This article is supplemental to “Genes and the Central Fallacy of Evolutionary Theory”, and can best be read in conjunction with that essay. Both pieces are part of a larger work in progress entitled: Toward a Biology Worthy of Life. Original publication of this article: February 28, 2013. Date of last revision: February 28, 2013. Copyright 2013 The Nature Institute. All rights reserved.
In February 1997 the general public learned that a several-month-old sheep named “Dolly” had been produced by somatic cell nuclear transfer, a form of cloning. Dolly’s parentage involved a normal sheep’s ovum (egg cell) from which the nucleus had been removed. The nucleus was then replaced with one taken from a fully differentiated cell of a second female sheep, producing a viable zygote, which then began more or less normal development. Finally, the resulting embryo was carried to term by a surrogate mother, a third sheep.
The nucleus from the original egg cell was haploid — that is, like gametes in general, it had only half the number of chromosomes characteristic of sheep. But the nucleus replacing it was diploid, containing the number of chromosomes found in an egg after fertilization by a sperm cell. So instead of a union of two haploid gametes, there was a union of one enucleated gamete with the extracted nucleus of a somatic cell containing the full (diploid) set of sheep chromosomes. No sperm cell entered into the process.
The somatic cell nuclear transfer producing Dolly showed that, not only can a single-celled zygote differentiate into all the cell types of the body, but a fully differentiated cell nucleus can — at least under artificially forced circumstances — “dedifferentiate” into a zygotic nucleus under the influence of an egg’s cytoplasm. Actually, this was known long before Dolly’s birth. For example, nuclei from adult frog brain cells were injected into frog egg cells at various stages of maturation. “In all cases the injected nuclei changed their activities to conform to those characteristic of nuclei of the recipient cell types” (Raff and Kaufman 1983, p. 110*). Brain cells do not divide and their nuclei do not normally synthesize new DNA. But once the nuclei were injected into eggs, DNA synthesis began. It’s the kind of thing that leads researchers to speak of the “powerful influence of the egg cytoplasm” (Pederson 2011*).
The entire field of induced pluripotency is based on the fact that differentiated cells can be at least partially “reprogrammed” (as the prejudicial phrase has it) back toward the less differentiated state of stem cells or gametes, even if at extremely low success rates. So in this “reverse direction”, too (the opposite of normal cell differentiation), we find “strong evidence for nuclear plasticity” (Yamanaka and Blau 2010*).
Contending spheres of influence. All this plays into a century-long debate about the relative roles of the DNA-containing nucleus and the surrounding cytoplasm of the cell. The dominant position was articulated well before the age of molecular biology — for example by pioneering geneticist Herman J. Muller in 1929:
The great bulk, at least, of the protoplasm was, after all, only a by-product, originally, of the action of the gene material: its “function” (its survival-value) lies only in its fostering the genes, and the primary secrets common to all life lie further back, in the gene material itself. (Quoted in Sloan 2012*)
I am far from wanting to take the opposite position, claiming that the cytoplasm “rules” all. What we see when we look at the cell as a whole is what we see if we look more narrowly, for example, at all the proteins bearing on gene regulation: the emerging picture shows that “no single protein or protein complex is more important than the rest; instead, they appear to be physically and functionally intertwined” (Fong et al. 2012*).
If the cell possesses an organic wholeness, and if the complete organism is a larger whole, then the corrective for the DNA-centered view of the past several decades is not to elevate the cytoplasm over the nucleus, but rather to see an integral unity. MIT historian of science Evelyn Fox Keller implied such an integral unity when she suggested that the crucial factor in Dolly’s cloning “lay in the relationship that had been established between nucleus and cytoplasm” (2000, p. 90*). Quoting Colin Stewart, Chief of the Laboratory of Cancer and Developmental Biology at the National Cancer Institute: “The key to success seems to have been in finding a method to make the donor nuclei more compatible with the cytoplasm of the recipient oocyte . . . The trick that [Dolly researcher Ian] Wilmut and his colleagues employed was to place the donor cells in a quiescent state” — something they achieved by partially starving the cells of nutrients (Stewart 1997*).
Both induced pluripotency and cloning initially produced huge excitement, but this was — as could have been expected — followed by the progressive realization that not everything was quite right. The results from the very beginning were scanty, with tiny success rates. The procedures were invasive and artificial, involving processes occurring out of their normal contexts and therefore producing inevitable “side effects”. There is a huge and growing literature showing the unexpected and often pathological aspects of the life processes resulting from “successful” procedures, so that researchers now do not hesitate to speak, for example, of “the dark side of pluripotency” (Pera 2011*).
Nevertheless, the experiments do show, in a perverse sort of way, the same truth we see in the positive picture of organismal development and cell differentiation: neither DNA nor any other element of the organism is “in control”. There are contexts within contexts, and nothing spares us the need to recognize, as far as we can, the never clearly bounded extent of the organism’s wholeness. And, so far as the experiments are concerned, one can hardly doubt that, as more and more contextual factors are recognized and brought into current experimentation, results will progressively improve.
It will always be possible to find situations where, with narrowed vision, we can see DNA “masterminding” something, just as we can find situations where this or that cytoplasmic factor — in truth, just about anything else in the cell — appears to be the “mastermind” of what is going on. This is why molecular biologists are forever telling us that one thing “regulates” or “controls” or “dictates” another thing. All one needs to do is to pick out the right circumstances or the right vantage point in order to make one or another aspect of the cell appear to be central. But the resulting picture will always be a limited one, abstracted from the overall life of the organism.
A little history. There is not a lot of mystery about how the nucleus with its DNA was made into a central controller of the organism. Evolutionary biologists Marc Kirschner and John Gerhart describe how, during the first half of the twentieth century, the pioneering geneticist, Thomas Hunt Morgan, narrowed his experimental procedures until they showed dramatic and easily measured “genetic effects”:
Morgan initially turned to inbred strains because animals from the wild, when mated, produced offspring with too much variation in their traits, such as wing size or eye color. But with this choice he turned from wild populations where the dynamics and variation of populations could be observed, to inbred laboratory strains where they could not. Variation, previously a source of fascination, was becoming an experimental nuisance. Selection was now performed in the laboratory by geneticists to identify traits that were easy to score, rather than traits that might be related to survival in the wild, or to embryonic development, or to evolution. The original impulse to understand how organisms evolved was lost (Kirschner and Gerhart 2005, p. 26*).
Researchers had to keep those fruit flies under the most uniform conditions possible — same diet, same temperature, same activities, and, in general, the same environmental, genetic, and physiological background. Otherwise, as geneticists Emmanouil Dermitzakis and Andrew Clark summarize the matter: “Modeling and prediction of complex phenotypes of inbred lines in the laboratory can be quite accurate, and yet when the same genes and phenotypes are projected into a free-living population, individual prediction entails too many additional variables and accuracy suffers” (2009*).
In other words, one uses constraining experimental procedures to block out the “interfering” aspects that arise from whole organisms in their varying environmental contexts. Isolated causes can then be identified — except that they lose their causal reliability as soon as other contexts are considered.
As one example among many: in a 1927 article in Science, F. R. Lillie, a University of Chicago zoologist and long-time director of the famous Woods Hole Marine Biological Laboratory, cited one of Morgan’s Drosophila mutants, which differed from the normal fly in a single gene — under one set of experimental conditions. But other conditions were possible. When raised in an ice chest, the mutant had “one, two, or even all, of its legs doubled, but if reared at room temperature none” (Lillie 1927*).
The problems raised by one’s choice of model organism go far beyond a few odd particulars. Researchers have, of course, preferred to work with small, rapidly reproducing organisms such as fruit flies and nematodes. However, as University of New Hampshire zoologist, Jessica Bolker, reminds us, “evolutionary selection for rapid development has broad implications. It seems to favour stronger genetic control during development and less plasticity (or flexibility). Compared with related species, development in the models is less responsive to external signals, whether adaptive or disruptive. Because plasticity and the role of the developmental environment are particularly hard to study in key models, these areas receive comparatively little attention” (Bolker 2012*).
It’s not that nothing was accomplished by the pioneering methods of Morgan and others. They performed truly ingenious and informative experiments, managing to correlate various mutated sites on chromosomes with observable changes in the organism. The results could be more or less systematized, and they demonstrated a not very shocking truth: the chromosome, in its own unique way, really matters. Furthermore, the peculiar exactness with which it (or, as we would now say, its DNA sequence) is transmitted between generations makes it an inviting thing to investigate in connection with heredity.
But some day it will be one of the great embarrassments to science that generations of researchers took the results of the genetic laboratories and converted them into an ideology of nuclear command and control. Nothing of the sort was indicated by the experimental data, and to this very day there is no basis for saying that a gene, or any combination of genes, is the unqualified cause of particular traits of the organism. The idea, in fact, is inconceivable as soon as we consider the reality of any organic process, which is always to some degree open-ended and subject to “outside” influences.
The nucleus and and cytoplasm are strongly differentiated parts of the cell, but the characterization of one as a command center and the other as recipient or executor of the commands is no longer tenable.
Bolker, Jessica (2012). “Model Organisms: There’s More to Life Than Rats and Flies”, Nature vol. 491 (Nov. 1), pp. 31-3. doi:10.1038/491031a
Dermitzakis, Emmanouil T. and Andrew G. Clark (2009). “Life after GWA Studies”, Science vol. 326 (Oct. 9), pp. 239-40. doi:10.1126/science.1182009
Fong, Yick W., Claudia Cattoglio, Teppei Yamaguchi and Robert Tjian (2012). “Transcriptional Regulation by Coactivators in Embryonic Stem Cells”, Trends in Cell Biology (advance epublication). doi:10.1016/j.tcb.2012.04.002
Keller, Evelyn Fox (2000). The Century of the Gene. Cambridge MA: Harvard University Press.
Kirschner, Marc W. and John C. Gerhart (2005). The Plausibility of Life: Resolving Darwin’s Dilemma. New Haven CT: Yale University Press.
Lillie, Frank R. (1927). “The Gene and the Ontogenetic Process”, Science vol. 46, no. 1712 (Oct. 21), pp. 361-8.
Pederson, Thoru (2011). “The Nucleus Introduced”, Cold Spring Harbor Perspectives in Biology 2011;3:a000521. doi:10.1101/cshperspect.a000521
Pera, Martin F. (2011). “Stem Cells: The Dark Side of Induced Pluripotency”, Nature vol. 471 (Mar. 3), pp. 46-7. doi:10.1038/471046a
Raff, Rudolf A. and Thomas C. Kaufman (1983). Embryos, Genes, and Evolution. Bloomington IN: Indiana University Press.
Sloan, Phillip R. (2012). “How Was Teleology Eliminated in Early Molecular Biology?”, Studies in History and Philosophy of Science, Part C: Studies in History and Philosophy of Biological and Biomedical Sciences vol. 43, no. 1 (March), pp. 140-51. doi:10.1016/j.shpsc.2011.05.013
Stewart, Colin (1997). “An Udder Way of Making Lambs”, Nature vol. 385 (Feb. 27), pp. 769-70. doi:10.1038/385769a0
Yamanaka, Shinya and Helen M. Blau (2010). “Nuclear Reprogramming to a Pluripotent State by Three Approaches”, Nature vol. 465 (June 10), pp. 704-12. doi:10.1038/nature09229
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Steve Talbott :: The Seat of Power: Nucleus or Cytoplasm?