Tuesday, January 31, 2006

Yes. You've Found Us Out. Crap.

So Fox News has gone further off the deep end than I would have guessed:

I swear to god it's real: the full page screen capture is here. Look on the left hand sidebar. It may even still be on the Fox News website, in which case let me know how the video is (I've been in class all day, so I haven't had time to check it out).

Perhaps there's a bit of intended irony in this, but it certainly seems like Fox is capable of parodying themselves much more successfully than anyone on the left ever could.

Thanks to Chris Mooney for pointing this out; and further thanks to him for his previous debunking of Bethel.

Big Brains, Small Genus

Sorry that my posting disappeared last week. I was running an experiment in the lab, which meant my days suddenly became 7-13 hour days not including time spent on coursework. With all the extra time spent in an internet dead zone.

Some notable newsworthies I'd managed to miss during the week, courtesy Seed's New & Notable:

A British team of researchers analyzing skulls spanning 30 generations has found that our cranial vaults are 20% bigger than they were in the 14th century. The researchers suggest that the increased skull volume might be related to a higher mental capacity. They also found that our ancestors had more prominent features than we do, leading scientists to believe that hundreds of years from now, everyone will look like the alien allegedly discovered at Roswell, New Mexico.
(source: BBC)...

...Trivial Pursuit: Genus Homo
A DNA comparison shows that humans and chimps have evolved at a very similar rate, even though we split from a common ancestor between five- and seven-million years ago. This lends support to the push to reclassify chimps from their current genus, Pan, to our genus, Homo. Some biologists think the chimps should stay in their own genus, because transferring them into ours might implicitly give them moral rights and responsibilities they don't deserve. Others believe that instead of moving them, we should suck up our pride and become Pan sapiens. The Discovery Institute would be thrilled about that one.
(source: Guardian)

I'm going to try to find that BBC article when I get a chance, but right now I have to run off to class.

Dance Dance DNA Revolution

Dance Dance DNA Revolution
Originally uploaded by mathowie.

A tip of the hat to Matt Haughey, for bringing this section of the Scripps Aquarium to our attention:

At the scripps aquarium near San Diego, they devote half the space to teaching kids about science. In a wing devoted to explaining gene expression they had some stuff about DNA and the coolest thing was this video game that taught you about building blocks of life, then proceeded to a real DDR game where you have to step to the DNA parts being shown on screen.

The best part was when one of the 20 amino acids were built, it would say the name. So you'd see A T T G C and so on... and then it would shout "Cysteine!"

This desperately needs to be being sold by someone somewhere. Whether it's the aquarium or Sony themselves, this seems like a great way to remind everyone how fun science is.

Because science is INCREDIBLY fun. Otherwise, all us scientists would run off and become supermodels or rock stars or something.

(via BoingBoing)

Sunday, January 29, 2006


Originally uploaded by Mal Cubed.

I've been around not at all the last couple days, so here you go some Deep Cerebellar Nuclei stained with Fluoral Ruby.

Friday, January 27, 2006

Suddenly, this can no longer be a family blog.

Parents, if your children are reading this along side you, cover their eyes.

Alright. Is it secret? Is it safe?

Here we go. Thanks to New Scientist:

Stuart Brody, a psychologist at the University of Paisley, UK, compared the impact of different sexual activities on blood pressure when a person later experiences acute stress. For a fortnight, 24 women and 22 men kept diaries of how often they engaged in penile-vaginal intercourse (PVI), masturbation or partnered sexual activity excluding intercourse. After, the volunteers underwent a stress test involving public speaking and mental arithmetic out loud.

Volunteers who'd had PVI but none of the other kinds of sex were least stressed, and their blood pressure returned to normal faster than those who'd only masturbated or had non-coital sex. Those who abstained had the highest blood-pressure response to stress (Biological Psychology, vol 71, p 214).

I really really really wish I had something to add to this. But you know? I think it really speaks for itself. Now go act on your knowledge.

Money talks... Infectious Pandemics Walk?

Thanks to Aetiology for pointing out this article (Nature sub. required) about developing a mathematical model for the spread of disease based on the circulation of money. Using Where's George. From MSNBC:

Money, like diseases, is carried by people around the world, so what better way to plot the spread of a potential influenza pandemic than to track the circulation of dollar bills, researchers reasoned.

Is there life after death? Would you know?

It's difficult to explain why I think Cognitive Daily post is so interesting without giving it away. And since I found the opening delightfully creepy when I first read it, I would hate to spoil it for anyone. So just go read it.

Thursday, January 26, 2006

I love this stuff a bit too much

Bush administration tries to make up science, gets called on it by actual scientists.

WASHINGTON - An acrobatic mouse is threatening Bush administration efforts to give Western developers an upper hand over endangered species.

The Preble's meadow jumping mouse is in fact a unique creature with "distinct evolutionary lineages that merit separate management consideration," says a
U.S. Geological Survey study presented Wednesday to senior Interior Department officials...

That finding contradicts research touted by Interior Secretary Gale Norton last February when she proposed removing the mouse from the government's endangered species list. Critics say it also undercuts the administration's claim that it uses the best science available in promoting fewer protections for imperiled wildlife.

Tuesday, January 24, 2006

Dedicated to my girlfriend

Science Blog: HIV Prevention Hope: Yogurt Bugs That Make Antiviral Drugs:

“We’ve found that you can engineer these bugs to secrete drugs – in this case, a viricide that disables HIV,” said Bharat Ramratnam, assistant professor of medicine at Brown Medical School and attending physician at Rhode Island Hospital and The Miriam Hospital. “The hope is to use the bacteria as the basis for a microbicide which can prevent sexual transmission of HIV.”

Ramratnam oversaw the bug-to-drug experiments conducted by an international team of scientists who recently published their results in the Journal of Acquired Immune Deficiency Syndromes.

Ramratnam hatched the idea a few years ago after reading about an intriguing discovery: A protein called cynovirin binds to HIV and prevents it from entering cells in the mucous membranes – a feat confirmed in both laboratory and animal studies. Ramratnam was already familiar with lactic acid bacteria, or LAB. They help make fermented foods such as yogurt and cheese by turning carbohydrates into lactic acid. LAB are also known for their “promiscuity,” or the ability to accept foreign DNA, then produce proteins called for in these new genetic recipes.

And now, since I've lost my ability to type, I'm going to bed.

So I Lied (Catching up on my random linkblogging)

I need to clear out some tabs. So fast and furious, here we go:

HealthDay News via Yahoo: Antibiotic Resistance Widespread in Nature:

"The density of resistance is surprising," said Gerard D. Wright, chairman of biochemistry and biomedical sciences at the university's Michael G. DeGroote School of Medicine. "Old compounds, new compounds, it doesn't seem to matter. They have all sorts of ways to get around these things."

That resistance doesn't come from exposure to antibiotics used in medical treatment, Wright noted. It's just the bacteria's way of surviving in a world full of perils, he explained, since they are surrounded by competing organisms that produce their own natural antibiotics.

Science Blog: Indigenous Amazonians display core understanding of geometry:

"Although there has been a lot of research on spatial maps, navigation and sense of direction, there is very little work on the conceptual representations in geometry," says co-author Stanislas Dehaene of the Collège de France in Paris. "What is meant by 'point,' 'line,' 'parallel,' 'square' versus 'rectangle'? All are highly idealized concepts never met in physical reality. Our work is a first start in the exploration of these concepts."

The work by Dehaene and colleagues suggests that such concepts are largely universal across humans.

Article: Methadone And Morphine in Depression
(Just linked to remind myself to look into this more.)

Science Blog: How the brain makes a whole out of parts:

"Humans do a rough categorization of objects very quickly," Connor said. "For instance, in just a tenth of a second, we can recognize whether something we see is an animal or not. Our results show that this immediate, rough impression probably depends on recognizing just one or more individual parts of what we see. Fine discriminations – such as recognizing individual faces – take longer to happen, and our study suggests that this delay depends upon emerging signals for combinations of shape fragments. In a sense, the brain has to construct an internal representation of an object from disparate pieces."

Substantia Nigra Pyramidal Cells

B8F6 40X Gold
Originally uploaded by Mal Cubed.

Sorry, no posting today but I've been putzing around the house sick as hell. Instead, you get a picture of some pyramidal cells in the Substantia Nigra--pars reticulata, if I recall correctly--taken at 40X after staining with Fluoral Gold.

Peace out.

Monday, January 23, 2006


Valentine's Day cards for the ridiculously wealthy. Wealthy and AWESOME!

Now you and your loved one can create the ultimate piece of art together. What could be more meaningful than creating a beautiful piece of art by combining you and your Valentine’s DNA on a single piece of canvas? Imagine his or her reaction when they receive the ultimate Valentines Day gift.


(via Worldchanging)

Statistics, Schmamistics

So Derek Lowe of In the Pipeline has this piece up on the Medical Progress Today site, about how the pharmaceutical industry is falling in sweet, sweet love... with Bayesian statistics.

It's a very interesting read, but I greatly suffer from my lack of knowledge of intermediate to advanced statistics. He does a good job of getting the general points across, but then I read sections like this:

Here's an illustration: Imagine a drawer full of socks, some white and some black. If you think you have a technique for picking out black socks without looking, you could test that by first closing your eyes and taking out ten socks in a row totally at random. That would give you your null-hypothesis data set. Then you would mix the socks up again, close your eyes, pick ten according to your best black-sock-selecting technique, then open your eyes and see how well you did.

That's a frequentist approach to the problem, run just like a basic clinical trial would be. Each difference you might find between your selected group and the random group would have a different P value (the bigger the difference, the lower the value, naturally).

And then I remember how much educational analogies make me want to bang my head into a wall. So for now, I'll just cry myself to sleep every night in sorrow at my lack of understanding of R-Squared.

They've come for evolution; who's standing?

Chris Mooney posted a link to Paul Nurse's editorial in Cell a few days ago, and there's been something hovering around the edge of my brain ever since, not quite fully expressing.

Today, I figured out what it was.

All in all, it's an interesting piece that I might recommend interesting. It's a discussion of current threats to biomedical research. The first half mostly concerns itself with funding problems: problems with the current boom-and-bust funding trends, suggestions of alternate ways to approach funding, and whatnot. It's very wonkish, so I thought it quite interesting, but there wasn't a lot of novelty there. The second half is also not necessarily new ground to me, but may be to others and is probably more intrinsically interesting. It discusses some of the political threats currently facing biomedical research in the US, and puts forward this passage (quoted by Mooney for the purposes of kudoing) that rather stands out:

Even senior leaders of US biomedical science seem to be rather nervous about taking a stand over the Creationism issue. When the NIH Director, Dr. Elias Zerhouni, was asked by Science magazine whether he was personally concerned about the Intelligent Design movement taking off in schools, he said, “I am very concerned about it. And I don't think it's a good direction.” But in the same interview when asked why NIH had not been very visible in the debate over Intelligent Design, his response was “Why should it? Why do you think NIH should be visible in that debate?” One answer is that if human pathogens are being intelligently designed in response to the evolutionary pressures brought about by prolonged exposure to antibiotics, changes will be required in the current NIH strategies used to combat infectious diseases. Dr. Zerhouni has a difficult job spanning the political and scientific worlds, but it is crucial that great US scientific institutions like the NIH are unequivocal in their defense of science, especially over an issue that is as fundamental to biomedicine as Darwinism. This is a very important matter because the failure of the leadership to robustly support science will eventually be damaging for the whole scientific enterprise in the US.

I certainly agree with both Nurse and Mooney here, and find this a sentiment to be applauded. But there are other groups out there whose vulnerability to political pressure is either on par with the NIH--and others who are less so--that could be stepping forward on this issue.

One that comes to mind is major universities. Most big universities have big biomed research programs--that's where a lot of the basic research gets done--and many of these schools also have lobbying relationships with their state legislatures, or even closer relationships, for the state-sponsored schools. And we do, I admit, see a lot of work coming out of these universities to keep ID out of public schools. But from my admittedly limited perspectives it seems to be more out of the work of individual professors--or even biology programs--than it is on an institution-wide level.

But what struck me like lightning this morning was the realization that there are multimillion and billion dollar biotech companies out there, whose incomes are dependent on biomedical and genomic research, who need to rely on a steady supply of quality biological scientists who know what they're doing. Why aren't we seeing them step to the plate? Why isn't there a biotech lobbyists association working to keep ID out of state legislatures? Are the Celeras and the Medtronics of America making it clear to states interested in bringing biotech facilities to their states that they have no interest in hiring employees who've been trained in creationism? After all, it's in their own best interest.

This is just a random musing. It's possible that this is, in fact, already publically out there and I just haven't been paying close enough attention to notice. But it occurred to me that this was something I hadn't seen, so I thought I'd throw it out there. What do you all think?

Sunday, January 22, 2006

It's so delicious, it should be Metallica

How could I resist linking to Carl Zimmer's latest post at the Loom? He manages to combine several of my favorite things:

A: Rats!
B: Cats!
C: Behavior-influencing parasites!

I didn't even know how much I loved (C), but I absolutely do! A lot!

So check it out, if only for this line:

Obviously, this manipulation would not do the parasite any good as an adaptation, since it's pretty rare for a human to be devoured by a cat. But it could still have an effect.

But really, it's all just a desperate excuse to copy his link to this article, so I can remember to read it later.

Maybe when I grow up...

That's the sort of thing I wouldn't mind being able to put on my CV: "Named Planet."

Saturday, January 21, 2006


So after looking over my previous post again, I've realized that another goal that I hope working on this blog will accomplish is an increase in my ability to form a cogent, structured argument and maybe a bit of help in editing myself.

We'll see how it goes...

Friday, January 20, 2006

Oversimplifications: Language and the Brain

So a couple days ago at Washington Monthly, Kevin Drum linked to this TNR article about the growing disparity between female and male college performance, which slowly morphs into an article about the disparity between boys & girl's reading skills. There's some interesting stuff in it, and some things that need to be said, but this passage sort of irked me:

[Ken] Hilton conducted a series of studies, culminating in the summer of 2004 with a large survey of 21 school districts across New York state. Twelve were blue-collar and middle-class districts just like Rush-Henrietta. Another nine were among the wealthiest school districts in the state. Here is what Hilton found: In the first group, the blue-collar and middle-class schools, girls not only excelled in verbal skills but each year put a little more academic distance between themselves and the boys. Even in math, long thought to be a male stronghold, girls did better. But the real leap for girls was in reading. Another significant find: In these districts, the big hit boys take in reading happens in middle school, as they hit puberty. That's when a modest gap in verbal skills evident in elementary school doubles in size. As for the wealthy schools, more on them later.

Combine Hilton's local research with national neuroscience research, and you arrive at this: The brains of men and women are very different. Last spring, Scientific American summed up the best gender and brain research, including a study demonstrating that women have greater neuron density in the temporal lobe cortex, the region of the brain associated with verbal skills. Now we've reached the heart of the mystery. Girls have genetic advantages that make them better readers, especially early in life...

...Hilton's research on the wealthiest schools is revealing. Girls still do better in verbal skills in those districts. But Hilton discovered an important distinction. When the wealthy boys enter middle school, they don't lose ground. And that holds steady through high school.
(emphasis mine)

Now, there's a bit that I'm uncomforable with here. But I'm going to issue some disclaimers, because there's probably going to be some foot-in-mouth action going on here shortly:
1. I have not read the Scientific American article referred to, nor am I intimately familiar with the research on which it's based.
2. I am also not intimately familiar with a lot of the published material on gender differences in the brain.
3. None of this prevents me from having an opinion, so just take everything I say from here on with a pinch of salt.

First off, let's just make clear that when we're talking about the temporal lobe, we're talking about a lot more than just reading skills here. The Wikipedia entry provides a good starter list of activities implicated in this general area: hearing--especially auditory processing--being primary, and recognition of complex visual stimuli are two of the heavy-hitters. But also of note are the hippocampus--key to memory and navigation--and the amygdala--key to the fear and stress responses, but also to emotions in general--both of which are temporal lobe structures. So if you wanted to make an argument that more dense wiring of the temporal lobe leads to greater reading skills, I'd really have to see an accompanying argument that it also leads to enhanced function in the rest of the activities implicated.

I should point out that the structure he's probably referring to is Wernicke's Area, which is key to language comprehension, and is found (generally but not always) at the junction of the temporal and parietal lobes. But the interesting thing here is that different parts of the brain seem to be responsible for language comprehension and language production, the latter of which seems to occur in Broca's area. I should throw out the caveat here that the distinctions we're going to refer to are incredibly simplified for purposes of explanation.

Now, unfortunately I can't seem to find the notes from the semester in which I covered this (I wouldn't dare to use the phrase "thrown away" without further investigations), but as I recall it, one of the really neat things ("neat" here means "morbidly fascinating to neuroscientists") about this distinction is that damage to each area produces a different variety of aphasia. Wernicke's aphasia is characterized by an ability to form normal sounding sentences with accurate syntax, that are overly verbose and frequently feature word replacement and repetition, leading to sentences that sound right but don't actually make any sense. Again, I can't find my notes so I'll just throw out Wikipedia's example because it's there:

I called my mother on the television and did not understand the door. It was too breakfast, but they came from far to near. My mother is not too old for me to be young.

Also of note is the fact that patients who have recovered from this type of aphasia consistently report a lack of comprehension of sentences that were spoken to them, and a similar lack of comprehension of their own speech.

Broca's aphasia, by contrast, basically results in a labored list of key words. Wiki's example:

"Yes... ah... Monday... er... Dad and Peter H... (his own name), and Dad.... er... hospital... and ah... Wednesday... Wednesday, nine o'clock... and oh... Thursday... ten o'clock, ah doctors... two... an' doctors... and er... teeth... yah."

Patients report a retention of comprehension ability, and recovered patients describe the experience as knowing what they wanted to say, but being unable to do so.

I may have derailed the train a bit at this point, but the point of all this is that the article seems to be trying to discuss not only differences in reading comprehension, but also differences in writing ability as well as other distinctions. Now, comprehension occurs in Wernicke's area, located in the temporal lobe. But Broca's, involved in expression, is located in the frontal lobe.

The argument that someone reading this has already developed in their mind at this point is, "But isn't it possible that Broca's area--or the frontal lobe in general--is also more densely wired in female brains?"

The answer to that is, I'd be willing to put good money down that such is the case.

Human brains are sexually dimorphic. As I understand it (and I could be wrong), the dimorphism is two-fold: the brains of males are larger, and contain a greater number of neurons. The brains of females, although smaller and containing fewer neurons, are much more densely wired. So what does this mean? Is bigger better, or is less more? This is something we're just starting to get a handle on, but the likely answer is that such a binary response is far too simplistic. For instance, keep in mind that there are also relative dimorphisms at work. One structure may be relatively larger in one gender than another, or may be more relatively densely wired, or an activity may even be controlled by a slightly different part of the brain. These things do happen.

So unless I'm totally barking up the wrong tree, saying "women have greater neuron density in the temporal lobe cortex" sounds to me a lot like saying "women have different reproductive machinery than men." If I'm totally wrong here, please let me know so I know when to start feeling like an idiot.

I had a bit more to say about this article here, but I think I'll leave it standing like I wisely utilized a single paragraph as inspiration for a lecture on language and the brain. That said, I leave you with this final quote that made me smile:

But, as Welsh pointed out, even these underperforming boys nearly always landed a spot in some college. That's due to one of the best-kept secrets in college admissions today: the affirmative action campaign to recruit men. Most admissions directors sifting through stacks of applications from men and women can only sigh at the contrast. The average male applicant has far lower grades, writes a sloppy essay, and sports few impressive extracurriculars. Those admissions directors face a choice: Either admit less-qualified men or see the campus gender balance slip below 40 percent male, a point at which female applicants begin to look elsewhere.

Jon to Scientific American: You Lose

So this is a story. It's a dumb story, but most stories are, which is why most of us haven't written best-selling memoirs. Yet.

So a friend posted a reference to an article in the latest issue of Scientific American, and that interested me enough that I thought about maybe subscribing. I've thought about that a bunch, but I am a college student and thus lost in the depths of poverty. Or so I keep telling myself. But I look up the subscription rate anyway, and I discover that it's $24.95. And I think, that's reasonable. And then I decide to look up the rate for a digital subscription, since it should be cheaper since it doesn't require acually mailing actual dead trees to my actual apartment.

And a subscription to SciAm online costs $40. 160% of the price of getting the actual thing mailed to your door. And I understand that it gives you access to stuff you wouldn't have otherwise, but that's a bit ridiculous. Especially since it means that in order to be able to both A: have a copy to read in the john and B: be able to tell your friends online about your important john-reading discoveries, you're paying $65 a year. Which seems a bit steep to my college-student pockets.

Maybe I'm just being overly stingy; but for a monthly magazine that is thoroughly classified in my head as falling into the "pop mag" category, that seems a bit ridiculous. I can get Time in the mail every week for $30, which seems to include full access to archives since 1923.

Access to scientific knowledge is a bit of a hot-button issue to me. One of the problems I see in America right now is that Americans don't seem to trust science, in large part because they don't understand it. Part of this is because science is taught at the grade school level about as poorly as it can be a lot of the time. But part of that is also because areas of science are overly insular to a certain degree. I'm a senior in a Neuroscience program, who's taken around 90 credits of science and math to get this far, including four semester of neuroscience classes and two semesters of directed research. And I still need a dictionary in one hand and a textbook in the other to follow half the journal articles I encounter that don't apply specifically to my area of research. Never mind how much it would cost for me to get access to them if I couldn't do so through my school... So when I see a magazine whose very purpose is to translate science into a format for the masses, it weirds me out to see the easy-access option to be priced somewhat prohibitively; or at the very least, prohibitive to those who might benefit most from it, the people who don't already have a grouded science education but might still be interestted in it...

Hrrm. This wasn't intended to turn into a big rant. I think I've just entered mountain/molehill territory, so I'm just going to leave it at this.

Brief Note & Friday Random Ten

First off, I'd like to let you all know that you should not expect a Thursday post for the duration of this semester. It's my eight straight hours of class day, which really doesn't seem that daunting until you've actually lived through it. Anyways, in the morning I'm going to either in the lab, studying, or asleep; and I get out of class at 9:30, and somehow I don't think I'm going to feel like posting when I get home at ten o'clock anytime soon. ("Should I blog? Or drink? Blog? Drink? Hmmm...")

So we'll do the best we can to make up for that the rest of the week.

Anyways, possibly the best part about having my own blog is now I can do the Friday Random Ten. Yes, it's the little things in life. Here we go:

1. George Sember - Shortnin' Bread
2. Drowning Pool - (Vrenna XXX Tweaker Mix)
3. Orbital - Acid Pants
4. Bob Marley and the Wailers - Mr. Brown (Electric Sky Church Remix)
5. Utah Saints - Beatle
6. Watts - Kundalini
7. Skinny Puppy - Chainsaw (Josh Wink Remix)
8. Euphoria - Delirium (Garry Hughes Dublirium Mix)
9. Front Line Assembly - Outcast
10. Scooter - Awakening

I'm not honestly sure I could place most of these songs out of a lineup... Hrm.

Thursday, January 19, 2006

Uh... What?

Although I'm really not quite a big fan of the argument from authority, there are occasions on which I might read a news article and be forced to conclude that the fact that people are experts on a given topic--and therefore presumably know more about it than I do--is the only reason I have to conclude that they're not deranged.

Today's case in point: the announcement that the NIH has halted a major AIDS study, one titled "Strategies for Management of Anti-Retroviral Therapy." The reason why:

Researchers concluded that those who took their medicine only when their immune systems waned were more than twice as likely to get sicker or die as people who took the drugs every day.

My initial response: uh, duh? But a bit later on in the article is a bit more of an explanation:

Combinations of potent anti-HIV drugs help patients live longer, and slow their progression from HIV infection to full-blown AIDS. But the combinations can cause serious side effects; it's inconvenient to take numerous pills a day, and the drugs are expensive.

While treatment guidelines back continuous therapy, earlier small studies had suggested it might be possible to take medication breaks and still control the virus while reducing side effects and cutting costs. So the NIH funded a bigger study — one of the largest ever done with HIV therapies — to see if those early results were real.

So here's my two cents. HIV is a particularly insidious virus, and one that I personally find morbidly fascinating. Part of the key of the virus' success is that it isn't actually very good at replicating itself (or, to be more precise, at reverse transcribing itself). This makes it a highly mutation-prone virus. Since the drugs prescribed for it are basically very powerful selection mechanisms, the HIV population in a patent's body can quickly become predominately resistant to any one drug. This is the logic underlying the current "drug cocktail" approach, known as Highly Active Anti-Retroviral Therapy, or HAART. Basically, the idea is that a patient can take multiple reverse transcriptase inhibitors (drugs that inhibit HIV's ability to insert itself into the genome by preventing it from reverse transcribing its genetic information--maintained as RNA--into DNA) and a protease inhibitor (a drug which inhibits protease, which IIRC is the enzyme HIV uses to cleave the proteins HIV tricks the cell into producing in order to prepare new virons). By administering them together, one can prevent the virus from becoming resistant to any one of the drugs administered. You see, any one mutation that confers resistance to one drug will probably not be beneficial to the other drugs--even if the mutation confers resistance to a specific reverse transcriptase inhibitors, it will be unlikely to confer resistance to another at the same time. And the odds of simultaneous mutations conferring resistance to a multitude of drugs a the same time or in short order are fairly slim.

However, there's a down side to this. As I'm sure everyone reading this is full aware, the side effects of all these drugs--even the current generation--are notoriously atrocious. AZT, the prototypical antiretroviral, was originally developed for treatment of cancer but was cast aside due to a considerable side effect profile. Its use in HIV treatment was only initially adopted out of sheer desperation--at the time, there was nothing else. Also, these drugs are also notoriously expensive, and most (if not all currently in use) are under patents that will be lasting for the foreseeable future. Since HIV is becoming more and more of an epidemic throughout much of the developing world, this is also problematic. So I do understand the motivations in trying to develop a protocol that reduces a patient's ongoing dependency on these drugs.

But at the same time? Any intro Bio student can tell you that on-and-off use of an antiviral or antibacterial regimen is a recipe for increased drug resistance. And although HAART minimizes occurrence of resistance, I wouldn't think it could eliminate it, especially in such a context. As I said above, I'm forced to assume that these people know more about what they're talking about than I do (and to be honest, they had pilot studies on their side, referenced in the quote above).

But apparently, they not only had an increase in illness and fatalities to deal with, they had another problem on their plate to boot:

Not only did that strategy not control the HIV virus, but there actually was an increase in side effects affecting the heart, kidney and liver in patients taking the drugs only episodically, NIH said.

The side-effect increase was counterintuitive, and researchers so far can't explain it, said Dr. Sandra Lehrman of NIH's AIDS division.

Again, these people hopefully know more on the topic than I do. But I'd guess that the answer to this one could be fairly simple: patients on a continued regiment probably acquire some amount of tolerance to the drugs in the HAART therapy. Of course, this is mostly a shot in the dark since I don't really have any knowledge of what tolerances are built to which effects of any of these drugs.

I will point out, however, that the idea that tolerance is developed to some effects of a drug but not others is not remotely novel. To draw on my own field, tolerance to negative drug effects is such an intrinsic aspect of heroin addiction that I've seen it claimed that first-time users don't even get to really experience the high due to their lack of tolerance to the drug's more harmful effects. I've also seen it claimed that dosages used by addicts are frequently several times the LD50 for drug-naive users. Sorry, I wish I could be more specific on these claims, but it IS two o'clock in the morning.

Anyways: for those who might be inclined to complain that I'm on my fifth post and I still haven't hit anything very neurosciencey, I will point out that a large part of my fascination with HIV was due to long conversations with my girlfriend about the mysteries of HIV-related dementia, a field she intends to go into research in. Which is just one of many reasons why she's incredibly hot. That wasn't TOO morbid a thing to say, was it?

Tuesday, January 17, 2006

Confessions Review & Brief Linkblogging

So I set some time aside to listen to the previously mentioned Philip K Dick piece on BBC radio while cleaning up around the apartment. A good idea, and one I should try to repeat in the future (ha ha ha).

All in all, it's a pretty decent piece. If one is already familiar with both the work of Mr. Dick and the events of 2-3-74, then it's mostly of intellectual interest; if not, then it comes heartily recommended. The use of the PKD android as a framing device makes it worth a listen regardless. It's rare to see a discussion of someone's work presented in such a fashion that elegantly demonstrates a deep understanding of the material.

Also, just in case anyone in publishing ever reads this, I would just like to point out that I for one would be willing to commit homicide most foul in exchange for a multi-volume set collecting the entire Exegesis. I realize that this will most likely never happen, but a guy has to have hopes and dreams.

Some random linkblogging:
As part of their recently revamped web presence, Seed Magazine has put their excellent article Built to Be Fans--a piece on mirror neurons and spectator sports--online. I'm an awed fan of Seed, since it almost seems to be a magazine designed specifically for me. And the article is worth a read.

Just how little can life get away with?
A short discussion of the J. Craig Venter institute's article just published in PNAS, Essential genes of a minimal bacterium. I wish I had time to read the article and give you my own thoughts, but this piece from Nobel Intent will have to suffice (and it does, in spades).

The Science Blog brings us news that researchers at Sandia National Laboratories are hard at work to develop a nano-size battery, intended for eventual use as a power source for an artificial retina. This is an issue that's fairly close to my heart, as one of my best friends has RP. My knowledge of the disease--and its potential treatment options--is small enough that I'm not clear at all if this would be useful for him and his endless quest for robot eyes (not to mention helper monkeys and ponies), but hope springs eternal.

The Science Blog also reports that the Biodesign Instute at Arizona State University has developed GM tobacco strains which can produce plague vaccine. This is something I'm just thrilled about. It's always nice to be reminded that I'm living in the future.

A salvo in my battle with procrastination

I need to start listening to BBC Radio specials. I have collected an impressive backlog of links that I intend to listen to someday, and haven't gotten around to yet. Two of note that I've just bookmarked:

Reith Lectures 2003: The Emerging Mind has series of lectures by noted cognitive scientist Vilayanur S Ramachandran. They should be delicious.
(via PsyBlog)

And yesterday was posted a BBC special titled Confessions of a Crap Artist:

Philip K Dick is now world famous, thanks to films like Blade Runner, Total Recall and Minority Report. But in the last years of his life he encountered something so strange and troubling he couldn't stop writing about it. Writer Ken Hollings asks: was it Phil's fault God talked to him or was it God's?

This holds some special significance to me. First off, Philip K Dick is probably my favorite author of prose fiction. Second, his collision with madness/enlightenment/outright strangeness had a strong influence in sending me towards neuroscience out of the desire to try to understand how the brain works--and to see if there was any room for a model to explain what had happened to him. So I'm hoping that this will be as interesting as it deserves to be.
(via Mind Hacks)

Introductions are in order.

Hello, my name is Jonathan Ehrich, and I'll be your blogger this evening.

I'm 27 years old, and am currently starting my last semester working towards a BS in Neuroscience at the University of Minnesota. If that seems a bit... old... to be finishing off an undergraduate degree, you'd be precisely right. But don't worry, I haven't spent the last decade working studying Neuroscience undergrad; this is actually my second Bachelor's, I also have a BA in Religious Studies from Macalester College.

Don't ask; it's a story that will probably be told someday, as part of some desperate attempt to make an obscure point. Patience is a virture, I'm frequently told.

My main areas of interest (today) are cognitive psychology, drug addiction, and ethnopharmacology. I've taken a couple classes on ethnopharm, studying under Dr. Dennis McKenna. I'm currently taking a class on the Neuroscience of Drug Abuse, and am doing my directed research in Dr. Mark Thomas' lab, where we primarily study plasticity in the Nucleus Accumbens. Don't worry, some day I'll get around to explaining to you exactly what that means. I think cognitive psychology sounds really neat. My long term plans are to go to graduate school for my Ph.D. and go into research.

This blog exists for a variety of reasons:

First and foremost, I love neuroscience. I love brains, I love neurons, I think glia are quite awesome. So this is, in part, an attempt to reserve some time in the day for me to think about neuroscience in an enjoyable context, rather than just the daily grind contexts of "I need to memorize this NOW or I'll look like a total dumbass in that test/discussion/lab meeting." And also, I'd like to spread a little of that love of neuroscience to the masses, if I possibly can.

Secondly, I want some practice writing about neuroscience. I spend a lot of time complaining about the arcane and impenetrable manner in which scientific articles tend to be written. So this is a bit of an attempt to put my money where my mouth is, and try and figure out how to explain the bleeding edge of the discipline to a casual observer.

So what can you expect out of this?
I'm not quite sure. I'm going to aim for posting at least five times a week, hopefully on each weekday. But I have to be honest and acknowledge that I'm a senior in a very hard discipline, and may not have a lot of time on my hands. So we'll see how it goes. A lot of posting will probably end up being regurgitations of some of my course material, just so I can try to digest it or use it as a tool for enlightening. Since I work in a lab studying drug addiction and am taking a course on the Neuroscience of Drug Abuse this semester, I imagine I should be able to keep it interesting for a certain demographic. Also, although most points will be brain-oriented (hopefully), there will be more than a healthy helping of whatever catches my eye, largely discussions of biology-oriented news and whatnot.

I'm also going to try and introduce the audience to the fundamentals of neuroscience over time, and also work a bit through how neuroscience is studied in the real world. Also expect to find the occasional review of a journal article that I may just happen to have to present in class the next week or something.

It sounds a bit dry when I write it all out like this, but trust me: it'll be fun. You'll love it.

A few caveats:
1. Man is mortal, and I'm a man. It seems like most of the science blogs around are either written by professionals, Ph.D.s, or at least people working towards their doctorate. I am none of those things (yet). So if you catch me when I inevitably screw up, please let me know. I may make some desperate attempt to cover it up and save face, but hopefully I'll just politely thank you and fix my errors.

2. Neuroscience is a high-level biological science. As such, it is frequently dependent on animal models of a behavior or trait being studied. Two examples: last semester, one of my courses involved a survival surgery performed on a rat in which we injected fluorescent dyes into its brain. We then sacrificed it a week later, before cutting its brain into sections. One of my main responsibilities in the lab I'm doing my directed research in is to perform experiments involving morphine addiction in rats. Yes, this involves shooting rats up with morphine and doing bizarre things to them. If this is the sort of stuff that disturbs you, I'm sorry but it will be talked about here. I will do the best I can to make sure the viewing of photos and discussions on this topic is optional, so that you can frequent the site without accidentally seeing something that makes you cry like a baby. If I screw up, I apologize in advance.

3. That thing about animal models? Now, obviously animal models wouldn't be useful if we didn't have some reason to believe that animals usefully modelled humans in certain respects. Like, say, there was some sort of evidence of a common descent. You know, perhaps that we had evolved from a common ancestor? Yeah, that. Some professors like to open the first semester of a biology class by stating that "in this class, evolution is considered a fact" or something along those lines. I'm going to one up:

A. Evolution is a fact. End of story.
B. On this blog, evolution shall be considered to be a law of nature when it comes to life forms. Like gravity for things with DNA.
C. We will not be having stupid arguments about creationism here. Just so you know. Intelligent, rational discussion allowed on both sides. But only I'm allowed to treat people like a total jerk, and I think you can guess which side of the debate I'll be entitled to go all jerky on.
D. Anyone who attempts to make fun of me for using the phrase, "go all jerky on" will be summarily crushed like an ant. The same goes for future liberties with the English language.

Any questions?

Monday, January 02, 2006

First post (ooh la la!)

Watch this space. If I'm not a total lazy ass, it is quite possible that something useful will happen here in the future.

Let's find out together, shall we?

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