Tuesday, July 31, 2007

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:


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.

Monday, July 30, 2007

Biology is noisy

We've known that for a long time. I have friends who choose not to study biology simply because it is so noisy.

I also have friends who assume that the noisiness of biological systems is an artifact of the less precise means we use to measure and control them. I like this article because it shows that if we were to remove the noise from biological systems, we would be removing some of their characteristics -- that noise has a purpose in biological systems. In fact, it's entirely possible that Bacillus cells amplify the noise inherent in a purely chemical or physical model of gene control through secondary measures. Basically, these bacteria want to be noisy, because that noise is the variation that genetics works with. In the overpopulated conditions at which Bacillus is competent, it is trying to take up new pieces of DNA in the hopes that some of them contain useful genes for dealing with the environment (similarly, heat-shocking some E. Coli strains will make them competent). But it's a chance - it's not certain that there's any DNA out there or even that any DNA that is out there won't kill the cell more surely than the overcrowding will. So in order for the species to survive, there has to be a mechanism by which some, but not all (and maybe not even most) cells turn competent. Hence the use of noise.

The one theoretical problem I have with the paper is that their method for reducing noise in the system seems flawed. They "remove" the noise by knocking down another gene - which reduces noise in gene expression but this might be because of a reduction in random noise or it might be because of a reduction in sensitivity to minute changes in the local environment. In the case of the former, then the researchers have indeed done what they set out to do. But in the case of the latter, then the researchers have simply said that when cells are less sensitive to their environments, they are less likely to react to their environments by becoming competent. Which is a bit obvious when put that way. The problem being, of course, that it's not easy to think of a way to remove that confounding variable. You can't test or control the minute variations around a single cell, since the system they are working with needs a large population of bacteria, and beyond stirring the media constantly (which they do) to get uniformity, well, there's not much of a choice. One would have to examine the effect of the mutation they use to knock down noise. There are other markers for response to crowding in Bacillus Subtilis than simply competency, or at least I imagine there are. Perhaps a slower cell cycle. One could perhaps test those secondary markers to see if they mirror the competency -- if they too are less likely, which would imply that the effect seen is a reduced sensitivity -- or if they oppose the competency -- if they do not change, indicating that the effect seen was in fact specific to the competency pathway.

And then the question is, is it worth it? Because in either case, noise and/or the amplification thereof is a necessary part of control of biological pathways. Which is perhaps a significant finding. Since it rather removes us from a strict deterministic paradigm and places us in a statistical one, I think (this is at first glance -- I might have to come back to the idea later). We're all fuzzy, noisy, there are no clear signals - and that fuzz is free will? Who knows.

This ranks right up there with the corn syrup experiment I am dying to do


And the corn syrup one is just pouring corn syrup into a bucket and seeing it spout back up after a bit. I think (actually, upon considering it) that water does the same thing. But less obviously probably because it is less viscous. Or something.

Yay kiddie science!

Friday, July 27, 2007


Lunch today was... odd.

Approximately weekly, I go out to lunch with a few of the postdocs in my lab (other days I have lunch alone or with undergrads). Usually it's a rollicking good time, and the conversations are interesting to say the least. My understanding of French is getting much better listening to Eric and Damien talk. I think I might even try to speak myself sometime; but that may or may not be the best idea. Eric thinks I don't understand the French, so often he'll explain it to me again in English. It was amusing when he was arguing with the second Damien about whether or not he had been where he said he would be when they were supposed to run an experiment together. The argument basically went; "I was there!" "No, I was there!" "No, I was there!" back and forth. Except in French.

In any case, a couple things were brought up today at lunch that got me thinking. The first is a meeting that several of my labmates recently had with an editor of Nature Immunology. The woman spends all of her time reading manuscripts and talking to people about what awesome science they are doing. That sounds like an amazing job. I would love to do that, if I couldn't (or don't want to) spend my time doing science myself. I'm sure that there are days when you just have too much to do and you have to bring it home, I'm sure there are manuscripts that are so awful you can't get through them, and I'm positive there are times when all the words run together because you're so tired, but reading and reviewing scientific manuscripts in a topic I enjoy would be an awesome job. So even if I don't make it in the research track, maybe I can look into that. Before today I hadn't even really thought about that as a job, but of course we need people to do that.

(A diversion: "Stick Shifts and Safety Belts" is playing on Roger's computer. This song unfailingly reminds me of Peter Russo and Richard Schnieder (sp? I always confuse the order of is and es in German names) spinning on stools -- the studs on stools, as they called themselves. Which reminds me of Peter doing so in Ms. Dyas' Linear Algebra class. Ms. Dyas was wonderful in her dubious amazement.

If anyone reading this actually understands that (except Mango), well, I'd be surprised.

Anyway, the song ended. Now "Perhaps, perhaps, perhaps" is playing. Which is less distracting. But Kristy says it's the theme song for Coupling, which I guess would be distracting if I watched that T.V. show.)

Back to the original point, another thing that was brought up a couple times was how important people skills are even in science. For example, the more editors of the more journals you know, the easier it is for your papers to get a serious look. Of course, editors are always accepting things from people they don't personally know, but if they know you they will probably look more closely at the paper. And on the other end, the reputation and quality of a journal depends directly on how many people know it and like it and read it -- which is sort of a tautology but implies that if you can get people to submit manuscripts to your journal because of a personal relationship, the journal does better. Of course a journal can't just publish the work of the friends of the editors, but those connections are still important. Anyone wanting to go into science to avoid politics will spend the rest of their lives closeted in a basement room calculating physical constants or something else boring; the exciting projects are done (and published) by people who are friendly and connected enough to find out about them and get them. Well, within a couple standard deviations.

I guess politics is slightly less important in science than it is in, say, the music industry, and there is a degree to which the data speaks for itself - if you do good work you get some rewards. But "Does good work but is a pain to be around" isn't really a stirring reccommendation, and even Francis Crick was in graduate school until something like his thirties because he couldn't get along with an advisor long enough to get out.

(It's all Cake all the time on the computer across the lab. It's kind of fun and kind of distracting.)

Finally, and maybe most interesting, is a thought that I had today based on a (very small) sampling of MD PhD prospectives. I had assumed, naively, that MD PhD folks were people who liked lab work and liked clinical work -- who wanted to do research in a lab and see patients as well, or who just wanted to do research in a lab, but thought that an MD would help them understand the bigger picture, understand the system better, or something.

I think maybe that I am wrong. I think that MD PhD people are, by and large, not actually interested in benchwork so much as they want to do clinical studies. And if they get caught in a real biology lab (as in really biology instead of medicine or something -- which isn't to say that medicine isn't real biology. Then again, maybe medicine is fake biology. You only care about part of the story) rather than a doctor's office or a drug testing lab or something, well, they aren't as happy.

Of course, my sample size is about two, so I can't draw any real conclusions from it, but Karen confirmed my suspicions that MD PhD folks aren't really into research as such, so that's something.

And if that was way too much stream-of-consciousness ramble for you, well, I understand.

Thursday, July 26, 2007

The protein from Hell and lazy RNA researchers

A few things that I thought of during the PCBio meeting, when I should have been paying attention:

1) Luciferase is the protein that goes flash! in fireflies. It is named Luciferase because it was Hellish to purify and isolate. Of course, many proteins since then have also been hellish to purify and isolate, but this one came at a time when there was no protein named after the devil, so it got the name Luciferase.

2) A Luciferometer would be awesome. I don't know what it would measure, though. Luciferase assays are measured using Luminometers. Since Luciferase makes light.

3) I am so glad I am taking pictures of large things (nuclei) instead of trying to dechipher Electron Micrographs. The presenter called it "A sadistic Where's Waldo". I squinted and tried to see molecules above the static.

4) Steve only has Words of Wisdom when you don't ask for them.

5) RNA researchers validate their existence by saying that DNA and Protein are "has-beens". DNA and protein researchers do not need to put down RNA to justify their existence. Sort of like some chemists and physicists: they put down biology in order to validate their own research, while biology doesn't even care. Also sort of like the U Chicago/Northwestern rivalry that Northwestern is unaware of.

6) Courtesy of Steve: People have been saying that RNA is the place to be since I was in elementary school. If they aren't making progress in the research, it's a laziness issue, not an under-staffed issue.

And the only response to that: That's cold, Steve.

At least they are all vaguely science related.

Also, to prove that I am not alone in my wandering thought in lab, I overheard a conversation today about how to take out a bear with a machete. It was decided that you should play dead and then catch it unaware.

I think that a hunting rifle would be more effective, and probably less dangerous.

Tuesday, July 24, 2007

At Ryan's Request

I have a post for real this time? Or for fake. Something like that.

This weekend was the weekend of Harry Potter Reckoning, so I dropped off the face of the muggle world and into one that is immensely more exciting.

A few general remarks, nothing specific to plot so don't be afraid to read it.

I think that Harry Potter is much more fun to read if you read it and analyse it with people. (i.e. the fandom community). There are a couple reasons for this: foremost, I think, is the fact that the books are good because of a thrilling plot full of clever twists and turns. This is made much more fun if you are experiencing it with people, hypothesizing and guessing as you go, rather than reading it in a bubble. However, almost as important are the characters. The characters are flat. They are all archetypes and almost nothing more. Few if any of them have complex motivations or conflicting emotions (except for teenaged angst, which gets old really fast) - the only complexity that is given is the fact that we might not know their motivations. Basically, people are either all good or all bad, all selfish or all selfless, nothing in between - and what we see as grey area is actually our misunderstandings of the characters. I'll use the very first book as an example -- Snape is all good, and we think for most of the book that he's all bad. That doesn't make his character ambivalent - it makes it all good and misunderstood.

However, with a group of friends, you can create the depth and the ambiguity that the characters lack in the books. You can create probable backstories, etc. And so when a character like Draco appears in the text, you don't just think of Draco as he is portrayed by Rowling (which is typical spoiled brat, nothing more and nothing less) but rather of the complex combination of typical spoiled brat, complicated rules and regulations of his family (a Malfoy code of conduct being a very common fandom notion), possibly questioning the morals he's been brought up with (for whatever reason - usually because Hermione beats him on all his exams) and so on and so forth.

Of course, in the past four years I have removed myself from the fandom community for a few reasons (foremost: I have been writing my own, original stuff) and as such didn't have these images in the forefront of my mind. Which left me with flat characters, a thrilling plot, and everything that everyone expects from Harry Potter books, no more and no less. And since I was half-expecting Fandom!Ginny and Fandom!Draco and Fandom!Snape, and even Fandom!Harry and Fandom!Ron and Fandom!Hermione, who are all deeper and more complicated than Canon!InsertNameHere, I must admit that I was a little bit dissatisfied with Rowling's characters, who do what they do because that is what they do, because that is their archetype and their stereotype or whatever other type you may have.

Er. Which isn't to say that I didn't love it, because I did. It is simply to say that I realized what makes Rowling such a good writer isn't her prose (which is straightforward and clear but not poetical) or her characters but her plot - which is thrilling and clever and keeps you laughing and crying and holding your breath until the last page. Everything is tied up into a neat little bow and you are left with the distinct impression that well, that's that. The story is over.

And that is exactly as it should be, and as it must be, and as it is.

I wanted to write a fanfic immediately after reading book 7. But that urge has subsided, fortunately. I say fortunately because it would not have been a very good fanfic, or a very good story, and because I have other better stories that I am working on. And the one good idea that I was going to use in the fanfic can be used in any number of other places, all of which probably suit it much better.

Tuesday, July 17, 2007

I have a post

But it might offend people, so I am reviewing it before posting. If this one is too much, I'll just write about the less offensive half.

In the meantime!

This is a cool article because it talks about using age to determine how much longer something will last -- the idea that a company that's been around for fifty years will probably be around for fifty more, but most new startups crash. According to that logic, the human race has between 5,100 and 7.8 million years left to go -- with a 95% confidence level. That flies in the face, I guess, of all those people who are rooting for the apocalypse in the next six months. Of course, there is always that 5% chance.

[EDIT: The aforementioned post is below.]

This is the old post.

In edited version. Perhaps you'll understand why I was tentative to send it out.

The Creationist's Atlas is being sent to scientists around the country.

Read about it here.

What is most troubling to me is that the general reaction isn't outrage or upset of any kind, it's "Well, we're used to this. It happens all the time." If we get used to people who think that intelligent design or creationism is valid, if we get used to people who invent invalid problems in the theory of evolution, if we don't fight against every single one of them, in a way, they win. The point is that the theory of evolution has corrolaries that are testable and have stood up to being tested, that we can see E. Coli evolving in jars, that there is no scientifically valid opposing theory. To say anything less than that - even if it is "People with certain religious views might not believe in the theory of Evolution and this is okay" - is just plain wrong, and for a scientist to accept the creationist view as something that isn't outrageous strikes me as, well, strikingly unscientific.

I don't really know how to explain my next point without probably offending a lot of my friends. I've purposely stayed away from talking about this side of neurobiology because I know it's contentious and when I have brought it up even with other atheist friends it has sometimes led to heated arguments. So maybe I should just stay away. But the segue is perfect and it's something I've been thinking about a lot. So, take this as a disclaimer: the following is my opinion, and I do not pretend to be an expert in neurophysiology. Also, even if I disagree with you, it doesn't mean I don't respect you as a person in every way possible. That being said, here goes nothing.

In what has become one of my favorite studies, (I should really find and read the paper), patients were wired up to a machine and told to wiggle their finger, basically, when they felt like it. The researchers saw something very interesting, because something like two hundred milliseconds before the subject moved their finger or decided to move their finger, every time the subject moved their finger, there was a specific impulse (called a readiness potential). However, the subject was not concious of any delay between when they willed moving their fingers and in fact moved their fingers; on the contrary, just as in normal life, one's decision to move his fingers happens nicely simultaneously with moving them - otherwise typing this blog post would be tediously slow.

In any case, it appeared that the biological determinant to moving one's finger happened two hundred milliseconds before the conscious choice to move one's finger. In other words, the decision to move the finger happened unconsciously (or perhaps subconsciously or aconsciously), before the conscious choice was made. Hence, the conscious choice to move one's finger could not have caused the motion. Instead, something else entirely had to be causing both the movement of the finger as well as the "conscious choice" to do so.

The way I look at it, there are a couple ways to interpret this study without simply throwing it out the window as faulty or ignoring it:

1) Since "conscious choice" cannot do what we think it does; it is an illusion and an artifact. In reality, our actions are caused by the sloshing about of chemicals in our brains, and we are, at base, automata. I think this is what Megan's boyfriend John believes, although I have not had a discussion with him so I am not certain.

2) Our idea of "conscious agency" is flawed, since the conscious choice does not determine the action. Instead, consciousness is a complex system designed to differentiate self from other - if an action is conscious, it was motivated by your self. If it is not conscious, it was motivated by some other. Hence, when I "consciously choose" to move my arm, it really is me - although it must be some deeper, unconscious me - that is moving my arm. However, when my arm moves because someone pulls on it, and I am not conscious of that choice, someone else is doing it. If my arm were ever to move without my "conscious choice" and without external impetus, something would be very wrong and I would go to see a doctor - which is an understandable safety mechanism for an organism. This is the view I espouse.

All of which is, I think, well and good and will offend few people, if any. The problem arises, mainly, from what I view as implications of this. The first, and most important, is the following: If consciousness does not cause our action, then it is unclear to me how our actions are different from the so-called instinctual actions of an animal. Indeed, a group of researchers recently looked at fly neurology when they were tethered, searching for "free will" in flies, and reports that even animals as distantly related to us as flies contain the ability to "be spontaneous" -- to take actions that are not direct, predictable responses to environmental stimuli (see a review here). If flies have a hard-wired spontaneity circuit in their brain, how much more likely is it that our "free will" is similar or identical to a homologous construct in the brains of mice, or cats, or dogs, or monkeys? Rats can be "altruistic" as I pointed out before in this blog. (Here is the link again, for those of you too lazy to confused to scroll down). I often get frustrated when watching the Discovery channel for anthropomorphising animals, but perhaps it is warranted. Maybe the same things that motivate us motivate them.

I have no problem owning my actions even if they cannot be described as "consciously willed." If the point of consciousness is to identify self versus other, then obviously the actions that are tagged as conscious are those that I chose to do - and conscious or not, it is still my organism. This is probably because I have, at base, absolutely no problem with a purely physical self. I am my atoms, I am my muscle and blood and bone etcetera etcetera etcetera, and that is all that I am. It is in some ways miraculous to me that consciousness could evolve, that neurons firing electrically could create the complex combination of sensory perceptions, emotions, and thoughts that I experience every day. That is wondrous and wonderful. It makes me almost giddy to think about. And, as it turns out, we are continually getting closer and closer to a point where we can begin to understand how that works. That is truly miraculous.

The problem, as I am sure some of you have realized by now, is that if the self is purely physical, there can be no soul. There is no "real" agency or free will. We're all animals, and the difference between myself and a chimp is even less than I ever thought it was.

Which brings me back to my initial point of the arguments about Evolution. I would love to argue that consciousness, and whatever it is that we have been referring to for so long as "the soul", evolved out of neuronal networks and the complex relations between them, that there is no bright line in the sand between ourselves and the rest of the animal kingdom and that in terms of consciousness and ensoulledness, there is a long continuum. However, that is a discussion that I simply cannot have. The evolution of physical traits is being questioned; if I cannot trust that my interlocutor agrees, at least, that evolution is the source for diversity in life on Earth, how can I even begin to talk to them about the new physical bases for consciousness, the revolution in neurophysiology?

Moreover, the idea of the duality between mind and body isn't just a religious notion. It is one that has inundated our thought for as long as western thought has been around, it seems. We are in the process of breaking that wall down. This is massive paradigm shift. This is a new world view. This is stuff on the level of "The earth revolves around the sun"!

It's the stuff scientists dream about. Or at least, scientists who have read Thomas Kuhn. The very way we look at the world around us is changing. The very kinds of questions that can be addressed are changing. The world is changing before our eyes.

And America is being left in the dust, because we cannot face down a bunch of idiots who still cling to creationism in the face of data; who still take pot shots at evolution because they aren't secure enough in their own humanity to not freak out at "being related to a monkey". Because they can't see that all living organisms are one part of the same thing, and that is more beautiful and miraculous than any special creation.

At least, in my opinion.

I hope you see why I've been editing and re-editing this post. I know, at base, that talking about the data that I've read about won't convince any religious person to abandon the notions of the soul and God. I don't honestly expect them/you to. I know that it's a personal thing, that it's Faith and the idea that His ways are not for us to comprehend. But I feel a little bit like I spend a lot of time toning down or holding in my views on stem cell research, abortion, ethics, and evolution because I know that at times they rankle my friends who disagree. And I guess this post is a resolution: I won't be offensive (or I'll try not to be offensive) and I will respect my friends, but that does not mean that I have to treat your beliefs with kid gloves, or stifle my own. I need to get over the fear of saying, point blank, "I disagree."

Monday, July 16, 2007

Movie Science?

First of all, a short article in nature described this paper. The general consensus was that asking movies to hold up to the same level of scientific reality that you ask of researchers or classes is silly. Everyone knows that Magneto defies the laws of physics, of course he does and of course no one can actually do that. Everyone knows similar for Superman, and most sci-fi movies. Well, duh.

What surprised me the most about the article was the fact that of all the problems in The Core, they chose the fact that the movie-makers show a human body sinking into lava, in defiance of buoyancy, and then talk about conservation of momentum with Superman, later on. I think the Superman example is a notably bad one, simply because, well, I had always heard that part of it being that Superman flies faster than the speed of light, reversing time and saving Lois, rather than the interpretation that the two authors gave it. However, there's a great problem with conservation of momentum in The Core, since if the earth's core stops spinning, in order to conserve momentum, the rest of the earth has to start spinning faster - and somehow, no one notices this.

Other wonderful moments that demonstrate a shocking lack of basic scientific literacy are moments such as when the main character has his two supposedly top-notch graduate students draw him a picture of the magnetic field of the earth (something anyone who has taken intro level physics should be able to do, along with many others) and when they have Orca whales singing. OR the repeated catch-phrase; Unobtanium converts Heat into Energy!

HOWEVER, it is my honest opinion that the writers of The Core knew exactly what they were doing and actually tried to break as many scientific laws as possible; to offend or mess up as many disciplines as possible. (Of that, they did a very good job, I think.) Since they were playing to stereotypes in droves, the stereotype of getting the science wrong is an easy one to play to.

ALSO, at the very beginning of the article in Nature (findable here), Mr. Ball mentions Jurrasic Park and the mad scientist in it, which brings me to my next golden find.

The New York Times, today, published an article talking about the possibility of re-engineering mammoths based on the DNA found from frozen corpses. The process is surprisingly similar to what would have actually had to happen were someone to do exactly what was done in Jurrassic Park to bring back Dinosaurs. First, using a newly developed sequencing technique, sequence the genome of the mammoth from the degraded DNA found in fossilized bones and frozen corpses. Second, engineer this genome into Chromosomes (we are getting to the point that we can get .5 million base pairs - which is only a couple orders of magnitude off, something the NY Times mentions). Third, find a way to package this with the proper proteins and methylation marks (something that we can do in bacteria, again noted by the Times). Finally, grow up the new Mammoth in an elephant's uterus. I find it fascinating and hilarious. And the best part is, people are trying to sequence the mammoth's DNA, the first step in this process. So, while perhaps we will never see Jurrassic Park, we are getting scarily close to going to a zoo to see Wooly Mammoths. Although global warming will probably make it a very unpleasant place for them to be.

Thursday, July 12, 2007

The problem of biology: You have to keep your cells alive

When I was in the eighth grade, ambitious little budding scientist that I was, I decided that I wanted to show that cells evolved in response to environmental stimuli (ala natural selection) for my science fair project. That's right, no baking-soda and vinegar volcano for me, I was going to single-handedly prove Darwin's theory of Evolution, and set aside all that pesky debate.

Of course, I didn't know that researchers had been growing e. coli in a variety of different conditions and doing the same exact thing since the time of my birth -- those are some damned cool strains of e. coli now. BUT that's beside the point.

I ordered algae (a strain of cyanobacteria called anabaena that is primarily single-cellular in unit) from Carolina Biological, along with the media to grow it in, and I set up cultures in my bathroom (after scrubbing it down with isopropyl rubbing alcohol). My mother taught me sterile technique and I carefully tended to the cultures. I grew them under green light, red light, white light, and no light, and at the end of about two months of growth I used flow cytometry to measure their color -- and get an approximate measure of the chlorophyll/carotene ratio. Idea being that cells growing in green light would have fewer green-reflecting chlorophylls and more green-absorbing carotenes as compared to cells growing in red light or white light.

I got my data and was happy, in that naive eighth-grade sort of way, and the mentor I had goen to for advice on methods and background and so forth suggested a stunning alternative hypothesis that explained my data as well: I had, simply put, killed the cells through overcrowding.

I was shocked, and decided to leave that part out of my science fair backboard. It was understandable; I was, after all, in the eighth grade.

I bring this up because today, in my PCBio meeting, one of the presenters showed a fairly interesting piece of data. She was using a rather strange system to try and determine melanin's photoprotective effects. She created and measured the presence of harmful oxygen radicals the following way: Compound S (rose bengal, I believe) was photoexcited (had light shone on it) in the presence of bubbled oxygen. Since rose bengal is a dye, it does a lot of funny chemistry that I don't really understand, but the end result is the creation of oxygen radicals. These oxygen radicals were then detected in a two step process: first they bind to histidine with some other funny chemistry that I only sort of understand, and then that complex binds to a reporter complex, changing its emission spectrum from 440 nm to 360 nm. Without any melanin in the system, she saw exactly what she expected: Over time, the peak at 440 nm disappeared and was replaced by a peak at 360 nm. Experiments with synthetic melanin showed only a "filtering effect" namely, the melanin was absorbing the light before it could hit the rose bengal, so before the chain reaction could take place. Hence, no oxygen radicals and no shift.

Next she used eumelanin (real melanin) in the form of cells from the Retinal Pigmented Epithelium (a layer of skin just behind your retina, which... er... has melanin). What she saw happening was that the cells would clump up together and fall out of solution, along with much of the rose bengal. Since RPE cells phagocytose dead or dying cones and rods in your eye, she (and her faculty mentor) guessed that the cells were phagocytosing rose bengal, and that for whatever reason this was causing them to clump together and fall out of solution.

What struck me most of all was that she was letting cells sit at room temperature in PBS for 20 minutes. To me, that seems like a very foolish thing to do if you don't want to kill your cells. Mammalian cells like physiological tempetatures, about 12 degrees celsius higher than room temperature, and PBS contains no nutrients or proteins to buffer them and feed them. However, I guessed that no faculty mentor would overlook something as obvious as "maybe your cells are dying."

I walked up to her after her talk and suggested it. She was just as shocked as my eighth-grade self had been when my mentor suggested it. One of the program leaders, Michelle, backed me up and said that it made sense. She said she would look into it. If experiments on cell lysates and purified components don't resolve that issue, well, then I'll be damned.

Which all goes to show that a little bit of common sense goes a long way. And that chemists (apparently) don't really think about things like cells dying. Or, perhaps more accurately, some chemists don't really think about things like cells dying.

Wednesday, July 11, 2007

Harry, you're pink!

I just discovered that the screenwriter for the most recent Harry Potter movie was responsible for the mauling of my childhood dreams in the latest Peter Pan movie.

And here I was looking forward to seeing it.

Tuesday, July 10, 2007

Two more articles

Because I have a lot of waiting to do today.

1) Big "bounce" hypothesis: Our expanding universe started not from a singularity, but from a very small, very heavy, particle existing at the end of a contracting universe. It makes me think of the universe being a sine wave, and also of the Doctor Who episode (The Satan Pit, I believe) where The Doctor says that you can't have anything "before time". Of course, it's a fairly blind guess. But pretty cool nonetheless.

2) Altruistic rats: When rats are done favors, they pay them back, or, failing that, they pay them forward.

(both were found on Monday.)

I get the feeling that no one much cares about the articles I find. However, I find them interesting, so I will be difficult and keep posting them.

Monday, July 09, 2007

I saw this in Nature first. I think


This article is interesting in pointing out goals (and the quote about taking over Mars, then Venus, and then Earth is quite amusing), but does a poor job of actually explaining the research. I think that's typical of the New York Times science section, though; in dumbing research down so the average lawyer can understand it, a lot of the cool science gets lost (and likewise for law -- dumbing things down so the average scientist can understand loses the nuance). If you want to read the whole thing, the article was published in Science on June 28. That should be enough to find it, I believe.

In any case, a search for that article led me to Science's website where I discovered that they are trying to reach out to Undergraduates (how convenient!). They even have a facebook group for AAAS -- American Association for the Advancement of Science -- with 95 members. It can't be more than 2 weeks old as a group, so that's pretty damn good. (Of course, most of them seem to be alumni or grad students, so maybe this facebook idea isn't too specific to undergraduates. But we knew that already, I think.)

Other things I found out today:

A study was recently done that polled people going to infertility clinics about what they felt was the most ethical thing to do with leftover embryos (their unborn children?) in which most people responded using them for embryonic stem cell research. Of course, this changes absolutely nothing about the issue and was really a foregone conclusion as well; few people would argue that killing an embryo by throwing it in a toilet and flushing is more ethical than killing an embryo by harvesting its cells for research which could potentially lead to cures for serious and life-threatening diseases. Most people would argue, on the other hand, that the very act of producing these embryos that cannot be born is unethical and we should do our utmost to stop that entirely, while perhaps (or perhaps not) retaining our ability to help infertile couples have children. Which is understood and probably wouldn't be argued against, but impractical in the short-term.

Buckyballs could help fight allergies, according to Nature. Previous studies have shown that they mop up oxygen radicals and protect nerve cells, and now it appears that they block the production of Histamine in human Mast cells when the cells are provoked with (basically) pollen. (The difference between +Buckyball and -Buckyball trials was fifty fold.) Similar results were shown in live mice. They're moving on to clinical trials next. So, in the future, asthma patients will have to remember to take their Buckminsterfullerenes.

Honestly, the more I read Nature and Science and other scientific journals, the more I think I'm living in the prelude to a science fiction novel. It's just incredible.

Friday, July 06, 2007

I have no idea what to title this.

I went to get rum for the party last night. Liquor stores have always been a bit daunting to me -- there is so much selection and since I like relatively little of it, I feel like if I am going to be pleased with my purchase I have to know what I am doing, and therefore that I have to find the needle in the haystack. I think that in the future I will stick to a few things I know I like or perhaps not go to liquor stores for myself at all - since I would rather have lemonade or iced tea than beer or wine.

But, all the same, what is a 21st birthday party without alcohol, so I bravely confronted my fear and stared at the rum selection - which was piddling, consisting mostly of differently sized bottles of the same rum. I selected the smaller one and a bottle of club soda, and made my way to the checkout, heart racing. I remembered the time in Binny's where I (and everyone with me) was kicked out surreptitiously, without an ID check. Of course, at that point I was under 21 so an ID check would not have been fruitful anyway. The woman at the register asked for my ID, and I gave it to her, and she typed something into a computer and asked "1986?"

I said yes.

She told me I wasn't 21 yet. I said that it was my birthday and I was fairly certain that I was 21. She called over the manager. The manager examined me, my ID, and the computer screen and then said "You typed it in wrong. This says the fifth."

The check-out lady wished me a happy birthday and I bought the rum.

Thing is, I have been looking forward to being carded for a while - if only to surprise people by the fact that I am, in fact, much older than I look. With my new haircut it's not as big a deal, but the point remains. So it was a tiny bit anticlimatic, but for my first trip to the liquor store, it was successful.

Thursday, July 05, 2007

Happy birthday to me!

And, as if on cue (?) I woke up today with "Follow the Fold" stuck in my head.

It's okay, though, because it fairly quickly changed to other things.

Also, this week's Nature reads like a science fiction story. And not just because part of it is one. You should check it out; their feature is on the Multiple Worlds Hypothesis -- which isn't a hypothesis so much as an implication of the hypothesis that Schrodinger's equations don't actually ever collapse (we just only see one of the superpositions). At least, that is how I understand it. I find it funny that the Multiple Universe theory is legitimate (although certainly not universally accepted) theoretical physics and not just crackpot science fiction. Then again, it is theoretical physics - which is about as close to philosophy as you can get and still be called scientific.

It also has an article about gene therapy actually working on mice. Which is astonishing. Hoorays! Maybe someday soon (read: in my lifetime) we will be able to *actually* have gene therapy! It's sort of like flying cars in that people have talked about it basically since they knew that genes sometimes lead to disease (not that people have been thinking about flying cars since they knew that genes sometimes led to disease. I think that people have been thinking about flying cars since they had cars and airplanes. Or something like that). But it's also sort of like flying cars in that no one has actually been able to implement it feasibly.

So, logically, if we can give gene therapy to mice, then we can make mouse-sized flying cars as well!


Tuesday, July 03, 2007

Prologue to a rewrite

Mango knows what that means.
The rest of you probably don't.

But here is the first chapter, in rough rewritten form. I chose this one because it actually has one of the supporting characters, as opposed to none of them. I would have posted the next bit - which includes/introduces the main characters, but that has yet to be fully written or sent to Kate for approval. Naiomi's last name might change. Maybe Andrews? I don't know.

So, chapter 1:

The ink on the letter shimmered and danced, black in the center and green-tinged on the edges, sparkling. Right now it said, “The Prime Minister’s daughter has been kidnapped by the Fairy King. He means war; he intends to invade your world and break the division.” A moment ago it had proclaimed a friendly greeting, and a moment before that it had been blank. Naiomi stared at the paper – a page from her own memo pad, proclaiming at the top in friendly bold-faced letters, “From the desk of Naiomi Watson”. The To: field had her name again in it, but the From: address was blank. Naiomi shook her head, wondering how this was possible and what it meant. Words slowly appeared at the bottom of the page.

“This is a telepathic letter – a little bit of my conciousness embedded in the paper. It is one of the few safe ways for me to communicate with you, because I am on the other side of the division – the side that the Fairy King means to free. Were I – were anyone – to break through this barrier between your world and mine, then anything could follow. The division is the invisible layer that keeps ideas simply ideas, stops all the childhood monsters, imaginary friends and feinds, ghosts and ghouls and goblins from coming out of the closet and pouring into your every day life. It keeps us from running amok. The barrier, in short, keeps what should be in Faerie in Faerie and allows you to have order instead of chaos and scientific reasoning instead of magic.” Naiomi frowned. It certainly sounded bad, unleashing chaos and so forth, but how could she tell any of it was true – except that something was certainly odd, because her memo pad didn’t normally behave in this way.

The words shifted again, melting into the page as new words appeared. “A tall, pale man with wings – an angel – stole the girl last night at two in the morning. Turn on your radio.”

Naiomi flipped the switch on her desk and heard a frantic reporter shouting over a crowd. “Disappeard last night after one a.m. and before six, according to her parents. They they have the police investigationg the scene, with reports of a ransom note from someone describing themselves as the “Fairy King”. Any information, please contact—” Naiomi switched off the radio and stared at the paper. “What do I do?” she asked, only vaguely aware of the ridiculousness inherent in asking a question of a memo pad.

“Send Victoria. She can get through to Faerie by going through a cave at the bottom of the pond in Kensington Gardens. Victoria will know how to get here.”

“I can’t send her alone,” Naiomi mumbled, the insanity of the proceedings finally getting to her. “She’s never been on a mission before, except for training. I have to send someone experienced along.”

The paper didn’t respond for a while, and then with an almost tangible frustration, the words appeared scribbled at the bottom, “You’ll send Roger.”

Naiomi rolled her eyes. Yes, she was intending to send Roger, but it was a good idea, a wise and thoughtful idea, not a foolish or reckless idea. “Well, shouldn’t I?” she asked.

This time the words came quickly. “No, you shouldn’t. If you send Roger, someone is bound to die. But you will send Roger anyway.”

Naiomi scowled. Who was this person at the other end, and why was she withholding information and insisting that Naiomi send agents to their death? The words shifted. “I am helping as much as I may. For you to know more at this point would be a paradox. Trust me – you have my assurance that when you send Roger along, only he will die. The Prime Minister’s daughter will be returned before the Fairy King’s plan reaches fruition, and with only minor sacrifice.”

The word sacrifice stood out on the page, almost bold-faced with emotion. Whose sacrifice? As if in response, the word “minor” disappeared to be replaced by “my”. The gaps on each side of ‘my’ made it look too small and too large, almost glowing.

Then the words abruptly disappeared. “I am not a person. At least, I am a person no longer. I gave up – or will give up – my place in your world. Time moves strangely here, as you will come to know, so I can’t tell you whether the event was in the future or the past or both. But now, I am simply words in your world, a narrator screaming in futility while the characters have their own way. I’m the chastising thought, the command, and so you may call me just that – Eirien.”

The words slowly faded to nothing, and Naiomi sat back in her chair, confused and mystified. Her secretary buzzed over the intercom and said, through the tinny speaker, that a police sergeant was here to see her about the Prime Minister’s daughter, and would she see him now? Naiomi answered to send him in, and after a few moments the young secretary opened the door and in walked a very nervous-looking police sergeant. Naiomi stood up to recognize the man and nodded to them both, as the secretary carefully closed the door behind her.

“Miss Watson,” said the sergeant. “I’m Sergeant Frank. I’m in charge of the Prime Minister’s case. I have gotten some information about it from an anonymous source, and he directs me to your department as one of the few – excuse me, the only – department capable of solving this case. I am here to request your assistance in the matter. I want to send your agents on what very well might be a wild-goose chase, searching for another world on the bottom of a pond, and I want to do it secretly so that the entire government does not look like foolish children. Besides that, we don’t know what we’re up against here, except that something very uncanny is going on, and we want people who are trained even more thoroughly than my men. People who are trained to handle the worst possible situations with the finesse that is clearly necessary in hostage situations such as this one.” Sergeant Frank cleared his throat nervously, obviously not expecting Naiomi to believe him.

Naiomi grinned warmly. “Don’t worry, Sergeant. I have two people in mind for your little spelunking outing already. You concentrate on finding the real kidnapper, I’ll send people out to debunk this witness of yours”

Sergeant Frank smiled with relief. “Absolutely, Miss Watson. I appreciate it.” He left with a clipped step, and after he closed the door Naiomi buzzed her secretary. “Send in Victoria and Roger. I have a new mission for them. And alert Michael and Joey that they’re backup – they should be ready to go in after Victoria should that become necessary. This might be dangerous.”

“Yes, ma’am,” came the secretary’s voice over the tinny speaker. Naiomi signed and glanced down at the memo pad. It now read “Perfect.”

“Well, I’m glad you think so,” Naiomi muttered, although she really wasn’t glad at all.