Monday, November 01, 2010

I can has published?

Continuing the trend of sending people elsewhere; you should check this out. It may sound familiar to some of you. I am pretty excited at the idea that someone has actually paid me (a small amount, but still) for a story.

Don't ask me about the picture though, it makes next to no sense as far as I can tell. Except, you know, sci fi == space.

Wednesday, October 06, 2010

Training Notes

On the way home from circus classes last night, waiting for the N (always waiting for the N), Chris and I saw a caterpillar dangling from a tree on a thread, slowly and painstakingly climbing and spiralling its way back up, winding its cocoon up around itself as it did, I think. I haven't tried to verify this by identifying the species and its cocoon-building habits, but upon close examination it was, tiny step by tiny step, hoisting itself back up towards the heavens.

Naturally, this led both of us in one direction, and the discussion of various Cirque Du Soleil caterpillar acts. There's a caterpillar act in Varekai, and one in Ovo, that we could think of. We decided ours would be better. Chris took a picture of the caterpillar as the Muni arrived.

I have been frustrated, lately, by the seeming impossibility of putting together and polishing an act with only one practice session a week. Last night was particularly bad; I wasn't able to get through even the small pieces of my act that I try to string together. Everything was more difficult because I hadn't slept well on Monday night, between staying up late grading and waking up early for class. But that was no excuse, I wanted to say. Putting together an act I could be proud of is increasingly seeming like a Sisyphean task - each week I fight against the atrophy that has occurred in the past seven days.

I'm at a difficult point with my training, in certain respects. I've been training for longer than all but a very few of my classmates, and I think that shows in my comfort on apparatus. But I don't have the time to train more than once a week, and that shows as well in my weakness and lack of flexibility. On the one hand, it might be helpful for me from a training perspective, if I want to perform, to drill the basics until I can do them absolutely effortlessly, with perfectly straight legs and pointed feet. On the other, if this is just for fun, why do I care if my toes are pointed and my legs straight? If it's just for fun, I might as well just goof off (or the equivalent) each week, doing tricks I enjoy, learning new ones occasionally.

I am having, in short, a problem of focus. Why am I training? Why am I taking these lessons? Do I have a goal - performing - or am I just there to get a good workout and crack jokes with the other students? And what do those different goals mean; what is their implication and significance?

Chris was surprised, and saddened, when I mentioned that maybe I should just give up on putting together an act. Or at least he seemed so. My coaches have agreed that that is the next place my training should go. It is certainly a hurdle, but it seems like such a big one: to go from one pose or a pose and a drop to an entire dynamic five minute act. And while I know that I have to work in small steps, even those small steps seem to come-and-go with the week. There are times, such as now, when I don't feel like I'm moving forward. From one point of view, that's okay; I had a generally enjoyable time last night, and what more could I want? From another, that's a shame.

Enough introspection. I'm stuck here writing this because I can't log into the website and finish my grading. This is infinitely frustrating to me. Every other website I've tried has worked fine; only the one where the problem sets are sitting, almost completely graded, is clogged. And it has been for the past hour and a half. I want to finish grading and go home and maybe make it to a yoga class. Instead I'm sitting, hitting the refresh key every couple minutes and hoping that this-time-it-will-work.

Isn't TAing fun?

Friday, August 27, 2010

Ask a Geneticist 2

Once again, I have a short essay posted for the "Ask a Geneticist" feature.

This one has given me no end of trouble, to be perfectly honest. I hemmed and hawed and obsessed and worried over it. I wrote three outlines and as many rough drafts that were binned before I sent them to the person editing it (who still insists on suggestions along the lines of "What I'm going to do for the rest of this essay is..." which still make my skin crawl). I procrastinated and I made jokes and I wrote several snarky introductions that I knew could never, ever, ever see the light of day.

All of that was a coping mechanism because I had trouble imagining the kind of person who would write in with that question. "I want my kids to look like me. How can I use science to do that?" There were just so many mental hiccups in the asking that I couldn't see where the person was coming from, that I couldn't identify with them, and that I couldn't write an essay explaining all the problems with the question.

I mean, first of all, on a certain level -- every kid looks like their parents. But who doesn't get that? Who wouldn't know that, or have noticed that? So it seemed to me that it was patently impossible that the question-writer simply wanted the all-around-family resemblance that every kid shares with their parents. It defied belief that someone would actually write into a museum asking about that.

Which makes me think, well, obviously the question is about making your kids look more like you - not a family resemblance but perhaps certain traits, or an eerie, clone-like resemblance. (Only one of these two is technically feasible with current technology.) And that, in turn, really freaked me out. In part because of how easily such technology could be misused ("Study finds blond-haired, blue-eyed children less likely to be bullied!") and in part because of how, well, narcissistic someone would have to be to not only think that the best appearance for a kid is one's own, but to desire to do something to ensure that outcome.

And then I thought, well, would I have felt better if my grandparents had cooed over how much of a Finn I looked, rather than doing that for my brother and my male cousins and conspiciously leaving me out? Do I feel some sense of connected-ness deriving itself from the fact that I look like my mother (albeit on a relatively smaller scale) and her sisters did at my age? Or that I have the body-shape of my Great Aunt? Or is my sense of belonging in my family mostly mediated by other things -- a shared love for Aristotle and Shakespeare, a perverse combination of dedication and stubbornness, a sense of strict justice, or the tendency to hold grudges? Those things seem to me to be at least as much mediated by how you raise a child as they are which genes you pass on (although certain components of personality are undoubtedly genetic in nature). And if the latter, how can I justify that in light of the fact that few of my more distant relatives share those features (although they might share my diminutive stature, or have the same brown eyes and small widow's peak).

On the other hand, the question was not "can I make sure my kid fits in with his extended family" but rather "can I make sure my kid looks like me" -- in which case perhaps only the comparison among my nuclear relatives is crucial. And so, to oversimplify greatly, do I identify with my mother because of our shared love of biochemistry or our shared facial structure? Do I identify with my father because of our shared memory for detail or our shared stature? Do I see myself in my brother because he has my hair color or because we are both intelligent, driven young people with a tendency towards worry and overanalysis? Or do I identify with these people because they are human, and because I know them well; because I love them and we are all more alike than different?

In the end, my essay for the Tech museum couldn't include philosophical ruminations. It wasn't - and isn't - the right forum for that. I gave a technical answer. (Your kids will probably look like you, because they're your kids. You could possibly choose a few simple traits like eye color, hair color, and gender, but to do that would be ethically dubious and you might have a hard time finding a doctor to help you. Anything else isn't possible yet and probably shouldn't be developed.) But I was dissatisfied with my response, because I felt like I didn't address what I read as the real concern -- a parent wanting to make sure his or her children to fit in, without knowing how best to do that.

Which is a question I am completely unqualified to answer.

Hopefully my dissatisfaction didn't come out in the essay. I can't help worrying that it did.

Thursday, July 01, 2010

Ask a Geneticist

My first "Ask a Geneticist" post just went live; you can find it here. It's written for schoolchildren, so it's pretty rudimentary and full of generalizations, but I'm reasonably happy with how it turned out. As a first (official) try at science-writing-for-laypeople, I think it's not so bad, although it has much more of a didactic/pedagogical aim and therefore more of a patronizing tone than I'm used to or perhaps comfortable with. It is possible, however, that I will be the only one to notice the unbearably twee condescension in what is by force a brief essay. (I can't imagine myself reading it aloud in my own natural speaking voice; only a higher-pitched, forcibly cheerful tone I use primarily when dealing with hyperactive children.)

The process of writing it was a bit of a lesson in and of itself. It was edited and vetted by the head of Stanford's program at the San Jose Tech Museum, a former research science who now focuses exclusively on community outreach and education. I had hoped, possibly foolishly, that because his focus was on outreach and education, that he would be able to teach me a good deal about clear communication of science. I had visions of my school essays in middle and high school, when I would get them back from my father: bloody and covered with red ink. Some combination of Strunk and White and the Little Red Schoolhouse course at Chicago that I only heard about second-hand from Ayn.

Let's just say I was disabused of my naive sentimentality. There was no secret knowledge handed to me in a manila envelope, 'Rules of Science Writing'. This isn't even science writing for adults, but science writing with an aim towards teaching schoolchildren, which is completely different. And I am enough of a snob about my style that I got into somewhat heated debates with the program director about word choice, sentence structure, and a few places where I detested his edits and changed them back repeatedly. One of his comments to me was "I noticed you don't like starting sentences with 'and'. It isn't necessarily the most proper thing to do but it can help shorter sentences in a row feel less choppy." As far as I could tell, that was the result of one specific place where I objected to starting a sentence with 'and'. In general, when it helps the flow, I don't mind starting a sentence with 'and' or 'so' or 'but'. Neither do I particularly mind sentence fragments. Especially in colloquial, online writing. But I don't think that "To know which test to choose, you have to know the difference between the tests. That means understanding how DNA works" is particularly choppy, or rather I don't think it's any more choppy than "To know which test to choose, you have to know the difference between the tests. And that means understanding how DNA works." In fact, in this situation, I feel that the 'and' is purely an extra word that clogs up the sentence and makes it, if anything, more choppy.

I suppose the reason this was difficult for me is that I wanted it to be more than it was; I wanted this to be an introduction to Science Writing, to fundamentally change the way I wrote about science or thought about writing. It didn't. If anything, I am more set in my ways and stubborn now than I was when I began the process of writing this essay. This wasn't a great learning experience which taught me new and interesting ways of conveying complicated scientific concepts to the unfamiliar masses. It was simply another writing assignment, something I can do reasonably well and reasonably easily, and something which perhaps would be easier still if I didn't care about the finished product as much as I do.

Tuesday, June 15, 2010


If you talk to me very often, and perhaps even if you don't, then you know that until recently I have been swimming in a thick, molasses-like sea of frustration. The reason for my erstwhile annoyance? My mice were not breeding. Without breeding, I could not get samples, and without samples, I could not do science. And lack of science makes for a very sad Elizabeth.

Well, one dissection two weeks ago, three last week, and two more today are confirmation that the dry spell is over and I now have more samples than I could ever, possibly, use (seriously. I showed one of my labmates my box-o-samples and he looked at me with an overwhelmed, pitying gaze). I mean, really, who makes 120 RNA libraries from 60 genetically identical individuals anyway? Grad students? Damn.

The bright side (apart from being on the road to data-ville) is that I saw some really cool things. Last week, I was pulling apart the yolk sac to get to the embryos, and two heads popped out. Turns out there were two embryos in there, sharing the same placenta and yolk sac. "Cool," I thought. "Monozygotic twins!" I hadn't seen that before in my dissections, of probably a few hundred mice. I showed Cheryl, the postdoc I'm working with who has seen a lot more mouse embryos than I have, and she had the same reaction. "Cool! I've never seen that before."

So I did a little bit of digging, and it turns out that monozygotic twins (naturally occuring ones, not artificially separated ones) are very very rare in mice. "Huh," I thought. "Nifty."

One week later, this time as I'm removing the embryo/placenta/yolk sac from the womb, I see two yolk sacs with embryos inside attached to the same placenta. "Whoah," I thought. "That's really weird. Twice in two weeks?"

And when we were subdissecting the placentas to prep them, Julie found another placenta that seemed to have been the product of two that fused at some point in development. She had never seen anything like it -- any of it -- and she has dissected thousands and thousands of mice.

It seems to me that there are two separate phenomena possibly occurring here: the first being a 'fused' placenta leading to two embryos in their own amnions and yolk sacs, and a placenta that still has the remnants of the fusion: a bright red line of giant cells in the middle showing the bifurcation. I would be willing to believe that this was in part a product of competition, possibly, in a large litter (the litters today had 10 and 12 pups respectively, which is on the big side but certainly not unheard of). Something like, two adjacent placentas are so close together in a large litter that they sort of grow into each other. This makes sense in the respect that the placentas that we saw with multiple yolk sacs were larger than usual and showed some remnants of the former separate structures. The second phenomenon is the 'monozygotic twinning' resulting in two embryos in their own amnions but sharing a yolk sac (or possibly two yolk sacs depending on when the cleavage occurred?) and a unitary placenta without any remnants of fusion. From what I've read, this seems like it would be much rarer?

One of the confounding issues being that mice have litters: multiple birth is the norm rather than being a relative exception. Only 1% of people have a twin, identical or fraternal. Just about every mouse has a few siblings that were born from the same litter. So in one way, 'twinning' in mice is much more common than it is in people.

On the other hand, about 1 in 500 people have an identical twin. (Most of them share a placenta but not an amnion: 60-70%. Some have separate placentas: about 36%. And sharing an amnion is even rarer: about 2%.) This is a lot harder to measure in mice (after all, lab mouse strains are all inbred and mostly have the same exact genome -- what does it mean to be an identical twin when all of your siblings and for that matter your parents have the same exact genome that you do? And how can you tell which siblings resulted from cleavage at a very early stage and which from multiple identical eggs being fertilized by multiple identical sperm?) But this is the phenomenon that seems to be utterly, excruciatingly rare. So much so that they can't use mice as a platform for studying monozygotic twinning in people. Sadly I can't access this article (just the abstract! Boo!) but the gist I can get is that out of 2000 mice born, none were monozygotic. In people, if you looked at the same number you would expect to find about four identical twins, or two sets. And of course there personal evidence like the reactions of Cheryl and Julie to the stories: neither of them had ever seen something like this before, and each have dissected thousands of mice.

On the other hand is this article (1965! a classic!) Which studies a strain of mice with, apparently, rather high rates of monozygotic twinning: they saw 9 pairs of 'identical' twins in 114 litters or about 500 mice. The problem with this paper being that the determination of 'identical' was based on cosegregation of 10 markers: 9 mutations and gender. And their values are barely statistically significant when you account for the fact that certain mutations and combinations of mutations kill the mice. So that's not very conclusive evidence of any monozygotic twinning at all in my opinion. The more recent paper which looked at 2000 mice (a different strain) used a more rigourous genetic panel and found that of 35 possible pairs (which fits with the 9 in 500 rather beautifully), none were truly identical.

But at base I'm less interested in what the probability is that any two mice from the same litter are genetically identical (almost 100% given the inbred strains I mentioned earlier). I'm more interested in the phenomenon of two embryos sharing the same placenta, either due to a hybrid placenta caused by fusion or due to cleavage at some early stage ala 'monozygotic twinning'. So it behooves me to look for embryological studies -- ones that examine the embryo at about the same time as I am looking.

I haven't found much to speak to sharing-a-placenta, and the rates thereof in mice. But possibly its rarity in the literature has something to do with its rarity in nature (in lab? is lab nature for a lab mouse?). Nothing to do but keep looking.

(Side note: turns out rabbits have conjoined twins, at especially high rates in a certain strain. As in, four partial duplicates in 250 or so animals in the study I saw. Siamese rabbits!)

Next time something more interesting to people who aren't me? Who knows. Probably not.

Thursday, June 10, 2010

Oryx and Crake

It has been two months. I will make up for my long absence by posting a novel (2,300 words, seriously). Tl;dr version: things are going well. I have lots of posts in the works. I was troubled by the novel Oryx and Crake. Scientists are good people, generally speaking. People are good people, generally speaking.

I have, according to blogger, five posts begun or drafted and not posted. I have, rather obviously, been having some trouble figuring out how I want to use this blog and what I want to post here. I have stayed away from any specifics about my research for a couple reasons, which I can go into at length but are most likely self-evident. On the other hand, my posts of 'this is what I have been doing' seem vapid and meaningless. Most of the posts are on scientific topics that have come up either in conversation with various non-scientists of my acquaintance or in my random wanderings through pubmed. I'll try to polish those up to readable-form. I'd like to turn these ramblings into thoughts on science, and science policy, and the interactions between science and laypeople, because that's something that I've been thinking quite a bit about lately and I don't imagine that will stop as I become more invested in science and scientific research.

I've written next to no fiction. I have a few ideas sitting around but I haven't found the right words for them, haven't found the right tone and characters or setting. They're amorphous and, well, embryonic -- the seeds of a story but not a story itself. And when I sit down to write them they slip away from me, much like the mouse embryos in a dish slipping past my forceps. (I've been doing a lot of dissections lately, can you tell?)

I have, however, been reading fiction. Which brings me to the title, at least. I just finished Oryx and Crake (Margaret Atwood's second-latest, I think?) and it puzzles me. In short, I found the world she created to be, frankly, unbelievable in the extreme. I liked the characters, I loved the interactions between them, and there were aspects of the plot that I really, really liked. But the speculative aspects of the 'speculative fiction' category just left me frustrated, slightly offended on behalf of scientists everywhere, and vaguely worried that such pop-culture and science fiction depictions of science really were indicative of a broader social attitude towards science and scientists.

To be brief: in her latest post-apocalyptic imagining, Atwood kills everyone off using genetic engineering. (As opposed to, say, A Handmaid's Tale, where she kills everyone off using Nuclear Power. And then she doesn't quite kill everyone off. Genetic engineering, it turns out, is much more efficient than a nuclear bomb.) But before she does that, she creates a dystopic, gen. eng.-ridden world run by big pharma and biotech (without drawing any line between the two). Literally. The lucky intellectual elites live in cookie-cutter company town suburbia, the plebeian masses being shunted off to polluted, out-of-the-way "plebelands" where they are exploited for what little money they have and experimented on without their knowledge. This tenuous equilibrium is broken (at the very last minute) by the genius of the novel, who kills everyone -- for a while we are left to believe every last human except one; at the end of the novel we discover three additional survivors -- with a genetically engineered ebola-like virus (quick death by hemorrhagic fever).

What rankled, basically, was the thesis, implicit in the novel, that scientists - or possibly engineers, but there is never any line drawn between the two - fit into one of two categories. Either they are incapable of seeing the bigger picture or understanding how their actions upset the natural balance of nature, or they are psychopathic zealots who are willing to kill off the entire human race with a smile. The latter, according to the novel, are the well-meaning ones. There's this tacit assumption that permeates the book, that if "word people" instead of "numbers people", by which I assume Atwood means poets, artists, dramatists, philosophers, and, to put a point on it, novelists, were more appreciated in their (our) society, the terrible future would never have happened. Because poets, artists, philosophers, novelists, can read the writing on the wall, whereas scientists and engineers are cursed with the tunnel-vision of Autism or Asperger's and therefore incapable. Or because scientists and engineers think they're Gods. Or, well, something.

There are several problems I have with that idea. The first is that she's creating an inaccurate and chimeric dichotomy that doesn't actually exist between 'numbers people' and 'word people'. The second is that it's an inaccurate and vicious depiction of scientists and engineers. The third, and perhaps most important, is that it overlooks what I see as the real danger and the real motivating cause of the potential dystopia she creates, which is corporate greed, and not science.

"Elizabeth," I hear you saying, "You're just bitter because an author cast your field of research as the cause of the apocalypse without creating a character you felt you could identify with." To which I respond, well, that's exactly the point. I'm a scientist, which, I guess, classes me as a 'numbers person' according to the rubric used in Oryx and Crake. I'm also very much a 'word person'. While I admit that people segregate themselves into camps, science versus humanities, I have never thought that that is all-encompassing. I'm a scientist who loves literature and philosophy and weird old words. I was in no way out of the norm in college. In fact I was surrounded by scientists who loved the humanities and philosophers who loved science. It was stranger to find someone who didn't have a broad interest.

Maybe part of that is the kind of person who goes to the University of Chicago instead of, say, MIT or Caltech. Although I have also met people from MIT and Caltech who have a more-than-passing interest in literature, philosophy, or history. But I think the dichotomy that Atwood created is more rightly a multi-dimensional continuum, different kinds of 'intelligence' for different people, in different quantities and combinations. Not just mathematical or linguistic intelligence, but tactile and visual and even olfactory. What do you say to the genius choreographer who can turn emotion into movement in a way that speaks to millions, but who cannot multiply seven by thirty-one or solve a simple crossword puzzle? Is he not a genius?

The point is that human genius takes on as many forms as does human culture, and that science and language are just two of them. "Numbers" and "Words" is an oversimplification and a false dichotomy.

But even in the world of "Numbers people" and "Words people", why are "Numbers people", in Atwood's universe, severely stunted socially, and without a sense of ethics? Sure, Autism Spectrum Disorders give people a way of looking at the world that can be incredibly useful and amenable to science and engineering, and while I will freely admit that one of the things I love as a scientist is that I can wear t-shirts and worn out jeans to work every day, that I don't need to wear makeup, and that the tomboyish aspects of my personality are accepted and smiled upon, I do not think that these are the defining characteristics of a scientific career or the personality of the typical scientist. That, I would say, is a sense of wonder and curiosity. A sense which was entirely absent from the 'science' in Oryx and Crake.

Moreover, even should the Asperger's-type be the defining norm in scientific academia, I would not say that this means we are without vision of the bigger picture. Which, in this case, was cast as having the responsibility to not utterly trash the planet. To be perfectly honest, I don't know whether scientists or people in technical fields are more or less likely to, say, recycle. Or drive a hybrid car, or bike to work. But at the same time, it felt like a bit of a specious argument. How do you define 'utterly trash the planet'? The fact of the matter is that even without a car or an air conditioner, even if I recycle and compost and grow vegetables in a small garden in my backyard, even if I keep my lights off, etcetera etcetera and so forth, my modest existence is not, likely, sustainable. Not even getting into the unsustainability of my workplace, full of disposable plastic pipettes, dishes, and rubber gloves, toxic reagents that have to be disposed of somehow, and so on and so forth. Stanford does a decent job trying to greenwash its campus but facts are facts, and without serious restructuring and quite a bit of alternative sources, the middle class existence is simply not something that the planet can sustain for some six billion-odd people.

But that's not, as I see it, a failing of science. If anything, science and engineering provides the route and roadmap towards alternative sources to help ameliorate this. If anything, science and engineering provide our way out of this mess. I won't say science and engineering are totally innocent. They provided the tools that got us here. But I'm very hesitant to use that fact to denigrate science and engineering, when it seems the real culprit is corporate greed and the exploitation/misuse of natural resources through science and engineering.

My problem with that argument being that it hearkens back to "Guns don't kill people, people kill people." Which is a terrible argument. And I guess that there are a couple caveats that differentiate my desire to exculpate science and engineering from such an argument against gun control.

First of all, I wouldn't say that science and engineering should be pursued without any oversight or guidance. Ethical committees and top-view oversight are absolutely necessary. At times government intervention, either to create regulations which limit certain kinds of research, or support other kinds of research, are absolutely necessary. These are fuzzy territories and each individual draws the line between 'good science' and 'bad science' in a different place, but it is an essential conversation to have, it is an essential topic to wrestle with, and to a certain extent we are having that conversation and wrestling with that topic right now. More would be better, of course, but these talks are happening. So in a way, I'm pro-science control in a similar way to being pro-gun control. I want scientists to be trained in ethics and safety, to be taught how to prevent disasters, and to be held to high standards just like I want the same things of gun owners. (Really, I'd like that for everyone. Wouldn't that be nice?)

Secondly, when considering any argument like "Guns don't kill people, people kill people", I guess what you need is an alternative. What else do guns do? A shovel is a neutral tool. There are uses that are perfectly legitimate: gardening. There are uses that are illegitimate: bashing someone's head in and burying the body. Admittedly, there are a lot more gardeners than there are shovel-murderers. Which is very much a good thing. A gun is, in some ways, less neutral. I think the majority of gun owners are sportsmen or women, target shooters and hunters. Some have guns for self defense or security. And a few have guns in order to threaten or commit violence. But the nature of a gun is de-facto violent, which makes it more difficult for people to accept than a shovel.

The tools of biological engineering have many legitimate uses. In a gross level, they are responsible for agriculture and domesticated animals. Modern medicine. You get the point. They are also capable of being used to commit ethically dubious actions, like Monsanto's creation of sterile corn crops (which is what allows them to stay in business from year to year, fund new and better products, and so forth, but also creates a monopoly and allows them to artificially limit supply and therefore increase prices). And unspeakable atrocities. It's the shovel analogy all over again. We have to weigh the good with the bad, and come to some compromise. It's not sufficient to say "Science is evil because Eugenics was used to justify Nazism." or "Engineering is evil because the atom bomb killed millions." And I felt like Oryx and Crake was, in many ways, trying to say just that, or rather, "Science is evil -- look at the misuses of genetic engineering! Scientists want to play God, and they don't see what they are doing is wrong!"

I tried, hard, to see the mitigating characters. Jimmy's mom, a biochemist who pleads with her husband to do "something basic" instead of creating a new 'cure for aging' or some such, and then runs away and turns traitor to the state/company/economy. And, of course, Crake, who sees the horror and chooses to end it all. But when presented as scientific heroes one ineffectual researcher and the mastermind who eradicates the human race, I was admittedly dismayed.

There were many parts of the book I loved. I adored Jimmy's interactions with Oryx -- the fact that he was willing to create a past for her, whole cloth, and she was willing to accept and develop the fiction was compelling and moving. The way Snowman deals with the Crakers, the stories he tells them and the ways he finds of explaining the world, the way he doesn't understand them and knows he never will but loves them anyway, is touching to say the least. But throughout the book there was a nagging thorn in my side, a thought in the back of my mind. It said two things. The first was how self-pitying it was for a novelist to write a novel in which the world ends because we don't care about literature enough. The second was, I hope people don't really think this is an accurate depiction of the scientific establishment. Because if so, they must hate us something fierce.

Wednesday, March 24, 2010

Happy Ada Lovelace Day!

An explanation shamelessly taken from the Finding Ada website: "Ada Lovelace day is an international day of blogging... to draw attention to the achievements of women in technology and science."

If anything, I have a surfeit of inspiration; I am a woman in science who has been fortunate enough to have female science mentors from day one. Which makes six strong women who have directly mentored me in beginning my career in science, and at least twice that if you count those who didn't work directly with me on a day-to-day basis but provided support and guidance. Not to mention the myriad famous women-in-science who I read about, and identified with or idolized to greater or lesser extents, or the multitude of relatives I have who went into nursing when that was about as close as a woman could reasonably get to science, without putting up a fuss (or my mother, who did put up the fuss, and probably has had the biggest hand in supporting my love for science). Like I said, a surfeit of inspiration. I have half a mind to write about a couple more people, in addition to my summary below, and if I do I might make some more general conclusions about women-in-science, but that all depends on how long my experiments take this afternoon.

That said, in honor of Ada Lovelace day, I'm writing about Barbara McClintock. She was awarded the Nobel Prize in Physiology or Medicine in 1983 for her discovery of 'jumping genes'. Her detailed work on genetics was absolutely ahead of its time: she was one of the first people to see meiotic recombination ('crossing over') events occur, she discovered the first DNA transposons, and she practically invented the concept of the distal enhancer or controlling element. In short, her work forced a transition from viewing DNA as a static molecule of inheritance to a dynamic molecule biochemically active within the cell and regulated in various ways. This at around the same time as the 'one gene one enzyme' hypothesis (it has since been rather spectacularly discredited by alternative splicing and noncoding RNAs) and the 'central dogma of molecular biology' (DNA is inherited, and transcribed into RNA which is translated to proteins -- and proteins are the truly functional parts of the cell -- which has also been rather spectacularly discredited). Biochemistry at the time, in other words, had not yet caught up to McClintock's ideas (it's arguable that it still hasn't quite gotten there, and the organization and dynamics of chromosomes is a very active field of study to this day).

McClintock was able to make the advances she did because she bridged cytology and genetics, and directly visualized chromosomes in the process of breaking and reattaching that takes place with every recombination or transposition. In other words, she was able and willing to pore over countless microscope slides, looking for the tiny breaks and joins in mitotic chromosomes, and changes in banding patterns that proved the jumps. Grueling, careful, detailed work to support her groundbreaking theories. However, in the middle of her career, she stopped publishing reports in major journals and instead communicated her findings only to a small group of friends and allies, because she felt her work was being ignored or discounted: "I stopped publishing detailed reports long ago when I realized, and acutely, the extent of disinterest and lack of confidence in the conclusions I was drawing from the studies." Ironic when so many of her theories were proven essentially correct, and largely generalizable, in the years following their discovery.

Monday, March 22, 2010

Alice in Wo-- Wait, what the hell?

As we waited for the new Alice in Wonderland movie to begin, I was giving a friend book recommendations; in particular I was describing what I liked so much about the 'Nightwatch' series of books. It seemed a fitting discussion just prior to watching a Tim Burton movie, in a way, because what I like about the Nightwatch series is that the world has a very unique, and imaginative, set up (mechanic?), which twists the world as we know it into something much stranger, and that every book in the series is unfailingly dark.

And then we watched the Alice in Wonderland movie, which might have looked like something out of the most tripped-out Goth's fever dream, but had the emotional murkiness and darkness of, perhaps, Cinderella. Oh, Disney.

To top things off, I just finished Jasper Fforde's latest book, which is also incredibly quirky (Fforde pretty much defines quirk for me, because everything he does is illogical until you realize it is powered by a pun) and also incredibly dark. Dark in that my vision of the world is mostly in gray scale, with a few bright points of - usually red - color (perfect for a Tim Burton movie, perhaps?) and dark in that after reading it my heart almost broke and I was left blinking and thinking "Oh no, this is the first book in the trilogy. Just how bad is it going to get?"

Which brings me to a bit of a quandary. Tim Burton didn't set out to make Alice dark, he set out "to try and make Alice feel more like a story as opposed to a series of events." (Quoth Wikipedia, Quoth a Comicon 2009 interview). But because it was Tim Burton I guess I pretty much assumed that it was going to be dark, emotionally as well as visually. To be fair, he did make a movie with considerably more plot than the episodic and often diffuse nature of Alice's Adventures in Wonderland. But given that he wanted a concrete plot, why choose one which ran so shallow? Given that he needed a good-versus-evil battle, why make good synonymous with 'likes fuzzy animals' and evil synonymous with 'callously abuses fuzzy animals'? I mean, I'm all for fluffy puppies, but give me an ethical quandary bigger than "We have to kill this vicious, man-eating dragon in order to end the iron-fisted, tyrranical, and arbitrary reign of Queen Evil McTortureson, but we don't want to kill anything because we're the Good Guys and Good Guys Don't Kill Things (TM)!"

So, a continuum:
1) Murderers versus cute puppies, and the puppies win! Tea and cookies all around!
2) Murderers versus cute puppies, and the puppies win, but sustain heavy casualties! Tea and cookies for those who survive!
3) Murderers versus cute puppies, and the puppies win, but sustain heavy casualties and end up compromising and/or killing other, even more innocent and/or cute, puppies who just wanted to keep their heads down and go about their business. Somewhat tainted tea and cookies for those who survive.
4) Murderers versus cute puppies, and the puppies win, but in the process realize that they're no better than the murderers. By now the tea has gone cold and the cookies are stale bricks of remorse.
5) Murderers versus cute puppies, and the murderers win. Murderers don't so much like tea and cookies, but they have some Lipton and a box of Chips Ahoy for appearances' sake.
6) Murderers versus cute puppies, and the murderers win, and in the process you realize that this is the only possible outcome. Lipton is cold and/or already steeped, and the Chips Ahoy has been left out and gone a bit stale.
7) Murderers versus cute puppies, except the murderers and the puppies are revealed to be exactly the same, and no one wins, because the battle goes on eternally, causing untold destruction for no real reason. There's no one left for tea or cookies, and no tea or cookies to be had anyway.

On that scheme, Alice in Wonderland is reveling in its (1)-ness, I think the Fforde trilogy is (3) or higher, and the Nightwatch series is squarely (7). Does the fact that I like Nightwatch best make me callous, cruel, depressed, or just realistic? (And does the fact that (7) is possibly overrepresented in Russian literature reflective of Stalinism, the cold Siberian winters, or both?)

Monday, March 01, 2010


A drabble. I think I finally have a beginning for the invisible-motorcycle story that has been bumping around my head for at least two years now, but I don't have a middle or an ending. We'll see if I can turn that into anything readable in the near future. Probably not.

Pablum: Something that is trite, insipid, or simplistic.

In other words, you should be very surprised that this is not about DNA. Or a collection of the responses I get when I say "I'm a geneticist."

There’s something that legitimizes dying wishes; your own rosy-tinted memory makes you comply, even if the request is absurd. I think my grandfather knew that, and that’s why he whispered, on his death bed, “Avenge me.”

It calls up all sorts of fairy tales, doesn’t it? Kill the evil baron who poisoned my grandfather’s wine, right countless yet-unknown wrongs, back in time for supper.

But things are never that simple. My grandfather died of a stroke. High cholesterol and higher blood pressure did him in: genetics and a lifetime of smoking, drinking, and eating red meat. Whose fault is that?

Tuesday, February 09, 2010

Disclaimer: I am not a poet

I had to write a short explanation of my research (to be put on the lab's website), and in the process of figuring out how to explain it concisely, I, in a fit of conceit, proclaimed that it would be just as easy to write it as a sonnet. My father suggested a Haiku. So here is the published (drabble: 100 words) version, a haiku veresion, and a sonnet version. I know the Haiku doesn't get into specifics, and the sonnet has some dodgy rhymes and phrasing, but they were written rather quickly.


I am interested in the epigenetic regulation of placental development, in particular the role of DNA methylation. The epigenetic profile of the placenta appears to be more flexible and dynamic than the embryo proper, as evidenced by significantly lower levels of total DNA methylation and striking loss of imprinting at many loci in extraembryonic tissues. However, knockouts or inhibition of the DNA-methylating enzymes (DNMTs) result in malformation of the placenta. I am examining the role of DNMTs in the placenta with tissue-specific knockdowns, and using high throughput sequencing techniques to clarify the extent of loss of imprinting in the placenta.
How cells interpret genomes
And environment
Though strictly controll'ed in embryo
The genome seems more flexible outside
And where development will progress slow
Environment must always be denied

Those marks which seem to regulation tied
Are rarer far in afterbirth than son;
And in placenta both alleles transcribed
Which fetus sees the choice of only one.

And yet those tissues with controls undone
In both the embryo and extra part
Are compromised and stunted every one
So necessary the controlling mark

I study why this freed placenta fails
And what its flexibility entails.

Friday, February 05, 2010

The first Friday of the Month...

Is, generally speaking, the worst day of the month in terms of getting anything done for me. Reason being, the first Thursday of every month is a fellowship meeting during which people present their progress over the course of the past year, and these presentations have almost always shaken my dedication to the scientific enterprise as a whole. They're poorly done, inconclusive, misrepresented, and it seems like almost everyone is just doing random, unconnected experiments, most of which do not work, in the hopes that someday they'll be able to find a thread that ties their experiments together and publish.

Seriously? This is science?

Yesterday's talks were made worse by one person who actually said that, as he was writing a manuscript at the time, he intentionally removed all identifying information from his single data slide. That, more than anything, struck me as very strange. I'm used to talking about everything to everyone. Talking through a problem is often my most effective way of figuring out how to solve it, and explaining a success is often my most effective way of figuring out where to go next, where the holes remain in hypothesis and theory that need to be shored up. What was he afraid of; that we would rush off and tell a competing lab, who would scoop him? Were he working with a company, and dealing with the nondisclosure and confidentiality clauses that allow for competition between biotech firms, I could understand his reticence, perhaps. On the other hand, in my idealized version of academia it is progress and the spread of ideas that is important, and not who thought of it first: Newton or Leibniz, the Calculus is the same.

Conferences and seminars can be full of unpublished or soon-to-be-published results; which is one reason why conference abstracts are largely misleading and often disproved later. And grants, of course, must be based on preliminary data; some comes from previous papers and my sense is that in the best grants, some comes from unpublished results. So in a way, it is true that communicating one's research even before it is ready to be published in a journal is an important part of science. What's more, this was a fellowship meeting -- a group which was designed and existed largely to support the research of the students who were presenting; it was not a thesis committee meeting, certainly, and it wasn't a lab meeting, but it was the next closest thing. What did this student have to fear, or think he had to fear, that caused him to remove all trace of data? On the other hand, I have several times balked from posting any specifics of my research here, in part because I don't think it would hold many people's interest, but mostly because it seems terribly unprofessional to post unpublished information on a private blog. That justification falls apart as well, I find, in an internal scientific meeting designed to be an annual litmus test of progress and provide support and ideas for those in need.

I'm not certain I remember this correctly, but I think when I went to hear James Watson speak, he said that the biggest difference between successful scientists and unsuccessful scientists was that successful scientists talked to everyone, absolutely everyone, about what they were doing. At the same time, fear of being scooped plays a huge role in The Double Helix. Maybe it would have been safer for them to say nothing, but to worry that every single thing they said would make it back to Linus Pauling, and provide for him the key to the riddle they were trying to solve, was not constructive. And in the end, it's hard to say whether the final breakthrough in that particular story was the result of any particular conversation, but it's likely that without as many conversations with as many different people as they did have, they would not have been able to make the discovery.

I'd like to think I live in a society (academia) where openness and collaboration is paired with success and progress more often than not. I think that the scientific enterprise requires communication, and not just because we see farther standing on the shoulders of giants. And when I feel like the status-quo, on the other hand, is secretive and reclusive and more focused on order of publications that spread of knowledge, it is yet another thing that disillusions me. On the up side, there was free food, and leftovers for today. It seems like a strange trade: we'll feed you, if you give us your hopes and dreams and idealism. But in a depressing sort of way, perhaps that's the trade that most people make every day of their lives. At least I only have to be reminded of it once a month before retreating back to my ivory tower.

Thursday, January 21, 2010

Momentous Occassions

Two absolutely life-shattering things happened today at work (and it's only 3:00!). The first is that I finally figured out how to submit stories to Futures (science fiction published in Nature). The second is that, for the first time ever, my cloning worked the first time around! Well, to be perfectly fair it worked in 3/5 cases, but I the remaining 2/5 are less essential, and possibly toxic to bacteria. I'll work on that.

It's a rare day when the experiment that is supposed to take a week actually only takes a week and a half. And all of that just goes to confirm once again that thunderstorms are my lucky charm.

Saturday, January 16, 2010


At least two significant things happened at dancing tonight. First, I finished the accelerating waltz with my feet on the ground and some semblance of rhythm and/or grace (a personal first!). All credit should go to my partner, of course, for taking smaller steps and reminding me to hold on for dear life. Otherwise I almost certainly would have skittered across the dance floor like the ball-bearing in the pinball machine, causing dismay, mayhem, embarrassment, and possibly a few broken bones. Not fun. But as opposed to previous accelerating waltzes in which at the end my feet leave the ground either out of centripetal force, my own clumsiness, or my partner's idea of something funny/interesting to do at 370 bpm, this time I ended on my feet. A miracle!

Second was a "difficult" Zweifacher -- a dance composed of waltzes and pivots in a repeating pattern -- which we were actually getting (by the end of the dance). The pattern was hardly a pattern at all: Waltz, waltz, pivot, pivot, waltz, waltz, pivot, pivot, waltz, waltz, waltz, waltz, pivot, pivot, waltz, pivot, pivot, waltz, waltz, and repeat. When the repeating unit is 9 and a half bars long (and since it's 'and a half', it's not really a repeating unit -- you then have to do it all on the other foot, which is different enough -- so the repeating unit is really 19 bars long), it ceases to be a step and becomes, well, a choreography. The only difference being that you could really hear it in the music. But it was great fun and my partner was a very good sport about the whole thing and by the end we were totally getting it.

Oh! And that's forgetting the wonderful cross step waltz/schottische cover of "Lucy in the Sky With Diamonds." That song made my night; the intro was 3/4, slow, and somewhat syncopated -- a cross step -- and then halfway through the first verse it switches to 4/4 and a bit faster -- a schottische. Besides the part where schottische is one of my favorite dances and Lucy in the Sky with Diamonds is one of my favorite songs, I was lucky enough to have a partner who not only knew what he was doing, but had a fondness for pivots and the "role-reversal" schottische (also known as the "sex change schottische" because for the second half the woman dances the man's part); fun times!

It is perhaps worthwhile to note that the most dizzying dances (the ones listed above) were probably also my favorites. At one introductory lesson a woman asked the teacher how to avoid getting dizzy while waltzing, and the teacher chuckled and informed her that the point of waltzing was to get dizzy. I don't entirely agree with that, and in any given waltz I'm unlikely to get dizzy (and glad that I don't get dizzy easily! How inconvenient would that be?), but one of the things I enjoy about waltzing, and especially fast waltzes, is the almost-dizzy feeling of one too many pivots (or is it just the right number since it's almost-dizzy and not outright dizzy?). So I guess it isn't surprising that the dances I generally like best are the ones that leave me slightly out of breath and slightly dizzy. Well, those and the Bohemian National Polka. You've just got to love the Bohemian National Polka.

Although, given the number of pivots in the BNP, and the fact that I often subconsciously try to add pivots (I mean, who wouldn't want to do 16 pivots in a row?), perhaps that one could be classified with the above as well.

Thursday, January 14, 2010


Inspired by the word-of-the-day; "Draconian", in addition to a conversation I had in lab today where someone asserted that a woman could get killed for committing adultery in the United States. I said "Um. No," although I was surprised to learn (thanks, wikipedia!) that some states have yet to decriminalize adultery (although it is hardly ever prosecuted anymore, and apparently there's at least one Supreme Court precedent that makes it difficult and questionable to apply any laws that still do happen to be on the books). The most amusing example was Maryland, whose punishment was a $10 fine -- which to me seems so very lenient as to be the worst of both worlds; it puts what is really a private thing between three people into the public, judicial, domain and it leans towards mocking the distress of the cheated-on. No good for anyone. And that sparked this:
You don’t seem to understand; I found her in bed with another man. In my bed, in my house, bought and mortgaged with my hard-earned money. With another man. I found my wife in bed with another man, she’s leaving me, and you seem to think that a ten dollar fine will just make everything better. Sorry for cheating on you, turning your suburban paradise into a twisted mockery of love and matrimony, how about I buy you dinner and we call it even?

Actually, you can’t buy dinner for ten dollars. That’s hardly even a cup of coffee anymore.
Clearly, my work today involved too many incubations/spins where I had fifteen minutes of empty time. Not enough to really read a paper, too much to just stare at the wall. So skimming wikipedia it is.

Tuesday, January 12, 2010

A drabble, off of the Word of the Day - "Torpor" - which I would have liked to be more rigid and angry but instead comes off instead as clinically depressed:
The dishes needed washing. The dishes needed washing, as did the laundry, and the bathroom should be cleaned, and the entire apartment was covered over by a fine layer of scrapbooking supplies. And the trash hadn’t been taken out. At the very least, she should get out. And instead, she sat, sheets smelling slightly of sweat, staring at the wall and then the ceiling and then the wall again. It was a peace-that-was-not-peace: if she didn’t acknowledge the outside world (or the mess), it didn’t exist. But she had never been good at isolation. And the dishes still needed washing.