ONTOGENY AND THE HIERARCHY OF TYPES

Abstract— The long history of belief in a parallelism between ontogeny and a hierarchical order of natural things is reviewed. The meaning of von Baerian recapitulation is analyzed and its implications for cladistic methodology are discussed at two levels: ontogeny and homology. The basic problem inherent in the purported parallelism is that the order of natural things (i.e., the taxic approach to homology) is part of the "world of being" of Platonic ideas, whereas ontogeny and phylogeny (i.e., the transformational approach to homology) belong to Plato's "world of becoming." These two "genera of existence," as Plato put it, being and becoming, are incompatible but complementary views of nature.     

Coming changes in accepted wisdom about "osteoporosis"

Here a voice from the past suggests 28 changes that will affect how people study, manage, classify and think about "osteoporoses" today. Those changes depend mainly on two things: (i) "Connecting the dots" between diverse evidence and ideas from many fields and sources in order to find larger "messages" hidden in mountains of often poorly-organized lesser details, (ii) and features of the still-evolving Utah paradigm of skeletal physiology. That paradigm sums contributions from many people who worked in many fields for over 100 years. In one view it is the most important development in skeletal physiology since Rudolf Virchow and others realized approximately 150 years ago that cells provide the basis for human physiology and diseases. This article emphasizes the above messages instead of the details. The messages affect ideas about the nature, pathogenesis, diagnosis, classification, study and management of osteopenias and osteoporoses, as well as some roles of muscle, drugs, hormones, other agents and fatigue damage, in those disorders. Those larger messages also concern how to classify "osteoporosis fractures", how to define bone health, the choice of absorptiometric methods for noninvasive evaluations of bones, osteopenias and muscle strength, and new criteria for selecting patient cohorts for "risk-of-fracture" analyses and in searches for genetic roles in "osteoporoses". Finally, those larger messages identify many new targets for research that should prove unusually useful in clinical and pharmaceutical domains and work.     

"The Image of Limited Good": Comments on an Exercise in Description and Interpretation

Thai peasants exhibit most of the behavioral characteristics that George Foster describes for peasants generally. But the Thai peasant's society is open, and there are things he values as important "goods" that he perceives as unlimited. Such observations make unclear to whom Foster's model of the Limited Good is to apply, and open to question the psychological premises on which his interpretation rests.     

"The orchids have been a splendid sport"--an alternative look at Charles Darwin's contribution to orchid biology

Charles Darwin's work with orchids and his thoughts about them are of great interest and not a little pride for those who are interested in these plants, but they are generally less well known than some of his other studies and ideas. Much has been published on what led to his other books and views. However, there is a paucity of information in the general literature on how Darwin's orchid book came about. This review will describe how The Various Contrivances by Which Orchids Are Fertilised by Insects came into being and will discuss the taxonomy of the orchids he studied. It also will concentrate on some of the less well-known aspects of Darwin's work and observations on orchids-namely, rostellum, seeds and their germination, pollination effects, and resupination-and their influence on subsequent investigators, plant physiology, and orchid science.     

The Obsolete "Anti-Market" Mentality: A Critique of the Substantive Approach to Economic Anthropology

"Analytic work begins with material provided by our vision of things, and this vision is ideological almost by definition. It embodies the picture of things as we see them, and wherever there is any possible motive for wishing to see them in a given rather than another light, the way in which we see things can hardly be distinguished from the nay in which we wish to see them. The more honest and naive our vision is, the more dangerous it is to the eventual emergence of anything for which general validity can be claimed. The inference for the social sciences is obvious, antl it is not even true that he who hates a social system will form an objectively more correct vision of it than he who loves it. For love distorts indeed, but hate distorts still more."     

On the Other "Phylogenetic Systematics"

De Queiroz and Gauthier, in a serial paper, argue that biological taxonomy is in a sad state, because taxonomists harbor "widely held belief" systems that are archaic and insufficient for modern classification, and that the bulk of practicing taxonomists are essentialists. Their paper argues for the scrapping of the current system of nomenclature, but fails to provide specific rules for the new "Phylogenetic Systematics"—instead we have been presented with a vague and sketchy manifesto based upon the assertion that "clades are individuals" and therefore must be pointed at with proper names, rather than diagnosed by synapomorphies. They claim greater stability for "node pointing," yet even their own examples show that the opposite is true, and their node pointing system is only more stable in a purely metaphysical sense detached from characters, evidence, usage of names, and composition of groups. We will show that the node pointing system is actually far LESS stable than the existing Linnaean System when stability is measured by the rational method of determining the net change in taxa (species) included in a particular group under different classifications.     

Growth of microbial populations in nonminimal media: some considerations for modeling

Ramkrishna and his co-workers have developed so-called cybernetic models which purport to describe, among other things, how microorganisms make choices when presented with two or more functionally equivalent, or substitutable, nutrients that are sources of carbon and available energy. In general, however, organisms are presented with choices not just between nutrients that are substitutable for one another, but also between sets of nutrients some of which are by no means substitutable for one another. It is postulated herein that the main ideas of cybernetic modeling apply to these more general choices as they seem to apply to the choices considered by Ramkrishna and his co-workers. Some consequences of the postulate are worked out for steady-state growth situations where two, or in one case three, nutrients limit or potentially limit growth rate. If predicted phenomena are observed experimentally so as to verify the postulate, a significantly improved basis for understanding growth of microorganisms in practical fermentation media as well as in natural situations will be provided by this application of cybernetic modeling ideas.     

God's magnificent law: The bad influence of theistic metaphysics on Darwin's estimation of natural selection

Conclusion It is natural for us — living after the Darwinian Revolution and the neo-Darwinian synthesis — to consider the adoption of evolution by natural selection as unconditionally rational, because it now seems the best theory or explanation of many phenomena. Nonetheless, if we take historical inquiry seriously, as allowing us to probe into the ground of our knowledge, the roots of even this rational Darwinism might be unearthed. Darwinian doctrine betrays a deceptive desire for unity and simplicity of principle, and belief that the mechanistic aspect of nature is of the highest significance. Such crucial but questionable presuppositions are more easily discerned historically, insofar as they chronologically preceded Darwin's particular theoretical conviction and were even set off as a metaphysics of divine law.We have seen how Darwin's teaching about nature emerged within that theistic metaphysics. It emerged in a prior metaphysical debate in his mind between the contemporary belief in special creations and the belief in a designed hierarchy of physical laws. One can hardly deny that Darwin favored the superior side in this contest; but the contest was a narrow one whose basic premises he never clearly criticized. On the one hand, of course, his conviction about a lawful genesis inspired him to take a broad view of things and to seek out important general phenomena. But, on the other hand, it ensured that his new empirical notions would be easily drawn into the preferred cosmology. Historically, this seems to have occurred in Darwin's adoption of Malthus' principle of population and his extension of it to the whole account of descent: Malthusianism was readily attached to an ultimate scheme of things. Consequently, the key concepts that Darwin developed out of his Malthusian views — perfect adaptation and selection — reflect his cosmological prepossession, his desire to express a total and teleological process of creation. Perhaps our most valuable, and most undervalued, token of Darwin's metaphysical orientation is his reliance on a human technique (selective breeding) to explain Nature's way. In sum, to understand Darwin's faith in his grand view of life, we should not ignore the metaphysics that preceded and structured it, the metaphysics that linked the principles of contemporary science to primordial creation. Nor should we fail to see that such a metaphysics leads natural philosophy into a shadowy realm, where system can come to look like science, and one insight like an absolute.     

The "unfrozen fraction" hypothesis of freezing injury to human erythrocytes: a critical examination of the evidence

This paper examines the experimental evidence presented by Mazur and his colleagues to support their hypothesis that the survival of slowly frozen human red blood cells is primarily dependent on the fraction of water that remains unfrozen, rather than on the high concentrations of sodium chloride produced by the formation of ice. This hypothesis is in direct conflict with the general belief that freezing injury under such conditions is caused by the concentration of solutes in the solution surrounding the cells: if the "unfrozen fraction" hypothesis is true, then much of the evidence supporting that belief must be dismissed as mere coincidence. We have reexamined Mazur's data, and have suggested an alternative explanation--that cells which are initially suspended in solutions that are not isotonic differ in their susceptibility to subsequent freezing and thawing, shrunken cells being more resistant and swollen cells more susceptible than normal cells. If this is true then the data can be explained without invoking a direct effect of the unfrozen fraction, solely on the basis of changes in the concentration of the solution surrounding the cells. We cite other experimental evidence, obtained in the absence of freezing, that red blood cells do indeed possess the required property. We further argue that the known effects of variations in cooling and warming rate, and in hematocrit, are able to account for the features observed by Mazur and his colleagues in their three published studies.     

Creation of first malaria vaccine raises troubling questions about "intellectual racism". Interview by Kirsteen MacLeod.

Some of the problems caused by malaria, which places a huge roadblock in front of economic progress in the Third World, may be solved by a new vaccine created by Dr. Manuel Patarroyo, a Columbian physician and researcher. "Imagine how things would be if Canadians had malaria," he says. "Episodes last 10 days, then there are 10 days of recovering. This leaves only 10 days each month in which to do some productive work. Then imagine killing the population of Toronto each year, and you can see the huge toll in terms of the number of yearly deaths globally from malaria." His discovery also raises the issue of "intellectual racism" because of criticism of Patarroyo''s methods by Western scientists. Patarroyo, meanwhile, turned down a $60-million offer for his vaccine, and instead donated the patent to the World Health Organization.     

Plant-pollinator interactions: from specialization to generalization * Waser NM, Ollerton J. eds. 2006. * Chicago: Chicago: The University of Chicago Press. $45 (paperback). 488 pp.

Highly specializedpollination systems, such as figs and their wasp or orchidsthat deceive bees in trying to make them mate with their floralorgans, are intuitively appealing to most people and have, therefore,gained far more attention both in popular and scientific literaturethan the more generalized pollination systems. For a long timethe dominant view was that many, or perhaps even most, plant–pollinatorinteractions were specialized. In 1996 Waser and his colleaguestried to stir things up by writing an article in which theyargued that, in contrast to common belief, generalization waswidespread in plant–pollinator systems. Ten     

Disease Etiologies in Non-Western Medical Systems

This paper argues that disease etiology is the key to cross-cultural comparison of non-Western medical systems. Two principal etiologies are identified: personalistic and naturalistic. Correlated with personalistic etiologies are the belief that all misfortune, disease included, is explained in the same way; illness, religion, and magic are inseparable; the most powerful curers have supernatural and magical powers, and their primary role is diagnostic. Correlated with naturalistic etiologies are the belief that disease causality has nothing to do with other misfortunes; religion and magic are largely unrelated to illness; the principal curers lack supernatural or magical powers, and their primary role is therapeutic . [disease, religion, and magic; ethnomedicine, medical anthropology, non-Western medical systems, shamans]     

The historical context of natural selection: The case of Patrick Matthew

Conclusions It should be evident from the foregoing discussion that one man's natural selection is not necessarily the same as another man's. Why should this be so? How can two theories, which both Matthew and Darwin believed to be nearly identical, be so dissimilar? Apparently, neither Matthew nor Darwin understood the other's theory. Each man's viewpoint was colored by his own intellectual background and philosophical assumptions, and each read these into the other's ideas. The words sounded the same, so they assumed the concepts must als be the same.¹²³ As Ghiselin has pointed out, historians attempting to evaluate Darwin's predecessors have been similarly blinded by a preoccupation with words, without regard to their proper context.¹²⁴ In the case of Matthew, the practice of quoting only brief passages from the appendix to Naval Timber and Arboriculture, without relating them to the rest of his work, has suggested a greater resemblance to Darwin's theory than actually exists.It is clear, both from the use which Matthew made of his ideas and from the philosophical roots of his natural world view, that he could not have arrived at the concept of natural selection by the same thought process which Darwin employed. His discussion of natural selection is presented not as an argument, but as an axiom. No theory is proposed, no evidence marshaled to support it. Natural selection is stated as a fact, a Law of Nature, unquestioned, and presumably, unquestionable.Despite his clamor for recognition as the discoverer of natural selection, Matthew recognized and acknowledged this very fundamental difference between Darwin and himself. In a letter to the Gardener's Chronicle of May 12, 1860, he wrote:To me the conception of this law of Nature came intuitively as a self-evident fact, almost without an effort of concentrated thought. Mr. Darwin here seems to have more merit in the discovery than I have had—to me it did not appear a discovery. He seems to have worked it out by inductive reason, slowly and with due caution to have made his way synthetically from fact to fact onwards; while with me it was by a general glance at the scheme of Nature that I estimated this select production of species as an a priori recognisable fact—an axiom, requiring only to be pointed out to be admitted by unprejudiced minds of sufficient grasp.¹²⁵ In the same letter, Matthew maintained that his ideas had not been accepted because the age was not ripe for such ideas.¹²⁶ Nor, he said, was the present age. He considered the inability of most of Darwin's critics to grasp his theory to be incurable. Yet he did not argue that natural selection should be accepted because of the evidence, but rather, that it should be accepted on faith:Belief here requires a certain grasp of mind. No direct proof of phenomena embracing so long a period of time is within the compass of short-lived man. To attempt to satisfy a school of ultra skeptics, who have a wonderfully limited power of perception of means to ends... would be labour in vain.... They could not be brought to conceive the purpose of a handsaw though they saw its action, if the whole individual building it assisted to construct were not presented complete before their eyes... Like a child looking upon the motion of a wheel in an engine they would only perceive and admire... without noticing its agency in... affecting the purposed end.¹²⁷ Here, then, is the final irony. In a passage urging acceptance of Darwin's theory, a theory which was to banish design and purpose from the natural world, we find echoes of Paley and of Providence.Loren Eiseley has lamented the fact that Matthew did not bring his views into the open, because the amount of ground he was able to cover in a few paragraphs suggests that he might have been able to sustain a longer treatise.¹²⁸ Now that the intellectual and historical context of Matthew's ideas are known, this statement is no longer tenable. Matthew was not a scientist, and his books were not written as biological treatises. His discussions of natural selection were not attempts to cover ground in advancing a particular scientific theory, but were simply reflections of his own assumptions about the natural world.Furthermore, despite Matthew's acceptance of evolution and natural selection, his biological thought was basically conservative on points where Darwin's was radical. Where Matthew saw a series of stable worlds interrupted by violent upheavals, Darwin saw a continuous process of change in an ever-fluctuating world. Where Matthew conceived of species in terms of Aristotelian classes and essences, Darwin revolutionized our concept of species by treating them as populations. Where Matthew saw a world of design and beauty functioning according to natural laws laid down by benevolent Providence, Darwin abolished design and Providence from nature and ushered in a world which cycles ever onward according to laws of chance and probability.It is not even particularly useful to point to Matthew as evidence that evolution was in the air prior to 1859.¹²⁹ His ideas did not represent the first wave of a coming revolution, but were the product of his own personal philosophical outlook, as expressed in the context of the biological thought of the 1830's. Matthew is important in the history of ideas, not simply because he accepted the concept of evolution or thought of something resembling natural selection, but because he did so without overthrowing, in his own mind, any of the basic philosophical assumptions which had underlain biological science since Aristotle. In recognizing Matthew's failure to do so, we are in a position to appreciate more fully the significance of the Darwinian Revolution.     

Bemerkungen zur Systematik der Lituolidae

In his recent publication onLituola grandis,Joseph H. Ziegler also discusses the classification of the Lituolidae in general. Since such evident morphological criteria of the test as type of coiling and apertural character are held to be of no generic value, some ofZiegler's conclusions differ considerably from those of the author and others. Attention is drawn to all the aspects concerning the morphological features of the group which should be taken into account for taxonomic purposes. Some misinterpretations and errors are pointed out and a supplementary list of publications dealing with lituolid Foraminifera is given.     

Introduction to "Cruelty, Suffering, Imagination: The Lessons of J. M. Coetzee"

For over two decades, Nobel laureate J. M. Coetzee has brilliantly addressed issues of interest to anthropologists: the brutal effects of racist tyranny and injustice in South Africa; the reach of empire; guilt and revenge; and the problem of language in particular historical and political moments. In his recent work Elizabeth Costello (2003a), Coetzee confronts a particularly pressing set of contemporary political and ethical concerns, ones to which anthropologists have much to add. In this "In Focus," anthropologists from each of the subdisciplines use Elizabeth Costello as a lens for working through such concerns, addressing a range of questions—including the nature of evil and its relationship to state power, the burden of belief, the legacy of colonialism, the ethical limits of representations of horror, what it means to live in a world of cruelty and suffering, and the power of humans' sympathetic imagination to confront such a world.     

Some of the best online Darwin resources

Ask most men or women in the street who Charles Darwin was and the chances are that they will know something of the work he did: the work that has revolutionised our understanding of the living world and our place in it. The 200th centenary of his birth was in February 2009. Over the 150 years since the publication of his seminal work On the Origin of Species by means of Natural Selection, the quality of his scientific thinking, experimenting and writing — leading to the formulation of his ideas about evolution — has had the single most profound impact on the development of modern biology. During this year a number of dedicated Darwin websites have been created and this edition of Webwatch describes a small number of the best of them.     

From "butyribacterium" to "E. coli": an essay on unity in biochemistry

New ideas in science frequently arise from neglected or distorted antecedents. This essay deals with the idea of biochemical unity, encapsulated in Jacques Monod's well-known phrase, dating from 1954: "Anything found to be true of E. coli must also be true of elephants." An earlier version of this phrase,--"From the elephant to butyric acid bacterium--it is all the same!"--was coined in 1926 by the Dutch microbiologist Albert Jan Kluyver. In that year Kluyver and his associate Hendrick Jean Louis Donker published a celebrated paper, "Unity in Biochemistry." The concept of biochemical unity had many antecedents, but these had never caught on. The Kluyver-Donker paper has often been regarded to provide a boost to biochemical and especially to microbiological thinking. Its interpretations and misinterpretations represent an encapsulated history of biochemistry. The present paper examines the history of the concept of biochemical unity from before to beyond Kluyver, investigates the two "elephant" phrases and their possible relationships, and ends with a discussion of the attractiveness of unifying ideas in science.     

利用“复杂性”解说经济生态发展模式

前言在研究生态经济问题时,常常感到理论上的虚弱,不能从理论上解说生态经济这一庞大、复杂的综合体是如何由生态、经济的相互作用衍变而成的。在生态和经济的复杂性的尺度上我们能把握多少?我们对于生态、经济关系能否及时调控和调控到什么程度?等等,如能从理论上给这些问题作出说明,相信会对生态经济理论及实践都有裨益。为此,我们对生态经济系统作了简化,只讨论了工业增长、农业增长和环境质量三者间的相互作用并用微分方程组表述,试定量说明生态系统、经济系统的复合系统的复杂性和发展。生态系统的复杂性自牛顿建立牛顿力学以来,尽管经典物理     

The design and analysis of microarray experiments: applications in parasitology

Microarray experiments can generate enormous amounts of data, but large datasets are usually inherently complex, and the relevant information they contain can be difficult to extract. For the practicing biologist, we provide an overview of what we believe to be the most important issues that need to be addressed when dealing with microarray data. In a microarray experiment we are simply trying to identify which genes are the most "interesting" in terms of our experimental question, and these will usually be those that are either overexpressed or underexpressed (upregulated or downregulated) under the experimental conditions. Analysis of the data to find these genes involves first preprocessing of the raw data for quality control, including filtering of the data (e.g., detection of outlying values) followed by standardization of the data (i.e., making the data uniformly comparable throughout the dataset). This is followed by the formal quantitative analysis of the data, which will involve either statistical hypothesis testing or multivariate pattern recognition. Statistical hypothesis testing is the usual approach to "class comparison," where several experimental groups are being directly compared. The best approach to this problem is to use analysis of variance, although issues related to multiple hypothesis testing and probability estimation still need to be evaluated. Pattern recognition can involve "class prediction," for which a range of supervised multivariate techniques are available, or "class discovery," for which an even broader range of unsupervised multivariate techniques have been developed. Each technique has its own limitations, which need to be kept in mind when making a choice from among them. To put these ideas in context, we provide a detailed examination of two specific examples of the analysis of microarray data, both from parasitology, covering many of the most important points raised.