are saying , but we need to remember that non-teleologists do not envision the cell coming together as a random assemblage of proteins. They propose a much more gradual emergence, starting with a simple self-replicating molecule (or metabolic circuit) that would randomly encounter other sequences that would happen to facilitate this process, step-by-step. I don’t think it is a convincing scenario, but probability arguments like these don’t play much of a role in my thinking. I think the problem is better seen from this perspective. https://designmatrix.wordpress.com/2009/04/05/abiogenesis-expects-life-to-be-multifarious/

    Hi BFast,

    I do recognize such constraints (see my first reply to Bilbo). The problem is in nailing them down. Unless and until they are objectively nailed down, I think the specified information arguments over-reach.

    As for most mutations, they are neutral. Just look at the vast sea of sequence in FlgE alone that has been drifting about.

    Hi Joe G,

    Yes, that is true. Chaperones aid in folding simply by preventing unproductive folding or by providing a micro-environment where folding can occur. Chaperones are important for two reasons – 1) protein synthesis occurs incrementally, yet folding is a global process; 2) the cell is chock full of proteins, meaning that two partially folded proteins could interact and collapse into gunk.

    I’ll say more later guys, but I’m going out of town for a few days. I will probably discuss a recent review on the design of proteins.

  18. I think a review of the protein design lit is in order. (IDers do your homework.)

    The use of reduced or simplified alphabets is explored. No doubt, it meliorates search for and optimization of functional sequences. (Albeit begging the question of why an extended alphabet is used in life.)

    It is also important to recognize the importance of context, the locus or position in the sequence and its occupancy. E.g., a specific position may be free to cycle through hydrophobic residues, but admits no substitution by any other type of amino acid w/o compromising function. This relaxes the constraint that a specific individual amino acid occupy the site, but retains the constraint that a specific type of amino acid occupies the site.

    I became interested in protein design back in college (thirty years ago), which is when some computer scientists pronounced (ala Levinthal) that the protein design (evolution) problem was “cursed” (N-P complete). The analyses were flawed (for the reasons mentioned). But reducing the alphabet still doesn’t solve the problem. It’s still “cursed.”
    Also, as observed, degeneracy is not a nuisance factor, but does perform a function(s). (Classically, it reduces and distributes loads and directs evolution along certain paths, “escape routes”.)

    Functions can be defined “negatively,” e.g., by not defining the function explicitly, but by adumbrating constraints, in effect by saying what a function is not, rather than what it is.

    Specificity, selectivity, and affinity are related biological concepts and should be understood.

  19. Zachriel cites Keefe & Szostak, Functional proteins from a random-sequence library, Nature 2001, for the 1 in 10^12 estimate.

    Mike writes: “we need to remember that non-teleologists do not envision the cell coming together as a random assemblage of proteins. They propose a much more gradual emergence, starting with a simple self-replicating molecule (or metabolic circuit) that would randomly encounter other sequences that would happen to facilitate this process, step-by-step.

    Yes, I realize that. I think one of the reasons they gave up on the protein-first scenario was realizing the very low probability of getting functioning proteins by chance.

  20. I read somewhere (Sci Am?) that the rate of amino acid transfer in the ribosome also affects the protein fold.

    This happens when a “silent mutation” occurs- different nucleotide sequence leading to the same amino acid- and the new codon has few matching tRNAs so it takes longer to reach the ribosome.

    Then there are prions which change the configuration just by contacting its “normal” sister.

    All I am saying is I don’t think that protein configuration can be reduced to amino acid sequence alone.

  21. You guys might find this interesting,

    Highly designable phenotypes and mutational buffers

    http://mobydick.ucsf.edu/~haoli/network.designability_pnas_2006.pdf

  22. Nick (Matzke)

    Hi Mike — why do you think this info, which has been extremely well-known about proteins for a long time, is such a surprise to the ID fans?

    PS: FlgE images — folks, the bacterial flagellum is only 30 nanometers wide, you can barely see bacteria with light microscopy (1000-2000 nanometers wide). To see the flagellum you need transmission electron microscopy, and even then the images are very fuzzy and are only images of highly prepared, chemically fixed specimens, where an image is built up by averaging dozens of individual specimens.

    In any event, FlgE is the hook which is the curvy part. See: http://www.talkdesign.org/faqs/flagellum.html#fig1 (the top bit)

    http://pandasthumb.org/archives/2006/08/friday-flagellu.html

    The animated cartoons etc. are neat to look at but are themselves highly simplified abstractions — well, cartoons — of the real deal.

    PPS: The FlgE story gets even more interesting when you realize that some of that small remainder of conserved amino acids are shared with *other* axial proteins in the rod/hood/linkers/flagellar filament tube.

    PPPS: Mike Gene writes: “Recall that I think the flagellum likely evolved.”

    Mike, correct me if I’m wrong, but I don’t believe this was your position back when we met in 2001 or so.

  23. Hi Nick,

    why do you think this info, which has been extremely well-known about proteins for a long time, is such a surprise to the ID fans?

    It goes to the distinction between EE and OE. Most ID proponents want some form of EE – some powerful demonstration that would cause even hardcore critics to acknowledge ID. “High information” proteins are supposed to qualify, as they are supposed to be beyond the reach of random processes. And what many ID proponents and hardcore critics share in common is an allegiance to the god-of-the-gaps approach – evidence of design as something that cannot possibly be explained by evolution.

    Mike, correct me if I’m wrong, but I don’t believe this was your position back when we met in 2001 or so.

    Here is what I posted to you on the ARN forum back in 2001:

    Now, when I infer ID behind the bacterial flagellum, I am focused on the core aspects that are shared by all bacterial flagella (I have previously explained how core IC modular systems are under functional constraint and surveying 3.5 billion years of evolutionary tinkering is a good way to detect such constraint). This core aspect of the bacterial flagellum is thus hypothesized to be essential to basic flagellar function in all bacteria while more peripheral elements, while important/essential in the context of individual species, can be tweaked in accord with the needs of the organism. And it’s when one focuses on the core constituents of “the bacterial flagellum” that we still find a hefty IC system that is not convincingly explained by cooption ,as (for one reason) there are no apparent precursors for all components of this core (remember we are talking about what happened and not about what could have happened). However, some have proposed such things as the type III secretory system and the F-ATP synthases. I simply don’t find such explanations convincing (the former probably post-dates flagella and the latter doesn’t look like a precursor). And it is not bias behind my skepticism, as both precursor states would nicely fit into a front-loading hypothesis (in fact, if anything, I’d love to fit the flagella into a front-loading hypothesis).

    At the time, the TTSS did not look like the F-ATP synthase, but since then, thanks to some of the stuff you and Pallin have found, it does look like a good candidate for a precursor. Like I said then, I was always eager to fit the flagellum into the hypothesis of front-loading, and your work made that possible for me. Thanks.

  24. Mike, Nick, and Rock, together again. I think I’m gonna’ cry. Somebody get me a hanky.

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