I just posted this on another thread, but upon reflection realized that that thread likely had a limited life-expectancy.

Here it is again:

quote:

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Trends Biochem Sci 2002 Feb;27(2):67-74

Evolution of enzyme cascades from embryonic development to blood coagulation.

Krem MM, Cera ED.

Recent delineation of the serine protease cascade controlling dorsal-ventral patterning during Drosophila embryogenesis allows this cascade to be compared with those controlling clotting and complement in vertebrates and invertebrates. The identification of discrete markers of serine protease evolution has made it possible to reconstruct the probable chronology of enzyme evolution and to gain new insights into functional linkages among the cascades. Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting and complement cascades. Extensive similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and from similar macromolecular building blocks.

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Here is the pubmed link.

To frame things in a way appropriate for this forum...

It seems to be agreed upon by everyone that natural processes can do *something* regarding complexity. The question is how much, and at what point does design need to be invoked?

If the author's conclusions in this paper are correct, what does an article like this imply for the design-oriented thinker? It seems like there are several possibilities...but which one is correct?

1) The blood-clotting and immune system complement systems are not IC/SC after all. (this would be in accord with the 'probablistic' definition of IC)

2) The blood-clotting and complement systems are IC/SC, but evolved via natural processes anyhow. (this would be in accord with the 'structural' definition of IC)

3) The blood-clotting and complement systems are IC/SC, but evolved via natural processes anyhow, but the necessary CSI was input by the fitness function (Dembski's NFL, option 1)

4) The blood-clotting and complement systems are IC/SC, but evolved via natural processes anyhow, but the necessary CSI was just obtained by reshuffling pre-existing CSI (Dembski's NFL, option 2).

All of these options appear to be commonly suggested as possibilities by either Behe or Dembski. But I'm not sure that they're all consistent with each other.

I propose a thought experiment: IF the conclusions of this article are correct, which of the above options, if any, should the design-oriented thinker take?

quote:

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From embryonic development to vertebrate blood clotting

Based on the experimental and phylogenetic data, we propose that an ancestral cascade of developmental or immunity serine proteases, and a pool of commonly inherited terminal substrates and auxiliary domains, gave rise to the developmental, immunity and clotting cascades of the protostomes and deuterostomes ( Fig. 2). Among currently known serine protease cascades, the Drosophila dorsal–ventral cascade appears to be the most similar to a developmental/immunity cascade that functioned before the divergence of the protostomes and deuterostomes. This is based on the primitiveness of the proteases in the cascade and on the fact that evolutionary remnants of the Toll-signaling-based effector arm can be found in organisms ranging from Caenorhabditis elegans to Homo sapiens [46,47] . The immune function of the dorsal–ventral cascade switched from a signal transduction-based mechanism to a clotting-based mechanism with the introduction of a spätzle homolog capable of polymerization, exemplified by coagulogen. Arthropod hemolymph cascades later began using the Ser195:TCN/Ser214:AGY/Pro225 lineage of proteases, exemplified by Sp14D. In the meantime, 2-macroglobulin homologs evolved into opsonins such as aTEP-I, giving rise to an advanced arthropod hemolymph immune system in which the new lineage of proteases activated opsonins rather than clotting molecules. Thus, complement was born in protostomes.

Deuterostomes appear to have drawn on the same ancestral genetic pool as protostomes for their complement systems, given the existence of modern-lineage proteases, sushi and EGF domains, and thioester proteins in both phylogenetic groups. The proposed ancestral developmental/immunity cascade probably gave rise to primitive deuterostome complement through a series of intermediates that recapitulated the pathway described above for the protostomes. The parallels between primitive deuterostome complement and advanced arthropod immunity are striking. Both are characterized by the appearance of Ser195:TCN/Ser214:AGY/Pro225-lineage proteases and both take advantage of 2-macroglobulin-type molecules as opsonins. However, auxiliary domain usage differs. Complement therefore seems to have evolved independently in both protostomes and deuterostomes.

The emergence of the advanced deuterostome complement system, featuring both the classical and alternative pathways, occurred by duplication of primitive complement proteins and recruitment of new proteases from the pool of ancestral building blocks. Factor C2 of the classical complement pathway probably arose from a duplication of complement factor B. Recruitment of Ser195:AGY/Ser214:TCN/Tyr225-lineage enzymes with complement-associated auxiliary domains, ancestral versions of factors C1r and C1s, completed the rudimentary classical pathway. The complement pathway was further modified with the addition of the membrane-attack complex effector arm, thus completing the basic elements of the vertebrate complement system [9]. Enzymes such as C1r and C1s subsequently gave rise to the ancestor of thrombin, with the major change being the replacement of EGF and sushi domains with a pair of kringle domains and a Gla domain. Also, new fibrinogen homologs developed that were specialized for polymerization rather than immunologic roles. The thrombin homolog then gave rise to the remaining vitamin-K-dependent clotting factors, marked by the appearance of the Ser195:AGY/Ser214:AGY/Tyr225 lineage and the replacement of the kringle domains with EGF domains. The modern mammalian clotting cascade was completed by the addition of serine proteases such as factors XI and XII, and cofactors such as factors V and VIII, which conferred additional levels of positive and negative feedback regulation [48].

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Sorry about whatever formatting gets lost...

Here is the caption for figure 2; I don't think it's possible to post the actual figure unfortunately...

quote:

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Fig. 2.
Evolutionary changes producing developmental, immune and clotting cascades. The central column, bordered by dashed lines, contains the pool of ancestral cascade building blocks jointly inherited by protostomes and deuterostomes. Cascade elements corresponding to serine protease domains are indicated by solid ovals, and auxiliary domains are collectively indicated by colored boxes. Names of representative proteins are listed to the side. Colors indicate the physiologic functional association of auxiliary domains: red, clotting; yellow, complement; green, development and/or immunity. Cascade elements corresponding to key non-serine protease substrates are indicated by dashed boxes. Text inside colored boxes and ovals indicates major changes in either domain structure or evolutionary markers of serine protease genes; blank circles correspond to Ser195:TCN/Ser214:TCN/Pro225. Text inside dashed boxes indicates the functional roles of non-serine-protease substrates. Upstream proteases corresponding to advanced arthropod immunity and primitive deuterostome complement have yet to be identified, so the upstream and middle proteases for those cascades are indicated by ovals with question marks; the blank boxes represent auxiliary domains that accompany these. The asterisk indicates that the steps leading to primitive deuterostome complement were probably similar to those leading to advanced arthropod immunity. Abbreviations: clip, clip domain; CUB, domain common to complement components C1r, C1s, Uegf and Bmp1; EGF, epidermal growth factor domain; Gla, -carboxyglutamic-acid-containing domain; kringle, kringle domain; MAC, membrane attack complex; sushi, sushi domain; unknown, undetermined domain structure; vWF, von-Willebrand-factor-type domain.

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For instance, this claim:

The proposed ancestral developmental/immunity cascade probably gave rise to primitive deuterostome complement through a series of intermediates that recapitulated the pathway described above for the protostomes.

Propose a test for this.

[ 01 March 2002: Message edited by: Paul A. Nelson ]

quote:

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Originally posted by Paul A. Nelson:
Drosera, how would Krem and Cera's scenario be tested?

For instance, this claim:

The proposed ancestral developmental/immunity cascade probably gave rise to primitive deuterostome complement through a series of intermediates that recapitulated the pathway described above for the protostomes.

Propose a test for this.

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Well, you could start by reconstructing the gene trees for the complement systems of a variety of early-branching chordate lineages. This should allow you to figure out in what order gene duplications etc. occurred. If this corresponds with the scenario, then you've got a confirmation result.

But perhaps you have an alternative scenario for the origin of these systems, and a proposed test for it?

Drosera

PS: Although this really isn't the topic I was proposing for this thread...

[ 01 March 2002: Message edited by: Drosera ]

Well, you could start by reconstructing the gene trees for the complement systems of a variety of early-branching chordate lineages. This should allow you to figure out in what order gene duplications etc. occurred. If this corresponds with the scenario, then you've got a confirmation result.

Have the authors done this? Has anyone?

There's little reason to take this speculative scenario seriously, as something ID theorists should worry about, until it grows up and is tested. Your "thought experiment" about responding to this publication therefore corresponds to wondering what a farmer should do if pigs sprouted wings. Should he put a canopy of chicken wire over their pen, so they can't fly away? Maybe.

quote:

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Originally posted by Paul A. Nelson:
Have the authors done this? Has anyone?

There's little reason to take this speculative scenario seriously, as something ID theorists should worry about, until it grows up and is tested. Your "thought experiment" about responding to this publication therefore corresponds to wondering what a farmer should do if pigs sprouted wings. Should he put a canopy of chicken wire over their pen, so they can't fly away? Maybe.

Or maybe not.

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Dear Paul,

I am afraid that perhaps you haven't read the article in question. Just because the authors haven't done a test that I just came up with out of the blue doesn't mean that the authors dreamed up their scenario from nothing.

On the contrary, they present a well-supported argument:

quote:

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Functional and organizational relationships among protease cascades

The cascades controlling dorsal–ventral fate determination, arthropod hemolymph clotting, vertebrate complement and vertebrate blood clotting share several organizational features. Each cascade has a functional core consisting of three required serine proteases (for clarity, referred to individually as the upstream, middle and downstream proteases) that undergo sequential zymogen activation, followed by cleavage of a terminal substrate by the downstream protease ( Fig. 1). Activation of the upstream protease might occur by contact with a non-enzymatic ligand or by cleavage by another protease. Furthermore, there are alternate routes of activating the middle and downstream proteases for some of the cascades, especially for vertebrate complement and clotting. However, for the sake of simplicity, the focus of this discussion is confined to the functional cores and terminal substrates depicted in Fig. 1.

In addition to its position within an individual cascade, each enzyme can be classified according to highly conserved evolutionary markers that divide serine proteases into discrete lineages and indicate the relative ages of those lineages [4] ( Box 1). When the above classification system is applied to proteases within the cascades ( Table 1), a clear pattern emerges: the upstream protease is from a more recently evolved category than the downstream protease. The middle protease belongs to the same category as either the upstream or the downstream protease, depending on the particular cascade. This suggests that each cascade began with the downstream protease cleaving the terminal substrate, and that levels of regulation were subsequently added in the form of middle and upstream proteases. Interestingly, dendrogram-based phylogenetic analyses indicate high sequence similarity for the upstream and middle proteases belonging to modern evolutionary categories in the four cascades [5,6] .

Classification according to evolutionary markers also distinguishes the functional cores of each cascade and enables the order of emergence of the cascades to be determined. The middle and downstream proteases of the Drosophila dorsal–ventral cascade ( Fig. 1a) belong to the most primordial lineage, Ser195:TCN/Ser214:TCN/Pro225. The upstream protease, gastrulation defective, belongs to the lineage Ser195:TCN/Ser214:TCN/Tyr225, a one-marker change from the primordial configuration. The middle and downstream proteases of the horseshoe crab hemolymph clotting cascade ( Fig. 1b) share sequence homology with snake and easter [7], and also belong to the most primordial lineage. The upstream protease, clotting factor C, belongs to the most modern lineage, Ser195:AGY/Ser214:AGY/Tyr225, a three-marker change from the primordial configuration. The lineage of clotting factor C suggests that hemolymph clotting, which mediates both hemostasis and host defense, evolved after the Drosophila dorsal–ventral cascade.

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Let me see if I can get one of the figs up after all...no, doesn't look like it. Ack -- well, I can't quote the whole thing. Suffice it to say that numerous lines of evidence are cited.

Why these variations, simpler functional systems, and similar systems with different functions should exist at all if blood-clotting and the immune complement system are IC & Behe's argument was correct, is another relevant question.

It looks like this is not an isolated article, either. Searching PubMed on 'Krem MM' gets us:

quote:

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1: Krem MM, Cera ED. Related Articles

Evolution of enzyme cascades from embryonic development to blood coagulation.
Trends Biochem Sci. 2002 Feb;27(2):67-74.
PMID: 11852243 [PubMed - in process]

2: Krem MM, Di Cera E. Related Articles

Molecular markers of serine protease evolution.
EMBO J. 2001 Jun 15;20(12):3036-45.
PMID: 11406580 [PubMed - indexed for MEDLINE]

3: Krem MM, Rose T, Di Cera E. Related Articles

Sequence determinants of function and evolution in serine proteases.
Trends Cardiovasc Med. 2000 May;10(4):171-6. Review.
PMID: 11239798 [PubMed - indexed for MEDLINE]

4: Krem MM, Rose T, Di Cera E. Related Articles

The C-terminal sequence encodes function in serine proteases.
J Biol Chem. 1999 Oct 1;274(40):28063-6.
PMID: 10497153 [PubMed - indexed for MEDLINE]

5: Krem MM, Di Cera E. Related Articles

Conserved water molecules in the specificity pocket of serine proteases and the molecular mechanism of Na+ binding.
Proteins. 1998 Jan;30(1):34-42.
PMID: 9443338 [PubMed - indexed for MEDLINE]

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I would venture to propose that Krem has worked quite a bit on this topic...

Drosera

PS: Looks like this lab has a pretty neat webpage also:

Serine Proteases: Evolutionary Trees

Enrico Di Cera's webpage

You wrote:

Just because the authors haven't done a test that I just came up with out of the blue doesn't mean that the authors dreamed up their scenario from nothing.

I'm quite sure they didn't dream it up out of nothing. But their scenario, and an ID-based analysis of the systems in question, are not even in hailing distance of each other. Here's the last sentence of their abstract:

Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting and complement cascades. Extensive similarities suggest that these cascades were built by adding enzymes from the bottom of the cascade up and from similar macromolecular building blocks.

This hypothesis rests entirely on "extensive similarities." Does that get us a testable mechanism for the origin of the particular systems in question? No. Therefore your four questions to ID theorists, in the first post of this thread, are at best premature.

[ 01 March 2002: Message edited by: Paul A. Nelson ]

quote:

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Originally posted by Paul A. Nelson:
I'm quite sure they didn't dream it up out of nothing. But their scenario, and an ID-based analysis of the systems in question, are not even in hailing distance of each other.

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Behe did an analysis of these systems in DBB. He says they're IC and must have been intelligently designed.

This peer-reviewed article disagrees & cites evidence to back it up. Therefore I was interested in *which* of the several possible responses was the "right" one from the ID perspective, *if* the article is basically correct. Several are floating about in the ID literature, but they seem inconsistent with each other.

*if* the article is basically correct.

About what? That similarities exist among the elements of various cascades?

Drosera, through his/her posts, has made some indirect/implicit statements about similarity, which I'd like to comment on, if I may... Both, the contested graphic which shows the various similarities between creatures, and the similarities between the various players in biological cascades, are often used by Darwinists with the implication that they are evidence for Darwinism (and I'm not making any statement with respect to Drosera's reason for posting them here). In neither instance can it be shown however, that such is the case. For in both instances, there are alternative explanations which are just as valid.

Take the graphic first, could not directed evolution (Ala Denton, Behe, Spetner) just as easily account for the hierarchy? What about progressive creation, surely it could account for the pattern of the graphic and even explain the gaps with a more natural fit. No mechanism is mandated by the pattern itself. No demand for natural selection + mutation here at all.

What about similarities between proteins in the cascades? Same thing, directed evolution or progressive creation could fill the bill. Again, no evidence that undirected mutation must accomplish the feat. And in fact, there is a tacit admission that functional intermediates are a problem:

quote:

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The identification of discrete markers of serine protease
evolution has made it possible to reconstruct the probable chronology of
enzyme evolution and to gain new insights into functional linkages among
the cascades.

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So the problem of unselected steps remains a threat to the proposal, as does the problem of integrative complexity, therefore (as Nelson correctly noted), there is a serious need for the testing of each step along the proposed pathway to ensure its viability.

Remember that similarity/relational hierarchies can be constructed from many different types of intelligently designed things, often times having extremely limited direct causal connection, consider the following............Wheel, Unicycle, Bicycle, Moped, Motorcycle, Car, Airplane, Jet, Space Shuttle. A natural progression, but is it due to Darwinism? No! Directed Evolution? No. Progressive Creation? Yes. The point here is not to call this evolution, and especially not Darwinian evolution.............................Cre8

[ 02 March 2002: Message edited by: Cre8ionist ]

quote:

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Originally posted by Cre8ionist:
Take the graphic first, could not directed evolution (Ala Denton, Behe, Spetner) just as easily account for the hierarchy? What about progressive creation, surely it could account for the pattern of the graphic and even explain the gaps with a more natural fit. No mechanism is mandated by the pattern itself. No demand for natural selection + mutation here at all.

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The thing is, the nested hierarchy prediction falls straight out of the proposition that descent is lineal, from parent(s) to child, with changes (however they occur) being inherited, but only vertical inheritance occurring. *If* this is how things work, then the nested hierarchy prediction falls straight out of this process.

(so, really, RM & NS is not what produces nested hierarchy, rather descent with hereditary modification produces it)

I see no particular reason why directed evolution or progressive creation would *necessarily* produce this pattern. Sure, they *could* produce the pattern, just as Last Thursdayism (god created the world last Thursday) could produce it as well.

Evan is discussing this well over on this ISCID thread:

http://www.iscid.org/boards/ubb-get_topic&f-6&t-000025

quote:

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What about similarities between proteins in the cascades? Same thing, directed evolution or progressive creation could fill the bill. Again, no evidence that undirected mutation must accomplish the feat. And in fact, there is a tacit admission that functional intermediates are a problem

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quote:

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So the problem of unselected steps remains a threat to the proposal, as does the problem of integrative complexity, therefore (as Nelson correctly noted), there is a serious need for the testing of each step along the proposed pathway to ensure its viability.

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The thing is, we *already know*:

1) Random mutations occur (including gene duplications & other 'macro' mutations -- point mutations are not the limit of mutation)

2) Natural selection occurs wherever reproduction outstrips carrying capacity

3) New genes can originate via these processes, e.g. as reviewed in this article in Current Opinion in Genetics & Development:

quote:

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Link: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11682312&dopt=Abstract

Curr Opin Genet Dev 2001 Dec;11(6):673-80
Evolution of novel genes.

Long M.

Much progress in understanding the evolution of new genes has been accomplished in the past few years. Molecular mechanisms such as illegitimate recombination and LINE element mediated 3' transduction underlying exon shuffling, a major process for generating new genes, are better understood. The identification of young genes in invertebrates and vertebrates has revealed a significant role of adaptive evolution acting on initially rudimentary gene structures created as if by evolutionary tinkers. New genes in humans and our primate relatives add a new component to the understanding of genetic divergence between humans and non-humans.

[...]

New functions evolved from gene duplications

The classic model for the origin of new gene functions is based on gene duplication [42], proposing that while one copy of a pair of duplicate genes maintains the original function, the other copy can accumulate mutations for further evolution of new functions. Although many theoretical models have been proposed to describe the gene duplication process, it should be emphasized that gene duplication is not synonymous with the gaining of new functions. A duplicate gene can have several evolutionary fates: first, it becomes a pseudogene; second, it maintains redundant functions; and third, it gains new functions. Walsh [43] examined the probability that a gene duplication evolves new functions under a simplified assumption incorporating only the first and third of these scenarios. He showed that a duplicate copy is in general much more likely to become a pseudogene instead of a new functional gene. He also showed that if a duplicated gene acquires an even slightly advantageous function, then it is unlikely to become nonfunctional in subsequent evolution. Ohta [44] proposed a probability model to examine the role of neutral mutation in the evolution of new gene functions. Gu [45] proposed a statistical method to detect potential functional divergence between duplicate genes.

There are many new functional genes evolved from gene duplications—for instance, hemoglobin genes in humans, in which duplicate copies are expressed at different developmental stages. A compelling case was reported recently in centromeric H3-like proteins in Drosophila [46••]. A member of this family, the Cid gene, in D. melanogaster functions in the centromere to determine the specificity of centromeric DNA binding. An evolutionary feature of centromeric DNA is the fast change of its component satellite repeats as a consequence of insertion of new mobile elements or loss of old repeats. For example, in a closely related Drosophila species that diverged for only 2–3 million years, the components of centromeric DNA diverged significantly. A biological question is how could the function of Cid respond to such rapid change in centromeric DNA? Malik and Henikoff [46••] find that Cid in D. melanogaster and D. simulans adaptively evolved new binding functions by equally rapid changes in its protein sequence. A recent laboratory experiment by Rosenzweig and co-workers [47] also showed that new duplicate copies of hexose transport genes in Saccharomyces cerevisiae originated only following 450 generations of selection in a glucose-limited medium. This interesting experiment, with early selection experiments in micro-organisms for the origin of new gene functions [48,49] demonstrated the significant role of selection in the origin of new gene functions.

[..]

The role of 'tinkers'

Various mechanisms for new gene evolution have been investigated, which often understandably point to deterministic optimization of the structure and functions of new genes. It may give insight to revisit the concept of 'tinkerism', the important but often overlooked idea of 'evolution as tinkering', proposed by Jacob [57] to describe how evolution works to generate novelties. In this view, evolution does not behave like a good engineer who always wants to do the best job with a well-prepared plan and specifically provided materials. Instead, evolution works like a tinker who uses whatever material comes to hand in making a device that crudely serves some new functions but does so in a far-from-perfect manner at first. Thus, a tinker can make a roulette table from an old bicycle wheel or a TV stand from a broken chair.

Nurminsky et al. [58] investigated the origin of Sdic, an evolutionarily new gene in Drosophila. It originated in the single lineage of D. melanogaster, after its split only three million years ago from its sibling species. Sdic is one of the two youngest genes known (the other gene, Jingwei, also in Drosophila, is under 2.5million years old) [59]. Remarkable in the early life of this gene are the unusual origins of various of its essential parts: deletion created the chimera; a new exon evolved from an intron of the Cdic parent; and the new testes-specific promoter formed from an exon in parent AnnX. As the resources for its various parts are so dissimilar to their eventual uses, both functionally and structurally, one could scarcely have predicted that they would be connected together. These changes provide evidence of tinkerism.

Furthermore, the high rate of protein evolution in the above examples indicates imperfection of the original parental genes or gene fragments for the novel functions they eventually serve. Otherwise, these proteins would not have been so rapidly changed by the force of natural selection. The high substitution rates of the shuffled exons, as shown in Sdic and other new genes [9,59] , however, suggests that the original exons were not adept in their new roles and needed further modifications by the diligent tinker. Thus, the concrete case of the Sdic gene and the rapid evolution of new genes known previously reveal tinkering evolution. This route of evolution, added to the powerful mechanisms of exon shuffling and duplication that provide novel but often imperfect genetic materials, would create a vast diversity of genes.

New gene functions follow Darwin's scenario

Whereas the mutation process that creates initial structure paints a dramatic picture for the first step in the evolution of new genes, the various evolutionary forces involved in the next step—the fixation of the new genes, at the various stages of their improvement in whole species— can next be considered.

Most new genes that originated from exon shuffling and gene duplication have undergone significantly elevated rates of evolution when compared to their parental genes. Jingwei has a significantly elevated rate of evolution in its protein sequence and gene structure, signifying strong protein adaptive evolution throughout its evolutionary history [59,60,61••] . Sdic evidences rapid sequence change and low within-species variation [58,62,63,64••] . Similarly, another new gene in Drosophila, Fannegan, which was generated by gene duplication 20 million years ago, also showed fast protein sequence evolution [65]. A plant cytochrome C1 precursor gene recruited a novel mitochondrial-targeting domain 100–120 million years ago, which evolved 30–50 times faster than its ancestral counterpart [9]. Ohta [66] noticed higher rates of evolution associated with functional divergence in some anciently duplicated genes. These examples are consistent with a role for Darwinian selection in shaping the structures of new genes.

Most attention has been focused on new genes that adopt different functions, a process shown to be governed by Darwinian selection. New progress has also been achieved in understanding convergent evolution. Novel genes in different lineages can evolve the same new function under similar selection pressures. The crystallins—eye lens proteins that contribute to the high refractive index needed for the lens to focus light—provide a good example for the same function being evolved from different proteins. Ancestral genes code for proteins as diverse as small heat shock proteins, lactate dehydrogenase B, and ornithine cyclodeaminase (e.g. [67,68] ).

Antifreeze proteins provide an explicit example of convergence from disparate origins [69–72] . The antifreeze glycoproteins (AFGPs) in polar fishes form a family of proteins that bind to ice crystals in the cells and block further ice crystal growth. Whether in Antarctic or Arctic fishes, these proteins have a similar molecular phenotype— many glycotripeptides (Thr-Ala/Pro-Ala)n interspersed with short peptide spacers—but these genes are very different in exon–intron structures, codon usage, and spacer sequences [69]. Furthermore, the AFGP in the Antarctic fish has very high similarity to trypsinogen genes, suggesting its recent origin (5–14 million years) from the latter gene [70].

Identification of a hybrid gene of AFGP and trypsinogen genes in an Antarctic fish, Dissostichus mawsoni, further confirmed the origin of the Antarctic AFGP [71]. Although it is unclear how Arctic AFGP originated, it is more parsimonious to infer a recent convergent origin for Antarctic AFGP.

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Once one knows that new genes/proteins in fact regularly originate via these kinds of processes, then the only question is can those processes get you to more complex multigene systems. The first article I cited indicates that this is possible.

quote:

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Remember that similarity/relational hierarchies can be constructed from many different types of intelligently designed things, often times having extremely limited direct causal connection, consider the following............Wheel, Unicycle, Bicycle, Moped, Motorcycle, Car, Airplane, Jet, Space Shuttle. A natural progression, but is it due to Darwinism? No! Directed Evolution? No. Progressive Creation? Yes.

---

But in fact, statistical studies of human-designed objects do not fall into robust matching nested hierarchies like organisms do.

Ack, talkorigins is down, so I can't reference the article, but see Doug Theobald's "29 evidences for evolution" FAQ.

[added in edit, here it is, with lots of references:

Prediction 2: A nested hierarchy of species ]

Regards,

"Mr." Drosera

PS to Dr. Nelson -- I cited a peer-reviewed article in TiBS, I'm not sure what else one can do. Obviously this is a new article so perhaps expecting a response this fast was unreasonable. But certainly, sooner or later the ID community will have to engage that kind of work at that high level, and present convincing arguments to those biochemists that the ID view (whatever it is, exactly) should be preferred over the current one. I'll leave that as my last thought on this thread.

[ 03 March 2002: Message edited by: Drosera ]

1. Please avoid excessively long quotations from outside sources. Links will do (thanks for your note about the subtelty of our links: we will be correcting that). I will begin to enforce this more strictly as soon as everyone at this forum has come to terms with the proper tone and focus of Brainstorms.

2. "PS to Dr. Nelson -- I cited a peer-reviewed article in TiBS, I'm not sure what else one can do. Obviously this is a new article so perhaps expecting a response this fast was unreasonable. But certainly, sooner or later the ID community will have to engage that kind of work at that high level, and present convincing arguments to those biochemists that the ID view (whatever it is, exactly) should be preferred over the current one. I'll leave that as my last thought on this thread."

Thanks for the note.

I don't like posting long quotes either -- but Dr. Nelson had written of my previous posts,

quote:

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I mean to be stubborn about this. This is an ID board. Loose standards of empirical demonstration may work elsewhere on the web (e.g., on talk.origins), but I for one want to see higher marks chalked on the wall here.

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...which has more than a few unkind implications. The way I see it, I cited a peer-reviewed article, and Nelson brushed it off with some undocumented assertions, and then accused me of "loose standards of empirical demonstration". Hopefully you can see how that led to my slightly sharper remarks.

My remarks about the ID community, however, were indeed overgeneralizing, and I retract.

It looks like another poster is interested in my original question. If the thread develops in this direction I may continue to contribute here, otherwise it will be on other threads.

You might be interested the following essay I wrote:

Irreducible Complexity ReVisited

Also, if you check out the TeleoLogic section, I am analyzing the bacterial flagellum with the level of detail that Drosera wants. See No. 10-13 (six more essays will follow to complete a 10-part analysis).

[ 03 March 2002: Message edited by: Mike Gene ]