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    The Demise Of The 'Genetic Blueprint' Metaphor
    By Massimo Pigliucci | December 18th 2008 04:40 PM | 21 comments | Print | E-mail | Track Comments
    About Massimo

    Massimo Pigliucci is Professor of Philosophy at the City University of New York.

    His research focuses on the structure of evolutionary

    ...

    View Massimo's Profile
    Metaphors are dangerous things. On the one hand, it seems pretty much impossible to avoid using them, especially in rather abstract fields like philosophy and science. On the other hand, they are well known to trick one’s mind into taking the metaphor too literally, thereby creating problems that are not actually reflective of the reality of the natural world, but are only perverse constructs of our own warped understanding of it.

    Take the metaphor of living organisms as analogous to complex artifacts, which led William Paley to articulate the most famous argument in favor of Intelligent Design -- an argument that, incidentally, has not changed in its broad philosophical outline since the early 18th century. David Hume -- rather presciently, since he wrote before Paley -- pointed out that the metaphor is flawed. Hume argued that living organisms are not like watches, to use Paley’s analogy. They are not machines that are assembled, but organic beings that develop gradually over time. Accordingly, the ID argument of “irreducible complexity,” as it is known nowadays, doesn’t make sense because it is based on the machine metaphor. To put it another way, biochemist Michael Behe doesn’t understand how the bacterial flagellum could have evolved because he doesn’t understand evolution and insists in thinking of the flagellum as a “propulsion engine” analogous to those built by Evinrude.

    Yet, even serious biologists (i.e., unlike Behe) have been guilty of enthusiastically pushing what is clearly a flawed metaphor: the idea that the DNA sequence of an organism’s genome is analogous to a computer “program,” and that it provides the “blueprint” for building said organism. Hence the wild (and, as it turns out, completely unfounded) claim a few years ago that sequencing the human genome will tell us everything there is to know about “making” a human being. The human genome has been sequenced, and what we have found is that genes, though playing a crucial causal role in development, are just one piece of a vast and as yet largely unresolved puzzle.

    Ironically, the harbinger of the demise of the genetic program-blueprint metaphor is the serious study of genomics itself. A recent article by Tanguy Chouard in Nature (20 November 2008) explains why. Researchers are finding out that what matters is not so much individual genes, but the way networks of genes function together. Take the example of the Bicoid gene in Drosophila: it was thought to be essential in establishing the form of the body in all insects, based on its effects on the development of body shape in fruit flies. No such thing, as it turns out. Once scientists looked for Bicoid-like genes in other insects they simply did not find them! Turns out that Drosophilais an exception (ah, the perils of “model” organisms), and that in species from wasps to beetles the job carried out by Bicoid is achieved by minor rearrangements of a large regulatory network encompassing a myriad of other genes.

    According to the same article, biologists are even beginning to document how evolution transitions from one regulatory network to another. Phylogenetically informed investigations conducted with different species of yeast, for instance, show nice intermediate stages from one arrangement to another, demonstrating that major changes at the genetic level can occur with minimal disruption of physiological or other phenotypic features. Finally, researchers have modeled the evolution of large regulatory networks and found that any particular phenotype can be underlined by a huge number of functionally equivalent genotypes, which implies that evolution of genetic networks can often be semi-neutral with respect to the organism’s fitness.

    All of this should dispatch once and for all ideas like “genetic program” and “genetic blueprint,” thereby also dramatically undercutting any claim to genetic determinism (as opposed to more mild “genetic causalism,” for lack of a better term). There is no program or blueprint because the developmentally-relevant information is distributed among different levels of organization, including but not limited to the level of gene networks. So phenotypes are truly emergent properties of gene-gene (and of course, gene-environment) interactions. This is completely different from the case of human-made programs and blueprints, which feature a relationship between input and output that is much closer to a simple one-to-one mapping.


    This is why living beings can evolve one complex feature after another without having to be “redesigned” from scratch. Hume was right: machines are simply not good metaphors for organisms, and it is time for stubbornly reductionist biologists to move on and search for better metaphors.

    Comments

    What a great paper! I wish you would do the same for physics: I always found that metaphors are very confusing. I remember reading about the train metaphor and thinking it was a flaw of human perception that made you unaware if the train was moving, not the absence of a frame of reference. It is thinking "it must be my fault" instead of "Oh, here comes a law of physics". Feynman lectures saved me from that. There is a case to be made for mathematics.

    Hank
    There's even a case to be made for teaching Feynman in school rather than trains, or headlights on cars at the speed of light, or apples and anvils.

    Growing up in the country the examples were always more practical anyway:   Deer A weighs 190 lbs. and you shoot it with a 160 grain bullet going 1300 ft/second.   Deer B weighs 170 lbs and you shoot it with a 180 grain bullet going 1600 ft/ second.    They're both on a ledge and fall over.  Where do they land?

    Answer:  I don't care, I am going back and getting a 4-wheeler rather than trying to drag them back up over that ledge.
    Hatice Cullingford
    Researchers are finding out that what matters is not so much individual genes, but the way networks of genes function together.
    True. That's why I wrote about Professor Abdi's research in "Chemistry, Drugs, and Rock-and-Roll: 2008 has 2 winners."

    You should see what the author sent me as a figure... when I can post it.
    Steve Davis
    "So phenotypes are truly emergent properties of gene-gene (and of course, gene-environment) interactions."
    "Researchers are finding out that what matters is not so much individual genes, but the way networks of genes function together."
    Which means that metaphors such as "survival machine" and concepts such as gene selection are nonsense.
    I suspect that in a decade or two Richard Dawkins will be regarded as one of the great buffoons of science, not because he was wrong,  but because he refused to recant in the face of contrary evidence, and his dismissal of opponents as fools.
    "It is time for stubbornly reductionist biologists to move on and search for better metaphors": would include the abandonment of the “Religion of Evolution”. It is bad enough that Darwin's original thesis was fatally flawed when his proposed different species turned out to be based on variations in the expression of a [beak] growth factor. Behe simply points out another example of why Darwin’s mechanistic view of evolution is wrong. Darwin failed, pulsatile evolution is abandoned, and punctuate evolution sounds like Genesis [while allowing no time for the immense changes that allow us to have this conversation].

    Furthermore, this article is unable to explain how a prototypical man and a woman were simultaneously birthed from a group of apes who happened to be living in close enough proximity to be able to find each other and mate Run the numbers: there simply weren’t enough apes or time for this to occur under the constraints of punctuate evolution. .

    While admitting the abysmal failure of the latest mechanistic concept of evolution, this author tries to "wish away" complexity with his brand of magical thinking. Congratulations, Harry Potter.

    I, too, would criticize this essay, but not because I'm a superstitious crackpot nor because my doctorate is in the evolutionary sciences. My doctorate is in reasoning, and this essay reads like an ad hominem attack based on strawman arguments and red herrings. It does not read like a reasoned position. For example: whence came that "wild claim" a few years ago that sequencing the human genome would tell us "everything there is to know about making a human being?" We don't know because the essay doesn't say. If such a claim was made, most likely it was made by some journalist. Behe and Dawkins probably never said any such thing; yet, the essay associates them with it. That is guilt by association. As for the argument about metaphors, the first thing the author needs to do is stop confusing metaphors with analogies. A metaphor is not "like" anything. A metaphor simply "is" something, thus: "a mighty fortress is our God." That's a metaphor: it refers to one thing as if it were something else. Thus, calling metaphors "flawed" is hardly revelatory. Of course they are flawed: they are emotional, not rational. If Paley in fact wrote that living beings were "like" watches ("clocks" or "clockworks" would have been more likely at the time), he was using an analogy, as the essay states. Analogies are not metaphors. Metaphors are poetical, magical, absolute fantasies. Analogies are often used as heuristics and, as such, they do not stake out a position; rather, as my dictionary indicates, they serve "to indicate or point out, stimulating interest as a means of furthering investigation." When we damn respected thinkers and scientists for using analogies we not only damn them for thinking in a very human way, we damn analogies themselves, and analogies are useful and probably necessary to rational thinking and the scientific process. Moreover, I am old enough to recall that, at least as early as the middle of the last century, scientists and educated laymen understood that there was no absolute answer to nature versus nurture; rather, that the development of an organism depended on both. Subsequent discoveries of the influence of various proteins or, as stated here, networks of genes, does not change that basic understanding. Consequently, I find it hard to believe that any scientist of my generation would refer to a "genetic blueprint" -- again, assuming any scientist did so -- without intending his remark as an analogy, a heuristic, to provoke challenge and debate, but not to be damned as if it were a heresy deserving of excommunication from the righteous cult of true believers.

    Mr. P needs to chill out.

    RG

    Steve Davis

    There's some basic flaws in Dr Gerber's comment. The first is that the author of the article did not find fault with metaphors but with their misuse. "Search for better metaphors" were his exact words.
    The second is that there is no reference to Dawkins in the article, the reference to Dawkins was in my comment, so there is no "guilt by association" that can be attributed to the author. The third flaw is that the term "genetic blueprint" has in the past been carelessly tossed about despite Dr Gerber having never come across it. And Massimo is not the first to be concerned by this. Gabriel Dover in his excellent "Dear Mr Darwin" (2000) included a sub-chapter titled "No Genetic Blueprints."
    Reluctant as I am to advise a doctor of reasoning on debating techniques, I would respectfully suggest that in future Dr Gerber should take a few deep breaths and calm himself down before committing pen to paper. Or just chill out.

    In response, I would have to say that, after referring to Richard Dawkins as a buffoon, Steve Davis has no right to tell anyone to chill out. Furthermore, the flaws he refers to are, for the most part, the same kind of strawman arguments and red herrings that appear in the Pigliucci's essay. To argue, as he does, that Pigliucci finds no fault with metaphors is a red herring. Pigliucci's first sentence is "Metaphors are dangerous things." He goes to state that they "trick one's mind" and he refers to them as "perverse constructs." Then he quotes favorably and relies heavily upon Hume's statement that "the metaphor is flawed." In addition, to imply that I argued in favor of metaphors or addressed the subject of their misuse, except as Pigliucci misused the term, is another red herring. I simply pointed out that Pigliucci does not know the difference between a metaphor and an analogy and explained the difference between them. Next, for Mr. Davis to argue that there was no guilt by association in the primary article because Dawkins is not mentioned there is both a red herring and utter chutzpah: a red herring because he evades the fact that the essay does associate named scientists in the "wild claim" of other people; chutzpah because, as Davis admits, he was the one who discovered Dawkins guilt by association. Finally, the strawman argument, the implication that the issues I address should be ignored because I have never heard of the term "genetic blueprint." I never said I was unfamiliar with the term. I said that if any scientist of my generation used the term, he or she almost certainly intended it as an analogy and a heuristic.

    RG

    Steve Davis

    My reference to Dawkins as a buffoon was merely my opinion, but I gave coherent reasons for coming to that conclusion. If Dr Gerber is not convinced, perhaps this extract from a Dawkins article of 1989 titled Universal Parasitism and the Coevolution of Extended Phenotypes should be considered. Dawkins gave an interesting description of the life cycle of the liver fluke, a parasite that spends part of its life in a snail then a sheep. Then came this: "A snail is just a fluke's way of getting into a sheep, and hence of getting its genes into the future." Now according to Dr Gerber that's a metaphor, a "poetical, magical, absolute fantasy," that is "emotional, not rational." I won't argue with that. The question we must ask is this; do such figures of speech have a legitimate role in scientific discourse. It seems unlikely if Dr Gerber's definition of a metaphor is accurate. They possibly have a role if used wisely, but wisdom was not even on the radar on this occasion, because Dawkins explicitly linked this metaphor to his "survival machine" metaphor in which an organism is merely a gene's way of getting itself into the future.
    This is why metaphors are, as Massimo said, dangerous things. The snail-fluke-sheep metaphor was nonsense, and it exposed the survival machine metaphor as nonsense.
    My opinion still stands.

    Gerhard Adam

    "For example: whence came that "wild claim" a few years ago that sequencing the human genome would tell us "everything there is to know about making a human being?"

    One example is from the National Human Genome Research Institute (www.genome.gov/10001772) where it states "...the HGP gave us the ability to, for the first time, to read nature's complete genetic blueprint for building a human being."

    Similarly one can go on to the "educational" portion of this website and be treated to all kinds of references to blueprints and how the proteins are like the bricks of a house (see the section "DNA as the instruction book").

    Whether analogy or metaphor, the approach is flawed when it comes to conveying an accurate picture of what is taking place.

    Mundus vult decipi
    HedgehogFive
    biochemist Michael Behe doesn’t understand how the bacterial flagellum could have evolved because he doesn’t understand evolution and insists in thinking of the flagellum as a “propulsion engine” analogous to those built by Evinrude.
    Thank you for that one, Massimo.  I am always pleased when someone shows succinctly what is wrong with ID or YEC arguments.

    As regards Paley and the watch, one must remember that he was a man of his time.  I don’t like him very much, he seems to me to be very much a man of the System (the Church of England as part of the Apparatus of State), but for many people his Natural Theology was something of an advance, inasmuch as he portrays things working on engineering principles rather that by “angels turning handles”.

    I see some people have brought Dawkins into the argument.  As a fighter against “Creation Science” he is compromised, because he has a deep hatred of Christianity and “C.S.” (mouthwash in Arabic be upon it!) assists his cause.  However, if one regards the Church as the Temple of God, “C.S.” is like dry rot in the intellectual rafters.
    I believe that Dr. Pigliucci was trying to make two separate points. The first, that the metaphor (or analogy or simile, as if the technicality of the term makes a difference) is a very useful yet dangerous tool in expressing scientific knowlege to those who have not had first hand experience in the particular feild being studied. This is true in both the sense that the metaphor may not have the same interpretation to the 'reciever' as it did to the 'speaker', and that the simplification of processes sometimes alienates the 'reciever' from 'being aware' of what they are 'not aware of'.

    The second point was that our view of how and to what degree the genomic code determines our phenotype is changing. We are learning that our hypothesis of (highly) genome-driven phenotype response is, while not entirely inaccurate, is only a smaller part of a giant picture. Much like Newtonian physics are not ignored or diminished in the light of Einstein's discoveries; Science is looking for better answers as much as better questions. Allow me to use a metaphor (or analogy, I'm sure Dr Gerber could tell me). Picture an organism as a football team, and the players as its gene's. Our previous assumption may have been that the higher quality player made for a more successful team, and that the better all the players are overall, the more likely the team will succeed. We see know that this isn't always the case. A team full of phenomenal players may not be as successful as a team of mediocre players that show better teamwork or can better deal with a variety or a particular feild condition (it's a poor metaphor I'm sure, theres not much place for a scrawny geek in the world of sports teams I was always cut from). Could poor shoulder pads represent methylation? Could replacing an injured player represent mutation? I suppose it doesn't really matter. What does matter is that we don't take a new scientific understanding as a complete degradation of our previous one, and that we careful to not let our metaphors misinterperate our message.

    And go easy on me, I'm just an undergrad!

    Gerhard Adam
    Actually that's a pretty good example.  It illustrates a particular concept but it also illustrates the danger of the analogy dominating the original idea.  In this case, one could take a familiarity with team sports and begin to conclude that they understand the behavior of genes because of their understanding of team sports. 
    Mundus vult decipi
    Steve Davis

    Eric, your analogy of a sports team as an organism was indeed a good one. It’s been used before, notably by Dawkins in The Selfish Gene, but he used a rowing team as the example and tied himself in knots, possibly because the tasks of rowers are similar, but in most sporting teams as in your football team, the tasks are varied, as are the roles of genes in an organism.

    You were careful to not take the analogy too far, unlike Dawkins who explained the analogy at length, then reached a conclusion that did not correspond to the explanation. He began his analogy (page 38) by stating; “One oarsman cannot win the <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" />Oxford and Cambridge boat race. He needs eight colleagues.” He returned to the analogy on page 84, restating that first observation as “Genes are selected, not as “good” in isolation, but as good at working against the background of the other genes in the gene-pool. A gene must be compatible with, and complementary to, the other genes with whom it has to share a long succession of bodies.” No problems so far, there’s a slight change in emphasis, but it still seems like organism selection to me, but not to Dawkins, who out of the blue came up with “It is possible to imagine a compatible combination of genes being selected together as a unit.” (his emphasis) Isn’t that what the boat race analogy was all about? A single oarsman cannot win the race, the team wins the race. The group is selected. What Dawkins was now doing was sleight-of-hand, he was trying to establish the Evolutionary Stable Strategy as a more likely explanation than group selection and a justification for accepting only gene selection. And incredibly he now had to plead “the rowing analogy is not really up to explaining this idea.” Not if you intend to fudge the argument, for his reasoning was faulty. On page 85 he stated “It so happens that the tendency for an individual to win races depends on which other individuals are present in the group of candidates.” This was the sleight-of-hand, the master illusionist at work. Previously he had stated (page 38) that “The pool of alternative candidates (for crew selection) is the gene pool.” That’s fine, but you cannot extend that to race winning as he did in the last quote. The gene pool is only a secondary consideration in selection, the primary consideration is the organism, or in winning races it’s the crew make-up. Was Dawkins confused or deceitful? What really matters is that he was wrong, and Massimo was right, metaphors are dangerous things. <?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />



     

    Thank you, Steve. I definitely tried to not take my analogy too far, as my knowlege of genetics is no where near anybodies on the blog. But I am continuing to learn, and I've had incredible lecturures for molecular biology and genetics classes. It's funny, because I like to use my analogies universally. The same one I used here I can use to explain gene's to my younger brother (who, after seeing me coming home from my university every day, has grown an admirable obsession with the living world).
    Analogies are intellectually dangerous, this has been discussed. But I also think they are invaluble, when used properly, for giving those who aren't involed in 'the fields' a better and more accessable visualization of complex concepts. This goes double for grade-school children, because when sciences and maths become intimidating and overbearing, kids lose interest. These concepts have to be more than something written in the textbook, they need to be seen as the actual, tangible, dynamic world around us.
    I though that the sport analogy was fitting enough to describe, loosely, how genes may work interdependantly and how this may be favored in natural selection over individual gene strength. I even convinced Mr. Adam that I know more about team sports than genetics (when in reality, I have as much knowlege in sports as Gerhard has taste in headwear). I really meant to take out Dawkins' 'Selfish Gene' to read during winter break, but I accrued $60 in late fee's when I forgot to return the "Blue Planet" dvd's until after finals, and I'm just too broke to pay it. You didn't seem too interested in it, though. Would you want to mail me your copy??

    Steve Davis
    I can certainly recommend The Selfish Gene, not because it's good science, but because it provides a lesson in how not to conduct a discussion of science. As for my copy, I'm Down Under so that might prove expensive. Also I was unable to get a second hand copy so it cost me $30 (how I hate giving royalties to Dawkins!) and I've got so much enjoyment from finding the many unjustified assumptions and instances of contempt for logic that I've developed a rather emotional attachment to it, I think it will give me pleasure for years to come. (I know, I gotta get a life!) I agreed with all your thoughts on analogies, but you're way off line with Gerhard's headwear. Us old blokes can get away with murder when it comes to style!
    Gerhard Adam
    Not only can we get away with it .... we look good doing it :)
    Mundus vult decipi
    Steve Davis
    That's what I keep telling myself Gerhard!
    Point well taken, considering I'm sitting here in an oxford, gym shorts, wool socks and sandals. I guess I'll just have to dust off my unread copy of "The God Delusion", see if it's any different than his other 20 something documentaries. I had no idea Dawkins stir's up so much animosity!

    mossnisse

    The basic idea with the problem of metaphors I actually agree upon. If it is an analogy all aspects of the things can’t be the same.  But when you come to the examples I think you are totally wrong.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />

    1. William Paley’s metaphor of living organisms as analogous to complex artefacts is really great. It shows that living organisms can’t have been just randomly created. That is no problem for evolution because we have natural selection that is not totally random. And the problem with reducible complexity is that the ID advocates don’t see the process how reducible complexity can evolve (it’s not obvious I recommend you to read the evolution of complex organs http://blogs.springer.com/evoo/?p=85) .

    2. I also like the analogy between computer programs and the genome I think it is because I have actually been doing some programming. It should maybe be a little bit ore specified it should be the computer program code. The program code is information it’s need to bee interpreted to make any sense like the code of the DNA must be in a cell to make anything. Modern source code have to be interpreted first by a compiler program and that can be a problem because it’s difficult to precisely define a programming languish so then different compilers can actually interpret the same program I slightly different ways, with the result that the code doesn’t work with others compilers. And it is actually no physical resemblance between the code and the resulting program. And often even the programmer doesn’t now exactly how his programs work there are so many variables that affect each other in complex patterns. As a programmer you have to do a lot of try and error and in that way we can make a loose analogy to evolution how a computer program develops. And the properties of the computer program is as truly emergent properties of the code as the phenotype of the genome.  The properties of the program is truly a complex interaction between variables and interaction between variables and the input from the user. It can be difficult to read others code to the level that it is easier to start over from the beginning especially if they haven’t done any comments and other documentation.

    I'm with you Steve Davis. I was furious after reading "The Selfish Gene" some twenty years ago. It is one thing to use metaphors for a professional audience but the general public can all too easily mis interprets the same. In any event Dawkins basic assumptions about what genes are was also deeply flawed. Dawkins helped promote a a type of genetic determinism throughout the general community. I'm not prepared to argue he is responsible for that but I think he is a good object lesson to scientists, and particularly physicists, in that great care needs to be taken when communicating complex ideas to those unfamiliar with the relevant discipline.