Sunday, October 28, 2007

In defense of biology in the classroom

Emblies posted about education in general, and Duff (in his comment) suggested that Biology should be taught in lab and not in class, since largely it does not use a mathematical framework. You should read their posts if you haven't already because they have many interesting things to say. But Duff's comment about biology not being appropriate for class learning piqued my thought and so as not to totally clog Emblies' response page, I'm responding at length here.

Duff says: "In biology, I've long wondered if things would be better served if they did away mostly with lectures, perhaps limited it to once a week for an hour and a half, and the rest of the time was spent working in the lab."

First (and foremost) is that "Biology" is an incredibly broad term. There are some areas of Biology (phylogeny, for instance, or most forms of ecology) which I know less about than I know about physics. Even in a specialty or sub-discipline such as Genetics, there are a huge range of things that people study. The principles may be the same, but the procedures and the questions asked in Harinder's lab (where I work now) are very very different from the procedures and questions asked in Bill's lab (where I worked in high school). I absolutely could not (cannot?) choose a field of genetics, much less a field of biology itself, without classes to introduce me to topics before setting foot in a lab. I know that ecology and phylogeny bore me because I've had to study them for classes at some point and they bored me. I know that molecular biology is interesting because when I read even text book sections for them, I find things that are amusing, interesting, and intriguing. I know that DNA studies interest me more than protein studies because I have taken classes focused on proteins, and I find them less interesting than the classes I have taken focused on DNA. I think that I want to be a molecular geneticist because of experiences that I have had in classes as well as lab. There would have been no feasible way for me to be introduced to as many fields and disciplines as I have been introduced to if I only had class 1.5 hours a week: a year of rotation for a graduate student typically has them visit and do small projects in 3 or 4 labs (as far as I am aware). And one hopes to actually do a substantive project at some of these places, which means that 2 years of rotation needs to be enough to find a lab. But only having interacted with 6 to 8 possible specialties (and that's maximum, with specialty very specifically defined) is certainly not enough to give people an idea of the variety that is biology. So I think that biology classes are a necessary part of training a biologist.

Secondly is the fact that walking into a lab without an understanding of lab principles or procedures is a very very foolish thing to do. My first year, I was in a biology lab class (an advanced introduction, so these were presumably more biologically-inclined people than most classes at the U of C, even for biology majors) in which people did not know (or could not figure out immediately) how to use micropipetters (or, as I like calling them because it's more awesome, pipettemen). They didn't understand sterile technique in the slightest, they got Bacteria everywhere and freaked out instead of swabbing with ethanol and trying again with more finesse, they couldn't load a gel, etcetera. Even in my biochemistry class in my Junior year, there were people who were graduating with a BA in biochemistry and could not load a gel without a guide. My TAs have been consistently impressed with my ability to do things that I consider very simple, such as load and run gels, set up PCR reactions and so forth. All of which tells me that most people are, at base, completely and totally incompetent in lab, and that that incompetence needs must be trained out of them before they set foot near any valuable experiments. I have trouble in lab about keeping everything sterile, pipetting accurately, and getting reactions to work without hitch - so if someone was worse than me at those standard procedures, well, I wouldn't know what to do with them. They would be a waste of time and money. It is ridiculous to expect post-docs and graduate students, who have their own work to do, to also take on training every single biology student who comes through a program. If they were expected to do so, they would never get any of their own work done. So putting people into laboratory situations right away is silly.

Duff goes on to say: "I've always been curious as to what it means to think about biology outside a lab context. That is to say, not that abstract thought about biology cannot be had, but that it must be tied to the laboratory, as biology often does not have a mathematical framework that one can think within."

Admittedly, I laugh about the idea of "theoretical biology" as well, but it does exist. (Harinder is especially good at it, actually.) And there are some principles of biology that can be learned in a classroom very well (and that are actually suited particularly for classroom instruction). Yes, biology is based in observation and experiment rather than theoretical mathematical systems, but that does not mean that it cannot be taught in a classroom. Because there are theoretical underpinnings to much of biology that can be taught, and a worldview that can be exposed, in much the same way that mathematical acumen is necessary to understand and practice physics. I'm trying to think of a really good example and I'm going to go with Dobzhansky's Dictum. Dobzhansky's Dictum is the following: Nothing in Biology makes sense except in light of Evolution. When I first heard it I was dubious. But that's just the point -- it's a theoretical underpinning and a way of looking at the world specific to biology. It forces you to see the connections and relationships between our environment and ourselves, between different parts of our environment, etcetera. It also forces you to see the relationship and interdependence between molecular biology, genetics, and macroscopic biology. Evolution works on all levels, and you can talk about it at the genomic level, at the gene level, at the organismal level, at the systems level, and it's always the same principle. But you have to learn how to look at the world before you start seeing the interconnectedness. You have to hear Dobzhansky's Dictum and think about it for a while, apply it to specific situations, before it makes any sense to you whatsoever.

So the point is that while all kinds of biology don't necessarily have a mathematical framework that one can be taught and can "work within" -- although many kinds of biology do, in fact, have mathematical frameworks that you work within; protein folding problems come to mind -- all kinds of biology do have theoretical frameworks and postulates that you can think about and use to hypothesize. After all, theory != math.

Speaking of which, then, what makes physics so much different than biology in its capacity to be theoretical, then? Because Mango, earlier, had the following gem: He had always thought of physics as science and biology as engineering. For Mango that came down to purpose: the purpose of physics was to understand the world, the purpose of biology was to make people's lives better by finding cures and treatments for diseases. Again, physics as a discipline is theoretical and abstract and attempts to understand existence while biology is tied to the day-to-day realities of life and disease.

But it doesn't have to be this way. At least, not in my estimation.

I've sort of lost my train of thought here, so I might come back and clarify/add later. But I think that's enough for now anyway.

Wednesday, October 24, 2007


I just finished sewing the pockets + collar for my new coat!

It is bright red, double breasted, knee-length, and super awesome!

I will have it done by thanksgiving at the latest!

This is very exciting to me!

Pictures will be forthcoming if I can get a camera.

Genetics, Epigenetics, and Life

As promised, the overuse of gene post.

I read, on one of my molecular biology binges, that the notion of a gene was becoming increasingly hard to identify. I don't know if I agree with the argument, but here's the general idea. A massive oversimplification of molecular biology says that each DNA sequence is transcribed and translated into a protein, and that each protein has one function. Given that assumption, then there is a one-to-one correlation between DNA sequences and proteins, DNA sequences and functions, and proteins and functions. Hence, a gene is a single DNA sequence, which corresponds to a single protein and a single function (or trait). We can, therefore, isolate the gene for blue eyes, the gene for tall pea plants, and the gene for purple flowers.

However, if we define a gene (as we have done above) as the DNA sequence which is transcribed and codes for the blue-eye protein and causes the phenotype of blue eyes, well, we have a problem. First off, not all of the DNA sequence that causes the phenotype of blue eyes is transcribed. Second, not all of the DNA that is transcribed codes for the protein. Third, not every protein that effects the decision between blue and brown eyes is coded by a single piece of DNA or even effects only that decision. Should things like transcription factor DNA sequences, which are necessary for "turning on" specific sequences and thus for the observed phenotype, be counted as part of the gene? Probably not. But should introns, which are transcribed regions of the DNA that have little effect on activity be counted as the gene? How about promoter regions immediately upstream? Enhancers that can be located long distances removed? The intervening sequences?

No matter how you look at it, it's a mess. Of course, there are rigorous definitions of gene (i.e. coding sequences) but if you use them you leave out the vast majority of the information in the genome (i.e. promoters, enhancers, insulators, microRNAs, other nontranslated RNAs, ...) . The authors of the book I was reading went on to say that, perhaps, the notion of the gene is obsolete.

Of course, I don't follow their final leap of faith that removing the word "gene" from the picture and using only the longer descriptive terms -- enhancer, promoter, coding sequence, exon, intron, etcetera -- would simplify matters. I think it would, if anything, make it harder for any non-biologist to understand what on earth geneticists were talking about. And I am decidedly against making myself harder to understand. But the central point of the argument; that the very idea of a single, isolated gene is an oversimplification and perhaps a fallacy, remains. Genes do not exist on their own. They exist in context and that context is incredibly important to determining what they will do.

In my last post I talked about birds who learn the calls of the birds in the nest where they were raised. That's a typical example of something called epigenetics. That call helps the bird find a mate and eventually find a nest to insert its eggs into, and is therefore heritable, but it is in no way "genetically coded". It can even be the basis of evolution by natural selection: birds who put their eggs into the nests of species who take care of their young well, who find food everywhere and are safe from predators will be more likely to have more of their young survive and therefore will be selected for. But it is not, at base, encoded in DNA and therefore is not genetic.

Epigenetics works at all levels; from the organismal level I've just discussed to levels of gene control and regulation, such as what I'm working on right now. Where a gene is in the nucleus has huge ramifications on transcription and regulation. The state of histones (the proteins that DNA is always wrapped around in the nucleus) creates a "histone code" that is independent of genetic code and controls much of gene activity. These things aren't coded for in the genome, but they are heritable and they do yield phenotypes.

Epigenetics (on both microscopic and macroscopic levels) is a growing field. Scientists are increasingly coming to the conclusion that, well, it doesn't just come down to your genes, even on a molecular level! Yes, I do believe that the entirety of my organism can be described with sufficiently sophisticated chemistry, but also that as a being I am constantly learning and adapting to my situation. I am always making connections between neurons, and those connections make it easier for me to make more connections and so on and so forth. My genes provided a scaffold upon which I could build, but it was only that.

And so whenever someone says that they want to isolate "the gene for intelligence", I cringe a little. Because everything I've just said holds true. The chance that there is a single DNA sequence mediating the immensely complex trait we call "intelligence" is tiny. The chance that there is a single protein mediating that trait is similarly tiny. The chance that we could select for a single gene and therefore raise our intelligence without other, unfavorable side effects is almost infinitesimal. The fact of the matter is that this subtle and complex trait is mediated by an enormous number of variables, from genetic elements to epigenetic ones to cultural ones. And saying anything else is a pathetic oversimplification.

Monday, October 22, 2007

Genetics and Racism

I think that this is a pretty nice summary of Watson's latest blunder. If you haven't already heard of it, well, you must have been under a rock.

James Watson made a few racist remarks, for whatever reason, and the backlash has been remarkable, swift, and decisive. Which is nice in some ways and not in others. The point, for me, is that Watson started from a scientifically relevant position - "there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically" - and applied it to a situation where it doesn't necessarily belong - basically, black people are stupid.

Personally, I think that it's entirely possible Dr. Watson made an honest blunder, or just got carried away or wanted to piss people off to sell more copies of his new book or something. As the article says, he has marketed himself as a trouble-child, so it's a lot to expect for him to toe the party line, no matter what party line that happens to be. (There's no such thing as bad publicity). And besides, in most circles it is well known that Dr. Watson is off his rocker (although not as much as some others, like Craig Vetner) and while brilliant scientifically, not someone to go to for advice that doesn't relate to molecular biology. (That puzzled me; many of the questions at his book signing at the U of C were not related to molecular biology. Part of me asks, what do I care what Watson's views are on religion or politics or... although his comments on religion were certainly hilarious. He's a good scientist, and I care about his views on scientific issues.) In any case, what bothers me more, to a certain extent, is the reaction that those comments have received.

First off is the feigning shock, the outrage and the revulsion, to the point that he's been suspended from his job and had interviews canceled. As I said, Watson has been marketing himself as someone who makes politically incorrect remarks since his first book, and the fact that anyone is particularly surprised that James Watson said something that was outrageous, politically incorrect, and just downright ridiculous is somewhat troubling. In the scheme of things, this ranks right up there with making all girls pretty, aborting homosexual babies, and saying that black people have bigger sex drives. It's stupid, it's prejudicial, and it's pure James Watson. That anyone should be surprised by it shows something about us that isn't necessarily a good thing; our ability to turn a blind eye and actually forget about the idiocies and unpleasant elements of our public figures. James Watson has always made this sort of absurd, bigoted remark. He has also always been a good scientist. Why should we think that anything has changed?

That was, again, my first reaction, and it has remained pretty much unchanged since I heard about his comments a week ago. What is new, however, is something that was only brought to light by the comments at the bottom of the blog post I linked to. I understand the impulse to defend what could be potentially valid remarks from a perceived over-political-correctness that makes much political discourse in this country utterly meaningless. However, some people go too far. Ignoring the one comment that seemed to tie Watson's lack of tact or forethought to the moral bankruptcy of the scientific establishment, slavery to abortion, and the second coming of Christ (more on that later, or rather, not), many of the comments seemed to be taking "Watson's side" on the issue - advocating to a larger or smaller degree the genetic basis for an IQ difference between blacks & whites, Americans & Africans. There are several problems with this, large and small. First, that I do not believe there is a significant genetic difference between blacks and whites, Americans and Africans and especially not one that would lead to a consistent and statistically significant difference in intelligence between those groups. Second, I think that people overuse genetics at the expense of environment and epigenetics. Third, people downplay the extent to which de juro or overt racism in our country and in the world has been replaced by a subtle, pervasive, and condescending sort of racism and sexism. Fourth, measures like IQ tests are inherently inaccurate. Finally, how can we say that Africans are genetically bad at governing themselves peacefully when there are obvious examples to the contrary?

If I talked about all of that, I would be here all night. I'm just going to cover the first part for now: my strong belief that there is no reason to assume that a genetic difference between populations causes the perceived intelligence gap.

I'm going to start from a few assumptions, which I'll probably dismantle in later posts (or not if I get distracted). Basically, what is the most valid I can make this argument that there is a genetic basis? I'll assume, to start with, that IQ tests give an accurate picture of intelligence. I'll also assume that there is a proven, significant correlation between how well your parents and relatives do on an IQ test and how well you do on an IQ test. That still doesn't prove to me that ability on an IQ test is necessarily genetic.

I'll give a few counter-examples. I doubt that anyone would argue (except perhaps Dr. Watson?) that religious belief is genetic. (Not even just belief in God, here, although that works too, but specific denomination and religion). However, the single greatest determining factor in someone's religion is the religion of their parents. Here it seems obvious that children who are raised in the faith, taught the faith from a young age, and (to an atheist's eyes) indoctrinated are more likely to profess that faith when they grow up. It has nothing to do with genetics and everything to do with environment; parents raise their children in the church and that experience of growing up in the church makes devout people out of their children.

You can even consider a species of nesting parasites (birds who insert their eggs into the nests of other birds). These birds develop the call of the birds whose nest they were hatched in. In fact, I believe that if you move the egg, the bird develops a different call. And the call determines mating patterns later in life - so it is not purely incidental. Here, where the bird grows up is a bigger deal for who its mate will be and what it will be like as an adult than its necessary genetic makeup.

Finally, it is (perhaps) a little known fact that the smartest children are not born to the smartest parents. Even given a correlation between IQ of parents and IQ of children, if Einstein and Marie Curie had children it is by no means necessarily true or even likely that their child would be particularly good at physics. In fact, the best determinant of childhood success in school appears to be the number of books in a house, which, like religion, is not genetic.

Given all of that, the question that I pose myself is: is it likely that environmental factors in a child's life could lead to the phenotype that we see, namely, a significant difference in IQ test-taking ability between Africans and Americans? And I am forced to answer that yes, it is very likely that environmental factors in a child's life could lead to that phenotype. Compared to the availability of books in middle class white neighborhoods, the number of books in most places in Africa is pitifully small. That alone would explain a significant difference between the populations.

So it seems obvious to me that even given a significant, apparently heritable difference in IQ between populations, there is no reason to believe that this difference is genetic and no reason to believe that any baby born in a remote village in Africa might not do very well on an IQ test were he or she raised from birth in a house with a lot of books and parents who read regularly.

Next up: Overuse of Genetics and the expense of more interesting subfields.

Saturday, October 20, 2007

Andrew Bird

Makes preparing graduate school applications and studying for midterms so very much better.

My favorite so far: Imitosis --

He's keeping busy, yeah he's bleeding stones,
With his machinations and his palindromes
It was anything but hear the voice
Anything but hear the voice
It was anything but hear the voice
That says that we're all basically alone

Poor Professor Pynchon had only good intentions
When he put his Bunsen burners all away
And turned into a playground a petri dish of single cells
That would swing their fists at anything that looks like easy prey
On this nature show that rages every day it was bound,
a part his intuition
To say we were all basically alone

And despite what all his studies had shown
What was mistaken for closeness was just a case for mitosis
Why do some show mercy
When others train for the show
and tell me doctor can you pull my file
'Cause he just wants to know the reason why

Why do they congregate in groups of four
Scatter like a billion spores
And let the wind just carry them away?
How can kids be so mean
Our famous doctor tried to glean
As he went home at the end of the day
In this Nature show that rages every day
It was bound a part his intuition, Say

We were all basically all alone
Despite what all his studies had shown
What was mistaken for closeness was just a case for mitosis
So fatal doses, malcontent to osmosis
Why do some show mercy
When others are paying for the shot
Well tell me doctor can you pull my file
reason why

Tuesday, October 09, 2007


This is amazing. I want to be a member!

Passion and Power

I was told today that when I present about my research, I have "Power" and that that "Protects me from people like Steve Kron." I find this greatly amusing, especially since I am reading the second book of the Night Watch series, Day Watch, in which that would take on a very specific meaning. I imagined myself casting some sort of shield spell to protect me from Steve's criticism.

What Elisabet meant was that when I present for PCBio I am obviously enthusiastic and excited about my research, and Steve sees that and appreciates that and so he won't find fault with what I do because the important things - learning about how to do research and how to discuss research - are two things that I am obviously enthusiastic about. Also that when Steve does make sarcastic comments or nitpick, I can rebuff or answer him succinctly and confidently, possibly because I am in presenter mode. (I go into presenter mode a lot. It is the mode I go into when I explain science to people. I enjoy explaining science to people.)

All the same, it would be much more awesome if I was really an Other going into the Twilight and casting awesome shielding spells or something.

Speaking of which, if you have not read Night Watch or its sequels by Sergei Lukyanenko, you should. Now. Or possibly yesterday. They are awesome. And I had a thought about them today that will not ruin them for anyone, so I will expound upon it here!

The premise of the books is that there are magically adept people among us, called Others. They are human in the biological sense that they are the children of humans and give birth to humans, but they are not human in the sense that they can do magic, live for much longer, and can access an alternate reality world called "the twilight". (of course it's more complicated than that, but I'm explaining very broadly here). They're witches and wizards and enchantresses and warlocks and magicians and werewolves and vampires and shapeshifters and so on and so forth, and there are Light Others and Dark Others.

Every Other gets his or her power from the emotions of the humans he or she comes into contact with. However, one principle difference is that Light Others feed on happiness while Dark Others feed on unhappiness. Which brings up an interesting point: when a Dark Other takes Power from a human's unhappiness, he or she takes away that human's unhappiness as well, leaving the person happier than previously. And vice versa for a Light Other: taking Power from people's happiness leaves them unhappy. Which brings up an interesting point, in my opinion, because if Light Others (who are, of course, supposed to be "good"), get power by making people less happy, and Dark Others (who are, of course, supposed to be "bad"), get power by making people more happy, then why are our classifications of "good" and "bad" set up the way they are? Possibly because if there were no misery in the world, Dark Others could not get any power, and hence they could not exist, and therefore Dark Others want there to be misery, while Light Others by the same logic want people to be happy.

But it's an interesting point, and merges nicely into another key difference between Light and Dark Others; that Light Others need to validate what they do constantly as "for the greater good" and so forth, while Dark Others just do whatever they please and don't care. Which makes sense if Light Others are basically making people less happy - people would get upset about that! - and Dark Others are basically making people more happy - people would not get upset about that.

In any case, some of the things that Lukyanenko does are obvious from the beginning; Light Others are obviously not all good and Dark Others obviously not all bad. Some of them are moralistic and preachy, but in general he does a good job of keeping you on your toes and the plots are amazingly intricate and well-woven. I can't talk about that without giving anything away, obviously, so you'll have to take my word on it.

Finally, and perhaps most awesomely, is this. Because you really wanted to know how to knit a Dalek.

Monday, October 08, 2007

Chocolate Ice Cream

Is better than God. At least, according to Jim Watson. I quote: "I like chocolate ice cream so much I don't need an afterlife. I can fulfill myself every day."

The talk was awesome. That was my favorite quote, followed shortly for wackyness by "I think Erectile Dysfunctional Disorder, which we can now treat with Cialis, has been evolutionarily selected for."

In terms of substantive stuff, he talked about how we can't get young people to want to be scientists unless we make it a fun place to be; interminable and badly paid graduate school, long postdoctoral careers with no way out, and the end-goal being paid less than a major league baseball Umpire. He also said it was silly for the P.I. to get his name on every paper leaving a lab, unless the P.I. really did contribute significantly to every paper in the lab. And that he thought going into science now was grimmer than when he was going into science.

He had his standard crazy things, talking about "new ways of thinking" that amount to pseudo-Darwinian semi-nonsense, for example the idea that Jews are smart because they were polygamous the longest; so extraordinary men had more wives and more children. His comment that "it might be wrong, but it's a new way of thinking" pretty much sums that one up in my opinion.

My favorite substantive comment that he made was on congeniality and science. What he said was, basically, that you absolutely have to talk to everyone you can in science. It doesn't matter if that person is mean, nasty, if you're afraid of them, if you're competing with them, whatever. You need to be able to walk into their office unannounced and talk about your project. Especially, he said, with competitors. Reason being that your competitors are the other people interested in your subject. One of the most interesting things he said was actually about Rosalind Franklin. He said that had she been able to sit down and talk to Crick, shown him her data and her stumbling block, Crick would have given her the missing piece to her logic and we would all be talking about Franklin's structure of DNA instead of Watson and Crick's structure of DNA. But she couldn't, and so she didn't, and so Watson and Crick are famous and have movies made about them and she died alone, bitter, and four years before she could have won the Nobel prize. Which is an interesting way of looking at it.

In any case, the talk was great, I have his new book, and man does James Watson have an annoying laugh.

A couple things

Craig Venter is an evil supergenius. See here. His comments on "A new philosophical age" and "Not everybody is going to be happy" are particularly creepy. Also the fact that he is knowingly and gleefully playing God, and seems to think this is purely a good thing. I particularly like his comments on our potential to make bacteria which pull carbon dioxide out of the air, since I have never, ever, ever heard of or seen an organism that could do that, and I'm sure that you haven't either. Also because there wouldn't be any problem with, for instance, pulling too much carbon dioxide out of the air, or deciding which byproducts these hypothetical organisms would turn the carbon dioxide into. I mean, honestly.

It has been said that I do not think like an evil supergenius. I am not sure I am ashamed of this. But I am sure I am going to be a mad scientist for Halloween. Possibly with a glowing rat. I think that would be fun. I would have something more traditional, like a ray gun or whatever, but I am after all a geneticist. A geneticist who has finished her GREs, though, which is exciting. Just in time to stress about my presentation to PCBio, where I will probably get yelled at by Steve for not making enough progress *wince*. But I can blame the fact that in the 100 clones I have screened, only 1 was good and only 1 other looks promising. AND I can say I'm trying new techniques to get clones, which will hopefully have better results. (I have 25 more clones ready to look at whenever Karen has time, and more on the way, but Karen is busy with paperness so I am on hold, working on getting bacterial constructs made for the next couple weeks.) That's not a lack of effort. That's a lack of luck?

Speaking of, I (hopefully!) get to hear James Watson speak tonight! I hope I have questions to ask him. I have also decided that Watson > Yoga and Heroes. Which I feel is the proper choice.
I should get his new book from the seminary coop. I liked Double Helix, it was really funny. (If you are a scientist, you should READ IT NOW. If you know many scientists, you should also READ IT NOW. It's wonderfully tongue-in-cheek making fun of paradigmatic scientists, and if you are one or know many, well, you'll see yourself and/or a lot of people you know reflected in the characters.)

In any case, maybe I'll post later tonight about the speech. And maybe I'll work on my problem set instead. We'll see, won't we?

Monday, October 01, 2007

While working on a problem set...

I happened upon this monthly blog: They talk about one protein each month. Some of them are obtuse, like the cupidin article (their article is a poem; the protein is also called Homer2 -- it is involved in neuronal signalling and cocaine sensitivity and apparently its deletion in mice makes them act like cocaine addicted rats. I think that the researchers would have compared to cocaine addicted mice except maybe we don't have those to study. Go figure). I still don't know why they called it cupidin. Some of their articles are also fictional -- such as the lamborghinin one; I really wanted there to actually be a protein named lamborghinin -- which is also unfortunate. But mostly the articles are pretty good. And now I am full of useless information about several random proteins!