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Ancestral Expression Patterns

by Bradford

This story is going around the blogosphere. The article entitled New genetic data overturn long-held theory of limb development is consistent with a theme notably advanced at Telic Thoughts. When I first started following threads at TT I was struck by a particular criticism of front loading, namely that it was indistinguishable from standard theories and likely to be cut down to size by Occam's razor. But would standard theories predict that a developmental toolkit for biological structures would appear in species who are ancestors rather than descendents of species in whom the structures are expressed? On the other hand would this not be exactly what one would expect to see predicted by a theory holding that the nature of subsequent evolution was loaded at the outset? From the article:

The paper, "An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish," shows that the genetic and developmental toolkit that builds limbs with fingers and toes was around long before the acquisition of limbs, according to the scientists, and that this toolkit exists in some primitive form in a living primitive bony fish, the paddlefish.

"We found that the genetic capability seen in tetrapods to build limbs is present in even more primitive fish," said lead author Marcus Davis, PhD, a postdoctoral fellow in Neil Shubin's lab at the University of Chicago.

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This entry was posted on Wednesday, May 23rd, 2007 at 7:31 pm and is filed under Evolution, Front-loading. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/ancestral-expression-patterns/trackback/

33 Responses to “Ancestral Expression Patterns”

  1. bFast Says:
    May 23rd, 2007 at 7:42 pm

    I was hoping that this story would make it to TT. Here's another story that needs to be hashed out on TT. It seems that feathered dinosaurs is a myth: http://www.physorg.com/news991...

  2. Comment by bFast — May 23, 2007 @ 7:42 pm

  3. chunkdz Says:
    May 23rd, 2007 at 10:10 pm

    How is the toolkit preserved if it is not being used?

  4. Comment by chunkdz — May 23, 2007 @ 10:10 pm

  5. Bradford Says:
    May 23rd, 2007 at 11:27 pm

    How is the toolkit preserved if it is not being used?

    It would have no selective value if it is not expressed would it? Yet how else could a front loaded concept operate if not by a selection anomaly?

  6. Comment by Bradford — May 23, 2007 @ 11:27 pm

  7. keiths Says:
    May 23rd, 2007 at 11:29 pm

    Bradford, chunkdz,

    You are misinterpreting the research. The genes associated with hands and feet were there before limb development, but that doesn't mean they were unexpressed. They were expressed, but as part of fin development, not limb development, as the article makes clear:

    The scientists studied the development of paddlefish fins to test whether the genes activated to make hands and feet in tetrapods were different from the genes activated to make fish fins. Davis working with postdoctoral fellow Randall Dahn, PhD, and Shubin, PhD, professor and associate dean for organismal and evolutionary biology at Chicago and provost of the Field Museum, disproved conventional wisdom.

    The team looked at Hox genes"”which play a vital role in limb development"”in the pectoral fins of paddlefish. To track where the Hox genes are active in the fin, the team inserted molecular markers and showed the activity pattern has similarities to patterns of these same genes in tetrapod limbs.

    Although this pattern of genes clearly helps to make hands and feet today in tetrapods, that may not be their original intent, Shubin said. "Here's a fish that doesn't have an autopod but is still using those genes in a second phase to help pattern out a fin that doesn't have fingers, never did, and is very far removed from tetrapods."

  8. Comment by keiths — May 23, 2007 @ 11:29 pm

  9. Bradford Says:
    May 24th, 2007 at 12:35 am

    Keiths, you may very well be right about the gene expression although the authors seem somewhat tentative. This would explain selection in the usual way but would not contradict a model showing that the seeds for adaptation were present before they needed to be expressed; at least with respect to hands and feet.

  10. Comment by Bradford — May 24, 2007 @ 12:35 am

  11. keiths Says:
    May 24th, 2007 at 1:05 am

    Bradford,

    I'm not sure what you're trying to say when you refer to the "seeds of adaptation" being "present before they needed to be expressed."

    It seems to me that there are four logical possibilities for the genes in question:

    1. not expressed
    2. expressed but not beneficial
    3. expressed but not beneficial, but with some heretofore unknown preservation mechanism to keep them unchanged until they are beneficial
    4. expressed and beneficial

    #1 is ruled out by the research, which shows that the genes are expressed. #2 is ruled out by the fact that the genes would quickly drift into oblivion if their function was not beneficial. Option #3 is logically possible, but nobody has any evidence for a mechanism that can preserve genetic information perfectly in the absence of selective pressure. That leaves only option #4.

    But if option #4 holds, then the paddlefish are just like any other organism we know of, wherein the genes that are expressed are the ones that are conserved. In that case there's nothing about paddlefish which suggests front-loading more than any other species.

    Are you thinking of something else?

  12. Comment by keiths — May 24, 2007 @ 1:05 am

  13. Bradford Says:
    May 24th, 2007 at 1:20 am

    Keiths, I concede there is no smoking gun but there is also an indication that genes involved in the expression of hands and feet do exist in ancestral species that do not have either. The point is consistency with theory. You claim that genes expressed are those that are conserved. But the question of the origin of such genes is not satisfied by this. Initial conditions are critical to an evaluation of what subsequently occurs and whether results are attributable to teleology or a rudderless process- at least with respect to a specified outcome.

  14. Comment by Bradford — May 24, 2007 @ 1:20 am

  15. salimfadhley Says:
    May 24th, 2007 at 9:09 am

    You are misinterpreting the research. The genes associated with hands and feet were there before limb development, but that doesn't mean they were unexpressed. They were expressed, but as part of fin development, not limb development, as the article makes clear:

    I concur; this shows that the same genes which code for certain fish fins also play an analogous role in limbs of other vertebrates. This is precisely what standard evolutionary theory predicts we would find. It is not evidence for front-loading (if by that you mean that evolutionary paths were pre-ordained), it is just more confirmation and refinement of the standard evolutionary model.

    But if option #4 holds, then the paddlefish are just like any other organism we know of, wherein the genes that are expressed are the ones that are conserved. In that case there's nothing about paddlefish which suggests front-loading more than any other species.

    Yep, this does not seem controversial, but it is good fundamental science that confirms what many evolutionary biologists have suspected for a long time.

    Front loading is an unusual departure from standard evolutionary; It seems to take the idea that later structures are derived from earlier structures, but turn that on it's head by claiming that the older gene somehow had an intent to become the newer gene.

    I'm not sure where this intentionality is said to exist, or at which stage in the gene's evolution this intent was allegedly acquired. I do not think that a strand of DNA can be said to have intent or desire.

    :-)

  16. Comment by salimfadhley — May 24, 2007 @ 9:09 am

  17. MikeGene Says:
    May 24th, 2007 at 9:22 am

    Hi Sal,

    I concur; this shows that the same genes which code for certain fish fins also play an analogous role in limbs of other vertebrates. This is precisely what standard evolutionary theory predicts we would find.

    You are already engaged in revisionism. I suggest you re-read the article:

    This finding overturns a long-held, but much-debated, theory that limb acquisition was a novel evolutionary event, requiring the descendents of lobed-fin fish to dramatically alter their genes to adapt their bodies to their new environments of streams and swamps.

    Prior to this find, scientists had little evidence of where the wrist came from. A popular theory, one Shubin himself subscribed to, was that it was a novel development"”that genetic variance gave rise to an entirely new function.

    This is not the first time "standard evolutionary theory" has failed to predict such deep homology.

    Such a study may not be evidence for front-loading (as opposed a non-teleological perspective), but it adds to the plausibility of front-loading:

    The capability of building limbs with fingers and toes existed for a long period of time, but it took a set of environmental triggers to make use of that capability.

    According to Shubin, in the Late Devonian, animals like Tiktaalik and its descendants acquired limbs with fingers using this primitive design, largely because their ecosystem"”the small streams that they lived in"”was new.

    "It had the tools," he said, "but it needed the opportunity as well."

    Y'gotta love that last quote.

  18. Comment by MikeGene — May 24, 2007 @ 9:22 am

  19. Nick Says:
    May 24th, 2007 at 11:46 am

    This is not the first time "standard evolutionary theory" has failed to predict such deep homology.

    As best I can tell, this data only supports front loading if one focuses exclusively on tetrapod limbs and HoxD. If one focuses on actinopterygian fins, then it looks more like a case for evolution of novel genetic mechanisms.

    The paired fins of actinopterygian fish and the limbs of tetrapods are homologous structures. Both are derived from the fins of an aquatic common ancestor. It was known that the developing fins of modern actinopterygian fish lack a developmental hallmark of developing tetrapod limbs (late phase HoxD expression). Since actinopterygian fins are morphologically more similar to the fins of the common ancestor, it was a reasonable hypothesis that the development of limbs was the evolutionary novelty and the development of fins was evolutionarily conserved.

    This new data suggests the reverse. Since the development of a fish whose ancestors branched off fairly early in the evolution of actinopterygians resembles that of the tetrapods, the development of limbs is probably controlled in a way similar to the development of fins in the common ancestor. The HoxD expression pattern in the fins of most modern actinopterygian fish is the evolutionary novelty.

    This is interesting and somewhat surprising, but I don't see how the new model is any more supportive of front loading than the old one. In both cases, one group of organisms has conserved an older developmental mechanism (i.e. "deep homology"), and one group of organisms has evolved a new mechanism.

    I suspect that "deep homology" of limb development seems more surprising than "deep homology" of fin development, because people tend to think of evolution as a ladder with limbs on a higher rung than fins, instead of a bush where the fins of modern actinipterygians and the limbs of tetrapods are both out on twigs equally distant from the common ancestor.

    Notice that the surprise was only with HoxD expression. The authors also looked at late HoxA expression which also differ in the limbs of tetrapods and fins of actinopterygians. The late HoxA expression in Polyodon resembled that of the actinopterygians, not tetrapods. So, if the tetrapod-like expression pattern of HoxD in Polyodon is consistent with front loading, then logically, the actinopterygian-like pattern of HoxA must be inconsistent with front loading, right? Or perhaps, both patterns have nothing at all to do with front loading?

  20. Comment by Nick — May 24, 2007 @ 11:46 am

  21. salimfadhley Says:
    May 24th, 2007 at 11:51 am

    This finding overturns a long-held, but much-debated, theory that limb acquisition was a novel evolutionary event, requiring the descendents of lobed-fin fish to dramatically alter their genes to adapt their bodies to their new environments of streams and swamps.

    Prior to this find, scientists had little evidence of where the wrist came from. A popular theory, one Shubin himself subscribed to, was that it was a novel development"”that genetic variance gave rise to an entirely new function.

    So what you are saying is that our understanding of vertebrate evolution was somewhat incorrect: The wrist was not a novel feature (as initially suspected) which suddenly appeared, but something that had clear genetic precursors in early quadrupeds.

    Or in other words, much smaller evolutionary changes than we suspected were required to produce limbs, from their precursor structure, the pectoral fins.

    "It had the tools," he said, "but it needed the opportunity as well."

    So not only have the scientists demonstrated that there is a continuous lineage between the genes responsible for fin and limb development, they have also shown that the evolutionary changes required are not 'dramatic'.

    I still do not see how this could be construed as evidence of front-loading or some kind of genetic intent.

    Mike, since you have read the entire paper, could you confirm if it's authors drew any particular conclusions that directly address the issue of "front loading", or is this your own independent interpretation of their findings?

  22. Comment by salimfadhley — May 24, 2007 @ 11:51 am

  23. chunkdz Says:
    May 24th, 2007 at 3:25 pm

  24. Comment by chunkdz — May 24, 2007 @ 3:25 pm

  25. MikeGene Says:
    May 24th, 2007 at 5:04 pm

    Hi Sal,

    So what you are saying is that our understanding of vertebrate evolution was somewhat incorrect: The wrist was not a novel feature (as initially suspected) which suddenly appeared, but something that had clear genetic precursors in early quadrupeds.

    Or in other words, much smaller evolutionary changes than we suspected were required to produce limbs, from their precursor structure, the pectoral fins.

    Sounds good. But I was under the impression that you were claiming this study was just something else that was predicted by conventional evolutionary theory. Yes, the fact that various "novel" structures actually trace back to genetic toolkits buried deeper back in time is something that makes front-loading all the more plausible.

    I still do not see how this could be construed as evidence of front-loading or some kind of genetic intent.

    What did I just write? Here it is:

    Such a study may not be evidence for front-loading (as opposed a non-teleological perspective), but it adds to the plausibility of front-loading

    Whether or not this example qualifies as a serious candidate for front-loading is another question, thus I am not talking about evidence FOR front-loading. I realize many people are in a rut, thinking that front-loading must somehow entail something that conventional evolutionary theory cannot possibly explain. But the truly interesting element of front-loading is to think about it from a design perspective with a design objective. That is, before we can even get to the "evidence for front-loading," we have to learn how to think about front-loading and we first need to resolve the plausibility of designing the future through the present (front-loading). This study adds to the plausibility of design-through-evolution. "It had the tools, but it needed the opportunity as well" could be a motto for front-loading.

  26. Comment by MikeGene — May 24, 2007 @ 5:04 pm

  27. Raevmo Says:
    May 24th, 2007 at 5:24 pm

    Mike:

    I realize many people are in a rut, thinking that front-loading must somehow entail something that conventional evolutionary theory cannot possibly explain.

    So what *do* you mean *exactly* by front-loading? I get the impression from your writings that it means little more than that initial conditions partially determine the final outcome. That sounds almost trivial, but I'm sure you must have something more profound in mind.

  28. Comment by Raevmo — May 24, 2007 @ 5:24 pm

  29. Thought Provoker Says:
    May 24th, 2007 at 5:28 pm

    Hi Mike,

    Raevmo wrote…

    …but I'm sure you must have something more profound in mind.

    Can I say "retrocausality" now? Can I? Can I?

    Hmmm, I guess I already did. :oops:

    Regards,
    TP

  30. Comment by Thought Provoker — May 24, 2007 @ 5:28 pm

  31. salimfadhley Says:
    May 24th, 2007 at 7:46 pm

    Sounds good. But I was under the impression that you were claiming this study was just something else that was predicted by conventional evolutionary theory. Yes, the fact that various "novel" structures actually trace back to genetic toolkits buried deeper back in time is something that makes front-loading all the more plausible.

    But these things were not buried; They were expressed genes that were strongly conserved which subtly changed over a very long period of time. The suprising thing was that radical changes in body appearance were shown to be the result of very small changes to the relevant genes. This stands in contrast to conventional wisdom which suggests that radical changes in DNA are required to produce radical changes in body-shape.

    I'm not sure what you mean by "Genetic toolkits", that sounds like an analogy too far: We know that all genes that exist today are adaptions of genes that existed some time ago, but to label one particular gene a "toolkit" because millions of years later it's sucsessor became important for some bodily feature. Why not call it what it is, it's a gene that evolved over time.

    I find the idea of front-loading interesting conjecture, I do not truly understand it, and I have never found a source of reference that fully explains the idea. These sort of questions have been puzzling me:

    For example, how might an original designer have determined which starting conditions would have resulted in producing human-beings? Did he have a way to just know, or did he run some kind of simulation? Perhaps the designer had no clear idea how his creation would turn out - but he just chose conditions that he knew would give-rise to complexity. What do you think?

    Suppose we expose a bacteria colony to a radically new antibiotic. We find that after a few generations of exposure, the bacteria acquire some kind of immunity to moderate concentrations of that antibiotic. We presume that the bacteria had been front-loaded with the code for immunity to that antibiotic and that it took a period of time to activate.

    How was this possible? Where was this information stored? If we found where it was stored and removed it from the bacteria, could we prevent a bacteria from being able to acquire any kind of immunity?

    If we were able to fully decode an organism's genome would we be able to predict what how subsequent generations of that organism would evolve?

    :-)

  32. Comment by salimfadhley — May 24, 2007 @ 7:46 pm

  33. MikeGene Says:
    May 24th, 2007 at 10:56 pm

    Hi Raevmo,

    So what *do* you mean *exactly* by front-loading?

    I think of front-loading as an attempt to design the future through the present. So I ask myself to what extent could evolution be used to carry out design objectives.

    I get the impression from your writings that it means little more than that initial conditions partially determine the final outcome. That sounds almost trivial, but I'm sure you must have something more profound in mind.

    LOL. Profound is something I would never claim to be or have.

    Hi Sal,

    For example, how might an original designer have determined which starting conditions would have resulted in producing human-beings? Did he have a way to just know, or did he run some kind of simulation? Perhaps the designer had no clear idea how his creation would turn out - but he just chose conditions that he knew would give-rise to complexity. What do you think?

    I have no idea if human beings were front-loaded. As far as I know, it was simply the appearance of multi-celluar life that was front-loaded. In other words, the objective of front-loading remains a completely open question.

    How was this possible? Where was this information stored? If we found where it was stored and removed it from the bacteria, could we prevent a bacteria from being able to acquire any kind of immunity?

    If we were able to fully decode an organism's genome would we be able to predict what how subsequent generations of that organism would evolve?

    These are all great questions. If the hypothesis of front-loading is to ever get off the ground, it is questions such as these that will fuel a research program.

  34. Comment by MikeGene — May 24, 2007 @ 10:56 pm

  35. salimfadhley Says:
    May 25th, 2007 at 1:13 pm

    These are all great questions. If the hypothesis of front-loading is to ever get off the ground, it is questions such as these that will fuel a research program.

    Okay for starters: Can you tell me what IS the front-loading hypothesis?

    From what I can infer, it seems to be a variation on directed evolution; specifically that the designer set the initial conditions with some degree of foreknowledge of what these conditions would lead to.

    Where it differs from directed evolution is that DE suggests that the designer is continuously, subtly choosing the outcome of evolution by small interventions. Front loaded evolution suggests that no or few interventions were made after the initial starting conditions were set.

    Did I understand it the same way that you did?

    Thanks

  36. Comment by salimfadhley — May 25, 2007 @ 1:13 pm

  37. keiths Says:
    May 25th, 2007 at 3:29 pm

    salimfadhley asks Mike:

    Okay for starters: Can you tell me what IS the front-loading hypothesis?

    Sal,

    Good luck in getting specifics out of Mike. Here's what happened when I tried on another thread:

    I wrote:

    Mike,

    You cite a couple of studies in your post.

    How, specifically, do they support a teleogical interpretation, and what do you think the data would look like if teleology were not operative?

    Mike responded:

    The studies are cited to support certain facts science has discovered and then I begin the process of incorporating them into a developing teleological gestalt.

    It all goes back to the words of Nobel Laureate Francois Jacob:

    To produce a valuable observation, one has first to have an idea of what to observe, a preconception of what is possible. Scientific advances often come from uncovering a hitherto unseen aspect of things as a result, not so much of using new instruments, but rather of looking at objects from a different angle. This look is necessarily guided by a certain idea of what this so-called reality might be. It always involves a certain conception about the unknown, that is, about what lies beyond that which one has logical or experimental reasons to believe.

    It's about a certain preconception of what is possible, looking at objects from a different angle, and a certain conception about the unknown. I'm trying to flesh out an attempt to see the forest through the trees. Things are still fuzzy for me, but they have been slowly and gradually coming into better focus over the years.

    How can you ask for specifics? Let the man flesh out his teleological gestalt! :razz:

  38. Comment by keiths — May 25, 2007 @ 3:29 pm

  39. MikeGene Says:
    May 25th, 2007 at 4:58 pm

    Hi Sal,

    Okay for starters: Can you tell me what IS the front-loading hypothesis?

    The working hypothesis is that the first cells were designed and that this design shaped subsequent evolution, channeling it toward some objective.

    From what I can infer, it seems to be a variation on directed evolution; specifically that the designer set the initial conditions with some degree of foreknowledge of what these conditions would lead to.

    It's not what these conditions would lead to. It's more like how these conditions would affect evolution.

    Where it differs from directed evolution is that DE suggests that the designer is continuously, subtly choosing the outcome of evolution by small interventions. Front loaded evolution suggests that no or few interventions were made after the initial starting conditions were set.

    Front-loading begins with the working assumption that a designer has one window of opportunity and from there, the influence of the designer (through the design) would be dependent on the propagation of the design(s).

  40. Comment by MikeGene — May 25, 2007 @ 4:58 pm

  41. MikeGene Says:
    May 25th, 2007 at 4:59 pm

    Hi Keith,

    Good luck in getting specifics out of Mike. Here's what happened when I tried on another thread

    The topic of this thread is not Mike Gene.

    How can you ask for specifics? Let the man flesh out his teleological gestalt!

    Indeed. I don't come to the table with some ready-made answer in hand and a set of specific beliefs about what did indeed happen. Why would anyone think I should? To have specifics, I need the "valuable observations" that Jacob mentioned, therefore I also first need "to have an idea of what to observe, a preconception of what is possible." For most people, the debate about evolution and ID is a debate between two opposite forces, as both sides seem to need conventional evolutionary theory to somehow, and at some place, be disproved. In their minds, only that would count as a "valuable observation." But I'm focused on how ID and evolution can interface. That's the perspective that needs to come into focus.

  42. Comment by MikeGene — May 25, 2007 @ 4:59 pm

  43. salimfadhley Says:
    May 25th, 2007 at 6:08 pm

    The working hypothesis is that the first cells were designed and that this design shaped subsequent evolution, channeling it toward some objective.

    So front-loading seems to be more of intentional replacement for a standard abiogenesis theory rather than a replacement for darwinian evolution. You are saying that a designer set up the original conditions with a purpose of setting life on earth into motion, but you are not claiming that the designer nececarily had spesific goals (e.g. to create a certain kind of fish or beetle), more a general goal to establish self-pepetuating life.

    What did you think of my thought experiment with bacterial immunity? Of corse none of us have access to the kind of genetics lab where we could carry out the experiment, but please humor me by predicting what you would expect to see. To recap: Imagine if we observe the way a number of genetically identical bacterial colonies adapt to the presence of antibiotic solution. We would expect that over time the colonies evolve some kind of resistance to that antibiotic.

    What has just occurred here: Is it a mindless process driven by a few fluke mutations which allowed certain members of the population to grow, or is there something more complex: Could it be that the bacteria had a latent gene that allowed it to avoid this novel antibiotic?

    Good luck in getting specifics out of Mike.

    It takes a while to formulate exactly what we mean by a new idea; and one of the ways we can do that is by debate. Lets thrash this one around for a bit and see where it leads.

    :-)

  44. Comment by salimfadhley — May 25, 2007 @ 6:08 pm

  45. MikeGene Says:
    May 25th, 2007 at 7:27 pm

    Hi Sal,

    So front-loading seems to be more of intentional replacement for a standard abiogenesis theory rather than a replacement for darwinian evolution. You are saying that a designer set up the original conditions with a purpose of setting life on earth into motion, but you are not claiming that the designer nececarily had spesific goals (e.g. to create a certain kind of fish or beetle), more a general goal to establish self-pepetuating life.

    The "original conditions" would be the population of first cells. I assume the designer had some goal in mind, as design is an attempt to achieve a goal. But before getting to "the goal," we first must establish the plausibility of designing-through-evolution. In fact, by focusing on this, it should give us information that can help us better define the range of possible goals.

    What did you think of my thought experiment with bacterial immunity? Of corse none of us have access to the kind of genetics lab where we could carry out the experiment, but please humor me by predicting what you would expect to see. To recap: Imagine if we observe the way a number of genetically identical bacterial colonies adapt to the presence of antibiotic solution. We would expect that over time the colonies evolve some kind of resistance to that antibiotic.

    What has just occurred here: Is it a mindless process driven by a few fluke mutations which allowed certain members of the population to grow, or is there something more complex: Could it be that the bacteria had a latent gene that allowed it to avoid this novel antibiotic?

    I would not put much stock the latent gene hypothesis. If life was designed ca. 3.5 billion years ago, any latent genes designed to counteract a specific antibiotic in the present would have likely decayed into oblivion long ago.

    Go back to your questions (with the minor tweaks I have in mind). I'm more focused on how is it possible to front-load X? Where would such information be stored? If we found where it was stored and removed it from biosphere, would X still evolve?

  46. Comment by MikeGene — May 25, 2007 @ 7:27 pm

  47. Nick Says:
    May 28th, 2007 at 3:16 pm

    Mike Gene:
    As far as I know, it was simply the appearance of multi-celluar life that was front-loaded. In other words, the objective of front-loading remains a completely open question.

    You and Bradford must have very different ideas about frontloading, and you were apparently wrong when you claimed upthread that this research "adds to the plausibility of front-loading." The research that started this thread has nothing to do with the origin of multicellular life, and therefore, has no relevance to front loading as you have just described it. Invertebrates don't even have a HoxD cluster, so the particular HoxD expression pattern that permits development of tetrapod limbs instead of fins cannot have been front loaded at the origin of multicellular life.

    Front loading is looking more and more like a kind of bait and switch. When it is convenient, almost any evolutionary conservation "adds to the plausibility of front loading." But when the specifics of a particular piece of research are discussed, front loading retreats to some vague event at the origin of multicellular life.

  48. Comment by Nick — May 28, 2007 @ 3:16 pm

  49. MikeGene Says:
    May 28th, 2007 at 7:01 pm

    Hi Nick,

    You and Bradford must have very different ideas about frontloading, and you were apparently wrong when you claimed upthread that this research "adds to the plausibility of front-loading." The research that started this thread has nothing to do with the origin of multicellular life, and therefore, has no relevance to front loading as you have just described it.

    Returning to the quotes provided by Bradford:

    The paper, "An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish," shows that the genetic and developmental toolkit that builds limbs with fingers and toes was around long before the acquisition of limbs, according to the scientists, and that this toolkit exists in some primitive form in a living primitive bony fish, the paddlefish.

    "We found that the genetic capability seen in tetrapods to build limbs is present in even more primitive fish," said lead author Marcus Davis, PhD, a postdoctoral fellow in Neil Shubin's lab at the University of Chicago.

    This shows us one way of designing the future through the present.
    BTW, multi-cellular life is just one possible objective of front-loading.

  50. Comment by MikeGene — May 28, 2007 @ 7:01 pm

  51. Nick Says:
    May 30th, 2007 at 8:58 am

    Hi Mike:
    "We found that the genetic capability seen in tetrapods to build limbs is present in even more primitive fish," said lead author Marcus Davis, PhD, a postdoctoral fellow in Neil Shubin's lab at the University of Chicago.

    And as I pointed out above, if the genetic capability to build tetrapod limbs is derived from genetic pathways present in primitive fish, then the capability to build modern actinopterygian fins must be a genetic novelty. The original hypothesis was that the ability to build tetrapod limbs was the genetic novelty, and the ability to build actinopterygian fins was derived from primitive capabilities. Either way, you've got one conserved mechanism and one novel mechanism in modern vertebrates. The competing hypotheses are equivalent with regard to front loading, so this new research adds nothing to its plausibility.

    This shows us one way of designing the future through the present.

    IOW, front loading is indistinguishable from descent with modification by Darwinian mechanisms. FL just has the added bonus of being vague and undefined with ever shifting scope and timing, so that any evolutionary conservation adds to the plausibility of FL, while genetic novelty does not detract from its plausibility. Perfect!

    BTW, multi-cellular life is just one possible objective of front-loading.

    The objective of FL isn't the issue, the timing is. You wrote that a basic assumption of FL is that "the designer has one window of opportunity." You also argued that the FL occurred at the origin of multicellular life or in the "first cells" (though it can't be both if there was a single window of opportunity). Therefore, this research adds nothing to the plausibility of FL, because it occurs after the critical period that you have defined. Since invertebrates lack HoxD clusters, they cannot have the overlapping pattern of HoxD expression. If FL occurred at the time multicellular life first appeared, then this genetic pathway is not a candidate for a front loaded process.

    This isn't a matter of trying to argue evolution versus ID, or worrying about the possible objectives of front loading. The issue is that FL, as you have described it in your comments, is incoherent and self-contradictory.

  52. Comment by Nick — May 30, 2007 @ 8:58 am

  53. MikeGene Says:
    May 30th, 2007 at 6:10 pm

    Hi Nick,

    And as I pointed out above, if the genetic capability to build tetrapod limbs is derived from genetic pathways present in primitive fish, then the capability to build modern actinopterygian fins must be a genetic novelty. The original hypothesis was that the ab ility to build tetrapod limbs was the genetic novelty, and the ability to build actinopterygian fins was derived from primitive capabilities. Either way, you've got one conserved mechanism and one novel mechanism in modern vertebrates. The competing hypotheses are equivalent with regard to front loading, so this new research adds nothing to its plausibility.

    The existence of true novelty does not render the front-loading of evolution implausible. It only renders the front-loading of that particular novelty (noise) implausible. The hypothesis of front-loading is not about pre-determining every aspect of evolution. On the contrary, a front-loading perspective asks just how much of evolution can be shaped by design given all the noise that it likely to occur.

    IOW, front loading is indistinguishable from descent with modification by Darwinian mechanisms.

    In the beginning (and maybe in the end), this may be true, as front-loading is about a designer recruiting descent with modification by Darwinian mechanisms. The alternatives for the designer would be to either ignore descent with modification by Darwinian mechanisms or work against it. IMO, recruitment is a better design strategy than ignoring it or opposing it.

    Besides, why would this bother you? If in the end we have a decent teleological perspective that embraces descent with modification by Darwinian mechanisms, is it the alternative teleological perspective that annoys you?

    FL just has the added bonus of being vague and undefined with ever shifting scope and timing, so that any evolutionary conservation adds to the plausibility of FL, while genetic novelty does not detract from its plausibility. Perfect!

    I'm not sure what "Perfect!" is supposed to mean, but are you under the impression that I am supposed to have a ready-made, rigorous, detailed Theory of Front-Loading? I have only begun to explore/investigate the front-loading perspective and must do so in my spare time.

    The objective of FL isn't the issue, the timing is. You wrote that a basic assumption of FL is that "the designer has one window of opportunity." You also argued that the FL occurred at the origin of multicellular life or in the "first cells" (though it can't be both if there was a single window of opportunity). Therefore, this research adds nothing to the plausibility of FL, because it occurs after the critical period that you have defined. Since invertebrates lack HoxD clusters, they cannot have the overlapping pattern of HoxD expression. If FL occurred at the time multicellular life first appeared, then this genetic pathway is not a candidate for a front loaded process.

    Where did I say that "this genetic pathway is a candidate for a front loaded process?" This example simply helps us appreciate one way in which the future could be designed through the present, adding to the plausibility of front-loading. "It had the tools," he said, "but it needed the opportunity as well."

    Since you are not happy with this, perhaps you can share what type of research finding would add to the plausibility of front-loading?

    This isn't a matter of trying to argue evolution versus ID, or worrying about the possible objectives of front loading. The issue is that FL, as you have described it in your comments, is incoherent and self-contradictory.

    On the other hand, perhaps your criticisms are knee-jerk reactions that satisfy a need to debunk?

  54. Comment by MikeGene — May 30, 2007 @ 6:10 pm

  55. Bradford Says:
    May 30th, 2007 at 9:29 pm

    Mike Gene: Besides, why would this bother you? If in the end we have a decent teleological perspective that embraces descent with modification by Darwinian mechanisms, is it the alternative teleological perspective that annoys you?

    This really gets to the heart of the matter. When the outcome and mechanism are not disputed but the perspective differs why then does this become such a problem for you Nick?

  56. Comment by Bradford — May 30, 2007 @ 9:29 pm

  57. Nick Says:
    May 31st, 2007 at 4:10 pm

    MikeGene:
    Where did I say that "this genetic pathway is a candidate for a front loaded process?" This example simply helps us appreciate one way in which the future could be designed through the present, adding to the plausibility of front-loading. "It had the tools," he said, "but it needed the opportunity as well."

    OK, sorry. I thought you were attempting to say something non-trivial. Since evolution, whether front loaded or not, is a historical process, the future always depends on the present (or the present on the past, if you prefer). The research that Bradford alerted us to is very interesting, but this quote from one of the authors is just banal. When does evolution not require both the tools and the opportunity?

    Since you are not happy with this, perhaps you can share what type of research finding would add to the plausibility of front-loading?

    You have have distinguished FL from directed evolution by limiting FLE to a particular time period in evolution. IIRC (and correct me if I am wrong), you also assume that standard Darwinian descent with modification occurred after the front loading event. IMO, then, research that adds to the plausibility of front loading would a) describe phenomena that occurred during the time period critical for front loading and b) predict a different outcome than Darwinian descent with modification. If the research doesn't fit a), then it might add to the plausibility of directed evolution, but it can't add to the plausibility of FLE. If the research doesn't fit b), then like the research that Bradford linked to, it might be neutral wrt FLE, but it won't add to its plausibility.

    Bradford:
    This really gets to the heart of the matter. When the outcome and mechanism are not disputed but the perspective differs why then does this become such a problem for you Nick?

    Heck, it's not a problem for me. It's just a mildly interesting topic to debate in the comments of a blog. If you are right that FLE uses the same mechanisms and results in the same outcome as Darwinian evolution, then I suspect that MikeGene's approach is doomed. Only a designercentric approach, confirming the existence of the designer and determining that entity's objectives, will add to the plausibility of FLE.

    The research that you originally linked to is interesting but I'm becoming much less interested in FLE, the further down these comments we go. It just doesn't seem to have any substance. You can have the last word.

  58. Comment by Nick — May 31, 2007 @ 4:10 pm

  59. Nick Says:
    May 31st, 2007 at 4:29 pm

    OK, so I lied about the previous comment being my last. I have one more question for Bradford and/or MikeGene. In the research described above, the old hypothesis was that the HoxD expression pattern controlling development of tetrapod limbs was an evolutionary novelty, and the HoxD expression pattern controlling actinopterygian fins was conserved. The new model is that the tetrapod pattern is conserved and the actinopterygian pattern is novel. Under which of these two models is front loading more plausible? Or, are the two models equivalent with respect to the plausibility of front loading?

  60. Comment by Nick — May 31, 2007 @ 4:29 pm

  61. Eric Anderson Says:
    May 31st, 2007 at 7:11 pm

    Thanks for the link bFast.

    Glad that a decent analysis is finally throwing some cold water on the ridiculous claim of the protofeathers. Unfortunately, it takes serious time and effort (i.e., actual scientific work) to analyze and demonstrate the falsity of such claims, while it is very quick and easy to get wild stories and evolutionary fantasies proclaimed to the world. Kind of like trying to swat down a population of files that multiply faster than they can be killed.

    Or controlling a large population of bunnies with a slow and plodding weapon. Oops, did I say that . . . ?

  62. Comment by Eric Anderson — May 31, 2007 @ 7:11 pm

  63. MikeGene Says:
    May 31st, 2007 at 9:29 pm

    Hi Nick,

    OK, sorry. I thought you were attempting to say something non-trivial. Since evolution, whether front loaded or not, is a historical process, the future always depends on the present (or the present on the past, if you prefer).

    Of course. If we are talking about originally designed entities, then connecting the present to the past is connecting the present to design. But we're still left with the question of just how plausible it is to design the future through the present. This research helps us see that such an objective is increasingly plausible.

    The research that Bradford alerted us to is very interesting, but this quote from one of the authors is just banal. When does evolution not require both the tools and the opportunity?

    Ah, but the conventional Darwinian view tends to tilt toward the notion that opportunity creates the selection pressure for jury-rigging the tools into existence. In this case, it was the tools that helped evolution find the opportunity.

    You have have distinguished FL from directed evolution by limiting FLE to a particular time period in evolution. IIRC (and correct me if I am wrong), you also assume that standard Darwinian descent with modification occurred after the front loading event.

    Yes, and because of life's design, it was RM & NS under control.

    IMO, then, research that adds to the plausibility of front loading would a) describe phenomena that occurred during the time period critical for front loading and b) predict a different outcome than Darwinian descent with modification. If the research doesn't fit a), then it might add to the plausibility of directed evolution, but it can't add to the plausibility of FLE. If the research doesn't fit b), then like the research that Bradford linked to, it might be neutral wrt FLE, but it won't add to its plausibility.

    I can see how failure to meet a) and b) leaves you unconvinced of front-loading, but I fail to see how it renders FLE implausible.

    As for a), I'm not quite sure what you mean by the "time period critical for front loading." Front-loading envisions the implanting of design at some point in time and then asks to what extent this design shaped subsequent evolution. One way to define "˜extent' is to define it as the time period by which the design can exert its influence. And that's the very question that is helped by the research Bradford links to. As for b), that does not make any sense. Did Darwinian descent with modification actually have a predicted outcome as far as this research goes? As you wrote:

    The paired fins of actinopterygian fish and the limbs of tetrapods are homologous structures. Both are derived from the fins of an aquatic common ancestor. It was known that the developing fins of modern actinopterygian fish lack a developmental hallmark of developing tetrapod limbs (late phase HoxD expression). Since actinopterygian fins are morphologically more similar to the fins of the common ancestor, it was a reasonable hypothesis that the development of limbs was the evolutionary novelty and the development of fins was evolutionarily conserved.

    This new data suggests the reverse.

    Unless Darwinian descent with modification is going to predict specific outcomes, how can FLE hope to predict something different?

    Furthermore, as I explained above, the recruitment of Darwinian descent with modification seems to be a rather wise design strategy. So why is FLE supposed to result in a different outcome than Darwinian descent with modification? What would one such possible different outcome look like?

    Heck, it's not a problem for me. It's just a mildly interesting topic to debate in the comments of a blog. If you are right that FLE uses the same mechanisms and results in the same outcome as Darwinian evolution, then I suspect that MikeGene's approach is doomed.

    Only time will tell.

    Only a designercentric approach, confirming the existence of the designer and determining that entity's objectives, will add to the plausibility of FLE.

    Huh? How? Let's say that life was indeed designed 3.5 billion years ago? Does this mean that we should necessarily be able to confirm the existence of the designer and determine that entity's objectives? Nope. So why hold a tentative design inference hostage to this demand? The designer-centric approach is an approach that is dependent on independent information about the designer. So why insist on it when no such independent information exists? We can either sit around and hope we stumble upon this information some day or we can begin pondering ways to get around the need for such independent information. Once this choice is seen for what it is, it becomes clear (at least to me) why so many critics demand allegiance to the designer-centric approach - sitting around waiting for independent information about the designer to poof into existence is a perfect way to make sure that no one is ever likely to detect any design.

    The research that you originally linked to is interesting but I'm becoming much less interested in FLE, the further down these comments we go. It just doesn't seem to have any substance. You can have the last word.

    I have a feeling that you'll find yourself wanting to talk about FLE sometime in the future. :grin:

  64. Comment by MikeGene — May 31, 2007 @ 9:29 pm

  65. Thought Provoker Says:
    May 31st, 2007 at 11:53 pm

    Hi Nick,

    If you have the time, please look at the ID and Consciousness thread. I have written a multipart thread that walks throught a quantum mechanical explaination that is potentially compatible with MikeGene's scientific research.

    My discussion starts here

    I really want someone to explain were Rodger Penrose and/or I have gone astray in the logic.

    Thanks and Regards,
    TP

  66. Comment by Thought Provoker — May 31, 2007 @ 11:53 pm

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