Causes that Make a Difference

Biologists studying complex causal systems typically identify some factors as causes and treat other factors as background conditions. For example, when geneticists explain biological phenomena, they often foreground genes and relegate the cellular milieu to the background. But factors in the milieu are as causally necessary as genes for the production of phenotypic traits, even traits at the molecular level such as amino acid sequences. Gene-centered biology has been criticized on the grounds that because there is parity among causes, the “privileging” of genes reflects a reductionist bias, not an ontological difference. The idea that there is an ontological parity among causes is related to a philosophical puzzle identified by John Stuart Mill: what, other than our interests or biases, could possibly justify identifying some causes as the actual or operative ones, and other causes as mere background? The aim of this paper is to solve this conceptual puzzle and to explain why there is not an ontological parity among genes and the other factors. It turns out that solving this puzzle helps answer a seemingly unrelated philosophical question: what kind of causal generality matters in biology

Ask Not "What is an Individual?"

Philosophers of biology typically pose questions about individuation by asking “what is an individual?” For example, we ask, “what is an individual species”, “what is an individual organism”, and “what is an individual gene?” In the first part of this chapter, I present my account of the gene concept and how it is used in investigative practices in order to motivate a more pragmatic approach. Instead of asking “what is a gene?”, I ask: “how do biologists individuate genes?”, “for what purposes?”, and “do their practices of individuating genes serve these purposes?" In the second part of this chapter, I propose that we use this approach when analyzing concepts of organisms and biological individuals. Following philosophical pragmatism, I argue that we should abstain from attempts to situate individuation of Darwinian individuals or of holobionts in a philosophy of nature. Instead, we should analyze practices of individuating organisms in terms of three-place relations between the world, ideas, and human purposes and actions. I conclude with three lessons: an ontological, an epistemological, and a meta-philosophical lesson, which I suggest, apply to philosophy of science generally and to philosophy and metaphysics at large

Ask Not "What is an Individual?"

Philosophers of biology typically pose questions about individuation by asking “what is an individual?” For example, we ask, “what is an individual species”, “what is an individual organism”, and “what is an individual gene?” In the first part of this chapter, I present my account of the gene concept and how it is used in investigative practices in order to motivate a more pragmatic approach. Instead of asking “what is a gene?”, I ask: “how do biologists individuate genes?”, “for what purposes?”, and “do their practices of individuating genes serve these purposes?" In the second part of this chapter, I propose that we use this approach when analyzing concepts of organisms and biological individuals. Following philosophical pragmatism, I argue that we should abstain from attempts to situate individuation of Darwinian individuals or of holobionts in a philosophy of nature. Instead, we should analyze practices of individuating organisms in terms of three-place relations between the world, ideas, and human purposes and actions. I conclude with three lessons: an ontological, an epistemological, and a meta-philosophical lesson, which I suggest, apply to philosophy of science generally and to philosophy and metaphysics at large

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

Infrared High-Resolution Spectroscopy of Post-AGB Circumstellar Disks. I. HR 4049 - The Winnowing Flow Observed?

High-resolution infrared spectroscopy in the 2.3-4.6 micron region is reported for the peculiar A supergiant, single-lined spectroscopic binary HR 4049. Lines from the CO fundamental and first overtone, OH fundamental, and several H2O vibration-rotation transitions have been observed in the near-infrared spectrum. The spectrum of HR 4049 appears principally in emission through the 3 and 4.6 micron region and in absorption in the 2 micron region. The 4.6 micron spectrum shows a rich 'forest' of emission lines. All the spectral lines observed in the 2.3-4.6 micron spectrum are shown to be circumbinary in origin. The presence of OH and H2O lines confirm the oxygen-rich nature of the circumbinary gas which is in contrast to the previously detected carbon-rich material. The emission and absorption line profiles show that the circumbinary gas is located in a thin, rotating layer near the dust disk. The properties of the dust and gas circumbinary disk and the spectroscopic orbit yield masses for the individual stars, M_AI~0.58 Msolar and M_MV~0.34 Msolar. Gas in the disk also has an outward flow with a velocity of $\gtrsim$ 1 km/s. The severe depletion of refractory elements but near-solar abundances of volatile elements observed in HR 4049 results from abundance winnowing. The separation of the volatiles from the grains in the disk and the subsequent accretion by the star are discussed. Contrary to prior reports, the HR 4049 carbon and oxygen isotopic abundances are typical AGB values: 12C/13C=6^{+9}_{-4} and 16O/17O>200.Comment: 42 pages, 14 figures, Accepted by Ap

Brown Dwarfs in Young Moving Groups from Pan-STARRS1. I. AB Doradus

Substellar members of young ($\lesssim$150 Myr) moving groups are valuable benchmarks to empirically define brown dwarf evolution with age and to study the low-mass end of the initial mass function. We have combined Pan-STARRS1 (PS1) proper motions with optical$-$IR photometry from PS1, 2MASS and $\textit{WISE}$ to search for substellar members of the AB Dor Moving Group within $\approx$50 pc and with spectral types of late-M to early-L, corresponding to masses down to $\approx$30 M$_{Jup}$ at the age of the group ($\approx$125 Myr). Including both photometry and proper motions allows us to better select candidates by excluding field dwarfs whose colors are similar to young AB~Dor Moving Group members. Our near-IR spectroscopy has identified six ultracool dwarfs (M6$-$L4; $\approx$30$-$100 M$_{Jup}$) with intermediate surface gravities (INT-G) as candidate members of the AB Dor Moving Group. We find another two candidate members with spectra showing hints of youth but consistent with field gravities. We also find four field brown dwarfs unassociated with the AB Dor Moving Group, three of which have INT-G gravity classification. While signatures of youth are present in the spectra of our $\approx$125 Myr objects, neither their $J-K$ nor $W1-W2$ colors are significantly redder than field dwarfs with the same spectral types, unlike younger ultracool dwarfs. We also determined PS1 parallaxes for eight of our candidates and one previously identified AB Dor Moving Group candidate. Although radial velocities (and parallaxes, for some) are still needed to fully assess membership, these new objects provide valuable insight into the spectral characteristics and evolution of young brown dwarfs.Comment: ApJ, accepte

The Time-Domain Spectroscopic Survey: Understanding the Optically Variable Sky with SEQUELS in SDSS-III

The Time-Domain Spectroscopic Survey (TDSS) is an SDSS-IV eBOSS subproject primarily aimed at obtaining identification spectra of ~220,000 optically-variable objects systematically selected from SDSS/Pan-STARRS1 multi-epoch imaging. We present a preview of the science enabled by TDSS, based on TDSS spectra taken over ~320 deg^2 of sky as part of the SEQUELS survey in SDSS-III, which is in part a pilot survey for eBOSS in SDSS-IV. Using the 15,746 TDSS-selected single-epoch spectra of photometrically variable objects in SEQUELS, we determine the demographics of our variability-selected sample, and investigate the unique spectral characteristics inherent in samples selected by variability. We show that variability-based selection of quasars complements color-based selection by selecting additional redder quasars, and mitigates redshift biases to produce a smooth quasar redshift distribution over a wide range of redshifts. The resulting quasar sample contains systematically higher fractions of blazars and broad absorption line quasars than from color-selected samples. Similarly, we show that M-dwarfs in the TDSS-selected stellar sample have systematically higher chromospheric active fractions than the underlying M-dwarf population, based on their H-alpha emission. TDSS also contains a large number of RR Lyrae and eclipsing binary stars with main-sequence colors, including a few composite-spectrum binaries. Finally, our visual inspection of TDSS spectra uncovers a significant number of peculiar spectra, and we highlight a few cases of these interesting objects. With a factor of ~15 more spectra, the main TDSS survey in SDSS-IV will leverage the lessons learned from these early results for a variety of time-domain science applications.Comment: 17 pages, 14 figures, submitted to Ap