Science Literature

In a Commentary essay, Carl Woese and Nigel Goldenfeld provide an analysis of biological thought that differs profoundly from that presented by those celebrating the Bicentenary of Darwin's birth and, incidentally, the recently published AP Biology Standards.

"This is the story of how biology of the 20th century neglected and otherwise mishandled the study of what is arguably the most important problem in all of science: the nature of the evolutionary process. This problem [ . . ] became the private domain of a quasi-scientific movement, who secreted it away in a morass of petty scholasticism, effectively disguising the fact that their primary concern with it was ideological, not scientific."

Procrustes was slain on his own bed by Theseus: an analogy for the microbial world liberating biology from the "Procrustean bed of dogma" that goes under the name of neo-Darwinism (source here)

The authors want to see biology liberated "from the Procrustean bed of dogma on which it has been cast for so long". A radical overhaul is warranted. The issues are comparable to the "transformation of the physical sciences" in the early 20th Century. This is when the foundations of Newtonian mechanics were undermined and the certainties of that approach were replaced by relativity theory and the statistical uncertainties of quantum mechanics. Just as physics then had to accept that there was much more to learn, so also biology today.

"Although 2009 will be marked by a plethora of celebrations on the subject of evolution, most of the attention is being bestowed on the personalities and historical circumstances surrounding the theory of natural selection, as if this and its synthesis with genetics in the first decades of the 20th century marks the culmination of the theory of evolution. It does not. The MMBR (Microbiology and Molecular Biology Reviews) community has been at the forefront of defying the standard wisdom; and thus it is, in many ways, its story that we now wish to tell."

This blog will refer to some of the themes developed in the essay. The first of these is reductionism. Newtonian physics is described as "deterministic reductionism, and safe in its completeness" and there is a direct link to neo-Darwinism: "the petrified form of evolution that emerged from the modern synthesis". This had adverse consequences for the study of living things: "Organisms, like pinatas, were there to be burst open in order to get at the (biochemical) goodies within - a view of microorganisms that, with justification, persists today among some subfields of microbiology."

"The discipline [of microbiology] clearly had a foundational issue. Biochemistry was simply not sufficient to serve as the basis upon which the study of the microbial world could rest. Neither the organism nor its ecology could be satisfactorily encompassed by this reductionistic perspective - an objection that could also be raised against all the sum-of-the-parts disciplines, such as molecular biology and genetics."

The second theme is the prokaryote hypothesis. In 1962, Stanier and van Niel sought to move microbiology on by declaring all bacteria to be prokaryotes. In their view, all bacteria shared a common cellular organisation and this allowed a common ancestry to be inferred. Woese and Goldenfeld write: "This notion, that all bacteria shared a common cellular organization, was to stand firmly in the path of microbiology's development for the better part of half a century." In their view, the assertion that "all bacteria were prokaryotes was an eminently testable hypothesis", but the microbiology community perceived the hypothesis as "the answer". Indeed, it became an axiom of microbiology. The test of the hypothesis came when Woese looked much more closely at the molecular properties of bacteria and recognised two distinct types: the archaebacteria and the eubacteria. Subsequent research widened the gap when it was realised that there was actually no common cellular organisation.

"[T]here were [. . .] many fundamental molecular properties in which the bacteria (declared to be synonomous with prokaryotes by Stanier and van Niel) differed from one another. The "archaebacteria (Archaea) had finally appeared on the scene, and their molecular properties were as distinct from those of the "eubacteria" (Bacteria) as either one's were from those of the Eukarya. The prokaryote hypothesis had been proven false."

The third theme relates to the concept of the gene. The root problem here is reductionism, but the consequences for genetics have been far-reaching. The mindset of the scientists was highly mechanistic.

"In this Newtonian world, the study of biology becomes a highly derived subdiscipline of the basic science of physics - in effect, an engineering enterprise; there is nothing "fundamental" about it. Biology becomes a study of machines made of assemblages of parts and the interactions among them, an exercise in describing, but not explaining, things as they are. [. . .] A discipline whose perspective is that of classical 19th century physics is inherently incapable of dealings with the problems of a nonlinear world, which is nonreductionist, nondeterministic (acausal), and works in terms of fields and emergent properties, not a static world of particles with linear relationships among them."

As a result, genetics was dominated by concepts of templating and translating that underplayed the "incredible and complex mechanism that can extract information (pattern) from the sequence of one type of macromolecule and "express", i.e., store, most of it as the structure (sequence pattern) of another macromolecule of a different type". Neo-Darwinism cannot deliver answers, because its vision of biology is fundamentally flawed.

"This turn in the road (of applying reductionist metaphysics to the understanding of the biological world) would become a superhighway that dead-ended before it reached molecular biology's ultimate goal, that of understanding the essence of "livingness" and directly answering the question of how molecules come to life."

This sense of biology entering a cul-de-sac is pronounced. Woese and Goldenfeld want to see a different approach to evolutionary thinking: for them, it is the key to moving the discipline forward. Their perception of the Modern Synthesis is that it has led to (a) stagnation (no new ideas) and to (b) safeguarding the consensus (looking after vested interests).

"The basic understanding of evolution, considered as a process, did not advance at all under its tutelage. The presumed fundamental explanation of the evolutionary process, "natural selection", went unchanged and unchallenged from one end of the 20th century to the other. Was this because there was nothing more to understand about the nature of the evolutionary process? Hardly! Instead, the focus was not the study of the evolutionary process so much as the care and tending of the modern synthesis. Safeguarding an old concept, protecting "truths too fragile to bear translation" is scientific anathema."

There is much more in this essay - happily it is open access. The vision of Woese and Goldenfeld warrants further discussion, as do their comments on the significance of horizontal gene transfer. However, this blog has an educational focus. Why are educationalists so keen to make neo-Darwinism the central pillar of evolutionary theory? Why are the AP Biology Standards affirming things that are here so vigorously contested? Why should students be given the impression that evolutionary theory is robust and settled? Woese and Goldenfeld comment:

"What makes the treatment of evolution by biologists of the last century insufferable scientifically is not the modern synthesis per se. Rather, it is the fact that molecular biology accepted the synthesis as a complete theory unquestioningly - thereby giving the impression that evolution was essentially a solved scientific problem with its roots lying only within the molecular paradigm."

Returning to the Procrustean bed of dogma, it is important to realise the significance of this imagery. Biology has been lying on a bed which has led to emasculation. To draw on the other images in the title, biology needs to be delivered from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis. These theoretical constructs have had serious negative effects on biological science, and yet we still teach them uncritically! In summary:

"Dogmatic thinking has prevailed all too often in our account, with disastrous consequences for the progress of the fields of microbiology, molecular biology, and the study of the evolutionary process. It led to the stagnant and scientifically invalid notion of the prokaryote; it led to the redefinition of the problem of the gene; and through a slavish adherence to the modern evolutionary synthesis, it led to a premature declaration of victory in the struggle to understand the evolutionary process."

How the Microbial World Saved Evolution from the Scylla of Molecular Biology and the Charybdis of the Modern Synthesis
Carl R. Woese and Nigel Goldenfeld
Microbiology And Molecular Biology Reviews, 73(1), March 2009, 14-21 | doi:10.1128/MMBR.00002-09

There must be no barriers for freedom of inquiry. There is no place for dogma in science. The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors.
-J. Robert Oppenheimer, The Open Mind, p. 114 (1955)

First sentence: This is the story of how biology of the 20th century neglected and otherwise mishandled the study of what is arguably the most important problem in all of science: the nature of the evolutionary process.

See also:

Tyler, D. Teaching goals for Advanced Placement Biology, ARN Literature Blog (21 September 2009)