Coyne and Bad Design

In his review of Dawkins most recent book, Jerry Coyne writes:

Even more evidence for evolution comes from the “bad designs” of animals and plants, which, Dawkins observes, look nothing like de novo creations of an efficient celestial engineer. His favorite example–and mine–is the recurrent laryngeal nerve, which runs from the brain to the larynx. In mammals it doesn’t take the direct route (a matter of a few inches) but makes a curiously long detour, running from the head to the heart, looping around the aorta and then doubling back up to the neck. In the giraffe, this detour involves traversing that enormous neck twice–adding about fifteen feet of superfluous nerve. Anyone who’s dissected an animal in biology class will surely agree with Dawkins’s conclusion: “the overwhelming impression you get from surveying any part of the innards of a large animal is that it is a mess! Not only would a designer never have made a mistake like that nervous detour; a decent designer would never have perpetuated anything of the shambles that is the criss-crossing maze of arteries, veins, nerves, intestines, wads of fat and muscle, mesenteries and more.”

Creationists often object to this sort of argument, saying that it’s not scientific but theological. God is inscrutable, they claim, so how could we possibly know how he would or would not design creatures? But this misses the point, for the “bad design” we see is precisely what we’d expect if evolution were true. The laryngeal nerve takes that long detour because, in our fishy ancestors, it was lined up behind a blood vessel, with both nerve and vessel servicing the gills. As the artery moved backward during its evolution to the mammalian aorta, the nerve was constrained to move behind it, although its target (the larynx, an evolutionary descendant of the gill arch) remained up in the neck. If you insist that such designs reflect God’s plan, then you must admit that his plan was to make things look as if they had evolved.

There is some sleight of hand to detect here.  Coyne/Dawkins begin with a “bad design” argument, but when confronted by the criticism that this argument is theological, they shift gears and insist they are really arguing that the mammalian nerve route is best understood by considering fish development and physiology.  In other words, it’s just an argument for homology. And since arguments for homology do not depend on something that looks nothing like de novo creations of an efficient celestial engineer, the whole bad design argument is superfluous.

The problem with Coyne’s complaint is that it is coupled to a double standard.  Bad design counts as evidence against design, but I doubt Coyne would acknowledge the other side of the coin – good design counts as evidence for design.  From his non-teleological perspective, it is “heads I win, tails you lose.” Bad design counts against an intelligent design and good design counts as evidence for how good the designer mimic can be.  All data are absorbed into the Duck.

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138 responses to “Coyne and Bad Design

  1. Here’s a recent study addressing that other old chestnut for design flaw arguments: the vertebrate eye. It expands upon a study done in 2007 on these Muller glial cells, which act like living fiber optics in the eye to transmit light through the optic nerves and other tissues to the “backwards” photoreceptor cells. I described the 2007 study, but I’ll have to write an update on the results from this new study, which describe how the passing of light through these Muller cells offers additional advantages over an eye w/o these kinds of cells.

    For the requisite “heads I win, tails you lose” response, see the editorial from New Scientist, esp. the statement by Kenneth Miller.

  2. LOL! My psychic powers on display. 😉

    Me:

    Bad design counts against an intelligent design and good design counts as evidence for how good the designer mimic can be. All data are absorbed into the Duck.

    Miller:

    Rather than provide evidence in support of intelligent design, the new work is actually yet another example of evolution’s extraordinary ability to create workaround solutions to problems arising from earlier iterations.

  3. I don’t believe that Coyne, Dawkins, Miller, or Gene have the slightest idea what constitutes “bad design”.

    It seems to follow the strange logic of “Well, I wouldn’t have done it that way”, which says far more about Coyne, Dawkins, Miller, and Gene than it does about the actual design or the actual designer.

    Good Lord. Dirt – raw dirt – turns into the mammalian larynx that Pavarotti uses to sing Ave Maria…

    …and you Bozos sit around pontificating about how YOU would have done it.

  4. chunkdz, I’m curious why you lumped Gene together in the group with Coyne, Dawkins, and Miller?

    Mike, I just realized that your final word was “Duck.” I don’t know what I thought you said when I first read your post, but it most certainly wasn’t “Duck….”

  5. chunkdz, I’m curious why you lumped Gene together in the group with Coyne, Dawkins, and Miller?

    Because like the other three, Gene considers the vertebrate eye to be irrationally designed.

  6. Chunkdz it looks to me like you’re lumping rationality and foresight together.

  7. Guts: “Chunkdz it looks to me like you’re lumping rationality and foresight together.”

    Mike gave the eye a -2 for rationality, even after considering the arguments in favor of an inverted retina.

  8. Hi Chunkdz,

    It seems to follow the strange logic of “Well, I wouldn’t have done it that way”, which says far more about Coyne, Dawkins, Miller, and Gene than it does about the actual design or the actual designer.

    Good Lord. Dirt – raw dirt – turns into the mammalian larynx that Pavarotti uses to sing Ave Maria…
    …and you Bozos sit around pontificating about how YOU would have done it.

    Then how are we supposed to determine if a design is an intelligent design? Or is the descriptor ‘intelligent’ superfluous to intelligent design?

    As I describe in the DM, the four criteria must be used as independently as possible. To score whether or not a system is rational we can’t be focused on ideas about dirt turning into the mammalian larynx. We have to look at the system as a designer or engineer would look at it and try to assess it in terms of engineering principles.

    Also, as I wrote in the DM, the score must be responsive to new data. So in 2007, I gave the vertebrate eye a Rationality score of -2 because it did not make sense to put the wiring in front of the sensors. In light of this new study, I would now move it to a 0; I can’t say whether the arrangement is rational or irrational. Perhaps after reading the paper, and dependent on my ability to grasp the technical points and dependent how well the analysis holds up over time, I would move it into the positive range. The authors do, after all, conclude: “The retina is revealed as an optimal structure designed for improving the sharpness of images.”

    There is one final big picture point to consider for those sympathetic to ID. Why in the world is it that two physicists from Technion–Israel Institute of Technology made this discovery and not someone from the ID movement? Talk about blown opportunities! Imagine if Miller and the scientific community had to credit researchers from the BioLogic Institute for this discovery. Ouch. So again, why is it that this discovery, waiting to be discovered, was missed by everyone in the ID movement? Could it have anything to do with eschewing “bad/non-intelligent design” arguments as “theological” while focusing on ways to convince people a gap really exists? I think so. Maybe if folks in the ID movement recognized the bad design argument as a legitimate criticism, someone would have been motivated to look more deeply into the issue and saw what Labin and Ribak saw. But if you simply wave away bad design arguments as theological complaints, as we can see, there isn’t much motivation to take such a deeper look, now was there?

    After all, pondering how I would have done it or not done has been a very helpful guide in outlining the case for front-loading evolution.

  9. “We have to look at the system as a designer or engineer would look at it and try to assess it in terms of engineering principles.”

    You hit the nail on the head there. Allow me to use an analogy from actual examples of engineering. There are many, but I will use a simple one.

    Your company is designing a video game and you hire consultants and developers that converge on an idea: Let’s pump thousands of dollars and man hours into developing a computer game. When we’re done, only the most powerful computers today can really see the beautiful graphics and the true functionality. Whereas, the average computer will only see average graphics and limited functionality. However, the demographic with which you expect to make the most profit only has the average computer. Since the demographic with which you expect to make the most profit only has the average computer, the design of your game is irrational. All that money? All that man power?

    The design may be irrational, but the designer isn’t, because computer technology is rising exponentially. The designer has the future in mind. So, there will be a time in the future that the average computer will be able to see the game in all it’s beauty and functionality without the designer having to constantly update the game engine. So there’s a big a difference between rationality and foresight and that’s why they should be kept independent.

  10. So again, why is it that this discovery, waiting to be discovered, was missed by everyone in the ID movement?

    Lack of resources.

    Maybe if folks in the ID movement recognized the bad design argument as a legitimate criticism, someone would have been motivated to look more deeply into the issue and saw what Labin and Ribak saw.

    Perhaps it wasn’t a good argument. The “bad design” argument appears to be based on ignorance.

    Also the eye of today is not the designed eye. Meaning “bad design” could have crept in over the generations.

  11. Hi Mike,

    It seems a bit unfair to fault the ID movement for not making this discovery. True, if this study had come from a known ID lab it could have been a prime example of how ID theory can lead to positive scientific results, but if we are charitable we can probably think of several valid reasons why this didn’t happen beyond just waving away these bad design arguments. Joe G cited lack of funding, but we can also consider the limited number of scientists working in labs who take an ID-centric approach.

    Also, we shouldn’t necessarily rule out that Labin and Ribak are not themselves proponents of ID. In their paper, they refrain from making any comments about how this finding could be explained from an evolutionary standpoint, which tends to be obligatory in these kind of papers (granted, their work was published in a physics rather than a biology journal). It is possible that they were guided by ID thought in conducting their study.

    Plus, do we know the motivations of those who conducted earlier studies that provide reasonable explanations for why the photoreceptor cells in the vertebrate eye are inverted? Michael Denton cited several in his paper on the inverted retina. Who’s to say that they were not also guided by a design-centric approach?

    I would also suggest that perhaps ID theorists realize that pointing out good designs in nature does not necessarily provide positive evidence for a designer, as it doesn’t close the door on later discoveries that provide a non-designer explanation. Thus, in regard to “design flaw” arguments it is enough simply to show that these arguments do not provide evidence against an intelligent designer, which is how these arguments are typically used.

  12. Guts,

    That’s a nice analogy. It maps well to the RNAP discussion. Compared to the bacterial RNAP, the archaeal RNAP looks like a clunker. But seen in the context of what was to come, the eukaryotic RNAP, the archaeal RNAP looks like the work of a genius.

  13. Ok, first I need to eat some words. Mike is not and has never been a “pontificator”. To the contrary he’s one of the most humble and carefully circumspect people I’ve never met when it comes to espousing his views.

    Also, it’s probably not wise to call a bunch of people smarter than I am “Bozo”.

    I guess I just picked the wrong week to stop sniffing glue.

    So apologies, Mike. My poorly stated point should have been said more simply and to the point.

    Nobody can tell whether something is good design or bad design without independent knowledge of the designer.

    And,

    irrational design does not equal bad design.

    I’ve expanded on these ideas a bit over at TT.

    http://telicthoughts.com/critical-thinking-exercise-bad-design/

  14. Guts, love that analogy.

    I’m a bit confused though why evidence of foresight does not then increase the rationality score. I have to admit that I have not read DM yet (forgive me) and this is probably covered there, but I did try searching in Mike’s blog for the working definitions of rationality and foresight used in the DM.

    If we understand that the reason the game developers released their game such that the average user only got limited functionality is because the developers were looking to the future advances in computer power (foresight), shouldn’t we then attribute rationality to the design of their game as well? While the advantages of the design may not be realized at present, the future profits that the game will garner as computer power catches up would seem to make the game, from a software developer point of view, a rational design.

    Now in reference to the vertebrate eye, Denton has argued that the inverted retina appears to be an essential feature to obtaining an eye w/ optimal visual characteristics, and that we’d be hard pressed to come up with any other design w/ comparable qualities that didn’t have this feature:

    The more deeply the design of the vertebrate retina is considered the more it appears that virtually every feature is necessary and that in redesigning from first principles an eye capable of the highest possible resolution (within the constraints imposed by the wavelength of light) and of the highest possible sensitivity (capable of detecting an individual photon of light) we would end up recreating the vertebrate eye–complete with an inverted retina and a choriocapillaris separated from the photoreceptor layer by a supportive epithelium layer and so forth.

    Denton then seems to call in the PREPA pattern in his conclusion:

    Why on any undirected model should such an unlikely, improbable arrangement–unique in the animal kingdom–have appeared in the first place some 600 million years ago in the earliest of vertebrates who had presumably no need for high acuity vision and in all probability possessed photoreceptors with metabolic rates perhaps one or two orders of magnitude less than those of higher warm-blooded vertebrates today? If the non-inverted retina works so well for the cold-blooded cephalopods why did evolution go to such trouble to invert the retina in cold-blooded vertebrates? And is it really just fortuity that this curious event resulted in an adaptation which turned out to be essential for high acuity vision in the most advanced terrestrial vertebrates that appeared on earth long after this remarkable choice was made.
    Rather than being a case of maladaptation, the inverted design of the vertebrate retina would seem to be a classic case of pre-adaptation–where an ancient adaptation was “chosen” long before its utility was of necessity. It is evidence for design and foresight in nature rather than evidence of chance. Evidently not all “tidy-minded engineers” get things right.

    What I get from this is that, rather than being an irrational design, the inverted retina was an intentional and essential feature all along, for without it high metabolism vertebrates would not have the visual acuity that they have today. The apparent foresight seen in the design of the vertebrate eye seems to make the inverted retina a feature that is more rational than not.

  15. In my analogy I give you all the answers. Unfortunately we don’t always have all the answers. So keeping the two independent is important in order to yield results in our investigation, IMO. When you are able to say to yourself “Ok, this design doesn’t make sense”, you can either throw your hands up and say “well maybe I don’t understand the designer’s intent” Or you could continue the investigation and start trying to make sense of it from the perspective of foresight. So you have rationality scores and you have foresight scores.

  16. Hi chunk,

    Interesting entry. I’m not trying to ignore you; I’m just extra busy at the moment. Caveman will share thoughts as soon as he can.

  17. Why in the world is it that two physicists from Technion–Israel Institute of Technology made this discovery and not someone from the ID movement? Talk about blown opportunities! Imagine if Miller and the scientific community had to credit researchers from the BioLogic Institute for this discovery. Ouch.

    I would think that would be a blow to biologists.

    It kind of tells me Miller and the rest of his ilk are focusing too much attention on erecting ID starwman arguments to refute instead of doing any actual research to substantiate their claims of inferior and/or illusory design.

    But anyway, I think it is funny that physicists are telling biologists about biology…

  18. Same here, Mike. I want to address your response when I get a moment.

  19. Hi chunk,

    Like I said, that was an interesting essay. You are correct in noting that all designs will entail a compromise.

    Compromised design is not a sign of irrational design. Why? Because design is ALWAYS a compromise. There will never be an aircraft with optimal stability and optimal maneuverability. There will never be an aircraft with optimal weight and optimal strength. There is always a compromise between a variety of design principles based upon – you guessed it – purpose and intent.

    I briefly explore this in the DM with the criteria of efficiency and flexibility. It is typically the case that one is enhanced at the expense of the other. That is why I encouraged people to take a holistic look, trying to factor all relevant criteria – a consilience of clues. I even suggested a matrix within the Matrix with this criterion. The “bad design” judgment is thus not rooted in isolated flaws, but is a judgment that the compromise itself is tilted in irrational direction.

    In the case of the vertebrate retina, we have a system where the wiring is placed in front of the sensors and this placement makes it necessary to incorporate a blind spot and makes the system vulnerable to break down. Furthermore, there is very good reason to think this arrangement is not necessary in any design sense – cephalopods have essentially the same eye, but the wiring is placed behind the sensors. Thus, on balance, I scored it as a -2.

    But once again, recall the DM scoring is a method of assessment. Its objective is to get people to lay their cards on the table and thus make it possible for an open-ended critical analysis and reanalysis to exist. If you think you can make a case that the arrangement is rational, make it. Lay out the reasoning, the evidence, and the score. If you think we can’t say either way, then score it as 0. In my opinion, it is only through this type of give-and-take that a true investigation can occur.

    Up above, I noted that Coyne/Miller are playing “heads I win, tails you lose.” There can be no evidence for ID, but there is plenty of evidence against ID. This explains why, over the years, critics have struggled immensely with simple questions – “What would cause you to suspect design?” and “What would you count as evidence for design?” Since the critic comes to the table with a closed-mind and already “knows” there can be no evidence for ID because ID is false (dammit!), they struggle to find something that could possibly happen, but know is unlikely to happen even if ID is true – they demand disproofs of evolution or want to see the designer with their own eyes. That’s the depth of their contribution.

    But there is a flip side, and that is that many in the ID movement likewise look like they are playing “heads I win, tails you lose.” There is all sorts of evidence for ID, but there can be no evidence against ID. Junk DNA is not junk, and even if it was, that would be a theological complaint and thus not relevant. Yet the fact that the ID movement cheers when functions for junk DNA are found is tacit admission that they recognize the validity of bad design arguments. So the questions to ask yourselves are this – “What would cause you to doubt ID?” and “What would count as evidence against ID?”

  20. Hi Mike,

    I have a couple issues with the way you applied the matrix to the mammalian eye. First, you note above that we should take a holistic approach when considering rationality. However, it appears that you leave out several key components in your analysis. You presume that the backwards wiring unnecessarily creates a blind spot and is therefore irrationally designed. But a truly holistic approach would recognize that the mammalian eye is designed to be one of a pair of stereovisual receptors, and that the mammalian brain is well equipped to compensate for the blind spot by multiplexing the information from both eyes.

    The second issue I have is that you pay lip service to the idea of bad design in biology and thus seemingly conflate an irrational balance of design decisions to “bad design”. I still contend that there is no way to judge whether something is bad design or not without knowing the designer’s purpose and intent. Otherwise we could fault the designer for not giving us the visual acuity of an eagle, the robust damage proof casing of a Hasselblad, and the wide spectrum sensitivity of a Hubble Telescope.

    Our eyes work reasonably well. That alone should indicate a positive balance on the rationality scale, but I don’t think you are wrong for scoring it a 0. But it should be totally seperate from the concept of bad design. As I noted in the essay, irrational design is often a signature of very good design. But we can only see this in light of the designer’s purpose and intent.

  21. “What would cause you to doubt ID?”

    Probably nothing. But my views about it have definitely changed since I began investigating.

  22. Hi chunk,

    Probably nothing. But my views about it have definitely changed since I began investigating.

    I truly appreciate your honesty, especially contrasted to the critics over the years who are unwilling to acknowledge there is nothing that would cause them to suspect ID. You come right out and lay your cards on the table while they will go to great extremes to keep their cards hidden from view.

    If you ever start to have serious doubts about ID, but also retain serious doubts about the non-teleological explanation, you should re-read the DM, as it will probably resonate more loudly from that viewpoint.

    Caveman will tackle your other response after sun rise.

  23. “What would cause you to doubt ID?”

    For me it would be:

    1- Some sound methodology for determining the design is illusory

    2- Something- anything- that demonstrates nature, operating freely, is all that is required

    and for Common Descent

    Something- anything- that demonstrates that the transformations required can be had by mutational accumulation.

  24. I don’t believe that Coyne, Dawkins, Miller, or Gene have the slightest idea what constitutes “bad design”.–chunkdz

    I was just reading an essay by John Avise about bad design in the PNAS. I don’t think the proper response to bad science and bad theology is more bad science and bad theology. Or more “bad design,” which Avise believes is “ubiquitous” in biology, and also “easy” to explain on evolutionary-theoretic grounds.

    I assume a more traditional Darwinian perspective: all things will tend to perfection, being tested and continuously refined under exacting conditions; and that life forms evince a higher workmanship, higher than man’s, (even if not quite up to God’s standards (LOL)) and it is “good design” that is the principal explanadum and explanans of theory.

    Avise thinks its “easy” for evolutionary theory to account for bad design. I don’t. (Sheesh! Why are things so difficult for me?)

    But from the more traditional perspective, it is the fit between organism and the conditions of its existence that determines whether it is a good or bad design.

    Not the subjective evaluations of anyone, not biologists or engineers, as to what is good, bad, or indifferent design. So I don’t give Mike Gene’s scoring of the “rationality” of the design much credence.

    Above, someone suggested a “software” solution, “multiplexing,” to the implementational issue. That sounds like a rational solution to the problem. Except now we’ve launched ourselves into the “spiral of complexity,” which in hindsight (designers don’t only have foresight) may have been the most irrational step we could have taken! Nonetheless, it may have been the only step we could have taken. (Sounds like a dynamic programming problem.)

    Just to illustrate that “rationality” is not a design panacea.

  25. Rock: I assume a more traditional Darwinian perspective: all things will tend to perfection, being tested and continuously refined under exacting conditions…

    I always thought the Darwinian perspective was: all things will tend toward extinction, being tested and continually assaulted under chaotic conditions.

  26. I always thought the Darwinian perspective was: all things will tend toward extinction, being tested and continually assaulted under chaotic conditions.

    The Darwinian perspective is that there is no plan and no goal.

  27. Alan Fox:

    The Darwinian perspective is that there is no plan and no goal.

    IOW an unscientific atheistic perspective.

  28. Joe, I’m not sure we should be meeting like this. But, what the heck.

    Ya see it’s the limitation of science that it can only deal with real phenomena. There may be a goal and a plan, indeed God’s plan, but that is invisible to science. Hence, from the Darwinian perspective, no plan, no goal.

  29. Hi Chunkdz,

    Before getting to your issues, let’s clear up some terminology. Instead of arguing about “bad design” and “good design,” let’s simply follow through on the I from ID. That is, both sides of the aisle here can probably agree the eye was designed, it’s a question of whether the designer was an intelligent agent or the blind watchmaker. As such, it would seem only productive and reasonable to consider if the design is intelligent or not. So let’s think about it in terms of intelligent design (if “ID” is to mean anything other than “it could not have evolved!”) and unintelligent design.

    Now, when we get to the first issue, the fact that the mammalian brain is well equipped to compensate for the blind spot by multiplexing the information from both eyes leads to a simple question. Why does it have to compensate in the first place? Given that eyes can be built without blind spots (see squidward), the fact that the brain has to compensate for the blind spot sounds like the brain has to compensate for a flaw, an unintelligent design.

    But even if you don’t agree, what does it get you to dismiss the blindspot as a signpost about the designer because the brain can compensate for it? It sounds to me like that pathway is a dead-end from an investigative perspective. No problem here, thus no reason to take a closer look.

    Yet if we acknowledge the blind spot is a problem for a design inference, then we can turn the same point into a hypothesis. That is, perhaps the blind spot has nudged the brain to develop along certain lines that enhance the power of the brain. Multiplexing the information from both eyes to solve the problem of the blind spot might preadapt the brain for greater tasks. Maybe it’s not a coincidence that our reasoning abilities is so ocular-centric. After all, when the brain compensates for the blind spot, the brain itself is actively seeing something the sensors in the eye did not detect. Kind of like thinking, eh?

    Again, I will simply point out that no one in the ID community discovered what two physicists from Technion–Israel Institute of Technology discovered.

    As for your second issue, I think function is closely related enough to purpose and intention that it can serve as the proxy when reverse engineering a system to judge whether or not the system was intelligently designed. I would agree that we should not make judgments about the rationality of a system because it lacks of particular function that would strike our fancy; but if we begin with the function it serves, then we can judge it. Of course, such judgments are tentative and dependent on the information the judge has.

  30. Hi Joe,

    For me it would be:
    1- Some sound methodology for determining the design is illusory
    2- Something- anything- that demonstrates nature, operating freely, is all that is required
    and for Common Descent
    Something- anything- that demonstrates that the transformations required can be had by mutational accumulation.

    In other words, you need someone to prove design is false or you need to see the blind watchmaker design something. The mirror image of the critic, who needs someone to prove evolution is false or to see the intelligent designer design something.

    No wonder you and Alan sound like twins separated at birth! LOL

  31. WRT to the (human) eye, the Darwinian hypothesis is that from the human population that exists today there is an unbroken chain of descent from parent to offspring back to the first living organisms. That each individual organism in that chain was itself viable enough to survive and that the development of the eye took place in small increments due to the favouring of advantageous traits by the process of natural selection.

  32. Hi Alan,

    WRT to the (human) eye, the Darwinian hypothesis is that from the human population that exists today there is an unbroken chain of descent from parent to offspring back to the first living organisms.

    The same holds with the Front-loading hypothesis. To design the future through the present, you’d need an unbroken chain to connect the two.

    That each individual organism in that chain was itself viable enough to survive and that the development of the eye took place in small increments due to the favouring of advantageous traits by the process of natural selection.

    Yes, this is conventional thinking that rests at a superficial level. We might ask if there is any evidence something like the human eye could evolve without Pax6. We might also wonder why you would insist on “small increments” when such an insistence misled Darwin on multiple occasions. And just how small is small in the “Darwinian hypothesis?” Is there any evidence that the vertebrate eye emerged in small increments?

  33. We might ask if there is any evidence something like the human eye could evolve without Pax6.

    It seems the fact that this gene is highly conserved across species and can trigger ectopic eye development makes it an essential ingredient. But we don’t know that there are not alternative genetic sequences that might work equally well. Is it one in a billion or a few million in a billion?

    We might also wonder why you would insist on “small increments” when such an insistence misled Darwin on multiple occasions.

    Darwin was not infallible and evolutionary theory today has moved on. I “insist” (actually, I don’t but I know how you like to play with words) on small increments because changes between parent and offspring need to be small to be viable.

    And just how small is small in the “Darwinian hypothesis?” Is there any evidence that the vertebrate eye emerged in small increments?

    The smallest possible increment is a single nucleotide mutation. There is no tape recording of the whole chain of events. there are many interesting organisms with different types of visual sensory system. Lots of homology, PAX6 for example!

  34. Douglas Theobold presents a good argument.

  35. Mike,

    I require positive evidence for something.

    I would think that is the way it should be.

    IOW I don’t understand your issue with what I posted- all I am looking for is positive evidence.

    No positive evidence = no science.

  36. Alan Fox:

    Ya see it’s the limitation of science that it can only deal with real phenomena.

    Design is a real phenomenon.

    Goals and plans are real phenomenon.

    Targeted searches are real phenomenon.

    There may be a goal and a plan, indeed God’s plan, but that is invisible to science.

    That is false.

    Just because some scientists have a blind spot that prevents tem from seeing a plan or goal doesn’t mean anything to science.

    IOW you are confusing some scientists short-comings with science.

    Hence, from the Darwinian perspective, no plan, no goal.

    That is an unscientific atheistic perspective.

  37. Alan,

    A formal test of common ancestry would be to take a reptile embryo and tinker with it until a mammal developed.

    Or a fish embryo to see if a tetrapod developed.

    However saying a formal test amounts to no more than it looks like common ancestry tells me the position is untestable.

  38. Again, I will simply point out that no one in the ID community discovered what two physicists from Technion–Israel Institute of Technology discovered.

    No one in the evolutionary biology community discovered it either.

  39. Again, I will simply point out that no one in the ID community discovered what two physicists from Technion–Israel Institute of Technology discovered.

    Mewonders if these physicists were driven to do this research because of the claim of the eye being poorly designed.

    Given the athletic abilities of some humans- the hand-eye coordination that is required for some/ most of what they do- the claim seems rather silly on the face of it.

    “But Joe if you close one eye and pull a piece of paper slowly towards your face you will notice you lose something in your vision before the paper reaches your nose.”

    Then it’s a good dam paper didn’t (slowly) rise up aginst us for reeming it! 🙂

    It’s about time someone from that mystic scientific community put that shiite* to rest.

    And you know there wasn’t any chance that some evolutionary biologist was going to do that. Not one without tenure anyway.

    *by design

  40. Perhaps it needs pointing out that from the Darwinian perspective, there is no design for an eye in the genome. The interplay of genes and their selective expression result in the growth and differentiation of cells in specific sites and at specific times result in the development of the visual system (which can be considered topologically as an outgrowth of the brain, which itself can be considered a development from ectodermal cells, i. e. skin!)

    No blueprint, rather a recipe.

  41. “as the embryo develops” may be added after “specific times”

  42. Or a fish embryo to see if a tetrapod developed.

    You should ask PZ Myers to give you some pointers to his research on zebra fish embryos. Evo-devo is a field that is developing (pun intended) rapidly!

  43. Alan Fox:

    Perhaps it needs pointing out that from the Darwinian perspective, there is no design for an eye in the genome.

    Yes Alan, we know.

    The Darwinian perspective is unscientific- ie it reaches a conclusion regardless of the data.

    The interplay of genes and their selective expression result in the growth and differentiation of cells in specific sites and at specific times result in the development of the visual system (which can be considered topologically as an outgrowth of the brain, which itself can be considered a development from ectodermal cells, i. e. skin!)

    IOW “it just happened”- unscientific.

    No blueprint, rather a recipe.

    A recipe is a plan with a goal.

  44. Alan Fox:

    You should ask PZ Myers to give you some pointers to his research on zebra fish embryos.

    When he publishes something worth reading I will read it.

    Evo-devo is a field that is developing (pun intended) rapidly!

    Evo-devo is your position’s last hope.

    However it doesn’t appear to support your position and science is not conducted via promissory notes.

  45. Hi Alan,

    It seems the fact that this gene is highly conserved across species and can trigger ectopic eye development makes it an essential ingredient. But we don’t know that there are not alternative genetic sequences that might work equally well. Is it one in a billion or a few million in a billion?

    Exactly. We don’t know. In other words, a key element of the Darwinian perspective is rooted in faith, not reality. Of course, it was the “few million in a billion” assumption which prevented evolutionary biologists from anticipating and predicting that fly and mouse eyes would share such similar pathways.

    Darwin was not infallible and evolutionary theory today has moved on.

    Of course. So why keep perceiving evolution as happening in small increments?

    I “insist” (actually, I don’t but I know how you like to play with words) on small increments because changes between parent and offspring need to be small to be viable.

    Do you think this is always true and has always been true for every life form that has ever existed on this planet? Would small increments between parent and offspring explain the emergence of the eukaryotic cell plan?

    The smallest possible increment is a single nucleotide mutation.

    Are you saying evolutionary transformations must occur through such point mutations? If not, then you have not defined how small small must be.

    There is no tape recording of the whole chain of events. there are many interesting organisms with different types of visual sensory system.

    No one asked for a tape recording (perhaps you are used to arguing with people who make extreme demands?). And yes, there are many different types of sensory systems.

    Back to the question – do you have evidence that the evolution of the vertebrate eye occurred in small increments?

  46. Hi Rock,

    I assume a more traditional Darwinian perspective: all things will tend to perfection, being tested and continuously refined under exacting conditions; and that life forms evince a higher workmanship, higher than man’s, (even if not quite up to God’s standards (LOL)) and it is “good design” that is the principal explanadum and explanans of theory.

    Don’t buy it. The blind watchmaker is blind, meaning that any “choices” it makes solve the immediate problem. The problem is solved by coming up with a way, any way, to get more kids out there than the next fella. That’s all. That’s it. Now, if you take this hyper-myopic approach, and fortuitously generate a more complex state by building on these choices, it’s quite possible the blind watchmaker will box itself in. The blind watchmaker is not good at erasing the blueprints to start over. It’s more likely to glom something onto the blueprint to merely lessen the problem. As there is no reason to think ancient choices – glommed on solutions to smooth things over – made for myopic reasons, will be inconsequential when it comes to future choices. That’s why we expect the blind watchmaker to spit out kluges. The standard for success is low and vague (make relatively more kids) and it’s tied to past solutions.

    You can almost think of evolution like a person’s life. Is a person’s life a constant series of ever-expanding choices that make him into a higher form of workmanship? Or is it that a person’s choices in the past continually winnow down the opportunities for choices in the future.

    The Darwinian perspective is tied to a historical perspective and does not constitute an atemporal search for the best solution.

  47. “That’s why we expect the blind watchmaker to spit out kluges.”

    We et imperium, Mike Gene? Ironic coming from you. You must mean you and Richard Dawkins. LOL

    For us rational design must necessarily fail, and “irrational” design is the only the only option. But its also common for scientists and engineers, and not just effecte avant garde artists-types, to deliberately defy “rationality.”

    A risky strategy, but sometimes very productive.

    None of that has anything to do with either the Divine Watchmaker or the Blind Watchmaker.

    Sorry!

  48. Hi Rock,

    We et imperium, Mike Gene? Ironic coming from you. You must mean you and Richard Dawkins. LOL

    Actually, I think you and Dawkins and wedded on this one. From my book:

    Biologist Massimo Pigliucci, from the University of Tennessee, spells out the implications of Jacob’s tinkerer. Pigliucci argues that organisms are “made of several parts that have no unique and irreplaceable function.” He adds:

    As biologist François Jacob put it, this is exactly what you would expect if natural selection worked like a bricoleur rather than a cunning engineer.

    {….}
    Ken Miller captures the essence of this form of design as he describes the genome as a product of the blind watchmaker: “In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival.”

    Like Pigliucci says, it is not too pretty. You would think such design should stand out against the blind, ignorant tinkerer’s haphazard cobbling. But then again, some contradict such claims and argue instead that the blind, ignorant tinkerer actually mimics the best of engineers. Richard Dawkins recognizes that many factors may be at work in evolution, yet he insists on one thing: “Wherever in nature there is a sufficiently powerful illusion of good design for some purpose, natural selection is the only known mechanism that can account for it.” He further pushes this point by noting that if “an engineer looks at an animal or organ and sees that it is well designed to perform some task, then I will stand up and assert that natural selection is responsible for the goodness of apparent design.”
    Apparently, while natural selection does not work as an engineer would, engineers would not know this.

    “None of that has anything to do with either the Divine Watchmaker or the Blind Watchmaker.”

    Agreed, as it’s not about divine vs. blind. It’s about whether or not evolution, as a process, was influenced by a mind’s eye or not. The Dawkins school, combined with the Pigliucci school, cover all the bases such that if evolution was indeed influenced by a mind’s eye, they would not be able to see it.

  49. …the fact that the mammalian brain is well equipped to compensate for the blind spot by multiplexing the information from both eyes leads to a simple question. Why does it have to compensate in the first place? Given that eyes can be built without blind spots (see squidward), the fact that the brain has to compensate for the blind spot sounds like the brain has to compensate for a flaw, an unintelligent design.

    We can’t possibly know this.

    We know that some planes can glide. An F-14 cannot glide unless it has a computer to compensate for it’s inherent instability.

    Is this a flaw?

  50. Hi chunkdz,

    We can’t possibly know this.

    Agreed. But a score is not a statement of knowledge. I don’t claim to know the design is unintelligent; it’s just the way the inferential winds are blowing from my perspective. The DM already incorporates your objection – the rationality score would be 0.

  51. “Is this a flaw?”

    Ya might think so when the engines flame out. LOL

    Might be interesting to consider how “rationality” is going to save you in that sitaution, when all the laws of physics are agin’ ya.

    I have no problem with the “mind’s eye” influencing biological evolution–that’s basically what design is, Mike Gene. Or that’s what I believe.

    Creationists and Dawkinists alike seem to treat design as if it were a “free lunch.” A miracle of Nature or of Nature’s God.

    Way beyond the spirit of Monod, Mike Gene.

  52. So why keep perceiving evolution as happening in small increments?

    Bit of a non-sequitur! “Small” in this context has a range from a single nucleotide substitution to too large to accommodate the offspring as a breeding individual in the gene pool. Obviously there is speculation about certain milestones such as sexual reproduction, symbiogenesis and multicellularity. However the origin of chloroplasts is best explained by a developing symbiotic process. The origin of multicellularity has several competing theories.

    I recommend The major transitions in evolution for a good source of material.

  53. Would small increments between parent and offspring explain the emergence of the eukaryotic cell plan?

    See previous comment.

  54. Back to the question – do you have evidence that the evolution of the vertebrate eye occurred in small increments?

    As you know I, like you, am a layman so I don’t research evolutionary processes with regard to the human eye. Wikipedia seems a good place to start. Lots of links to peer reviewed papers.

  55. So all Alan Fox has are literature bluffs?

    LoL!!!!

    However the origin of chloroplasts is best explained by a developing symbiotic process.

    Best explained to people who reject, a priori all alternatives.

    Can we test this symbiotic relationship?

    IOW can we repeat what allegedly occurred so we can study it?

    If not then it ain’t science…

  56. Can we test this symbiotic relationship?

    Yes.

  57. Alan,

    You are nicely demonstrating how the “Darwinian perspective” encourages a superficial perspective on evolution, as it clearly does not inspire deep thinking about these issues. We’ve seen that you have been content to believe on faith that countless alternatives to Pax6 would have been available to the blind watchmaker. And in your latest round of replies, it turns out the “small” in “the development of the eye took place in small increments due to the favouring of advantageous traits by the process of natural selection” can mean whatever you want it to mean. At least Darwin made an attempt to define small: “Natural selection can act only by the preservation and accumulation of infinitesimally small inherited modifications, each profitable to the preserved being.”

    Not only can’t you tell us how small ‘small’ is supposed to be in that “Darwinian perspective,” such subjectivity is coupled to an inability to provide the evidence. When I asked for evidence that the vertebrate eye evolved in small increments, you pointed me to the Wikipedia page and its references. But Joe G nicely called that as a “literature bluff’ as I found nothing to answer my question. Here, try it this way. Consider a study from two years ago:

    Early evolution of multifocal optics for well-focused colour vision in vertebrates
    O. S. E. Gustafsson, S. P. Collin and R. H. H. Kroger
    Journal of Experimental Biology 211, 1559-1564 (2008)
    Jawless fishes (Agnatha; lampreys and hagfishes) most closely resemble the earliest stage in vertebrate evolution and lamprey-like animals already existed in the Lower Cambrian [about 540 million years ago (MYA)]. Agnathans are thought to have separated from the main vertebrate lineage at least 500 MYA. Hagfishes have primitive eyes, but the eyes of adult lampreys are well-developed. The southern hemisphere lamprey, Geotria australis, possesses five types of opsin genes, three of which are clearly orthologous to the opsin genes of jawed vertebrates. This suggests that the last common ancestor of all vertebrate lineages possessed a complex colour vision system. In the eyes of many bony fishes and tetrapods, well-focused colour images are created by multifocal crystalline lenses that compensate for longitudinal chromatic aberration. To trace the evolutionary origins of multifocal lenses, we studied the optical properties of the lenses in four species of lamprey (Geotria australis, Mordacia praecox, Lampetra fluviatilis and Petromyzon marinus), with representatives from all three of the extant lamprey families. Multifocal lenses are present in all lampreys studied. This suggests that the ability to create well-focused colour images with multifocal optical systems also evolved very early.

    It would seem reasonable to me to argue that the vertebrate eye was quite developed in the last common ancestor of all vertebrates. So let’s next look at their closest relatives – the tunicates and lancelets. There, you find examples of very simple eyespots (clusters o of light sensitive cells). Where are all the “different types of visual sensory systems?”

    Of course this does not rule out the possibility that the vertebrate eye evolved by “small increments” (whatever that means), but I don’t see the evidence that is did evolve by small increments.

    Ah, the advantages of the front-loading perspective – inspiring critical thinking to ask questions that make people with assumptions uncomfortable.

    Alan, the Darwinian perspective is just that – a perspective. Don’t confuse it with reality and turn it into reality with assumptions.

  58. Ah, the advantages of the front-loading perspective – inspiring critical thinking to ask questions that make people with assumptions uncomfortable.

    OK maybe you are at last ready to explain what the advantage of the front loading perspective is and how it is any better explanation of the observed diversity and distribution of living organisms.

    Your perceiving holes in evolutionary theory isn’t getting us anywhere and I concede evolutionary theory is incomplete and inadequate to explain everything. Where does your front loading hypothesis do any better?

  59. Had a look at that paper, Mike:

    The presence of multifocal lenses in representatives of all vertebrate classes studied thus far and their absence in cephalopods suggests a monophyletic origin for this lens design. Convergent evolution in so many vertebrate lineages is unlikely.

    It doesn’t seem that the authors consider they are challenging evolutionary theory.

  60. Alan,

    Originally you spelled out the “Darwinian perspective.” I then posed three basic questions that have stumped you.

    I asked you if something like the human eye could evolve without Pax6 and you admitted you didn’t know.

    I asked you to define how small the “small increments” must be and you could not do it.

    I asked you if there is any evidence that the vertebrate eye evolved in “small increments” and you could not provide any.

    Given this poor showing, you are now trying to shift attention away from these legitimate questions. You write, “OK maybe you are at last ready to explain what the advantage of the front loading perspective is and how it is any better explanation of the observed diversity and distribution of living organisms.”

    First of all, in this particular case, I made it quite clear what the advantage was – “inspiring critical thinking to ask questions that make people with assumptions uncomfortable.” The three questions I asked you flushed out your assumptions.

    Second, as for the larger issue of front-loading, it is dishonest of you to write, “maybe you are at last ready to explain” as if I have been unwilling to explain. I explained that in my book back in 2007 and have been explaining, expanding, and illustrating it on my blog for the last two years. Your unwillingness to read and understand my actual position/arguments is not my problem. Your history of doing just that tells me you are not interested in any answer but just want to redirect focus from the fact that you advocate beliefs without evidence, which is ironic given your misguided pontifications about “science = reality.”

    You also write,

    Your perceiving holes in evolutionary theory isn’t getting us anywhere and I concede evolutionary theory is incomplete and inadequate to explain everything. Where does your front loading hypothesis do any better?

    A couple of things to notice here. First, you activate the Puffer Fish defense, as note how the “Darwinian perspective” has magically inflated into “evolutionary theory.” But that just makes matters worse, as it now appears that it is evolutionary theory that cannot answer some basic and important questions about evolution.

    Secondly, notice the way you frame the theory as if I am asking it to “explain everything.” No, I did not and am not asking it to explain everything. I’m asking some basic questions about what it actually proposes – how does it define its terms and what is the evidence that supports the proposition.

    But then it gets worse, as you next write, “It doesn’t seem that the authors consider they are challenging evolutionary theory.”

    Since I never claimed the authors considered themselves to be challenging evolutionary theory, your point amounts to hand-waving. I interpreted that study to mean – “It would seem reasonable to me to argue that the vertebrate eye was quite developed in the last common ancestor of all vertebrates.”

    Now, try and follow the argument from there, Alan:

    So let’s next look at their closest relatives – the tunicates and lancelets. There, you find examples of very simple eyespots (clusters o of light sensitive cells). Where are all the “different types of visual sensory systems?”

    Of course this does not rule out the possibility that the vertebrate eye evolved by “small increments” (whatever that means), but I don’t see the evidence that is did evolve by small increments.

    So you see, I’m not denying eye evolution, Alan. I’m looking for the evidence that supports your truth claim. Where is the evidence of “small increments” that connects the simple eyepots of the vertebrate’s closest relatives to the complex eyes of the lineage that reflects the most ancient vertebrate? It would seem to me the most intellectually honest thing to do here is to drop the “small increment” requirement, acknowledge the eye evolved, and acknowledge the actual mechanism remains obscure.

    As for your last reply/link, that fits very nicely within the hypothesis of front-loading evolution and I may incorporate it into a future blog, so thank you.

  61. Alan Fox,

    All you have is “it looks like chloroplasts are ancient bacteria”.

    IOW there isn’t any way to test the premise.

    We cannot go into a lab and perform an experiment that demonstrates one bacteria can engulf another and the engulfed bacteria becaomes and intergral organelle.

  62. BTW Alan I am fully versed on endosymbiosis.

    Lynn Margulis’ work is not foreign to me.

    But all she has is “it looks like bacteria”….

  63. Michael: Agreed. But a score is not a statement of knowledge. I don’t claim to know the design is unintelligent; it’s just the way the inferential winds are blowing from my perspective.

    I guess this is where we differ. You see an irrational feature and tentatively conclude irrational design.

    I see an irrational feature, but firsthand knowledge tells me the eye works really, really well. So my first instinct is to look at the entire system and find out how an irrational feature might actually be a rational decision. Lo and behold, a couple of physicists in Israel discover just that.

    Perhaps the holistic approach should really begin with the entire system. In other words, “Man, that F-16 really can fly!” That way, we don’t waste our time wondering why this or that particular feature looks “irrational”.

  64. I asked you if something like the human eye could evolve without PAX6 and you admitted you didn’t know.

    Why would you expect me to know, Mike? You know I, like you, am a layman. If you know and think I should know, enlighten me. If not, you can always post a link. Actually on re-reading the question, my answer is most definitely yes. Say there was an extinction event on Earth tomorrow and only bacteria remained, so that there was another dawn of life, I would expect after 2 – 3 billion years maybe that multi-cellular life would emerge and that organisms would develop organs of sight (via small increments of course). Due simple physics, the light sensing organ should be of broadly similar morphology. But will PAX6 re-emerge? The brain-eye structure that may emerge may emerge could involve entirely different gene sequences and proteins. There be many ways to arrive at a very similar organ. Of course feel free to point out that this is speculation and unfalsifiable, which it is.

    I asked you to define how small the “small increments” must be and you could not do it.

    I beg to differ, Mike. I clearly said, (and indeed you quoted it) “The smallest possible increment is a single nucleotide mutation.” There is no possible smaller increment. The limit on how large a genomic change can occur between parent and offspring is impossible to define specifically but one essential factor is that the offspring is not so different as to cause reproductive isolation from other members of the gene pool. I am ruling out Goldschmidt and his hopeful monsters, notwithstanding a single nucleotide change can result in a large morphological change. Or were you wanting to indulge in semantic games with how small is small. Is Mercury a small planet?

    I asked you if there is any evidence that the vertebrate eye evolved in “small increments” and you could not provide any.

    Well, the Darwinian hypothesis is that evolution generally proceeds by small increments. See above for clarification on small. It’s sort of a central tenet and if you could demonstrate it false in one case, you would have certainly struck Darwinism a severe blow. Frankly, there is so much evidence that evolution (let me qualify, once we are into sexually reproducing organisms) proceeds by small increments that it’s hard to know where to start. Are you serious about this?

    Given this poor showing, you are now trying to shift attention away from these legitimate questions.

    See above for responses to your legitimate questions. This is projection, Mike. Why keep dodging on your front loading ideas?

    Second, as for the larger issue of front-loading, it is dishonest of you to write, “maybe you are at last ready to explain” as if I have been unwilling to explain. I explained that in my book back in 2007 and have been explaining, expanding, and illustrating it on my blog for the last two years. Your unwillingness to read and understand my actual position/arguments is not my problem. Your history of doing just that tells me you are not interested in any answer but just want to redirect focus from the fact that you advocate beliefs without evidence, which is ironic given your misguided pontifications about “science = reality.”

    “Buy my book” is not an explanation. “Read my blog” is not an explanation. If there is a specific explanation of your front loading idea here on your blog, how difficult can it be to cut and paste? Why not a FAQ?

    “Misguided pontifications”?

    Science=reality in the sense that science is limited to the study of real phenomena. How is it possible to disagree with that? Do you disagree?

  65. So you see, I’m not denying eye evolution, Alan.

    Never thought you were a Young Earth creationist, Mike.

    I’m looking for the evidence that supports your truth claim. Where is the evidence of “small increments” that connects the simple eyepots of the vertebrate’s closest relatives to the complex eyes of the lineage that reflects the most ancient vertebrate?

    Mainstream evolutionary theory posits small (within the upper and lower limits stated above) increments in general. With regard to the vertebrate eye and it’s proposed monophyletism and where hagfish fit in, I wonder if Professor Lamb, the author of several papers, including the one I linked to and the earlier one reviewed by PZ Myers might help us out. I’ll email him if you like. Unless you prefer to contact him yourself, I’ll cut and paste your questions.

    It would seem to me the most intellectually honest thing to do here is to drop the “small increment” requirement, acknowledge the eye evolved, and acknowledge the actual mechanism remains obscure.

    It has always puzzled me why intellectual is needed to qualify honesty. I honestly think evolution proceeded in general in small increments (caveats above). Of course the specific sequence of events for any lineage is obscure.

    PS I’ll acquire a copy of your book. I am tempted to ask Dave Rintoul if he wants to sell his copy. On the other hand, if I purchase through Amazon USA, I can post a review! I would just like your assurance that your alternative mechanism(?) that you refer to as “front loaded evolution” is clearly set out and explained there. A page number or chapter heading would be a bonus.

  66. Oops, seems I messed up tags. Freudian nested hierarchy of quotes. Doesn’t seem to affect the sense, though.

  67. BTW Alan I am fully versed on endosymbiosis.

    Never doubted it, Joe.

    Photosynthetic seaslugs

  68. Alan Fox: Say there was an extinction event on Earth tomorrow and only bacteria remained, so that there was another dawn of life, I would expect after 2 – 3 billion years maybe that multi-cellular life would emerge and that organisms would develop organs of sight (via small increments of course).

    Lol!

    Alan just came up with his own theory of front-loaded evolution!

    He even “expects” it to be true. Hey Mike, how come you are not as certain about your theory as Alan is about his? Lol!

  69. Frankly, there is so much evidence that evolution (let me qualify, once we are into sexually reproducing organisms) proceeds by small increments that it’s hard to know where to start. Are you serious about this?

    The tenet that evolution proceeds by small incremental change alone is being challenged by empirical data from many independent sources, from phenotypic plasticity to nongenetic inheritance, etc. The very fact that we can have evolution experiments on life-history characters in the laboratory shows that Darwin’s repeated emphasis on small incremental steps was his second mistake.

  70. The tenet that evolution proceeds by small incremental change alone is being challenged by empirical data from many independent sources…

    See, Mike, this is how it’s done. Nelson points out that there is empirical evidence that refutes incremental change, thus falsifying the prediction.

    I guess his next comment will list what that evidence is.

  71. Hey Mike, how come you are not as certain about your theory as Alan is about his?

    Prediction met – wrong poster! 🙂

  72. Already listed them.

  73. small incremental change alone

    In case you are interested,Nelson, “alone” was never part of my claim.

  74. I didn’t see you mention anything else. Non incremental change is actually a huge property of biological organisms and complex systems in general and it explains the non-incremental change frequently observed in the record of paleontology.

  75. Non incremental change is actually a huge property of biological organisms and complex systems in general and it explains the non-incremental change frequently observed in the record of paleontology.

    Huge as in bigger than small? 1%, 10%, 50%?

    Evidence for non-incemental change? What do you mean by the term, by the way?

    What other complex systems and what do they have in common with living organisms?

  76. I’d give you some citations but

    1. I doubt you’d understand them.

    2. You’d just hand wave them away like you do when I link to Mike’s blogs that discuss the evidence for front-loading. So thanks but no thanks.

  77. Already listed them.

    “phenotypic plasticity to nongenetic inheritance” is not evidence. How, for example does “phenotypic plasticity refute the concept of incremental change.

  78. I’d give you some citations but…

    Mike’s book is ordered! So no need, all will be revealed and I’ll let you know when the review is posted.

  79. Looking forward to it!

  80. Looking forward to it!

    “1 item will be shipped to Alan Fox from Amazon.com, LLC. Estimated delivery June 14, 2010 – July 2, 2010”

    And I have to read it! Hope this turns up the evidence for front loading you mistakenly advised me I would find here.

  81. Ah! Is it using two tags together that causes the nesting?

  82. Alan,

    Say there was an extinction event on Earth tomorrow and only bacteria remained, so that there was another dawn of life, I would expect after 2 – 3 billion years maybe that multi-cellular life would emerge and that organisms would develop organs of sight (via small increments of course). Due simple physics, the light sensing organ should be of broadly similar morphology. But will PAX6 re-emerge? The brain-eye structure that may emerge may emerge could involve entirely different gene sequences and proteins. There be many ways to arrive at a very similar organ. Of course feel free to point out that this is speculation and unfalsifiable, which it is.

    I appreciate the fact that you point out this is an unfalsifiable speculation as, in essence, it is the non-teleological perspective in its raw form. But you are missing another aspect of this general line of thinking – it led evolutionary biologists astray. Because biologists in the 80s assumed evolution works this way, they were completely caught off guard by proteins such as Pax6. It was thought the emerging developmental pathways for flies and mice would be composed of entirely different gene sequences and proteins because of this thinking. And therein lies one of the advantages of front-loading – it predicts deep homology.

    I beg to differ, Mike. I clearly said, (and indeed you quoted it) “The smallest possible increment is a single nucleotide mutation.” There is no possible smaller increment.

    You are answering a question that was not asked. I never asked you to define the smallest possible increment. I asked you to define what you mean by “small.” Unless you are willing to insist that all evolutionary transitions must occur through nothing larger than single nucleotide mutations, you have not answered my question.

    Well, the Darwinian hypothesis is that evolution generally proceeds by small increments. See above for clarification on small. It’s sort of a central tenet and if you could demonstrate it false in one case, you would have certainly struck Darwinism a severe blow.

    So the central tenet is built around the vague concept of “small” and make things worse by incorporating an escape hatch – “generally.”

    Frankly, there is so much evidence that evolution (let me qualify, once we are into sexually reproducing organisms) proceeds by small increments that it’s hard to know where to start. Are you serious about this?

    I don’t deny that evolution can occur in “small increments”; I question those who would insist evolution must occur in “small increments.” If you can agree that evolution need not occur in “small increments,” then we have no problem.

    But you really should pay attention to some of my blog entries, Alan. Consider this one

    Eugene Koonin outlines the principal concepts of the Modern Synthesis.
    [….]
    3. The beneficial changes that are fixed by natural selection are ‘infinitesimally’ small, so that evolution proceeds via the gradual accumulation of these tiny modifications.
    [….]
    Koonin then reviews how well these concepts (predictions?) have held up in light of the massive new information from genomics:
    3. False. Even single gene duplications and HGT of single genes are by no means ‘infinitesimally small’ let alone deletion or acquisition of larger regions, genome rearrangements, whole-genome duplication, and most dramatically, endosymbiosis. Gradualism is not the principal regime of evolution.

    You write, “See above for responses to your legitimate questions. This is projection, Mike.”

    And the responses leave us at this point: We don’t really know if eyes would have developed without Pax6, but many share in the unfalsifiable speculation that it could have happened. “Small” means anything from point mutations to symbiogenesis, generally speaking, that is. And the data that indicate the vertebrate eye emerged in small increments is the central tenet and your incredulity that it might not apply in this case.

    Why keep dodging on your front loading ideas?

    If you take a few seconds and survey this blog, you’ll find a section called “Tags.” Can you now tell me which tag has the largest font? Can you tell me why that tag has the largest font?

    Sorry Alan, but I have long demonstrated a willingness to discuss front-loading with any skeptic as long as I don’t think I’m wasting my time with someone who is just playing games or culture warring. For example, I recently used the perspective of front-loading to propose a testable hypothesis and then discussed it with a very knowledgeable skeptic who did not strike me as one who is just playing games. You can read this here and here and here.

    “Buy my book” is not an explanation. “Read my blog” is not an explanation. If there is a specific explanation of your front loading idea here on your blog, how difficult can it be to cut and paste? Why not a FAQ?

    In the About section of this blog, I clearly begin by noting, “This blog will build on the various themes that are outlined in my book.” If you go to the tag cloud, you find me building on the various themes, with primary focus on front-loading. The closest thing to introductory essays (that I can quickly point to at the moment) would be here and here and here and here and here and here and here and here.

  83. Alan,

    I am not doubting endosymbiosis.

    I am doubting the evidence for the origin of chloroplasts (and mitochondria) points solely to endosymbiosis.

    You do understand the difference, don’t you?

  84. Alan Fox:

    I would expect after 2 – 3 billion years maybe that multi-cellular life would emerge and that organisms would develop organs of sight (via small increments of course).

    Why is the “solution” to evolution- “throw deep time at it”?

    There isn’t any evidence that bacteria can “evolve” into anything but bacteria.

    But if we add enough time then abbra cadabbra- metazoans with complex vision systems!

    Magical mystery mutations.

    So that is what passes for science these days?

  85. Michael: The closest thing to introductory essays (that I can quickly point to at the moment) would be here and here and here and here and here and here and here and here.

    Lol!

    If an invitation to the buffet didn’t satisfy Alan then spoonfeeding certainly won’t.

    Something tells me Alan doesn’t like what’s being served.

    -Still, one wonders why he keeps asking for the recipe…

  86. (Wondering why you couldn’t have provided links right at the start, after I was directed here by Nelson with the assurance I would find scientific evidence of “front loading”)

    First link is to a thread titled “Nudge”.

    Front-loading would thus take this strategy of nudging, a form of design, and build it into the “choice architecture” of life – it’s form and composition – to improve the “choices” evolution would subsequently make without “forcing” it to do so.

    Nudging/front-loading represent a subtle and sophisticated form of design. If life’s designer was clever enough to develop carbon-based nanotechnology, why think anything less subtle and sophisticated was involved with the design of evolution?

    I don’t see any kind of a setting out of a proto-theory or how to link the previous part about “nudging” as social engineering to an idea called “front loading”.

    Or is it the comments section?

    In other words, here is my telic outline:

    1. Planet seeded with single-membrane bacteria begin terraforming.
    2. Symbiogenesis creates double-membraned bacteria – terraforming enhanced, stage set for next leap.
    3. Symbiogenesis creates eukarytotic cell plan – stage set for next leap.
    4. Symbiogenesis creates metazoan body plan.

    The puzzle pieces are all falling into place, where symbiogenesis events are the consequence of front-loaded nudges.

    It’s not falling into place for me, yet. Is there something I’m missing or is that it for the first link?

  87. Link 2: Nudging evolution.

    Is it possible that evolutionary events currently envisioned to occur once (monophyly) actually happened several times over, but the signal for multiple origins is blurred by convergence as a result of front-loading?

    “As a result of front loading” means what exactly?

  88. Link 3 has a bit more meat in the sandwich.

    “Four Expectations From Front-Loading.”

    The hypothesis of front-loading evolution posits that life was designed with evolution in mind. As such, the design objectives would not only take evolution into account, but would use and exploit evolution as a mechanism in reaching those design objectives. This attempt to design the future through the present leads us to expect at least four things from evolution.

    I am having a job parsing anything much more specific than wishful thinking here. What am I missing?

  89. You’re missing science, Alan Fox. But you may be forgiven for that, because what Mike Gene is doing is not science.

    But I don’t forgive you for that: Ignorance of science, natural and applied, is no excuse.

  90. Ignorance of science, natural and applied, is no excuse.

    No excuse for what? Is “Front loading”some kind of secret society? What is “front loading” is all I am asking? What the *insert expletive* has forgiveness to do with science?

  91. Link 4 looks promising:

    “Misunderstandings about Front-Loading”

    The original front-loaded state had sufficient information that would bias evolutionary trajectories needed to evolve complex, multi-cellular organisms.

    What’s a front-loaded state? What do you mean by information? “Needed to evolve”?

    I don’t see any coherence, let alone an explanation.

    To borrow one of Mikes phrases, can it get worse?

  92. Just reflecting here. It’s almost like Mike is coming up with the phlogiston theory of evolution but after the discovery of oxygen. Terraforming bacteria rather than bacteria falling into the open environmental niche that is forming and shaping therm.

    P S @ Mike

    Interested in an approach to Trevor Lamb?

  93. LOL Forgiveness has everything to do with science, Alan Fox! I forgive you for being ignorant, because that’s where all science begins.

    But, as a scientist, I can not forgive ignorance either willful or due neglect.

    In your ignorance and negelct you are doing nothing but forwarding that whole ID-agenda.

    Mike Gene loves you, Alan Fox. If you didn’t exist he would have to invent you!

  94. Mike Gene loves you, Alan Fox. If you didn’t exist he would have to invent you!And I love you guys, too.But I’m really wanting to know what is “front loading”?

  95. Obviously not enough to pay attention to blockquotes!

  96. But enough to buy his book! €22.97 including postage!

  97. Link 4

    “Misunderstandings About Front-Loading 2”

    (I wish I could get as far as misunderstanding front loading!)

    Front-loading assumes that life began with a consortium of different genomes that, as a group, contained sufficient information needed to bias evolutionary trajectories needed to evolve complex, multi-cellular organisms.

    “bias evolutionary trajectories”?

  98. Alan,

    Wondering why you couldn’t have provided links right at the start,

    Er, I did provide you most of those links…..when I tried to explain front-loading to you the first time around – 7 months ago. Then again, you do have a history of ignoring links that I provide you, making me wonder why you complain about not getting links after you get them.

    So I see that after 7 months, you have finally decided to breathlessly skim though some of them. But what’s the rush? Let’s slow down on think about some of this.

    Let’s start with the Nudge essay (one of the links I provided you 7 months ago). Since you “don’t see any kind of a setting out of a proto-theory or how to link the previous part about “nudging” as social engineering to an idea called “front loading,” let’s pause to see if you understand the social engineering strategy known as nudging. Do you understand what a ‘choice architecture’ is?

  99. Alan Fox:

    But I’m really wanting to know what is “front loading”?

    Dawkins’ “weasel” program is an example of front-loading Alan.

    So are all the “evolutionary” algorithms which have a target.

    Targeted searches are front-loaded, Alan.

  100. Do you understand what a ‘choice architecture’ is?

    “…the careful design of the environments in which people make choices, he said. “If anything you do influences the way people choose, then you are a choice architect,” Thaler said.”

    But do I understand what Mike Gene means by “choice architecture”? Probably not. I’ve got three weeks to fill till your book arrives, so carry on and explain.

  101. …I tried to explain front-loading to you the first time around…

    Looking back, I see the thread where Nelson first brought me claiming I would find scientific evidence of FLE.then here last October. I think I more or less gave up on getting any explanation on FLE then. Anyway, looking on the bright side, maybe the book will reveal all.

    Why not try a “Front loading for dummies” post? You could even keep it as a “FAQ” page. I am sure I am not the only dummy reading your blog.

    *glances at Joe*

    BTW, Mike, any thoughts on Trevor Lamb?

  102. Is that a glitch, Mike? Or did you mean to switch pre-moderation back on?

  103. Alan,

    Looking back, I see the thread where Nelson first brought me claiming I would find scientific evidence of FLE.then here last October. I think I more or less gave up on getting any explanation on FLE then.

    Yes, your vendetta is still in play (it turns out I was right in scoring it as a “bottomless” vendetta). Clearly you are still upset about being banned from TT and are here for revenge. As to your point, you seem to be confusing “scientific evidence of FLE” with an “explanation on FLE.” I asked you to clarify what you meant by “scientific evidence” and you never came through on that.. Apparently, since you didn’t get what you wanted, you decided to put your hands over your ears when I tried to explain front-loading to you, as nicely demonstrated by the manner in which you ignored the links with explanations.

    Anyway, looking on the bright side, maybe the book will reveal all.

    Alan, when you post your review on Amazon, would you be willing to include a link to my response to your review? You can link to this blog in the review and go back an edit it to link to my response after I post it.

    Why not try a “Front loading for dummies” post? You could even keep it as a “FAQ” page. I am sure I am not the only dummy reading your blog.

    Well, I can expand on the whole nudge theme. Too many posts to write and too little time.

    BTW, Mike, any thoughts on Trevor Lamb?

    It’s not my style to draw people into the seedy world of internet spats as there are a lot of people who dislike that. If you want to contact Dr. Lamb, that’s entirely your call and your choice. But last time you did something like this, you primed the person to elicit a position statement. If you decide to contact Dr. Lamb, your best approach would be to be respectful, acknowledge you accept the evolution of the eye and Darwinian evolution, but note you are unclear as to the nature of the evidence that indicates the vertebrate eye evolved only in small increments. Perhaps you might want to ask him to define what a “small increment” is and then point to the evidence that indicates only small increments were involved as the chordate eyespot transitioned to the complex eye of the last common vertebrate ancestor.

  104. Alan,

    Is that a glitch, Mike? Or did you mean to switch pre-moderation back on?

    I realize you are a little paranoid and hyper-sensitive about pre-moderation, but you should have paused to consider why one post got through and the other did not. The one that got held up had two links in it and comments with two or more links are automatically sent to moderation to help cut down on the spam.

  105. Alan, I decided to repost the essay on Nudge so we can discuss it on that thread.

  106. …you should have paused to consider why one post got through and the other did not.

    Erm? The post immediately prior to my query was the post that went into moderation. Prior to that, all posts went through. The very fact that the post immediately after went through confirmed a glitch (or rather the 2 link rule I was unaware of) but only on posting it.

  107. Clearly you are still upset about being banned from TT and are here for revenge.

    I never made a secret about my initial reason for commenting at your blog. Nelson etc…

    Plus I make no secret of being sceptical that “front loading” holds any promise as a a useful idea, scientific or not. But as I still do not grasp what your idea is (though possibly you have clarified some things that it is not), I am prepared to persevere.

    …links with explanations…

    Links to other threads, yes. Explanations in the sense that is helping me grasp the essence of “front loading”, no.

    But I’ll pick up on the other thread and see how we go.

  108. Alan, when you post your review on Amazon, would you be willing to include a link to my response to your review? You can link to this blog in the review and go back an edit it to link to my response after I post it.

    Of course! I wouldn’t want anyone to be unaware of my confirmation bias. 😉

  109. If you want to contact Dr. Lamb, that’s entirely your call and your choice.

    Fine. I thought (assuming he finds time to respond) his views on phylogeny of the vertebrate eye wrt to hagfish would be interesting. I’ll copy the relevant part of your comment in my email.

  110. Alan Fox:

    Plus I make no secret of being sceptical that “front loading” holds any promise as a a useful idea, scientific or not.

    Perhaps if you applied a little scepticism towards the blind watchmaker we would take you seriously.

  111. Alan,

    Plus I make no secret of being sceptical that “front loading” holds any promise as a a useful idea, scientific or not.

    Given that I have found front-loading to be quite a useful idea (see here and here for just two of the recent examples), your skepticism is irrelevant.

    Of course!

    Thanks.

    Fine. I thought (assuming he finds time to respond) his views on phylogeny of the vertebrate eye wrt to hagfish would be interesting.

    Agreed. But remember that phylogeny is not the issue – it’s whether the emergence of the vertebrate eye occurred in small increments.

  112. Origin of the Vertebrate Eye

    As we shall discuss, there is now overwhelming evidence that the vertebrate eye did indeed arise through an evolutionary sequence involving countless tiny steps.* However, a full picture of the historical sequence remains hidden from our view for two major reasons. Firstly, the most important advances in the organization of what would eventually become the vertebrate eye occurred over 500 million years ago (Mya), prior to the evolution of hard body parts (like a bony skeleton), and as a result, many such advances in the arrangement of the vertebrate eye occurred in animals that are either not preserved, or else are very poorly represented in the fossil record. Secondly, each of those eye arrangements that was superseded by a better arrangement is very unlikely to have survived for hundreds of millions of years in the face of competition from animals possessing better eyes, and as a result, very few extant species retain eyes with the intermediate features.

    (* my bolding)

    It would seem superfluous to email Professor Lamb, who makes his position clear in the paper quoted.

  113. I’m no biologist, so I’ve differ to others to explain the validity of these statements from Prof. Lamb’s paper (empasis mine):

    Then, at metamorphosis, the lamprey eye changes substantially: the retina differentiates fully; the lens, cornea, and extraocular muscles develop; and the eye enlarges and erupts at the surface in the form of a vertebrate-style eye. In other words, it is as if metamorphosis in the lamprey converts a hagfish-like non-visual organ into a vertebrate-like image-forming eye. We suggest that this process of metamorphosis reflects evolutionary developments that occurred over some 30 million years , as indicated in Fig. 1f–g. Furthermore, we suggest that an analogous process occurs at a very much faster rate in the development of the retina of jawed vertebrates, as we discuss now.

  114. Hi Alan,

    Thanks big time for the link to that article, as I’ll flush out the possible echoes of front-loading sometime in the future.

    It would seem superfluous to email Professor Lamb, who makes his position clear in the paper quoted.

    Well, as I explained, I wasn’t asking about Lamb’s position; I was looking for the evidence that the vertebrate eye emerged in small increments (your claim). And after reading through the paper, I don’t see this evidence.

    The first paragraph is interesting. It begins with a bold statement about “overwhelming evidence” for “countless tiny steps” but then the bulk of the paragraph undercuts that bold statement in trying to explain why there is not that much evidence for the countless tiny steps – fossils poorly preserved and the countless, gradual intermediates all went extinct. But then that second explanation is undercut by noting some intermediates have escaped extinction. It’s quite awkward, if you ask me.

    But let’s get to the driving issue. I noticed that the authors never defined what they meant by “countless tiny steps.” So we have “overwhelming evidence” for an ill-defined intuition? Then, when it is time to get to the data, the “countless tiny steps” are morphed into “numerous stages.” Do you think “countless tiny steps” = “numerous stages?” The seven stages look good to me, but hardly qualify as “countless tiny steps.” Then, as we get toward the end, we’re back to Darwin’s “numerous gradations.”

    So where does it leave us? I see no overwhelming evidence that the vertebrate eye did indeed arise through an evolutionary sequence involving countless tiny steps. I see evidence that the vertebrate eye evolved in several stages over a relatively short period of time. In fact, it effectively completed its emergence in the last common ancestor of vertebrates and has since not changed all that much:

    This rapid period of vertebrate eye evolution occurred over an interval possibly as short as 30 million years, with the modern vertebrate camera-style eye having evolved roughly 500 Mya (by the time that the predecessors of lampreys diverged from the lineage that gave rise to jawed vertebrates including humans). Further refinements to the form of the vertebrate eye have, of course, continued to evolve through to the present day, better adapting the vision of modern species to their distinct photic environments and visual behaviors. However, it seems that the fundamental pattern was already so exquisite by the time jawed vertebrates first appeared that relatively little change has taken place in the form of the vertebrate eye during the last 400 million years.

    I find it intriguing that an eye that evolved to service the needs of a lamprey would eventually find itself to be quite well-suited to service the needs of primates and eagles.

  115. Hi Kendalf,

    I liked that section. In fact, I think folks should consider the possibility that metamorphosis may be a better way to think of such an evolutionary transition than “countless tiny steps.”

  116. I wasn’t asking about Lamb’s position; I was looking for the evidence that the vertebrate eye emerged in small increments (your claim). And after reading through the paper, I don’t see this evidence.

    Not my claim, solely, or at all, really. What interests me is whether there is any substance to the FLE. Incidentally, I have pointed out some generally accepted mainstream aspects of evolutionary theory. As I have previously conceded (and as Professor Lamb points out) evidence is incomplete and probably will always remain so.

    Your statement “I don’t see the evidence” (for small {or even “tiny”} increments is understandable but it would be hard to catalogue every evolutionary step from half a billion years ago.

  117. I find it intriguing that an eye that evolved to service the needs of a lamprey would eventually find itself to be quite well-suited to service the needs of primates and eagles.

    Me too! Does FLE better explain what evidence we do have?

  118. Not my claim, solely, or at all, really.

    Your claim: “the development of the eye took place in small increments due to the favouring of advantageous traits by the process of natural selection.”

    What interests me is whether there is any substance to the FLE.

    If there was, given that you are motivated by a vendetta, you would not admit it. But considering the fact I have shown above that your non-teleological views entail unfalsifiable speculations, truth claims that cannot be defined, and historical claims without evidence, let’s just say your position is no better than FLE. So I can understand your desire to lash out.

    Incidentally, I have pointed out some generally accepted mainstream aspects of evolutionary theory. As I have previously conceded (and as Professor Lamb points out) evidence is incomplete and probably will always remain so.

    No one asked you to be omniscient. I was simply asking for the evidence that the development of the eye took place in small increments/countless tiny steps.

    Your statement “I don’t see the evidence” (for small {or even “tiny”} increments is understandable but it would be hard to catalogue every evolutionary step from half a billion years ago.

    No one asked you to catalogue every evolutionary step from half a billion years ago. I just want to know what the evidence is for this insistence on strict gradualism. Do you at least acknowledge that “countless tiny steps” is not equivalent to “numerous stages?”

    Me too! Does FLE better explain what evidence we do have?

    You forgot the central metaphor – it doesn’t have to be better. Only a reasonable and plausible alternative. In this case, there are indeed some intriguing clues that fit a general pattern of evolution quickly piecing a solution together than turns out to be very useful much later in deep time. Remember – the blind watchmaker/tinkerer has no foresight.

  119. Your claim

    you misunderstand. Not my claim. In the course of trying to establish what FLE is, I have discussed mainstream arguments. I make no claim about the theory of evolution, other than as it crops up in the to-and-fro. It would be better to discuss such matters with working biologists. In this context (your blog) I am interested in your FLE.

  120. I just want to know what the evidence is for this insistence on strict gradualism.

    The point I made was that the largest change from parent to offspring has to not so large as to isolate the offspring from the gene pool. John Davison’s semi-meoisis hypothesis, based, I believe on Goldschmidt, attempts to get around this.

  121. Just for clarity, could I ask:

    Do you think that the RM + NS process happens?

    Does your FLE process happen instead of or in addition to RM + NS, in your view?

  122. Do you at least acknowledge that “countless tiny steps” is not equivalent to “numerous stages?”

    Both phrases need to be defined and placed contextually to have a precise meaning, otherwise it’s just verbal decoration.

  123. You forgot the central metaphor – it doesn’t have to be better. Only a reasonable and plausible alternative.

    OK, so what is the reasonable alternative?

  124. Alan,

    you misunderstand. Not my claim. In the course of trying to establish what FLE is, I have discussed mainstream arguments. I make no claim about the theory of evolution, other than as it crops up in the to-and-fro.

    Okay, but you were outlining the Darwinian perspective and we have seen there is no evidence for this particular expression of that perspective.

    It would be better to discuss such matters with working biologists. In this context (your blog) I am interested in your FLE.

    Actually, the topic of this thread was the use of the criterion of rationality as it relates to a design inference. But yes, I have once again tried to make room for your interest in FLE.

    The point I made was that the largest change from parent to offspring has to not so large as to isolate the offspring from the gene pool. John Davison’s semi-meoisis hypothesis, based, I believe on Goldschmidt, attempts to get around this.

    Do you think this would apply when it comes to the origin of the eukaryotic cell plan?

    Just for clarity, could I ask:
    Do you think that the RM + NS process happens?
    Does your FLE process happen instead of or in addition to RM + NS, in your view?

    I clarified this back in October: “What you describe, Alan, can be viewed as random variation and natural selection (RV + NS). Front-loading does not deny either one. Front-loading views RV + NS as being under some form of control.”

    To make sure I am clear, let me answer again.

    Do you think that the RM + NS process happens?

    Yes. Not only that, but as you will see in the book, I acknowledge that RM + NS can function as a designer-mimic – the blind watchmaker. Why else do you think many ID proponents are displeased with my book?

    Does your FLE process happen instead of or in addition to RM + NS, in your view?

    Not instead, but more like ‘in addition’. In addition in the sense that RM + NS have been placed under some degree of control.

    Here’s a simple way to break it down:

    Mainstream science: RM + NS can mimic a designer.

    Mainstream ID: RM + NS cannot mimic a designer.

    FLE: The designer-mimic is under some form of control/guidance.

    Mainstream ID will reject FLE because it does not deny the designer mimic. Mainstream science will reject FLE because of its teleological undercurrent.

    Both phrases need to be defined and placed contextually to have a precise meaning, otherwise it’s just verbal decoration.

    Both phrases are used in the Lamb paper that you provided.

    OK, so what is the reasonable alternative?

    That evolution involves some element of foresight or planning.

  125. Sometimes it takes an Act of God to shut my mouth, but @Biologos they have a word limit on the comments. Presuming Mike Gene’s indulgence (forgive me—which I know you must LOL) I thought I would post my comments here, since they wouldn’t fit there. (If MG feels these are inappropriate then I would take no offense to him deleting them.)

    http://biologos.org/blog/jerry-coynes-insufferable-argument/

    Like Coyne, I was a bit surprised by Avise’s PNAS essay. Utterly w/o any scientific merit, as far as I can tell, which nonetheless passed peer review. LOL

    You guys know your Scripture better than me, but I thought God copped to the charge and confessed that he created evil. “I create weal and woe…,” etc. Rather than “allowing” evil, which doesn’t get him “off the hook,” he actually created evil! I recall one incident where God commits misprision of felony or subvention by eliciting a “lying spirit” to wreck the plans of the kings of Israel and Judah. It’s not an isolated incident. Given that, theodicy is not a question of whether or not God is evil, but why he is evil.

    I am assured (by my religious friends) that God does nothing w/o a purpose, and I assume a “principled” approach on his part, a plan. A method to such (appalling)madness.

    But even we recognize the basic principle in law: Sometimes a “lesser evil” must be committed, by necessity, to effect a greater good. So we allow the police to break the speed limit to chase people who break the speed limit, e.g.

    It’s the only rationalization, justification, or defense of God that made any sense to me. Quite traditional, as I understand, but not repeated here (there). Apparently not a very satisfying answer to the question?

    Mike Gene makes much of the false dichotomy presumed by so many in these discussions, and maybe this is just another case of such reasoning, a false moral absolutism—holding God to a standard (hypocritical on our part) that even God can’t meet! God, rightly, scoffs at our notions of right and wrong. In the Book of Job, God is imperious, and hardly deigns to respond to the complaints of Job and his friends. Instead, God commands Job to pull up his trousers and start acting like a man! Maybe there is a bit of an “unmanly” moral squeamishness on our part. An attempt to evade the moral dilemma God created for us when he created evil?

    That God is not either black or white, good or evil, makes him a far more interesting person, from my perspective. Maybe God isn’t quite who and what religious people think he is… Maybe his devotees need to admit that God is a bit more complicated, and however uncomfortable it may make them feel, admit that God is more like us than we are wont to recognize.

  126. “If this temporal universe be but a tapestry woven by God from end to end, to be revealed in it’s fullness at the appointed end, then how much more beautiful that it be woven with threads of black and white, of grey and of gold, and adorned with the contrasting colours of anguish and exultation?”

  127. I’m a poet at heart, as my Mom says, and not a real scientist, philosopher, or theologian, chunkdz.

    What are you quoting from?

  128. Nobody that you would have heard of. Just a good friend. Your comment brought it to mind.

  129. “Real isn’t how you are made,” said the Skin Horse. “It’s a thing that happens to you. When a child loves you for a long, long time, not just to play with, but REALLY loves you, then you become Real.”
    “Does it hurt?” asked the Rabbit.
    “Sometimes,” said the Skin Horse, for he was always truthful. “When you are Real you don’t mind being hurt.”
    “Does it happen all at once, like being wound up,” he asked, “or bit by bit?”
    “It doesn’t happen all at once,” said the Skin Horse. “You become. It takes a long time. That’s why it doesn’t happen often to people who break easily, or have sharp edges, or who have to be carefully kept. Generally, by the time you are Real, most of your hair has been loved off, and your eyes drop out and you get loose in your joints and very shabby. But these things don’t matter at all, because once you are Real you can’t be ugly, except to people who don’t understand.”

  130. Do you think this would apply when it comes to the origin of the eukaryotic cell plan?

    Yes, in essence. There is an overlap between phagocytosis, symbiosis, parasitism, symbiogenesis and it is reasonable to envisage small steps.

  131. In addition in the sense that RM + NS have been placed under some degree of control.

    That is quite clear now. It does not seem very different, though, from the Catholic churches position or theistic evolution, where God works through natural means of achieving His ends. Science cannot observe God at work, therefore and can make no claim about His existence.

    Is FLE also immune from scientific study? If FLE is RV + NS under teleological control, presumably the evidence that points to RV + NS will not address the validity of FLE.

  132. Maybe a little off-topic but here is a paper that relates to the “one in a billion” or “a million in a billion” poins about protein sequences.

    From the abstract:

    Our results show that proteins are fairly close to random sequences. The entropy reduction due to correlations is only about 1%.

  133. Yes, in essence.

    Sorry, but your point was as follows: “the largest change from parent to offspring has to not so large as to isolate the offspring from the gene pool.” Bacteria do not depend on matings to generate offspring.

    There is an overlap between phagocytosis, symbiosis, parasitism, symbiogenesis and it is reasonable to envisage small steps.

    It depends on what you mean by “small steps.” Dr. Koonin, a working biologist who has published over a hundred papers on evolution, maintains that symbiogenesis does not qualify as a small step (gradualism). Lynn Margulis herself would likewise be skeptical of framing symbiogenesis as a neo-Darwinian small step.

    Is FLE also immune from scientific study? If FLE is RV + NS under teleological control, presumably the evidence that points to RV + NS will not address the validity of FLE.

    FLE generates testable hypotheses which in turn have been supported by empirical data.

    Maybe a little off-topic but here is a paper that relates to the “one in a billion” or “a million in a billion” poins about protein sequences.

    Thanks. Just remember that front-loading does not depend on the outcome of that debate.
    It would be more interesting to ponder to what degree the blind watchmaker has been dependent on proteins themselves. For example, could a replicating system evolve into something akin to a bacterial cell without proteins?

  134. And of course I butchered it. It should be:

    “If this temporal universe be but a tapestry, woven by God from warp to weft, and to be revealed in it’s fullness at the appointed end,

    How beautiful then that it be arrayed with threads of black and white,
    of greys and golds,
    and lovingly adorned with the contrasting colours of anguish and exultation?”

  135. Bacteria do not depend on matings to generate offspring.

    Indeed. the emergence of sexual reproduction is hard to explain via the process of RM + NS. Though there do seem to be a few theories.

  136. I had a look at the paper on protein sequence entropy. It looks like the authors acknowledge that the statistical support is actually just a “rough estimate”. It’s interesting though, that there are not global constraints on what sequences can serve as a functional protein (per se). However, there are strong constraints on what sequences can serve to support a particular protein function, for example DNA binding. The homeobox is a 60 amino acid domain in a family of proteins called HOX proteins, and this sequence is almost entirely conserved in HOX proteins in different species, even in species that have not shared an ancestor for more than 500 million years. It appears that changing many conserved residues presumably destroys protein function.

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