Abstract
“Which came first, the chicken or the egg?” For all its innocence, this is a question which, as this paper will show, obliges one to think deeply about the terms in which one ultimately seeks to explain biological systems. “A hen is only the egg’s way of making another egg”, in Butler’s (1878)1 apt phrase, sums up the view that organisms can most simply be explained as the results of causes laid out in the egg or, in contemporary terms, as the results of their inherited sets of genes. Today’s biologist might well extend the metaphor and say that “organisms are only expressions of a sequence of the four nucleotides of DNA”. This eminently successful way of explaining biological systems is examined in the first part of the present paper. Yet there remains a nagging worry about this viewpoint. Can this really be the whole story? In the second section, I attempt to identify the possible missing element and consider whether the other attributes of organisms might be more than mere genetic epiphenomena. In the third section I suggest how, due to the continuing impact of now outdated methodological assumptions, we face a choice of methods which greatly affects our ability to tackle the real problem of biological organization.
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Notes and References
Butlers. S. 1878, Life and Habit. London: Trubner.
Preformation dominated eighteenth century thinking about the origins of biological systems (Hartsoeker’s drawing dates from 1694), chiefly due to the overturning of the notion of spontaneous generation, on which the earlier idea of “epigenesis” had depended (see
Needham, J., 1934, A History of Embryology, Cambridge: Cambridge University Press.
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The “provisional theory of pangenesis” in Darwin, C., 1868, The Variation of Animals and Plants under Domestication, London: Murray.
It is difficult for us now to put ourselves back in Darwin’s conceptual framework, in which heredity and embryonic development were in effect indistinguishable. The embryo as such was poorly understood, even descriptively. His contemporary, Haeckel, considered embryonic stages (seen as recapitulating phylogenetic stages) to be the actual manifestations and vehicles of heredity. Against this view, His argued that embryogenesis must be explained in terms of physical causes at the time of development.
Weismann, A., 1893, The Germ-Plasm. A Theory of Heredity, London: Walter Scott. His theory was originally proposed in 1885.
Weismann hypothesized a process of assignment of specific nuclear formative factors to an organized pattern in the egg cytoplasm. Hertwig and Wilson, whose writings vividly illustrate the struggle to clarify the domains of genetics and embryology at the time, recognized clearly that Weismann’s theory implied preformed egg organization and that it did not explain embryonic regulation (first shown by Driesch in 1891) or regeneration.
Hertwig, O., 1896, The Biological Problem of To-day, London: Heinemann; Wilson, E.B., 1896, The Cell in Development and Inheritance, London: MacMillan.
Thompson, D’A. W., 1917, On Growth and Form, Cambridge: Cambridge University Press.
D’Arcy Thompson’s influence is notoriously difficult to characterize, but is probably considerable (see.
Medawar, P.B. in Thompson, R.D’A., 1958, D’Arcy Wentworth Thompson. The Scholar-Naturalist, 1860–1948, London: Oxford University Press.
Like His, his aim was “The study of organic Form by methods which are the common-place of physical science. It is the skilled and learned mathematician who must ultimately deal with such problems” (Preface). He was unconcerned with genetics or with embryology as such. As theories of development or evolution, modern versions of his approach (e. g. approaches based on the concepts of allometry and heterochrony) are very limited: they fail, for example, to explain changes in number or differentiation of body parts (see.
Horder, T.J. 1989. Syllabus for an embryological synthesis. In Complex Organismal Functions; Integration and Evolution in Vertebrates. Wake, D.B. and Roth, G., eds, pp 315–348. Chichester: Wiley.
“Neo-Darwinism” or “the modern evolutionary synthesis” of the 1930s and 1940s was primarily aimed at bridging the divide between genetics and evolution. Gradualistic evolution and adaptation were shown to be compatible (through population genetics) with the discrete effects of genes and mutations. The aim was achieved at the cost of considerable abstraction and detachment from specific data, particularly concerning phylogenesis, the specific forms of organisms and the actual phenomenology of embryogenesis. Changes in adult morphologies were seen as the results of gradualistic “growth” changes, using concepts like allometry, in turn linked to genetics in concepts such as “rate genes” and statistical gene combinations (Wright’s “shifting balance”). For analysis of methodological limitations see;.
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Horder (1989) (op cit).
Regeneration, metaplasia and embryonic regulation all demonstrate the retention (and potential expressibility) of the entire genome in most cells throughout the life cycle, later confirmed by nuclear transplantation.
Figure 14.8.
Boveri, T., 1910, Die Potenzen der Ascaris-Blastomeren bei abgeanderter Furchung: Zugleich ein Beitrag zur Frage qualitativ ungleicher Chromosomenteilung, Festschr. R. Hertwig, Jena. III; 133-214.
Harrison, R.G., 1945, Relations of symmetry in the developing embryo, Trans. Conn. Acad. Arts Sci. 36: 277–330.
Spemann, H., 1938, Embryonic Development and Induction, New Haven: Yale University Press.
Waddington, C.H., 1940, Organisers and Genes, Cambridge: Cambridge University Press.
Waddington, C.H., 1957, The Strategy of the Genes, London: Allen and Unwin.
Figure 14.9; Derived from.
Wolpert, L., 1974, “The Development of Pattern and Form in Animals”, Oxford Biology Reader No 51. Oxford: Oxford University Press.
Figure 14.10; For details see.
Lawrence, P.A., 1992, The Making of a Fly. The Genetics of Animal Design, Oxford: Blackwell Scientific Publications.
On the positional information model, cells must have morphogen receptors capable of discriminating levels to a degree equal to the number of morphological positions at which cells undergo alternative forms of differentiation. A particular difficulty for locus-specific control mechanisms concerns the differentiation of identical structures at multiple, different locations: on the positional information model, specificity would still be needed at each locus even if the same cell type differentiates (as acknowledged in the associated concept of “non-equivalence”). This independence of locus receptivity and differentiation makes it difficult to see how evolution could change pattern, since two, matching mutations serving the two functions would always be needed simultaneously.
Lewis, E.B., 1978, A gene complex controlling segmentation in Drosophila. Nature 276: 565–570.
“It has become almost a truism to assume that the position of a gene, either on a chromosome or else within a nucleus, is of critical importance to its functional capabilities”.
John, B. and Miklos, G., 1988, The Eukaryote Genome in Development and Evolution, London: Allen and Unwin, p193.
The concept of master genes — hypothesized as functioning to control and integrate groups of genes mediating pattern or mediating the differentiation of specific cell types (see
Davidson, E.H. and Britten, R.J., 1979, Regulation of gene expression: possible role of repetitive sequences. Science 204: 1052–1059.
MacIntyre, R.J., 1982, Regulatory genes and adaptation: past, present, and future, Evol. Biol., 15: 247–285.
— carries preformationist implications. Such overall control elements may be unnecessary given that control might be explained as the result of a cascade, whereby the products of one structural gene are used as signals for another, and so on in a chain reaction.
Although maternally imposed patterning in the egg cytoplasm is well established, this mechanism has occupied a diminishing place in developmental theories. Adequate testing increasingly reveals other mechanisms (e. g. see.
Lambie, E.J. and Kimble, J., 1991, Genetic control of cell interactions in nematode development. Ann. Rev. Genet. 25: 411–436). Most maternal factors are involved in forming the egg cell as such and their role in pattern control must be restricted if they are not to limit zygotic variation and rates of possible future evolution. Compared to other patterning mechanisms, their role is always very limited and is minimal in vertebrates.
Examples of functional modulation of morphology are reviewed in.
Goss, R.J., 1978, The Physiology of Growth, New York: Academic Press.
Horder, T.J., 1983, Embryological bases of evolution. In Development and Evolution, Goodwin, B.C., Holder, N. and Wylie, C.C, eds, pp 315–352. Cambridge: Cambridge University Press.
Holmes, S.J., 1948, Organic Form and related Biological Problems, Berkeley: University of California Press.
Why such evidence has not generally featured in theories of development is unclear; apart from the Lamarckian overtones and the difficulties of defining the underlying genetic and cellular mechanisms (in common with many developmental phenomena), 20 there is perhaps a tendency to think of “environmental factors” as external to the organism: i. e. to disregard “internal environmental” factors.
Darnell, J., Lodish, H. and Baltimore, D., 1990, Molecular Cell Biology, New York: Scientific American Books.
Three types of cause, commonly combined in biological phenomena, can loosely be distinguished; the source of the specificity of the factor or function under consideration (an “instructive” cause); the conditions needed to trigger or regulate events (“elective”); and other preconditions necessary for events, but not directly contributing to them (“facultative”, “permissive”).
There are many contending definitions of the term “genetic”.
Kitcher, P., 1982, Genes Brit. J. Phil. Sci. 33; 337–359.
Even the nearest to an ultimate definition — the description of a specific DNA sequence — involves ambiguities (e. g. whether to include variations between individuals, introns, initiating and control regions). The concept of “genetic” factors is not just difficult to define: it is ultimately meaningless, because it cannot be separated from “environmental” factors. The two types of consideration will always interact, because no genetic effects can occur unless they are expressed and expression depends on factors extrinsic to the DNA sequence itself. What is more, there is no complete way of determining the extent of involvement of either consideration, given the complexity of their interactions and the practical impossibility of testing all possible environmental variants. Despite the importance and frequency of the appeals to a supposed separability (as in “nature/nurture” discussions), these points are rarely made and the literature on the subject is extraordinarily restricted. For the best available attempts at clarification see.
Oyama, S., 1985, The Ontogeny of Information. Developmental Systems and Evolution, Cambridge: Cambridge University Press.
Rose, S., Kamin, L.J. and Lewontin, R.C., 1984, Not in Our Genes, Harmondsworth: Penguin Books.
For an important critique of geneticism see.
Tauber, A.I. and Sarkar, S., 1992, The human genome project: has blind reductionism gone too far? Perspect. Biol. Med. 35: 220–235.
The gene concept has always referred primarily to a structural entity. In practice “identifying the gene for a function” means localizing an involved chromosomal site, or sequencing it or its products. These operations are usually merely handles for further practical procedures: the specificity of the products and their functions are usually in themselves of secondary importance. Compared to their structure, the functions of genes, via their products, are difficult to investigate and can never be delimited with certainty. Despite the problems, the search for genetic explanations continues apace.
Owen, M. and McGuffin, P., 1992, The molecular genetics of schizophrenia, Brit. Med. J. 305: 664–665.
Alper, J.S. and Natowicz, M.R., 1992, The allure of genetic explanations, Brit. Med. J. 305: 666.
Figure 14.11; adapted from.
Patten, B.M., 1946, Human Embryology, London: Churchill.
The phenomenon of induction is massively documented and Figure 14.11 summarises many of the known cases. See also.
Nakamura, O. and Toivonen, S., 1978, Organizer — a milestone of a half-century from Spemann, Elsevier: Amsterdam.
Regulation, coordination and precision (potentially to the level of individual cells) of adult pattern (the main reasons for hypothesizing gradients) are explicable by the developmental cascade, as are varieties of distributions and combinations of differentiated cell types. Induction has been a focus for much dispute, largely due to methodological problems (e. g. multi-causality due to double assurance, involvement of competence, reciprocal interactions between inductor and induced tissues) inherent in the analysis of any higher level embryological phenomena. For reviews of these problems and the role of morphogenetic movements and receptivity to inductors see.
Horder (1983) (op cit).
Horder, T.J., 1976, Pattern formation in animal development. In The Developmental Biology of Plants and Animals, Graham, C.F. and Wareing, P.F., eds, pp 169–197. Oxford: Blackwell Scientific Publications.
Induction and positional information are opposing concepts. In induction the control of one cell’s fate is locally determined; only “position” in relation to neighbouring cells is relevant and it is unnecessary that a cell has information about its position in the embryo as a whole. For further discussion see; Hinchliffe and Horder (this volume).
The genetic analysis of Drosophila development (Figure 14.10) illustrates some of the limitations of genetic methodology in general. It is essentially descriptive. Increasingly, it is becoming clear that a full explanation of development requires more than just the identification of genes or description of their products and their spatio-temporal patterns of expression; it also requires explanation of the distributions and interactions of these products, since it is these considerations which determine succeeding gene switches. It is likely that any one switching factor (e. g. the bicoid gradient) is only responsible for a limited number (around three) of spatially distinct patterns as expressed in the next round of gene switches. Pattern is therefore actually built up gradually (i. e. involving multiple interactive, dependent stages — the gene product of one stage having free, direct access to the promoters of other genes which are then selectively switched14 — so that final adult differentiation is not the result of direct one-to-one read out of initial position, e. g. as defined by the bicoid gradient; interactions include induction and morphogenesis.
Horder, 1983, op cit.
Early embryogenesis and mutations affecting segmentation in Drosophila may be poor models for other organisms; e. g. Drosophila embryos do not regulate (see.
Sander in Goodwin et al. (1983) (op cit).
and equivalent (“homeotic”) mutations are unknown in vertebrates.
Horder, 1976;1983, op cit).
See Horder (1989) (op cit).
which includes arguments against the notion of pattern (e. g. limb pattern) genes. There is a wide spectrum of possible relationships between genes and their ranges of effect morphologically; e. g. genes may be locus or organspecific, cell-type specific (with mutations often leading to patchy effects) or may affect metabolism (with mutations having diffuse effects). In all cases pleiotropy may be due to knock-on effects, secondary to the primary gene action. There are major limits to our ability to analyse the genetic programming of pattern; e. g. due to incomplete identification of genes or mutations and difficulties in separating component genes in situations of polygenetic control.
On the evolutionary flexibility of chromosomal organization see.
Berry, R.J., 1977, Inheritance and Natural History, London: Collins.
Wasserman, M., and Wasserman, F., 1992, Inversion polymorphism in island species of Drosophila, Evol. Biol. 26: 351–381.
O’Brien, S.J., and Seuanez, H.N., 1988, Mammalian genome organization: an evolutionary view, Ann. Rev. Genetics 22: 323–351
John and Miklos (1988) (op cit).
As an example of the dispersed mapping of protein molecules originating by duplication from one ancestral form, see.
Wilkie, T.M., Gilbert, D.J., Olsen. S.A., Chen, X-N., Amatruda, T.T., Korenberg, J.R., Trask., B.J., de Jong, P., Reed, R.R., Simon, M.I., Jenkins, N.A. and Copeland, N.G., 1992, Evolution of the mammalian G protein alpha-subunit multigene family, Nature Genetics, 1: 85–91.
Haemoglobin sub-units illustrate dispersed mapping of a single final molecule: see also.
Wissinger, B., Schuster, W., and Brennicke, A., 1991, Trans splicing in Oenotheran mitochondria: nad1 mRNAs are edited in exon and transsplicing Group II intron sequences, Cell 65: 473–482.
Bacteria may not be good models here; they typically show integrated polycistronic genome control and very stable gene sequences in evolution.
Riley, M. and Krawiec, S., 1987, Genome organization. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Neidhardt, F.C., Ingraham, J.L., Low, K.B., Magasanik, B., Schaechter, M. and Umbarger, H.E. eds. pp 967–981. Washington: American Society of Microbiology.
In general gene organization, in higher organisms, tends towards random order. Given appropriate control mechanisms14,22 this is entirely compatible with integrated function. Many special factors may explain instances where particular gene sequences show close relationships; e. g. recent evolution by gene duplication, “supergenes”, “position effects”, linkage disequilibrium, “gene complexes”. On the lack of effect of dissociating neighbouring genes see.
Struhl, G., 1984, Splitting the bithorax complex in Drosophila, Nature 308: 454–457.
John and Miklos (1988) (op cit).
See Horder, T.J., 1991, Molecular biology and evolution: two perspectives. In Developmental Patterning of the Vertebrate Limb, Hinchliffe, J.R., Hurle, J.M. and Summerbell, D. eds, pp 423–438. New York: Plenum.
Horder, T.J., 1993, Three glimpses of evolution. In Formation and Regeneration of Nerve Connections, Sharma, S.C. and Fawcett, J.W., eds. pp 222–238. Boston: Birkhauser.
Nei, M. and Koehn, R.K., 1983, Evolution of Genes and Proteins, Sunderland, MA: Sinauer.
Li, W-H. and Graur, D., 1991, Fundamentals of Molecular Evolution, Sunderland, MA: Sinauer.
“Causality” in the organism may sometimes come to differ widely from the causal chain of events in evolution; e. g. in the case of DNA as the “cause” of RNA and in turn proteins, it seems likely that the evolution of RNA preceded that of DNA (see.
Darnell et al. (1990) (op cit).
Chapter 26). However, other characters (such as the DNA genetic code itself) are so constant and universal among organisms that we can confidently infer their early origin and subsequent evolutionary inflexibility. Sequences of developmental events in extant organisms often provide direct evidence on which evolutionary inferences can be based and sometimes “recapitulate” or retain the record of the evolutionary sequences of events.
Horder, 1993, op cit.
Recombination is evidently almost as basic a property of DNA sequences as the DNA code itself. Maintaining the “integration” of a genome tending towards random order becomes a matter, not only of the selective advantages, matching and compatibility of structural gene products, but also of the regulation of the units of DNA rearrangement.
Plasterk, R.H.A., 1992, Genetic switches: mechanisms and function, Trends in Genetics, 8: 403–406.
and expression control, 11,14 by other, nonexpressed DNA components.
It is easy to think of natural selection as only operating directly on the adult; however, despite its protected circumstances, the embryo is indirectly under even greater selective pressures because multiple adult characters depend on each developmental step; hence the relative evolutionary stability of developmental processes (Horder, 1993, op cit).
The available terminology is inadequate;39 the term “epigenesis” comes closest to covering the concept we have attempted to characterize, but is unsatisfactory because of its connotations as the antithesis of preformation and of genetics.
Roll-Hansen, N., 1978, Drosophila genetics: a reductionist research program, J. Hist. Biol. 11: 159–210.
On vitalism, physico-chemical reduction and the origin and use of “models”, see.
Hall, T.S., 1969, History of General Physiology, Chicago: University of Chicago Press.
Oppenheimer, J.M., 1967, Essays in the History of Embryology and Biology, Cambridge: M.I.T. Press.
Haraway, D.J., 1976, Crystals, Fabrics, and Fields. Metaphors of Organicism in Twentieth-Century Developmental Biology, New Haven: Yale University Press.
Oyama (1985) (op cit).
On the origin of embryological concepts, see.
Needham (1934) (op cit).
Holmes (1948) (op cit).
Oppenheimer (1967) (op cit).
Haraway (1976) (op cit).
Horder, T.J., Witkowski, J.A. and Wylie, C.C., 1985, A History of Embryology, Cambridge: Cambridge University Press.
Gilbert, S.F., 1991 A Conceptual History of Modern Embryology, New York: Plenum.
In this area of biology — notable for its importation of ex-physical scientists, e. g. Turing, Schrodinger, Whitehead, Weiss, Wolpert — many concepts have been borrowed from the physical sciences; e.g. field, polarity, system, double assurance. On the coextensivity of thinking in physical and biological sciences see, for example.
Stebbing, L.S., 1937, Philosophy and the Physicists, Harmondsworth: Penguin.
Hull, D.L., 1974, Philosophy of Biological Science, Englewood Cliffs: Prentice-Hall.
Yoxen, E.J., 1979, Where does Schroedinger’s “What is Life?” belong in the history of molecular biology? Hist. Science, 17: 17–52.
As case histories, see.
Whyte, L.L., 1963, Focus and Diversions, London: Cresset Press.
Fischer, E.P. and Lipson, C., 1988, Thinking about Science. Max Delbruck and the Origin of Molecular Biology, New York: Norton.
“The purpose of this paper is to discuss a possible mechanism by which the genes of a zygote may determine the anatomical structure of the resulting organism. The theory does not make any new hypotheses; it merely suggests that certain well-known physical laws are sufficient to account for many of the facts”.
Turing A.M., 1952, The chemical basis of morphogenesis, Phil. Trans Roy. Soc. 237B: 37–72.
Problems of biological explanation often revolve around a conceptual dichotomy or antithesis, both elements of which very often turn out to be interrelated and equally relevant in the end (e. g. nature/nurture)19 or the bridging of the domains of evolution and genetics.
Horder, 1989, op cit.
Such disjunctions often originate in the way in which data are initially categorized and classified; e. g. the distinguishing of genetics and embryology (as described above), pre-functional and functional phases of development.
Holmes, 1948, op cit.
or morphogenesis from pattern formation and differentiation (see).
Waddington, 1957, op cit.
Wolpert, 1974, op cit.
Many biological concepts are used in a disjunctive or all-or-none manner (e. g. homology, species, phases of life cycle, genotype/phenotype, nature/nurture) leading to typological and saltationist thinking, which can often be seen to create artefacts which misrepresent the underlying continuities of biological processes.38.
It could be argued that in practice what has happened is that, caught between the far more coherent and well-developed fields of genetics and evolution theory, embryology has been conceptualized in conformity with assumptions and expectations derived from other fields.
On the theory of “reducibility of theories” and transitions between levels, see.
Nagel, E., 1961, The Structure of Science, London: Routledge and Kegan Paul.
It has become increasingly recognized that reduction cannot be fully realized in practice, even in the paradigm case of translating between Mendel’s laws and molecular genetics: the rules of translation cannot themselves be closely enough specified (see.
Rosenberg, A., 1985, The Structure of Biological Science, Cambridge: Cambridge University Press.
Hull (1974) (op cit).
Hull, D.L., 1976, Informal aspects of theory reduction, Boston Studies in the Phil. of Science, 32: 653–670.
Similar problems apply to axiomatization; see.
Ruse, M., 1975, Woodger on genetics. A critical evaluation, Acta Biotheoret. 24: 1–13.
Given a large enough scale of view, biological functions and processes (with very few exceptions and in marked contrast to biological structures) can be seen as continuous; e. g. continuity of genome and cell organization across generations, morphogenesis, phases of the life cycle, growth, morphological integration. The discrete manifestations of evolution immediately available to us (e. g. the individuality of organisms, gaps between known species, the quantal nature of mutations) encourage disjunctive thinking.35 However, there must be limits to the size of unit steps of evolutionary change compatible with the survival of intermediate stages (particularly given the requirements for genome integration)11,28 and the concept of the species as a gene pool containing a reservoir of possible variants implies a diffuse, statistical basis for change: the nature of embryogenesis provides strong grounds for inferring a close continuity of morphologies during phylogenesis.
Horder, 1993, op cit.
The term “emergence” refers to the appearance of new (and, by implication, unpredictable) properties as the result of the combination of elements in a complex system.
Nagel, 1961, op cit.
As Nagel argues, whether new properties are “unpredicted” all depends on how well understood the contributing elements are in the first place: if the complexity of the system is adequately recognized the emergent properties become less surprising. A single complex molecule is often a sufficient and fully understandable explanation for high level physiological functions (e. g. haemoglobin). A type of thinking based on emergence underwrites many anti-reductionist claims about biological systems.
Simpson, G.G., 1963, Biology and the nature of science, Science 139: 81–88.
Polanyi, M. 1968, Life’s irreducible structure, Science 160: 1308–1312.
Weiss, P.A., 1971, Hierarchically Organized Systems in Theory and Practice, New York: Hafner.
On laws in biology, see.
Rosenberg (1985) (op cit).
Due to the opportunistic nature of evolution, it is inevitable that there will be few broad generalizations in biology and that most will eventually have exceptions. Only at the level of chemistry (i. e. molecular biology) will laws (in the usual sense of absolute rules) apply. High level concepts such as evolution are more like generalizations than laws.
Fundamental to what I have been saying is the importance of an awareness of the procedures involved in the use of data and of the concepts needed to link them. Embryology has been dogged by the inadequacies of its heritage of concepts and terminology (e. g. epigenesis, organicism, holism, emergence, etc): suspicions regarding their imprecision, abstractness or merely metaphorical character, and of the theories built on them, were often justified.
That the priorities of philosophers of biology should lag behind those of biologists is perhaps inevitable given the philosophers’ dependence on the state of already established scientific knowledge and their traditional affinities with the physical sciences.
Hull, D.L., 1969, What philosophy of biology is not, J. Hist Biol. 2: 241–268.
Hull (1974) (op cit).
For a penetrating analysis of the requirements of scientific method in biology (as applied to psychology), see.
Kaplan, A., 1964, The Conduct of Inquiry, San Francisco: Chandler.
Nagel (1961, op cit).
defines “explanation” as “systematized knowledge”.
Kaplan (1964, op cit, p329).
as “concatenated description… each element of what is being described shines, as it were, with light reflected from all the others”.
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Horder, T.J. (1993). The Chicken and the Egg. In: Othmer, H.G., Maini, P.K., Murray, J.D. (eds) Experimental and Theoretical Advances in Biological Pattern Formation. NATO ASI Series, vol 259. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-2433-5_14
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