June 28, 2008

The utilitarian vampire

As I mentioned earlier, Netflix Instant Viewing (and hence the Roku) is pretty heavy on the cheezy 80s TV shows. Mrs. EG and I have been catching up on Forever Knight, the existential tale of a vampire living in Toronto, trying to become human, and making up for his sins by posing as a Canadian cop named Nick Knight (though not that polite, so you can tell he's not really Canadian). Anyway, in the Forever Knightiverse, it seems you can get along OK by drinking cow's blood, so we're back to the situation I alluded to in an earlier post, vampirism as an immortality treatment with some annoying side effects. Given that, it occurs that Mr. Knight would do a lot more good for people by starting a cow blood production operation and saving the lives of the terminally ill by turning them into vampires. Just saying.

Posted by ekr at 9:56 PM | Comments (0)

June 15, 2008

Stop smelling like food & find out how DEET works

Ditzen, Pellegrino, and Vauxhall had an interesting paper in science a few months ago about the insect repellent DEET and its mechanism of action. Their results seem to indicate that a significant fraction of the effect of DDT isn't so much insect repellence as blocking the attractant effect of 1-octen-3-ol, which is present in human breath. The figure below summarizes the observed behavioral results on drosophila:

At high concentrations of DEET and/or when flies can come in direct contact with the DEET, flies are repelled. I.e., they prefer an empty chamber without DEET to one with DEET. If you reduce the concentration of DEET to 10% and cover it with a perforated polypropylene barrier, the repellent effect is eliminated, and the flies end up equally in both vials. However, if you take the same pair of vials (one without DEET and one with DEET) and put food in both of them, then the flies far far prefer the one without DEET.

This is confirmed by direct studies of the fly (drosophila) and mosquito (anopholoes gambiae) sensory systems which show a significantly reduced response to 1-octen-3-ol in the presence of DEET (The other major attractant is CO2, but DEET doesn't seem to have much effect on that.) This kind of explains why DEET has a relatively short range of action: this NEJM article claims 4 cm, while Ditzen et al. claim 38 cm (I can't read either of the original sources) but in either case, it's pretty short. I wonder if part of the issue is that mosquitos are still attracted to other chemicals you're emitting (e.g., CO2) but they get confused when they can't smell the 1-octen-3-ol, so they get close but don't want to actually land on you. What you really want, though, is something that will convince mosquitos they want to be far away from you, not just that they don't want to be near you.

Posted by ekr at 10:30 PM | Comments (2)

May 31, 2008

Prediction of fMRI activation patterns

Predicting Human Brain Activity Associated with the Meanings of Nouns
Tom M. Mitchell, Svetlana V. Shinkareva, Andrew Carlson, Kai-Min Chang, Vicente L. Malave, Robert A. Mason, Marcel Adam Just

The question of how the human brain represents conceptual knowledge has been debated in many scientific fields. Brain imaging studies have shown that different spatial patterns of neural activation are associated with thinking about different semantic categories of pictures and words (for example, tools, buildings, and animals). We present a computational model that predicts the functional magnetic resonance imaging (fMRI) neural activation associated with words for which fMRI data are not yet available. This model is trained with a combination of data from a trillion-word text corpus and observed fMRI data associated with viewing several dozen concrete nouns. Once trained, the model predicts fMRI activation for thousands of other concrete nouns in the text corpus, with highly significant accuracies over the 60 nouns for which we currently have fMRI data.

This paper is pretty interesting. Basically, they have measured fMRI activation data for 60 words. So, voxel v has activation level A_v_w for word w. For each word, they have measurements of a bunch of linguistic parameters P_1, P_2, P_3..., etc. They then fit a predictive model for the effect of each parameter on the activation level of each voxel, so for instance you could say that if a word is associated with "sight" (i.e., it appears near "sight" in text corpii) that increases the activation of voxel v by .1 units. This is fairly straightforward regression modelling stuff.

Once you have the model fitted, you can then predict the activation of each voxel for a novel word by taking its linguistic parameter values and plugging them into the model. Their results are actually pretty good. They have a corpus of 60 word/fMRI pairs and they use 58 as a training set and 2 as a test set. They then try to differentiate the two test words by asking which predicted activation pattern is closer. The results are significantly better than chance: mean=.77 for what appears to be arbitrary words and mean=.62 when the words are from the same semantic category (e.g., "celery" and "corn"). Moreover, a significant amount of the error appears to come from head motion by the subjects.

I'm not sure how to interpret this from a scientific perspective. It's a long way from knowing which brain cells are used in processing certain words to knowing how the brain actually processes those words. On the other hand, it's not clear you ned that deep an understanding to build a brain-scanning fMRI gizmo that does something useful. Though we're a long way from that too. Even ignoring the fact that we don't understand the brain well enough, hanging out with your head in a noisy magnet probably isn't a lot of fun.

Posted by ekr at 9:14 PM | Comments (0)

May 24, 2008

Baffling

For some reason I checked out Conservapedia today. Sort of an amazing artifact, if basically insane. It's like—well, it actually is—they want to create a whole alternate reality where the normal rules of intellectual discourse don't apply. Here's the (somewhat famous) article on the kangaroo:
According to the origins theory model used by young earth creation scientists, modern kangaroos are the descendants of the two founding members of the modern kangaroo baramin that were taken aboard Noah's Ark prior to the Great Flood. It has not yet been determined by baraminologists whether kangaroos form a holobaramin with the wallaby, tree-kangaroo, wallaroo, pademelon and quokka, or if all these species are in fact apobaraminic or polybaraminic.

After the Flood, these kangaroos bred from the Ark passengers migrated to Australia. There is debate whether this migration happened over land[6] with lower sea levels during the post-flood ice age, or before the supercontinent of Pangea broke apart[7] The idea that God simply generated kangaroos into existence there is considered by most creation researchers to be contra-Biblical.

Other views on kangaroo origins include the belief of some Australian Aborigines that kangaroos were sung into existence by their ancestors during the "Dreamtime" [8] and the evolutionary view that kangaroos and the other marsupials evolved from a common marsupial ancestor which lived hundreds of millions of years ago.[9] In accordance with their worldviews, a majority of biologists regard evolution as the most likely explanation for the origin of species including the kangaroo.

Uh, yeah. Incidentally, that passage contains links to Baraminology, the study of Biblical kinds. I almost expect there to be a page on the Turtles all the way down theory of cosmology. I was going to try to make a serious argument about this, but it's just laughable.

Incidentally, Mrs. G noted the weird juxtaposition of Pangea and flood theory. Unsurprisingly, there's a footnote pointing to this uh, explanation about how Pangea is compatible with flood theory. In case you're curious, it's that the rate of geologic activity was higher during the flood.

Posted by ekr at 9:32 PM | Comments (1)

May 16, 2008

Gastroesophageal reflux and body position

Interesting fact: there's a significant amount of evidence that sleeping on the left hand side as opposed to the right hand side significantly reduce GERD. For instance: Khoury et al. (1999(:
METHODS: Ten patients, three female and seven male (mean age 47.6 yr, range 30-67 yr) with abnormal recumbent esophageal pH <4 on 24-h pH-metry participated. A standardized high fat dinner (6 PM) and a bedtime snack (10 PM) were administered to all patients. GER during spontaneous sleep positions was assessed with a single channel pH probe placed 5 cm above the lower esophageal sphincter (LES) and with a position sensor taped to the sternum. Data were recorded with a portable digital data logger (Microdigitrapper-S, Synectics Medical) and analyzed for recumbent percent time pH <4 and esophageal acid clearance time in each of four sleeping positions. Time elapsed between change in sleeping position and GER episodes was also calculated.

See also Katz et al. (1994), van Herwaarden et al. (2000). The mechanism doesn't appear to be entirely clear, however.

Posted by ekr at 5:29 PM | Comments (1)

February 9, 2008

Diet and metabolic syndrome

Lutsey, Steffen, and Stevens report study of dietary intake and "metabolic syndrom" (MetSyn), described as "a cluster of cardiovascular risk factor abnormalities associated with increased risk of type 2 diabetes mellitus, cardiovascular disease, and all-cause mortality." Here's what they found:
Background--The role of diet in the origin of metabolic syndrome (MetSyn) is not well understood; thus, we sought to evaluate the relationship between incident MetSyn and dietary intake using prospective data from 9514 participants (age, 45 to 64 years) enrolled in the Atherosclerosis Risk in Communities (ARIC) study.

Methods and Results--Dietary intake was assessed at baseline via a 66-item food frequency questionnaire. We used principal-components analysis to derive "Western" and "prudent" dietary patterns from 32 food groups and evaluated 10 food groups used in previous studies of the ARIC cohort. MetSyn was defined by American Heart Association guidelines. Proportional-hazards regression was used. Over 9 years of follow-up, 3782 incident cases of MetSyn were identified. After adjustment for demographic factors, smoking, physical activity, and energy intake, consumption of a Western dietary pattern (Ptrend=0.03) was adversely associated with incident MetSyn. After further adjustment for intake of meat, dairy, fruits and vegetables, refined grains, and whole grains, analysis of individual food groups revealed that meat (Ptrend<0.001), fried foods (Ptrend=0.02), and diet soda (Ptrend=< 0.001) also were adversely associated with incident MetSyn, whereas dairy consumption (Ptrend=0.006) was beneficial. No associations were observed between incident MetSyn and a prudent dietary pattern or intakes of whole grains, refined grains, fruits and vegetables, nuts, coffee, or sweetened beverages.

Conclusions--These prospective findings suggest that consumption of a Western dietary pattern, meat, and fried foods promotes the incidence of MetSyn, whereas dairy consumption provides some protection. The diet soda association was not hypothesized and deserves further study.

(Full article behind a paywall, but I have sources).

So, working through the actual analysis, it looks like what they did was cut the level of consumption of each pattern or individual food group into quintiles and then compare the relative risks in each quintile. So, for instance, the highest quintile of the Western diet has an 18% (1.03 - 1.37) higher risk of MetSyn than the lowest quintile. At some level, this is good news if you tend to eat an "unhealthy" diet. An 18% increased risk really isn't that much, and you might well be willing to absorb it in order to keep eating stuff you like all the time, especially because the second quartile has a 13% increased risk, so you'd need to make pretty dramatic changes in order to see much improvement.

One question I'm having trouble extracting here is the extent to which the effect of the "Western Diet" is dominated by consumption of meat and fried foods (the only factors tha are significant in this model.) It's certainly possible that you could get away with eating all the sugar you wanted as long as you stayed off the chicken fried steak. On the other hand, it doesn't look like eating your vegetables helps at all.

The other result that's gotten a lot of press here is the association between diet soda consumption and MetSyn (34% in the highest tertile). As the authors say, it's hard to know if this is a cause or an effect, and needs some more study.

Posted by ekr at 6:34 PM

November 3, 2007

On prostate cancer mortality

Ezra Klein points out that while the US death rate from prostate cancer is more or less the same as in other developed nations, the survival rate is a lot higher because the US screening program is so effective.

Figure from: Cancer Research UK

A natural question to ask at this point is: what's the point of a massive screening program if it doesn't improve the death rate? There's more to the issue here than the cost of the screening, since you need to followup with other tests, eventually culminating in a biopsy, and then treatment isn't fun. And of course it's probably kind of stressful to find out you have prostate cancer, even if it's not eventually going to kill you.

Posted by ekr at 8:40 PM | Comments (3)

October 7, 2007

Ovulation and lap dance tipping

ScienceNow reports on an interesting research project out of New Mexico:
The researchers used ads and flyers to sign up 18 lap dancers from local clubs. Each woman was asked to log on to a Web site and report her work hours, tips, and when she was menstruating. Lap dancers generally work 5-hour shifts with 18 or so 3-minute performances per shift. They average about $14 per "dance"--all of which is called a "tip" because it is illegal to pay for sex in New Mexico.

Over a 60-day period, the researchers collected data from 5300 lap dances. They divided the answers according to whether the dancers were in the menstrual phase, the high-fertility estrous phase, or the luteal phase. The result, as they report online this week in the journal Evolution and Human Behavior: Of the 11 women with normal menstrual cycles, those in the estrous phase pulled in about $70 an hour--compared with $50 for those in the luteal phase, and only $35 an hour for those who were menstruating. The other seven women were on birth control pills. They earned less across the board, and there was no peaking at the estrous phase.

The numbers suggest that men can tell when a woman is most fertile, although the message seems to be conveyed by "subtle behavioral signals" that evade conscious detection, the authors say. They add that the study couldn't identify whether it is scent or other physical changes that cue the men in, but they don't think it's anything obvious such as type of dance moves or "conversational content."

That's an interesting result. The paper doesn't seem to be online, but it would be interesting to know whether the variation is in the number of dances (18 over a 5 hour shift as opposed to 100 potential is a fairly low hit rate) or to the amount of tipping per performance. That might provide some indication of the nature of the effect.

Posted by ekr at 9:04 PM | Comments (7)

September 16, 2007

Bimodality in cancer survival improvements

This article in Science reports on the lack of improvement in cancer treatments for Adolescents and Young Adults (AYAs). Here's the depressing figure from the article, showing the situation from 1975 to 1999:

It's not really clear what the issue is. The dominant theory seems to be that pediatric cancers and adult cancers are fundamentally different and that AYA tumors mix them and so adult treatment, at least, doesn't work. It's unclear if pediatric treatment will work better, but the specialists seem skeptical.

Also, note the negative progress in the 30-35 cohort. I wonder if that's real or just noise.

Posted by ekr at 9:40 PM | Comments (1)

September 3, 2007

Oh, hi, I'm tracking your cell phone

The NY School system has just fired a carpenter for submitting false time information. The evidence is that his cell phone has GPS tracking and that the locations don't match where he claimed to be:
August 31, 2007 -- Schools Chancellor Joel Klein yesterday fired a veteran worker whose movements were tracked for five months through the GPS device in his cellphone, leading to charges that he was repeatedly cutting out early.

"This individual was getting paid for not working," said schools spokeswoman Margie Feinberg, explaining Klein's decision to accept an administrative law judge's recommendation to ax John Halpin, a longtime supervisor of carpenters.

Halpin had worked in the school system for 21 years and was conscientious enough to show up as much as two hours early for his 8 a.m.-to-3:30 p.m. shift.

He said he was never told that the cellphone he was given in 2005 could be used to monitor his every move and questioned the accuracy of the data it produced.

But neither argument swayed administrative law Judge Tynia Richard, who found Halpin guilty of submitting false time records when he left early on numerous occasions between March and August 2006.

She issued a decision saying the Department of Education was under no obligation "to notify its employees of all the methods it may possibly use to uncover their misconduct."

I generally don't think much of the Theory X management style of rigorously tracking what employees do. Certainly I wouldn't want to work that way. But even if that is the kind of shop you want to run, it's not clear to me that what you want to track people by is their cell phone. Presumably a lot of the reason you give your employees cell phones is so you can reach them. If the phone is also being used to track them, then they certainly have a lot less incentive to make sure that they have it on them at all times.

From a security guy perspective, it's also worth nothing that this technique is fairly easy to cheat. The tracking system works based on where the handset is, so you just need to get a second handset and then arrange for your phone to transfer calls to and from that handset. Probably, it's as simple as turning on call forwarding on your employer provided line. That certainly could be detected but I doubt the providers currently check for it. There are also a number of more sophisticated and harder to detect techniques.

Posted by ekr at 12:04 PM

August 27, 2007

And right on cue..

In the comments section, Todd complains about the accuracy of my characterization of ACT UP SF (reformatted for easier reading).
"One strange twist to this story is that San Francisco ACT UP (though not other ACT UP branches) has become not only HIV denialist but also AIDS denialist"

They are neither. They are HIV/AIDS Dissidents. And ACTUP has been so for over a decade. Do you make any attempt to be accurate at all ?

Yes, I do, and I think this phrasing is accurate. ACT UP SF's refers to AIDS as the "AIDS $CAM". Here's a quote from their web site:

The fact is that there is no plague of contagious AIDS. Every year of the so-called AIDS "epidemic" in the United States more people died from car accidents than from AIDS. Government estimates of the number of HIV positive Americans has been continually revised downward from 1.5 million in the mid-1980s to between 400,000 to 600,000 today. In addition, the life span of HIV positives that refuse toxic AIDS treatments is over twenty years -- as long as HIV has supposedly been around.

So what's going on? Some big government conspiracy? Not likely. Think of AIDS as a tragic medical mistake where in an era of greed and fear non-contagious illnesses were blamed on a virus. Where societal disapproval of gay men was exacerbated by alarmist media reports and a massive amount of government and big business corruption. Think of AIDS as a scam not a scourge.

Sounds like denial to me.

Moroever, at least one ACT UP chapter has dissociated themselves from ACT UP SF. See, for instance, this from "Survive AIDS" (formally ACT UP Golden Gate). (This link was in the original article).

"This bit about "fair play" is really important. One of the underlying norms that makes science work is that people to some extent adjust their beliefs in response to contrary evidence. Obviously this doesn't happen all the time, but when you're dealing with someone who's not interested in the evidence at all but merely using it as a sort of prop to attempt to defend their position then that isn't an argument, it's just contradiction. At some point the proper response becomes to just ignore the offender, but then they claim that the orthodox community won't listen to them. It's obviously very hard for a layman to disentangle who's right. "

Actually, it does "happen all the time". It's a hallamrk of good science, to adjust and adapt a hypothesis, if it still works, to fit the evidence.

I can see how this might not have been clear. What I meant to say was that while scientists strive to adapt their beliefs, I concede that it doesn't always happen. Yes, it's a hallmark of good science but scientists are human.

Speaking of evidence, it's odd how "the deniers" talk constantly ABOUT the evidence, and how people such as yourself, do little more than 1. name-call, 2. misrepresent facts, and 3. refuse to discuss the facts, yet write on the issue without any notion at all what the big points of disagreement even are.

You can dismiss an argument you've never heard and don't know any of the details of, but don't call yourself "scientific" or even "honest".

Uh huh.

As it happens, I have taken the time to familiarize myself with some of the arguments raised by the AIDS denial community and satisfied myself that the "evidence" you're talking about is unconvincing. Luckily, it's not necessary for me to take the time to debunk these claims personally because others have already done so.

Posted by ekr at 11:28 AM | Comments (9)

August 26, 2007

HIV denial

This PLOS Article by Tara C. Smith and Steven P. Novella, paints a pretty grim picture of the HIV Denialist movement. Now, you may have thought that this was pretty much limited to Thabo Mbeki and Peter Duesberg, but no, it turns out that the world is full of whackjobs. Smith and Novella aren't interested in arguing that HIV causes AIDS—a proposition which is fairly clearly true—as discussing how movements like this survive. The parallels to other anti-scientific conspiracy theories (with creationism being the most obvious example) are striking:

Although the HIV deniers condemn scientific authority and consensus, they have nevertheless worked to assemble their own lists of scientists and other professionals who support their ideas. As a result, the deniers claim that they are just on the cusp of broader acceptance in the scientific community and that they remain an underdog due to the "established orthodoxy" represented by scientists who believe that HIV causes AIDS.

...

Further, deniers exploit the sense of fair play present in most scientists, and also in the general public, especially in open and democratic societies. Calling for a fair discussion of dissenting views, independent analysis of evidence, and openness to alternatives is likely to garner support, regardless of the context. But it is misleading for the HIV denial movement to suggest that there is any real doubt about the cause of AIDS.

...

Of all the characteristics of deniers, repeatedly nudging back the goalpost--or the threshold of evidence required for acceptance of a theory--is often the most telling. The strategy behind goalpost-moving is simple: always demand more evidence than can currently be provided. If the evidence is then provided at a later date, simply change the demand to require even more evidence, or refuse to accept the kind of evidence that is being offered.

This bit about "fair play" is really important. One of the underlying norms that makes science work is that people to some extent adjust their beliefs in response to contrary evidence. Obviously this doesn't happen all the time, but when you're dealing with someone who's not interested in the evidence at all but merely using it as a sort of prop to attempt to defend their position then that isn't an argument, it's just contradiction. At some point the proper response becomes to just ignore the offender, but then they claim that the orthodox community won't listen to them. It's obviously very hard for a layman to disentangle who's right.

One strange twist to this story is that San Francisco ACT UP (though not other ACT UP branches) has become not only HIV denialist but also AIDS denialist:

The fact is that there is no plague of contagious AIDS. Every year of the so-called AIDS "epidemic" in the United States more people died from car accidents than from AIDS. Government estimates of the number of HIV positive Americans has been continually revised downward from 1.5 million in the mid-1980s to between 400,000 to 600,000 today. In addition, the life span of HIV positives that refuse toxic AIDS treatments is over twenty years -- as long as HIV has supposedly been around.

ACT UP SF now seems to be primarily in the medical marijuana business. There must be a really fascinating story behind that.

Posted by ekr at 8:30 AM | Comments (4)

June 3, 2007

Sympathy for the VAMPire

Rumor has it that the scientists over at NIH have developed a new life extension technique: Viral Augmentation and Mortality Prevention (VAMP). Subjects treated with VAMP develop substantially improved strength, reflexes, and eyesight. They also develop dramatically faster healing and appear to have significantly improved life expectancy, at list four times as long in animal models.

Like any medical procedure, VAMP has side effects. The two big ones are extreme sensitivity to sunlight and severe, chronic, anemia. As a consequence, subjects require frequent transfusions of whole blood. Obviously, this is an undesirable side effect and one we'd like to fix in future development, but one would expect that plenty of people would be willing to trade off a bit of a blood dependency for being immortal and superstrong. That seems like an especially good trade if you were old, terminally ill, etc.

So, ignoring the issue of whether the FDA would approve VAMP, is this something good for society? Once we get past objections about how immortality is inherently bad, we've got a situation that's inherently exclusive. Each subject requires a support base of some number of normal humans to provide transfusions for them, so this means that only a small fraction of the population can be treated—at least until we find some way to produce blood in vivo, which is likely to suddenly become a pretty high research priority, along with finding a version of VAMP without these side effects.

Even with the current set of conditions, though, it's not clear that VAMP is unacceptable. There are lots of drugs we can't afford to give to everyone, but that doesn't stop us from manufacturing them. Of course, VAMP is slightly different in two respects. First, you voluntarily acquire the condition but then we have to treat the side effects, but it seems to me that you still stand in the same relationship to the poor schlubs who can't afford the treatment. Second, while the side effects are unpleasant, being treated with VAMP arguably puts you in a superior position to others, rather than an inferior position, as with, say, HIV.

Of course, VAMP doesn't exist, but it's a useful way to think about vampires, or as they prefer to be known, vampiric-Americans. Vampires basically have a disease with some positive side effects (long life, strength, fast healing), and some negative ones (sun sensitivity, garlic allergy, etc.) And of course, the need for blood, but as we saw with VAMP, that's just a matter of a missing market for blood. If we had some cool blood mass production technique, then vampirism would just become another treatable condition. Without it, vampires are reduced to uh... freelance blood collection. With it, people would be lining up to get bitten.

Posted by ekr at 10:12 PM

March 5, 2007

It could be lupus!

I happened to come across WebMD's Symptom Checker and thought I'd give it a shot. Here's what it offered me when I gave it the symptoms for illiotibial band syndrome:

I also fed in the symptoms of poison ivy on my arm and got:

First, note that poison ivy is an allergic reaction which causes contact dermatitis, which is a form of dermatitis, which just means a skin inflammation. Second, narcotic abuse???? I wouldn't have this drug problem if my lupus didn't hurt so much!

Posted by ekr at 11:13 PM | Comments (2)

December 16, 2006

Genetic variation, lactose tolerance

While nearly all children are able to digest milk, a large fraction of adults lose their ability to process lactose (milk sugar) as they age (lactose intolerance). However, in many cultures (e.g., the Masai, dairy is a major part of the diet, so being able to consume milk is an obviously desirable adaptation, or rather four adaptations.

In this week's Nature Genetics (behind paywall, this post based on the Science summary above). Tishkoff et al. report on a study of African populations finding three novel mutations that allow the digestion of lactose (add this to a previously known mutation found in Finns). As with altitude adaptation, we see that there's been a remarkable amount of separate adaptation to the same problems in different human populations.

Posted by ekr at 8:02 PM