FILES!

I started - or rather, continued - rewriting it tonight. And I have some passages that don't give much of anything away, because I had to tell people and Mango and Kate had already gone to sleep.

This was the most humiliating situation he had ever found himself in. Except perhaps that time he had gotten caught in the dolphin tank without his trousers, and everyone insisted they hadn’t seen a foxy red-headed dolphin training seductress anywhere near the aquarium.

This was almost as embarrassing as that. And it was made worse by the fact that the person pointing and laughing at Roger's predicament wasn’t some pimply janitor who probably couldn’t get a sexy red-head in (well, half-in) a wetsuit to lure him to almost-certain death in the dolphin tank if he asked nicely, but rather Roger's own coworkers. And as much as Roger would like to deny it, while Michael would be too much of a prude to be caught without his trousers, well, he had after all inherited his father's looks as well as his employment, and so it would probably not have been for lack of trying on the part of the woman in the tightly fitting neoprene.

That's probably my favorite quote from the new stuff.

Roger is such a melodramatic character though, so over the top. It's such fun to write, even if he's rather despicable.

Is this Biochemistry?

I have reached the unfortunate conclusion that I am a molecular biologist pretending to be a biochemist. Most of the time I do not even pretend. After all, I chose to be a molecular biologist and not a biochemist for a reason: Namely that I am more interested in genetics than in protein science, and not particularly interesting in reaction kinetics (whether that be for a folding reaction, a binding reaction, or an enzymatic reaction). Also I, in general, appreciate working with more natural systems rather than more artificial ones (namely, if studying biological systems, we should perhaps use biological systems, like cells and animals, rather than non-biological systems, like test-tubes and monolayers). (I also note that there is a time and a place where the non-biological systems are incredibly useful and that my own systems are, in many ways, very artificial themselves). In any case, none of this would be an issue if I didn't want to write an honors thesis. Which I do, and since I am majoring in biochemistry (primarily), I feel like that should be in biochemistry. So my question: does this sound like biochemistry?

Gene regulation in eukaryotes is an incredibly complex process which is not completely understood. Until recently, the model for transcriptional control has been based on a view of DNA as linear, neutral, and controlled by the function of transcriptional activators and repressors – proteins designed to interact both with DNA and with the transcription complex. However, DNA is, in reality, in a dynamic nuclear environment not solely determined by the various transcription factors present. Long-distance DNA-DNA interactions such as chromosomal kissing disprove the linearity of DNA, and the effect of nuclear localization on gene expression disproves the transcription-neutrality of its position in the nucleus. My project attempts to determine the significance of this localization effect in gene expression. To do this, I have created a system called TCIS (Tagged Chromosomal Insertion Site) with which I can repeatedly insert pieces of DNA into the same, easily visible, genomic location. This site is usually found in the center of the nucleus but can be tethered to the edge of the nucleus as well. I will insert various promoter regions into this TCIS, tether them to the edge of the nucleus, and measure the difference in expression levels between tethered and untethered samples.

I know it's rough, I'll work on that once I get something that actually might convince someone I'm almost a biochemist (if they're being really generous).

Well, this is not that celebratory, but I NEED to post it

Or rather, it's absolutely awesome.

First, www.freerice.com is awesome in that it makes you less guilty for procrastinating with online video games; you're helping the UN to end world hunger with each correct answer. (I've "bought" 13690 grains of rice. Woot.)

Second, it shows you awesome (and counterintutive?) words like the following:

Pulchritude == physical beauty
Fuliginous == sooty
Panjandrum == self-important dignitary
Gallimaufry == hodge-podge
and many others.

Also, quote of the day: "For real, though. Who threw that wedding at me?" - Ayn.

99th post

My next post is my 100th post. So it should be significant.

But since this is just the 99th post, well, it can be about something silly; like a teenager beating up a bear.

http://news.bbc.co.uk/2/hi/americas/3667399.stm

My favorite is the caption:
"Unarmed humans rarely come off best against bears."

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.

COAT!

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.

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.

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

OOTSSOERAAAP

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.

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?

While working on a problem set...

I happened upon this monthly blog: http://ca.expasy.org/spotlight/snapshot. 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!

Hooray!

Public service announcement

Aristocratic Octopus is no more.

GRE

I have vanquished the GRE! Go me! Now I just need to similarly vanquish my subject test and the math methods test and I can maybe get into graduate school!

Yay?

Also

Is it just me, or is the Eckhart library set up particularly well for a rousing performance of "Marian the Librarian?" I mean, the partial second floors are just too perfect. As is the large central area full of desks for dancing on. Unfortunately, there aren't any of those rolling/sliding ladders that are so awesome. At least, I couldn't find any.

But it still bears thought. Seriously, guys. Take a look if you haven't.

I am no longer dead to the world!

In fact, I am out and about today! Hooray! If by 'out and about' I mean 'at work and studying' then... yes.

I recently got an e-mail about the test that I have to take to prove that I can do some math, so the Chemistry department won't disown me and ostracize me from the elite group of Biochemistry majors into to the masses of Biology majors. That would be scary. There are so many pre-meds there.

I laughed at first, because the concepts on it (n-space, linear dependence, eigenvalues) were all things I remembered learning in high school but have long since vaguely forgotten about. I don't mean to sound snide -- I'm sure the college course here on basic linear algebra is much more demanding than my high school course on basic linear algebra, even if it isn't the course here on abstract algebra which sounds like so much more fun and I'm somewhat disappointed I never really got a chance to take.

However, I understand now why the Chemistry department won't simply take my year of Analysis as proof that I can do this math - because while some of the concepts in Analysis are based on the concepts of linear algebra, and while Analysis is really much much easier if you know a little bit of linear algebra, the topics above, especially eigenvalues, are not covered in Analysis. So it would be entirely possible to pass through Analysis and not know what an eigenvalue is. (Which would be a shame because then you couldn't throw things at Peter Parker when he mistakenly gives one a unit.) Of course, I've almost forgotten what an eigenvalue is, so it's time for me to break out the book and get studying.

I can't believe that it's the weekend before first week and I have 1 test to take and 2 to study for. This year is going to be awesome. If I survive it.

What is so hard about getting my name right on an ID?

I am 1 for 4, on people getting my name right on IDs at their first try. But at least DMVs are full of hijinks for me. I guess that's a good thing. Certainly makes something very boring somewhat exciting.

Today there were two adventures: First, I presented my 19-year-old social security card (with stub containing an address in Roger's park) and my much more recent Maryland Driver's License. They accepted the Social Security card as proof of my residency in Illinois. I am now registered to vote here. At no point did they ask for any sort of more recent mail. I know that they do for some people, because I heard them asking people in line in front of me. They also tried to put the roger's park address as my current address. But I caught them there. When she asked "Is this your current address?" I was shocked enough to sort of double take. I was not aware that the stub to the social security card contained an address. But it does. What's more, I think that wherever I go in life and whatever I do, I will be able to get an Illinois Driver's License. Which is more than a little bit absurd.

The name mistake is much less funny, because it wasn't really their mistake. My (and my brother's) social security cards say "Hauener" instead of "Havener" for the middle name. The woman, therefore, typed my middle name with the U instead of the V. This was, fortunately, easily corrected with my passport which clearly says "Havener". I didn't show her the erroneous social security card again, and I am perhaps lucky she did not ask. But she was fairly apologetic, which was nice. Or something.

Also, the inside of the DMV in Chicago (on a weekday at about 2 pm in the middle of the month) is actually not much of an ordeal. The people are polite, friendly, and intelligent, and they move you through remarkably quickly. (for a DMV).

That is all.

Wacky?

In this week's Science table of contents, this caught my eye:

Production of Trout Offspring from Triploid Salmon Parents

Now, at first I stared at it and said, well, how can a Salmon give birth to a Trout? The answer, it turns out, is if the Salmon is only externally a Salmon, and has Trout-derived reproductive cells. The researchers took sterile Salmon and transplanted by microinjection (so basically injected into the fish eggs) Trout progenitor cells for reproductive cells. Surprisingly enough, the fish grew normally and were, for all intents and purposes, Salmon with Trout eggs/sperm cells.

Which raises the question, biologically, are they closer to Salmon or closer to Trout?

Also, how wacky and awesome is it that Salmon can give birth to Trout?

Those terrorists...

So, I need to renew my driver's license. I went to the Illinois DMV armed with my old driver's license, my passport, a canceled check, and a piece of mail, thinking that with all of these things I would be set. However, they turned me away immediately for not having my social security card with me. I told them I knew my number, they were not impressed (this is understandable), I told them I could get it faxed to them in a matter of minutes, they were not impressed. Finally, in a bit of a tiff, I asked them why they needed my social security card when I had two forms of U.S. photo I.D. with me, as well as proof of my residency in Illinois. Their response, and I quote, was "To prevent fraud after 9/11."

Now, excuse me for a second while I ponder this statement. First off, I was unaware that there was a particular increase in identity theft concurrent with the attacks of September eleventh. Second, I am confused as to how preventing people from getting an Illinois driver's license will a) prevent them from getting on an airplane and crashing it into a building or b) prevent them from committing any other form of atrocity except, perhaps, living in Illinois and owning and driving a car. Third, I am very baffled, since social security cards are perhaps the easiest piece of identification to fake, as they have only a number, name, and signature, and they are printed on plain blue paper. In fact, had I actually lost my social security card, I imagine that it would be easier and less time-intensive for me to forge a new one using photoshop and online images than it would be to go to the social security office and get a new one sent to me.

Fourth, I am unaware as to how giving my social security number to the idiots at the DMV will prevent fraud. Excuse me if I am wrong, but it really does seem to me that the reason we have a problem with identity theft and social security fraud is, quite simply, that there are quite a few transactions where the only identifying information on them is a social security number and name. Every time that I give my social security number to someone else, it goes into another database to be stored with a bunch of other people's social security numbers. The more times I give out my social security number, the more possible times there are for someone to steal it. Making an easily forged social security card necessary for a driver's license in fact does nothing to ensure the safety of my social security number; if anything, it makes it more dangerous for me.


Finally, since this doesn't prevent terrorists from flying in our planes, trains, buses, and taxi-cabs, perhaps with dirty bombs tucked away in briefcases or boxcutters with which to hijack whatever, well, the question is what does this rather useless rule do? It seems like a simple rule to, generally, make life harder for immigrants and keep those gosh-darned illegal immigrants off of American soil. One more hoop for them to jump through before they can be treated as human beings. Of course, it's easy to hijack the public's fear of anti-American terrorists coming over and doing evil things to keep everyone else out as well, which in some ways we've already done (one look at the signs on American customs outposts convinces you of this - the 'welcome measures' include fingerprinting for all non-U.S. Citizens who enter the country, I believe). This is just one more example.

Of course, it could also be to prevent terrorists from stealing my social security number and crashing it into a building. You know, like they do.

Evolution!

People from societies with diets that have historically been rich in starch are twice as likely to have at least six copies of the Amylase gene.

Amylase is one of very few genes that exhibits significant differences in copy number between individual humans. It encodes for the protein in saliva that begins the digestion of starches, and is necessary to get nutrition out of grain. What's more, contrary to what happens in some other places, the "extra" copies of the amylase gene are fully functional and do lead to more amylase protein being produced, which in turn leads to faster and more effective digestion of starches. Also, since the differences in sequence between the three copies of the amylase gene in the reference human genome sequence are so small, it seems that this duplication might have happened quite recently; even perhaps since the birth of modern humans. Which means things like the development of agriculture and therefore the increased levels of starch in some societies' diets might very well have effected the evolutionary path of those societies. Which is cool -- we are effecting our own evolution. And not just by killing genetically diseased babies, like certain geneticists would want us to.

Nature, Futures, and the coming dystopia

The past two stories in Nature's "Futures" column have both been in reference to a futuristic society in which certain aspects of life (photography and weapons manufacture, respectively) are monitored automatically via computer, ala failsafe. In the first, guns turn against their owners and start deciding who gets shot based on entries in a police database-in-the-sky. In the second, all photographs are stored online (by requirement) for some reason - and darkroom procedures hence outlawed, a compromising picture of a government official appears in a chemistry lab.

It vaguely reminds me of the Cybermen; the little ear-bud phone service that turns against you, hijacks your brain, and turns you into an automaton. And I wonder what the fascination with such dystopic futures is. At one point, progress was considered universally good, we were on the path to utopia, and so forth. Now it seems more imprinted on the common imagination that we are descending into a police state, that our parents were freer than we are and we are freer than our children will be, and that there is no turning back on this irrevocable path. When did we go from Marx, with the revolution being imminent, to Mill, with no more revolutions and the gradual death of our species from lack of freedom, argument, and passion?

EDIT: I know the answer to that question is, potentially, when Marx's communism turned into just such a controlling police state.

Fall

There is a certain joy that can only be achieved by nestling into freshly washed, still-warm-from-the-dryer, sheets with the window open and letting in air that is just a tad colder than comfortable. And it is a joy that cannot be had in summer in Chicago. (There are plenty of awesome things about summer in Chicago, such as swimming in the lake and sudden thunderstorms, but that is not one of them). But last night was just such a night, and that is a sign, perhaps, that fall is on the way (or already here).

Joy!

My experiments worked! Joy!

Also, I have a new project: Bright red wool coat with polka dotted lining; double-breasted and really full bottom; approximately knee length; big white buttons. Wish me luck! I will post pictures if I ever get a camera that works.

November is closer than you think

I just realized, recently, that November is really quite close. Which means that the insanity of writing a novel is closer than I think. Which also means that the insanity of applying to NSF grants and graduate school while writing a novel is closer than I think. I tried the writing-a-novel-in-December last year, and while I succeeded it wasn't nearly as much fun without the online community (or any community to speak of, really). It was my second year doing it, and I think that the product I ended up with was better than the first year. But I can do better. I have a few ideas for my novel this year. Most of them are stories that I want to write eventually, so I'll have plenty of fodder to keep doing this for years to come no matter which I choose. The three best ones are as follows; first, the story that I originally envisioned as a fanfic, but doesn't have to be, second, the story vaguely based on my experiences with circus people and diving, and third the science-policy dystopic story. I've had ideas for first chapters to all of them in the recent past, but I'm working on the fic-one right now. At the moment I think I'll do that one, but I think the other two are probably better stories. Or I could combine the first two, but that seems a bit much perhaps? It would need outlining to work right. The problem being that the first two are both vaguely retellings of Peter Pan or The Wizard of Oz (or Alice and Wonderland I guess, but I'm less familiar with that). I feel a little bit like that is the only plot I can really write, because it is arguable that the story I wrote last year also follows that paradigm in plot:

Main character runs away from/is spirited away from normal life to adventures, has adventures but in the process realizes that they really want to be home having normal life/normal life is the true adventure/some corny moral and returns home to cheers and fanfare. It's the typical children's story I guess. So maybe I want to write the science one simply because it's different.

In any case, this useless post brought to you by the fact that November is NATIONAL NOVEL WRITING MONTH. You should all write novels in November with me, so that I will have company.

Now this is cool.

It seems like it is a corrollary of the theory of Natural Selection that the most highly conserved regions of the genome will be those which are necessary for existence -- if a region is not necessary then it will slowly mutate away and if it does not do this there must be some reason why mutations in that region are selected against. This is particularly interesting in the context of certain "ultraconserved" regions which do not code for proteins -- long regions that are conserved between fish, frogs, and men and which can be very distant from any coding region. For a while, it was supposed that these regions were necessary regulatory elements. However, conservation does not imply necessity, a recent study points out:

It is widely believed that the most evolutionarily conserved DNA sequences in the human genome have been preserved because of their functional importance and that their removal would thus have a devastating effect on the organism. To ascertain this we removed from the mouse genome four ultraconserved elements—sequences of 200 base pairs or longer that are 100% identical among human, mouse, and rat. To our surprise, we found that the mice lacking these elements are viable, fertile, and show no apparent abnormalities. This completely unexpected finding indicates that extreme levels of DNA sequence conservation are not necessarily indicative of an indispensable functional nature.

I find this very cool. I have no idea what it means, but it's very very cool.

My new project?

I am probably certifiable, but I am going to try and make a jacket based on this for a part in a halloween costume (I'll make the whole costume as pictured, with a slightly different jacket). My idea being to make it black + off-white, with trim around all the seams and a design on the front bottom openings and around the neckline and on the sleeves, instead of everywhere. Probably a more tailored and fuller cut too, because I like those. Wish me luck; if I succeed it should be totally awesome.

Peter Breaks In

Wendy locked the front door from the inside, waving goodnight to her coworkers with half a smile. Mr. Darling had told her there were a lot of bills to take care of and the budget needed balancing; from the looks of the ramshackle filing cabinet in the back room, Wendy had a full night ahead of her. Darling Toys was thriving; it seemed like they couldn't keep the toys on the shelves, but for some reason they were still barely in the black. When Mr. Darling had promoted Wendy to assistant manager last week, he told her that her first job was to find out why.

She pulled one of seven tea bags out of her purse at random - it was apple-cinammon black tea - and took a mug off of the shelf, filling it with steaming water from the coffee machine. She set the tea to steep and turned to the sheet of plywood, balanced on a filing cabinet and a massive old computer, that Mr. Darling called a desk. It was covered in children's toys - dolls and wooden trains, a remote control car, and even one of the heavy-duty, high-quality lightsabers. She cleared the desk, booted up the computer and held her mug of tea up to her face, breathing in the cinnamon-flavored steam and leaning back into the folding chair. She wished that Mr. Darling hadn't been so very... frugal with his purchases for the administrative part of the store. But perhaps there hadn't been much of a choice, if things really were as bad as he claimed.

Mr. Darling founded Darling Toys with his wife, twelve years prior, when they realized that they would not be able to have children. The Darlings loved children, and wanted nothing more than children of their own, but they hadn't even met until Mrs. Darling was thirty-five and past her reproductive prime, and so by the time they were ready to make the commitment to eachother that a child would bring she was forty and simply too old to conceive. Even the adoption agencies turned them down as too old. Mr. and Mrs. Darling fought the decision, sent calm petitions and angry diatribes and everything they could think of to nearly ten agencies, but simply could not get results. And so they sat down one night, and Mr. Darling looked Mrs. Darling in the eyes, and said to her, "My dear, why don't we just start a toy store, and spend all the rest of our lives making children happy?"

And so they took a loan out of the bank - for while having a child is much easier when you are twenty, getting enough money to start a store is much easier when you are fifty - and they rented a space and they began to sell toys to children. Of course they struggled in the beginning, because Mr. Darling had to scale back his psychological practice and Mrs. Darling was only a school teacher, but they squeaked by just barely and slowly grew their inventory and the store until they could move to a bigger location, which they did on the fifth year of the store's history.

And so they came to their present location, a friendly little corner store taking up the basement of a red brick three-flat, and until Wendy came it was just the two of them and their customers. Wendy walked into the store, a bit tentatively, two weeks into her first term at a nearby University and desperate for a job. It being a Saturday, Mrs. Darling was working the register and she took one look at the nervous girl in front of her and knew, instantly, that the girl would be just the right fit for the store. It didn't take long to convince Mr. Darling, and it took even less time to fill out the proper forms and hire Wendy officially. The Darlings came to look at her as a surrogate daughter, and she admired their love. Mr. Darling wasn't sure they would be able to pay her at first, but he and Mrs. Darling went into the back room and calculated expenses and insurance and decided that they could give her nine dollars an hour.

After Wendy, John, a boy who grew up in the neighborhood and was going to the local highschool, was hired (with much the same fuss). John was followed everywhere by his younger brother Michael, but no one really minded except John, because little Mike had too sweet a disposition to be much of a problem to anyone, and besides, he swept up and reshelved the toys for free.

There had been marginal raises and bonuses over the years, and Wendy was now managing to get by, in her third year at the University, working as many hours as she could at Darling Toys.
John was due to leave at the end of the summer, and Michael was already a freshman in highschool. Wendy realized now, of course, now that she was privy to the account book, that Darling Toys had only ever just squeaked by by the very skin of its teeth before, and that it had perhaps not been wise to move into the larger space, or take on any employees at all. But they had made do, and they formed quite the little happy family to the passer-by, and truth be told it was a very good place to work, if Wendy's judgement was to be trusted.

Wendy took a gulp of her tea while the computer finished booting up. It was a relic, a dinosaur, but all Mr. Darling asked it to do was run Microsoft Excel, and so it managed to limp along. Wendy opened the accounting spreadsheet and tapped her fingers against the keys of the keyboard, thinking.

The accounts were a mess, scrambled and unintelligible. Wendy sighed and opened a new file, and then pulled the bills and inventories from the past year out of the filing cabinet, spreading them on the floor. She began to categorize them; into regular expenditures she placed rent, electricity, the phone line, costs for advertising, her salary and John's. The security system she put in a different pile, resolving to investigate if perhaps there wasn't a better system available. She sorted the inventory by company and calculated the rate of return for each toy company, which jumped off the shelves and which they ended up giving away at a loss. She noticed that they lost toys regularly, but not so regularly that anyone would see anything amiss, and not with any pattern. She assumed that it must just be random teenagers or small children stealing on occasion, and was tempted to write it off as simply a regular expense. By the time she was done, she was down to two tea bags. She took a sip of her tea - mango green - and rubbed her eyes and back. Then she turned to the computer and began to set up a new spreadsheet.

There was a soft clatter in the front of the store, just barely enough to hear over her typing, but audible nonetheless. She froze, looked around for something to use in case of an emergency. She wasn't sure if she should call the police or if the security system would automatically do that, but she guessed that the security system would call someone, who would know better than Wendy what to do. Then she heard laughter. It was one person, alone, and with such a charming and innocent laugh that she felt her fear melting a little. She could, perhaps, explore, she decided, and so Wendy grabbed the heavy toy lightsaber from the ground by the desk and made her way to the front of the store. "Who's there?" she called, cautious.

The person fell silent, but she heard another soft clatter as something fell to the floor, and then footsteps moving towards the door. "Stop! Thief!" she shouted, and ran to catch him, but all Wendy saw was a bright green hooded sweatshirt before he was out the door. She turned back to the shop and began to check the shelves. As far as she could tell, nothing expensive was missing, although she would recommend a full inventory the next morning. The only disruption appeared to be pieces from the wooden train set scattered on the floor.

She told Mrs. Darling about what had happened the next morning, and Mrs. Darling told Mr. Darling, and together they reached the consensus that Wendy must have been dreaming. Michael and John helped with the inventory but nothing was missing, and it was impossible for someone to get into the store after it was locked without setting off the alarm system. And so it was settled, and left at that, although there always were the train pieces picking at the back of Mrs. Darling's brain, just unlikely enough to have fallen out of their box that it made her wonder.

In truth, it made her wonder enough that a week later she spent the night at the store, bringing an air matress and sleeping on the floor behind the register. She dreamed that night that someone had opened a store across the street from hers, and that all the children in the area preferred this other shop, and that Darling Toys was going out of business. But somehow, she was calm in her dream until she saw Wendy, John, and Michael peering into the windows of the new Toy Store with awe. She woke with a start to see a face through the window by the door, a boyish round face surrounded by a cotton sweatshirt hood. He looked her straight in the eyes, as if he knew she was there although it was dark in the store so he couldn't possibly, laughed in audibly through the glass, and then walked away.

This week's Futures

Is awesome. In part because it's clever and creative, in part because it tells something about humanity and life, and in part because it's based on really really real science. My mom told me about those parking-lot things, and some of the kids in her class have the high-pitched ring tones. She got lucky; even at age 54 she can still hear them, but most teachers can't and her students were shocked when she would go up to them and tell them to give her the ringing cell phone. They would actually say "But you can't hear that!" And she would stare and answer "Yes I can." So it's not very futuristic, I guess, which is what some people like about science fiction - wacky and futuristic - but I think I like this better.

In short, everyone should read it because I really like it. Here it is.

Edit: I think that I have a post about sexuality in mice, and possibly a short (Doctor Who related?!) story about it too (it's going to be awesome) but it bears some more cogitation. *cogitates*

Edit 2: I am victorious over fear. I got blood drawn today. On friday I will know if I have mono or if my immune system is just insane.

Science and Magic!

This is an awesome article. I like most of its ideas.

My grandmother and the kitchen floor

According to my mom, my maternal grandmother would say that if you can't sleep, you should scrub the kitchen floor. If you feel antsy and anxious and can't do anything about it, at least do something useful and clean the house. As I was scrubbing the floor today with Cake playing loudly in the background, I thought of her, and my mother, and the days I would spend as a kid with my mom and brother cleaning the house. We would always scrub the floor by hand; we only got a mop when we hired cleaning ladies. As a result, I am perhaps more comfortable getting down on my hands and knees and scrubbing than I am weilding a soapy mop.

Which isn't to say that I don't want a mop in the apartment.

False Alarm

Never mind the joy of the last post. I'm still in cloning hell. And playing hooky today to not deal with it. I'm good at that; not dealing with stuff. It just might be one of the few things I am good at. Unfortunately, you can't make a career out of ignoring problems.

Thursday is still full of meetings

But won't be next week.

This week's meeting was not as awesome and hilarious as last week's, but I did not bring a notepad to take notes, so I cannot blame myself for it. Julie made a big deal out of it being the last meeting for some people, and Steve said, utterly unconvincingly, "I'll really miss you all." When we laughed, Julie said that he really did mean it, to which Steve responded, in the same tone of voice, "Yes, I'll really miss you all." We laughed again. Then Steve said "I'll miss the lunch," which was kind of even funnier.

In personal science news, I *finally* have the construct which I have been working on off and on since December made (it's a long story involving being sent the wrong plasmid, a postdoc not doing what he said he would and us having to change plans three times in the cloning process)! At least, I think so. I am sending it off to be sequenced on Friday morning, and I have one more diagnostic digest to do tonight to verify the previous two semi-positive results. But that is exciting; I might not have to do much more cloning! Hoorays! Because, as Chauncey said at lunch yesterday, cloning sucks.

The Scarlet Letter

Richard Dawkins has Atheist tee-shirts for sale. They have bright big, scarlet, As written on the front. I think the comparison is fitting.

Sam Harris in Nature

I quote: "There are bridges and there are gangplanks, and it is the business of journals such as Nature to know the difference."

Here's the article.

His argument is an argument that I have heard before (I think it's his standard argument); that religion - any religion - is out of keeping with science, and as such the battle has to occur. Tolerance on the part of either side will simply end with that side being taken advantage of. Namely, in Sam Harris' case, the atheists have to take a strong view espousing reason at all costs - and particularly at the cost of God - in order not to be abused. To be utterly honest, it is a tempting view especially after seeing atheism blasted in various forums, and being told that I am not a good person or am going to Hell. Of course not all of my religious friends have told me that, and in fact a few of them have told me that they don't believe it, but it is a striking statement that the fact that some of my religious friends have told me that or things like it does not mean that I am not friends with those people anymore.

(P.S. Please don't read this as a plea to have my religious friends tell me I am not a bad person. It isn't. After a lot of deliberation I have decided that I couldn't care less what someone else thinks of my actions. At this point in my life, I can honestly say that I regret none of my actions, and that I do not think I behaved poorly in any major occasion and did not at least try to make up for it. Except that time I shot four men in Vegas. But you know what they say; what happens in Vegas stays in Vegas.)

In any case, the man brings up some good points; basically amounting to the fact that at least in a scientific journal, we don't have to lower ourselves to the kind of politically correct "Of course there are no contradictions between science and religion" that we do in other forums, and that since we do not have to stoop to that sort of, well, lying, we shouldn't. For example: "In his Commentary, Sardar seems to accept, at face value, the claim that Islam constitutes an "intrinsically rational world view". Perhaps there are occasions where public intellectuals must proclaim the teachings of Islam to be perfectly in harmony with scientific naturalism. But let us not do so, just yet, in the world's foremost scientific journal."

I think a nicer way to phrase his point, in general, is that religion never constitutes a rational world view, but that it doesn't even attempt to. It is impossible for religion to be rational because its agents are by their very definition arational or superrational. And perhaps there shouldn't be a value judgement attached to that.

The problem is where to draw the line. If you let someone believe something of which there simply cannot be any evidence or something which is simply a personal opinion (such as the existence of God or when life starts, respectively), you aren't saying that when faced with contrary evidence they should deny it. The existence of God or a Universal soul or merely something cannot really be proved or disproved, and so there is nothing requiring someone to deny reason and evidence simply because they believe in God. So we can say that the belief of God is perfectly in harmony - or could be perfectly in harmony - with the practice of science.

Then you get to things that we simply don't know yet. They are potentially knowable, but we don't know them. I'd put things like the physical cause of "the soul" (will and consciousness), here. There are a lot of people trying to figure it out, and it's possible that in the future some religious belief will be contradicted by evidence and reason. But at the present time, we don't know - all anyone has right now is a belief or a hunch or a gut feeling. In this case, perhaps, most people who lean towards atheism lean towards one answer and most people who lean towards religion lean towards another. But that's all there is - a lean - there isn't a clean line and there isn't a clean disharmony between the two views, at least in principle.

Of course, there are quite a few things that we do know, and that are hard to contest using reason and evidence, but are still contested issues simply because religious people make them so. For example, evolution. We've seen evolution take place in petri dishes (see here) and the paleontological and genetic evidence of relation between humans and other primates is huge, but there are still crackpots and religious nutters saying that all of that means nothing, because of a passage in the Bible or the Koran or whatever that says God created man in his image, period, end of story. Or who are masquerading as scientists saying that life is "too complex" to have developed through a process of natural selection (something which is, it seems to me, complete bullshit). This one, in my opinion, comes down pretty clearly to religion versus science. Either you believe what is written in the Bible or you believe in what we have learned and theorized and figured out. You can't believe both. Here, religion and science are directly at odds. There are religious people who believe in Darwin's theory of Evolution through Natural Selection, but they are choosing which parts of their religion to believe. And that's a slippery slope, because if you only believe some parts of the Bible literally, then why should you believe any of it? If you don't believe the Bible when it tells you that the ratio between a circle's circumference and its diameter is 3, why do you believe the Bible when it tells you that homosexuality is a sin, and why do you believe the Bible when it tells you that Man was Created in God's image?

But the point is that it's a continuum. There are plenty of things that the scientific community isn't quite certian of and religious views push you one way or another on. There are all sorts of intermediates. And you have to draw a line somewhere, except there's absolutely no clear place to do it. And so 44% of Americans say they judge atheists harshly, and people like Sam Harris say that the "forces of unreason" are attacking science, and we have to fight back or we will be defeated.

To prove that I am not that sad

Article: Peace in the Middle East through surfing

But of course it doesn't do that much immediately. Which is unfortunate but not surprising. It brings to mind a few things; how much someone can do and how little it can matter. How a common activity brings people who hate eachother together and builds unity. And how the zen state you acquire when you're concentrating fully on your body and not on anything else -- a state that is easiest to acquire through athleticism in my opinion -- can wash away anger and hatred and frustration. But not for very long.

Also, the fact that now that Hamas is a governmental organization, the rest of the world has to start treating it as such or cease helping the people of Gaza. It's sort of like the Cuba problem (although arguably much more severe). The United States' boycott against Cuba was meant to destabilize Castro, but instead it simply hurt the Cuban economy and through that the people. It didn't shorten Castro's reign at all - it is very likely that he will officially be president until he dies of natural causes, although his duties will be (and are) carried out by his healthier brother Raul. I don't know how accurate the parallel between Hamas and Castro's communism is, I'll have to think about that some more.

It would be interesting to ask that surfer again and see how much he likes Hamas now. I don't think that he has much reason to change his mind, though. I also think that one critical step in acheiving peace in the middle east is for Isreal and the West to convince Palestinians that they should not feel threatened. I think that in large groups people act with gut instinct, in a sort of animal response, rather than with logical, calm reasoning. And hence, since Palestine as a state is probably threatened, Palestinians feel threatened and violence ensues - just like a bee will sting if it is scared, or a dog (no matter how well domesticated) bite.

And so maybe things like this - uniting specific people with specific other people through common interests, charity, and friendship - is the most that anyone can do to help the situation. Perhaps in some ways that has more of an effect than any official state action, because it gets people to look eachother in the face and say "Well, I hate their leader, but I don't hate that person." And in my mind it isn't far from "I don't hate that person" to "I don't hate that kind of person" and from there to "If I take this action against that institution, it will hurt that kind of person, and I don't want to do that."

And once you're there you can start talking about peace.

A la recherche du temps perdu

Someone once said that of all the senses, smell was the most entwined with memory. I think it was Proust, but that might just be an image of madelaines and sadness. A la recherche du temps perdu. I smell like chlorine now, and it's bringing back all sorts of memories, good and bad, all of them lost now and covered in a fine layer of dust. I have been avoiding them, but the smell brings them back, whether I would or no.

It's that smell, and the feeling of the tight, disinfected and dried skin on my face, the feathery quality my hair takes on, and the rubbery tinge to my legs as they get used to walking on land again instead of kicking against water. That and the electric buzz of cicadas that forever will remind me of summer, and being at Glenwood, and belonging; what is summer without cicadas?

I went to Ratner today. I swam because they would not let me dive. I wanted to dive. I can't tell if that's a good thing or a bad thing, if it is prudent or foolhardy for me to step on a board again; whether it will give me comfort and pride, or sorrow and longing, whether it will lead to increased confidence or another injury. I can't tell. I don't know what the future holds, but I want to try it, and the ache in my legs and my stomach when I see a diving board and forbid myself from standing on it, feeling it move beneath my feet (because it's such a tactile sport, such a rhythmic sport), and then launching myself off of it into the air, well, I can't take it anymore. I want to be younger, I want to be freer, I want to fly.

I always have.

It's a peculiar feeling to float. Relaxation is key -- for whatever reason, a clenched muscle sinks to the bottom of the pool but a relaxed muscle responds and stays afloat. You start out level, and then slowly your hands and feet sink down, pulling your arms and legs with them and your torso. Your chest pauses at the surface before sinking too, and then all that is left is your head. If you kick, your feet stay above water and you can stay floating by slowly, gently kicking your feet so that they don't sink. Some people float better than others. I do not float as well as my mother.

The water gets in your ears, plugs them up so you hear the gentle rush of water leaving the pool by the drains and being replaced at the vents, the tinkle of your feet and hands splashing as they enter the water, and nothing else. If you close your eyes and float, it is perhaps like being in utero again; except colder, and when your face starts sinking less receptive to life.

If you sit at the bottom of a pool and look up, you feel like you are at the bottom of a bowl; the index of refraction is high enough that the light bends around you and the walls look like they swoop up. Apparently the atmosphere in Venus does that too. So walking on Venus would be like walking on the bottom of a pool, but much hotter and more sulfuric (I think?).

Since your vocal chords are open to air and not water, you cannot be heard if you shout underwater unless you shout very loudly. Instead, you make vague noises and expell bubbles through your mouth; it looks like the words escape in the bubbles and if someone was to sit up above you and put their ear to the bubble, they would hear what you were saying. I don't think it works that way in real life. But it would be awesome.

The floor in the Ratner locker room is made up of many small-to-medium sized white tiles arranged in a grid with dark brown mortar between them. The shower curtains fold and sway on them in some complex curve. I don't think I could model it, but I'm sure that you could write a series of sinusoidal functions whose sum was the path of the shower curtain on the tile grid. I only know this because any curve can be expressed that way.

Today I stared at the floor of the showers and thought; this is the shower I warmed up in after the accident. These are the tiles that I couldn't focus on then. The thought made it hard to focus today. Several times today tears came to my eyes, but they mixed with the chlorine and the water and neutralized themselves as they ran down my face or I submerged myself to keep from making a scene.

People don't appreciate pools. They go to pools and swim laps, and think about their days or their bills or work or their families. They don't empty their mind and stare up at the perfectly white rafters and think; how does one clean rafters so high up? For surely they must be cleaned every now and again, just like everything else in this world. They don't find all the little dots in the windows that block some of the light. They don't match those dots to the dots in the ceiling. They don't see the curve of the roof or the lines of the bleachers. They only see the black cross on the wall that marks where they should do their flip turn. They don't listen to the vents and the drains, to the splish-splash of their own strokes. I know this because when I was a swimmer, I didn't think about any of that; except perhaps occasionally about the shape of a cloud as I did backstroke -- I told myself that one day there would be a message in those clouds, and I would decipher it and it would mean I was special. I sang songs in my head, I counted strokes, I counted lengths, I futzed with my goggles and my cap.

But a swimming pool is a thing of beauty -- water just deep enough to being to turn blue of its own accord, smooth white tiled walls and floor, or rough concrete instead. In a swimming pool, you can escape into your own bubble and not notice someone until the wake of their strokes disturbs your own. You don't have to hear, or see, or feel or smell or taste anything other than the cool clear water that surrounds you, and you have no choice but to hear and see and smell and taste and feel it, immediately upon entrance and constantly thereafter. Perhaps the only exception is sight, but the sting of chlorine in my eyes is enough to convince me to close them usually unless I am wearing goggles - and goggles are such a sign of the quotidien, of the lap-swimmer, that I usually avoid wearing either of my two pairs.

I went to the swimming pool today, and sunk to the bottom to let myself think for a while. There, in the cool and clean and quiet water, everything was calm, and I couldn't afford not to be. I came of age in a swimming pool; I grew from a small child into an adult in a swimming pool, and like a mother's womb when I was finally ready for something else, I was rudely shoved away from its waters. I tried to return today. But it didn't feel the same. It wasn't home, it wasn't comfort. All that is left are memories. And I think I was the last person to figure that out.

My non-science post

I was going to post about not-science. It was going to be novel. However, I started writing the post and then I started reading the post and it was rambly and discontinuous and not well argued or thought out. So I'm putting it on the back-burner, and maybe I'll post it when I've thought about that stuff some more. But I'm pretty pre-occupied with my biology stuff now, so maybe I'll just keep talking about that.

So. This New York Times article is neither exciting nor news, but it is interesting. Better than this New York Times article which is just plain silly (and which we discussed last night over pizza and beer, hah).

Article #1: Americans have to drastically rethink two things: the label "Dumb Jock" and the idea that your brain stops developing at an early age. It turns out that in mice and in humans, excersize stimulates the hippocampus and prompts the development and maturation of new neurons. Aerobic excersize is better than stretching in the elderly. So take a jog, and you'll be able to do that problem set better!

Other things that supposedly increase bloodflow to the hippocampus and prompt the regeneration of neurons are: moderate alcohol use (although too much and you're hurting your brain), marijuana, a social life, and chocolate. Things that hurt your brain are stress and fast food.

Article #2: If you accept the "reasonable" hypothesis that some civilization reaches a point when they can create computers capable of modelling thousands of brains, then it is likely we are all simulated. There are several problems with this idea, and more problems with it being in the science section of the New York Times. Really, it is dubious that the assumption that thousands (or really millions) of brains will ever be able to be well modelled in a computer simulation. Especially not well enough to lead to the complexity and diversity we see in nature. At the moment, we have trouble modelling three electrons on the largest supercomputers. AI is incredibly basic and does not come anywhere near an actual sentience or even a facsimile of sentience. We can program supercomputers to play chess and solve checkers, but in the end we cannot make a computer that can have a normal conversation. Imagine not just the processing power but the skill in computer science necessary to overcome that barrier and model not just one being, but millions.

It's funny that one of the explanations given as to why this was a reasonable assumption to make began with the phrase "assuming a planet-sized computer" which is another assumption that I hope is self-evidently absurd. People can imagine planet-sized computers, but imagine trying to build one. And that ignores all the problems of finding a place to put such a computer where it would stably remain and be easily accessable but wouldn't interfere with life on earth. Basically, to do that it seems we would need faster-than-light-speed data transfer, unless it wasn't really a planet-sized computer but rather a moon-sized computer, and even then it would be incredibly unweildy to make and position and so on. Again, not only do we not have the technology, but we are nowhere close to having the technology.

We really will need to reach the technological singularity before any of this will happen. And given that the human race has a maximum of 7.8 million more years to live, and 1794 more years to travel in space, (taken from this, another nice pseudo-scientific article by the same dude) well, we'd better hop to.

This is all ignoring the fact that, well, presuming that some society did make it to a point where they could model the world, they wouldn't have come to similar conclusions as ourselves and realized that modelling sentient beings is, well, kind of sadistic. And if the question comes down to "Are we sentient or do we just think we're sentient?" well, then I ask you why you are asking such a silly question. Because in the end that is a bit meaningless.

Besides, the only conclusion you can really come to from the idea that maybe we're all just simulated in a computer is the fact that, okay, maybe we're all just simulated in a computer, but that doesn't have any repercussion on my every day life, what's right or wrong or in between, and so forth.

Rather than supporting Ethanol powered cars...

Why don't you just plant a tree? You will probably do more good for the environment. (See Science news article here.)

Basically, forestation of a piece of land X will sequester (take out of the atmosphere) 2 to 9 times the amount of carbon dioxide that we avoid producing by using that piece of land for production of corn, sugar cane, and other ethanol-producing crops, using a variety of estimates. Plus forestation helps with loads of other things, like not driving animals to extinction by taking away their habitats, keeping soil fertile, and apparently even stabilization of regional weather patterns. Which implies that to best fight global warming (and all sorts of problems that we cause in the environment), we should convert the farmland that is not being used for food into forested land rather than farmland being used for ethanol production (of course, there are even more complicated elements here because adult forests take a very long time to grow; plant succession and all of that). BUT! The point is, supporting industries like solar/wind powered electricity to reduce carbon emissions and planting more trees will (in the long term certainly and the short-term probably) do more good for the environment than supporting research into plant-based substitutes for gasoline and diesel fuel.

In conclusion; what you were taught in elementary school was right at base -- if you want to help mother nature, plant a tree. Or, if you can, plant a forest.

GRE

I just signed up for the GRE general test. It was pretty terrifying.

But what is more terrifying is that it won't let me sign up for the GRE Biology online. Wah!

Thursday is full of Meetings

PCBio for lunch and NSF for dinner. Which means I am up two free meals today. Which is pretty awesome. And they were fun, funny meetings too. Which is even more awesome. BUT since I had lunch and dinner at meetings, I am at work after dinner, which is less awesome. But it won't be too late, so that's more awesome again.

PCBio was full of projects I have trouble really getting into on their own merits: Computer modelling of protein folding, mapping energy surfaces for small molecules found mainly in the troposphere, and determining conditions for crystallizing proteins. So two out of three were certainly bio related, but in the very chemical-biology or computational-biology sense. But that's okay. Because the presenters were really good and got you to see the merits and excitement behind their projects, and Steve was in a great mood, actually, so it was absolutely hilarious.

I should really start taking notes, because there were a lot of absolutely hilarious things going on. But here are the few I remember, in the order I remember them and not the order they took place.

To the physical chemist (EmJ) who proclaimed, somewhat guiltily, "This project has zero relevance to biology, so I am not going to try to give it any," Steve responds: "That's a challenge."

Later in the same presentation, EmJ mentioned coal. Steve: "Where does coal come from?" It was followed by awkward silence, because everyone knew where it was going but no one really wanted it to go there. Finally someone responds that it's compressed oil, and Steve says that oil comes from compressed plants, and it's all well and good. He asks where the Sulfur in EmJ's molecule comes from, and got Methionine and Cystiene. "That's your biological relevance," Steve said. "The true meaning of plants, which is to eventually make fuel for our cars."

Later on in the same presentation, EmJ confides that her molecule is incredibly reactive, reacting even with the teflon that she used to coat her reaction vessels. She's going to try glass next. Maybe that will work better. Steve makes her flip back to an earlier slide which has a picture of her molecule on it, and asked why that molecule would react with teflon. There were a few people who answered seriously; Sulfur is particularly unstable with four bonds, etcetera, but the best answer is that MeOSOCl is "Smokin' hot." For the rest of the day, everything was "Smokin' hot." In fact, Julie decided that it was her new word. So "Smokin' hot" is "Smokin' hot."

Steve brought up the interesting idea that protein crystal structures do not, in fact, show a very accurate picture of that protein in action. In fact, NMR structures often have many equally valid solutions -- many different possible structures for one protein. Which is an interesting way to look at it; if a protein has multiple conformations that are valid, and in fact equivalent in terms of energies of atoms and the other things measured by NMR, a crystal will exclude those structures which are different -- thereby giving you a static picture of something which is actually dynamic. I'm sure that's not an actually particularly new opinion, but it is interesting nonetheless. There was a very funny dynamic when for about a minute or so Steve kept interrupting Alexander (the presenter for that bit) about random things and making witty remarks. I cannot replicate that exchange, but it was priceless.

I know there are other things, but I cannot remember them all today. Maybe next week I'll take notes. But if I bring things with which to take notes, it won't be as funny, I'm sure.

Oh well.

ALASKAXORS

I have just returned from Alaska! I saw Orcas and Dolphins and Seals and Otters and Eagles (lots of Eagles) and a Porcupine. It was tons of fun. I think we got the only 5 days of sunny weather all year, which was awesome. I could post a long story all about everything that I did in Alaska, but I think that in the end that would be boring and repetitive. You should instead ask me. I will tell you all about whatever parts I remember at the time. But Alaska was awesome, although not as much fun as Cuba. (It would be hard to be as much fun as Cuba without involving Swaney, seven of my best friends, and the whiff of fear whenever Costello would shout "DONDE ESTA FIDEL?".) In any case, I definitely recommend it, especially in August when it is miserable anywhere else.

Futures

Is a segment in Nature where they publish a short science fiction story each week. They select them for a wided variety of reasons, obviously, but I would hope that not least among these is realism or something like that. A nice balance between realistic science and creativity. These are scientists who are going to be reading it, after all.

In any case, I read it every week because it's a cool idea, and most weeks I really like what I read. I went through the archives a bit ago and found this amazing story. Creepy and awesome at once. I really love it. In the new issues of them, this and this are my favorites. Enough wacky to keep you wondering and for it not to seem too mundane, and enough normal for my scientist part not to rebel. (Of course the first is very Matrix, and the second very... There's a word for it but I can't place it).

In any case, this week's futures story is about genetic engineering -- sort of. And I don't like it. The idea that we could mistakenly turn a person into a fish rather than simply cause a miscarriage is, to put it bluntly, patently unbelievable from a biological standpoint. I do not believe that we will be able to turn people into fish until we really want to and really know what we are doing.

In other words, merpeople are still a long ways off for genetic engineering. And that's the problem -- the practical procedures that are cited in the story (replacing all the junk DNA with markers) haven't been developed in the slightest, while the key idea that the scientists came to too late (junk DNA isn't junk at all) has already been reached. It would perhaps work in an Alternate Universe where we are very slow to pick up on all the various signals and miRNAs and so forth that are in "junk" DNA, but since the segment is called "Futures", well, I always took it as "This is a potentially plausible future if we're really cool."

Which is something that has always frustrated me about science fiction in general. Science fiction writers are not, by and large, scientists really. (For example, the guy who wrote "Junk".) The writers who are scientists are, in my opinion, better writers because they actually take the time to research the science, even if they are writing outside of their area of expertise. There is little more frustrating to me than "serious" science fiction that disregards scientific discoveries that are easy to find online or in a text book.

If you want to write fiction, great, wonderful, awesome. If you want to write weird and wacky speculative fiction, great, wonderful, awesome. If you want to write science fiction, you have to remember that half of that name is science. So maybe you should take out a subscription to Nature or Science or at least regularly read the NY Times science section. If you aren't at least vaguely interested in science (not doing it, but reading about it and thinking about it and wondering about it), why are you interested in writing science fiction?

Mnar.

It's a little bit like grammar and poetry. Poets who break the rules of grammar are rampant and cool. But poets who don't know the rules of grammar are lame posers. You have to know the paradigm in order to break it in meaningful ways.

More noise!

Since the last post was on how noise was good for some genes, it seems suitable to say that noise is, of course, bad for others:

http://www.nature.com/ng/journal/v39/n8/full/ng2071.html

Says that essential genes cluster in low-nucleosome areas due to the decrease in noise that such a cluster will cause. Basically, since misexpression of said genes will cause severe phenotypes, they are clustered in places where misexpression is less likely to happen randomly, even for a short time -- hence less noise. Kind of an interesting result. I like the idea that noise in gene expression is caused by chromatin remodelling. It's clever.