Gould's article contains an important fallacy, maybe several. He infers from the relative paucity of "human" genes that the "central dogma" (one-way directionality of explanation from DNA through protein) is false, because so few genes cannot produces od many proteins, and infers from that we must reject "reductionism," understood as explaining "higher level" phenomena, e,.g., biological, or maybe even psychological and social phenomena, in terms of lower level phenomena, e.g., genetic or even biochemical phenomena. None of these inferences will hold.
I should remark that years ago I wrote a dissertation defending a sophisticated reductionsim about the mind (roghtly taht we ould expklain mental phenomena in physical terms) against abd philosophical objections. I published several papers out of it, then lost interest, since it seemed to me that I was saying oveer and over again that either the scientists would produce reductions, in which case the philosophical objections were obviously wrong, or they wouldn't, in which case the issue would lose its urgency. I no longer care very much about reductionism. But I do know a lot about it. And despite Gould's immense scientific learning, far greater than mine, what he has presented here is another bad philosophical objection, not a scientific refutation.
OK, the first step: few genes, many proteins. That refutes the idea that there is a single gene that by itself turns on each protein in every circumstance. It does not even refute the idea, however, that there is a single gene that turns on each protein in some circumstance. Nor does it show that discrete combination of genes do not make each particular proteins in some or all circumstances. If only two genes are required to turn on or make each protein, we have already got a huge increase in the number of explananda in the explanatory base. This means that the central dogma stands, unless we identify it with the one gene-one protein view. The paucity of genes does not by itself tell us anything about the explanatory direction.
Now, the second move: from the failure of the central dogma to the falsity of reductionism. This is a bad argument for several reasons. The first is already indicated; since several genes, or single genese in particular circumstances, may make single proteins, the lower level phenomena, so understood, may still explain the high level ones.
Second, I remark that is is somewhat difficult to imagine how else it could be: is Gould suggesting that there are genetic explanations for biochemical phenomena? That, say, the laws of population genetics explain how RNA encodes information from DNA and makes proteins? How could that be? Maybe he just means that there are several ways that the biochemsitry of DNA/RNA means proteins, that, in the jargon of the discussion, the manufacture of proteins is multiply realized. It's true that multiple realizability is often taken to be a refutation of reduction, but it isn't. It just shows that there are several reduction bases.
But even if the "central dogma" is refuted by the results of the human genome project, and we accept that there are emergent properties that can affect lower-level ones, evolutionary properties that can affect biochemical ones somehow, that does not show that reductionism is false, that we cannot explain higher level phenomena in terms of lower level ones, even exhaustively. It just shows that explanation can run both ways. It would take more argument to show that exhaustive explanation of the higher levels in terms of the lower levels is impossible; that does not follow from the premise that explanation in the reverse direction is possible.
I comment that "reduction" is not elimination: no onme argues that there are no proteins just becaust or if we can esxplain their behavior in biochemical terms.
I don't see why any of this discussion has any implicatiosn for "bourgeois" thought one way or the other.
--jks
>
>[Gould is too discreet to say it this way, but quite a blow to
>conventional bourgeois thought.]
>
>New York Times - February 19, 2001
>
>Humbled by the Genome's Mysteries
>By STEPHEN JAY GOULD
>
>Two groups of researchers released the formal report of data for the
>human genome last Monday - on the birthday of Charles Darwin, who
>jump-started our biological understanding of life's nature and
>evolution when he published "The Origin of Species" in 1859. On
>Tuesday, and for only the second time in 35 years of teaching, I
>dropped my intended schedule - to discuss the importance of this work
>with my undergraduate course on the history of life. (The only other
>case, in a distant age of the late 60's, fell a half-hour after
>radical students had seized University Hall and physically ejected
>the deans; this time at least, I told my students, the reason for the
>change lay squarely within the subject matter of the course!)
>
>I am no lover, or master, of sound bites or epitomes, but I began by
>telling my students that we were sharing a great day in the history
>of science and of human understanding in general.
>
>The fruit fly Drosophila, the staple of laboratory genetics,
>possesses between 13,000 and 14,000 genes. The roundworm C. elegans,
>the staple of laboratory studies in development, contains only 959
>cells, looks like a tiny formless squib with virtually no complex
>anatomy beyond its genitalia, and possesses just over 19,000 genes.
>
>The general estimate for Homo sapiens - sufficiently large to account
>for the vastly greater complexity of humans under conventional views
>- had stood at well over 100,000, with a more precise figure of
>142,634 widely advertised and considered well within the range of
>reasonable expectation. Homo sapiens possesses between 30,000 and
>40,000 genes, with the final tally almost sure to lie nearer the
>lower figure. In other words, our bodies develop under the directing
>influence of only half again as many genes as the tiny roundworm
>needs to manufacture its utter, if elegant, outward simplicity.
>
>Human complexity cannot be generated by 30,000 genes under the old
>view of life embodied in what geneticists literally called
>(admittedly with a sense of whimsy) their "central dogma": DNA makes
>RNA makes protein - in other words, one direction of causal flow from
>code to message to assembly of substance, with one item of code (a
>gene) ultimately making one item of substance (a protein), and the
>congeries of proteins making a body. Those 142,000 messages no doubt
>exist, as they must to build our bodies' complexity, with our
>previous error now exposed as the assumption that each message came
>from a distinct gene.
>
>We may envision several kinds of solutions for generating many times
>more messages (and proteins) than genes, and future research will
>target this issue. In the most reasonable and widely discussed
>mechanism, a single gene can make several messages because genes of
>multicellular organisms are not discrete strings, but composed of
>coding segments (exons) separated by noncoding regions (introns). The
>resulting signal that eventually assembles the protein consists only
>of exons spliced together after elimination of introns. If some exons
>are omitted, or if the order of splicing changes, then several
>distinct messages can be generated by each gene.
>
>The implications of this finding cascade across several realms. The
>commercial effects will be obvious, as so much biotechnology,
>including the rush to patent genes, has assumed the old view that
>"fixing" an aberrant gene would cure a specific human ailment. The
>social meaning may finally liberate us from the simplistic and
>harmful idea, false for many other reasons as well, that each aspect
>of our being, either physical or behavioral, may be ascribed to the
>action of a particular gene "for" the trait in question.
>
>But the deepest ramifications will be scientific or philosophical in
>the largest sense. From its late 17th century inception in modern
>form, science has strongly privileged the reductionist mode of
>thought that breaks overt complexity into constituent parts and then
>tries to explain the totality by the properties of these parts and
>simple interactions fully predictable from the parts. ("Analysis"
>literally means to dissolve into basic parts). The reductionist
>method works triumphantly for simple systems - predicting eclipses or
>the motion of planets (but not the histories of their complex
>surfaces), for example. But once again - and when will we ever learn?
>- we fell victim to hubris, as we imagined that, in discovering how
>to unlock some systems, we had found the key for the conquest of all
>natural phenomena. Will Parsifal ever learn that only humility (and a
>plurality of strategies for explanation) can locate the Holy Grail?
>
>The collapse of the doctrine of one gene for one protein, and one
>direction of causal flow from basic codes to elaborate totality,
>marks the failure of reductionism for the complex system that we call
>biology - and for two major reasons.
>
>First, the key to complexity is not more genes, but more combinations
>and interactions generated by fewer units of code - and many of these
>interactions (as emergent properties, to use the technical jargon)
>must be explained at the level of their appearance, for they cannot
>be predicted from the separate underlying parts alone. So organisms
>must be explained as organisms, and not as a summation of genes.
>
>Second, the unique contingencies of history, not the laws of physics,
>set many properties of complex biological systems. Our 30,000 genes
>make up only 1 percent or so of our total genome. The rest -
>including bacterial immigrants and other pieces that can replicate
>and move - originate more as accidents of history than as predictable
>necessities of physical laws. Moreover, these noncoding regions,
>disrespectfully called "junk DNA," also build a pool of potential for
>future use that, more than any other factor, may establish any
>lineage's capacity for further evolutionary increase in complexity.
>
>The deflation of hubris is blessedly positive, not cynically
>disabling. The failure of reductionism doesn't mark the failure of
>science, but only the replacement of an ultimately unworkable set of
>assumptions by more appropriate styles of explanation that study
>complexity at its own level and respect the influences of unique
>histories. Yes, the task will be much harder than reductionistic
>science imagined. But our 30,000 genes - in the glorious
>ramifications of their irreducible interactions - have made us
>sufficiently complex and at least potentially adequate for the task
>ahead.
>
>
>We may best succeed in this effort if we can heed some memorable
>words spoken by that other great historical figure born on Feb. 12 -
>on the very same day as Darwin, in 1809. Abraham Lincoln, in his
>first Inaugural Address, urged us to heal division and seek unity by
>marshaling the "better angels of our nature" - yet another
>irreducible and emergent property of our historically unique
>mentality, but inherent and invokable all the same, even though not
>resident within, say, gene 26 on chromosome number 12.
>
>Stephen Jay Gould, a professor of zoology at Harvard, is the author
>of "Questioning the Millennium."
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