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Author
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Topic: Front Loading: A Research Program (based on the ideas of Christian Schwabe)
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John Bracht
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Member # 5
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posted 01. May 2002 11:47
I just want to say that I really appreciate charlie d. and Drosera's participation on this board and I do not, in any way, view them as "trolls." They have a valuable differing viewpoint that deserves to be heard. I hope they stick around and continue to offer that viewpoint to enrich our discussions. I, for one, think they are NOT to be "dismissed."
That said, charlie, I think you might want to go back and edit your post. I went back and re-read your original comments (which the moderator cited) and you certainly seem to be saying that Mike and I are espousing a front-loading view specifically because we want purpose or meaning to life. Comments like "It seems to me that even within a front-loading context, designed to do away with the uncomfortable concept of human life as a random event..." are certainly prone to be interpreted as implying that Mike Gene and myself are embracing a front-loading view at least partly because we're not strong enough to take the hard, cold reality of the meaninglessness of human existence. Not only do you assume the point in question, but you are implicitly assuming some things about our objectivity and character. You can claim that you meant something different, but I suggest that you alter the post to make it agree with what you meant.
Finally, (getting back on track a bit), I think it's worthwhile to point out that purpose is definitely a part of front-loading; neither Mike nor I ever pretended that front loading wasn't a teleological perspective. The problem comes when people dismiss front-loading as merely a metaphysical coping strategy for those uncomfortable with a purposeless, meaningless universe. That begs the question and implies an ad-hominem to boot. Let's get back to the original topic and investigate front-loading and its associated purpose from a scientific point of view.
John Bracht
[ 01 May 2002, 12:12: Message edited by: John Bracht ]
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Janitor@MIT
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posted 01. May 2002 12:33
There exists a considerable body of research into complex adaptive systems that is not predicated on traditional biological theory of origins. You’ll find it under headings of artificial intelligence, machine learning, adaptive and robust control, etc.
There may be some skepticism that such systems can be built to handle real-world exigencies, but of course that is exactly what the designer intends: that the system adapt to changes unanticipated by the designer and unpredictable by him. And of course there are systems that do indeed observe, predict, and anticipate adaptation to even extremely rare and improbable events, such as an asteroid impact. The objective of the designer of such a system is to equip it with robust adaptive control strategies. The technological ideal would be a system that emulates the designer himself (as in AI).
Genome size is a bit of a red herring here. Since its not a question, from an engineering perspective, of loading the genome with genes anticipating all possible contingent uses or all possible developmental (“evolutionary”) vectors; but loading it with generalized and effective adaptive strategies that enables it to evolve “intelligently,” so to speak, to contingencies that cannot possibly be predicted (at least over some arbitrarily large interval).
I’ve noted here (ISCID) that some of these strategies are to be found in the very design of the code: forcing adaptive searches forward through neutrally structured design spaces, e.g.
Biologists might have been well advised fifty years ago to take seriously the code/program metaphor they adopted. They may by now have come around to the view that a genome is not merely ad hoc adapted to impositions of necessity or the vagaries of chance, but is actively and strategically adaptive. The antique view that life adapts “accidentally” by the skin of its teeth is unworkable and leads to all sorts of amusing interpretations of results that reveal life actively searching for solutions to the problems of its own continued existence and evolution.
Mike Gene considers the role of duplication in genomic expansion and I am also considering the same thing. My predicate is that genome expansion systematically exploits naturally given recurrence relations that exist and emerge from highly integrated complex systems, just as occur in complex analysis and dynamic programming. I’ve simply presumed that evolution occurs according to how a mathematician understands the “evolution” of a system of equations, rather than how Charles Darwin understood it. (Why should I have this unholy regard for Darwin?--since Darwin wouldn’t know a gene if it bit him in the butt!) Hackers could also provide some interesting insights into how complex programs “evolve” iteratively and imperatively, rather than accidentally and haphazardly.
Why not consider the possibilities of looking at things a little differently? Why all that “junk DNA”? Using Mike Gene’s presumptive teleology I go to an expert (a communications engineer, not a geneticist) and ask why she includes long and simply repetitive and apparently random sequences in a message she transmits? First she gets that indulgent and bemused look on her face, you know the one, where you’ve asked a perfectly naīve question that has a very simple and straightforward answer, but answering it tests the patience of experts in suffering fools. Then she explains why there is a perfectly rational reason for doing so--including long repetitive or random sequences in a message.
(Any ambitious grads in biology out there? Go ask the expert, type up his answer as an abstract, hustle it off to PNAS. It’ll look good on your curricula vitae. You can always toss in a reference to ole Charles. His imprimatur is always helpful. Kinda makes it look official. The engineer will understand. We’re used to anonymity. LOL)
Now “purpose” isn’t even a scientific question, at least as it has been posed, from the traditional perspective. But if Mr. Moderator will indulge me, and with no intention of expanding the topic or allowing it to go off track, I will offer some speculation of how “purpose” relates. If the design objective is to emulate the intelligence of the designer, then there is of course no inherent or intrinsic, or imposed “purpose” for the design other than emulation. The very “purpose” is to enable it (the design) to search for and discover “purposes” of its own, if you know what I mean. Adaptive design at this level absolutely requires a high-level of autonomy. Imposing some “purpose” on the design effectively circumvents the very objective of enabling adaptability. There is no usual engineering trade-off here, as the objectives of some rigid “purpose” and adaptability are irreconcilable. A hammer is an example of a dedicated design. Its purpose is to drive nails. It implements little adaptability. Whereas a computer is a highly adaptable design in a broader, but still limited, context. It is a very generalized data processor, and so is pre-adapted to adapt to a multitude of such tasks. The theory is now quite old, but you’ll find it under the headings of self-reproducing automata, universal machines, and universal constructor. It is the object of all AI and machine learning research and even occasionally of “science fiction.”
(If Mr. Moderator feels that this has too much potential to spin out of control, he should feel free to redact the offending “unscientific” speculation. I don’t know how you guys do that, that’s why I appear to be habitually tentative about my posts. I don’t require any notification or anything like that, e.g. Just do whatcha gotta do. I understand perfectly.)
The traditional view is that evolution “just happens” to life, but I take the opposite view, evolution is what life does. If evolution is what life does, than a restricted teleological perspective occurs quite naturally. That something “just happens” is not a scientific theory at all. It’s a placeholder for our ignorance of what’s really happening. The traditional view is subtly but profoundly misinformative, and it could use the injection of some fresh and original insights and possibilities. A “rational reinterpretation” of biology is past due. Evolution is not fact, and its not theory: Evolution is applied science.
[I should include a disclaimer here. I haven’t a clue that Mike Gene’s (or anyone else's) and my thoughts correspond on any detailed level. But I have nothing but words of encouragement. Look at things differently. It’s the scientific way.]
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Moderator
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posted 01. May 2002 14:10
As I'm in the business of coming down hard on people (I'm glad people are aware of me as they write!), I've recently been convicted to "come up" hard on people. Does that makes any sense!
Anyway, Janitor, I love your posts. I look forward to reading them, both for the humor and the novel angles you take on these ideas. I think that your clarification of "enabling design" or "dedicated design" is very helpful. The purpose for the design may well be in the emulation...as you state.
In any case, great post. ![[Cool]](cool.gif)
[ 01 May 2002, 14:12: Message edited by: Moderator ]
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John Bracht
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Member # 5
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posted 01. May 2002 17:41
I just came across a jewel of a quote from Simon Conway Morris that really agrees with some of the ideas we've been discussing:
quote:
Molecular biology enlarges our horizons, but without a firm basis in evolutionary theory, the most interesting questions still elude us. There do, however, seem to be some trends. First, the diversity of life is, in molecular terms, little more than skin deep. Most, perhaps all, of the basic building blocks necessary for organismal complexity were available long before the emergence of multicellularity. How and when the gene networks and regulatory mechanisms that led to complex organs and functioning organisms were assembled is largely obscure. Cooptation and transfer of function could be equally important, but here, too, we can do little more than articulate general principles. Just as the phenotypic diversity of life excites the imagination of a naturalist, so the range of molecules and the sophistication of their biochemistries impress the molecular biologist. In comparison, the underlying constraints on form and the inevitability of convergences have recieved far less emphsis. Why should this be so? There seem to be two reasons. The first is that if evolution is in some sense channeled, then this reopens the controversial prospect of a teleology; that is, the process is underpinned by a purpose. It is no coincidence that interest in the Anthropic Principle, which broadly seeks evidence for the boundary conditions of the Big Bang and the ensuing physics and chemistry uniquely favoroing the emergence of life, is being extended to the fields of biochemistry and molecular biology. Second, the study of evolution is strongly historical, and the prospect of a seemingly unique trajectory of circumstances for the history of life may be discoureaging to those who are seeking general principles. Yet here, too, the search for convergences may yield unexpected insights, and the work by Travisano and coworkers on the replicability of evolution in bacteria is of particular importance.
[From: Morris S. Evolution: Bringing Molecules Into the Fold. Cell 7 Jan 2000;100:1-11. Emphasis added. Note: This paper is a real treasure and well worth reading if you're not familiar with it.]
Compare the first bolded section from the Morris quote above with this quote from Christian Schwabe:
quote:
Multicellularity, single cellularity, the difference is genomic complexity, nothing changes fundamentally as life proceeds from one to the other.
In other words, it's almost as if life were given all the "building blocks" at the beginning and it simple re-shuffled and re-expressed those genetic elements over time. Evolution is not the acquisition of new genes and information; its the rearrangement and re-expression of the information that was loaded into it in the beginning. In fact, the beginning of the paper discusses these ideas with some concrete examples:
quote:
The fact that the arm that brandishes the newspaper, the eye that scans the room, and the heart that pumps the blood, and even the entire orientation of the body all find corresponding genomic counterparts (e.g., Pax-6, tinman, etc.) in the fly buzzing around the room is almost too well known to require further emphasis. And such deep and pervasive similarities amongst the metazoans seem to be the rule. Consider, for example, the sponges, which by general consent are the most primitive living metazoans. Nevertheless, their biochemistry includes elements that seem to foreshadow the immune system of vertebrates. Sponges do not have nerve cells, but paradoxically they possess neuronal-like receptors. Moreover, in one group of sponges (the hexactinellids), electrical impulses have been detected. Even though their unusual syncitium might be peculiarly conducive to such propagation, some evidence suggests hexactinellids are the most primitive of the sponges. With such features, sponges seem to be almost "animals in waiting": everthing is in place but nothing happens. This, however, is a distorted view. First, many of the basic building blocks and processes found in the metazoans are very widespread among eukaryotes and must have originated much earlier than the first animals. Second, sponges are well adapted, abundant, and diverse. They are highly organized, capable of coordinated response, and despite the relative simplicity of their bodyplan, some sponges demonstrate a radical reorganization concomitant with a shift to carnivory.
And skipping down one paragraph:
quote:
At a more advanced level, the amphioxus (the most primitive living chordate, widely regarded as a sort of pre-fish) also provides some good examples of such inherency. Molecular data strong support the notion that this animal is the most primitive living chordate, notably in terms of its possession of a single Hox cluster. Conginuing genomic investigations and careful historical studies of such features as the eye, the nervous system, and the organ known as the endostyle (prmitively a ciliated gutter on the floor of the pharynx that ultimately gives rise to the thyroid) again reveal a "vertebrate in waiting." In this case, however, the evidence for gene duplications, and presumably new regularoty pathways, could allow a closer tracking between genomic innovation and the emergence of the vertebrate bodyplan.
I like the term "animals in waiting" or "vertebrate in waiting"; these terms indicate that the necessary genomic components were pre-loaded and ready to go. Gene duplication and evolution of new regulatory pathways could have been the mechanism by which the inherent potential was actualized. This accords well with Janitor's notion that life is "actively and strategically adaptive." Consider the very last few sentences from the Morris paper:
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Evolution obviously occurs in the river of time, and in many ways the world of the Cambrian, let alone the Archaean, is very different from that of today. Yet, as discussed earlier, the very similar genetic architecture that underpins the arm with which I write this article and the wing of the passing fly introduces the sobering possibility that much of organismal architecture is dependent on a set of "toolboxes," each opened as and when the need arises. And this is perhaps the central conundrum of evolution: how do we balance the process of change against the emergence of form?
It sounds to me like the opening of toolboxes is more of a teleological process than a purely chance-driven one. Perhaps a case of derived intelligence?
John Bracht
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charlie d.
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posted 01. May 2002 19:03
Hmmm... I think that the concept of evolution as a tinkerer (or, more accurately, and much better-sounding, in french, a "bricoleur", is 40 years old, give or take a few). That all existing genes can be eventually tracked back to genes in more ancient organisms is in fact a paradigm of evolution. Of course amphioxus looks like a vertebrate-in-waiting: vertebrates are evolved protochordates. But why aren't mollusks, or insects, anything-in-waiting? That seems to me is the real teleological question (and I'll get back to it).
I think the most telling sentence in John's Morris quote in fact is:
quote:
This, however, is a distorted view. First, many of the basic building blocks and processes found in the metazoans are very widespread among eukaryotes and must have originated much earlier than the first animals. Second, sponges are well adapted, abundant, and diverse. They are highly organized, capable of coordinated response, and despite the relative simplicity of their bodyplan, some sponges demonstrate a radical reorganization concomitant with a shift to carnivory.
That is, while evolution must work with the set of tools it has been given by the contingencies of past history, every step of the way also must follow the contingencies of local adaptation. That is why, of course, sponges and protozoa and bacteria also possess an equally large number of genes that got lost, or were never co-opted into novel and different forms and families in later organisms. That is why eukaryotes had to "reinvent" the flagellum, different species of arctic fish used the same basic strategy to generate anti-freeze proteins, but all started from very different precursors, and insects, birds and bats all came up with different engineering solutions to generate aerodinamic surfaces useful for flying.
I also strongly disagree with Janitor that the "traditional view" (I imagine he means the "darwinian" view) is that evolution "just happens". Evolution is an unavoidable consequence of the chemistry of life. The moment there was an imperfect self-replicator, evolution had to happen, with faster, more stable, more (but not entirely!) accurate replicators replacing their predecessors. It seems quite likely at this point that a self-replicating ribozyme will be generated in a lab within the next decade or so, and the moment that molecule will exist, it will start evolving (if allowed to by us, of course).
In the end, teleology can of course explain everything: what is not useful today, can be useful tomorrow. Like all the junk in my 6-year-old son's pockets, which can be come a plaything at any moment, our pseudogenes could be a testimony to engineering foresight, rather than a burden we have to cope with. Like Janitor's expert's string of senseless code, they may have some mysterious role to play at some point (ah, don't experts have an answer for everything! That must be the reason for all the junk in Microsoft's programs...).
That is why I think if teleologists want to play this kind of game, the question of purpose IS crucial. Of course, they don't have to: Mike seems to say that the progenote was given the ability to evolve in every possible direction simply according to random changes and local adaptation. Who am I to argue with that? Schwabe thinks all the "purpose" we see may be the result of some yet-unexplained quantum mechanics "trick": purposeless teleology, I guess.
But if, like John seems to suggest, protochordates truly (and not just figuratively)are vertebrates-in-waiting, the question must be answered:
what's so special about vertebrates?
[ 01 May 2002, 20:16: Message edited by: charlie d. ]
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Drosera
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posted 01. May 2002 21:45
I thank Charlie D. there for making the points I was going to make, and probably more clearly than I would have.
The great thing about Conway Morris is that he really strives for a complete, integrated, and balanced view -- perhaps somewhat in reaction to Gould's interpretation of his work I suspect. I think that if one looks at the overall theme of his work, it quickly becomes clear that his position is devasting to all of the traditional ID arguments relating to the origin of the Cambrian phyla -- i.e., he identifies transitional forms between some of the supposedly disparate phyla, argues that the "Cambrian Explosion" was preceded by a fair bit of multicellular-but-soft-bodied, near-microscopic planktonic/wormlike forms and in general has strongly advanced the case that the origin of complex metazoans can be understood without resort to anything very radical.
The quote that Charlie D. pointed out, where Conway Morris rather specifically debunks the "sponges are animals in waiting," front-loading type notion, is a case in point.
Me, I think that humans are echinoderms-in-waiting, as humans still retain the primitive bilateral symmetry in our adult forms that the more-highly-derived echinoderms long ago replaced with secondary five-fold radial symmetry.
(Here is another recent article by SCM in PNAS)
(here is the whole free PNAS special issue on "Evolutionary Developmental Biology", with many articles in addition to Conway Morris' on the origin of metazoans)
(Here is a very recent (2002) review of the Cambrian "explosion" by Valentine, wherein he concludes:
quote:
Some of the factors that may have influenced the explosion events have been briefly noted above. They presumably included evolutionary responses within the fauna to those taxa that were emerging with novel bodyplans and occupying new regions of adaptive space, the sorts of adaptive feedbacks that can be imagined as marine ecosystems evolved from Neoproterozic to Phanerozoic styles. As emphasized by Budd & Jensen (2000), the explosion does not require a radical explanation, at least now that it can be seen how the evolutionary modes involved in the explosion included at their core the evolution of developmental systems and not simply the changes associated with structural gene substitutions. Conditions during the Early Cambrian clearly permitted diversity increases among the explosion taxa, and perhaps the extent of the explosion was influenced by those factors as many workers have suggested. Just how far Neoproterozoic metazoans reached along the trajectory of increasing complexity that culminated in the bodyplans of the explosion fauna, and just how diverse the Prelude faunas were, remain uncertain. Future studies that combine geological and paleontological evidence with molecular tools should take us significantly closer to the answers.
)
Switching gears a bit...
"New" information
Regarding recent suggestions about "reshuffling information" vs. "new information", I'm not sure that there is any principled distinction that can be drawn. Certainly clear criteria would have to be set up to define these terms if any serious arguments are going to be based on them -- if this doesn't happen then there is the great danger that there will simply be a replay of older antievolution arguments about supposedly distinct "kinds" "basic types", "major groups", etc., none of which ever received a respectable, stays-in-one-place definition.
When, exactly, is something "new"? One obvious example where this is problematic is hox genes in "lower" metazoans -- e.g., sponges, sea anemones, etc. appear to have Hox genes, but only a few. When these are duplicated many times, resulting in a dozen or more genes, and specialized for more specific functions, how can this not be both an increase in information and complexity on any reasonable definition?
Similarly, how can the origin of developmental, immune, and blood-coagulation systems from a common ancestral system, as discussed in some detail in the paper below, not be an increase in information and complexity on any reasonable definition? Brushing these types of things off as "reshuffling" seems to do them an injustice.
quote:
link
Trends Biochem Sci 2002 Feb;27(2):67-74
Evolution of enzyme cascades from embryonic development to blood coagulation.
Krem MM, Cera ED.
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St Louis, MO 63110-1093, USA.
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.
Drosera
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Drosera
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posted 01. May 2002 21:53
Here's that Budd & Jensen (2000) paper that Valentine referenced, it again is provocative to many traditional views about the "explosion".
quote:
A critical reappraisal of the fossil record of the bilaterian phyla
Budd GE, Jensen S
BIOLOGICAL REVIEWS OF THE CAMBRIDGE PHILOSOPHICAL SOCIETY 75 (2): 253-295 MAY 2000
Abstract:
It has long been assumed that the extant bilaterian phyla generally have their origin in the Cambrian explosion, when they appear in an essentially modern form. Both these assumptions are questionable, A strict application of stem- and crown-group concepts to phyla shows that although the branching points of many clades may have occurred ill the Early Cambrian or before, the appearance of the modern body plans was in most cases later: very few bilaterian phyla sensu stricto have demonstrable representatives in the earliest Cambrian. Given that the early branching points of major clades is an inevitable result of the geometry of clade diversification, the alleged phenomenon of phyla appearing early and remaining morphologically static is seen not to require particular explanation. Confusion in the definition of a phylum has thus led to attempts to explain (especially from a developmental perspective) a feature that is partly inevitable, partly illusory. We critically discuss models for Proterozoic diversification based on small body size, limited developmental capacity and poor preservation and cryptic habits, and show that the prospect of lineage diversification occurring early in the Proterozoic can be seen to be unlikely on grounds of both parsimony and functional morphology. Indeed, the combination of the body and trace fossil record demonstrates a progressive diversification through the end of the Proterozoic well into the Cambrian and beyond, a picture consistent with body plans being assembled during this time. Body-plan characters are likely to have been acquired monophyletically in the history of the bilaterians, and a model explaining the diversity in just one of them, the coelom, is presented. This analysis points to the requirement for a careful application of systematic methodology before explanations are sought for alleged patterns of constraint and flexibility.
Drosera
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Mike Gene
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posted 02. May 2002 00:42
Charlie,
Let me again clarify that I am not arguing the validity of FLE, as it is much too early for this. As I said, I'm fleshing out a completely different heuristic perspective, one that has additional conceptual tools. You write, "So, to paraphrase Mike, the real question is: how do you directly design a seeding organism without really knowing what the environmental conditions are going to be like in a few thousand years, let alone a billion?" Yes, that is the real question. But while you apparently think the answer is in, and are ready to throw in the towel at the first sign of difficulty, I would simply note that any attempt to take this hypothesis off the table comes with little or no experimental effort to answer the question. As our ability to design organisms improves, I think this question will lend itself to experimental analysis. Thus, my interest is to initiate new ways of thinking to prime other teleologists to take the lead into this uncharted territory.
Now, the question is just how far we can extend a front-loaded state. There are many reasons to think this is feasible. For example, the very fact that evolution relies so heavily on borrowing means that evolution can tap into your design. Better yet, it means your design channels evolution. If things can be pre-adapted, then with a sufficient knowledge base, one can design things to be pre-adapted. But the important key is to rid oneself of determinism and stop thinking of FLE as a preprogrammed event. Instead, think of it as biasing a random walk or increasing the odds that a future target state might be reached.
You write, "the sheer number of potential evolutionary routes is staggering, and any prediction meaningless." Really? Are there many studies attempting to design through evolution, resulting in complete failure to realize targets? Furthermore, the ubiquity of convergence suggests that the routes are not quite as staggering as they would seem. Neither do the number of phyla suggest this. Likewise, the diversity we see at the macroscopic level is quite misleading when we turn to the cellular level. Merely observing human beings and baker's yeast might lead people to think the cellular processes must be fundamentally different in a staggering number of ways also. But as I'm sure you know, the similarities at the cellular level make it possible to think of humans basically as reshuffled/tweaked yeast.
Back to predictions. If I were to design a protozoan and endow it with highly efficient 9+2 flagella, I would know that I had now introduced into evolution an effective barrier to evolving another type of flagellum, as any attempt to compete against this machine is likely to fail (IC itself may also contribute to this barrier, not by making evolution impossible, but by biasing the biosphere toward that 9+2 flagellum). Given this, I might very well predict that had multicellular creatures evolves, needing tissues to move fluids, or needed mobile gametes, they would coopt this 9+2 flagellum rather than invent some novel motility solution. My design gets carried through time.
Finally, you write, "Certainly, starting from a bacterium there is a lot of free space to go up, and not much to get rid of, so probably multicellular life is indeed unavoidable, at the fringes of life (major asteroids permitting, of course)." Yet we are only guessing here. What is needed are data. After all, one might also argue that if life is simply about replicating DNA, you can't do any better than bacteria, unless you "go down" as the viruses did. Thus, it is not clear there would be any impetus to "go up." In the other hand, if unicellular life forms were endowed with the pieces and parts not essential to unicellular life, but essential to multicellular life (and this case seems to be growing), we may have fingerprints of front-loading. Remember that while both teleological evolution and non-teleological evolution recognize the opportunistic nature of evolution, the latter is quite myopic, while the former can be hyperopic (which in turn amplifies the opportunistic nature of evolution).
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RB
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posted 02. May 2002 12:58
But Mike, other cilia that aren't 9+2 have evolved (though from the 9+2 arrangement). What will be fun will be to see if future findings show a different arrangement evolving from the less structured cilia. As diversity sampling increases this may occur. But perhaps since it still ultimately came from an original 9+2 ancester this would still be front loaded in your model.
Also, Mike, can you define myopic and hyperopic in terms of your last post.
[note from Moderator: this message was edited to merge two posts into one, not content was removed]
[ 02 May 2002, 16:22: Message edited by: Moderator ]
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Mike Gene
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posted 02. May 2002 22:44
Hello RB,
Concerning flagella, I should again clarify that I am not arguing the validity of any particular model. I raised this issue in response to the notion that predictions about long-term evolution are meaningless. Perhaps a better example than eukaryotic flagella would be the genetic code itself. If the code was designed, one prediction we could make would be that the code would remain largely intact in all subsequent descendants. That is, creatures evolving billions of years later would still be drawing from the original design. And it would seem that this would be useful information from a perspective of front-loading, as the code itself, coupled to the originally designed sequences, could be fitted into a rather advanced model used to bias things.
As for the terms myopic and hyperopic, that's just near-sightedness and far-sightedness. Traditional evolutionary mechanisms are strictly near-sighted, focused only on what helps the current organism produce more offspring. The culling that takes place selects for anything that just happens to increase immediate fitness. It would thus seem to suffer a great risk of painting evolution into a corner, where something selected to increase the efficiency of unicellular life, for example, would be a bad design if employed by a metazoan that reproduces through the production of gametes. Of course, such short-sightedness happens in evolution, but front-loading may be a way of poking through some of this noise.
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Mike Gene
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posted 02. May 2002 23:08
Hi Janitor,
You write: Biologists might have been well advised fifty years ago to take seriously the code/program metaphor they adopted. They may by now have come around to the view that a genome is not merely ad hoc adapted to impositions of necessity or the vagaries of chance, but is actively and strategically adaptive. The antique view that life adapts “accidentally” by the skin of its teeth is unworkable and leads to all sorts of amusing interpretations of results that reveal life actively searching for solutions to the problems of its own continued existence and evolution.
One of the neat discoveries over the last several years has been the realization how cell's attempt to exert control over their future. If DNA is randomly mutated by environmental conditions, the cell doesn't seem to "approve" of this evolutionary raw material. Instead, an array of circuits plugged into checkpoints prevent the cell from replicating this DNA until it is repaired. This comes in very handy from a multicellular perspective, where cells have to function as a team, rather than selfishly propagate themselves. In this case, if a cell can't fix itself, it commits suicide. From the unicellular perspective offered by baker's yeast, the cell's circuitry senses and answers at least three basic questions before it is licensed to replicate. Are there enough nutrients in my surroundings? Yes/No. Am I big enough? Yes/No. Is my DNA damaged? Yes/No. If the answer is Yes, Yes, and No, the cell will commit itself to dividing. Shapiro also argues that most of the mutations that are generated and used as variability are intrinsically generated, and not the result of environmental insults.
[ 03 May 2002, 18:28: Message edited by: Mike Gene ]
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Janitor@MIT
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posted 03. May 2002 11:50
Hi, Mike Gene.
Continuing your thought: You’d think that researchers such as Eric Davidson and Michael Savageau (just to name two of the earliest entrants into the field) would stare at those representations of genes-as-Boolean circuits long enough to come to the realization that what is evolving here is the logic of the design, and the (changing) form-function is purely epiphenomenal upon the logic. But that would seem to be impossible unless we adopted a certain “teleological” perspective: there is a prior and imperative logic to the design of life.
The form-function ontogeny of biological theory is exactly backwards! Its not etiology > teleology. Its teleology > etiology! Form-function emerges not as necessity/contingency, but as design sufficiency, in what can only be described as a “conception” of design. Probably nobody appreciates it more than yourself that this is a radically different perspective and potentially quite productive. But old habits (of thought) die-hard.
Programmed cell cycles are a few pages ahead on my research agenda, but these kinds of checkpoints, where a cell monitors its state, compares it to a model, and makes “decisions” as to its next state, are places where I will look for any evidence of recompiling of the model, if you know what I mean.
(I’m so radical I’m gonna buy a beret and start smokin’ gauloises! “Viva la gauche!”)
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James A. Barham
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posted 03. May 2002 17:49
Janitor:
I think that we teleologists should alter that slightly: "Vive la gauche aristotelicienne!" (to paraphrase Ernst Bloch on the subject of "die aristotelische Linke").
Watch those Gauloises---they are real killers . . .
-- James
[ 04 May 2002, 08:31: Message edited by: James A. Barham ]
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Mike Gene
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posted 04. May 2002 11:07
I thought I would repost something I wrote earlier (and elsewhere) since it relevant to this discussion.
I just finished re-reading Simon Conway Morris' article, Evolution: Bringing Molecules into the Fold. (Cell 100: 1-11, 2000). Morris makes many arguments that fit nicely into my developing views concerning front-loading evolution. In fact, the article is so good that I will discuss it at length.
Morris argues that our understanding of evolutionary processes and its mechanisms is fundamentally incomplete (that is, we are not simply missing mere details). I could not agree more. The non-teleological view of evolution is that it is not really a biological process, but instead is the consequence of many smaller biological processes. Or look at it this way: the purpose of life is not to evolve; it just happens. But a teleological view of evolution likens it to a biotic process (roughly/weakly analogous to ontogeny). Evolution was intended/anticipated. I suspect much of the so-called junk DNA comes into play here. Is evolution really nothing more than a by-product of messy molecular interactions or is it far more sophisticated (itself being designed)? Concerning the cell and its contents, Bruce Alberts noted, " But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. " More and more, I am coming to seriously think that in another few decades, another leading scientist will write, " But, as it turns out, we exist because evolution has been much more elaborate and sophisticated than anything we students had ever considered. "
Back to Morris. He begins his article by pondering the meaning behind that fact that "deep and pervasive similarities amongst the metazoans seem to be the rule." There is something more here than mere evolution. He first considers sponges, generally accepted as the most "primitive" form of metazoan life:
their biochemistry includes elements that seem to foreshadow the immune system of vertebrates. Sponges do not have nerve cells, but paradoxically they possess neuronal-like receptors….With such features, sponges seem to be almost "animals in waiting": everything is in place but nothing happens.
Morris adds that this is, however, a distorted views for two reasons. First, much happens with sponges; they just exist as sponges and not "animals." Secondly, "the basic building blocks and processes found in metazoans are very widespread among eukaryotes and must have originated much earlier than the first animals."
Elsewhere, Morris drives this point home as follows:
the diversity of life is, in molecular terms, little more than skin deep. Most, perhaps all, of the basic building blocks necessary for organismal complexity were available long before the emergence of multicellularity.
Observations like these constitute good evidence of front-loading. What this means is that all the hardware needed to form all the various metazoan life forms already existed in unicellular organisms. While this may be commonly seen merely as evidence for common descent, a bigger picture emerges from a deeper look.
(1.) First, it would appear more and more that a designer could design mutlicellular life through unicellular life forms. This is front-loading.
(2.) Secondly, our perception of evolution has been skewed over the last century. This is not surprising, as science is limited by the perceptions its tools can deliver. Yet how has the perception been skewed? From a morphological and behavioral perspective, life is immensely diverse. But the molecular perspective shows such diversity to be "skin-deep." Thus evolution, as evidence by the fossil record, has not been about developing novel hardware to solve adaptive problems. It has been more about reshuffling, testing, and deploying the molecular endowments it has been given. Put bluntly, all the evolution contained in the entire fossil record and inferred by our phylogenetic trees has been largely a footnote in the development of life. The really interesting and important questions concern the origin of this "animal in waiting" hardware that was infused into protozoan life forms.
(3.) Thirdly, one can always attribute the origin of such hardware to non-teleological processes, but what a coincidence all this would be. That is, selective pressures shaping protozoan life forms for millions of years just happened to find solutions that would just happen to become essential for metazoan life.
Returning to Morris, he introduces a concept called molecular inherency which he defines as "a gene known to be of major importance in organogenesis in a higher animal also occurs in a more primitive group." This is very similar to one way in which I infer front loading. Morris lists a few examples:
a. Sponges contain equivalents to many Pax genes.
b. Otx is a gene family important in the development of the brain/head of arthropods and vertebrates. But it is also found in Hydra (cnidaria), where it plays only a role in cell movements.
c. Genetic and tissue studies of Amphioxus show a "vertebrate in waiting."
Again, all of this speaks to front-loading. For example, if one wanted to design a vertebrate, they would not need to design vertebrates. They need only design Amphioxus and evolution is then rigged to evolve vertebrates.
Cooption and Constraint
Morris also speaks of cooption. Front-loading, or genomic inherency, lead us to expect cooption. After all, it is cooption that exploits and draws out the potential of the front-loaded state. It seems (at least to me) that Morris is hinting that the phenomena of cooption is not an evolutionary "free-for-all" but instead occurs under high-order constraints. For example, Morris quotes Davidson and Ruvkun who "gently question received orthodoxy by reminding us that cooption of genes might be analogous to plugging of particular computer "chips" into a new program." The program is not the product of cooption, it is what is designed to make use of cooption. Yet as Morris notes, the "how, why and when cooption occurs is, however, only now beginning to be explored."
A further word on cooption. I have expressed skepticism concerning the notion that this phenomena explains the origin of IC molecular machines. However, that cooption may not be a good explanation for the origin of IC molecular machines does not mean that is was not involved in helping to generate the diversity of morphological forms that followed from the front-loaded state(s). That is, if cooption is played out on the stage set up by front-loading (which is maintained, at least in part, by the interplay of molecular machines), trying to use cooption to explain the make-up of the stage is like putting the horse before the cart.
Shared ancestry or convergence?
Morris touches on the significance of the disconcordance between genotype and phenotype. He explains, "a much more interesting problem [is one] that questions whether genetic similarity, however striking, can be equated in any simple fashion with a shared ancestry." He then provides a very provoking quote from Nagy:
Should vertebrate and insect limbs be considered homologous because they are patterned by similar gene networks? Or is the similarity an example of molecular convergence, representing not an extreme conservation of limb construction throughout metazoa, but merely a consequence of a limited number of molecular tools an organism has available to change its form?"
As a rule, evolution is not going to design new molecular tools. It is merely going to make use of the tools it has been given. This is front-loading. And this also points us to the design of evolutionary mechanisms.
Morris also brings up sea urchin development that may contain an important clue:
may have wildly different ontogenetic trajectories, with fertilized eggs developing into very different types of embryo that subsequently converge on similar adult forms.
and
Multiple genomic pathways in ontogeny are probably the rule, but in our present state of knowledge, this seems rather surprising given that once a particular pathway is established, the advantages of altering it, when the end-product remains unchanged, are obscure.
Thus, here we have an example that demonstrates there can be multiple pathways to a very similar endpoint in ontogeny. If evolution is a biological process, rather than merely a consequence of many smaller biological processes, why can't we extrapolate this to phylogeny? And thus, the whole phenomena of 'convergent evolution' comes into play. Is this yet another clue to front-loading and the design of evolution? After all, convergence is, by definition, similarities not reflecting a common ancestral state.
Morris writes:
The question we need to ask is whether a structure (molecular or organismal) is similar because it shares a common ancestry and thus is homologous or because there is no (or very few) alternative. The former approach, of course, underpins most evolutionary thinking and has potentially a strong historical component. Convergence, on the other hand, points towards adaptive constraint in which the historical dimension is relatively unimportant.
The concept of adaptive constraint is another reminder that evolution is not an adaptive free-for-all. Evolution is constrained by the very substrate upon which it is played out. Thus, it is the substrate of evolution, and not evolution itself, that is of primary importance in these origin disputes. Morris then cites some very interesting examples of convergence which show that "remarkably similar endpoints can be arrived at from quite different starting points." I'll come back to these in a follow-up.
Let me finished with a provocative quote from Morris:
Just as phenotypic diversity of life excites the imagination of the naturalist, so the range of molecules and the sophistication of their biochemistries impress the molecular biologist. In comparison, the underlying constraints on form and the inevitability of convergences have received less emphasis. Why should this be so? There seems to be two reasons. The first is that if evolution is in some sense channeled, then this reopens the controversial prospect of teleology; that is, the process is underpinned by a purpose.
Let me merely say that we have just begun to understand evolution and I think we will one day find that the processes of evolution are far too sophisticated to fit comfortably in the Modern Synthesis. Darwin helped us to understand things like finch beaks and the spread of antibiotic resistance. His concept has been extrapolated to all other origin events merely because we don't understand evolution very well and have no better explanation. Those days are changing.
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Mike Gene
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posted 04. May 2002 23:52
Charlie writes: Evolution is an unavoidable consequence of the chemistry of life.
If we are to define 'evolution' as change over time, I think you are right. And if such evolution is a necessary consequence of chemistry, it stands to reason that any designer behind life would know about this. Thus, we might very well expect any designer to factor this into the design. Ironically, this would mean that any good designer would make good use of evolution and many later on would view this evolution to mean the original design/designer was superfluous.
In another thread, edmund writes:
quote:
Cooption could, as Mike Gene suggests, be a sign that an organism was pre-designed for future evolution. But it also fits exactly with the Darwinian view that evolution makes do with whatever it has on hand. In general, a lot of the intelligent-design scenarios seem to converge, when discussed in detail, to predict the same observations we would predict from "natural" evolutionary mechanisms. This is a problem, because Dembski suggests that design should then drop out of the scientific discussion as superfluous.
Maybe, maybe not. It would all depend on how things shake out after a systematic investigation has taken place. There are at least two ways teleologists can go about studying the natural world. One way is to look for features that clearly cannot be explained by non-teleological explanations. There is nothing wrong with this approach. In fact, it holds potential for developing new insights and methods, along with helping to better define the dispute. But there is another way that can complement this approach. This way simply begins by looking for things that one might expect to follow from design. This way follows the examples of mainstream science. Take OOL research. Scientists do not look for things that could not be explained by teleologists. They are not looking for phenomena that rule out telic causes, therefore rule in non-telic causes. On the contrary, they begin with squishy, vague scenarios about how something might have happened and then see if something in the lab or nature can be fitted into such a scenario. What becomes important here is the development of a track record and a scenario that gets less and less squishy. I see no reason why teleologists cannot likewise adopt this approach.
So if we go back to cooption, it's not a question about highlighting differences between front-loaded evolution and darwinian evolution. It's a question of whether front-loading would likely employ cooption. Would we expect a designer to design life with the ability to coopt? If so, how, when, and why?
One almost gets the impression that some critics of design think the designer should have designed something that was both fragile and stupid, rather than robust and smart.
[ 04 May 2002, 23:53: Message edited by: Mike Gene ]
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