Field Notes Digitzation

Together with another student in the CUNY Graduate Center, I was able to get a grant from the Provost"s Digital Initiatives Grant. This grant allows us to start something exciting, the digitization of the notes taken by scientists in the field.
There's a few jsutifcations for this type of project. On the one hand, field notes are an important part of thproduction of science.  Workers record observations ---actual data--- in their notebooks and use that later on to produce scientific ideas and publications. Nearly everything else we do is heavily computerized and digitized, But taking an iPad out to a field station is very rarely a realistic option. If it's not clear why, field sites are often remote, with no electricity and no connectivity. Field sites are also often harsh, without proper shade; high temperatures; extremely high humidity, all things that can wear on electronics. Despite that however most of us still take our cell phones into the field. But paper and pen, that's a technology that continues to stand up to the field environment.   Field notes are also a pastiche of what in the digital world are multiple types of media: sketches of an outcrop; maps of field sites; tables of data; lists of GPS coordinates; alongside spontaneously recorded blocks of text. Most digital solutions to this mixture of media are simply replications of paper and pen notes on a screen. Digital pens reverse the process of digitization; they insert digitzation into our already existing processess.
But why digitize at all? Digitizating your field notes creates a back up of them. Most of us do this by photocopying and scanning the pages in our notebooks. This is a timeconsuming nuissance that sometimes still produces unreadable sections of our notes. Some people go so far as to cut out the spine outof their notebooks in order to make scanning easier. With a digital pen, the only extra work to produce a visual backup of your notes is turning syncing to your phone or simply turning on your phone and opening an app before writing. This alone makes the digitiation of field notes through smart pens worth investigating.  As long as  pen system can be found that fits into research budgets; that produces accurate renditions of handwritting; and that is manageable and portable, you've got something worth investigating and potentiallyy incorporating.
But I think smart pens offer us a lot more than redundant back ups. They make field notes shareable. Even if you previously had a set of scanned pages from your notebook, sharing them can be difficult. The files tend to be large if they're high quality. You may've scanned to PDF or TIFF,  and that decision may've dependded on the scanner you were using. Whoever you want to send the files too may need you to make the files smaller, or even the email program their campus uses may require that! And if you didn't bundle every page together, that'd mean you have to batch resize every file. A digital pen system should manage your files, it should let you send entire notebooks or ranges of pages in a choice of formats
If another worker, or you yourself, want to search for a particular passage or subject in your notes, digitzation has tremendous potential to aid in that. When I use a notebook, I put a table of contents or index in the first few pages and I add to it over time. That's how most of us make our notes "searchable". Really important things I flag with a post-it type of sticker. Usually I put a header on each page. When I really start getting desperate I'm drawing stars, using highlighers, or anything to make a page stand out; because more often than note when I'm searching through a notebook I'm flipping through the pages quickly and need something jarring to make a page or passage stand out. A digital system should be able to do that and expand beyond it. A digital system should handle indices and tags, but also should make note searchable from the start. When we're evaluating these systems, handwriting recognition and searchability are prime criteria.
Not all field notes are spontaneous. A lot of field notes are very patterned and regular: you're measuring or estimating the size, colors, rock types, strike and dip of beds at an outcrop, thickness of beds, etc. Or you're recording the location, body mass, length, species, and sex of a dozens of living specimens at multiple locations. We're doing that because this data will be used later on. We're building databases from our notes. For most of us this means getting back from the field, to our labs and computerrs, cracking open our notebooks, marveling at the amount of dust they've taken in, and then entering by hand all of the data. Sometimes we're lucky enough to have junior lab workers that can be assigned this tasks, and often we're the more junior worker that get's assigned it. With smart pens we should be able to save time, by writing the notes we should be also be generating text that can then be copied as a whole into a database. In fact we should be able to have that entire process automated. And if we have some connectivity at our field locations, we should practically be able to build databases in real time or nightly. But one thing that should be apparent in academia is that saving time often isn't much of a draw. What does the PI care if a digital process saves a student's time? Well one added benefit of digitization is that it can result in less errors. The data entered into fields can be set to be numbers, text, or a mix of both, just like in a spreadsheet. This prevents the handwriting recognition system from mistaking a "7" for an "h" or something along those lines. Or it can at least throw a flag up for a human to review when it hits a contradiction like that. It also allows for errors to be addressed while there is still someone in the field. Even with a notebook alone, there can be confusion about what's recorded. If it's months later, even the person who took the notes can be unsure of what they were recording and why. Having the people back at the lab able to contact a field worker while on location can clear up errors and make us more confident in our decisions regarding how we've resolved errors.

There are a few other possibilities and abilities that digitzed notes offer beyond handwritten notes. By having searchable text, the frequency and co-occurence of words can be tabulated and studied. This potentially can tell us something about how a worker learns about their field site. Perhaps there are differences in word occurence between people new to the location and others who are experts about the field site? Perhaps there's a difference, or similarity, between expert scientists and expert non-scientists about the site. Those are more distant possibilities for this project. At the moment, we're just trying to figure out what digital processes and practices work best for a variety of scientific fields.

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.

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.

More on webpages

I was having a bit of a problem getting a viable web page up and running before. Our campus's document sharing system (Xythos) seemed to be working, but the webpages I was making just weren't functioning well. I had been using Microsoft Publisher 2007.
I then tried using Adobe Illustrator, but that ended up not being too easy to use, I could get a layout setup and create slices, but I really have no idea how to work it as html, all I had were images.

Then I found out about KompoZer, which is a 'what you see is what you get (WYSIWYG) editor. I've been able to get a two-page website up and running. It's really uninteresting right now, and exceptionally plain. I suspect that the coding is excessive for such a simple site too. But, now at least I have something I can work with:
https://wfs.gc.cuny.edu/rschenck/www/index.html

Pre-Grad School

I'll be starting in the CUNY Grad Center's PhD Program in Earth & Environmental Sciences this fall. I need to sort some things out before that. I've already been through a Master's degree program before, at Adelphi University; the MS was through their Biology Department where I was lucky enough to work with Dr. Beth Christensen on paleoclimate-paleoceanography. So on the one hand I have some idea of what Graduate School is like, keeping in mind that a PhD program is going to be different. I know I do good work in a lab and do good research and that I have some trouble writing up that research; I never published my Masters as a separate article in a journal, but I have done poster presentations on my subject matter, and I've done an oral presentation at an AGU conference. Clearly the big hurdle I need to make it over here is actually submitting and publishing in a journal.

I've done research, and I've applied for and obtain small grants, and I was also lucky enough to be responsible for equipment purchasing on a big grant where I work. But I haven't obtained and administered a big grant on my own. That involves a lot of paperwork and management, its not the sort of thing that you normally think about as being associated with doing science. Business, sure, that can be expected, but you tend to think of the work of science being spent either looking down a microscope or pouring over research papers; if a spreadsheet's involved its for tabulating data, not doing accounting. I'm expecting to see lots more of that as grad school progresses; I'll need to obtain funding just for taking credits/tuition, if that's doable, or maybe I can get a fellowship or some sort of grant for doing research while at school. I don't actually expect much 'support' in that sense from the program. In some ways, they shouldn't be providing that sort of support, students need to develop those skills, and sink or swim is a way to do that.

So I understand that scientists spend a lot of time doing things other than science. How much, I can't really say. I'd hope that the program can help make that clearer, but its not what we usually think of the doctorate curricula are.