Pursuing praxis

I’m generally a pretty nice person, I think. My attitude averages on the positive side of neutral, and two standard deviations don’t stray considerably far from that average, with a noticable tail end in the "quite happy" range.

However, I have recently had the inadvertent opportunity to simulate what I would be like as a peri-homicidal psychotic: dump me into the deep end of computer programing with zero experience and expect 3 hours of "programming for n00bs" lecture to make it all better. I get so frustrated my head wants to explode, and I spend hours managing my rage in order to preserve relationships and stay on the good side of the law. In these situations, judging myself to be bitchy is a good thing - it means I’m only bitchy.

At root, I think I can reasonably attribute it to the self-taught-programmer/professor who learned it 15 years ago and is so competent now that he thinks you can just pick it up, no sweat, in a weekend or two of considered work. No "C++ for Dummies" or "Read this if you value your sanity" pointers or tips or anything. Just a copy of his half-finished draft of his book-in-progress that assumes you know how to program, and then you’re dumped in the deep end with the sort of sympathy that rings exceptionally shallow after a dizzying 80 minute watch-me-program-while-speed-typing-and-juggling-three-windows-on-the-screen lecture. Arrghhh!!

The good news is, I’ve also discovered how to terminate this simulation: drop the damn class.  

My blood-pressure, neck muscles, proto-wrinkles, lab-mates, neighbors and boyfriend are all silently thanking me, I’m sure. But it’s nothing compared to how much I’m thanking myself, lol, especially for having the foresight to take enough research credit hours that I’m not in hot water for dropping the class.

Back to work! 

Well, close.

I have the awesomest lab and labmates. My natural inclination (with anyone) is to decline social invitations to lunch, dinner, etc. in order to "get work done." Which may or may not happen as envisioned. But still, the drive to work is very seductive, especially when I’ve made the resolution to leave blocks of time - whole days, in fact - to "focus on my research."

But, for the price of an enchillada, I learned the basics of how to procure, maintain, and use a dermestid beetle colony, at home or at work. Dermestids are the beetles used to clean up carcasses and leave a nice clean skeleton. I also learned about some rather ignoble people and practices surrounding institutional colonies, mainly resulting from a staggering degree of irresponsibility and failure to be considerate. And I learned that the dermestid beetle colony housed at the Smithsonian has been reproducing in isolation for so long that those beetles now can’t breed with non-Smithsonian dermestid beetles. Evolution in a test tube, I’m telling you. Or bathtub or cardboard box or other container, context depending.
 

Teaching starts today - 14 weeks of functional human anatomy smashed into 8 weeks, plus 40 hours of geometric morphometrics this week.

If it’s got form and function (and a backbone), I’m on it!

So, no field work for me in South Africa, despite some fairly well-sketched plans for it. There’s the overabundance of work at the museum, but what tipped the balance was a nation-wide strike by public service workers. "Talks" had been going on for several weeks - perhaps even months - with the union demanding a 12% salary hike, and the government only willing to give 6% (7.25% as of June 15th). The strike started around May 25th, and is continuing.

This means many government-run services like the courts are either just creeping along, or not working at all, many public schools aren’t open, so kids are out and about. Although nurses and the police have contractual agreements that they’re not allowed to strike, public hospitals have been minimally staffed, meaning private hospitals are over-booked, and many striking healthcare workers are now being fired, along with other strikers.

Firing union members - even with warnings, ultimatums, and deadlines - is one of the surest ways to piss these people off, so some of the demonstrations have recently turned violent. (Teachers burning tires and trying to shut down a provincial hospital in Kwa-Zulu Natal on Thursday night). Newspapers this morning quoted President Mbeki telling union members to "behave themselves," (as if that works for 8 year-olds, much less a group of hundreds of thousands of adults who feel entitled to use physical force as a means of getting what they want - which is what unions do). The papers also announced that some 200,000 police officers will might be striking as well. That’s right, they’re considering breaking their contractual agreement to the contrary, right when people aren’t behaving themselves. It is as I predicted: if police officers are members of the same union that is striking and breaking the law, the situation simply cannot turn out well. It’s an inherent conflict of interest - yet another fantastic reason unions only ever make things worse - and in this country, I don’t have too much motivation to assume the best about people.

Oh yeah - and many private taxi companies are joining the strike as well - I think at the behest of the union - on the arguement that much of their business comes from public service workers, and the taxi companies are best served by not operating (i.e. not making any money) and further crippling those people and businesses that keep the country running while others sit on their hands in petulant self-righteousness expecting to keep their jobs, get higher pay (and back-pay while striking!), and return to a friendly work enviroment as if they hadn’t just threatened their bosses. Isn’t that extortion?

These are some of the same taxi companies that gained worldwide infamy in the late ’90s by warring with each other over "territories" and routes, and shooting up each other’s vehicles and killing scores of passengers. Looks like the ‘wars’ started up again, just before the strike. Needless to say, I won’t be taking any of those taxis to the airport (the South African equivalent of matatus - 14 passenger minibuses). Better to pay an arm and a leg for a private yellow cab, which was my plan anyway.

The good news is, the airport hasn’t been affected yet, so hopefully things will not disintegrate so fast that I’m delayed getting out of here on Saturday.  

True enough, other researchers here have succeeded in doing field work, but in my book the facts that I don’t have a travel partner or assistant, that I’m female, and that I haven’t traveled around the country much yet, tip the scales in favor of staying put in the museum. I’m quite alright with this. Pity I’d (finally) gotten a grant to reimburse field work costs! Hopefully I can persuade them to let me use the money for other research costs coming up.

For the record, I’d planned to go to the Hluhluwe/Umfolozi Game Reserve in Kwa-Zulu Natal province to see nyala, one of my dear tragelaphine antelopes, and the only one not present in East Africa. They’re the fashionistas of their tribe, males having elaborate coats with stripes and long white hairs along the spine that they can make stand up to look bigger and more impressive. Their horns are very similar to sitatunga horns, and the females are similar to most of the other tragelaphine females. Nyala are rather rare, but locally numerous. I figure they’re not going anywhere too quickly, and I can deal with them later.

I have my microscribe, in my own hot little hands. AND it works! It passed all its accuracy tests with flying colors, despite my extreme skepticism given the small size of the box, the 20 days of transit, and the fact that it was packed upside down. I now store it behind three locked doors (two of which I have the only keys to) and today I can start on the backlog of specimens cluttering the aisles of the osteology department.

“Hello? May I please speak to someone with a functioning brain?”

Such is my Microscribe Saga – the month and a half exercise in frustration that began with Virgin Atlantic breaking my microscribe (a bit of computer equipment for recording and importing shape data from objects – antelope skulls, in my case), followed by a week trying to wring a repair/work-order number out of the parent company before I could ship it, followed by a $500 bill (paid by yours truly) to mail it back to the US for repair, followed by a $2000 bill (very kindly covered by my advisor’s research funds) to upgrade it to the new model because they don’t make some parts for the old model anymore. (And mind you, when I asked about the difference between the new and old models, I was told: color, and a USB port, neither of which was broken on my otherwise mangled microscribe). Finally, after 2 weeks to diagnose, and 2 weeks to actually fix and calibrate it, they posted my microscribe on Feb. 28^th, by FedEx International Priority, to arrive in 2-3 days’ time, at the museum address I had provided.

Now the fun begins. First, the FedEx contractors (a courier service at the airport) failed to reach me on my cellphone, which has been in service continuously since Jan. 19^th. Did they leave a voicemail? No. Call back, try again? No. Try the ubiquitously popular text message? No. Call the museum, the name of which was on the box and is a well-known landmark in the city? No. Call the other fellow, head of department, whose name was also on the box? No. Do anything besides sit on their hands and wait for a bolt of lightning or burning bush to tell them what to do? No.

And, thanks to FedEx’s backlogged tracking number service, I was under the distinct impression my dear microscribe had been sitting in some British town for a good six days. After 2 days of phone calls and emails, I learned it was actually in Nairobi, and likely had not spent an inordinate amount of time in Britain at all. In fact, it had probably been sitting in Nairobi for nearly a week at this point. Remember also, I came out here in large part to USE the microscribe in the collections. All my work to date has been second-priority stuff, with a ruler, string, and notebook, which doesn’t justify the $400 research permit or the daily bench fees – not including the plane tickets, housing, paperwork headaches, or the bureaucratic bullshit I’ve been putting up with for the last several months.

But what of my dear MS? The holdup was due to its declared value - $2000 (about a third of the replacement cost, actually). High-value items of this sort need a PIN number for delivery. (I’ll hold off on asking Why??) Who knew? Not the company in California, for sure. Nor FedEx International, apparently, nor the museum whose missing PIN jammed up the delivery works. And of course, the museum person with PIN codes was out of the office last Friday, when I figured all this out. The secretary kindly passed it on in his absence (probably a no-no), and I phoned it in to the FedEx guy, leaving it in a message with a co-worker, and a clear request that he call me No Matter What, Today.

Nothing. So I nagged him again Monday morning. Did he have the PIN? “Huh?” The PIN and message I left last Friday. No, of course not. So I gave it to him, and asked when I might expect the delivery. This afternoon, perhaps? “No, it will take 2-3 days to process the PIN.”  

WHAT?!? … Apparently it takes a long time to crunch through a string of nine letters and numbers. But what could I do? I told him in no uncertain terms that that was Ridiculous, the package was Urgent, and to please deliver it As Soon as Humanly Possible.

Speaking with the head of supplies at the museum on Monday (because of course no one works on Saturdays, or before 9:30am, or really after 4pm, and certainly not during lunchtime, from 1-2pm, or really the half-hours bordering that time), I learned there was also an issue of a clearing charge. For what, exactly, I am still ignorant. For delivery? But I already paid for that. Apparently, if the goods are for research by museum staff, the museum will cover it. If it’s for personal use, I have to pay it (and it’s about a hundred bucks, I think, to get it across town, which is nearly half what it cost to ship it to the other side of the planet – and in 1/7^th of the time!).

One of my contacts here volunteered to write a memo to the supplies guy (by hand, since there was no power that day), basically lying that it was for use by various department staff so I could dodge the fee, because he fully understood it’s mine, and for my use, and while I’m happy to demonstrate and share knowledge, I haven’t any mind to let others risk breaking it – not that I really have time for that now, I’m so pressed as it is. So, memo written and submitted, I should have had it Tuesday. I gave the supplies guy the FedEx guy’s info, the tracking number, the situation, everything. I passed it off as cleanly as I knew how. Full information disclosure. Cards on the table.

Two days later I called the FedEx guy to see what the heck was up with my still-missing package. He claimed there was an issue with the clearance fee. I said it had been handled, the museum would pay it. He then dodged to a problem with the clearing agent – hadn’t heard from him. So basically, one or both parties failed to get my baton in the hand-off of the Delivery Fiasco. I went to bug the supplies dept guy. The secretary assured me the clearing agent would talk to FedEx today. Hopefully I should have it tomorrow. That is, Friday, March 16^th, 2 weeks later than expected.

Evidently by “tomorrow” it’s understood here to mean “Sometime this week. Maybe. Be sure to remind me at least a half dozen times. Then I’ll see what I can do about it at the 11^th hour, by which time it will probably be too late to do anything about it until tomorrow.”

So, I have ranted to various individuals about the mess, including taxi drivers, the guesthouse cook, the receptionist, my travel agent, and now a recurrent boarder at the guesthouse here (a civil engineer working near the Ugandan border), who has been very kind, and perhaps the most conscious and intelligent person I’ve yet met in Kenya. Instead of chuckling softly and shuffling away (like one prominent museum staff member today), or shaking his head and smiling (like the taxi driver), or feigning sympathy and indignant outrage without effecting any change at all (like the other museum staff member), this guy actually looked me in the eye and listened, then offered novel suggestions about what to do.

Like call the US embassy tomorrow, or even the head of the airport. The embassy? I don’t need a stamp or to be med-evacked, thanks. No, he insisted, this was a real problem, and right up their alley. They can talk to the blooming idiots at the delivery company, and get the wheels rolling, because it’s patently ridiculous that as a student and researcher here to do work, I’ve nearly wasted a third of my time because of administrative crap and blatant ineptitude and poor service.

So, if my dear microscribe isn’t waiting for me tomorrow morning when I arrive, I will call the FedEx guy, give him hell, make a trip to the supplies office (because face-time is how things work here, if they work at all), and then call the embassy, give them my sob story (in as professional a tone as I can muster), then try to forget the whole issue so I can measure as many eland skulls as humanly possible before closing time (to the tunes of KMFDM, drowning out the static-clogged Indian music and references to Allah being piped over the lab radio) and tomorrow take off for two days of sunshine, driving, and hopefully lots of bovids. And hopefully on Monday I can finally do what I came here to do.

And if my microscribe has not survived over two weeks of transit… well…. I just might give it up, cry for the first time in my professional life, and resign myself to doing a PhD with old, unsophisticated, second-rate methods, supplemented by suggestive but ultimately inconclusive microscribe data taken from too few of the wrong specimens to really be of any use at all.

But by golly, I plan to see lesser kudu this weekend. Crack of dawn, there I am, binoculars and camera in hand, tracking down the wiley wascals of the northern bush of Tsavo West Nat’l Park, some 50 miles northeast of Mt. Kilimanjaro. My plan is to see all those bovids that can most reasonably be seen in Kenya – lesser kudu having a fair distribution through Ethiopia, Somalia, Kenya, and Tanzania – thereby removing any reason I might have of visiting this country (or region) again in the next 20 years, if ever.

–3/16/07. PS: On the brighter side of this bureaocratic nightmare, the US Embassy got back to me right away, although the fellow was not terribly helpful, saying "Welcome to Kenya. Their bureaocracy is not as evolved as ours." Well, it’s too evolved, in my judgement, but that’s largely an issue of semantics. I threatened the FedEx guy with harassment from the US Embassy, and paid a special visit to the supplies department at the museum, and was told it should arrive this afternoon. Although my outlook now mainly consists of "The proof is in the pudding," the good news is that they haven’t yet promised to deliver it by a specific date or time. The fact that they said ‘this afternoon’ is therefore a ray of hope in an otherwise bleak landscape for science (and business in general) in Kenya. We will see. I am considering returning to Kenya (red tape depending) after Egypt if I cannot get the minimum amount of work done to justify my trip. Better to shell out a little extra, then have a heap of only semi-useful data to struggle with for the next two (or ten) years.

As for work – I’ve learned loads, and there’s months of work I could do just at Florisbad. Sadly I didn’t get to the fossils, but I’m so swamped with living bovids (and I’m not doing bovines, true cows, so Pelorovis wouldn’t really apply anyway) it’s hard to know what portion of fossil-studying to carve off. As it is, I’m taking some 20-32 measurements, 55+ notes on sutures, notes on dentition, and 4-8 photos per specimen (if available – some are partial or broken skulls, etc.) That’s a ton, though I have extreme difficulty imagining paring back. If anything I may try to swap out photos for the suture notes – see if I can get them from photos later.

But it’s been really exciting to see how just a couple of the different tribes differ in their suture fusion patterns – among adults, and also as it happens through developing juveniles. The patterns and trends aren’t watertight – there’s a lot of variation, and I’m sure I’ll encounter more, but I’m starting to get a picture of it for some taxa, and it varies consistently among the tribes.

To talk more concretely (on the off chance you’re dying to know…) it’s really interesting how, for example, in eland and kudu, the skulls start out with these really large gaps between some of the bones, and then how these gaps close, and stitch together, and then get remodeled by bone maintenance till you can’t see them in the adults – you’d be hard pressed to know that there were originally two bones there. But it doesn’t happen for all sutures that way, and when it does, the timing of it depends on the suture, and on the species. In the kudu and eland, the suture down the midline of the skull (between the left and right frontal bones, which the horns grow on) disappears lickety-split. And the suture it connects to at a right angle, between the frontal and parietal bones (parietals are right behind the frontals, also part of the skull dome, so you get a T-shaped intersection just behind the horns), also disappears lickety-split, but reappears on the side of the head, below the horns, just before it gets to the temporal bone. Chock it up to horns? Naw – the hornless female kudu do it too. And the heavily-horned Hippotragines (sable, gemsbok, roans) and some of the larger Reduncines (waterbuck, lechwes) have totally visible F-F and F-P sutures all the time, no hint of remodeling them out of existence. And trust me, some of the skull+horns of each of these groups are very heavy – it’s not a product of horn size, that’s for sure. Move to the smaller blesbok (Alcelaphines), and you get juveniles whose F-F suture goes from open and simple at the nasal bones, to zig-zagged and smooth between the eyes, to crazily complex between the horns with big gaps between fine struts of bone in the midst of being fused and remodeled like mad, and by the time it gets to the parietal bone, its already being remodeled and turned invisible. This is in the span of about 5-6 inches. Crazy! And – why??

And I haven’t even gotten to the wildebeest or the teeny tiny dik-diks and duikers yet. But from a couple casual looks, the teeny tiny ones don’t seem to reach the remodeling stage for any major suture, even when they start hyper-ossifying their craniums. (I’ve got a couple cool pictures of these tiny skulls with loads of extra bone deposited in quasi-random patterns on the forehead and vicinity – like lace or an incipient coral reef. For their size, it’s clear these skulls weigh a fair bit more than your typical midget bovid skull). The bones just come together, sit in place, the line remains visible and uncomplicated, and that’s that – you’ve got a skull that stays together and does what it’s supposed to do, even when the “make more bone!!!” switch has been turned on, as with the lace-headed bovidettes. This is interesting because - if that generalization about the small guys holds true, and I connect the dots well enough (and that’s a fair task) - it suggests how the little guys grow to little sizes, and the big guys grow to big sizes – because there are a couple of options for how to do it, and how one achieves X size can, like most other traits, give clues to evolutionary pathways taken, and relationships (both historical and current) among species.

How does one become small (that is, become smallER compared to an ancestral stock)? Assuming a rubric of typical development – that is, the ancestral stock had a typical growth trajectory of small baby to big(ger) adult, and adults look characteristically different than the babies (pretty safe assumptions here) - what are your options? Well, you can either slow down your rate of growth while zooming through the steps to maturity, basically ending up as a miniature version of the ancestral adult. Alternatively, you can keep growth rates similar and just stop development earlier (save some key reproductive changes for sexual maturity), which results in comparatively infantile looking adults. (Something along this line is hypothesized to have happened in human evolution – the quick rationale or explanation is: just look at a baby chimp; in terms of proportions, we look a lot more like a baby chimp than an adult chimp, which of course assumes our common ancestor looked kind of chimp-like; there are probably better, and worse, descriptions of this unknown ancestor). Of course, those are two extremes of a continuum, and in most cases there’s probably a mix. But it’s good for keeping peas and carrots straight in your mind.

What about for getting big? Same idea – you can simply increase the rate of growth, while keeping the same sequence of steps to looking like an adult – they’re just stretched out in terms of the number of pounds or inches between each step. Or, you can add steps, so that you zoom past the previous “adult” form and achieve something relatively new (or do a combination).

How’s this possible? Well, the simplest way is to just extend the duration of the developmental program – that is, some parts of your body (in my case, I’m interested in heads) grow faster than other parts,or grow in this direction vs. that, (and at different times to boot). Thisresults in changes in the proportions of that body part. If you just think about these as basic instructions (“grow this region of the bone a third faster than that region”) there’s no built-in stopping point. The halt signal comes from elsewhere in the body or program. So if you change the timing of that halt signal, you’re going to get a head shaped a bit differently than normal. That’s all. Do it just a smidge, and a scientist probably won’t even notice, or will chock it up to “normal variation.” Do it a lot, and they start to take notice. Do it repeatedly over tens of millions of years, and some people will say you were deposited on earth as-is a few thousand years ago.

Of course, adding genuinely “new” traits (new instructions for development) is very interesting, and more complicated (“new” being completely relative and contextual, and on the whole a misleading but common word). And on that reason alone, it’s reasonable to think it happens less often. So, my strategy is to keep a good eye out for the things most likely to happen, and among those cases, keep another eye out for oddballs, and see if and how they might go together. Because, given the fact of inheritance, systematic widespread features don’t just come out of left field, although history has a nasty habit of deleting the data that would make that obvious. I mean, when you get down to it, nothing comes out of left field, even the unpredictable congenital defects, “monstrosities” and the like – it’s just unexpected (to us) given a backdrop of experience. If one knew about the genetic abnormality prior to it being obvious, then the resulting abnormality would not be “new,” left-field, or spontaneous – we’d view it as the result of a known cause. That is, stuff acting in accordance with its identity (in this case, dynamic, organic, biological stuff, but still stuff just the same). The gambols of evolution are no less causeless, but a trifle more cumbersome to nail down, given the number of things involved, the time involved, and the patchiness of the data (and several orders of magnitude fewer people working on such questions as compared to, say, biomedical research).

1/30/07

 

Now, before you think all I’m doing here is dealing with pathetic, not-especially-African wildlife, rest assured that’s not true. I’ve been measuring a lot of heads and wishing I had a voodoo doll for the people at Immersion, who will be (supposedly) fixing my broken microscribe. I can’t mail the thing in until I have a work order number. I’ve been waiting for a week! And it’s not for lack of effort on my part. 7pm, 11pm, 2am, doesn’t matter, I call them up and explain, and explain, and leave messages, and call back, and remind, and I get nuthin’ out of them. Couple friendly voices, and a one-in-ten follow-through rate (and that’s generous).

 

But, I’ll cut that rant short. It could definitely go on a while. I’ve been entering data, organizing various things, couple trips to town, and I still have a ton to do. I’ve even got a rough sketch of my semesterly activities through mid-2009. Scary, eh? Me, a friggin’ doctor (of sorts). Man I hope this work turns out all right, cuz I need a job at the end of this little stint, and I oscillate between hot-stuff and useless-to-the-world. And I’ll be almost 30!

 

Ok ok, enough of this debilitating talk. Photos hopefully soon. I’ll likely just be dumping them on my Fotki site. It takes a long time to upload them, and then go back and link to my photos in posts and such. If I get limitless free high speed internet at some point on my journey (hahahahahahaha) I’ll make some beautiful blogs with embedded pics. Till then, I’ll just try to name and label my pics in a useful manner.

 

–

PS: Monday, 1/30: I got my work order from Immersion, and the microscribe is on its way in. Of all the 20 things that could go wrong between now and when I get it back, I hope none of them happens, and I can happily forget about my crippled technology for the next month.

The foregoing logistics aside, my trip has started off quite badly, actually. When I unpacked my microscribe, I noticed one of the joints sounded a bit crunchy (nnnnnnnnot good), and two parts of the accuracy tests it failed, one horribly so (on the wrist joint). I spent all weekend fiddling with calibration blocks, power supply and adapter configurations, re-reading the manual, you name it, trying to characterize how it was off and if I’d be able to apply a correction factor to my data afterwards. No such luck. It’s off by a good 10% on each measurement, and that’s regardless of size. Up from about <0.2% error a couple weeks ago. You name it, I probably tried it. No go. The MS is belly-up for my purposes. Which sucks, cuz I came to digitize stuff.

 

It obviously got damaged in transport, and what I think happened was security people opened up the case to have a look, then didn’t put it back together properly, and the joints traveled in a bad position and got tweaked with the rough and tumble (despite the Fragile tag and my request to have my bag plastered in Fragile stickers, which they didn’t do.) I also think they were rough or careless, because they ripped off about a quarter of the lining in the bag, and one of my calibration blocks was out of its spot in the foam. Of course, the airline absolves itself of responsibility for baggage (unless they completely lose it, which now I wish they had), especially for electronic and fragile items. I spent the weekend feeling extremely incompetent and a waste of good air, but hammered out a string of options and strategies for making the most of my time here, and for the next 4 months too.

 

Long story short, I’m sending the MS back to California for diagnostics and (hopefully) fixing, at which point they’ll charge me an arm and a leg and send it back to me (if it’s repairable at all). I can probably get it back in a month, which is just enough time for them to send it to the museum in Kenya, where I’ll meet it when I get there on March 1^st. Then, I should have a functional MS for the bulk of my collections work there and in the museums in South Africa in May. The collections here are good, but small compared to the other places, and I’ve only got a shed of springbuck skulls to get through in Namibia, as it’s mostly field and observation work out there. I’ll gather qualitative data on specimens here, as well as some old fashioned linear measurements with the trusty old ruler and string (and calipers, though using a 12 inch ruler I can get to within 2-3mm on larger measurements, and 1mm on smaller ones with just my eyeballs, and the ruler is often faster), as well as photograph some of the more important ones, like juveniles, on which I can hopefully do 2D morphometrics later on (the MS lets me do 3D morphometrics). If you haven’t heard me yabber on at length about my work yet (or in a while): morphometrics is the study of shape. It captures all the same data as linear measurements (if you do it right), but also captures the location of all the end-points relative to each other, so you can study shape and not just single linear measurements. It’s kind of a glorified connect-the-dots. Yeah, that’s what I’m getting a PhD doing: playing connect-the-dots. Dear lord. I won’t be telling the insurance people that or they’ll never take me seriously.

 

The excellent news came in tonight: I talked to KP, explained what happened and what my strategy was, and asked if he had any suggestions for getting reimbursed for this prohibitive but unexpected research expense. In about as many words, he said have them send the bill to me, I’ll pay for it out of my research funds because you really need to have this fixed, and your plan of action for this and the intervening time sounds great, carry on, give my best to James. Whew! It’s funny how not being out a thousand bucks, and not having your advisor think you’re a useless idiot, will really put the spring back in your step.

 

Now, I just have to find a better camera, cuz mine totally sucks. To my knowledge, it has taken one good picture out of (now) hundreds. For the life of me I cannot get it to alter the shutter speed or exposure time. I think I’ve tried every combination of buttons; it is permanently stuck on 1/16^th s shutter speed and 1/20^th s exposure time. The good pic had 1/64 and 1/81. I don’t know what happened. But it’s useless, and I need to avoid image distortion in addition to poor quality if I’m to document specimens and do morphometrics, so tomorrow I’m going camera shopping in Bloem. Hopefully they have something, and hopefully tomorrow morning the South African rand takes a nose dive and I can get more buying power with my struggling US dollars (man I wish they were in pounds! It’s over $2/lb right now). Yet another item I should have been more prepared on, and thought ahead for, a good camera for back-up 2D morphometrics, although 2D is such a poor substitute for 3D in bovids, it’s perhaps a lost cause. It’d be different if I was studying piranhas or blades of grass or sand dollars or fly wings or something existing mainly in two dimensions. Curly bovid horns just don’t fit the bill very well, and like hell I’m surrendering to the world of tooth-specialization and forget what the dorsal surface of my critters looks like. I will not spend all my research time labeling, counting and measuring tooth cusps. I’d rather splice a gene into bacteria, and there’s a reason I’m no longer doing that.

 

So, tomorrow I make my first trip into town and, re-remember how to drive a stick, but on the other side of the car and the other side of the road. Good thing bad driving is the norm here; I’ll be going grandma-slow and checking every direction three times. And, given the habitual nature of driving, I’ll be going to bed now so that I don’t make tired, automatic US-driving decisions and crunch the tin can of a car they’re lending me. I don’t need whiplash or more paperwork at this point in my trip. To say the least.

I once knew a lady named that.

Nevertheless, today I’m referring to the South American ratite bird, Rhea americana, which can be described as a gray-white mini-ostrich, standing maybe 5 feet tall and weighing 60-70 lbs. A labmate procured a headless frozen rhea (how many times has that phrase been uttered in the history of mankind?) and offered to share the experience of dissecting it. He’s after the leg bones, for comparison of bird/ratite bone microstructure (aka histology) with that of dinosaurs. And other peri-lab person wanted to measure wingspan and look at shoulder and arm joints, and another labmate wanted the heart (still not sure why…). And how often do you get to dissect a rhea? That’s right, never. So about 10 of us showed up and helped thaw and pluck and photo the thing. Fair bit of work. Probably twice the size of a very, very large turkey. Finally it was warm enough (and featherless enough) to skin and begin dissecting the legs. After much ado, we procured the desired longbones of the leg, and left the rest for the next day.

I opted out of today’s festivities for work though, so I can’t report on the internal structure of the bird, although we got a few glimpses yesterday (like the clavicular airsac, what I’m guessing is the superior vena cava, plus the esophagus and trachea, plus the external sternal callosity, and the remnant claws on the stumpy digit left on the wing). Despite some great shots with my new camera, I will refrain from posting them here. If some people are grossed out by dressing a chicken or gutting a fish… well this shouldn’t be any worse. But I expect the psychological element of it would outweigh the coolness factor in many cases.

Haha, maybe I should make a myspace page for the rhea. Wonder how fast it would get deleted. Hm, let’s find out! point people to Dr. Vector’s post (as well as his post yesterday) where he’s already posted some images, licketysplit. Warning: visceral material. (See also his emu dissection - a considerably… fresher experience).

I friggin love mine. I’m playing rockstar in the lab at 2am, singing along to a Romanian song I can’t even pronounce, and thinking about stuff I love to think about, thinking new thoughts and devising simple ways to get at complex questions I’m not sure anyone’s ever thought of quite my way, and I’m actually happy I’ve got this massive 40 page paper to write (not counting references, figures, tables, table of contents, index or appendices, lol) and a 15 minute presentation to devise, in less than eight hours. It’s an open ballfield! I get to talk about horn and antler development till she tells me to sit down! And then she has to read my paper on it. I have a captive audience that volunteered. … I was about to say you can’t pay for that sort of thing - but that goes without saying if you insist on volunteers. Would I rather be sleeping? Maybe tomorrow night :o). Why live if you don’t allow yourself to do what you aim to do, whenever you have to do it, whatever it takes to do it? I’m baffled by people who just work so they can spend their off time not-working, which is different from doing something. If I ever settle down with someone, we’re going to have to have a serious understanding about how I don’t work - I live, and by definition one does that all the time till you haven’t got any time left. We’ll also have to have an understanding about schedules, routines and some aspects of reliability - cuz I don’t do those things very well. I’ve been called uncivilized. I say: for what? I can’t think of anything outside what I consider work that I’ve got to do at a certain time on a regular basis. Let’s just say I’m pre-adapted for leaving for the other side of the world on a moment’s notice.

Uncivilized? Pshaw. I haven’t had a dirty dish in my sink in weeks. Hm, come to think of it I’m not sure I’ve eaten a meal at home in weeks. I’ll make up for it by polishing my piano and baking cookies this week. Hahaha. No really, that’s what I’m going to do. Hopefully my gingersnaps won’t qualify for NHL-grade pucks this year. Can you believe I used to win cooking contests? Like five lives ago. I figure it’s one of those bicycle type skills. There’s no sense in riding a bike unless you have a reason to ride a bike, right? Right.

Cool cow of the day: the southeast Asian banteng.

Oh, and how’s this for scary-cool: Ever wonder why there are quite a few big ol’ herbivores, and they never seem to live around big ol’ predators? Like moose. And the caribou, which is about a third larger than a muledeer. And the elk. I mean really, what eats a moose? Or something with basically a dozen blunt-ended spears pointed at you if you screw up? A grizzly? IF they live in the same area - I don’t see a grizzly being that stupid. Moose are damn mean. And I don’t know many animals, not even predators, who fancy a good goring before breakfast. Besides, there are so many smaller, easier Whitecastle-hamburger type meals out there in nature, like baby moose and deer and beaver and salmon and fermenting berries and whatever else bears eat. Well, as the eminent Valerius Geist pointed out in his very cool 1998 book "Deer of the World: Their evolution, behavior and ecology," moose and such evolved at a time when there were damn big predators. Saber-toothed cats and the North American short-faced bear (Arctodus simus). It was as tall as a moose. Just to remind you, moose can stand 7.8 feet tall at the shoulder, and of course the head’s a bit higher than that. Well, the picture in front of me makes me feel like sushi. The bear matches the moose in every major dimension, save antlers (it’s got 20 claws and a mouth full of crunch-your-femur teeth), plus being a bit longer, with bigger legs and, well, a big ol’ bear head, which never looks deceptively dumb like a moose head. 

 

Lesee, where was I….

Oh yes. We’ve said buh-bye to Stanford and Davis, Silicon Valley is either soggy or has moved to high ground (not without considerable cost), SF is now two islands instead of one, Berkeley’s enjoying fresh fish n’ chips… what about the precious salt-marshes, and the 12,000 breeding pairs of god-knows-what birds (let’s call’m schmatzels; I never had a Polish grandmother)? And the three recently-identified sub-species, upstream on the Sacramento River, that (now that we know about them) are also threatened?

Now, let’s take an historical perspective on marshes too. A marsh, being a combination of certain kinds of plants, and a certain depth of water, is highly subject to changes in water level. Too much water, the plants drown, and you’re left with more bay/lake/river/ocean/whatever, and the critters using the marsh are SOL (for that marsh). The SF bay is a fairly recent phenomenon (c. 8000 years it started trickling in), so all the marshes here (or that were here in the 1800s) are a pretty darn recent phenomenon. And given that most established species last on the order of 100,000- 1-million years, 1) 8000 years is a drop in the bucket even for species, and 2) it’s reasonable to infer that most organisms have ways of moving (individually, and between generations) and repopulating (even if a region of critters gets wiped out). That is, a lineage of organisms *not* capable of withstanding and/or accomodating (over the long haul) significant change would be highly unlikely to get beyond the toddler phase of specieshood.

And in fact, the long-term pattern of ecosystems is one of colonization, expansion and adjustment, stabilization, destabilization (several reasons), collapse/transformation, repeat. And most lineages of organisms suffer regional extinction one or more times, only to recolonize from populations elsewhere and do it all again. In fact, regional death and re-colonization can be part of the meta-strategy/niche of the group. Hard to tell. More research is needed (way way way more research) before we determine that holding things still as best as possible is the best feasible short-term solution to a long-term problem. It makes a lot of effectively arbitrary assumptions about the biological world, many of which are suspect if not false on their face. That’s what scientists *aren’t* supposed to do.

So the SF Bay marshes are an historically recent phenomenon, and only about 5% of marshes (from the 1800s) remain. Understandably this crimps the style of a lot of marsh-using critters, and it’s therefore expected that there are fewer critters than there used to be. A lot fewer. Only 12,000 breeding pairs of schmatzels or whatever. But, it’s not like these marshes were always there, and in terms of biotic and abiotic history, they represent an unprecedented regional surplus of opportunity for marsh-dwelling critters. So really, maybe we’re looking at the whole "low numbers" problem the wrong way. Maybe we’re coming off a local maximum of bird population numbers, and effectively returning to the norm of the last 40,000 years or so.

Well, the bird aspect of this story was the topic of a seminar attended by our hero in the not-so-distant past. The historical aspect of this story, extending beyond 250 years ago, was part of what our hero discussed in seminar yesterday, and a perspective he conveyed to the ornithologist at the end of that talk. The ornithologist, visibly agitated by that challenge to the welfare of local schmatzels, eventually burst out with, "Won’t you leave!!" Our hero pressed his point, and the angry ornithologist spouted forth with, "I don’t give a shit about the last 4.5 billion years, and I don’t give a shit about the next 4.5 billion years!!" A little more discussion, and our hero got the A.O. to admit that he didn’t care about anything after his own death. Being a conservation biologist in addition to an A.O., this is eyebrow-raising to say the least. Then our hero learned that not only was the A.O. not a graduate student (as he had assumed), but he was the chair of the department!

God save the schmatzels. With folks like this making policy recommendations, He’s the only one who can.  

But, then again, seeing’s that schmatzels have gotten along without the aid of god for… well if you trace it back, you’ve got 3.5 billion years of life continuity, without His divine non-existent help. Not only can the schmatzel take care of itself jim-dandy-thank-you, a few informed scientists and rational policy makers can make sure both humans and schmatzels are here well into the next centi-millenium.

 
Next time: "Hitting bottom, or, Why the Bay might not be totally fucked: A perspective from benthic foraminifera, Pleistocene to Present."

I’ll be here all week. Don’t forget to tip your waitresses. 

Fortuitously (given yesterday’s rant on rhinos), and hilariously, the following anecdote came up in a seminar today:

The speaker, (micropaleontologist and world expert on shelly protists, foraminifera, a deep thinker on deep time, and funny as hell to boot), recounted how he was attending a conservation biology seminar, where the speaker was talking about endangered birds requiring marsh habitat in the bay area if they are to survive. Something about only 12,000 breeding pairs of X species locally.

Back up a sec, and let’s talk about the "recent" history of the SF Bay area. Recent in geological terms means the last 125,000 years. Or even 8000 years, since that’s when the first humans (probably…) arrived, and started leaving giant mounds of clam shells around the bay area. Around 125K years ago, the earth was doing it’s glacial cycling, where you have a little ice age followed by warming, and it does this like 5 times or something, over 10s of thousands of years. And in fact the ocean levels were a bit lower than they are today, when this was happening. Then about 40,000 years ago (or was it 11000? nuts…) we had a glacial maximum, and everything was #@*$ing cold. Like, the line practically bored through the bottom of the graph. That cold. (haha).

Now, to step this out for the kiddies, that means there was a lot of ice. And ice is made of water. And that’s a lot of water. And that water has to come from somewhere. That water comes mostly from the oceans, since most of the water on earth is in the oceans. And when you freeze up a bunch of water at the poles, that means there’s less left for everywhere else. This means that ocean levels fall - quite a lot, actually. In the SF Bay area, they were about 360 FEET lower than they are now. That is, if you stood on the easy bay mountains and looked out where the Golden Gate Bridge is across the bay - you just MIGHT be able to see the water on a clear day. And this was normal, for a long time.

But, the good news is (well, not good - it’s just news, cuz it’s just the facts) since that glacial maximum is in the past - everything’s been warming up since then. And the interesting facts are these: Unlike the previous lukewarm-cool cycles that were happening 125K years ago, it’s been an almost continuous increase in ocean levels since that maximum cold. None of that up-down cycling bit, although there have been greater and lesser plateaus. And, some 8000 years ago, there was really just this piddly little body of water that was where the bay is now. Just pathetic. And it’s been slowly increasing ever since. By about 2000 years ago, we crossed the previous high water mark (of 100K years ago, give or take). In comparison to the last 125K years, sea levels are the highest they’ve ever been - but just a little bit (probably within 10 meters). This is also at the tail end of a very long upswing in sea levels. (I should probably point out the obvious and say that sea levels and global temperatures are positively correlated). And it is true that the slope of the graph is a bit steeper over the last little bit (500 years? 1000 years? Bit hard to tell on a graph covering that amount of time), than say 5-10,000 years ago.

Now, this raises a few very practical points, the insanity about global warming not withstanding. Because earth temperatures have been warming (period) over the long haul, and because the rate of increase is slightly steeper more recently, we might reasonably expect temperatures to increase slightly over the next 50 years. And, reasonable projections indicate a rise in bay water levels of maybe 3 feet. 50 years and 3 feet are chump change for paleontologists, but even paleontologists are land-owners and (usually) law-abiding, tax-paying citizens, and have some investment in the 100 years of their existence on this hunk o’ rock. So, applying our knowledge of historical patterns, and looking at a detailed topographic map of the bay area water levels, present areas of settlement, industrialization, and major economic import (including the marshes - I haven’t forgetten about the story), the following is indicated:

Some of the most important companies of Silicon Valley, which evidently have arrayed themselves along the western shoreline of the bay, including Sun Microsystems and others I recognized by can’t now recall (BIG names), fall within this 3 foot span. Yessiree, it’s true. 3 feet of water - for any reason, and "NASA, we have a problem." Gone, guys. Unless these companies pick up shop and move, they’re toast. Of course, they won’t go without a fight, but even dikes (or is it dykes? I can’t remember) and levees and seawalls are short-term fixes for a major problem - a gagillion cubic tons of water pressing in from the bay, non-stop. Better to re-locate uphill than fight such a brainless behemoth. Hopefully that’s what they will do - becuase unless it’s a tsunami or something, 3 feet doesn’t happen overnight. Still, this is a major, major economic drain for a very, very important sector of the global economy. I expect stocks to rise in the dredging industry, however. 

But wait, it gets better. Our valiant speaker informed us that, without a doubt, 3 feet of water will wipe Stanford off the map. Simultaneously, the island of SF will be cut in half with a straight of water running NW-SE through Colma. Next goes UC Davis, which sits well upstream on the Sacramento (I think) River, but will nonetheless be subject to the effects of higher water levels, and will get swamped. The hikes uphill on the Berkeley campus do indeed have a long-term benefit beyond my heart, quads and ass: Berkeley will remain untouched. In fact, there’s this nice little restaurant about five blocks down from the western-most border of campus that, with a slight shift in its business strategy, is exellently located to exploit the "fresh fish n’ chips" corner of the market. New student hangout?? We’ll see…

More later… must run. The fate of the marshes and the character of a prominent conservationist remain to be seen…. 

Continued tomorrow.

So, SVP was lovely. Ottawa is a very beautiful city - plus I’m partial to cities on grand but not huge-and-muddy rivers, like Prague on the Vltava, Boston on the Charles, NYC on the Hudson. The conference was good; I made several contacts I needed to, and saw some cool talks. Jenny McG and I hung out with Megalosaur Roger from the UK, who saw my logic talk a couple months back while he was in town. Cool guy, though I definitely have trouble seeing through that whole British-persona thing. Anyway. A lot of talk, a lot of coffee and drinks, and far too many stories about things about people I didn’t need to know. Some very, very funny though. But that’s all I’ll say about that.

My trip on %*#@ing Delta was another matter, but no need to discuss that either. I still love traveling, although I had an eerie flash of fiction-recollection while I was arguing, dumbstruck, against the staggering ineptitude and un-thinking of several Delta employees - a flashback to the pre-Taggart-tunnel scene in AS. Just… no one home, everyone doing the run-around cuz it’s their job, too afraid to not blame Federal Regulations, to actually identify the immediate cause of the problem… But anyway. I do like Vogue magazine. And ear-plugs. And brainstorming on blank paper. Makes a five-hour flight go much faster.

I’ve decided to start a semi-regular series here - vignettes from evo-devo. Stuff you never knew you never knew. Development is so incredibly complex, powerful, and we’re just *just* scratching the surface of it. Genomics is to genetics what the arch was to piles of rocks. And genetics is to development what an untouched granite quarry is to an architect - pure creative potential, with no current way to predict the final product. So, given that the field of evo-devo is about 30 years old, and really on 15 years old if you look at the existence of major research programs - I thought I’d pass around the tray of Stories That Make You Go "Wow" "Whoa" and "Duuuuuuude…". No, that’s not the official title of the series. But it is 4am (7am eastcoast time) and I should get to bed. 

But - a quick view of what’s in store: tweak the flow of some signaling proteins in the embryo of a developing chicken, and you restore the fibula (small shin bone - which is long gone in all birds; it’s that tooth-pick like bone on the drumstick) and its articulation with the ankle joint in one fell swoop - and guess what? It looks like the set-up we see in Archaeopteryx. And then there’s the gain and loss of ancestral and adult traits throughout the development of… loads of taxa (i.e. critters) - therizinosaurs being the most recent example. Then there’s the bipedal goat story, round 2 of antlerogenesis (antler growth), the fin-lobe-limb embryo and fossil work (simply….. stunning; I wanted to work with these guys at Chicago, but I didn’t get into the program there). We could do the evolution of the flight stroke, but that’s pretty over-done. I want to do the stuff that’s not well-known. There’s all the bone biology stuff I’m learning… for class… tomorrow…

Time to go to bed.