Friday, August 8, 2008

An open letter to Health and Human Services Secretary Mike Leavitt

Secretary Leavitt,

First and foremost, let me state that you are an economist. You have no medical or scientific expertise; in fact, you only have a bachelor's degree in a completely unrelated field. You are unfit to take the helm of a position that requires you have comprehensive knowledge of American health. I am appalled that Bush appointed you, and I am appalled that you accepted his appointment (although the last Democratic appointee, Donna Shalala, a former chancellor of my university, was about as qualified as you were, and I'm not too happy that the last three HHS secretaries were political scientists).

Secondly, the text of the memo clearly states that you will redefine abortion as "Any of the various procedures -- including the prescription and administration of any drug or the performance of any procedure or any other action -- that results in the termination of the life of a human being in utero between conception and natural birth, whether before or after implantation.". That is unequivocally a statement that tries to redefine contraception as abortion. "No comment" is NOT AN ACCEPTABLE ANSWER, MR. SECRETARY. You have a duty to the nation, and you cannot shirk it. You owe us the truth.

Thirdly, you are clearly not listening to your scientific advisors here; you would do well to solicit the opinion of Dr. Elias Zerhouni, the director of the NIH. Pregnancies are not viable until they implant in the uterine wall amid the endometrium. If a fertilized egg is not implanted, it remains a fertilized egg and does not grow. Two medical dictionaries, a Zogby poll, and a bunch of conservatives' religious beliefs do not change scientific fact, besides the fact that the Zogby poll and a bunch of conservatives' religious beliefs are unscientific and probably come from a bunch of people who don't know squat about human reproduction. We who are in the scientific community and who are in the know about human reproduction think, bluntly, that your pandering to unscientific individuals is about the most disingenuous thing you can do in your position. As I said on your blog, by your logic, I have an abortion every month when I menstruate, and by your logic, every man who masturbates has fifteen million abortions every time he has a wank.

Fourth, you would do well to listen to some of the stories of women who have had to deal with birth control, and consider not only the numerous non-contraceptive reasons why people use contraception, but also the contraceptive reasons, and ESPECIALLY listen to women's reasons for having abortions. There are women who are glad they had them; every child should be wanted. Seeing as you are a man, you have never had to be in this position. Listen to those who have had to be in this position.

You are the Secretary of Health and Human Services, Secretary Leavitt, not a Bush toady. Do your job.

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Thursday, July 31, 2008

Genetic diversity and intelligence

From a paper in Animal Cognition, we find out that mules are smarter than horses and donkeys.

This raises interesting questions about hybrid vigor and, especially, in humans, if multiracial individuals or people with more diverse genetic ancestry have a higher IQ on average than people from a more uniform ethnic background.

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Monday, July 28, 2008

Caffeine (or why Dr. Drew is full of shit)

LOL at a comment from Dr. Drew:

Is there a culture of restriction at treatment facilities? For example, what is the tolerance for lesser vices like caffeine, or sex?
Sex is a no; relationships are what take people out. Caffeine is not actually a stimulant. It removes a nervous system depressant so the brain can feel stimulated. Addicts will always put things in their mouth. They always try to alter [their perception] automatically — that's their orientation. Of course we want that behavior to stop. However, there's no evidence that caffeine alters their course [of recovery]. We used to say the same thing about nicotine. Now there is evidence that we should be focusing on stopping nicotine early.
Caffeine is a stimulant. You can find a better post explaining why this is so at Chris's website. Refer to this article too.

'Stimulant' by definition means at least removing a nervous system depressant; in addition, the effects of caffeine on the body are well-documented.

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Thursday, July 24, 2008

PZ finally does what many of us have been dying to do

Reading this post felt great .

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In which I expound on my frustration

Warning: Rant. If you do not want to read this, page down.

Sometimes I come across things which are supremely stupefying in their simplemindedness and their illogic; the long list of things that are wrong with them is so long and interwoven that I don't even know where to begin describing them. I comprehend the problem, but it is difficult to translate it into words and organize the points sometimes.

Mostly, I am not sure how much to explain some things sometimes. I come from an upper-middle-class family, for example, the progeny of two parents who have masters' degrees, and am planning to get a PhD in neuroscience (as you all know, I am currently in college studying neuroscience), which is actually fairly easy for me, compared with how hard it seems to be, from the reactions I've gotten from many whom I've told about my studies, for many others. Sometimes, when for example I have to communicate with someone who has less than a high school education, I wrack my brain trying to tell them about various intricate concepts in simple terms. Even people in other fields, who may be as educated or more educated than me, make me wrack my brain in telling them things in ways they can understand. I really only have a certain amount of ease communicating with people who study what I study; I don't have to do a whole lot of explaining.

(As an aside, though I have a distaste for Mooney, Nisbet, Olson and their ilk, the sentiment that we could do a little better in communicating science to people is true, though I disagree with them on how.)

As for social criticism, I have some of the same problems - I cannot muster the words, no matter how much grandiloquence I can wedge into my posts, to express how utterly disastrous the world is right now. I make no move to hide my misanthropy. I mean, yes, it is informed, to some extent, by a past that I mostly vigorously shove to the back of my mind where I am seldom reminded of it, though it is also informed by what I read in the news and my understanding from my point of view. Sometimes the explanations I muster are long enough that I do not have the patience to say everything I want to say, that the other person probably doesn't have the time to listen to me, and sometimes they're also filled enough with harsh and well-deserved criticism, which is usually fairly angry even if somewhat eloquent, that emotionally it makes me feel like retreating into a room for a while and either beating the shit out of an inanimate object or crying. Anger is tiring. I make no move to hide the fact that I have much of it, and it tires me daily.

Sometimes my blog posts sound a little clipped; honestly, I don't get enough feedback in my comments to know what the apparent several hundred people who've read this blog think of what I write. Those are usually because sometimes, on some topics, it's hard to know where to start - some are so wonderfully or nastily complex that no one angle seems quite adequate to explore what I'm writing about.

I tried to make this post somewhat organized, and I think I didn't organize it much; I was already reluctant to post this anyway, because of what a reader might think, and because I've been shit on enough for just bringing up some of my own problems - I mean, seriously, there's a shortage of people who seem to really care when their friend has problems instead of pushing them away for temporarily being a sad sack, even though everyone has problems at some point (man, if this loses me any friends at Wisconsin - I know some of you read this blog from time to time - I'm not gonna be happy), but I got tired of being quiet about this.

I'm tired, I'm tired, I'm tired.

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Wednesday, July 23, 2008

Monday, July 21, 2008

Rotating objects

Via Cognitive Daily, older people are worse at some visuospatial tests than younger people.

Mélanie Joanisse, Sylvain Gagnon, Joshua Kreller, Marie-Claude Charbonneau (2008). Age-related differences in viewer-rotation tasks: Is mental manipulation the key factor? Journal of Gerontology: Psychological Sciences, 63B (3), 193-200

This is very interesting - not only for the whole neuroscientific aspect, but because I have also tested as having much higher visuospatial abilities than other people my age. The study looked at three different methods of presenting an object to a viewer - updating, ignoring, and imagining. See the Cognitive Daily post for the study methods.

What is cool about this is the fact that some aspects of mentally rotating objects decline in older people but not other methods, which makes me wonder whether these aspects are controlled by different areas of the brain - different parts of the visual cortex or the intraparietal cortices? Do older people lose particular synapses? Does this vary by original visuospatial ability?

Put an fMRI in there - I want to see the activity of the parietal lobe in this study.

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Exercise slows down Alzheimer's syndrome

An article in the journal Neurology says that exercise may prevent your brain from shrinking if you have Alzheimer's.


Well, exercise has some neuroprotective effects. It increases the flow of blood to the brain and promotes growth factors and neurochemical protectivity. It's not going to hurt your brain.

There is no idea what causes this, but there was four times less brain shrinkage in Alzheimer patients with moderate physical activity than in Alzheimer patients with slight physical activity.

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Sunday, July 20, 2008

Meta stuff .

It may take a few days for me to put up another post. Things are hard right now.

Emotional support is welcomed.

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Saturday, July 19, 2008


Congratulations to Karl and Ariela, who are now no longer Mogel and Haro but Haros von Mogel.

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Thursday, July 17, 2008

The frustrations of trying to find research - a window into undergraduate life

Most science blogs out there are from graduate students or faculty members. I'm still in college, and I'm looking pretty feverishly for research.

Part of the problem is personal issues; I've got a few pretty difficult ones to deal with, and I'll hopefully deal with them by the beginning of the semester. I'm not going to tell readers what the issues are, but they suck.

I'll admit my grades are not what they should be, either, because of these personal issues. One of the things that has been helping me keep my head up is Brian Switek's series of posts at Laelaps, telling the reader about his own struggles, which are different than mine, but reading the advice there keeps me from crumbling.

My first attempt at finding research was back in 2007, when I emailed a neurogeneticist at my university who was doing work on Drosophila. There was a lot of back-and-forth with emails until he said 'I can't train you' and I just went batshit until his graduate student said 'Hey, I'm looking for someone to help me' and I volunteered and he said 'I can't train you'.

Fall of 2007 was spent grumbling about the missed research and doing my classes. Spring of 2007 was when I started trying to pick up more research, but after contacting at least six or seven different people, there was nothing to do.

This semester will be spent trying to pick my grades up, and after that I'll probably try a few other places and reapply, since my grades will be higher. My advisor, another professor in my department, and a few others are good sources of information.

But I spend most of my precious little free time on campus reading blogs from fellow science people, reading new information, and sucking up every bit of knowledge I can find. I have a passion for what I study - neuroscience is my life. I've gotten encouragement from my fellow students; one who works at the VA hospital that's near the university hospital has given me some useful advice on trying to find a lab.

I'll get my degrees. I have to.

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Sunday, July 13, 2008

PZ gets death threats

Lest you think tolerance of stupidity and fanaticism is a good thing, read this blog post and some of the comments beneath it (luckily most of the comments are sensible).

I mean, srsly, death threats? The fuck?

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Saturday, July 12, 2008

This is madness

Via Mike the Mad Biologist, from Driftglass .

If you replay the video, and listen under Stephanopoulos' interruption, this is point Koppel was trying to get across:
"And I think there is just a small but significant fraction of Americans for whom...the truth in this instance is never going to matter."

Which sounds like a small thing, but for me it was almost a cultural event, because it is almost the only time in my memory when a Big Time Newscritter sat in front of a camera and called bullshit on some specific, identifiable group other than "bureaucratsinwashington" or "liberalelites".

Because in Stephanopoulos' world (as in fairy tales of old) knowing and using the True Name of things comes with the possibility of dire fucking consequences, and so one must never, ever, ever, ever, ever call the 27%-ers out by their True Name lest All Conservative Hell break loose.

And so, in Stephanopoulos' world the 27%-ers are people who have merely been somehow bamboozled by the medium through which the message passes.

They are innocent naifs, bedazzled by Teh Sparkly Internets.

The inhabitants of Stephanopoulos' world will never come within a million miles of even forming their mouths to say the words "Jesse Helms was a despicable, racist motherfucker who stayed in power for as long as he did because his supporters and admirers were and are despicable, racist motherfuckers, one and all."

Instead, the inhabitants of Stephanopoulos' world believe that on the occasion of the death of this evil man we should toddle down to the Piggly Wiggly and buy some brand of Kiwi shoe polish powerful enough, to buff this turd of a human being to a shine high enough, so that he can be buried under a gooey, compromise word like "Controversial" or "Provocative".

But Koppel -- admittedly in the weakest, most tepid way possible -- was trying to at least hint at the terrible truth that dare not be spoken, because its implications are so enormous.

The truth that, fundamentally, it's not that our courts that are broken. Not our roads and bridges. Not our schools.

Not something from which science or engineering or manufacturing will rescue us. Not something we can figure out, prototype and then make a fortune selling a million units for a buck apiece.

Because it is we ourselves that are broken.

When I look at Dubya's poll numbers staying absolutely dead-level week after week after week regardless of what he has fucked up this week, or how badly, I learn nothing new about George W. Bush. But A-B-Cs behind just about everything else I need to know about America stand painfully revealed. Those numbers confirm for me for the unmpteenth time that inside the mushy skulls of the 27%-ers there is nothing but a hatbox of junk machine parts, still twitching and clattering mindlessly along on corrupted software that was already obsolete before men walked on the Moon.

The 27%-ers are slugs madly fighting for the right to jump into the salt bucket and drag us all down with them, and any solution to the problems that vex us must begin with their grotesquely mutant versions of patriotism, economics, virtue and civilization being discredited, sequestered and driven into oblivion.

Our first, great, national problem is that our fellow citizens -- in their millions -- are damaged beyond repair.

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Friday, July 11, 2008

Wednesday, July 9, 2008

A short introduction to the neuron

Doing my part to contribute to basic science blog posts on the Web.

This blog is, as stated, mostly a neuroscience blog. In this post, I'll be teaching those of you who don't know, perhaps, a friggin' thing I'm talking about about the basic component of the nervous system.

The neuron is the basic building block of the nervous system. There are several different shapes of neurons, which I'll describe later, but here's a basic neuron:

(Carlson, Niel. A. (1992). Foundations of Physiological Psychology. Needham Heights, Massachusetts: Simon & Schuster. pp. 36)

There are some parts of the neuron that aren't labeled here, including the nodes of Ranvier, but this is a basic neuron. A basic description of the parts -

Dendrites - These receive synaptic signals and contain receptors on them for neurotransmitters.
Soma - The cell body contains the nucleus and all that other cellular shit.
Axon - The tunnel which electric and chemical signals travel down.
Myelin sheath - The insulating cover for the axon. Gets eaten in people with MS.
Nodes of Ranvier - The axon between the myelin sheaths. Electrical signals travel in saltatory ('jumping') motion between the nodes.
Terminal button - These send synaptic signals.

The most important part of a neuron is its cell membrane. This is what receives electrical and chemical signals. Here is a diagram of a neuron membrane:


There are ion pumps in the cell walls. There are three ions which are important to the neuron: sodium, potassium, and calcium. These make your electrical impulses work. Gradients of charge across a cell produce potentials, which are differences in the voltage across a cell membrane and which drive electrical charges, known as action potentials, which do the work of your nervous system. Here is an action potential:


Action potentials always begin with a stimulus and depolarization - once the voltage across the membrane approaches a threshold (in this case a small negative voltage), the action potential is triggered. Action potentials are an all-or-nothing action, kind of like an orgasm, where the voltage becomes positive then drops down again and undershoots a tad.

There's an equation which relates the charge in a cell given the concentrations of ions, which is called the Nernst equation (which relates to a lot of other cells, but is used in neurons) and something one of my professors called the Extremely Important Equation.

The Nernst equation:

E = \frac{R T}{z F} \log\frac{[\mbox{ion outside cell}]}{[\mbox{ion inside cell}]}
where E = equilibrium potential, RT/F = 59.1 mV, z = the number of electrons transferred, and the words in brackets should be self-explanatory.
The Extremely Important Equation, which I think is called the Goldman equation:

E_{m} = \frac{P_{K^+}} {P_{tot}} E_{K^+} + \frac{P_{Na^+}} {P_{tot}} E_{Na^+} + \frac{P_{Cl^-}} {P_{tot}} E_{Cl^-}
where Em = equilibrium potential of the membrane, E(ion) = equilibrium potential of an ion, P(ion) = the permeability of the ion in arbitrary units, usually siemens for conductance, and Ptot = the total permeability of all permeant ions.

And here's some basic physics equations:

Here's some different types of neurons, categorized by function:

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Ah, fascism.

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Mercury militia wackjobs

Discussion at Respectful Insolence.

Jump in the fray, it's fun to make fun of idiotic parents who don't know the first thing about autism and are likely making their offspring and other people's offspring susceptible to other diseases.

I wonder if they've heard of genetics.

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Tuesday, July 8, 2008

Time for a bit of shaming

This morning, I stumbled across this heinous post, in which some asshole decided to use my blog's content in an attempt to justify his racism:

This is the content he used from my blog, which comes from this post:

"NOT SO. I can name a couple of genes and not much more that influence intelligence:

Human neuropsin
and a small amount of genes on chromosome 4"

And this is what the asshat wrote in the rest of his article:<


"Some comments on Jim Manzi’s article at above link. This is well written and thought out. However, we can measure IQ racial differences at the top of the column easily. Very few blacks produce great math. One exception is David Blackwell and there are others.

"To tell if two bodies of water are the same height you look at the top. Same with trees, people, etc. You don’t have to know the chemistry of the insides of the lakes, trees, or people to tell that one is higher than the other. Its the same with intelligence. We look at the top of the races and see a huge difference. That is the measurement. We can look at the societies and civilizations and see a large part of the distribution.

"If blacks can’t figure out not to eat lead, that is an indication of intelligence. Whites did figure that one out. Claiming its lead or whatever in the environment doesn’t explain why one group can figure out lead is a problem and avoid it. If lead was the problem, then liberals say its whites fault for not keeping blacks from ingesting lead."

Someone doesn't understand much about intelligence, does he. Nor does he understand shit about logical fallacies.

Let the shaming commence!

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Monday, July 7, 2008

It really drives you insa-a-a-a-ane

Hernandez-Gonzalez M, Guevara MA, Agmo A (2008). Motivational influences on the degree and direction of sexual attraction. Ann. N.Y. Acad. Sci. 1129: 61–87

Motivation can be defined as a class of central nervous processes determining the likelihood of display of a behavior and the intensity of the behavior if displayed. All behavior is, according to this definition, caused and controlled by motivation. Although the concept of motivation eventually could be replaced by an entirely mechanistic explanation of the causes of behavior, in terms of neural events, such explanations would be overly complex for everyday use. This is particularly the case with regard to the momentaneous fluctuations in the intensity of a behavior, like those occurring during copulation in rats. Thus, the concept of motivation will remain useful even when mechanistic explanations become available. Even though the propensity to perform sexual responses is determined by sexual motivation, another element is required for the execution of such responses. This other element is an appropriate stimulus, a sexual incentive. For a male rat, an appropriate incentive could be a sexually receptive female. For a human, it could be a mental representation of a sexual partner. The incentive activates approach behaviors, and the intensity of these behaviors will be determined by motivation and by the quality of the incentive stimulus, its attractivity. Much work has been done with the purpose of identifying the nature of the incentive stimulus or stimuli emitted by rats and other mammals. While visual stimuli seem to be of limited importance, auditory and particularly olfactory stimuli have been found to have incentive properties. Soluble chemicals may be important for some aspects of copulation, but copulatory motor patterns are basically under the control of tactile stimuli. The processing of sexual incentives in the rat brain has been studied with electroencephalographic techniques, and data show that the prefrontal cortex (PFC) participates in the identification of sexual incentives. Furthermore, there are important differences between the medial and orbital frontal cortices. The medial PFC, as well as the ventral tegmental area, also seem to participate in the generation of pelvic thrusting.

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How antidepressants work

What you thought about depression is about to be up-ended.

Recent studies from Yale and Princeton and a university in Italy suggest that depression is a mild neurodegenerative disease. Instead of simply disturbing your brain's neurochemistry, depression destroys neurons. (This is bad for the 10% of people in the United States who are depressed.)

Antidepressants work depending on each individual's neurochemistry, but they supposedly perform another function: they prevent neurons from dying. My question is - how do the neurons die? What biochemical trigger makes them die? If we dissected the brains of a happy rat and a depressed rat, what would we find? Loss of neurons has been already found in the hippocampus - so maybe SSRIs help protect the hippocampus.

The gamut of drugs for already-identified neurodegenerative diseases is acetylcholinesterase inhibitors, NMDA receptor inhibitors, L-dopa (dopamine), dopa decarboxylase inhibitors, dopamine agonists, MAO-B inhibitors, MAOIs, and other drugs. MAO inhibitors are a class of antidepressant reserved for those cases that cannot be treated with other antidepressants, and antidepressants and antipsychotics are used to decrease symptoms of depression and psychosis in people with neurodegenerative diseases.

Depression is a disorder which contains some wacky brain chemistry, which would no doubt kill a few neurons. The neurotransmitters affected in depression are serotonin, dopamine, norepinephrine (the catecholamines), and possibly GABA and glutamate. A lot of brains also secrete excess amounts of MAO-As, where the MAOIs come into play.

As we further understand the processes of neuronal death in depression, treatment will advance. Some treatments for more advanced neurodegenerative disease might, in small doses, cure depression.

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Friday, July 4, 2008

Japanese neuroanatomical drawings

Via Neurophilosophy, the Kaibo Zonshinzu, a set of medical illustrations from the 1800s.

An exposure of the meninges and their vasculature.

The cerebral cortex.

The cortex opened exposing the corpus callosum and the cranium.

The cerebellum opened and the ventral view of the cranium, showing cranial vasculature and how the brain is oriented in the cranium .

The ventral view of the brain, showing the brainstem, olfactory bulbs, pons, pineal gland, and medulla.

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Thursday, July 3, 2008

Reader censuses

Comment open season:

I have temporarily enabled anonymous posting so I can get a better idea of who's reading and what posts they've liked and what they haven't liked so far. Please, feel free to include or not include this information in your post:

- A little bit about yourself - where you're from, a broad idea of what you do
- Critique of the blog

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Death and the brain

Today I'm going to post about death.

This post is dedicated to my canine buddy whom I knew for thirteen years, Hot Shot (don't laugh; I got the dog when I was seven, and I called him that for thirteen years - I'm 20, and I got him when he was a mere sixteen weeks old - he died at the ripe old age of thirteen, which, if you use the 7 years to one human year rule, is equivalent to a 91-year-old human. He was an elderly ), who I euthanized two days ago after finding he suffered from a tumor on his enlarged heart, a tumor on his testicles, chronic kidney failure , and a stroke. He was beginning to convulse as I held his furry little body while the veterinarian sedated him, and the only indication that he'd died was his stopped heart, his lack of breathing, and some spasms. He died peacefully, and I'm glad he has no more agony, even if he is no longer alive. I feel like shit, as you can guess, and even though I look mildly stoic on the outside, I am grieving for my old very small friend who is, at least, going to do his part for nature after he has croaked by feeding organisms. Eat up, bacteria.

When the brain dies, all electrical activity ceases. Simple.

The problem is, how do you determine the brain has died? The American Academy of Neurologists has a set of criteria for determining brain death.

Brain death is defined by the American Academy of Neurologists as 'the irreversible loss of function of the brain, including the brainstem'. The brainstem is an important part of the definition because it controls your basic bodily functions - breathing and heartbeat.

The criteria are listed thus:

- Directly quoted from the list of criteria, clinical or neuroimaging evidence of an acute CNS catastrophe (which is our term for a critical occurrence in the brain or spinal cord) that is compatible with the clinical diagnosis of brain death
- Exclusion of complicating medical conditions that may lead to a different assessment - rule out various disturbances in the body's chemical milieu
- No poisoning
- Core temperature higher than 90 degrees F (32 degrees C)
- Three cardinal findings: coma/unresponsiveness, absence of brainstem reflexes, and apnea
- Eyes: Unresponsive to bright light, normal to dilated, no oculocephalic reflex if there is no apparent fracture or instability of the cervical spine, no deviation of the eyes in response to ear irrigation
- Facial sensation and motor responses: No corneal reflex, no jaw reflex, no grimacing in response to pressure on sensitive parts of the body
- Pharyngeal reflexes: no response to stimulation with tongue depressor, no cough response to bronchial suctioning
- PCO2 pressure higher than 60 mm Hg

Visual observations that can still be seen in brain death include spontaneous movements of limbs other than pathologic flexion or extension response, respiratory-like movements, sweating, blushing, tachycardia, normal blood pressure without pharmacologic support or sudden increases in blood pressure, absence of diabetes insipidus, deep tendon reflexes, superficial abdominal reflexes, triple flexion response, and the Babinski reflex (quoted almost directly from the criteria).

Tests that can be performed to diagnose brain death include conventional angiography, EEG, transcranial Doppler ultrasonography (except in ten percent of patients, who may not have temporal insonation windows, which are structures in the temporal bone of the cranium allowing sound waves to provide a picture of your brain), small systolic peaks in early systole without diastolic flow or reverberating flow, technetium-99m hexamethylpropyleneamineoxime brain scan, and somatosensory evoked potentials.

These criteria are vital in determining when a patient has died so the family may take them off life support, harvest their organs for donation, and a physician may declare them legally dead. There have been people declared legally dead who are still alive. There is a bunch of hemming and hawing about when death occurs, mostly split along religious/ideological lines (as an atheist, I think when their brain goes, they're effectively dead). Even among physicians, there are variations. - according to 'Greer et al. (2008) Variability of brain death determination guidelines in leading US neurologic institutions. Neurology; 70: 284-289', there is significant variability in 'requirements for performance of the evaluation, prerequisites prior to testing, specifics of the brainstem examination and apnea testing, and what types of ancillary tests could be performed, including what pitfalls or limitations might exist'. Does brain death stop, for that matter, when consciousness stops? Consciousness comes from our frontal lobe; we would have to find a way to judge when those neurons fall silent. (But that gets into a big argument about what consciousness is, and philosophy of mind is, as you know, one of the things I love to hate, as a person in neuroscience who is highly positivist, highly materialist, and absolutely hates dualists. Why the hell are they still debating whether the mind is part of the brain when we've already established it and are doing more research? Let us people in neuroscience do research on the brain; you go sit over there with your Kant, especially you bloody dualist bastards, who can keep your Descartes, the worthless frog)

If the diagnosis of brain death is this shaky, a few limitations might exist in determining it: misinterpretation of tests, unreliable test results, complicating comorbid symptoms, unknown factors in the neurological milieu (likely neurochemical processes), and other bits of human imperception.

I expect, as we grow in our knowledge of the healthy living brain, that we can use it to determine when that brain stops being living.

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Friday, June 27, 2008

A rendition of 'Boom De Yada'

In honor of the Discovery Channel's awesome new commercial, I bring you my folksy song dedicated to my field. Because we neuroscience people have a sense of humor.

I love my neurons
And all their dend-r-ites
I love my foramen
I love my astrocytes
I love my whole brain
It's such an awesome organ
Boom de yada
Boom de yada
Boom de yada
Boom de yada

I love my dopamine
I love adrenaline
I love my GABA
And seroton-in
I love my whole brain
It helps me think and shit
Boom de yada
Boom de yada
Boom de yada
Boom de yada

I love my spinal cord
I love my frontal lobe
I love my thalamus
And my temporal lobe
I love the human brain
It is my favorite thing
Boom de yada
Boom de yada
Boom de yada
Boom da yada

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Monday, June 23, 2008


Today's post is about nicotine.

Before I launch into a rather calm treatment of the neuropharmacology of this, let me say that smoking is bad and your nervous system is not to be messed with, because it can have irreversible issues.

Nicotine is a stimulant of nicotinic acetylcholine receptors, specifically two kinds of receptor: the ganglion type nicotinic receptor and the CNS type nicotinic receptor. Nicotine interferes with the reception of acetylcholine by nicotinic acetylcholine receptors and can be blocked by curare and hexamethonium. Since it blocks acetylcholine, it produces a high. In the ganglion type nicotinic receptor, it stimulates production of adrenaline, and in the CNS type nicotinic receptor, it stimulates production of dopamine. Therefore, it makes you feel awake and good. This is why people often smoke when stressed - nicotine gives them a jump.

The most little-known side effect of nicotine is the fact that it raises the heart rate (duh - it releases adrenaline into the body) and releases the body's stores of fat into the blood. Nicotine by itself can cause strokes.

Therefore, reducing addiction to nicotine would require simply inhibiting nicotine's ability to attach to the receptors, right? Varenicline (Chantix) is a drug that has been tried, but it causes suicidal thoughts in drug users, probably due to the fact that it prevents acetylcholine from bonding to the receptors. Acetylcholine is important for cognitive function and mood, and inhibiting it would cause symptoms similar to depression. The only way to safely stop nicotine is to quit cigarettes cold turkey.

And nicotine is only one of many drugs that make you feel good when you take them, but do some really stupid shit to your body when you take them - so don't use drugs.

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Friday, June 20, 2008

Architeuthis peezeemyers

...has been discovered lurking somewhere in Lake Superior. It is the first species of squid known to reside in the Midwest.

Catch footage of it here, along with one of its three offspring:

Spore may not be strictly an evolution game, but it features it as a theme. Spore is about the biological pressures on a species. Check out the Creature Creator.

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Wednesday, June 18, 2008

Bullshit from the Associated Press

From A Blog Around the Clock and BoingBoing, we get a shining example of stupidity from the Associated Press:

The Associated Press wants people to pay how much for QUOTING their articles? As several people have said already, this violates Fair Use. From the U.S. Government copyright website:

The 1961 Report of the Register of Copyrights on the General Revision of the U.S. Copyright Law cites examples of activities that courts have regarded as fair use: “quotation of excerpts in a review or criticism for purposes of illustration or comment; quotation of short passages in a scholarly or technical work, for illustration or clarification of the author's observations; use in a parody of some of the content of the work parodied; summary of an address or article, with brief quotations, in a news report; reproduction by a library of a portion of a work to replace part of a damaged copy; reproduction by a teacher or student of a small part of a work to illustrate a lesson; reproduction of a work in legislative or judicial proceedings or reports; incidental and fortuitous reproduction, in a newsreel or broadcast, of a work located in the scene of an event being reported.”
One day, if this crap keeps up, we will no longer be able to criticize anything.

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Tuesday, June 17, 2008

Uppity delicate religious idiots on MY campus?

Most frightening things I've read all week.

Via The Friendly Atheist and the NYT courtesy of Chris.

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Gender differences and sexual orientation in the brain

From the Beeb and several other sources comes an article about which I already kind of knew the answer:

Homosexual brains are similar to heterosexual brains of the opposite sex.

The survey was different, though, in that it measured hemisphere volume. Lesbians and heterosexual men had asymmetric hemispheres, while gay men and heterosexual women had symmetric hemispheres.

What this says about people who are bisexual or pansexual or who are transgender or who are intersex, I don't know. Nature, however, is not quite as cut-and-dry as to make a clear-cut dichotomy for sexual orientation and sex, even though individuals on neither end of the dichotomy don't appear often, so this study has some flaws, but that's another post.

Most studies I've seen about this have been mostly about hormones, in which lesbian women have elevated levels of testosterone and gay men have elevated levels of estrogen or where lesbian women have more or less activation in a certain area of their brain or where gay men have more or less activation in a certain area of their brain than heterosexual people of their sex. What we do know is that sexual orientation is biological.

There are also differences in symmetry of synaptic junctions in the amygdala.

What I'd like to see is a study on people who fit neither end of one or both of the continua to see how similar a brain in, say, a bisexual or pansexual person is to heterosexual or homosexual people.

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Sunday, June 15, 2008

On gay marriage

A comic that briefly summarizes my sentiments about the homophobic troglodytes who want to ban it.

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Wednesday, June 11, 2008

Of birthdays and booze

I have to keep up with my friends' birthdays a little bit better.

, my friend and proprietor of The Uncredible Hallq, is now 21. Send him alcohol.

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Saturday, June 7, 2008

A short history of human civilization

Contains some gore and genitals. May not want to maximize this if at work.

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Blogging is one of many steps we need to take to spread atheism

Two more months and a week or so until I make a 16-hour long drive with my stuff, which my folks are looking after right now while I'm visiting them this summer, back to Madison. I'm visiting my folks right now, and it is nothing short of a pain in the ass (mostly because of where they live).

It occurs to me that much of my sentiments about atheism and about the stupidity of religion have been expressed elsewhere. I am not sure that repeating the same true things - which are true; at the same time, repeating them does not contribute much to the conversation or the movement - will make much of an impact in helping us atheists to at least be recognized as a group which deserves as much equality as anyone else and helping people to realize that religious conservatives are killing the world. In the end, it will be about writing letters to Congressmen, staging protests, educating people, and donating money to those who will help us.

Blogging certainly helps, but we cannot keep saying the same things - we have to keep explaining them further and make sure people are aware of where we have said these things, and we have to show by our actions that we are a group that needs to be listened to.

Ultimately, we will make religion meet its demise if we do it in a way that destroys it by bringing people to atheism. Religion was originally designed as a way to fill gaps in the human knowledge of the day before we figured out the scientific method - and it is important to make the point to people that atheism is a characteristic of we educated and we knowledgeable masses and has been for millennia. We are atheist because we know better. I am an atheist because I see no evidence for any deities; any evidence anyone has posited has incontrovertibly and always eventually been shown to be explained by purely scientific processes. Atheism is logical.

Karl Marx was astute when he said:

Religion is, indeed, the self-consciousness and self-esteem of man who has either not yet won through to himself, or has already lost himself again. But man is no abstract being squatting outside the world. Man is the world of man—state, society. This state and this society produce religion, which is an inverted consciousness of the world, because they are an inverted world. Religion is the general theory of this world, its encyclopedic compendium, its logic in popular form, its spiritual point d'honneur, its enthusiasm, its moral sanction, its solemn complement, and its universal basis of consolation and justification. It is the fantastic realization of the human essence since the human essence has not acquired any true reality. The struggle against religion is, therefore, indirectly the struggle against that world whose spiritual aroma is religion. Religious suffering is, at one and the same time, the expression of real suffering and a protest against real suffering. Religion is the sigh of the oppressed creature, the heart of a heartless world, and the soul of soulless conditions. It is the opium of the people. The abolition of religion as the illusory happiness of the people is the demand for their real happiness. To call on them to give up their illusions about their condition is to call on them to give up a condition that requires illusions. The criticism of religion is, therefore, in embryo, the criticism of that vale of tears of which religion is the halo.
Let me explain the quote: Marx makes the inference, quite correctly, that the vast majority of people - the unwashed, idiotic, poor, resourceless, uneducated masses - do not have the ability to understand and/or access the resources we have. What are they to assume, until they learn what a thunderstorm really is, what a thunderstorm is? Do they think it is the physically-manifested anger of, perhaps, an entity swinging a big invisible hammer or an angry sky god, which we know is nonexistent and completely impossible, but which they think is real? The part where he says 'Religion is the general theory of this world, its encyclopedic compendium, its logic in popular form, its spiritual point d'honneur, its enthusiasm, its moral sanction, its solemn complement, and its universal basis of consolation and justification' is an indication of the times which he lived in, a time where, quite frankly, many people were idiotic and/or uneducated.

Establishing rationality, reason, and ultimately atheism in society may be dependent on establishing an environment where every single person on the earth has access to all information and lives under a government where they are free, justly-protected citizens with all the rights and responsibilities inherent therein and has both an adequate support system to support them when they fall and the discipline to pull themselves up and get to wherever they want to be in society.

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Wednesday, June 4, 2008

My friend Mr. Plush Neuron is happy

Because Obama has won the primary and he is way more electable than Hillary. He is very pro-science, mostly (except for his apparent non-opposition to the mercury militia).

This bodes well.

(As an aside, if anyone wants to get me a plush neuron from, I will be quite happy about your gifting of such plush object)

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Monday, June 2, 2008


Via A Blog Around the Clock, the LOLPLoS submissionfest.

Science is awesome. Science humor is nearly as awesome.

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Thursday, May 22, 2008

Neuroscience and epigenetics

Chris has a new site up at If you read his site, redirect your links there.

The quality and frequency of my posting has been rather shitty these days, mostly because I have a lot to deal with.

Anyway, here's a real post.

Epigenetics is the ancillary system of your genes which causes them to be expressed in different locations by different stimuli. For example, it is why you are not a blob of uniform cells, but rather a person made of different types of cells which have the exact same genetic information.

There are a few terms in epigenetics you should be familiar with if you want to know anything about it:

- DNA methylation: DNA methylation is the addition of a methyl group to the carbon-5 position of cytosine residues ('residue', in this context, is a fancy word for an individual nucleic acid) that are followed by a guanine (at least, in 99% of cases of methylation ). A methylated cytosine followed by a guanine is called a CpG dinucleotide. The human genome doesn't have a lot, which is due to the deamination of these methyl-cytosine complexes, which are called 5-methylcytosine. This is important in cancer.

- DNA histone: DNA histone is the stuff that makes DNA curl into chromatin - if you didn't have histones, you would almost certainly not be alive, because without histones, DNA is a 1.8-meter long tangled mess of crap. With histones, DNA condenses into 90-millimeter bits of chromatin that are tightly packed in the nucleus, which is more condensed into 90-micrometer chromosomes during mitosis. Different folding of histones would change the folding of DNA.

- Transcription factors: Transcription factors enable the replication and transcribing of DNA into RNA, which is translated into proteins.

- Prions: Prions are proteins gone nuts. They can infect cells and catalytically convert other native state versions of the same protein to the infectious state.

Why is epigenetics so important in neuroscience? Epigenetic abnormalities cause a number of neurological issues, and has been implicated in a number of seemingly non-developmentally-related conditions such as schizophrenia (which is sort of our favorite illness to speculate about the causes of, as it is very poorly understood and very devastating and very interesting in its symptoms.) It is indeed also a factor in neural stem cell developmental issues, and is also implicated in differences in things such as intelligence.

Much research has been devoted to the role of epigenetics in psychiatric disorders. It's going to become much more important in the next few years; I suspect those of my fellow neuroscience people who investigate the psychiatric will do more gene-based research surrounding these things.

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Wednesday, May 21, 2008

The stupidity of dignity

Via EvolutionBlog, an article on the stupidity of dignity, which is a much-needed topic to discuss.

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Thursday, May 15, 2008


I had been mystified by this subfield until now, and it is profoundly relevant to research of neurological disease, both somatic and psychological:

The brain is extremely immune-protected, since there is a blood-brain barrier made by the glia surrounding our neurons (astrocytes). Very few substances get through the blood-brain barrier, and the molecules that get through produce some interesting effects, but viruses and bacteria which enter the nervous system are acted on by molecules which also affect the nervous system - in a sense, these molecules possess a double duty , particularly cytokines and chemokines.

Psychoneuroimmunology, in particular, is very interesting. It focuses on the 'mind-body connection', which is largely a lot of stuff about placebos and nocebos and how attitude affects your immune system and things of such ilk. What I'd like to see psychoneuroimmunologists address is microbes and mental illness.

As stated before, viruses and bacteria can cause mental illness - schizophrenia might be caused by a virus. I know little of how the blood-brain barrier is formed, but presumably, for example, if a pregnant woman has a virus, it might be easier for it to cross the BBB and wreak all sorts of shit.

I am not sure about how encephalitis and other brain-affecting disorders affect the neuroimmune system, but there seems to be a major role filled by cytokine RNA in detecting it. Cytokines, for those of you who don't know what they are, are proteins that are used in cellular signaling. Activation of them can affect sleep and disposition, and their actions are controlled to an extent by psychological triggers. Presumably, this is probably the biological basis of 'laughter is the best medicine' and other sorts of adages which are the same in meaning.

The entire immunological makeup of a person, however, will affect the brain. Human Genome Sciences, for example, is developing a treatment called belimumab, a human monoclonal antibody, for the treatment of lupus. Lupus has neurological symptoms, among them seizures, psychosis, and abnormalities of the CSF. Given the fact that lupus is triggered by environmental factors, belimumab should be effective in minimizing the development of lymphocytes which act against the body; specifically, it inhibits the b-lymphocyte stimulator. Given the interaction of lupus with the nervous system, one can make a few inferences about how this drug might act: the drug will keep B cells from interacting with the cytokines and chemokines in the nervous system, since it will reduce the B cell count, and reduces the amount of harmful B cells in the cerebrospinal fluid (since the CSF acts as immunological protection).

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Sunday, May 11, 2008

Florida sucks, and the evolutionary significance of amusing gastric phenomena .

Florida should not be a state.

Luckily, however, we have one more piece of evidence to add to the already-quite-massive amount of evidence for evolution: hernias, farts, and hiccups prove we evolved.

Farts: our surprising ally in the quest for a more reasonable America.

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Auditory processing.

Via Pure Pedantry, an article on the double dissociation of 'what' and 'where' in the auditory cortices of cats.

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We are just another species

I haven't driven this point enough: humans are just animals. I hate using the word 'people', because it implies we're elevated above every other species.

Elevating ourselves above another organism may be our way of emotionally reconciling the fact that we have to eat another organism to survive - vegetarians, for example, won't eat meat, because they are causing the death of a living, possibly sentient organism, and it has been ground into us from birth that murder is wrong. I, for example, am not vegetarian, but will not eat animals that have been demonstrated to have intelligence equivalent to a human's at any age - I will not eat ham, beef, or octopus - or that have not lived their full life - I will not eat veal or lamb. (I have no problem eating chicken, turkey, and fish - they're fairly stupid animals, and I am perfectly happy to help eliminate the world's population of stupid.)

We have to consume organisms, though, because we can't eat rocks - we require certain molecules to survive, and these molecules are only found in organisms.

So there is a quandary about whether specific morality that we apply towards humans ought to be morality that we apply towards other organisms. I see the problem that if we acknowledge that species we share the planet with are our equals, we will effectively have less resources to draw from because we will have to allocate enough resources to them to survive - pets and animals in zoos would be tantamount to slaves (I have no problem with getting rid of zoos and replacing them with educational centers on the premises of an animal rehabilitation center, but I have a problem with the whole pet thing on a personal level - my folks have a dog and it's pretty much a member of the family, and they're domesticated so they can't very well survive in the wild unless they're more genetically identical to wild canine animals.), and civilization will go to shit because it would not exist unless we had agriculture, which involves essentially enslaving entire populations of species (except non-conscious organisms who don't have a fully-developed nervous system or who don't have one at all; I don't give a shit about the ones no other organism needs to consume to survive nor do I give much of a shit about embryonic organisms, they're effectively non-living).

Spreading across the galaxy would be little help, since it would just create the opportunity for more humans and more planets full of 6.8 billion idiots, so we need a better solution to conducting ourselves sanely, maintaining human rights, and respecting the other species that we share the universe with.

1) Higher intelligence. I have devoted my life to researching the neurogenetics of intelligence, and together with those who prefer researching mechanical ways of improving intelligence, we can make people more able of accurately processing the information we receive.

2) Better perception. We need better eyes, better noses, better ears, better tongues, better senses of touch, better senses of balance, better senses of temperature, and better senses of what's going on in our bodies.

3) Less people. Make birth control more economical, make elective sterilization free and legal on demand for all ages, make abortion free and legal on demand everywhere that it isn't, and counsel people on how much money it actually takes to raise a well-educated, competent person - and institute a licensure system for people who want to reproduce, because frankly, nobody has the right to raise a neglected, undereducated kid, and put MASSIVE pressures on groups who are idiotic enough to be reticent about making sure people have reproductive freedom. (This has the added advantage of mostly getting rid of the poverty and abuse problem - more resources and better-adjusted people.) Populations are already declining in some countries, but they're declining in the wrong countries among the wrong people.

4) Better education. To paraphrase Bush-o-lini, the nation's children is not learning.

5) More money for research. We need to halve the defense budget and divide the money which the government saves evenly among the Department of Education, the Department of Energy, the Department of Health and Human Services, the Department of the Interior , and the NSF. Science is the backbone of civilization.

6) Better healthcare. There is an entire continent where 99% of its population receives substandard healthcare. This is stupid. (Let's take away asshole Mugabe's fortune for a day and make him live like the poorest people in his country - see how he likes it. Kim Jong Il, the Burmese junta, and the janjaweed blow just as much.)

7) No religion. I think, if you read my blog, you can see why I subscribe to antitheism and why I'm an atheist. We do not need mass superstition or cults.

8) A very inculcated respect for everything we share the world with (the Native Americans got this right). This will be difficult, but this is vital to the success of our species in the long run.

Some of these are obvious; I wish these were more obvious.

Right now, the universe is a bad joke that keeps telling itself; we need to make the universe a more amusing place.

I find it funny how the topic of humans being another species leads, quite simply, to a very general solution for lots of other problems.

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Saturday, May 10, 2008

Beating down the fundamentalist jihad

I have no more tolerance for the creationists - especially the way they behave toward me and my fellow atheists.

I say we start protesting.

They want to wage wars? Let's wage our own war of reason.

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Friday, May 9, 2008

Depression and drugs

Apparently, the gub'mint has released a statement that depression and marijuana are not to be mixed, particularly in people between the ages of 12 and 17. Is it based on sound science, though?

While drug use in anyone under the age of 18 is completely idiotic, the report is poorly cited and makes poor logical conclusions:

Millions of American teens* report experiencing weeks of hopelessness and loss of
interest in normal daily activities, and many of these depressed teens are making
the problem worse by using marijuana and other drugs. Some teens use marijuana
to relieve the symptoms of depression (“self-medicate”), wrongly believing it may
alleviate these depressed feelings. In surveys, teens often report using marijuana
and other drugs not only to relieve symptoms of depression, but also to “feel good,”
or “feel better,” to relieve stress, and help them cope.
However, recent studies show that marijuana and depression are a dangerous
combination. In fact, using marijuana can worsen depression and lead to more
serious mental health disorders, such as schizophrenia, anxiety, and even suicide.
Weekly or more frequent use of marijuana doubles a teen’s risk of depression and
anxiety. Depressed teens are more than twice as likely as their peers to abuse or
become dependent on marijuana.
Alarmingly, the majority of teens who report feeling depressed aren’t getting
professional help. They have not seen or spoken to a medical doctor or other
professional about their feelings. For parents, this means they need to pay closer
attention to their teen’s behavior and mood swings, and recognize that marijuana
and other drugs could be playing a dangerous role in their child’s life.
Nowhere in the paper are the citations even mentioned, and to my knowledge, a lot of people use drugs because they're depressed - biochemically, however, THC binds a cannabinoid receptor - CB1 - neuropharmacologists are currently debating the causality of the correlation of psychotic symptoms and THC (for the record, since neuropharmacology is an entirely different field of neuroscience than the field of neuroscience which I am studying, I can only give my personal experience - I have known a few stoners, and to my knowledge, they are not psychotic). The most common hypothesis is the self-medication hypothesis, which attributes the use of marijuana among depressed individuals to substance abuse by many who are mentally ill and who do not have access to the proper treatment. More disturbing is the list of statements made by the DEA without assessment of information:

Executive Summary
Two million teens report feelings of depression and loss of interest in
daily activities during the past year.
Depressed teens are twice as likely as non-depressed teens to use
marijuana and other illicit drugs.
Depressed teens are more than twice as likely as their peers to abuse
or become dependent on marijuana.
Using marijuana can cause depression and other mental illnesses.
Marijuana use can worsen depression and lead to more serious
mental illnesses such as schizophrenia, anxiety, and even suicide.
Teens who smoke marijuana at least once a month are three times
more likely to have suicidal thoughts than non-users.
The percentage of depressed teens is equal to the percentage
of depressed adults, but depressed teens are more likely than
depressed adults to use marijuana and other drugs.
Teen girls who use marijuana daily are more likely than girls who do
not use marijuana to develop depression.

There the feds go again with their causality. I wonder if NIMH and NINDS have started any sort of stink about this - SAMHSA is independent of the NIH, though, which is highly suspect, and their citations don't say anything about causal implication.

Here's the report - though I do not condone or support marijuana use by anyone who is not legally an adult, I think it is fallacious and idiotic to make unsupported statements about a drug .

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Thursday, May 8, 2008

PZ Myers is coming to Madison

PZ Myers, proprietor of Pharyngula and the most awesome evolutionary biology professor in the United States (tied with Sean Carroll), is coming to Madison in September, provided I can set stuff up properly.

Maybe we can get in touch with his younger son and see if there's anything else we might need to know.

Also - pimping his daughter Skatje's blog, Lacrimae Rerum - it's some good shit. The Myerses may just be my favorite atheist family.

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Wednesday, May 7, 2008

Neuroscience jobs for the pre-doctoral student (graduate and undergraduate)

So, as I have said before, I am an undergraduate at the University of Wisconsin - Madison. I have been trying to find a lab job, even one as small as dishwashing that has the chance to turn into a research project.

It's pretty hard to find one - couple that with the fact that due to financial constraints I have to visit my folks this summer in their hole in Northern Virginia, which makes me more hard up for a lab job due to the fact that it is much easier to get a lab job at my university than it is to get a summer internship for the NIH or a biotech company which most likely demands at least a bachelor's degree or a freaking 4.0 GPA, and I'm trying to get at least two years of research experience before grad school because it is competitive. (Mom, I know you read this because your IP shows up on my sitemeter; try to understand my plight before you bring down the NO-YOU-MUST-VISIT-ME-THIS-SUMMER hammer.)

This is not nearly as difficult as the situation of a friend of mine who has even stricter financial constraints than I do. I honestly feel bad for her and have been trying to help her when I can by searching for resources.

I am fishing for comments on this post; please comment if you have tips or possible job postings or anything that might help a financially strapped student (even scathing but constructive criticism is welcome, I won't fault you if it's genuinely constructive and will usually learn from it!). Or, if you know my email, email me.

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Tuesday, May 6, 2008


The vast majority of people don't know this, but neurology has been known to have its own pandemics to deal with . While the world is on the subject of H5N1, I'll post about some neurological diseases that have developed into epidemics.

-Encephalitis and encephalomyelitis

Encephalitis - this is a nasty disease and is an inflammation of the brain. There are two main encephalitides that have developed into epidemics: Japanese encephalitis and La Crosse (yes, Wisconsin has its very own encephalitis!) encephalitis. The main symptoms of encephalitides are sudden fever, headache, vomiting, stiff neck and back, impaired judgment, drowsiness, weak muscles, a clumsy and unsteady gait, and irritability (from NINDS Fact Sheet on meningitis and encephalitis). Epidemics occur in East and Southeast Asia, where 30,000-50,000 cases occur annually. Case fatality is anywhere from 0.3-60%, depending on the population and age.

Kuru - also known as the zombie disease, due to the fact that it mostly occurred among cannibalistic tribes of Papua New Guinea via eating a dead person's brain. This is a prion disease, and is similar to CJD in that it produces spongiform encephalopathy. Luckily, this disease was wiped out by 1980.

Meningitis - Also a nasty disease and is the inflammation of the meninges, which are the membranes surrounding the brain (arachnoid, dura mater and pia mater; this is one of the two diseases here which every college student is or ought to be vaccinated for. It occurs sometimes in college dormitories, and has many of the same symptoms as encephalitis. Case fatality is low, but it occasionally kills in as little as 48 hours!

Polio - The FDR disease. Most people in the United States are vaccinated against this. Polio, oddly enough, was endemic to Europe for thousands of years until it hopped across the pond, and it preferentially infects motor neurons - which means that when you get it, you may stop breathing and be quite paralyzed. Iron lungs were used quite frequently for this; nowadays, biphasic cuirass ventilation replaces the iron lung in situations where patients cannot breathe (see also Ondine's curse for another interesting and sad condition where people cannot breathe, albeit not autonomically.)

Trypanosomiasis - What we call trypanosomiasis is called by laymen sleeping sickness and Chagas's disease. This disease makes people sleepy and is caused by a small parasite in the saliva of tsetse flies, in the case of sleeping sickness, and mosquitoes, in the case of Chagas's disease. Its symptoms are fever, headaches, and joint pains; in addition, Chagas's disease causes conjunctivitis.

Enjoy wondering how it might be to get one of these little suckers.

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Thursday, May 1, 2008

A rant on funding, again

We need a science White House. At this point, I am almost past caring whether it is Democratic (though I would prefer a Democratic White House) or Republican (OH SWEET REASON NO), I just want them to give more money to the NIH and NSF. The Department of Defense doesn't need all the crap it gets. No military in the world is nearly as technologically advanced as ours.

The reason I say this is because there is good research that is getting tossed by the wayside because it doesn't have enough money or there are laboratories that cannot afford to hire an adequate number of researchers.

For example, John McCain showed his ignorance of all but the most obvious research when he made a snide comment about a bear DNA investigation that was part of investigating ecological dynamics in a key species. McCain is a man who has no understanding of science, although we can't fault him more than a reasonable amount because he's not science-educated.

There are plenty of PhDs who are unemployed because of the shortage of fundings. GrrlScientist is an ornithologist who has been unemployed for the past while, for example, and she delivers an interesting and rather exquisite rant on her own unemployment.

This is research not getting done because of governmental ignorance. How much development would we have had if Bush was not in office? Let's think of research topics that might be done if the government gave us more money:

- topics concerning keystone species which are vital to their environment
- research into rare diseases
- more investigation of the neural bases of intelligence

There is also a lamentable lack of science education. We American-born scientists (in this number are also counted mathematicians, computer scientists, and engineers in addition to biology, chemistry, physics, and medicine) are a small bunch; apparently, we have to import the rest of our colleagues from Asia and Europe because the vast majority of the rest of you can't be arsed to have as motivation for your job anything other than money. I don't give a flying crap how much I earn as long as I'm doing neuroscience; I would live in a space similar to my friend Bill's crusty old attic if I had to (although with sufficient weatherproofing and maybe a space heater).

We would have more American-born scientists if the vast majority of the aforementioned rest of you stopped being greedy and had some discipline and actually knew something about science. (Interestingly, this reminds me of a discussion I had at Atheists, Humanists, and Agnostics at UW-Madison, the atheist group that I am a member in, when we were talking about the theists' so-called 'miracles'. None of the theists who were arguing this point - I say this because the only theist who usually sides with us, my friend Rachel the Spinozan panentheist, is as far as I know majoring in science and wasn't really participating in the conversation, and the theists I personally know who are scientists are comparably sane to my fellow scientist atheists - were majors in science, and Chris, Nick, Travis and I, who are all science majors and all atheists - well, Chris is also a philosophy major - were using probably the most substantive arguments which arise mainly from science to argue that the rather fundamentalist theists were full of shit, and our arguments apparently went over their heads - they apparently went over the heads of the other atheists, too.)

And no, we're not going to resort to framing and marketing it like some sort of product. Is the American public really this stupid?

Seriously, if it gets much worse, I WILL bail on the United States after I get my PhD, as one more scientist who takes their talent to where it will be acknowledged. You can say hello to me in Amsterdam.

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Saturday, April 26, 2008

The problems with phenomenology

Sorry about the lack of posts for a week. I've been under stress.

In philosophy club Saturday, we discussed whether the scientific method was a method which produces most truth.

I argued that it was about the best thing we've got, and we can't understand what it's like to be anything else - for example, to use the classic philosophy of mind example, we can't understand what it is like to be a bat . We cannot echolocate, we do not have very good hearing, and we cannot fly.

Phenomenology examines first-person experiences. I think phenomenology is going to be stuck between what we learn of consciousness in the next decades and the fact that you cannot reproduce an individual's experience because it is so complex at the moment. We have a limited ability to reason logically which is constrained by our perceptions.

So can we in fact know what it's like to be a bat? Well, there are two factors in this:

- the bat's neurological milieus
- the bat's experiences

Generalizing from one bat to all bats is dangerous; there are different species of bats, and each one has different abilities. For example, a hawknose bat does not know what a vampire bat's perception of blood is, and within species, I suspect one bat does not know how exquisitely satisfying another bat's recent meals were.

The research by Tristan Bekinschtein, whose work I have cited before in this blog, deals with consciousness in patients with 'disorders of consciousness' - dementia, PVS and Alzheimer's. His research seems to suggest that there are significant impairments in affective cognition and theory of mind in such individuals (for those of you who don't know what theory of mind is, here is a Wikipedia article that describes it extremely well.)

This does not seem to mesh with how philosophers define consciousness, though, which is to say, they don't limit it to simple awareness of the self and of one's environment.

Subjective experience, by definition, is how we perceive a thing. Now, in my studies of neuroscience, our perception of something first goes through our sensory system. To use a complex example from my own experiences, say you are at a party, you are sober, and you are sitting next to someone who is drinking a beer. Your senses are not impaired, so you perceive the situation as accurately as possible. You smell the alcohol, see the color of the bottle, and see the person who is drinking it. The visual, olfactory, auditory, tactile, possibly gustatory, proprioceptive, nociceptive, and thermoceptive aspects of the situation all trigger certain responses in your sensory system. These varied responses are compared to your previous experiences, whether you have experienced it firsthand or heard about it.

You know, I think this can be best summed up in one angry sentence: Philosophy uninformed by science is sophistry.

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Monday, April 14, 2008

Race and intelligence

I'm gonna get more fire on this one. I'm not going to talk about this from a comparative standpoint but am going to present general information; I am not going to talk about this in controversial terms until I'm a professor and I've got tenure, because I know who probably reads this blog and I need to make it clear, in no uncertain terms, that I am an individual of no significant prejudices. ('No prejudices' would be a misnomer, because everybody's got them.)

Race is undoubtedly a factor in intelligence because members of certain cultural groups tend to mate with people of their own cultural group - interracial offspring are becoming more common, yes, but there is still a strong trend in organisms to stick to their own. An example of selection for intelligence is Steven Pinker's article in The New Republic (admittedly a conservative paper which I usually will not read because of its sheer stupidity, but Steven Pinker writes mostly good stuff, though I still thoroughly disagree with him on his rather sexist defense of Larry Summers) about selection for intelligence in individuals of Ashkenazi Hebrew background ('Jewish' is a misnomer; 'Jewish' describes an adherent of a religion, not a member of an ethnicity.) Pinker writes:

The appearance of an advantage in average intelligence among Ashkenazi Jews is easier to establish than its causes. Jews are remarkably over-represented in benchmarks of brainpower. Though never exceeding 3 percent of the American population, Jews account for 37 percent of the winners of the U.S. National
Medal of Science, 25 percent of the American Nobel Prize winners in literature,
40 percent of the American Nobel Prize winners in science and economics, and so
on. On the world stage, we find that 54 percent of the world chess champions have had one or two Jewish parents.
Does this mean that Jews are a nation of meinsteins? It does not. Their average IQ has been measured at 108 to 115, one-half to one standard deviation above the mean. But statisticians have long known that a moderate difference in the means of two distributions translates into a large difference at the tails. In the simplest case, if we have two groups of the same size, and the average of Group A exceeds the average of Group B by fifteen IQ points (one standard deviation), then among people with an IQ of 115 or higher the As will outnumber the Bs by a ratio of three to one,
but among people with an IQ of 160 or higher the As will outnumber the Bs by a ratio of forty-two to one. Even if Group A was a fraction of the size of Group B to begin with, it would contribute a substantial proportion of the people who had the highest scores.

The CH&H theory can be divided into seven hypotheses. The first is that the Ashkenazi advantage in intelligence is genetic in the first place. Many intellectuals dismiss this possibility out of hand, having been convinced by Stephen Jay Gould's book The Mismeasure of Man that general intelligence does not exist and that there is no evidence for its heritability. But a decade ago, the American Psychological Association commissioned an ideologically and racially diverse panel of scientists to review the evidence. They reported that IQ tests measure a stable property of the
person; that general intelligence reflects a real phenomenon (namely, that measures of different aspects of intelligence intercorrelate); that it predicts a variety of positive life outcomes; and that it is highly heritable among individuals within a group. This does not imply that differences between groups are also genetic, since one group may experience a difference across the board, such as in wealth, discrimination, or social and cultural capital.
The most obvious test of a genetic cause of the Ashkenazi advantage would be a cross-adoption study that measured the adult IQ of children with Ashkenazi biological parents and gentile adoptive parents, and vice versa. No such study exists, so CH&H's evidence is circumstantial. The Ashkenazi advantage has been found in many decades, countries, and levels of wealth, and the IQ literature shows no well-understood environmental factors capable of producing an advantage of that magnitude. It remains possible that the advantage is caused by some poorly understood environmental cause. Environmental hypotheses tend to get a free pass in intellectual life, but they must be scrutinized as well. The possibility that Jewish mothers produce smarter children is unlikely in light of abundant evidence that families have no lasting effect on intelligence. Siblings reared together are no more correlated in IQ than siblings who were separated at birth, and adopted siblings are not correlated at all. Growing up in a given home within a culture seems to leave no
lasting stamp on intelligence.
But parents are just one aspect of the environment, and the cultural milieu is surely more important. Yet it cannot be taken for granted that Jewish culture favors achievement in physics, philosophy, or chess. ...

Also worth remembering is the saying that if wishes were horses, beggars would ride. Mere expectations cannot produce a brilliant mind. So an environmental explanation of the Ashkenazi advantage in intelligence is also unproven, though it certainly cannot be ruled out.

The second hypothesis is that Ashkenazim tended to marry their own during most of their formative history. This is necessary, because natural selection cannot change the genetic composition of a population if new genes are constantly flowing in from the neighbors and diluting its effects. CH&H cite the Jewish traditions of avoiding intermarriage, proselytization, or conquest. They mention historical accounts attesting that intermarriage was indeed rare, and genetic evidence pointing to an admixture of about 0.5 to 1 percent of neighboring genes per generation. Note that over many centuries this is enough to make Ashkenazim genetically similar to their European neighbors, so the notion of a distinct "Jewish race" is indeed nonsense. But the two populations are not identical: the genetic overlap due to interbreeding is around one-third to one-half, depending on which genes you look at.

The third hypothesis is that Ashkenazim were concentrated in mercantile, managerial, and financial occupations at a time when their neighbors were likely to be peasant farmers, craftsmen, or soldiers. Jews presumably had an accidental head start in these occupations because of their religious obligation of literacy, their ability to network with one another across far-flung communities, and their role as a go-between amid Christian and Islamic civilizations. In the Middle Ages they were funneled into middlemen professions by their exclusion from guilds, their inability to own land, and the niche opened up by the Christian prohibition of usury. CH&H cite historians who have documented that a majority of Jews were middlemen during the Middle Ages, many of them moneylenders.
The fourth hypothesis is that in traditional Ashkenazi occupations higher intelligence led to greater economic success. CH&H cite contemporary data that IQ predicts income and occupational success in every profession, and that the minimum IQ requirements for financial and managerial occupations are higher than those for farming, crafts, and the military. Presumably, numeracy, verbal skill, problem solving, and social intelligence are invaluable in calculating slim profits and interest
rates, in assessing creditworthiness, in anticipating trends, and in meeting other cognitive demands of the middleman niche. Cultural historians have noticed that these skills seem to be cultivated among contemporary middleman minorities.
The fifth hypothesis is that richer people had more surviving children during the centuries in which Ashkenazim were middlemen. Today the wealthy tend to have fewer children, but before the demographic transition (which began with the industrial revolution) wealth brought better nutrition and healthier surroundings, and hence more children who survived to adulthood. CH&H cite historians who made this point about the Ashkenazim in particular.
The sixth hypothesis is that the common Ashkenazi diseases are a product of natural selection rather than genetic drift, the other mechanism of evolutionary change. In any finite population, some genes can go extinct and others can take over the population by sheer chance. Imagine an island on which a lightning bolt happened to kill everyone but the redheads; the descendants would found a redheaded race, despite the lack of any advantage to redheadedness. As the example suggests, drift is most potent in small populations. It can leave a genetic stamp on an inbred community that was founded by a small number of pioneers, or that suffered a bottleneck in population size and subsequently rebounded, multiplying copies of whatever genes were possessed by the few lucky survivors.
Most medical geneticists believe that drift is to blame for Ashkenazic genetic diseases. CH&H respond with two lines of evidence, based on the logic that drift affects all genes equally, be they advantageous, neutral, or deleterious. Bottlenecks tend to reduce heterozygosity, or the state of having different versions of a gene from one's mother and father. That is because if only a few ancestors were around at some point in the past, they would have had fewer gene variants to leave to their descendants, increasing the chance that a gene would meet a copy of itself when a couple conceives a child. CH&H adduce evidence that Ashkenazim, unlike other small populations, have degrees of heterozygosity similar to their more numerous European neighbors. They also suggest that Ashkenazim have a distribution of neutral genes similar to that of Europeans in general. A problem in evaluating this hypothesis is that arguments for and against genetic bottlenecks are often sensitive to assumptions built into the models, and we can expect CH&H to be debating their critics for some time.
Perhaps the most interesting biological fact addressed by CH&H is that Ashkenazi
genetic diseases tend to cluster in a small number of metabolic pathways. Genes involved in different stages of a single biochemical assembly line are often scattered throughout the genome. The presence of mutations in a set of these genes is a fingerprint of natural selection, because the only common denominator is their effect on the organism, which is what selection, and selection alone, can "see." Random drift is unlikely to collect genes scattered hither and yon that just happen to take part in the same biochemical process.
It has long been known that Ashkenazi diseases cluster in groups with a common
metabolic pathway. They include disorders of storing sphingolipids ("sphinx-like fats"), such as Tay-Sachs and Gaucher's, and disorders of DNA repair, including the BRCA1 gene, which increases the odds of breast cancer. Using a functional genomic database, CH&H try to calculate the a priori probability that these clusterings could have arisen at random, and dismiss it as infinitesimal.

The seventh and really pivotal hypothesis is that the common Ashkenazi diseases are by-products of genes that were selected because they enhance intelligence. The alternative is that they were selected for something else, such as resistance to infectious disease. CH&H discount disease resistance for most of the genes in question because the genes are not shared by other Europeans, who must have been victims of the same germs.
Harmful genetic by-products can arise in two major ways. In heterozygote advantage, a gene confers an advantage on possessors of one copy (heterozygotes or carriers), which outweighs the disadvantage it encumbers on possessors of two copies (homozygotes). The best-known example is the sickle cell gene, prevalent in malaria-ridden parts of Africa, which leads to malaria resistance in homozygotes but to anemia in heterozygotes. CH&H suggest that a similar trade-off could have produced the Ashkenazi diseases, though the evidence is paltry. They note that increased levels of sphingolipids foster neural growth in developing rodent brains, and that the normal version of the BRCA1 gene inhibits neural growth; but that is a long way from human intelligence.
The other kind of by-product comes from antagonistic pleiotropy: a single copy of a gene has multiple effects, the good ones outweighing the bad ones on average. The
evidence here is a bit better. People with the genes for torsion dystonia,
non-classical congenital adrenal hyperplasia, and Gaucher's disease tend to have higher average IQs, or tend to be concentrated in professions such as physics and engineering. But the numbers are small. So the evidence that Ashkenazi disease genes boost intelligence is extremely iffy. Still, the hypothesis is testable: compare the IQs in a large sample of sibling pairs, one of whom is a carrier of a disease gene, the other a non-carrier. If the carriers are not smarter, the hypothesis is wrong. The study could easily be done in Israel, with its centralized records of health care, education, and military service.

Pinker's hypotheses seem to state that certain genes are going to be selected for in certain populations and some populations are more prone to select for intelligent genes. So there are, certainly, some mild genetic correlations, but I have to issue a warning: this does not mean one race has superior intelligence to another. Even if one race has a higher average IQ, you cannot generalize from a population to an individual. The mean is not the median. People of different races are very spread out among the continuum of IQ.

One of my favorite academics in my field is J. Philippe Rushton, an evolutionary neurogeneticist at the University of Western Ontario. Dr. Rushton nearly lost his job because of his article 'Evolutionary Biology and Heritable Traits (With Reference to Oriental-White-Black Differences)' . Pinker and Rushton make the point that there are clearly differences between people of different ethnic backgrounds, but that there is potential for misuse. Intelligence researchers will have to deal with - and I am absolutely afraid of having to deal with this in the future, but I will need to deal with this - human rights groups such as the NAACP. Their purpose is noble and I am a LOUD supporter of civil rights for folks, but censoring science because they may not want to know information gathered in an ethical, honest way is going too far - and they will most likely misinterpret it, because frankly, not too many people in most human rights groups about anything lately have any science background, and people in general are also morons.

Before we tackle race and intelligence, though, we still have to figure out the neurological basis of it. As I said, I aim to be one of the researchers who does significant work in this area. We have a tiny list of genes, and a comprehensive neurologic model of intelligence is not going to be possible until we have the rest of the genes.

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