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Thursday, December 18, 2008

The demise of the genetic blueprint metaphor

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 Drosophila is 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.


  1. This is at best tangentially related to the subject, but it has bothered me ever since I read the line a month or so ago:

    "Time is to clock as mind is to brain. The clock or watch somehow contains the time. And yet time refuses to be bottled up like a genie stuffed in a lamp. Whether it flows as sand or turns on wheels within wheels, time escapes irretrievably, while we watch. Even when the bulbs of the hourglass shatter, when darkness witholds the shadow from the sundial, when the mainspring runs down so far that the clock hands hold still as death, time itself keeps on. The most we can hope a watch to do is to mark that progress." - Dava Sobel, Longitude

    Time is not an emergent phenomena of a clock! A better analogy would have been time is to clock what distance is to ruler.

  2. "Those interested in the sciences must remember that scientists often must speak in metaphor since reality is not required to fit into our language."
    I was writing about the whole "information in DNA" fallacy a few days ago. It's amazing how often people take the metaphor too far.

  3. "...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..."

    Uh boy! I am trying to figure out if this means that biologists need to rethink all quantitative genetics. :)

  4. The demise of the genetic blueprint metaphor

    And that of the computer program, so that we may be spared the blatherings of creationist computer programmers who think DNA is a program written in something like C++ or Fortran and is therefore as brittle in the face of mutation as they are.

  5. I think the problem is not machines per se that are the bad metaphor, but machines that have intentionality. When genes do things they do it as part of a major set of machinery, but the idea that genes are "information" relies on a bad analogy with designed machines, and should be dropped. Mechanism is physical - we can measure it. Information is entirely relative to the description of the system and some ancillary assumptions, and should be treated as arbitrary.

  6. Funny, I always said that use of mechanical metaphors for biological phenomena is a tip off that you're talking to an intelligent design advocate... being as they indicate features are unchangeable and that rubs the wrong way with biologists. I think a big part of the problem with teaching the public evolution is that everybody acts like it's a simple, but really, iterative, dynamically interacting processes across huge numbers of generations... it's kind of mathematically complex.


    But isn't that how so much of science works in practice? One can sometimes identify a pseudoscience by its inability to produce such surprises.

  8. Didn't Richard Dawkins argue against the "machine" metaphor in "A Devil's Chaplain"? He said that the way genes build a living being is more akin to a recipe than a blueprint; the difference being that a machine can be erverse-engineered to recreate a blueprint, in which every component has a specific location, wheras reverse engineerign a cake will not give you the exact location of every current and sultana according to the recipe.

  9. Kimpatsu,

    yes, he did. Unfortunately Dawkins is also single-handedly responsible for the second worst metaphor in this field: the selfish gene...

  10. While we are attacking metaphors, I'd like to have a go at "adaptive landscape". Phenotype-fitness gives enough trouble already, but genotype-phenotype or genotype-fitness landscapes get crazy. "Rugged" hardly captures it. "Discontinuous" is a more accurate word. The metaphor of a landscape hardly is an intuitive picture of an object with a huge number of dimensions, each with possible genotypes at one locus containing no natural ordering along an "axis".

  11. Each time I hear Huckabee spout off his '23 chromosomes from the father and 23 from the mother, and that's it, it's all set, you have the entire blueprint for human life' I grimace, and say "but the mitochondrial DNA all came from the mother, is that a 'sub-set of blueprints', and environmental factors in utero, those have no influence..." Over-simplification using black and white metaphors, the retreat of the simple-minded and the willfully ignorant.

  12. Joanna,

    oh, I completely agree. Jonathan Kaplan and I devoted an entire chapter of Making Sense of Evolution to criticize the adaptative landscape metaphor. Jonathan also edited a special issue of Biology and Philosophy on the topic, it's coming out early next year.

  13. Alright, I'll take the bait. Perhaps one can get something useful out of the bluprint metaphor. It is just not as simple as we once thought, a chracteristic of much of what I learned in biology.

    Give the same building blueprint to the same contractor, with the same client, on the same terrain, in the economy with the same access to the same materials, with the same building inspectors, etc. and you will get nearly the building.

    It is simplistic to believe that you can look at the pages of a complex blueprint for structure, HVAC, electric and plumbing, etc. and think the outcome is predetermined without awareness that there are layers of systems which affect how the blueprint is implemented.

  14. Fantastic post.

    I have been reading a lot of the physicist David Bohm, and he made a similarly Hume-ian refusal of the machine metaphor. If I remember correctly, it is actually the last thing he said in his last book, and he really emphasizes the point with gravitas.
    Bohm would argue that these different levels of organization are levels of "implicate order" within the DNA/organism's structure. Such disorder as observed by the Intelligent-Design people would be explained as an implicate structured order that has yet to be properly understood.
    The ID camp revels in what Bohm would describe as a primary confusion, a confusion where one is caught up in the stress of not understanding something, and cannot concentrate on solving the problem.

  15. Max, how do you mean that the "selfish gene" is a bad metaphor? Is is because you don't subscribe to the gene's-eye view of evolution?
    I do remember Dawkins complaining how his publishers had completely mangled the meaning he wanted to convey with the covers they chose for the various editions of his books. (But then again, Michael Shermer said much the same thing at TAM 3.)
    Are you sure you're not confusing Dawkins himself with some editor's hyperbole?

  16. I can see how the metaphor of genes as 'blueprints" could be a bad one -- particularly if you don't know anything about architectural blueprins(I've seen them), and constructing a building(which I've also seen done). If it's your house you're building from a "plan" you know that the architect's blueprint only tells you how much house you will end up having. It says nothing about what you will end up putting into it. I see genes as being somewhat like that. Your genetic makeup provides the parameters of "you", but it doesn't define "you", because what an organism turns out to be, depends on so many factors, both genetic and environmental, that simply knowing your genome, or the whole human genome, won't explain "everything".

    By the way, and just to make things absolutely clear, I am not in any way, a proponent of "design". I don't believe evolution works that way, nor are we, or any other organism, "fixed" by whatever our genetic makeup happens to be. And yes, I also know that the way genes interact with each other and with whatever environment they're in, is also incredibly complicated, so in that sense, any metaphor is probably inadequate.
    Anne G

  17. Kimpatsu,

    my problems with Dawkins' metaphor are on both fronts: on the superficial one, "selfish" is often taken to be a new version of "nature red in tooth and claw." This isn't what Dawkins meant, but he should have foreseen it. It was not by chance that the CEO of Enron said his favorite book was The Selfish Gene.

    More substantially, right, I don't buy his gene-centric view either, especially as presented in The Selfish Gene, but even the milder version of The Extended Phenotype. But that's not a problem with the metaphor as much as with the science behind it.

  18. Surely this sums up the gene-centric problem with the Selfish Gene metaphor: "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." Dawkin's "genes" are analytic not biochemical - arguably simplistically matching a one gene to one phenotype - contrary to the actual regulatory dynamics that occur, as Max emphasizes in this article. Could Dawkin's "Selfish Gene" therefore be renamed "Selfish Phenotype"!? ;-)

    The again IMHO his use of "selfish" is equivalent to succesful, and confuses the process/product distinction, we usually read "selfish" - even in a just behavioural, third person sense - as the process (a possible means through which success is achieved) not the product(the success itself).

