From differential display to DNA microarrays--a personal account

This article is a tribute to Dr. Arthur Pardee, one of the most innovative and brilliant scientists of our time, on the occasion of his 85th birthday. In this partially perspective and partially review piece, I look back how fate, by twist and turn, has led me eventually to his lab at Harvard where we worked out the Differential Display technology from scratch, how the method has revolutionized the field of gene expression analysis and where DD is taking us in the "era" of DNA microarrays.     

INTRODUCTION

The Oak Spring Garden Library, a legacy of Rachel Lambert Mellon (1910–2014) and now part of the Oak Spring Garden Foundation, contains the archive of John Bradby Blake (1745–1773), a young trader who worked for the British East India Company in the late 1760s and early 1770s in Canton (Guangzhou) and Macau. The archive provides an unusually detailed insight into Bradby Blake's life and botanical work, including his attempts to send living plants back to England. The archive also contains almost 200 pieces of exquisitely detailed early British‐Chinese hybrid botanical art, which Bradby Blake prepared with a Chinese artist, Mauk‐Sow‐U. With their emphasis on botanical detail and careful depiction of the detailed structure of flowers, these illustrations are as accurate as any produced at this relatively early date in the post‐Linnaean development of botanical science.     

Pictures of microbiology -- the biofilm imaging facility under Dr. David C. White

This contribution honoring David C. White (DC) summarizes the five years I interacted with him on a daily basis in his laboratory. Over this time we worked on many different projects all tied together by the unifying principle now recognized as central to bacterial life in nature: biofilms. My goal is to convey some of the excitement and joy of working with DC and, from my perspective, that means telling how the Biofilm Imaging Facility at the Center for Environmental Biotechnology (CEB) came into existence and describing some of the projects on which DC and I worked.     

New data on the distribution of the Upper Lena form of grayling (Thymallidae) in the basin of Lake Baikal and its taxonomic status

The habitation of the Upper Lena form of grayling in the upper reaches of the Tiya (the northwestern tributary of Lake Baikal) and Barguzin rivers, where Baikal grayling Thymallus baicalensis Dyb. also occurs, was established. The listed forms can be diagnosed from the body coloration, dorsal fin pattern, combination of meristic characters, as well as by molecular-genetic methods. The sympatric habitation of the Upper Lena and Baikal graylings in the northern tributaries of Baikal, considerable phenotypic and genetic differences, as well as the absence of individuals with intermediate characters, make it possible to consider them as independent species. The results indicate the need to revise the intraspecies structure of the Arctic grayling T. arcticus (Pall.) and the entire genus Thymallus. The localization of populations of the Upper Lena grayling in the upper reaches of Baikal tributaries testifies to its possible penetration of the Baikal basin by means of temporary river catchments that formed in the past and which are probable at present at watersheds with the Lena River. A wider distribution of this form is apparently hindered by the pressure of aboriginal species.     

Demarcating public from private values in evolutionary discourse

What I suggest we can see in this brief overview of the literature is an extensive interpenetration on both sides of these debates between scientific, political, and social values. Important shifts in political and social values were of course occurring over the same period, some of them in parallel with, and perhaps even contributing to, these transitions I have been speaking of in evolutionary discourse. The developments that I think of as at least suggestive of possible parallels include the progressive encroachment of public values into the private domain of post-World War II American life, the cold war, the rise of consumerism, and the flowering of what Christopher Lasch calls a narcissistic individualism.³⁵ In popular language, the 1960s gave birth to the me generation. Perhaps the most tantalizing analogue is suggested by Barbara Ehrenreich's argument for the emergence of a new meaning (and measure) of masculinity — an ideal of masculinity measured not by commitment, responsibility, or success as family provider, but precisely by the strength of a man's autonomy in the private sphere, his resistance to the demands of a hampering female.³⁶ It is tempting to speculate about possible connections between changes in scientific discourse and developments in the social and political spheres, but such connections, however suggestive, would clearly have to be demonstrated.For now, however, I want to focus on another kind of change —a transformation not so much in the social or political sphere as in the scientific sphere. I make this turn, or return, in support of a more complex account of scientific change that incorporates reverberations within the scientific communty along with social and political changes.     

Ernst Mayr: Biologist-historian

Ernst Mayr's historical writings began in 1935 with his essay Bernard Altum and the territory theory and have continued up through his monumentalGrowth of Biological Thought (1982) and hisOne Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought (1991). Sweeping in their scope, forceful in their interpretation, enlisted on behalf of the clarification of modern concepts and of a broad view of biology, these writings provide both insights and challenges for the historian of biology. Mayr's general intellectual formation was guided by the GermanBildung ideal, with its emphasis on synthetic and comprehensive knowledge. His understanding of how to write history was inspired further by the example of the historian of ideas Arthur Lovejoy. Some strengths and limitations of this approach are explored here through attention to Mayr's treatment of the French biologist J.-B. Lamarck. It is contended that Mayr's contributions to the history of biology are not restricted to his own very substantial historical writings but also include his encouragement of other scholars, his development of an invaluable archive of scientific correspondence, and his insistence that historians who write about evolution and related subjects acquire an adequate understanding of the principles of Darwinian biology.This paper was originally delivered at the biennial meeting of the International Society for the History, Philosophy, and Social Studies of Biology, held in Brandeis in July 1993, in the special session organized by John Greene on Ernst Mayr's contributions to systematics, evolutionary theory, and the history and philosophy of biology. The paper is presented here with only slight modifications of the original, oral presentation. As indicated in the text, a full assessment of Mayr's historical work, including situating that work in the context of Mayr's other work and contemporary developments in the history of science, would require a much more extensive study than I have been able to undertake here.     

Husserl's Crisis as a crisis of psychology

This paper places Husserl's mature work, The Crisis of the European Sciences, in the context of his engagement with--and critique of--experimental psychology at the time. I begin by showing (a) that Husserl accorded psychology a crucial role in his philosophy, i.e., that of providing a scientific analysis of subjectivity, and (b) that he viewed contemporary psychology--due to its naturalism--as having failed to pursue this goal in the appropriate manner. I then provide an analysis of Husserl's views about naturalism and scientific philosophy. Some central themes of the Crisis are traced back to Husserl's earlier work and to his relationship with his teacher, Franz Brentano, with whom he disagreed about the status of "inner perception" as the proper scientific method for a phenomenological analysis. The paper then shows that Husserl was well aware of at least one publication about the crisis of psychology (Bühler's 1927 book), and it teases out some aspects of the complicated relationship between Husserl and members of the Würzburg School of thought psychology: The latter had drawn on Husserl's writings, but Husserl felt that they had misunderstood his central thesis. I conclude by placing Husserl's work in the wider context of scientific, cultural, and political crisis-discourses at the time.     

Thomas huxley: Fossils,persistence, and the argument from design

Conclusion In struggling to free science from theological implications, Huxley let his own philosophical beliefs influence his interpretation of the data. However, he was certainly not unique in this respect. Like the creationists he despised, he made many important contributions to the issue of progression in the fossil record and its relationship to evolutionary theory. Certainly other factors were involved as well. Undoubtedly, just the sheer inertia of ideas played a role. He was committed to a theory of type and was heavily influenced by von Baer, who argued that one could not rate the different types as being higher or lower than the others. By the mid-1850s his animosity toward Owen had become extreme and he tried to discredit the man whenever possible; yet, as I have pointed out, he also was more than willing to cite Owen's early work when it suited his needs.But I believe the crucial factor in Huxley's eventually accepting progression was that he finally disassociated it from the idea of divine plan. This happened gradually through the 1860s and 1870s, as more and more fossil finds provided support for Darwin's theory. In evaluating this new evidence that supported gradualism, Huxley also realized that progression was an intrinsic part of Darwin's theory:The hypothesis of evolution supposes that at any given period in the past we should meet with a state of things more or less similar to the present, but less similar in proportion as we go back in time... if we traced back the animal world and the vegetable world we should find preceding what now exist animals and plants not identical with them, but like them, only increasing their differences as we go back in time, and at the same time becoming simpler and simpler until finally we should arrive at that gelatinous mass which, so far as our present knowledge goes, is the common foundation of all life.In concluding his first lecture to the Americans, he told them: The hypothesis of evolution supposes that in all this vast progression there would be no breach of continuity, no point at which we could say This is a natural process, and This is not a natural process.⁸⁵ Finally for Huxley, progression was no longer linked to Divine Plan.     

Ultrastructural localization of monoamines in the central nervous system of Lumbricus terrestris (L.) with remarks on neurosecretory vesicles

Summary The cerebral ganglion and the ventral nerve cord of Lumbricus terrestris have been studied with the electron microscope. The results are as follows: In the neuropile small granular vesicles (300 to 500 Å) occur in some varicose nerve fibres after fixation with potassium permanganate. This indicates the presence of noradrenaline. Sometimes only a few of the vesicles produce a positive reaction. After incubation with -methyl-noradrenaline the numbers of nerve terminals with small granular vesicles greatly increase, indicating the presence of dopamine and/or 5-hydroxytryptamine. In this case the reaction is now complete. The number of small granular vesicles is largest in the terminal swellings.These findings are consistent with histofluorescence, chemical, and microspectrofluorometric analyses, which have demonstrated noradrenaline, dopamine, and 5-hydroxytryptamine in neurones in the central nervous system.Large granular vesicles (600 to 900 Å) are to be found in some perikarya, not identical with neurosecretory cell bodies. In this case the granular vesicles in the axon are smaller and fewer. This indicates a simultaneous proximo-distal transport and gradual decrease in size of the granular vesicles. The intraneuronal distribution of the vesicles is in agreement with the distribution of the fluorophores in the fluorescent neurones.Neurosecretory neurones are found most likely not to contain monoamines.This work was supported by grants from the Helge Axison Johnson Foundation, the Magn. Bergvall Foundation, and the Roy. Physiographic Society at Lund.I am greatly indebted to Mrs. Lena Eriksson, Miss Rita Jönsson, Miss Inger Norling, Mrs. Lena Svenre, and Mr. Henryk Keff for their excellent technical assistance.     

Pathogenesis and antigenic characterization of a new East European subtype 3 porcine reproductive and respiratory syndrome virus isolate

Background  

Porcine reproductive and respiratory syndrome virus (PRRSV) is divided into a European and North American genotype. East European PRRSV isolates have been found to be of the European genotype, but form different subtypes. In the present study, PRRSV was isolated from a Belarusian farm with reproductive and respiratory failure and designated "Lena". Analyses revealed that Lena is a new East European subtype 3 PRRSV isolate. The main purpose of this investigation was to study the pathogenesis and antigenic characteristics of PRRSV (Lena).     

Mendel's experiments: A reinterpretation

Conclusion My conclusion is that Mendel deliberately, though without any real falsification, tried to suggest to his audience and readers an unlikely and substantially wrong reconstruction of the first and most important phase of his research. In my book I offer many reasons for this strange and surprising behavior,⁵³ but the main argument rests on the fact of linkage. Mendelian genetics cannot account for linkage because it was based on the idea of applying probability theory to the problem of species evolution. Central to the theory is the law of probability according to which the chance occurrence of a combination of independent events is the product of their separate probabilities. This is the common basis of Mendel's first and second laws, but this is why Mendel's second law on independent assortment is enunciated in too general a way. From Morgan's work we now know that characters may not always be independent if their genes are located very close one to the other on the same chromosome. And this was also the basis of Mendel's personal drama: he surely observed the effects of linkage, but he had no theoretical tools with which to explain it. So he presented his results in a logical structure consistent with the central idea of his theory. Had he described the real course of his experiments he would have had to admit that his law worked for only a few of the hundreds of Pisum characters — and it would thus have been considered more of an exception than a rule. This is why he insisted on the necessity of testing the law on other plants, and this is why in his second letter to Carl Nägeli he admits that the publication of his data was untimely and dangerous.⁵⁴.We can argue that already in 1866 Mendel was less confident that his so-called second law had the same general validity as the first — and that later he lost his confidence altogether. Contemporary testimony indicates that in the end he became as skeptical as all his contemporaries as to the scientific relevance of his theory.⁵⁵ But he was wrong. His research is in no way the fruit of methodological mistakes or forgery, and it remains a landmark in the history of science. He was only the victim of a strange destiny in which the use of probability theory was responsible, at the same time, for the strength and for the weakness of his theory. We must still consider him the father and founder of genetics.     

COMMENT ON RECENT PUBLICATIONS

Mr W. Gilbert Hartley was the Convenor of the Electrical Fishing Working Party for E.I.F.A.C. and until his retirement he worked at the Salmon and Freshwater Fishery Laboratory of the British Ministry of Agriculture, Fisheries and Food. He is recognised internationally as an expert on the use of electricity on fish. We are therefore privileged to publish his comments on this subject .
E ditor     

李济先生与周口店研究：纪念李济先生诞辰100周年

李济先生是中国考古学的奠基人,中国第一位人类学家。他毕生从事考古学研究,著作等身,桃李满天下。他的功绩主要体现在安阳殷墟的发掘与研究上,考古学的其他方面亦建树甚丰。本文仅就李先生在中国旧石器考古草创时期,特别是在周口店本世纪３０年代初发掘方法改革中的贡献等方面作简要的介绍。以此纪念济先生诞辰１００周年。为使读者了解他取得巨大成就的历史背景,对其生平亦作点录。     

Observations on the differentiationin vitro of mouse metanephros

Summary Metanephros of mouse embryos was explanted at the 11th day of gestation and culturedin vitro on the surface of a plasma clot for up to 7 days. Microscopic sections were cut from cultures fixed every day; the differentiation process was followed and compared with development under normal conditions. The ureter branches out and gives rise by means of dichotomous division to straight canals, lined by a light, columnar epithelium, which correspond to collecting ducts. Around the blind ends of their terminal branches, mesenchyme condenses and forms caps, in which the layer of cells in contact with the ducts acquires a palisade-like appearance. Subsequently, vesicles differentiate from the caps, representing the first rudiment of the nephron. The next stage is the change of the vesicle to an S-shaped tubule, the lower end of which becomes crescentic or bowl-shaped and is the first anlage of Bowman's capsule: the upper end connects with the collecting duct.The developmentin vitro goes on at a much slower rate than in normal conditions, and the nephron does not go beyond the stage of S-shaped tubule; however, the general pattern of development is the same in both situations, except for the absence in culture of blood vessels and therefore also of the glomerular anlage. It should be assumed that glomerular vessels are not necessary in order to shape the first anlage of Bowman's capsule. The connection of the nephron with the collecting duct, generally recognized to occur at the S-tubule stage, was sometimes already found at the vesicle stage, both in cultures and in normal development.Dedicated with warm affection to Prof. Antonio Pensa on his 94th birthday — Research done with the help of means provided by the U.S. Atomic Energy Commission (NYO-3355-30), Euratom (043-65-1 BIOI) and the Italian C.N.R. — Thanks are due to Dr. Elena Vivori for her very kind help in revising the English text.     

Personal reminiscences about Morton Grossman and the founding of the Center for Ulcer Research and Education (CURE)

The Center for Ulcer Research and Education (CURE) from its onset was primarily the work of one man: Professor Morton Grossman, or "Mort" as he was known and called by all. Mort's legacy includes a large body of scientific publications, the first National Institutes of Health Digestive Diseases Center (CURE), and, most importantly, a group of scientists who have become academic leaders and who have made important contributions in the fields of upper gastrointestinal (GI) tract secretion, hormones and receptors, mucosal defense mechanisms, the design and conduct of randomized clinical trials, and ulcer epidemiology. Indeed, Mort is considered to be a founding father of modern academic GI research. I was fortunate to have known and worked with Mort and would like to memorialize his contributions so that his memory can inspire the next generation of academicians.     

Studies on the nephron of an elasmobranch fish Scyliorhinus stellaris (L.)

Summary The nephron of the elasmobranch Scyliorhinus stellaris was studied by macerating kidneys of newly hatched specimens in a solution of arsenic anhydride and by sectioning material of the same age and of late embryos. It was found that each nephron consists of (a) a dorsal conical portion containing a skein of canals, loosely intertwined and immersed in blood sinuses, (b) a Malpighian corpuscle, (c) a ventral portion formed by a tightly packed bundle of five tubules. It was not possible to disentangle the ventral tubules so as to recognize their sequence. It may be stated that the neck, originating from the corpuscle and coming back to it after a bend, forms two of such tubules; two more are similarly connected at the distal end by another loop; one forms the collecting duct. The dorsal part of the nephron contains two canals, greatly folded and interlaced. When completely dissociated they appeared to consist of (a) a larger and longer one, corresponding to the brush border portion of all vertebrates (it is thick for most its length, but becomes thin at one end), and (b) a smaller and shorter one, lined by low cells throughout, with no brush border. Although it is not possible to decide so far which of these canals precedes the other, it was ascertained that they are not continuous with each other inside the dorsal portion, but are connected by means of a loop situated in the ventral bundle. The renal tubule passes by, and adheres to the corpuscle four times. The small dorsal canal, although it does not correspond, either in topography or in structure, to the features of the alleged special segments, may be something peculiar to elasmobranchs.Dedicated to Professor Wolfgang Bargmann on his 60th birthday. — Research carried out under contracts with the U. S. Atomic Energy Commission (NYO-3355-3) and Euratom (043-65-1 BIOI), and supported by the Italian C. N. R. and Ministry of Education. — Thanks are due to Dr. P. Dohrn and the staff of the Zoological Station for their help in securing the material and to Dr. Elena Vivori who revised the English.     

Intramolecular charge transfer in the bacteriorhodopsin mutants Asp85-->Asn and Asp212-->Asn: effects of pH and anions.

The photovoltage kinetics of the bacteriorhodopsin mutants Asp212-->Asn and Asp85-->Asn after excitation at 580 nm have been investigated in the pH range from 0 to 11. With the mutant Asp85-->Asn (D85N) at pH 7 no net charge translocation is observed and the signal is the same, both in the presence of Cl- (150 mM) and in its absence (75 mM SO4(2-)). Under both conditions the color of the pigment is blue (lambda max = 615 nm). The time course of the photovoltage kinetics is similar to that of the acid-blue form of wild-type, except that an additional transient charge motion occurs with time constants of 60 microseconds and 1.3 ms, indicating the transient deprotonation and reprotonation of an unknown group to and from the extracellular side of the membrane. It is suggested that this is the group XH, which is responsible for proton release in wild-type. At pH 1, the photovoltage signal of D85N changes upon the addition of Cl- from that characteristic for the acid-blue state of wild-type to that characteristic for the acid-purple state. Therefore, the protonation of the group at position at 85 is necessary, but not sufficient for the chloride-binding. At pH 11, well above the pKa of the Schiff base, there is a mixture of "M-like" and "N-like" states. Net proton transport in the same direction as in wild-type is restored in D85N from this N-like state. With the mutant Asp212-->Asn (D212N), time-resolved photovoltage measurements show that in the absence of halide ions the signal is similar to that of the acid-blue form of wild-type and that no net charge translocation occurs in the entire pH range from 0 to 11. Upon addition of Cl- in the pH range from 3.8 to 7.2 the color of the pigment returns to purple and the photovoltage experiments indicate that net proton pumping is restored. However, this Cl(-)-induced activation of net charge-transport in D212N is only partial. Outside this pH range, no net charge transport is observed even in the presence of chloride, and the photovoltage shows the same chloride-dependent features as those accompanying the acid-blue to acid-purple transition of the wild-type.     

The excluded philosophy of evo-devo? Revisiting C.H. Waddington's failed attempt to embed Alfred North Whitehead's "organicism" in evolutionary biology

Though a prominent British developmental biologist in his day, a close friend of Theodosius Dobzhansky, and a frequent correspondent with Ernst Mayr, C.H. Waddington did not enter the ranks of "architect" of the Modern Synthesis. By the end of his career, in fact, he recognized that other biologists reacted to his work "as though they feel obscurely uneasy"; and that the best that some philosophers of biology could say of his work was that he was not "wholly orthodox" (Waddington 1975c, 11). In this essay, I take Waddington's self-assessments at face value and explore three potential reasons why his work did not have more of a direct impact: Waddington's explicit support for the philosophy of Alfred North Whitehead; a lack of institutional support; and Waddington's occasional marginalization from the core network of American neo-Darwinians. Though excluded from the Modern Synthesis in the mid-20th century, it now appears that Waddington's work does undergird the emerging evo-devo synthesis. Whether this indicates concomitant, if implicit, support for Whiteheadian philosophy is an interesting question not explored here.     

The decay of linkage disequilibrium under random union of gametes: how to calculate Bennett's principal components

How rapidly does an arbitrary pattern of statistical association among a set of loci decay under meiosis and random union of gametes? This problem is non-trivial, even in the case of an infinitely large population where selection and other forces are absent. J. H. Bennett (1954, Ann. Hum. Genet. 18, 311-317) found that, for an arbitrary number of loci with an arbitrary linkage map, it is possible to define measures of linkage disequilibrium that decay geometrically with time. He found a recursive method for deriving expressions for these variables in terms of "allelic moments" (the factorial moments about the origin of the "allelic indicators"), and expressions for the allelic moments in terms of his new variables. However, Bennett no where stated his recursive algorithm explicitly, nor did he give a general formula for his measures of linkage disequilibrium, for an arbitrary number of loci. Recursive definitions of Bennett's variables were obtained by Lyubich. However, the expressions generated by these recursions are not the same as those found by Bennett. (They do not express Bennett's variables as functions of the allelic moments.) Lyubich's derivations employ genetic algebras. Here, I present a method for obtaining explicit expressions for Bennett's variables in terms of the allelic moments. I show that the transformation from the allelic moments to Bennett's variables and the inverse transformation always have the form that Bennett claimed. (This transformation and its inverse have essentially the same form.) I present general recursions for calculating the coefficients in the forward transformation and the coefficients in the inverse transformation. My derivations involve combinatorial arguments and ordinary algebra only. The special case of unlinked loci is briefly discussed.     

THE THREE G's Meeting the Invertebrate Cell Culture Pioneers: Goldschmidt, Gaw, and Grace

It was my good fortune to meet personally the three invertebrate cell culture pioneers,Richard Goldschmidt,Zan-Yin Gaw,and Thomas D.C.Grace (Fig.1).In 1951 I met Goldschmidt at a symposium in Cold Spring Harbor,but I only knew that he was a prominent geneticist.I had no idea about his insect cell culture work at Yale University and daily contacts with Ross G.Harrison.In 1959 Zan Yin Gaw in Wuhan successfully cultured monolayers of silkworm cells for more than one year.I reported his breakthrough achievement at the 11th International Congress of Entomology in Vienna in 1960,but his work was completely ignored outside China.In 1982 Gaw invited me to Wuhan where he told me that he studied in the United States in the 1930s,working as postdoctoral scientist at the Rockefeller Institute,where he was daily meeting William Trager,and later at Yale University in the Osborn Laboratory,where he was inspired by Harrison.T.D.C.Grace worked in my laboratory at Rockefeller University during 1957 and 1958,then returned to CSIRO in Canberra,Australia.