Adapiformes

The Adapiformes are primitive euprimates who's fossils range from the early Eocene to the late Miocene. Famously, the first discovery was mis-identified as an early ungulate and thus named Adapis parisiensis, as in 'towards Apis, the sacred and mythical bull'.

Groups

The major adapiforme groups are:

1. Notharctidae (North American adapiformes)
1. Notharctinae
2. Cercamoniinae
2. Adapidae
1. Adapinae (European adapiformes)
3. Sivaldapidae (south-east Asia adapiformes)

Additionally there are problematic taxa, particularly from Asia and Africa (which here includes Oman).

The Notharctine Cantius is the earliest adapiforme in North America and also one of the earliest in Europe.

Bodies

Body sizes range from around 1kg to 7kg for Notharctus robustior, with a few species weighing less than 500g, and one, Anchomys gaillardi weighing around 50g. Gingerich (1977) famously showed a gradual evolutionary trend for body-size increase amoung some Adapiformes. Gould and Eldridge cited this case in their famous punctuated equilibria discussion as an example however of the data not meeting the gradualistic interpretation matched with it (Figure 1).

Figure1 

Adapiformes have sloping facets of their ankle bones and and characters of the distal tibia (presumably that link with the ankle features) that associate them with Lemuriformes (lemurs and lorises). They possess a post orbital bar, thus linking them with all other euprimates. Adapids had a dental formula of 2143 (early ones at least), lack a hypocone, have an elevated trigonid, and an unfused mandibular symphysis. Adapids have a petrosal bulla with a ring-like ectotypmanic included within the bulla (bullar morphology receives a lot of attention in primate systematics).  In the cheiridia, adapiformes have opposable first digits for grasping. Their orbits are obliquely facing allowing for some stereoscopic vision and the lacrimal is included within the orbit. Their snouts are large and have lots of turbinates. Some workers have been able to pick out (in some specimens) boney features (such as a gap between the upper incisors) that might correlate with the wet-nosed' condition of modern strepsirrhines. Some have, in a heterodox position, listed a set of features thought to link adapiforms to anthropoids, in particular the cercamoniine adapiformes.

Adapiformes generally have mobile shoulder joints, which makes sense for active arboreal species.

Some notharctines were potentially vertical clingers and leapers, having short and high trochlea with the capitulum extending below the trochlea. For these  potential VCL-ers, the elbow may not have allowed the forearm to fully extend, but the forearm may have had good twisting ability. Potentially arguing against the VCL hypothesis, none of the notharctines have knees like those of tarsiers and galagos, which are specialized leapers.

Adapines were different; they were possibly slow-climbing arboreal quadrupeds, agile but non-leapers. They were potentially loris like in their habits.

Diet

Some adapiforms have good zyogmatics and saggital crests suggesting more frugivorous or folivorous diets. The tiny Anchomys had insectivore-like teeth, and other small forms may also have been insectivorous. Most other species are over 1kg and were likey frugi/folivores. Covert (1986) found a high molar shearing coefficient (`spikiness' of teeth) for Adapis, Leptadapis, Notharctus, Caenopithecus, and Smilodectes (which are also larger adapiforms). The Sivaladapids also have folivorous molar shearing coefficients.

Climate

Figure 2

The Paleocene-Eocene Thermal Maximum (PETM) was the warmest period on Earth throughout the Cenozoic. The early Eocene was very warm, likely tropical with little seasonality. Climate declined and cooled throughout the Eocene, by the end of which Antarctic icesheets had formed. Around the end of the Oligocene the climate started warming again, fluctuating through most of the Miocene until heading into the decline the eventual leads the the episodic Ice Ages of the later cenozoic (Figure 2). Adapiforme diversity and geographic spread basically follows this same story of a peak in the early/middle Eocene followed by a long decline. By the middle Miocene all that's left are Sivaladapids in south asia.

Fantastic Bridges

This was pointed out to me by someone else, it's an odd glitch in google maps.

  The map shows south Brooklyn. Manhattan Beach is on the east-end of a  bit of land on the southern base of Brooklyn, with Coney Island at the west-end. The long strip at the bottom of the screen capture is a barrier island, made up of  Breezy Point and the Rockaways.  This map shows a bridge extending from Breezy Point into Manhattan Beach. There's no such bridge.

Here we're zoomed in on the north end of the 'bridge', and it actually is shown running into the CUNY Kingsborough Community College campus.
In fact a big chunk of the campus here is mysteriously shown as under water.
There's nothing like any of this in the satellite view, shown below.

Outside of this being a weird map rendering issue---and the error is not normally there, I've checked this map before---my first thought was, maybe it's a projection involving potential sea-level rise. But that wouldn't explain the "bridge", which is also rather wide for a bridge. Plus, the campus has a high sea-wall running all around it, so if the south end of it was flooded, the whole campus should be flooded. Water could be coming in to the west, off campus, and run into campus, but I'd think if that was the case then there'd be more flooding overall. Anyway, it's probably not the case that 'someone' at Google accidentally put in data from some imaginary flood scenario into the standard Google Map.

I actually wish this bridge did exist, it'd be better taking the Southern Parkway and driving through the Rockaways, and then over this bridge, than taking the dread Belt Parkway.

Colin Groves - Carl meets Karl: The case for testability in Primate Taxonomy

Dr. Colin Groves is a well known primatologist from the Australian National University. Amoung other things, he was one of the people who named Homo ergaster. His books include the textbook: Primate Evolution, 2001's Primate Taxonomy, and 2011's Ungulate Taxonomy. He's been called "primatology's latter-day Linnaeus" [Rosenberger 2009 (pdf)], which figures in the talk's topic.

The ~hour long talk---"Carl meets Karl: The case for testability in Primate Taxonomy"---was held at SUNY Stonybrook's Anatomic Sciences Seminar room (HSC T8-025) Monday July 1st at noon. Dr. Jungers did the introduction.

The two Carls are Linneaus and Popper, as might be guessed from the issues of testability and taxonomy.  

A little Background

Dr. Groves was making an argument for the use of the Phylogenetic Species Concept (PSC) in Primatology/Anthropology, in lieu of the Biological Species Concept (BSC). In brief, species concepts are attempts to define what we actually mean by species, which is no small task. Effectively there is no one universal species concept today, and debate on the issue can get quite heated.

The BSC defines a species as a population capable of interbreeding: if you have two populations that can't produce fertile offspring, you have two separate species. This is the species concept of highschool biology courses, but of course it was advocated by no less a figure than Ernst Mayr. 

There are three different types of Phylogenetic Species Concepts (Wilkins, 2009) :

1. Hennigian: species are unbroken & unbranched lineal segments of an evolutionary tree
2. Phylogenetic Taxon: the smallest unit in a phylogenetic tree is the species
3. Autapomorphic: species are set by diagnostic associations of unique characters

The bulk of the Talk

Groves says that the BSC is not testable because in most cases where we wonder "are these two species or one?", the populations have an allopatric distribution. They're geographically separated and there's no test of reproductive isolation. The BSC then falls outside the limits of Popper's demarcation criterion (that science must be testable). In the few instances where we can test inter-fertility (when the populations are in sympatry or the populations are housed together in, say, a zoo) interbreeding between putative good species often occurs, the BSC fails the test.

Groves explained that some good primate species, like Trachypithecus pileatus, have been shown to be hybrids (via Y-chromosome and mtDNA studies). He also showed a map of the distribution of baboon species across Africa, and then showed an African baboon mtDNA haplotype map, which broke up some of these species and, he said, gave evidence for hybridization between some species.

So, for Dr. Groves at least, the BSC is either unscientific (and thus should be rejected) or often falsified (and thus should be rejected).

Dr. Groves reviewed a few alternatives to the BSC, such as:

1.  Ghiselin 1996 - Species as individuals
2. Van Valen's Ecological Species Concept
3. Paterson's Recognition/Fertilization System Concept
4. Templeton's Cohesion Species Concept
5. Mayden's Genetic Distance Species Concept

But Groves ultimately rejects them all in favour of the PSC. Groves, following the standard usage, attributes the PSC to Eldridge & Cracraft. Groves also notes that Darwin anticipated some aspects of the PSC (that species are just like sub-species, but with wide gaps between them as intermediate forms go extinct), and that Gerrit Miller (who recognized that the Piltdown jaw was actually from a non-human ape) felt that if there are no morphological intermediates between two populations, then they must rank as separate species.

Groves defines the PSC as "the smallest population or aggregation of populations which has fixed, heritable differences from other such populations."
There are, apparently, many species of Mangebey (Cercocebus) monkeys, with different people sorting them differently. Groves performed a discriminant analysis which he claims showed absolute differences between the populations, and that thus each of these groups is a good, phylogenetic, trait-based species.

So Groves's major points is that the biological species concept at best fails when tested, and that the phylogenetic concept is more objective and testable; therefore anthropologists should explicitly use it.

In the brief question session, Groves was asked about what he meant by "fixed", he said he was talking about a binary 'yes/no short/long' difference between populations, but at the same time seemed to say that there was a good amount of wiggle room there.
Another important questions was: how far should someone take this method? Taxonomy & Systematics has long been divided over the 'lumper/splitter' issue. Groves rather strongly felt that the default should be that an operational taxonomic unit (OTU) is a species, and that one would need to demonstrably show that it was a subspecies otherwise.

My reactions

So one thing to note here is that Groves is using the Autapomorphic "flavour" of the phylogenetic species concept, that a species is something that is 'diagnosable', and that species are the terminals of a cladogram. Some people treat this concept as meaning that the pattern of characters is real, but that pattern doesn't tell us anything about how the groups of species evolved. Thus there's a pattern vs process arguement amoung advocates of the Autapomorphic concept (and often this is called an problem of ontogeny-epistemology). 

Wilkins (2009) reminds us of a case where workers had identified the species of seals and were now considering   whether mtDNA haplotype data supported them. But under the PSC definition, each haplotype has to be considered a separate and distinct species. The authors in that study ended up resorting to biogeography and breeding data to justify their original choices of species, but that invalidates using the phylospecies concept in the first place.
This problem is taken to an extreme by Vrana & Wheeler (1992), who argue that the terminal taxa in a cladistic analysis should be individuals, not species. The only way to group individuals in a cladistic analysis (under this concept) would be if all members of the group were identical for all characters considered. Vrana & Wheeler also note that this would be a major problem for conservation biology, because the taxonomic units that people try to conserve aren't real.^*

Groves believes that his usage of the PSC works in the modern day, and for any given 'slice' through paleontological/evolutionary time. But a problem here is highlighted by some of his listed antecedents. In the past, intermediate forms and slight gradations would connect what today are separate species with 'fixed' characters. So what's a species, based on morphology, today, somehow wasn't a species, based on the same morphology, in the past. Groves thus has, ironically, speciation by extinction. 
A question actually came up for what Groves and the PSC means for paleontologists, since Groves was using soft-part anatomy (like pelt coloration) to mark new species. But it should be obvious that the PSC can be applied to paleo-species, it's just that the characters are going to be preservable ones. Of course, the major problem here is that a paleontologist today, and a hypothetical neotologist in the distant evolutionary past, would practically never identify the same species.
This all weakens the falsifiability claim that Groves makes for the PSC, the concept becomes extremely subjective in his rendering, much more so that, say, testing for reproductive isolation (the hallmark of the biological species concept).

Further, does the biological species concept really fail in the instances cited? In the case of two allopatrically separated 'obviously good' species that are brought into captivity, mate, and produce fertile offspring, what has been tested? A particular hypothesis (that there are two species) has been tested, and it failed, there's really one species in this scenario, according to the biological concept, which wasn't itself tested.

The existence of hybrids also is certainly not a new challenge to the BSC, plant species apparently easily hybridize, producing fertile offspring, in fact plant species can sort of self hybridize, they can fertilize themselves and instantly produce a new species with twice the chromosome number of the parental species. 

Further, the phylospecies is distinguished from the morphospecies when the characters have undergone a cladistic analysis: that's how the autapomorphies are identified as such (as unique, derived traits specific to the group).
There was very little discussion of phylogeny in Groves talk and no cladistic analysis presented. Perhaps this is just because he was giving a condensed talk to a small group and he's explained this elsewhere.

The question over species concepts has been around for an extremely long time and isn't likely to be settled anytime soon. Coyne and Orr's [2004] recommendation that workers adopt a definition that best addresses their particular question is probably where the issue stands today, which isn't much help.


* Vrana & Wheeler continue by stating that, even if the 'species' isn't real, this could still mean, if a cladistic analysis reveals it, that there's structure within that 'species', and so a conservationist now has an argument for preserving each lineage within that, an appeal for preserving "cladistic diversity"


References

Coyne, J. A., & Orr, H. A. (2004). Speciation (p. 545). Sunderland, MA: Sinauer Associates.


Rosenberger, A.L. 2009. History of Primatology: The Alpha Taxonomist's View. Book review of: Extended Family: Long Lost Cousins. A Personal Look at the History of Primatology. Colin Groves. Arlington VA, Conservation International. Evolutionary Anthropology, 18: 79.

Wilkins, J. S. (2009). Defining species: a sourcebook from antiquity to today.  American University Studies. Series V. Philosophy. Vol. 203. Peter Lang Publishers.

The Past as Prologue - Michael Mann

Penn State University Climatologist Michael Mann. After: Physicist and climatologist Michael Mann. Photograph: http://www.guardian.co.uk/environment/2012/mar/05/climate-change-hockey-stick-michael-mann

Dr. Michael Mann is going to give a talk at the CUNY Graduate Center, Thursday May 9th. The talk will be on the 4th Floor in the Science Center, room 4102. This talk will start at 530pm. As usual, after the talk we'll have an informal reception.

Michael Mann is a well known climate researcher who's 1998 publication "Global-scale temperature patterns and climate forcing over the past six centuries" (pdf) is the source of the famous (well, famous as statistical graphs go) "Hockey Stick" graph.

A version of the "Hockey Stick Graph"., showing temperatures more or less stable for the past millenium, and then sharply spiking upwards in the modern era. After IPCC TAR WG1 (2001) Figure 5. 

The subject of the talk, however, is "The Past as Prologue". Dr. Mann will review work over the past decade aimed at establishing the nature of, and factors underlying, patterns of large-scale climate variability in past centuries.  He will discuss evidence from proxy climate reconstructions spanning the past millennium, the comparison of proxy reconstructions with simulations with climate model simulations forced by past natural and anthropogenic forcing, and results from climate modeling experiments in which proxy evidence is assimilated directly into coupled ocean-atmosphere model simulations. He will also discuss recent work suggesting the possibility that equilibrium climate sensitivity may have been underestimated in some past studies comparing model simulations and paleoclimate reconstructions.

  

This will be a moderately technical talk, which is appropriate since the students that organize the GEOS talks as PhD candidates within the Earth & Environmental Sciences program. However, Dr. Mann has explained that he expects to talk about other issues related to his research. So non-academics are certainly welcome and can expect an exciting talk!

If you can't make it to the Grad Center for the talk, you can also check it out on our livestreaming channel:

http://videostreaming.gc.cuny.edu/videos/channel/44/

Click here for a Flyer with more information (pdf)

(This entry is cross-posted at the GEOS group blog: http://opencuny.org/geos/?p=143)

Gould & Eldredge 1977 or G&E Strike Back

reading: Gould and Eldredge. 1977. Punctuated Equilibria: the tempo and mode of evolution reconsidered. Paleobiology. 3

I previously talked about an earlier paper where Eldredge and Gould put forward their concept of punctuated equilibria. This was a rather controversial concept at it's time. I think it's gone through the infamous 'stages of truth' series (which weirdly are tied up with Darwin's bulldog Huxley and famed embryologist von Baer as detailed here); first ridicule, then violent opposition, and then the claim that it's trivially and obviously true. 
Or, as the claim was initially stated by Schopenhaur:

"To truth only a brief celebration of victory is allowed between the two long periods during which it is condemned as paradoxical, or disparaged as trivial."

Reading these papers you see a lot of work that seems trivially obvious today: allopatric speciation, local sections don't necessarily represent the wide ranging species, speciation is a process of branching, etc. But some other aspects of these papers haven't had their brief victory celebration yet (species selection and speciation through regulatory gene revolutions).

Gould and Eldredge's major gripe is that gradualism prevents examination of the tempo and mode of evolution, and that in particular gradualism can't be refuted by fossil evidence because the evidence has been heavily interpreted under the gradualistic framework. Punctuated Equilibria, they argue, allows for fair assessment of evolutionary tempos, and once we understand that we can make some inferences about the mode that evolution operates through. They state that if the tempo is punctuational, then the mode is 'speciation' or branching.

By "Tempo", G&E borrow from George Gaylord Simpson (a leader in the Modern Synthesis) and mean variation in rates of evolution between lineages, while "Mode" is the mechanism that produces the variation in rates.
Tempo, once the blinkering effect of gradualism can be removed, can be observed empirically, and punctuated equilibria is  a mode that can be inferred from it. G&E feel that punctuated equilibria will be 'orders of magnitude' more important than phyletic gradualism, and that phyletic gradualism occurs 'hardly ever'. Importantly in this work, the fossil records sometimes failure to display radical morphological change, rather than being a 'failure to record' information is actual information, stasis, they reiterate is data. This is a necessary implication of applying the neontologist's allopatric speciation to the paleontologist's fossil record.

G&E also make it clear that they want two major changes to occur in the way paleontologists do their work (or rather did, since the initial paper on this topic was from more than 30 years ago); 1) evolutionary trends are the result of (higher level) species selection; and 2) workers need to quantitatively study the evolution of entire ecosystems and their members. They particularly want for workers to quantify geographic variation within a population and compare that to stratigraphic variation along and between lineages before anyone can really talk about stasis or punctuation (although they seem to relax that standard sometimes when people make claims of finding punctuation).

They then go through a number of studies that have supported or contra-indicated punctuated equilibria and tests for it, amoung them Stanley 1975 (pdf); Hecht 1974 (a longstanding and well-respected Chair of Biology at CUNY Queens College); Hayami & Ozawa 1975;  Makurath & Anderson 1973; Gingerich 1974, 1976, 1977 (pdf); and Klapper & Johnson 1973 (whom they seem to paint as what I will call 'naive gradualists'). They also take to task workers who publish on evolutionary trends when all they really have are three data points, an original population, and then say one where the individuals are bigger on average, and then a third population where they're a little bigger again, on average. Trends really have to be based on many points, not just a few, G&E go through some basic statistics on why this is so.
G&E also look at a few cases where other authors have calculated the rates of gradualistic change, finding rates along the lines of 10% per million years. This means a fantastically small amount of change per year or per generation, which should just be wiped out by genetic drift. It also implies uninterupted multi-million year long selection pressures, which is terribly odd, and also seems to beg the question of why not select for more change over a shorter span of time?

Speciation Theory

All of this is well and good and most workers today try to follow these recommendations, good papers carry them out fully, examining entire faunas, gathering solid data for statistical analysis, paying attention to stratigraphy, etc, and really great papers make explicit statements about null & multiple working hypotheses and put their theoretical assumptions up front.
Beyond this, G&E start trending into more controversial territory. They enter this territory by way of an opening analogy: 

"speciation is the raw material of macroevolution, and genetic substitution within populations cannot be simply extrapolated [into macroevolution] [...] We therfore challenged [that] change in gene frequency within populations is hte building block of major evolutionary events"

Species selection/species sorting is selection at a heirachical level higher than the cannonical individual, it is something that is still strongly debated today. As they presented it here and in their 1972 paper, marginal species randomly enter peripheral environments. These sub-populations respond especially well to their surroundings in some types of peripheral environments. From this, an overall effect arises, a trend. Lets say a population is exposed to cold conditions at multiple points (and even at many times) along the edge of it's range, and that this species always tends to strongly react to 'cold' by forming thicker fur, bulkier body-types, etc. This means that, of the varieties of this species that are out there, a bunch of them are going to be cold-adapted, and over geologic time-scales, you're often going to have cold-adapted sub-types pop up. There's a good chance that the cold-adapted subtype, simply by the numbers, and through the actions following allopatric speciation, will tend to be successful and replace it's parent variety/sub-species/species. And this process repeats. The "net effect" is a trend in body-type, fur, etc. 
This is a messy idea, and a big problem is, what are G&E saying is actually going on? To continue with the above example, does the trend towards 'cold-types' happen because of differential reproductive success of some individuals within a population, or is it happening because of the success of the species as a whole? How do we distinguish selection for cold-type individuals against selection for cold-type species? 
Also, in the above, and maybe this is just my misunderstanding, the overall environment doesn't need to get cold, the whole lineage can show a trend towards the 'cold-type' while the temperature across the overall range remains the same, the cold-types win out because there's always a bunch of them around and they can expand out of their limited allopatric range. Perhaps that'd be a good test for species selection, a non-adaptive trend that starts out as an adaptation to a local environment (this is the opposite of how Gould often talks about adaptations, with most current 'adaptations' starting off in a different functional context, or iow as 'exaptations', in his coinage).
G&E talk about their ideas about trends and species selection being a necessary/logical consequence of two things, 1) the occurence of punctuated equilibria (itself a logical consequence of allopatric speciation applied to the fossil record) and 2) that the morphology associated with a speciation event is random with respect to the direction of evolutionary trends within the group (their so-called "Wright's Rule").

G&E also wander a bit too closely to the line of '"explains everything" when it comes to punctuated equilibria also. They consider anagenesis to be simply the result of species selection over many, many splitting events (making it something like a trend). But anagenesis is most people's word for "phyletic gradualism". So they appear to be saying that punctuated equilibria can actually explain the very process that it's set up antithetically to, perhaps this dialectic 'negation of negation' is the Marxist-Hegelian spirit at work in Gould. Regardless, a theory that explains everything in the universe is a useless theory (consider the "godidit" idea, even contradicting evidence can be explained as "godidit"). Perhaps, similarly, a theory that can explain everything under it's ambit is a little too good (and by implication we're probably deceiving ourselves and the theory is ultimately wrong or more limited). Along these lines, G&E even claim that punctuated equilibria can now explain events below the species level, especially within asexual species; we already have a theory that explains those phenomena, it's the standard modern synthesis, there's no need to tack on punctuations.
G&E also step into what I think is unfamiliar territory for them, and they really step on it. Perhaps in the 70s it was debateble if they were right or wrong, but their idea that speciation occurs with a 'genetic revolution' (admittedly this is attributed back to Mayr), and that this revolution involves drastic re-structuring of the regulatory parts of the genome, is terribly wrong. When you start writing things like  (and this is actually Carson 1975 that G&E are quoting):

No, not that Carson

"Speciation is considered to be initiated when an unusual forced reorganization of the epistatic supergenes of the closed variability system occurs"

you know you're in trouble: time to take a step back and re-evaluate (see here for a more sympathetic and fuller discussion). 
G&E are particularly wedded to the idea that evolution occurs through variation in the tempo and mode of development, which is why Gould is so interested in heterochrony and paedomorphy. Perhaps Carson's statements were just too 'in line' and tempting with their thinking to prevent them from stepping into this topic. I just want to be clear, this issue of the genetics of speciation was a lively topic for a long period of time, there's nothing 'invalid' about it obviously, it just seems to me the G&E overstepped, widely, by taking a side on this issue in this paper.

G&E, despite getting some things very wrong, got a lot right. In particular, Figure 1 shows how they see punctuated equilibirum, with it's branching pattern of speciation (they call it a 'v' pattern and contrast it with what others call a 'y' patter). Figure 1 (Figure 8 in their paper) is basically what any phylogenetic tree looks like in modern papers today.

Figure 1

Compare this to Figure 2, from Klapper and Johnson 1975, a paper they examine in some detail (and showing the 'y' shapped pattern). Figure 2 is the sort you commonly see in older papers, you very rarely see a phylogenetic tree presented in this manner. 

Figure 2

This is a minor point in some ways perhaps, but it illustrates that G&E were definitely on the right side with respect to branching and clades.

On Punctuated Equilibria

Reading Eldridge and Gould, 1972. Punctuated Equilibria: An alternative to Phyletic Gradualism. in Schopf (ed) Models in Paleobiolgoy. Freeman, Cooper, & Co. 

E&G begin by noting that research is not conducted in a vacuum and that we don't observe data with a "viewpoint from nowhere": we use theory to organize and interpret data. they call this a "picture" rather than a paradigm/research programme/etc, explicitly trying to avoid the longstanding debate over those terms.

Stepping off from this, they claim that most paleontologists hold a conceptual picture of evolution walking along with slow and small steps; they term this "phyletic gradualism" and link it with sympatric speciation. Importantly they feel that paleontologists haven't been keeping up with the mainstream of population biology, where allopatric speciation is (or at least was in the '70s when the paper was written) was all the rage.

So with that hypothetical apparatus in mind (that "picture" influences theory and paleos currently work under a gradualist picture), they consider how allopatric speciation would look in the fossil record. E&G look at two fossil groups and attempt to establish that the data can be explained, and can possibly be more "interestingly" explained, under the allopatric model.

First they consider Poecilozonites, a genus of pulmonate snails from Bermuda. Using different pictures, they can argue in support of allo- or sympatric  speciation. The species under consideration are all subspecies of P. bermudensis that are marked in being paedomorphic; the adults retain juvenile features. A story of gradual cumulative change can be laid out, but when you start including geographic information, more support is seen for allopatry.

Second they review Phacops rana and related trilobite species from Devonian New York--Ohio strata. In particular the discussion focuses on changes in one 'character' (although it's a complex character with many related components, as the 
authors point out), the number of "dorso-ventral files" in the eye.  They find that the mainline species has 18 of these eye-files, and argue that marginal populations arise with variable number of eye-files. These marginal peripheral populations then expand/migrate, overtaking the mainline. This is the allopatric model in essence. In each case of these triblobites there's a reduction of the number of files in the eye (see Figure 1). 

Figure 1 - Hypothetical Phylogeny

I don't really know anything about the eyes of trilobites, other than that they're complex/compound and insect-like, but are not related to insect eyes. Eyes are fascinating structures, famously Darwin seemed to waiver that natural selection could produce something so complex, and who's function seems so reliant on the interdependence of parts. But of course Darwin immediately recognized that the eye could evolve in stages, and he even cited some fossil examples of probable stage. In fact, one would think that that was a lucky accident and that eyes turned up once in a primitive ancestor and have been inherited by all eyed organisms today-- or maybe they evolved twice, one for organisms with eyes 'like ours' and one for compound eye type organisms). But that's not the case, eyes of various sorts have independently evolved many times amoung animals, up to 100 times.
The only other thing I know about trilobite eyes is that their lenses are made of calcite, a mineral. Our eyes lenses are nothing like this, they contain crystallin, which is a protein, not  a mineral (despite what its name might suggest to some) and our lenses are metabolically active.
So this business of "dorsoventral" whatever seemed like it was worth looking into. Trilobite eyes are compound, similar to an insect's, but independently evolved (they're possibly the oldest eyes we have on record). Each facet is made up of a small calcite lens (and other tissues), and a string of lenses is what E&G is referring to as a "dorso-ventral file". There's more to the eye, with the visual unit, capped by a lens, being called an ommatidia. Lines of lenses that run between the dorsal and ventral surface of an eye are called d-v files, and lines of lenses that run horizontally across an eye are simply called rows. The number of files is used in the determination of species within trilobites.

Figure 2 - Trilobite eye structure

Interestingly, the some of the specimens referred to by E&G are from the Marcellus Shale in NY (a source of hydrofraked natural gas).

E&G go on to state that there's an expectation amoung paleontologists that successively higher taxonomic ranks should have progressively more and more taxa within it, they believe this incorrect assumption is a result of the "picture" of phyletic gradualism; as time goes on more and more species are produced. The reality is that there are, infamously, lots of higher ranks that are species poor, so we in some families there are hundreds of genera each containing dozens of species and good sub-species, but often enough we can have Orders with a few monotypic genera. Allopatric speciation can explain this as repeated splitting with either 1) the parent species going extinct and only marginal ones surviving; 2) when geographic isolates adapt through new modes of feeding/motion/protection/etc; and 3) when it involves a small isolated lineage.

Finally E&G address that exemplar of phyletic gradualism, the evolution of long-term (and especially adaptive) trends in a lineage. They feel that allopatry can result in the appearance of  a trend by way of analogy to how random mutation in a population can still result in the overall production of a trend within that population. Selection pressure moves the population in one direction, and something that would eventually become called "species sorting", IIRC, similarly produces the trend at a higher level. They point out a mechanism in a little more detail, relying on something like the genetic and historical constraints of the mainline species tending to result in marginal species reacting strongly and in the same way to particular to similar marginal environments--say, developing thick skin in desert environments; the net effect is an overall trend for the group of species.

You can see a lot of anticipations of Gould's later work on hierarchical levels of evolution in this work, along with some material that, probably through uncharitable readings, was used to charge Eldridge and Gould with being monstrous saltationists.

I have to wonder at some of their examples though and if they really show a signal of allopatry. With Phacops, we see a few marginal populations developing, in these cases through paedomorphosis, in different locations and then expanding over the ancestral range. E&G note that the mainline population is invariant, with 18 d-v files, while the marginals are at first more variable, and then later less variable with a reduced number of d-v files. But why isn't this just a large, general population with variability in the number of d-v files, why consider the variable population to be an isolate?  If you look at any one slice through time, you find a wide-spanning population with variable d-v file numbers, some living in epeiric seas, other in marginal seas, which aren't terribly different environments either. 

Figure 3 - Some notes on the hypothetical Trilobite phylogeny. Red lines 1--3
are samples at a particular time, the green arrow is a possible trendline.

Figure 3 show populations (marked with red lines) with 1) 18--17 d-v files; 2) only 17 d-v files; and 3) 15--17 d-v files. Further, the green line in Figure 3 shows that in epeiric seas as you move through time the number of d-v files changes 18 to 17 to 15, a trend of reduction in this group at this location. The authors posit that migration has occurred  not evolution in place over a long period of time.

 Obviously the justification for allopatry must be in Eldrige's (and others) stratigraphic and geographic work on the group, but it'd be more helpful to have some discussion of that.

One other thing that really sticks out in this work is that E&G are heavily operating within the adaptationist programme, ironic given that Gould is such a critic of that. Whether they're considering allopatry or sympatry, they can find adaptationist explanations for all the features. Perhaps shells became thinner as an adaptation to living in limey soil, or perhaps that was just the result of drift, a meaningless fixation. It's hard to believe that you can have a wide ranging population of Phacops trilobites with something like the structure of the eye varying so much, and that this is the result of selection pressure for the number of d-v files, rather than just meaningless variability in their number. Eldridge, and others, promoted the idea of identifying species within the trilobites by counting (presumably amoung other things) the number of dorso-ventral lines. Perhaps that 'picture' of trilobite evolution coloured his ideas here.

Disinteresting Star Trek Conventions

Reading: Dear, Peter. 2001 Science Studies as Epistemography. in The One Culture, A Conversation about Science. Labinger & Collins, Eds.

This essay makes the point that Science Studies needs to be disinterested, by which the author means 'not interested in the scientific truth of the matter under study'. If the researcher used normal scientific methodology in order to study his subject, he'd be introducing an 'interest' that could bias the results.
But the problem with this is that the scientific truth of the matter at hand is relevant to the study of science, to the history of science, and why certain theories are accepted while others are not.

In Science Fiction, the reader is asked to suspend disbelief over a few technical issues in order to provide the setting and backdrop against which the story takes place. This, by way of analogy, is like Dear's disinterest. But there is a major problem with this type of disinterest and suspension of disbelief: it's one thing to think about Warp Drives and allow them to exist in order to be entertained and educated by the stories in Star Trek, it's quite another thing to actually go around believing that, yes, Warp Drive does exist. While that belief might seem insane to most people, there is a tendency amoung Trekkies to in fact believe that the Science of Star Trek is real science, or a likely and reasonable projection of what science will be like in the future; it's not science today, so we need to suspend our disbelief in that sense, but one day it will most likely come to fruition, it's believable.

A Star Trek Technical Manual, 
yes, that's "a" manual, there are 
several and they'll explain the 
physics and engineering challenges 
involved in incorporating the 
Bussard Ramscoop into the 
Warp Nacelle, or that a 
Nanocochrane is a billionth 
of a Cochrane, itself a measure of 
the subspace field stress.

Given that this tendency or trend exists (and competes with a similar trend to realize that Star Trek is not about real science), what is the better way to analyze and critique Star Trek? Based on it's literary value or on it's scientific accuracy? Surely most would agree that literary criticism of Star Trek is more sensible than Scientific criticism. And so, by analogy, it might seem that criticism/evaluation/analysis of science should "stand-off" from the truth, that scientific accuracy shouldn't be a criteria through which we analyze the social development of a scientific research program.
But that's wrong, the analogy fails, because Star Trek is literature, it's not the truth and doesn't claim to be scientific. The truth of scientific correctness of a research program or theory is very much a part of the how and why it's successful. The truth of a sci-fi story is not, in fact in a way it's explicitly not, a part of why the story is successful.

Scientists don't just happen to stumble on the truth, the scientific enterprise (see what I did there) builds upon previous successes in order to achieve more success: science progresses. Maybe not in straight lines, and certainly not inevitably, science does form columns and march right into progress, but, nonetheless, it does progress. So it's grossly inadequate to evaluate science from a sociological perspective without taking into account the scientific correctness of the theory, research program, or even researcher, under study.
Clearly there are other influences. Going back to the Sci-Fi analogy, IF you ask the audience to suspend disbelief too much, then at the very least you cross genres and end up in Science Fantasy Land, where hobbits have ray guns, and that's just plain stupid.

No Comment on either.

In the sociology of science, there is a tendency to reject experiment and empiricism, largely because of conventionalism: explaining experimental failures through auxiliary theories that represent an ad hoc defense of the core theory. Philosophers of science like Karl Popper insist that we make a "bold" decision to refrain from conventionalism (and also to design experiments that test our theories where they'd be the weakest, to try to disprove our theories rather than merely confirm them). This has a parallel in science fiction.  The science of Star Trek has been laid out in books and articles and is moderately well established; you can argue about the results of hypothetical actions in the Star Trek universe, and arrive at canonically consistent results (whereas you can't do this in the Dr. Who universe, because time is merely all wibbly wobbly). Star Trek Conventionalists can criticize a Star Trek story if, say, it involves ship speeds greater than Warp 10. If there's a story where this happens, we know that this is not allowed by the fictionalized science, and so some other explanation has to be offered, or instead we could say that a story must stay within the conventions of Star Trek (not to be confused with Star Trek Conventions of course). Popper wants us to avoid that kind of conventionalism and to make what's arguably a quantum leap: that a theory which hasn't technically been completely falsified, should nonetheless be discarded, and we should move on to another. If you do that in Star Trek, what you get are arguable disasters like Enterprise or Andromeda (as far beyond Star Trek as Trek was beyond Today).

Actor Scott Bakula, playing Dr. Sam

Beckett playing Capt Jonathan Archer,

who's hoping that his next leap will 

be his leap home.

In Science, researchers are supposed to,of course, be disinterested; they're supposed to not be interested in one particular theory over another because it's more popular; it's what their lab director has a research program in; or because it's what the government is providing funding for--a literary critic of Star Trek isn't supposed to be interested in, say, the Romulans coming out on top, and if that doesn't happen well dammit the story was flawed! A science fiction critic is supposed to be interested in the story. A scientific researcher is not supposed to be disinterested in the truth.

Responses and Reactions to Threatened Paradigms

There have been a few responses to Dupré's column on a crisis in Evolutionary Theory; Dr. Jerry Coyne's and Dr. Massimo Pigliucci's.

Coyne's arguement

I think Dr. Coyne's argument would be seen by many as the standard fare to expect from most researchers on this issue. A crisis is an extraordinary thing, and it requires, so the saying goes, extraordinary evidence to support it. Dr. Dupré instead offers some interesting things that perhaps Ernst Mayr would've found really surprising, but not an Kuhnian indictment of Evolutionary Theory. 
Dr. Coyne's main beef is that we tend to hear the evolution is in crisis from a lot of quarters, and they're usually wrong. This is not to say that there aren't any debates between biologists, just that we aren't in the stagnation followed by revolution stage of Kuhn, nor near it.

Pigliucci's Points

Dr. Pigliucci's essay is as much a response to Coyne as it is to Dupré. Some would argue that a mainstay of philosophy is to use reconciliation between opposing camps to better get at the 'truth' of any particular matter, and that is what Pigliucci attempts here.

A major disagreement between Coyne and Pigliucci is over rare events and important events. Obviously an event can be both, and Pigliucci cites the Big Bang as a good example of just that. However, while Inflationary Theory is important, did it result in a re-writing of the Standard Model in Physics? While Margulis hit on something amazing in biology, does the endo-symbiont hypothesis really challenge the Modern Synthesis?

Another contentious point is the importance of 'causal arrows' that don't extend out of the genome. I don't think most would consider Coyne a genetic determinist, certainly not in the way that Dawkin's is usually accused of being, but he does seem fairly set in the idea that most of the important stuff traces back to the genome, and things that don't are just ancillary, not revolutionary.

This entire argument really tracks back to, or at least mimics in some ways, reactions to Kuhn's Structure of Scientific Revolutions (pdf). Many felt that what Kuhn was describing was the way science normally operates, that he hadn't hit on anything really interesting, and for others his shifting paradigms concept was a truly revolutionary way of understanding change in science, of addressing the 'problem of progress'. For the people who felt Kuhn wasn't saying anything new, well, it was just that, he was describing things events that were already well known, understood, and accepted. His small problems that a standing theory couldn't address (and that eventually were involved in the theory's downfall), weren't capable of bringing the theories down (in this contra-Kuhnian line of thinking). The small problems were relegated to the side or worked on further in the normal process of science, and only added to the existing theory. Thus it is with Dr. Coyne's assessment of Dr. Dupré's crisis claim, the small issues are just that, small, and while they're real, and affect evolutionary theory, they don't represent a crisis.
Prof. Pigliucci seems to feel differently, even if he isn't happy with Dupré's use of 'radical' to describe the changes, and he rattles off a list of concepts that are foreign to the Modern Synthesis.


The biggest challenge to the Modern Synthesis, in my mind, was Genetic Drift and Neutralism, even tho some might argue that they're 'fully' accounted for in MS. And they were successful challenges, and they defeated the Modern Synthesis, or at least the MS-based claim that they couldn't contribute to an organism's evolution and history. But the MS was formulated around a hundred years ago; I don't think that Dr. Coyne is trying to defend the traditional MS in this piece. Dr. Dupré explicitly mentions the MS, and his 'threats' are threats to the MS, but haven't we moved away from the MS already anyway? That's been my impression for a while now, so while Dupré would certainly be right that the traditional Modern Synthesis, which is pretty explicit about what counts in Biology, is challenged to the point of crisis (Kuhnian or not) by the 'threats', or rather, it already had been challenged by those threats and had to give in to them.

Threatened Paradigms?

Dr. Dupré is the Director of the Economic & Social Research Council's Centre for Genomics in Society. He considers speciation by branching and genetic determinism to be  "Threatened Paradigms", as detailed in his column, Evolutionary Theory's welcome crisis. Here are my thoughts on his threatening paradigms.

Horizontal Transfer

This is not a new phenomenon, in fact it's something that's so well established and argueably uninteresting that it's made it's way into high school textbooks. If our focus is on largish mutlicellular animals, then yes, we're probably not appreciating the quantity of horizontal tranfers that goes on in life, but the bigger problem there is that we're focused on largish mutlicellular animals in the first place! Microbes are by far the greater moiety that makes up life, and there horizontal transfer is rampant. While the recognition that microbial life is where the bulk of the action of life is 'at' is an important recognition, it's not one that Dupré actually calls out; it's not something that really changes our understanding  of evolution; and it's not a new idea.

Epigenetics

Again, this is not a new phenomenon, and while it wasn't in my high school textbooks, I honestly wouldn't be surprised if it was in then now. Dupré also overstates the case when it comes to epigenetics, it's not like the outside environment sends molecules into the organism that then alters the genome or suppresses/activates large segments of it, it's the genome that largely does the control work for epigentics. Much like "Evo-Devo" as a phrase, epigenetics is something that seemed to claim something radical, but as a program, hasn't altered the status quo much. 

Also, note that what  Dr. Dupré claims here is that, these are not merely interesting addenda to the Modern Synthesis, but rather they're 'Radical Restructuring of Evolutionary Theory'.  From what I can tell, if Stephen J. Gould's ideas, as worked out in his magnum opus "The Structure of Evolutionary Theory" were to take over the majority of thinking in evolution and biology, that would be a radical restructuring, not paying attention to drift, methylation, and horizontal transfer.


I 'get' that maybe  Dupré 's main point was that it's the disagreements between evolutionary theorists and biologists and the like that really shows how evolution (in fact science itself), shines, but that claim doesn't require the non sequitor of radical restructuring.

Dr. S. Pekar on ancient changes in Antarctic Ice Volumes

The first GEOS talk for the Fall 2012 semester will be a great one, from Prof. Stephen Pekar on ancient changes in Antarctic Ice Volumes.  Prof. Pekar is a researcher at the Lamont-Doherty Earth Observatory, as well as an instructor at CUNY Queens. The talk will begin at 5:30 on Thursday, September 6th, in the Graduate Center, in the 4th Floor Science Center (Room 4102).   Dr. Pekar is heavily involved with the Integrated Ocean Drilling Program and the Antarctic Drilling Program (ANDRILL) and has served on expeditions to the Antarctic, where ocean floor sediments, including important proxies for past climate, have been retreived. Prof. Pekar studies the make-up and stratigraphy of these materials in order to better understand changes in the all-important Ice Volume of the Antarctic Ice Sheets. At points in Earth's past, the Antarctic was ice-free, but of course today the continent is layered in a thick sheet of ice. The stability of this ice sheet is a terribly important question when it comes to predicting future changes in sea level. In the Mesozoic, when both poles were ice-free, the middle of the United States was submerged under the great "Western Interior" Sea, in fact North America was broken up into three island-continents because of this.  Today much of that water has been pulled out of the oceans and is held, frozen, in the Ice Sheets. The onset of Ice Sheets in the Antarctic is also one of the areas in paleo-climate studies that is somewhat controversial, some workers believe that once the Ice Sheets were established they remained unchanged, and Antarctica was essentially "dry"  (despite the ice cover, there was little free flowing water). Other workers believe that the Ice Sheets were much more dynamic, with periods in which they grew and shrank, and times when there was free water on the continent. Dr. Pekar has been heavily involved in this scientific debate, and his talk will likely touch on this and other climate-science issues.

 Please follow the link below for a promotional flyer for Dr. Pekar's talk: Past Climate and Ice-Volume Changes in Antarctica: Looking Back to Our Future

(This entry is cross-posted at the GEOS group blog: http://opencuny.org/geos/?p=118)