posted 15. February 2003 03:24                   

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I think re the reptile-mammal jawbone-earbone transition, we are really dealing with a transition that is inferred based upon some fossils that close the gap to a limited extent, not because of actual fossils documenting the jawbone-earbone transition itself. I think it's an urban legend that needs to die.

Also, this last quote makes me wonder if John's analogy might work with this transition. It seems that some pretty radical renovation of the bone structure is necessary for this to happen, perhaps this is a good example of John's hypervolume at work.

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Figure 1.4.3. A comparison of the jawbones and ear-bones of several transitional forms in the evolution of mammals. Approximate stratigraphic ranges of the various taxa are indicated at the far left (more recent on top). The left column of jawbones shows the view of the left jawbone from the inside of the mouth. The right column is the view of the right jawbone from the right side (outside of the skull). As in Figure 1.4.1, the quadrate (mammalian anvil or incus) is in turquoise, the articular (mammalian hammer or malleus) is in yellow, and the angular (mammalian tympanic annulus) is in pink. For clarity, the teeth are not shown, and the squamosal upper jawbone is omitted (it replaces the quadrate in the mammalian jaw joint, and forms part of the jaw joint in advanced cynodonts and Morganucodon). Q = quadrate, Ar = articular, An = angular, I = incus (anvil), Ma = malleus (hammer), Ty = tympanic annulus, D = dentary. (Reproduced from Kardong 2002, pp. 274, with permission from the publisher, Copyright © 2002 McGraw-Hill)

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Since Figure 1.4.3 was made, several important intermediate fossils have been discovered that fit between Morganucodon and the earliest mammals. These new discoveries include a complete skull of Hadrocodium wui (Luo et al. 2001) and cranial and jaw material from Repenomamus and Gobiconodon (Wang et al. 2001). These new fossil finds clarify exactly when and how the malleus, incus, and angular completely detached from the lower jaw and became solely auditory ear ossicles.

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Gish simply does not understand how gradual transitions happen (something he should understand, obviously, if he intends to criticize evolutionary theory). These fossil intermediates illustrate why Gish's statement is a gross mischaracterization of how a transitional form should look. In several of the known intermediates, the bones have overlapping functions, and one bone can be called both an ear bone and a jaw bone; these bones serve two functions. Thus, there is no reason to expect transitional forms with intermediate numbers of jaw bones or ear bones. For example, in Morganucodon, the quadrate (anvil) and the articular (hammer) serve as mammalian-style ear bones and reptilian jaw bones simultaneously. In fact, even in modern reptiles the quadrate and articular serve to transmit sound to the stapes and the inner ear (see Figure 1.4.2). The relevant transition, then, is a process where the ear bones, initially located in the lower jaw, become specialized in function by eventually detaching from the lower jaw and moving closer to the inner ear.

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posted 16. February 2003 03:58                   

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No, you don't have the type III secretory system since it most likely evolved from the flagellum.

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You seem to be trying to have it both ways. If evolution predicts we won't be able to find the precursors for the flagellum, then why the talk about knowing only a tiny fraction of proteins in extant organisms?

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Besides, if there is a time limit in which evolution predicts we will not find evidence of its happening, lay it on the table. It doesn't make much sense to complain the flagellum is too old when Miller et al. claim to have evidence for the evolution of the Krebs cycle.

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posted 23. February 2003 12:59                   

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However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under [the classical model], and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene.

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However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under [the classical model], and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation.

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The antifreeze example is even weaker. The lowering of the freezing point of a solute only requires that there be some solvent dissolved in it, so the only requirement for an antifreeze protein is that it be water-soluble. There is not even a need to alter the protein itself, it just has to get accidentally mis-directed into the bloodstream. This would definitely not qualify as an invention in TRIZ; I'm not even sure it would get a patent in the USA. Certainly, no contradiction was overcome and no invention was made.

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posted 23. February 2003 13:26                   

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Portions of the endo16 cis regularatory system of Strongylocentrotus are to date the most extensively explored of any, with respect to the functional meaning of each interaction that takes place within them. What emerges is almost astounding: a network of logic interactions programmed into the DNA sequence that amounts essentially to a hardwired biological computational device

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posted 23. February 2003 13:48                   

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"Phylogenies of most or all of the flagellar proteins follow those of the source organisms with little or no lateral gene transfer suggesting that homologous flagellar proteins are true orthologues. We suggest that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems."
J Mol Microbiol Biotechnol 2000 Apr;2(2):125-44 Phylogenetic analyses of the constituents of Type III protein secretion systems. Nguyen L et. al.

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posted 24. February 2003 01:33                

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However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under [the classical model], and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene.

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The phrase here is unambiguous. As far as the examples that do produce new function, we see that they clearly not relevant to the type of inventiveness discussed in the paper.

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Subfunctionalization is defined as the fixation of complementary loss-of-function alleles that results in the joint preservation of duplicate loci. For example a gene that is originally expressed in two tissues may diverge into two copies, each being expressed uniquely in one of the two tissues.

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Numerous examples now exist for the presence of independently mutable regulatory sequences associated with developmental genes. Consider, for example, the bmp5 gene in the mouse.

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Although the DDC process is based entirely on degenerative mutations, there are at least three ways in which it may play a significant role in creative evolutionary processes. First, by stabilizing duplicate genes in the genome, the DDC process extends the time period during which genes are exposed to natural selection, thereby enhancing the chance that rare beneficial mutations to novel functions may arise (as compared to the situation under the classical model, where a gene is removed from selection once it has become nonfunctionalized). Second, the partitioning of gene expression patterns by the DDC process may reduce the pleiotropic constraints operating on single-gene loci, thereby allowing natural selection to more closely tune the duplicate members of a pair to their specific subfunctions. Third, gene duplicates that have unresolved subfunctions at the time of a reproductive isolation event provide a powerful mechanism for the development of reproductive incompatibility, i.e., speciation. The degeneration of orthologues in different ways in two sister taxa effectively causes a divergence in genetic maps (Haldane 1933) and a consequent loss of some aspects of gene expression in hybrid progeny.

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There is, however, nothing inherent in the DDC model that denies the significance of gene duplication in the origin of evolutionary novelty. Indeed, the subfunctionalization process may facilitate such evolution by preserving gene duplicates and maintaining their exposure to natural selection and/or by removing pleiotropic constraints.

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Finally, we note that we have couched all of the theory in this article in terms of loss-of-function/subfunction mutations. However, some evidence suggests that gain-of-function mutations may be quite common, perhaps as common as loss-of-function mutations (Clark et al. evolution. Am. Nat. 67: 5–9. 1995). A key feature of the DDC model is how mutations in duplicate genes are perceived at the level of natural selection, so the extent to which our results would have to be modified in the face of gain-of-function mutations depends on their influence on fitness. If such mutations are dominant and have a negative influence on fitness, then they may be effectively purged from the population and contribute little to the long-term evolutionary dynamics of gene duplicates. On the other hand, gain-of-function mutations may prolong the life of gene duplicates by resurrecting previously impaired copies. empirical and theoretical studies will be required to clarify these issues.

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"We are not aware , however, of any convincing evidence that the majority of duplicate copies have acquired new functions that did not already exist in the ancestral genes."

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An alternative reason for the failure of the classical model to explain the fates of most duplicate loci may be an overly simplistic view of gene structure. …

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… This model is quite distinct from the classical model, under which degenerative mutations can only lead to gene loss and beneficial mutations are the only route to gene preservation.

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The only examples that we see where gene duplication evoke a new function were very simple examples. That "sometimes new functionality develops from gene duplication, then new functionality is a capability or potential result of gene duplication" is irrelevant, as we are discussing whether gene duplication would likely result in the type of inventiveness discussed in John Bracht's paper. Lets stay focused. If gene duplication truly results in an increase in dimensionality, you are doing a good job of hiding it.

As paper states:

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As we noted earlier, even the most basic premise of the classical model of duplicate gene evolution--that gene duplicates are preserved only by the evolution of new functions--has never been tested.

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… Unlike the classical model, the mutational mechanisms that lead to gene preservation by DDC are distinct from those responsible for the origin of new gene functions. On the other hand, by expanding the time period for which genes are exposed to selection, the preservation of duplicates by the DDC process facilitates subsequent opportunity for the evolution of new functions. If the evolution of new gene functions is the only mechanism of duplicate gene preservation, then it should be possible to empirically reject our alternative subfunctionalization hypothesis. We now consider some potentially fruitful avenues for future research.

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That re-working of the "rules" of gene expression and embryonic development, along with adding extra genes, is what I'm referring to as an inventive change in biology. I've never seen an example where that sort of change was observed to be the result of Darwinian processes.

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[Speaking of the paper “Ohno (1970)”:]

Ohno concludes:

Thus, gene duplication emerges as the major force of evolution.

Onno’s provocative thesis is supported by the discovery of pairs of proteins with similar sequences of DNA and similar sequences of amino acids, but different functions (Nei 1987; Maeda and Smithies 1986; Dyson and Sherratt 1985; Brooks Low 1988; Patthy 1991; Go 1991; Hood and Hankapiller 1991). Examples include

• myoglobin and the single subunits of monomeric hemoglobin of lamprey and hagfish,
• myoglobin (used for storing oxygen in muscle cells of vertebrates) and the four subunits of hemoglobin (used for transporting oxygen in red blood cells),
• trypsin and chymotrypsin,
• the protein of microtubules and actin of the akeletal muscle, and
• the light and heavy immunoglobin chains.

For the Escherichia coli bacterium, a relatively simple organism, it is known that the more than 30% of its proteins are the result of gene duplications (Lazcano and Miller 1994; Riley 1993). Those proteins include its DNA pllymerases, dehydrogenases, ferredoxins, glutamine synthetases, carbomoyl-phosphate synthetases, F-type ATPases, and DNA topoisomerases.
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The midge, Chironomus tentans, provides an additional example of gene duplication (Gallli and Wislander 1993, 1994). In particular, consider the contiguous sequence of 3,959 nucleotide bases from this midge that is archived under accession number X70063 in the European Molecular Biology Laboratory (EMBL) database and the Gen Bank database. The 732 nucleotide bases located at positions 918-1,649 of the 3,959 bses of the DNA sequence involved become expressed as protein containing 244 (i.e., one-third of 732) amino acid residues. The 759 nucleotide bases at positions 2,513-3,271 become expressed as a protein containing 253 residues. The 732-bae subsequence is called the C. tentans SP38-40.A gene and the 759-base subsequence is called the C. tentans Sp38-40.B gene. The bases of DNA before positions 918, the bases between positions 1,650 and 2,512, and the bases after position 3,271 of this sequence of length 3,959 do not become expressed as any protein.

But both the “A” and the “B” proteins are secreted from the midge’s salivary gland to form two similar, but different, kinds of water-insoluble fibers. The two kinds of fibers are, in turn, spun into one of two similar, but different, kinds of tubes. One tube is for larval protection and feeding, while the other tube is for pupation (the stage in the development of an insect in which it lies in repose and from which it eventually emerges in the winged form).

[continues with details on “A” and “B” proteins]

[References discussed excerpted:]

• Brooks Low, K. 1988. Genetic recombination: A brief overview. In Brooks Low, K. (ed.). The Recombination of Genetic Material. San Diego: Academic Press. Pp.1-21.
• Dyson, Paul; and Sherratt, David. 1985. Molecular mechanisms of duplication, deletion, and transposition of DNA. In Cavalier-Smith, T. (ed.). The Evolution of Genome Size. Chichester, England: John Wiley & sons.
• Gali, Joakim; and Wislander, Lars. 1993. Two secretory protein genes in Chironomus tentans have arisen by gene duplication and exhibit different developmental expression patterns. Journal of Molecular Biology 231:324-334.
• -----, 1994. Structure of the smallest salivary-gland secretory protein in Chronomus tentans. Journal of Molecular Evolution 38:482-488.
• Go, Mittko. 1991. Module organization in proteins and exon shuffling. In Osawa, S.; and Honjo, T. (eds.). Evolution of Life. Tokyo: Springer-Verlag.
• Hood, Leroy; and Hankapiller, Tim. 1991. Modular evolution and the immunoglobin gene superfamily. In Osawa, S.; and Honjo, T. (eds.). Evolutoin of Life. Tokyo: Springer-Verlag.
• Lazcano, A.; and Miller, S. L. 1994. How long did it take for life to begin and evolve to cyanobacteria? Journal of Molecular Evolution 39:546-554.
• Maeda, Nybuyo; and Smithies, Oliver. 1986. The evolution of multigene families: Human haptoglobin genes. Annual Review of Genetics 20:81-108.
• Nei, Masatoshi. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press.
• Ohno, Susumu. 1970. Evolution by Gene Duplication. New York: Springer-Verlag.
• Pathy, Laslo. 1991. Modular exchange principles in proteins. Current Opinion in Structural Biology. 1:351-361.
• Riley, M. 1993. Functins of the gene products of Escherichia coli. Reviews of Microbiology 32:519-560.

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posted 24. February 2003 02:25                   

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Already I am seeing how much Theyeti's essay is causing confusion (see a forthcomming reply at ARN since I feel partly responsible for the essay, given my posts at Antievolution.org about ID not necessarily being antievolution, but I digress). Mouse traps and molecular systems like bacterial flagella have this in common: they are multi-part systems with well-matched parts that are assembly-dependant, and dependant on assembly from scratch. What we have with the ear-bone system is a system that are not built like mousetraps or molecular machines, they are dependant on the evolution of developmental systems.

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Furthermore, it's another quite simple example of the reshuffling of pre-existing parts, and 3 measly parts at that. So even if this was a molecular example, it would be just as trivial as the PCP degradation pathway or the antifreeze example.

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What I find *really* entertaining is how, with practically every example I raise, the reaction is something like (1) Much doubt and objections that there is no evidence that the example in question evolved (2) followed by argument and citation of more evidence followed by (3) an assertion that, OK, maybe the example evolved but it's really trivial and doesn't meet whatever ill-defined IDist criteria is popular this week.

You, Nelson, just called this:



...set of finely-crafted, delicately matched, sound-conduction devices -- from jawbones, of all things -- a "trivial" acheivement. Despite the fact that, as the above graphic shows, it represents the very defining characteristic of mammals that distinguishes them from mammal-like reptiles. Humans have even given the bones names on analogies with human devices, and refer to their function in terms of lever action, impedance matching, etc. The analogy with a mousetrap is rather close -- transfer of energy via physical mechanisms such as levers, to deliver it somewhere else.

If you concede that such a thing is a trivial thing for evolution to accomplish, then you've just conceeded that IC is a trivial thing for evolution to produce, and there goes your argument for ID.

yersinia

PS: Regarding gene duplication and the origin of information, you've got a lot more to deal with than just antifreeze genes. There are dozens of published examples of the detailed origin of new genes, although since no one here has given a non-goalpost-moving definition of "inventive" or "technical contradiction" there is no way to know which ones would meet the criteria.

But here is a very partial list anyhow.

And some more examples, focusing on cooption but also the origin of new genes

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Although the type III systems are simpler than flagella, they are also IC, and not only that, to tell a co-option story about how you can add the other parts of the flagellum, requires co-option of multi-component systems. Again, see the 6-part essay at ]http://idthink.net

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J Bacteriol 2002 Aug;184(15):4219-32

Origins of the 2,4-dinitrotoluene pathway.

Johnson GR, Jain RK, Spain JC.

Air Force Research Laboratory, U.S. Air Force, Tyndall Air Force Base, Florida 32403, USA.

The degradation of synthetic compounds requires bacteria to recruit and adapt enzymes from pathways for naturally occurring compounds. Previous work defined the steps in 2,4-dinitrotoluene (2,4-DNT) metabolism through the ring fission reaction. The results presented here characterize subsequent steps in the pathway that yield the central metabolic intermediates pyruvate and propionyl coenzyme A (CoA). The genes encoding the degradative pathway were identified within a 27-kb region of DNA cloned from Burkholderia cepacia R34, a strain that grows using 2,4-DNT as a sole carbon, energy, and nitrogen source. Genes for the lower pathway in 2,4-DNT degradation were found downstream from dntD, the gene encoding the extradiol ring fission enzyme of the pathway. The region includes genes encoding a CoA-dependent methylmalonate semialdehyde dehydrogenase (dntE), a putative NADH-dependent dehydrogenase (ORF13), and a bifunctional isomerase/hydrolase (dntG). Results from analysis of the gene sequence, reverse transcriptase PCR, and enzyme assays indicated that dntD dntE ORF13 dntG composes an operon that encodes the lower pathway. Additional genes that were uncovered encode the 2,4-DNT dioxygenase (dntAaAbAcAd), methylnitrocatechol monooxygenase (dntB), a putative LysR-type transcriptional (ORF12) regulator, an intradiol ring cleavage enzyme (ORF3), a maleylacetate reductase (ORF10), a complete ABC transport complex (ORF5 to ORF8), a putative methyl-accepting chemoreceptor protein (ORF11), and remnants from two transposable elements. Some of the additional gene products might play as-yet-undefined roles in 2,4-DNT degradation; others appear to remain from recruitment of the neighboring genes. The presence of the transposon remnants and vestigial genes suggests that the pathway for 2,4-DNT degradation evolved relatively recently because the extraneous elements have not been eliminated from the region.

[...]

[snipping many paragraphs of analysis before the final summary]

Inferences from the comparison of the structural genes of the 2,4-DNT pathway suggest that the pathway came together from three sources. The initial dioxygenase appears to have originated from a naphthalene degradation pathway like that of strain U2 (17). A large portion of the salicylate hydroxylase oxygenase component is retained but is not functional. The MNC monooxygenase was probably derived from a pathway for degradation of chloroaromatic compounds. The presence of the vestigial (with respect to 2,4-DNT degradation) ortho-ring fission dioxygenase is consistent with its recruitment from a pathway for chloroaromatic compounds. The true ring fission enzyme for 2,4-DNT degradation has a different origin. The sequence of DntD is quite dissimilar to all other described meta-ring fission enzymes, including those from naphthalene and chloroarene degradative pathways. The distinctive sequence of the ring cleavage enzyme reflects the substrate specificity observed for the THT oxygenase (28). The distant relationship between homogentisate dioxygenase and DntD and the association with homologs from amino acid metabolism (dntE and dntG) indicate that the lower pathway operon arose from a gene cluster for amino acid degradation.

The disparate origins of the various dnt and associated genes described in this study are consistent with the difficulties that bacteria face to achieve efficient metabolism of synthetic compounds like 2,4-DNT. The organization of the pathway genes suggests there is a progression towards a compact region en-coding the entire pathway. In that progression, remnants from assembly persist, such as the benzenetriol oxygenase (ORF3), putative maleylacetate reductase (ORF10), and putative trans-posase (ORF4). No role in nitroarene degradation is apparent for the remnants; their presence might indicate an intermediate point in the evolution of an optimal system or perhaps some of the proteins could be used in other pathways when another substrate is available.

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posted 24. February 2003 04:06                   

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Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indrect route drops precipitously.

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posted 26. February 2003 00:10                   

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The essential insight is that trial and error may only operate within a given hypervolume—but it may never jump to a new, higher-order hypervolume. The unbridgeable gaps between hypervolumes correspond to the technical contradictions in TRIZ theory.

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posted 26. February 2003 03:36                   

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But I'm not hopeful--it seems that most of my critics aren't willing to think that hard and consider what sorts of genetic changes they're dealing with.

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The essential insight is that trial and error may only operate within a given hypervolume—but it may never jump to a new, higher-order hypervolume. The unbridgeable gaps between hypervolumes correspond to the technical contradictions in TRIZ theory.

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The point I've been trying to make is that a given dimension of a hypervolume, along which the Darwinian process can move, is itself determined by MULTIPLE fundamental parameters, which themselves do not evolve but determine the hyperspace in which evolution can happen.

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However, the ideas I'm dealing with are a good bit more sophisticated than that, and don't admit to easy simplification to the superficial (and therefore likely incorrect) level you want

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posted 26. February 2003 12:07                

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A duplicated gene that evolves is still going to be interpreted in light of the "old" genetic network, and will only be able to produce (at best) variants of what existed before. Genuine novelty (of the inventive sort I'm talking about) simply cannot come about this way because you're just moving around in the hypervolume of possibilities--you're not re-engineering it to make new possibilities available to be explored.

Several people have argued that the icebreaker example could be just a "duplication" of the hull or that you just need to "add a hole" to the hull to get this inventive change. But let's think a little more clearly about this scenario. Imagine that we just add a hole in the hull of the ship. Obviously, this could cause some serious problems. A hole in the hull will quickly sink the ship (assuming it's below water-line). Getting a sealed hole through the hull (such that it's still water-tight) is no minor change--it's a fundamentally different morphology in which the hull has a highly specific, tightly constrained opening added. The opening cannot "halfway" be added--it's fully functional or else the boat sinks. Further, imagine that we add the right sort of hole, but in the direction perpendicular to the direction of motion. Certainly, this does nothing to provide a better icebreaker, since the ice still cannot move through the hull. Additionally, the side walls of the new hole in the hull need to be thin enough to provide improved functionality, and the hole has to be "deep" enough to allow the entire thickness of the ice sheet to pass through. So you can see that the constraints on the system are a bit more severe than just "add a hole to the hull". Similarly, just duplicating the hull won't do it either. The most obvious result of hull duplication is to make a catamaran. It's not at all obvious how these two hulls would then join beneath the ice, or how they would be thin enough to slice through ice (esp. if the original hull was not thin for slicing). If we duplicate vertically, one still has to do massive re-working of the upper and lower sections--one can't just duplicate the hull as-is and have a working boat. It's always a case of "duplicate AND do A,B,C..." which is required--and I see the A,B,C... part as being very teleological and non-Darwinian in nature.

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• Force, A.; Lynch, M.; Pickett, F. B.; Amores, A.; Yan, Y. and Postelethwait, J., 1999 Preservation of duplicate Genes by Complementary, Degenerative Mutations Genetics 151: 1531-1545.
• Lynch, M.; Force, A. 2000 The Probability of Duplicate Gene Preservation by Subfunctionalization Genetics 154: 459-473.

posted 26. February 2003 13:07                    

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Bottom line: none of the examples presented in this thread, as counterexamples to my arguments have been this sort of inventive change. Simply showing that genes can duplicate and evolve is not enough. The question is: can gene CONTEXTS evolve such that genes are imbedded in the regulatory networks in ways that produce novel structures? A duplicated gene that evolves is still going to be interpreted in light of the "old" genetic network, and will only be able to produce (at best) variants of what existed before. Genuine novelty (of the inventive sort I'm talking about) simply cannot come about this way because you're just moving around in the hypervolume of possibilities--you're not re-engineering it to make new possibilities available to be explored.

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posted 26. February 2003 13:32                    

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b) Cases like the flagellum, and other examples you bring up in your earlier post (sexual reproduction, multicellularity, etc.) which are extremely ancient. It seems to me that assessing the inventiveness of a given artifact (be it biological or human) one must have a fairly complete record of what other artifacts existed at the time. How could be determine if a given Babylonian artifact showed TRIZ like inventiveness unless we had a complete record of what other similar artifacts the Babylonians had? The complaint concerning ID is that inventiveness is only found where that kind of record is missing.

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