Tuesday, February 15, 2011

Facilitated Variation

I've prepared a bunch of exam questions for my students and given them out two weeks before the exam. I promised them that I would post some of these questions on my blog to see how you would answer them. I'm hoping that you, dear readers, will show my students that there really is some controversy.

Here's the first question. It's based on Gerhart and Kirschner (2007).
What do you think of Kirschner and Gerhart’s "Theory of Facilitated Evolution." Is this something that has to be incorporated into a new extended version of evolutionary theory? What, if any, are the limitations of the theory and what, if any, new insights into evolution does it provide?


Gerhart, J., and Kirschner, M. (2007) The theory of facilitated variation. Proc. Natl. Acad. Sci. USA 104 Suppl 1:8582-8589. [doi: 10.1073/pnas.0701035104]

86 comments:

  1. Interesting that John Gerhart was IDer Jonathan Wells advisor at UC Berkeley....

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  2. The reference link should be to http://dx.doi.org/10.1073/pnas.0701035104 (you have to include the http://)

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  3. Thanks Joel. I usually check the links but it looks like I forgot this time.

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  4. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological
    processes in which core components serve, in particular by the processes’ modularity, robustness, adaptability, capacity to
    engage in weak regulatory linkage, and exploratory behavior.


    This is from the abstract. Oh boy. Could someone translate it into normal language? The paper is A LOT of words with no data and no illustrations. Do I really need to read???

    Instinctively I am against any special "core" components that can be generalized in evolution. Particularly of the type that can actively do this: "some conserved core processes appear to search and find targets in large spaces or molecular populations."

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  5. For contrast, here is an incredibly well written paper:
    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001067

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  6. For contrast, here is an incredibly well written paper:

    Criticism of naive population genetics? I'm in!

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  7. I never understood what they meant. What is 'facilitated'? Nothing specific, lots of wordy talk. I even reviewed the book, but I never got as far as understanding what they might be aiming at. Direct adaptation to the environment as an inbuilt property of the genotype, without any selection? K&G in the book rejected some simplified version of first year population genetics (not even a version any one would advocate), but how to test whatever they might be advocating?

    I put this book into the pile fluffy-headed books, together with the book by Mary Jane West-Eberhard and anything by Jablonka & Lamb. However, such views seem fairly popular! I cannot understand why.

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  8. "Interesting that John Gerhart was IDer Jonathan Wells advisor at UC Berkeley...."

    That could explain why many IDcreationists have insisted that their book is at least friendly to ID. I got into a discussion on a facebook page with a creationist who insisted that their book supported ID. I happened to have had the book, but not yet read it, and I predicted that the creationist was overstating his case. I read it and documented the fact that I was correct - they do not in any sense support IDcreationism and make it clear that mutation is at the heart of evolution.

    I found their thesis interesting if not compelling. I have not looked into much of the original source material, but it seems plausible.

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  9. I don't understand what they mean by 'weak linkage', and why that is advantageous.

    I understand the other two reasons...

    This paper was wordy, needed the dictionary next to me.

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  10. I just came across this term for the first time and had a skim through the paper and was struggling to find anything new in it. I also found it pretty hard to work out what they were saying, and really don't (yet) understand why they chose to call it "facilitated variation". Facilitated in what sense? By stuff just being the way it is? Is that not just "variation"?

    I'm very glad to see I'm not alone in this. I'm tempted to try and deconstruct the paper a bit at a time and see if I can get to the bottom of what they are actually saying. And to see if what they are saying makes any sense to what I see day to day as a molecular evolutionary biologist working predominantly in protein-protein interactions and networks. Is anyone interesting in reviving this comment thread for a bit of a discussion about this?

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  11. @cabbagesofdoom:
    Three Sandwalk items apart from this one. I appear in the comments of the first.

    http://sandwalk.blogspot.com/2007/03/animal-chauvinism.html
    http://sandwalk.blogspot.com/2007/09/evo-devo-innovation-and-robustness-in.html
    http://sandwalk.blogspot.com/2008/01/plausibility-of-life.html

    I didn’t know this article, but I read ‘The Plausibility of Life’, and was not impressed. In ‘The Plausibility of Life’ the idea ‘facilitation’ was never made clear, and the view on Neo-Darwinism or the Modern Synthesis or whatever the authors called evolutionary biology was narrow.

    This does not seem impressive either, at a first glance. Much of it seems standard: biology needs a better grasp of the genotype-to-phenotype trajectory, and until we have that, evolutionary biology cannot be complete. I wonder whether anyone will disagree with that.

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  12. Thanks, heleen. I had found the "Plausibility of Life" post and it seemed to say much the same as this one (also in the comments). I'll check out the other posts.

    My problem is that I hate to just dismiss things out of hand just because I have a (albeit) strong hunch that it is all hype and no substance, but the writing style and language makes it so hard to extract the core message of what they are really saying.

    It is undeniable that interaction networks seem to be modular and even have core conserved components but I do not see this as particularly new or insightful. We also know that elements (whole genes/proteins) are gained and lost, and the network is rewired by the gain and loss of interaction sites, so I am far from convinced that it all comes down to changes in expression, if that is what they are suggesting?

    I guess the fact that I had not come across "Facilitated Variation" until this week despite working in a neighbouring field gives some indication as to the (lack of) impact of this idea!

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  13. "I don't understand what they mean by 'weak linkage', and why that is advantageous.
    I understand the other two reasons..."



    In systems terms it relates to "coupling" (and "cohesion").
    "Weak linkage" corresponds to low coupling which is a sign of good module design.
    (High cohesion is also good design).
    http://en.wikipedia.org/wiki/Coupling_(computer_programming)
    "Low coupling is often a sign of a well-structured computer system and a good design, and when combined with high cohesion, supports the general goals of high readability and maintainability."

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  14. "Interesting that John Gerhart was IDer Jonathan Wells advisor at UC Berkeley...."

    That could explain why many IDcreationists have insisted that their book is at least friendly to ID. I got into a discussion on a facebook page with a creationist who insisted that their book supported ID. I happened to have had the book, but not yet read it, and I predicted that the creationist was overstating his case. I read it and documented the fact that I was correct - they do not in any sense support IDcreationism and make it clear that mutation is at the heart of evolution.
    I found their thesis interesting if not compelling. I have not looked into much of the original source material, but it seems plausible."


    By "mutation" you mean "change".
    Change is at the heart of evolution.
    Right?

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  15. cabbgaesofdoom has put his finger on something significant when he says:
    "I guess the fact that I had not come across "Facilitated Variation" until this week despite working in a neighbouring field.."


    This is an example of the fact that the people who work in the field are not familiar with ideas in their own field that are even a little different than the consensus thinking.
    This more than anything explains why new insights come from people outside the field.
    Those in the field are in their own little bubble and new ideas do not reach them.

    This is a well known phenomena and not just in biology.

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  16. Anonymous, go away and play, and leave the discussion to the adults.

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  17. The problem is that those here who think of themselves as "adults" display childish school-yard traits such as taunts, insults and personal attacks.
    And they are not familiar with ideas outside their own little consensus world. The result is that within their limited scope they mistakenly think they are the "adults".
    But it is hardly worth arguing about this obvious point.
    The claim to be "adults" is simply humorous.

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  18. Gerdien de Jong posted:
    "I never understood what they meant. What is 'facilitated'? Nothing specific, lots of wordy talk. I even reviewed the book, but I never got as far as understanding what they might be aiming at. Direct adaptation to the environment as an inbuilt property of the genotype, without any selection? K&G in the book rejected some simplified version of first year population genetics (not even a version any one would advocate), but how to test whatever they might be advocating?

    I put this book into the pile fluffy-headed books, together with the book by Mary Jane West-Eberhard and anything by Jablonka & Lamb. However, such views seem fairly popular! I cannot understand why."


    Could they be popular because there is something in there that is important that you have not yet understood? You have been upfront in saying that you do not understand it.

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  19. Let's imagine that the authors want to show us that there are a number of processes/structures of the genome that make it possible for a small amount of change to produce a viable, large effect.

    These "facilitators" include:
    "modularity, robustness, adaptability, capacity to engage in weak regulatory linkage*, and exploratory behavior."

    http://www.pnas.org/content/104/suppl.1/8582
    "The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior."

    The authors continue:
    "These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population."

    So they are saying that "the number of regulatory changes needed" is REDUCED.

    From this they conclude:
    "By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation,".


    I suspect that people have trouble understanding this because they do not like the sound of it - and not because of any inherent complexity of the ideas. It is a rule of human nature that we have difficulty understanding something that we do not want to accept.


    *I referred to weak linkage and low coupling earlier.

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  20. This is mind blowing:
    http://www.pnas.org/content/104/suppl.1/8582.full
    "Although the signal seems superficially to control the response, it invariably turns out that the responding core process can produce the output by itself but inhibits itself from doing so. This self-regulation is built into the process. The signal, then, merely interferes with the self-inhibition (the intermediate agency), thus releasing the output, which may be much more complex than the signal and needs little instruction from it."

    Brilliant design.

    In the systems area, is this part of object-oriented programming?

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  21. For those who may not be familiar with design ideas notice the following:

    http://www.pnas.org/content/104/suppl.1/8582.full
    "Although the signal seems superficially to control the response, it invariably turns out that the responding core process can produce the output by itself but inhibits itself from doing so. This self-regulation is built into the process. The signal, then, merely interferes with the self-inhibition (the intermediate agency), thus releasing the output, which may be much more complex than the signal and needs little instruction from it."


    The signal does not even interface with the process! It interfaces with an intermediary. That means that the signal does not even need to be designed specifically for that process. It just needs to be designed to work with the more general intermediary.
    That is design at its highest.

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  22. For those who are familiar with these design issues, this all shows that the system was not built bottom-up. It was built top-down.

    It takes a GREAT deal of planning and thought to build a system like that.
    And you also have to know a huge amount about design principles.

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  23. For those who are familiar with these design issues, this all shows that the system was not built bottom-up. It was built top-down by the intelligence of Nature.

    It takes a GREAT deal of planning and thought to build a system like that. Nature continues planning.
    And Nature also has to know a huge amount about design principles. Especially as the design principles have to be carried through the saltations when speciating a new type of creature.

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  24. Once again the desperate person pretending to be me, by combining some of what I said with his/her additions.
    This is of course dishonest.

    This person has taken the discussion of ideas VERY PERSONALLY.
    It is a shame.

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  25. I'm not really sure what there is to not like about the general observations. I certainly don't think evolutionary biologists, myself included, would be inherently hostile to an idea that meant that small variations can lead to large changes - we know this to be true and have documented examples. Similarly, robustness etc. is well known. I think the key bit - and the least clear bit - is exactly how they link these things to both genotypic and phenotypic variation (and those to each other) and then what they conclude.

    Speaking for myself, I just have trouble extracting the core novelty of their idea from all the slightly non-biological language: I think it was written by a Systems Biologist, not a Systems Biologist, if that makes sense?

    Oh well, I think I am just going to have to read it carefully for myself. I'll report back when I am done. (Might be a while!) I've seen enough hostility to Systems Biology as a discipline to wonder whether all the backlash is deserved, but I've also enough papers trying to make small tweaks to old ideas sound more exciting and revolutionary than they are. I suspect the truth may lie somewhere in the middle. (It usually does.)

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  26. If one acknowledges the ideas expressed by Gerhart and Kirschner about modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior
    then here is the significance of that acknowledgement:

    1. The design of the processes is exceedingly "facilitative" for rapid genome re-organization (saltation)
    2. The design is not what a bottom-up process would result in.
    3. It has all the hallmarks of a top-down design. It employs exceptional design ideas.
    4. A top down-design and particularly one of this immense beauty and elegance requires planning and thought.

    If anyone is accepting of those ramifications, then good.

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  27. http://www.pnas.org/content/104/suppl.1/8582.full

    The following is the old thinking I have mentioned:
    "Darwin noted the rapid divergence of beak morphologies by Galapagos finches. If we think mostly about selection and not phenotypic variation, we might imagine that selection acted repeatedly on many small changes occurring independently in the upper and lower beaks, adjacent skull, and head muscles to coordinate and order them into viable intermediate beaks throughout divergence. Many regulatory changes and many selections would be needed for this detailed coevolution of parts."

    The following is the new thinking I have mentioned:

    "Recent results, however, make a different impression. Tabin's group has compared two Galapagos finches, one with a large nutcracker-like beak and another with a small forceps-like beak (37). In beak development, neural crest cells migrate from the neural plate to five primordia around the mouth. The primordia of the large-beaked finch express Bmp earlier and at higher levels than do those of the small-beaked finch. To test the importance of this difference, they introduced Bmp protein into the primordia of a chicken embryo, which normally develops a small pointed beak. The experimental chick developed a deep, broad beak, like the large-beaked finch. The beak was not monstrous; its parts fit together and properly adjoined the head. Recently the same group demonstrated that elevated levels of calmodulin, a ubiquitous calcium signaling protein, correlate with increased beak length, and experimental increases of this protein in the developing chick beak caused coordinated increases in beak length (38)".

    This is really fascinating stuff.

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  28. http://www.pnas.org/content/104/suppl.1/8582.full
    "These properties* reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population."


    The reduction of "the lethality of genetic change" is an interesting effect.
    On the face of it, it seems that "random" changes would be even more successful in generating new species. That would seem to bolster current evolution thinking.

    I wonder if anyone sees any problem with that line of thinking.



    *modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior.

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  29. If one acknowledges the ideas expressed by Gerhart and Kirschner about modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior
    then here is the significance of that acknowledgement:


    1. facilitation is phenotypic, not genetic, and will not lead to rapid genome re-organization
    2. facilitation is a bottom-up process, as for instance in linking nerves and bloodvessels to muscles
    3. it has all the hallmarks of self-organisation
    4. organisms are facilitated by a self-rganisation and made robust by natural selection

    If anyone is accepting of those ramifications, then good. If anyone is not accepting of those ramifications, then Anonymous make garbage of them

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  30. http://www.pnas.org/content/104/suppl.1/8582.full
    "In defining weak regulatory linkage, we stress two points: (i) the signal input and response output interact indirectly through an intermediate agency and hence do not require stereochemical complementarity to each other, and (ii) the output can be much more complex than the regulatory input because it has been previously built into the core process, independent of the nature of the signal."

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  31. http://www.pnas.org/content/104/suppl.1/8582.full
    "In defining weak regulatory linkage, we stress two points: (i) the signal input and response output interact indirectly through an intermediate agency and hence do not require stereochemical complementarity to each other, and (ii) the output can be much more complex than the regulatory input because it has been previously built into the core process, independent of the nature of the signal."


    It would be an interesting exercise for someone to present how this sort of design could evolve through evolution mechanisms such as random, mutation, drift etc.

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  32. http://www.pnas.org/content/104/suppl.1/8582.full
    ".. and adaptability implies that a process changes with the conditions in ways still to achieve the objective."

    Is the process achieving an objective?
    That sounds like the opposite to the principle of evolution theory.

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  33. http://www.pnas.org/content/104/suppl.1/8582.full

    "For the most part, though, animals since the Cambrian have repeatedly reused the processes and components that had been evolved long beforehand to generate novel traits of anatomy and physiology."

    They say that the core components evolved first. Once they were in place, gene duplications and neo/subfunctionalisation could increase the number of different uses by re-wiring the input/output. Look up GPCR signalling if you want some examples. They also discuss compartmentalisation in the paper, which is another way at a different level of organisation. All can be subject to random mutation, drift and selection.

    "Is the process achieving an objective?
    That sounds like the opposite to the principle of evolution theory."

    In that case they are using ill-advised language. It is very easy to lapse into language that anthropomorphises evolution but it is wrong to do so. The problem lies with the use of language, not the process.

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  34. cabbagesofdoom said...
    http://www.pnas.org/content/104/suppl.1/8582.full

    "For the most part, though, animals since the Cambrian have repeatedly reused the processes and components that had been evolved long beforehand to generate novel traits of anatomy and physiology."

    This too: 'reused', 'generate', is ill-advised language. It distorts the observation that animals use pre-animal signalling systems in a different way into something that reads as confusing goal-directed thinking.

    Many signalling systems used in multicellular animals are found in unicellular eukaryotes. Finding the genes in unicellular eukaryotes is easier than finding their function there, I imagine. The wording by K&G disguises or glosses over the important point, what induced the gene system to be involved in something different.

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  35. http://www.pnas.org/content/104/suppl.1/8582.full
    "In defining weak regulatory linkage, we stress two points: (i) the signal input and response output interact indirectly through an intermediate agency and hence do not require stereochemical complementarity to each other, and (ii) the output can be much more complex than the regulatory input because it has been previously built into the core process, independent of the nature of the signal."


    It would be an interesting exercise for someone to present how this sort of design could evolve (WHEN IT EVOLVED EARLIER) through evolution mechanisms such as random, mutation, drift etc.

    I am not saying that it could not arise from evolution mechanisms. I would just like someone to describe how that happened.
    It would be an interesting exercise for Moran's students and for the people here.

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  36. I have an extensive background in systems design so perhaps what is obvious to me is not obvious to others here.
    Here are the basics:

    When the first form of the design appeared it would be a "hard-coded" from signal to process. The signal would be tailored to the specific process that it would trigger.
    That is how a programmer codes who does not feel a need to make the program easily modified for future adaptation/modification.

    And if further functions are needed they would take the same form of direct hard-coded linkage.

    On it's own it would NEVER evolve intermediaries because the intermediaries add NO survival value.

    It is only when you plan and think about the future that you design a flexible system like that described by the authors.

    As I say, this is immediately obvious to me, since I have been involved in both types of designs.
    It takes a great deal of planning and thinking to produce a "facilitated variation" type of design.
    That is the kind of design work done by "systems architects".

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  37. I think this is another case of engineers approaching biological systems with a design mentality, rather than an evolutionary one. You seem to be arguing that X would not have happened because it is bad design unless a future Y was planned. Evolution is imperfect and does not start from a blank canvas with pre-determined goals, so it will generate sub-optimal solutions to problems and have redundant features sometimes. As a general rule, we do not see the hallmarks of good design in nature. We see some wonderful adaptations and some crazy mistakes (giraffe nerves, flatfish eyes, human retina etc.) that make sense in the absence of forward planning but not if designed.

    For many systems there are also good functional reasons for intermediates - signal amplification (or dampening), for example - even in the absence of multiple functions. It is not hard to imagine gene duplication and sub-functionalisation slowly increasing complexity of inputs or outputs, adding branch points etc. Convergent evolution at the molecular level and exon (domain) shuffling can add new interactions, again slowly increasing the complexity of the system.

    Do you have any examples of "core processes" that have "intermediates" that are useless outside the context of facilitated variation? It's a pretty big claim to make about all core processes, so you should be able to throw out a handful of clear examples if it is true.

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  38. cabbagesofdoom, I am not entering into discussion with you based on previous interactions.

    My knowledge is both in design and biology. So your premise is incorrect. But I am not wasting time with you.

    Your post is filled with errors but I am not wasting time trying to straighten you out. Your mind is not open to anything beyond what you have been programmed to think.

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  39. Anonymous said...

    But I am not wasting time with you.

    I am not wasting time trying to straighten you out.


    I'm wasting my time commenting here.

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  40. So, Anonymous, you follow us all to a comment thread that I re-awakened after six months of dormancy and then refuse to engage in discussion with me? Not sure I understand your motivation there. Thanks for the insight into Design Mentality, though. It's nice to get a better idea where (and who) these ideas come from, and whether they are to be taken seriously.

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  41. By the way we can see cabbagesofdoom slyly twist what I said into:

    "You seem to be arguing that X would not have happened because it is bad design unless a future Y was planned."

    I guess he cannot help but slyly twist things.
    How many times does he need to be caught? Is he trying to surpass Moran?

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  42. Nothing sly. Just trying to make sense of what you wrote. You can't hold me responsible if you refuse to explain or clarify your position.

    Correction. You shouldn't hold me responsible. But, I know you will. Against my better judgement, I decided to engage your comments in this thread, ignoring the baggage from the other but I acknowledge that you are unable to do this and I am sorry for wasting both of our time. I shall go back to ignoring all "Anonymous" posts as before; it seems that we will both be happier that way.

    FYI, you can still approach biology with a "Design Mentality" even if you know about biology - many biologists (especially biochemists) make this mistake, not just engineers. "Adaptionists" sometimes do it too and have done for many years - Stephen Jay Gould warned against such things back in the 70s in his famous "Spandrels" Nature paper. If you stopped taking everything as a personal insult, you might learn something. (And if you also started answering our questions, we might too.)

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  43. I wish I had a dollar for each time someone absurdly distorts what I said and when I point it out, they claim that I have not been clear.
    One of those tired old dodges.
    But we would expect no less from cabbagesofdoom.

    I expect if we looked back we would have seen that tactic from Moran as well.

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  44. Here is one of those unclear statements.
    "On it's own it would NEVER evolve intermediaries because the intermediaries add NO survival value."

    Unclear to anyone not familiar with the English language.

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  45. Anonymous, we both know that your (unsupported and purely speculative) statement was framed by comments about design, which lead me to believe that your reasoning for making such a bold (and unsupported) statement came from design thinking. (It certainly isn't an obvious conclusions from biology, which indicates it is empirically false.) Here is that sentence in the original context (my bold):

    "When the first form of the design appeared it would be a "hard-coded" from signal to process. The signal would be tailored to the specific process that it would trigger.
    That is how a programmer codes who does not feel a need to make the program easily modified for future adaptation/modification.

    And if further functions are needed they would take the same form of direct hard-coded linkage.

    On it's own it would NEVER evolve intermediaries because the intermediaries add NO survival value.

    It is only when you plan and think about the future that you design a flexible system like that described by the authors.!

    As I say, this is immediately obvious to me, since I have been involved in both types of designs."

    I then inferred: "You seem to be arguing that X would not have happened because it is bad design unless a future Y was planned."

    Despite all your bluff and bluster, I still do not know which bit of this you object to. Would you be happier if I had said: "You seem to be arguing that X would not have evolved because it is bad design unless a future Y was planned." ?

    If so, just say so. (And explain why that makes any difference.) Note: I am not being sly, I am asking you a direct question about your meaning, giving you an opportunity to unambiguously clarify your position.

    The problem with a Design Mentality such as you appear to (forgivably) display in your post is that you are assuming that the inputs and outputs were set as such from the outset and any intermediates were subsequently added. It is perfectly possible that the intermediates were originally inputs and/or outputs themselves and that they only became intermediates when additional ("better") bits were bolted on. If you approached the problem with a evolutionary hat on, you would not run into these false impasses.

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  46. I have already told you cabbagesofdoom that I am not wasting my time on you.
    I would be spending all my time just exposing your spin.

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  47. Anonymous, you are free to waste your time however you choose. I was just responding to your slander. (Pointlessly, of course.)

    I don't understand what you think I have to gain by "spin" but I doubt that you would care to explain that, either?

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  48. Anonymous said...
    "On it's own it would NEVER evolve intermediaries because the intermediaries add NO survival value."
    Unclear to anyone not familiar with the English language.


    Given that it should be "on its own" as "it's" is short for "it is", it might be wise to keep the English language out of it.

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  49. And what about those not familiar with the English language? Some of my best friends have English as a second (or third) language.

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  50. http://www.pnas.org/content/104/suppl.1/8582.full
    "The adaptability and robustness of normal muscle, nerve, and vascular development have significant implications for evolution, for these processes accommodate to evolutionary change as well. In the case of the evolving wing, if bones undergo regulatory change (driven by genetic change) in length and thickness, the muscles, nerves and vasculature will accommodate to those changes without requiring independent regulatory change. Coevolution is avoided. Selection does not have to coordinate multiple independently varying parts. Hence, less genetic change is needed, lethality is reduced, larger phenotypic changes are viable, and phenotypic variation is facilitated."

    This is quite a different picture than the evolutionist idea we have all been raised on.
    It is a shame that this is not taught from the beginning.

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  51. Anonymous said...
    "In the case of the evolving wing, if bones undergo regulatory change (driven by genetic change) in length and thickness, the muscles, nerves and vasculature will accommodate to those changes without requiring independent regulatory change.

    This fact of development can be found in quite a number of books, and is general knowledge.

    Nobody ever stated separate mutations for nerves, muscles and blood vessels were necessary if one wants to select for a longer wing or whatever. It is a wild misunderstanding of evolutionary biology to suppose it has that position.

    It is a major failing of K&G, both in this article and in their book, that they understand so little about evolutionary biology that they (K&G) seriously seem to have proposed evolutionary biology only worked with independent point mutations that specified every feature of an animal, down to the trajectory of each blood vessel.

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  52. Anonymous said...
    This is quite a different picture than the evolutionist idea we have all been raised on.

    No, it is standard biology, including standard evolutionary biology.

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  53. What I meant was taught from the first day in grade school.
    Then the new crop of youngsters will not have the incorrect ideas that we have all been taught.

    But this is not worth arguing.
    Everyone here believes that young people should be taught correct ideas.

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  54. Anonymous said...
    What I meant was taught from the first day in grade school.
    Then the new crop of youngsters will not have the incorrect ideas that we have all been taught.


    I've no idea whatever Anonymous has been taught, and I actually don't know what type of school 'grade school' is.

    Nobody ever gets or got taught that separate point mutations are necessary for every extension of blood vessels or nerves in selection on wing length or beak depth or whatever. Simply because noboydy ever had that idea. What nowadays is likely to be taught in schools is that the heritability of beak depth is 0.66 (about, in Geospiza fortis). Selection on beak depth includes everything whatsoever in developmental terms that has to do with beak depth. Selection is not on a single gene for beak depth, and to work with selection is is quite unnecessary to know the developmental detail.

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  55. I imagine that everyone is aware of the tricks and the spin within heleen's posts. He/she is striving to catch up with the others in the sly category.
    But keep in mind that Moran has been at it for years so he is probably not catchable at this point.

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  56. heleen writes:

    Nobody ever gets or got taught that separate point mutations are necessary for every extension of blood vessels or nerves in selection on wing length or beak depth or whatever.

    Indeed, this is one of the central points, repeated many times, in Sean B. Carroll's award-winning 2005 book, "Endless Forms Most Beautiful," which I highly recommend.

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  57. @heleen. I have come to the conclusion that "sly" just means "right". How "sly" of you to argue using facts and truth. You are totally right, in my experience. I have never encountered this strange caricature of evolution that is somehow being over-turned.

    I think that Systems/Engineering principles can teach us some interesting things about the ways signals are propagated etc. in biological systems. They can even tell us some interesting things about possible evolutionary trajectories. They just need to tone down a bit on the whole revolution/paradigm-shift business. (Sigh. If I had a dollar for every time I've made that complaint.)

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  58. heleen writes:

    "Nobody ever gets or got taught that separate point mutations are necessary for every extension of blood vessels or nerves in selection on wing length or beak depth or whatever."

    Indeed, this is one of the central points, repeated many times, in Sean B. Carroll's award-winning 2005 book, "Endless Forms Most Beautiful," which I highly recommend.


    Ooh, I've been meaning to read that one. I feel I should also point out that this same point is why Dawkins et al. are constantly pointing out that DNA "is not a blueprint". This stuff is old. Important, yes. Interesting, yes. Nice to have examples of, yes. Ground-breaking and revolutionary, no.

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  59. Well the folks here are continuing to pretend.

    When children are introduced to evolution ideas they are given exactly the wrong idea - the wrong idea that people here are correctly repudiating.

    That is my point.
    When children are given the correct idea about the obvious intelligence of Nature, things will begin to change.

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  60. Anonymous, you have just made a case for better science education. I think we can all agree with that part. Such science education should include the truth about evolutionary theory and not the lies/mistakes that you have obviously been taught, which is a shame. (I won't ask where - too personal.) It is not too late for you, though. Read "The Selfish Gene", written in the 70s and containing many of the correct idea that you are claiming we are merely "pretending" exist.

    One of these correct ideas is not the Intelligence of Nature. If I ever had a child in a school that teaches that, I'm getting that poor kid out of there. No need. No evidence. No mechanism. No resemblance of a coherent scientific idea.

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  61. Actually, I might be thinking of "The Blind Watchmaker" (1986). Read them both.

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  62. Anonymous said...
    When children are given the correct idea about the obvious intelligence of Nature, things will begin to change.

    Nothing I said has anything to do with 'the intelligence of Nature'.

    Anonymous simply does not know two hoots about evolutonary biology.

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  63. @Cabbagesofdoom:
    see comment 32 in:http://whyevolutionistrue.wordpress.com/2011/09/05/free-kindle-edition-of-evolution-book/#comments

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  64. I have seen expert spin-meisters in action. But I must say that cabbagesofdoom is right at the top.
    His genius is to present a subtly distorted position as if I have said it. Then he derides that distorted position.
    His subtly and slyness is a marvelous thing to behold.
    People would be better to take what I actually have said rather than cabbagesofdoom's sly distortions.

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  65. More slander, Anonymous. I express explicitly what I think you are saying and ask you to clarify if it is not, which you do not.

    I quite like the term "spin-meister", though! Makes me sounds like a DJ.

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  66. cabbagesofdoom - why reword what I have said?
    Just work with what I actually said.

    This is why talking with you is a waste of time.
    I am supposed to deal with whatever distorted way you put it.
    Just work with what I actually said.

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  67. Anonymous: "Just work with what I actually said."

    That's fine with me. This is what you actually said:
    "When the first form of the design appeared it would be a "hard-coded" from signal to process. The signal would be tailored to the specific process that it would trigger.
    That is how a programmer codes who does not feel a need to make the program easily modified for future adaptation/modification.

    And if further functions are needed they would take the same form of direct hard-coded linkage.

    On it's own it would NEVER evolve intermediaries because the intermediaries add NO survival value.

    It is only when you plan and think about the future that you design a flexible system like that described by the authors.!

    As I say, this is immediately obvious to me, since I have been involved in both types of designs."


    Working with just this, you state: "On it's own it would NEVER evolve intermediaries because the intermediaries add NO survival value."

    Does this not assume that the "signal" and "process" to which you refer are the same throughout the evolutionary process and that any intermediaries were subsequently added as intermediaries? [Note: A question, not a re-wording.] Why is it not possible that the intermediaries were originally signals or processes themselves and that they only became intermediaries when additional ("better") bits were bolted on?

    I think it is less likely that intermediates would have evolved directly as intermediaries, not so much because of the lack of selective advantage ("survival value") - they could add buffering, feedback or amplification, for example - but more that it would involve multiple steps.

    Do you have any examples where you believe that intermediaries were added to an existing direct signal-process coupling? Part of my problem in understanding what you mean is that "signal" and "process" do not have precise biological meanings and so I do not really know what you are referring to. It would be helpful if you could expand on your statements/ideas accordingly.

    Can you also please define what you mean by a "direct hard-coded linkage". Is this a direct protein-protein interaction? If protein A produced metabolite X and protein B recognised X, would that be "direct hard-coded linkage" in these terms? (Only A and B are "hard-coded" by the genome.) Or is metabolite X an "intermediary"?

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  68. "Signal", "process" and "intermediate" are the words the authors use.
    http://www.pnas.org/content/104/suppl.1/8582.full

    You spin this as if I came up with those words. And as if I have to define them for you.
    Read the article.
    Use the examples the authors use.

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  69. "Just work with what I actually said. "

    This is why talking with Anonymous is a waste of time.

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  70. I am starting to see the problem. You do not understand design principles and you do not understand the article.

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  71. First you say: "Just work with what I actually said."

    Now you want me to add what you say to what they and somehow synthesise the ideas myself?

    You say: "On it's own it would NEVER evolve intermediaries because the intermediaries add NO survival value."

    They say: "For the most part, though, animals since the Cambrian have repeatedly reused the processes and components that had been evolved long beforehand..."

    Do you see why I have a problem with that? They present no examples to support your argument because they do not make it. Are you saying that there are no examples to support your position? [Question, not spin.]

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  72. "I am starting to see the problem. You do not understand design principles and you do not understand the article."

    That is possibly true. What certainly true is that I do not have the same understanding of the article as you. If, therefore, you tell me to read it, I will read it and get the same understanding as I did before. If you answer my questions and tell me how you understand it, I might know what you are talking about.

    Is that not, after all, the point of such a discussion?

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  73. Let us say you have a module that accepts an input and processes the input into particular outputs.
    The module must receive the input (the signal) in a PARTICULAR format. It is a hard-coded relationship. If the signal is not in exactly the format that that particular module expects the module cannot work with the signal.

    Here is a different (more flexible) design. The signal does not interact directly with the module.
    The signal interacts with an intermediate and the intermediate interacts with the module.
    In this case the signal does not have to be EXACTLY formatted for that particular module. It simply has to interact with the intermediate. And the intermediate is already designed to work with the module. This is of course much more flexible. (I could expand on that but perhaps you understand this).

    Here is how the authors put it:
    "The regulator need not inform the response or be stereochemically compatible with it. Regulation does not need to coevolve with the functional response."
    and
    "Thus, a simple signal, which can easily be moved, replaced, or modulated, regulates the time, place, and amount of the very complex developmental response. The ease with which simple signals can entrain complex processes reflects the capacity of core processes to engage in weak regulatory linkage."

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  74. What I have called hard-coded the authors call "strong linkage".

    "Conceptually, the alternative is “strong linkage” (e.g., cofactors and substrates), which, we argue, requires more complex, precise, informative, and direct interactions from the input to make a process give a particular output. Constraint to change would be greater; more genetic change seems required.

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  75. OK. I understand all of those last two posts and agree with it, as far as I can tell.

    What you/they describe fits very well with my understanding of signalling pathways. Often the point of "detection" for a signal involves a hard-coded "strong linkage" between signal molecule and receptor but I cannot think of any receptors that generate a complex output all by themselves - the signal is invariably propagated through intermediaries, which will recognise and pass on different "formats" of intermediate signal.

    I still do not see any problem for the evolution of such core modules.

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  76. I do not understand what you have said. You have again put it into your own words rather than using the words and ideas the authors use.

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  77. "I do not understand what you have said. You have again put it into your own words rather than using the words and ideas the authors use."

    I have converted the language of "systems" into the language of biology. This is essential if we want to understand the biological implications of the systems ideas. I am sorry if I made too much of a jump or explained it poorly. (I am probably assuming a lot of molecular biology knowledge.)

    I am of the opinion that you can never really know if you understand an idea, unless you can put it in different words and keep the meaning. That is why I re-phrase things. If the meaning gets lost in translation, it means that I have misunderstood, or explained poorly. If the meaning remains clear, then we know we are on the same page.

    If you can tell me which bits you do not understand, I will try to explain it better. (But later. I have to dash now...)

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  78. Don't put it into your own words. Use the words that the article uses.

    I already said I am not wasting time straightening out the distorted way you re-word these ideas.
    It is not only the words but the actual ideas that you distort.

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  79. cabbagesofdoom writes:

    Is that not, after all, the point of such a discussion?

    It might be to you, but consider your audience.

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  80. I am not that interested in "systems design" implications for evolutionary theory if they cannot be framed in biological language. I interpret that as meaning that the systems theory in question has little or no relevance to actual biology.

    I'll still try to get to the bottom of that Facilitated Variation paper some time, though. My gut feeling is still that it's old news wrapped in new language but perhaps there is more real biology in there than my first read-through identified.

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  81. cabbagesofdoom, again you have spun this. As if it is design versus biology when it is all biology.
    This is why discussion with you is pointless.

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  82. I did not say design versus biology. I said design language versus biological language. Ideas are inherrently shackled to the language in which they are expressed. A biological idea must ultimately be expressed in biological language.

    I'm getting bored of all these accusations of spin (by, ironically, distorting my words), so I bid all Anonymids farewell. Let me know (using a stable pseudonym) if you ever want to actually discuss any of these ideas.

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  83. It would appear that caggagesofdoom is not used to being called on his spin.
    When he is called on it he has nothing further to contribute.
    But that is not unique to him.
    I have seen this tactic a number of times before.
    I met one guy who was so good at it that even cabbagesofdoom would be impressed.

    If anyone else would like to discuss the significance of facilitated variation I am certainly interested.

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  84. cabbagesofdoom posted:
    "I did not say design versus biology. I said design language versus biological language."

    In fact that is incorrect.
    cabbagesofdoom did not say "design language".
    Does he/she not realize that we can scroll back and see what was said?

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  85. You are right, I did not use the phrase "Design language". I said "Design Mentality"

    and

    "I have converted the language of "systems" into the language of biology."

    Apologies for any confusion. I don't even know if either of these posts were what provoked your needless accusation.

    Although I was not trying to make it about design "versus" biology, design and biology are different.

    But this is not worth arguing about.

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  86. At least cabbagesofdoom acknowledges that what he said was false.
    Even if he feels the need to present a convoluted justification for his false statement.

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