Thursday, February 26, 2015

Becoming a Scientist ~ A Very Short Introduction to Keith Stewart Thomson

It was inevitable that, after I discovered the Oxford University Press’ Very Short Introductions (VSI) series, I would discover the preeminent evolutionary biologist Keith S. Thomson.  I should have known about both the series and the scientist long ago.  But, perhaps, the best in this sequence of discoveries is coming upon the brief autobiographical essay titled Becoming a Scientist that Thomson included in The Common But Less Frequent Loon and Other Essays (1993).  I will treat each of these discoveries in the order in which I made them.

Very Short Introductions

The VSI series is twenty years old, its first volume published in 1995.  How could I have missed these short (an average of 133 pages each), pocket-friendly books written by experts in their fields?  These slender volumes cover such a wealth of subjects, from metaphysics to stars, the devil to terrorism, probability to magic, the Magna Carta to the U.S. Supreme Court, climate to Malthus.  You name it, VSI has a title on point or probably will have shortly.  Four new titles came out this past January – the American West, Love, Exploration, and Psychotherapy.

There are now 413 titles in the series of which I’ve read a total of 3 – Teeth by Peter S. Ungar (2014), Dinosaurs by David Norman (2005), and Fossils by Keith Thomson (2005).  Yes, a crappy sample size, for sure, so I wont make any broad pronouncements about the overall quality of the offerings in the VSI series.  But, in this tiny slice of VSI were two brilliant hits and one miss (well, mostly a miss).

Teeth is informative, well-written, accessible, and substantive (a difficult combination to achieve, for sure).  It wasn’t the obvious choice for the first VSI volume I read though it did exactly what these works are intended to do:  it served an immediate need for an authoritative, albeit quick, overview of a subject   I drew on it for a blog post last year.

Dinosaurs is the one that mostly disappointed me.  The paleontologist author David Norman, a renowned expert on dinosaurs with much work on the Iguanodon, not surprisingly places that particular dinosaur at the center of the story, too much so in my opinion.  A better title might be Iguanodon:  A Very Short Introduction.

And then there is Fossils, an outstanding, thoughtful and thought-provoking introduction that provides the basics and much more in its scant 147 pages.

Thomson has brought not only his extensive expertise to this 2005 effort, but his well-honed literary skills as well.  This volume reflects Thomson’s own dictum that “there is a simple positive correlation between the quality of the thought and the quality of the writing.”  (The Literature of Science, The Common But Less Frequent Loon and Other Essays, p. 69.)

Though the fundamentals are here – such as the fossilizing processes themselves, and some stories of fossil hunters in the 19th century – Thomson’s reach is broader.  He begins with the earliest human perceptions of fossils and considers the revolutionary implications (theological, cultural, and scientific) of the developing understanding of what fossils actually are.  He explains well, and at some length, why and how fossils became keys to our knowledge of the evolution (speciation and extinction) of life on this planet, and of the evolution of the planet itself.  In the process, he succinctly summarizes debates within the scientific community over the processes and pace of evolution, highlighting the role that the fossil record has played in shaping those debates.  Thomson’s research and writing on evolutionary development (“evo-devo”) of organisms is reflected in the latter parts of this volume though, even then, he maintains a clear focus on the contribution of fossils.

Perhaps I really did not need to read another introductory treatment of fossils, though given my porous memory and my haphazard introduction to paleontology, I had no doubt, when I first cracked the binding, that the book was likely to offer some things new and refresh the memory of things mislaid.  What I have come to appreciate most about Fossils:  A Very Short Introduction is its introduction to Keith Thomson.

Keith Thomson

Thomson, who was born in England in 1938 and grew up there, has had educational and academic careers of the first rank.  He’s been associated with some of the leading institutions in the research of . . . no other way to say it . . . natural history.

Among the milestones in those careers are a Ph.D. in biology from Harvard University (1963); a two-decade career as professor of biology at Yale University during which time he also served as the Peabody Museum of Natural History’s curator of vertebrate zoology, and, for two years, its director (1965-1987); the presidency of the Academy of Natural Sciences in Philadelphia (now the Academy of Natural Sciences of Drexel University) (1987-1995); and appointment as professor of natural history at the University of Oxford concurrent with his election as director of the Oxford University Museum of Natural History and fellow of Kellogg College (1998-2003).  Thomson is currently the president of the American Philosophical Society.

I remain awestruck by this vita – a surfeit of rich accomplishments.

His early research was on ancient fishes, air-breathing, and the transition from marine to terrestrial life.  In the mid 1960s, he conducted the initial study of a freshly-caught coelacanth.  Fossils have played a central role in his work.  His work on evolutionary development has drawn him into myriad subjects.  As the Kellogg College (Oxford) description of Thomson’s work puts it, the overarching objective of his scientific research “was to understand fossils in the same physiological, biomechanical, and ecological terms as we study living animals.”  (Kellogg College (Oxford) website,)  More recently, he has focused on the history of science, particularly the challenge that the emerging understanding of fossils, evolution, and deep time posed to the theological and cultural status quo of the early 19th century.

Becoming a Scientist

In the delightful essay Becoming a Scientist, Thomson tells the story of his conversion from a lackluster, uncommitted student to a scientist, a process that hinged on the intervention of adults who recognized his potential and, as he puts it, “took me seriously.”  There’s a moving poignancy to some of this account.  In school, his favorite teacher was Phillip Allen who taught English.  For some unknown reason, he was called "Ticker" Allen to distinguish him from another teacher also named Allen who was called “Tocker.”
Ticker Allen was perhaps the worst teacher in the school, at least for small boys whose innate need to read Shakespeare was very hard to uncover. . . . Everyone else hated English.  I looked forward to it.  I felt such sympathy with that quiet man sadly trying to teach us something he loved. . . .  But I look back and wonder if Ticker Allen ever knew how much his classes meant to me.  (p. 59)
What a beautiful, profound phrase – that quiet man sadly trying to teach us something he loved.  And how painful that Ticker Allen may have never known his influence.

As Thomson describes it, his transition from school to university was awash in teenage angst.  The drama and conflicting emotions embedded in this brief, matter-of-fact description almost beggar the imagination.
I fell in unrequited love with the girlfriend of a best friend (he was off in the army), failed in a competitive examination to win a scholarship to Cambridge, and was accepted to read zoology at the University of Birmingham.  (p. 59)
Once at Birmingham, Thomson discovered he could succeed adequately without trying – “Life was one long party . . . .”  (p. 60)  That is, until he was captured by one tutorial assignment to write an essay about the process of neural transmissions.  It was an issue that, unbeknownst to Thomson, had no answer in the early 1960s.  He worried the issue to death, discovering that the challenge, even without an answer, was “exhilarating, a real-life mystery story with me as detective.”  (p. 60)  At one point, in his research, he consulted with a resident fellow in his hall, a physiologist who clearly took him seriously and ultimately steered him to research in zoology.

His transition to graduate study at Harvard was partly because his acceptance to the University of Oxford came with no financial assistance, and also because Harvard offered an opportunity to study with the renown vertebrate zoologist Alfred Sherwood Romer.  Not surprisingly, Thomson discovered a truth about graduate education, one learned by countless others who chose a graduate institution because of who was teaching there:  “Romer was one of the very great men of American science, so naturally I did not see a lot of him:  he was always off lecturing or collecting fossils in South America.”  (p. 61)

Rather, Thomson writes, his real graduate education took place at the regular afternoon coffee klatches with those paleontology professors who were around, technical staff, and students.  They would gather in an outside stairwell at the Museum of Comparative Zoology where they could smoke.  “This is where I learned paleontology and evolution, not in the classroom.”  (p. 62)

At some point, whether in graduate school or in the ensuing couple of years, when he, after earning his Ph.D., married and returned to London for a stint at the University College, London as a temporary lecturer in zoology, Thomson took “control of my own fate.”  “From this mysterious moment, . . . , I felt free to follow my own interests wherever they would take me.  I was independent of any fashion, fad or faction. . . .  I had freedom to tackle my own choice of biological mysteries.”  (p. 62-63)  What a heady realization.

But, actually, it’s the second paragraph of this essay that perhaps captures best what attracts me to Thomson’s sensibility and his prose with its flow, understatement, and irony.
My grandfather had a brass microscope, and on rare occasions, when a very small child, I was allowed to help him set it up and to look through it. . . .  I wish I could report that my grandfather and I had a lot of fun with that microscope, but he was a disagreeable man and only got it out to amuse himself, with me and my sister as an audience.  Little did he realize that his selfish displays put me on course for a life in science.  (p. 57)

Friday, February 13, 2015

Surprising Mesh-Size Effects

Though I shouldn’t have been, I was surprised at the effects different sized sieves can have on the screening of fossil-strewn matrix.  Turns out, I seem to have some company among professional paleontologists, which is, itself, also surprising.

Here’s the source of my first surprise.  My previous post featured a picture of a plastic container with roughly one and a third cups of matrix.  For the past couple of weeks, I’ve been slowly working through that Miocene Epoch material in search of fossils (both macro- and micro-).  My early finds were mostly large fossils, shells and shark teeth primarily, spotted with the naked eye.

Then, as I worked deeper into the container, my finds shrank in size . . .

and, when the microscope swung into play, the finds were that much smaller, many shells from foraminifera and several from ostracodes.  Foraminifera appear in the image below (scale bar is 500 microns which is 0.5 millimeters).

What mesh size had I used originally to screen this material?

Well, it didn’t take long in this process to realize that this material hadn’t been washed or screened at all.  It was just as I’d gathered it, which means it was the equivalent of using a sieve mesh with no openings in it.  In the two systems of sieve mesh-size measurements with which I’m familiar, as the numbers assigned to sieves increase, the mesh sizes decrease (though not, I’m sure, to zero).  Here are a few examples from the U.S. Sieve Size and Tyler Mesh Size systems:

U.S. Sieve Size Tyler Mesh Size Opening in Millimeters Opening in Microns
No. 10 9 Mesh 2.000 2,000
No. 18 16 Mesh 1.000 1,000
No. 35 32 Mesh 0.500 500
No. 60 60 Mesh 0.250 250
No. 80 80 Mesh 0.177 177
No. 200 200 Mesh 0.074 74

(Tables offering more sieve sizes appear widely on the web.  One source is Appendix E:  Particle Size – U.S. Sieve Size and Tyler Screen Mesh Equivalents, in Fundamentals of Turbulent and Multiphase Combustion, by Kenneth K. Juo and Ragini Acharya, 2012.)

So, given no screening of this material, I shouldn’t have been surprised (but was) at what happened as I got down to the dust-like dregs of the matrix – the silica frustule of a diatom caught my eye, a kind of fossil I’d never found before.

The scale bar in the picture above was chosen deliberately because the smallest sieve that I own and use is a No. 80 in the U.S. Sieve Size system which has mesh openings that are 177 microns or 0.177 millimeters wide.

Yes, the frustules of these algae can be larger than what I found and, yes, they can be very abundant, but many are much, much smaller.  So, essentially, any fossils smaller than 177 microns, many of them presumably diatoms, that make it all the way through my stack of sieves (large mesh on the top, small mesh on the bottom) are never to be seen by me.  But, this issue is not mine alone.   Writing apropos of a non-paleontological context (quantitative analysis of extant marine ecosystems), marine biologist Kevin Zelnio noted:
The sieve size I use at the bottom, . . . , is the most important.  It is my cut off.  Essentially, I’m saying I’ll ignore anything that can fall through this size hole.  Ideally, this should be as low as possible, but I’m often limited by what sieve size my colleagues have used in past studies.  This is important because our results need to be compared to each other.  ((Sieve) Size Matters, EvoEcoLab, Scientific American blog, March 5, 2012.)
Seems so obvious – what can fit through the openings of the mesh in the final sieve eludes analysis.

Here’s my next surprise, another one that I should have anticipated because science is introspective and correcting.  Since, in paleontology, as well as in biology (. . . and in most of the rest of life), one may make decisions with significant consequences and sometimes not know or fail to keep those consequences in mind, there has developed a large body of (often strongly cautionary) literature analyzing the effects of mesh sizes on the findings of paleontological and biological research.

This is an important issue because sifting matrix through sieves is a core paleontological endeavor.  Indeed, one paleontologist has gone so far as to assert that “the real work of paleontology comes in extracting and identifying individual fossils from a bulk sample of rock or sediment (collecting bulk samples is as easy as digging a hole) . . . .”  (J. Bret Bennington, Confessions of a Statistical Paleontologist, Hofstra Horizons, Fall 2011, emphasis added.)  Though, certainly, not every paleontologist spends his or her time sieving samples, extracting and identifying the different fossil species contained in those samples, and counting individual specimens, many do, particularly those exploring the paleoenvironment of specific sites.  My efforts are not so ambitious.  Actually, I’m more of a tourist, visiting ancient environments to get a glimpse of what lived there.  I’m just passing through.

From my reading of just a fraction of the literature on mesh-size effects, the central (and not earth-shattering) conclusion is that what is kept and analyzed makes a fundamental difference for research findings.  In general (and not surprisingly), smaller sieve mesh sizes serve to increase, among other results, estimates of the biomass of extant organisms, the number of identified species, the number of individual specimens collected, and the retention of juvenile forms.  Yes, less is more.  All of this stands to reason given that species (fossil or otherwise) can vary in size, and juvenile specimens of a species are likely to be smaller than adults.  (A few papers from this literature are listed at the end of this post.)

Geologists Michał Kowalewski and Alan P. Hoffmeister have observed that “even studies that share virtually identical research goals and target the same groups of fossils collected from the same time intervals can vary greatly in mesh size.”  (Sieves and Fossils:  Effects of Mesh Size on Paleontological Patterns, PALAOIS, Vol. 18, No. 4/5, October 2003, p. 460.  This is hiding behind a paywall, sorry.)  To demonstrate mesh-size effects, they used a detailed database describing a large number of fossil marine benthic mollusks from two Miocene Epoch sites and simulated the use of different mesh sizes on the sorting of these fossils.  Certain paleontological patterns that have been studied over the years were affected by changes in mesh sizes.  For example, they found that, as mesh sizes increased, bivalve representation in the selected population decreased, and the percentage of mollusks with predator holes increased as did the percentage of encrusted specimens.  They concluded, “What matters here is the observation that if the Miocene dataset were originally obtained with coarser sieves, different results would have been reported . . . .”  (p. 465)  Though some species-diversity measures seemed to have been little affected by mesh sizes for this particular dataset, there were differences in the impact of changes in mesh sizes between the two sites that provided specimens to the dataset.  “The new insight offered by this analysis is that ensuring that a standard mesh size is used in comparative analyses is insufficient – the outcome may depend on the choice of that standard.”  (p. 465)

There are trade-offs, of course.  Keep too much and the analytical tasks may exceed the resources researchers have available to them (I know, I still a lot of the fine lees from that container of matrix to go through).  It’s also true that, in some instances, finer mesh sizes may negatively affect the analysis (see, for instance, Susan Kidwell’s paper listed below).

Mesh-size effects – often surprising, and, usually, they shouldn’t be.

Selected Additional Literature

John D. Gage, et al., Sieve Size Influence in Estimating Biomass, Abundance and Diversity in Samples of Deep-Sea Macrobenthos, Marine Ecology Progress Series, Volume 225, 2002.

Susan M. Kidwell, Mesh-Size Effects on the Ecological Fidelity of Death Assemblages:  A Meta-Analysis of Molluscan Live-Dead Studies, Geobios, Volume 35, 2002.

Antoine Morine, et al.,  Sieve Retention Probabilities of Stream Benthic Invertebrates, Journal of the North American Benthological Society, Volume 23, no. 2, June 2004.  (Hidden behind a paywall.)

Frank Peeters, et al., A Size Analysis of Planktic Foraminifera From the Arabian Sea, Marine Micropaleontology, Volume 36, 1999.  (Another paywall, it would appear.)
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