CFP "More Too Funky Causation" (Funky III), February 23-24, 2011, Ghent.

The Department of Philosophy and Moral Sciences, Ghent University, Belgium, is proud to announce a call for papers for:
"More Too Funky Causation" (Funky III), February 23-24, 2011.
Keynote speaker is Jeffrey K. McDonough (Harvard): "Leibniz on Agency and Optimal Form"
The conference is the third to explore *funky* notions of causation in historical perspective.
'Funky' causes are defined negatively as those notions of causation that are neither final nor (Humean) efficient causation.
We welcome paper proposals that explore a funky cause in depth. Topics need not be limited to Early Modern topics or figures,
but we would especially welcome papers on formal causation.
Abstracts (no more than 500 words) prepared for blind review should be mailed to Eric Schliesser (nescio2@yahoo.com) by December 1. Inquiries can be directed to same address.

Ravello meeting on Chance and Necessity, part III (last one)

I am at the Ravello meeting on Chance and Necessity in biology, on the 40th anniversary of Jacques Monod's seminal book, and will be posting a few entries while the meeting is going on this week.

The gathering is organized by Giorgio Bernardi, sponsored by International Union of Biological Sciences and Istituto Italiano di Studi Filosofici.

What follows are the raw and somewhat selective notes only, in order of presentation of the various speakers. Hopefully this will provide a feeling for what the meeting is about and generate some discussion. Throughout, parenthetical comments are my own, unless otherwise noted.

Denis Duboule, Constraints (necessity) and flexibility (chance) in the evolution of vertebrate morphologies.

Across vertebrates the structure of proximal bones is strongly constrained, while there is a lot of variation in distal structures, like the number and shape of digits. This pattern appears to be related to the pattern of deployment of a cluster of Hox genes during the development of vertebrate limbs. It is the differential regulation of distal Hox that generates the type of phenotypic variation that shows up in evolution. The reason the proximal pattern of the limb is much more constrained is because its regulation has been co-opted from the trunk, and the latter is obviously resistant to evolutionary change. (Nice and elegant explanation.) There are exceptions, like limbless lizards and snakes. But in those cases, obviously, you do also observe dramatic changes in the trunk. There is a similar reason why tetrapods cannot have symmetrical limbs: the developmental genes that cause the asymmetry are co-opted from the trunk, and changing the pattern would affect the trunk in inviable ways.

Walter Gehring, Chance and necessity in eye evolution.

Jacques Monod compared the eye to the camera to highlight both the similarities, as in the relation between form and function, and the difference between teleonomy - for the eye - and teleology - for the camera. Monod's insight is confirmed by modern research on how genetic control is deployed during the development of the eye: the observed patterns are clearly not the sort of thing that an engineer would put in place, but are instead the kind of hodgepodge that results from sequentially overlapping historical events. Eyes of vertebrates, insects, Cephalopoda, and other invertebrates have been thought as non homologous because they are morphologically different and because they develop differently. Molecular biology however shows a "deep homology" in the fact that all these eyes are affected by different version of the Pax6 gene. (But of course that raises the thorny question of the degree of congruence of homology at different levels: is the genetic one more fundamental than the developmental one? On what grounds?)

Takashi Gojobori, Chance and necessity in the evolution of connections between sensory and nervous systems.

Starts out with gene expression in Planaria brains, the most primitive of all structures that we recognize as brains. Turns out that half of known Planarian genes expressed in the head are shared by humans. Next, what about Hydra, which does not have a central neural system, just a diffuse nerve set? Again, half of the relevant genes are also expressed in human nerve cells. What about sea urchins, which have lost a central nervous system? Sure enough, gene expression patterns show that the arm of sea urchin larvae are degenerated from an ancestral more fully developed nervous system. Looking for connection between sensory and nervous systems back in the Hydra, because of the simplicity of their nervous system. Focus on gap junctions as precursors of fully formed sensory-nervous connections. (Once again, not much here about Monod, chance or necessity, but it’s near the end of the meeting...)

Ravello meeting on Chance and Necessity, part II

I am at the Ravello meeting on Chance and Necessity in biology, on the 40th anniversary of Jacques Monod's seminal book, and will be posting a few entries while the meeting is going on this week.

The gathering is organized by Giorgio Bernardi, sponsored by International Union of Biological Sciences and Istituto Italiano di Studi Filosofici.

What follows are the raw and somewhat selective notes only, in order of presentation of the various speakers. Hopefully this will provide a feeling for what the meeting is about and generate some discussion. Throughout, parenthetical comments are my own, unless otherwise noted.

Werner Arber, Contingency of spontaneous genetic variation.

Talk started with a (somewhat peculiar) historical overview leading from Darwinism and the Modern Synthesis, through Watson and Crick and genomics, to a broader "synthesis" concerning molecular evolution. Different definitions of mutation if issue considered from phenotypic or molecular perspective, of course (just like the definition of gene itself). (Long-winded) introduction covering basics of molecular genetics. (Not clear at all what the point of this was, other than giving us a quick molecular genetics 101.)

Masatoshi Nei, Hugo de Vries and species formation: new perspectives from recent genomic data.

de Vries was famous for his experiments on mutations in Oenothera plants (and for contributing to the rediscovery of Mendel's work). These mutations were soon shown to be the result of chromosomal rearrangements and abnormalities, as opposed to the sort of point mutations discovered at the time by Morgan in Drosophila. Stebbins referred to de Vries' mutationist theory as a figment of imagination, even though polyploidy is very common in plants and other groups (this can't be right, Stebbins was well aware of polyploidy and it's role in speciation). Modern molecular genetics suggests that following genomic duplication there is a reduction in gene numbers that leads to incompatibility and speciation. (Lots of refs to Nei's own work on hybrid sterility back from the '70s and '80s.) Nei doesn't like Coyne and Orr's critique, in 2004, of his neutral model of hybrid speciation, proposed in 1983, suggesting that neutral models are under appreciated. (On this one I think Coyne and Orr were correct, actually.) (Overall, Nei seemed to want to significantly scale down the evolutionary importance of selection in favor of mutation, though I don't think his arguments were very coherent.)

Eviatar Nevo, Stress and evolution at micro- and macro- scales.

Importance of a variety of environmental stresses as major drivers of adaptive phenotypic evolution. (This has been a theme of Nevo for decades now.) Documented differences between, for instance, underground and above ground mammals, range across morphology, behavior, and even fine aspects of physiology. No question that life style drives phenotypic evolution. Evidence for a positive relationship between genetic diversity and levels of environmental stress. Similarly, indices of sexual activity, as opposed to asexual reproduction, increase with stress. (This morning we've steered pretty clear from Monod, chance and necessity. Hopefully better this afternoon, judging from the titles.)

Eugene Koonin, The role of extremely rare events in the evolution of life.

Major transitions in evolution are examples of extremely rare events and how important they can be, e.g., origin of life, nucleotides, cells, eukaryotes, or multicellularity. How do we explain the origin of replication and translation processes? Neither natural selection nor exaptation are adequate since both processes require replication and translation to get started. One popular answer is the RNA world type scenarios. However, known RNA replicases are ligases, not polymerases. (Somehow) the answer is related to inflation in cosmology... Which leads to a multiverse with island universes, of which ours is one, and in which the big bang becomes a local event... (Apparently) this is relevant because the number of times a given macroscopic history is repeated in an island universe is infinite. (Voila, by epistemological sleight of hand we solved the problem!) So anthropic (so called) selection would have preceded Darwinian selection.

Tomoko Otha, Near-neutrality, robustness and epigenetics.

Starts with brief history of neutral and near-neutral theories of molecular evolution. Neutral theory predicts that rate of evolution is same as rate of neutral mutation; near-neutral theory predicts rate of evolution to be inverse to population size. Much recent comparative genomic data compatible with near-neutral expectations. Robustness of gene networks made possible by near neutrality (this agrees with work by both A. Wagner and S. Gavrilets.) While robustness implies that many genotypes can result in the same phenotype, epigenetics results in the opposite: many phenotypes can be produced by the same genotype. (Not entirely clear what the role of epigenetics was here, but I take Otha to imply that it increases the range of near-neutrality as a theory of molecular evolution.)

Giorgio Bernardi, The neo-selectionist theory of evolution.

The two major determinants of gene expression are cis factors and chromatin structure. Lots of stats followed about the differential abundance of the various classes of DNA trinucleotides in the human genome. Selection favors certain types of chromatin structure in vertebrates, namely those that stabilize the thermodynamic properties of the chromatin itself. Indeed, patterns concerning the distribution of GC-rich chromatin is conserved across a hundred million years of mammalian evolution. (Not clear why this is “neo-selectionist,” however.)

Ravello meeting on Chance and Necessity

I am at the Ravello meeting on Chance and Necessity in biology, on the 40th anniversary of Jacques Monod's seminal book by the same title, and will be posting a few entries while the meeting is going on this week. The gathering is organized by Giorgio Bernardi and sponsored by International Union of Biological Sciences and the Istituto Italiano di Studi Filosofici.

What follows are the raw and somewhat selective notes only, in order of presentation of the various speakers. Hopefully this will provide a feeling for what the meeting is about and generate some discussion. Throughout, parenthetical comments are my own, unless otherwise noted.

Agnes Ullman, In memoriam of Jacques Monod.

Monod was prominent in the critique of Lysenko and his brand of anti-scientific ideology. Shown charming early photos and even family drawings of young Jacques. I Did not know that Monod early on almost turned to a career as orchestra director before concentrating full time on genetics. He was active in the French resistance during WWII as a chief, a dangerous position that had cost three of his predecessors their lives. After WWII Monod immersed himself in the work on bacterial protein regulation that resulted in his Nobel in 1965. The latter was made possible by the intense collaboration with Francois Jacob, who eventually shared the Nobel. Their work led of course to the classic papers on the concept of the operon and of allosteric regulation of enzymes. In the late '60s Monod was politically involved with the student protest movement. In 1969 he gave four lectures at Pomona College, on "modern biology and natural philosophy," which became the core for Chance and Necessity - the book became an unexpected best seller in the early '70s. Monod then became a very effective manager and fund raiser, starting the first French institute of molecular biology, which now carries his name. He remained involved in politics, for instance in defense of abortion rights, until the premature end of his life.

"A beautiful theory may not be right, but an ugly one must be wrong." -JM

Bernardino Fantini, Monod's vision of life and the theoretical structure of contemporary biology.

Monod's philosophical work is largely under appreciated. It is true that he did not have a professional grounding in philosophy, but he was awake to the importance of philosophy in the biological sciences. According to Francis Crick's obituary of Monod in Nature, Chance and Necessity presented a vision of life that is shared by most practicing scientists, and yet feels alien to the majority of the public: life is an accident and Darwinian evolution is the impersonal causal mechanism that shaped it. Monod was interested in the apparent paradox of living organisms functioning in a way that cannot be explained only by the laws of physics and chemistry, which constitute the foundations of our scientific understanding of the world. He saw molecular biology not as a branch of chemistry, but rather as a biological-Darwinian understanding of biochemistry. Emphasis on biological form rather than specific matter constituents ("Plato sometimes is right" -JM). Monod saw evolution not as a law or a principle of life, but rather as an emergent result of complexity and certain environmental conditions. Monod attributed the idea that everything is the result of randomness and necessity to Democritus, though no specific quote to that effect can actually be found in the Greek atomist. For Monod life is bound by the laws of physics, but requires additional causal principles when it comes to the specificity of biological information. Delbruck quasi-seriously suggested to give the Nobel to Aristotle for the discovery of the basic principle of molecular biology, that DNA plays the role of the unmoved mover in biology. Many biologists rejected this idea that structure and function, form and information, can be conceptually separated in a way reminiscent of Aristotle's causes. Monod's ideas here derived naturally from his experimental work separating the control of enzymatic function from the biochemical function itself: allosteric control is entirely independent of the structural details of the functional enzyme.

Massimo Pigliucci, Biology as a historical and experimental science: the epistemic challenges of chance and necessity.

My talk was about situating the concepts of chance and necessity, in their broader sense, within the context of recent and ongoing discussions about the structure of evolutionary theory - from the Modern Synthesis of the 1940s to the newly proposed Extended Synthesis. I discussed the classic debate between Fisher and Wright, then moved to Gould's emphasis on contingency, at the same time that he was trying to establish paleontology on nomothetic grounds. I then used Cleland's distinction between prediction of future events and postdiction of past ones to mediate between experimental and historical aspects of evolutionary biology. I concluded with an overview of the Extended Synthesis as outlined in a MIT Press volume that I recently co-edited with Gerd Muller.

David Haussler, The genome 10k project, what we might learn from sequencing 10,000 vertebrate genomes.

Cost of DNA sequencing going down faster than cost of microprocessor power. Hence the idea of starting on a 10,000 - out of 60,000 known - vertebrate species genome project. Interested scientists and tissue samples sufficient for sequencing are available already for 16,000 species. Work made difficult by the structural / architectural changes in the various genomes over time, which superimpose on sequence-level changes. Still, one can follow both the birth of new genes, via duplication, and their death, via mutation causing a stop codon. The (rather naive?) long term scenario is to map genomic changes to phenotypic ones, thereby mapping the evolution of vertebrate form at the genomic level. An interesting early result is that early on in the phylogenetic history of vertebrate clades we observe an excess of regulatory innovation affecting transcription factors. This excess then tapers off, and regulatory elements become just as likely to mutate as other parts of the genome. On the other hand, changes in receptor binding sites become more important later in evolution, also eventually dropping off. Finally, more recent evolution is marked mostly by changes in intra-cellular signaling. So, early importance of developmental changes, intermediate period targeting intercellular-level changes, and finally intra-cellular changes. (This was an interesting talk on its merits, though it is hard to see what it had to do directly with the theme of the conference. I suspect this will be true for several other talks over the next couple of days.)

Gill Bejerano, Change and constancy in the evolution of the human genome.

Consider the contrast between having 20,000 protein coding genes vs about 1,000,000 genomic switches controlling the expression of those genes. A large number of cis non coding regions seem to have evolved under purifying selection. (Must admit that my eyes glaze over when slide after slide explains the various techniques used to gather the relevant molecular biology data...) (Still asleep, in the last two talks I have not heard the words "Monod," "chance," or "necessity" very much, if at all.)

Daniel Hartl, Chance favors the prepared genome, copy number variation and the origin of new genes.

Whole gene and partial duplications are frequent, though most of them are lost quickly. Chimeric combinations often lead to the evolution of new genes in Drosophila. The estimate is of about 100 duplications peer million years, 10% of which are chimeras. The two types of genes are then lost at the same rate. The rest of the talk focused on a couple of specific examples of the evolution of particular chimeric genes, one of which has been the locus of a recent - 15,000 years ago - selective sweep. The second example presented the case of a large number of structural events - deletions and insertions - which would maintain functionality only if they happened simultaneously. The way this happened was not by intelligent design ;-) but by way of resolving a stalled replication fork, which would have caused cell death at the moment of division. In other words, a number of molecular events that normally would be interpreted as having happened over a large number of generations likely occurred in a single molecular reshuffling inside an individual cell. (Talk about non-gradual evolution...)

CALL FOR ABSTRACTS WORKSHOP: Discovery in the social sciences: Towards an empirically-informed philosophy of social science

University of Leuven, Belgium, March 22-23, 2011
Submission deadline for abstracts: 31 December, 2010.
Notification of acceptance: January 15, 2011.
Keynote speakers
Alison Wylie (University of Washington)
Jack Vromen (Erasmus University Rotterdam)

Call for papers:
The aim of this workshop is to bring together scholars who are working in the philosophy of the social sciences, especially those interested in scientific practice. The theme is discovery in the social sciences.
We invite submissions of extended abstracts (about 1000 words), and we are especially eager to hear from young researchers, including graduate students, postdoctoral fellows, tenure-track professors and other recent PhDs, working in the philosophy of the social sciences or related fields. We are interested in both case studies that examine specific instances of discovery in social sciences, and in more theoretical or methodological papers that are informed by scientific practice. We take 'discovery' in a broad sense, meaning discovery of empirical phenomena, theories and laws. 'Social sciences' refers to a broad range of disciplines, including (but not limited to) economics, anthropology, history, archaeology, psychology (including neuroscience), linguistics, and sociology.

Possible topics (not an exhaustive list) include:
- What is specific to discoveries in the social sciences?
- What is the epistemic role of artefacts in discovery, for example in neuroscientific research?
- Can we discern patterns in discovery in the social sciences?
- The discovery of laws in social sciences.
- Case-studies of discovery in specific social sciences.
- Creativity in social scientific practice.

Please send your abstract, preferably as pdf or rtf to Helen De Cruz, using the following e-mail address philosophy.social.sciences @ gmail.com (remove spaces) by December 31 2010. Please also indicate your position (e.g., graduate student, postdoc, assistant professor, etc).
Scientific committee: Helen De Cruz (University of Leuven), Eric Schliesser (Ghent University), Farah Focquaert (Ghent University), Raymond Corbey (University of Leiden and Tilburg University).
This workshop is supported by funding from the University of Leuven and Ghent University.

Postdoc: Mellon Postdoctoral Fellowship at Wisconsin

The University of Wisconsin Madison invites applications for Mellon Postdoctoral Fellowships in the humanities and the humanistic social sciences. The theme for 2011-13 is Life, broadly construed.

Details about the fellowship can be found at http://www.humanities.wisc.edu/programs/mellon-postdocs/call.html

The deadline for applications is November 15, 2010. Applications should be sent electronically to: fellows@humanities.wisc.edu.
If you have questions, please contact Jessica Courtier, Mellon Postdoctoral Fellows Coordinator, at that email address or phone her at 608.516.8109.

Leiter concedes, redoes poll

Brian Leiter has graciously accepted the arguments (http://www.newappsblog.com/2010/10/philosophy-of-science-in-20th-century-.html) that his original poll on the most significant philosopher of science was marred by oversight: http://leiterreports.typepad.com/blog/2010/10/most-significant-philosophers-of-science-of-the-20th-century-one-more-time.html

I am very pleased that Duhem, Michael Polanyi, Moritz Schlick, David Lewis, Frank Ramsey, and David Hull are now all included (but no Weber, Russell, and Weyl, alas!!!). I suspect only Lewis will make a big dent on the list, but I think it is important to avoid encouraging the already existingbias toward the recent past in such polls, which do help shape the discipline's self-perception

Most significant 20th century philosophers

Brian Leiter is running a poll of interest to readers of this blog:
http://leiterreports.typepad.com/blog/2010/10/most-significant-philosophers-of-science-of-the-20th-century.html

He has acknowledged some significant oversights (Schlick and Hull). But as I point out here: http://www.newappsblog.com/2010/10/philosophy-of-science-in-20th-century-.html
I think the situation is worse without Duhem, Russell, Weyl, and a few more controversial others (Husserl, Foucault, Zilsel, and Weber).
Chime in, and vote!

Job: Tenure stream position in the HPS department at the University of Pittsburgh

POSITION: Tenure stream assistant professor in the Department of History and Philosophy of Science, pending budgetary approval.

Area of Specialization: History and philosophy of science and related areas that naturally complement departmental strengths. We have interest in strengthening areas of history and philosophy of neuroscience, physics, and general methodology.

Rank: Assistant professor

Responsibilities: Undergraduate and graduate teaching; regular departmental duties.

Applicants must submit the following materials, which will not be returned:

• A curriculum vitae.
• At least three confidential letters of reference.
• Relevant academic transcripts.
• Evidence of teaching ability.
• Samples of recent writing.

The department regrets that it cannot solicit missing materials from applicants, or return any materials.

Please direct all inquiries and application materials regarding this position to:

The Appointment Committee
Department of History and Philosophy of Science
1017 Cathedral of Learning
University of Pittsburgh
Pittsburgh, PA 15260.

The University of Pittsburgh is an Affirmative Action, Equal Opportunity Employer. Women and members of minority groups underrepresented in academia are especially encouraged to apply.

Deadline for Applications: November 15, 2010

Please note that by accident this ad was not included in the October issue of the Job for Philosophers.

The financial corruption of the economics profession

[Apologies for x-posting this from Apps: http://www.newappsblog.com/2010/10/the-financial-corruption-of-the-economics-profession.html, but the regulars here are familiar with my self-promotional activities!]
In general I argue that philosophers and citizens more generally ought to be more economically literate than they tend to be. In my view a lot of criticism of contemporary economics is based on conflation between political rhetoric and the complex reality of economic research. (Such criticism also often conflates a lot of different trends within economics.)

Nevertheless, there is a class of economists that have leveraged their economic expertise and have become part of revolving door between academia, industry, and government. (Often they also become apologists of worst abuses by foreign dictatorships from Left and Right!) What is significant about the piece below is that it exposes the financial incentives that tempt economists. It may be well over due that when economists publish journal articles and textbooks that they reveal not just research grants, but also their consulting fees/sources? It would be strange if economists, of all people, would think that (financial) incentives don't matter.

http://chronicle.com/article/Larry-Summersthe/124790/