Perhaps this is advice to reiterate a little closer to the (northern hemisphere) growing season. But without any other pressing topics asking me for a rant at the moment, I would like to warn would-be gardeners out there to pay attention to what you are planting.

If you can, avoid big-box gardening centers such as Walmart and Home Depot. While I avoid them for other reasons as well, a biggie is that they distribute similar plants and seeds to all their stores around the country. So, many plants native to different areas (and different countries) are distributed to where they do not belong. I know that the Walmart in Butte, Montana goes so far as to sell seeds of plants forbidden by the state's Noxious Weed list. Every single year, the local weed folk have to go to Walmart and have them remove the illegal seeds from their shelves, because they don't bother to learn from their mistake - I suppose there are no legal repercussions available, which is unfortunate. Apparently the idea of being a good corporate citizen hasn't occurred to them either, when put up against the cost of keeping noxious weeds from non-native areas. The homogenization of our business communities and the homogenization of our landscape are not just parallel phenomena, they are inextricably intertwined.

Seeds meant for planting are not the only source of invaders - checkout the Invasive Species Weblog for info on an attempt by Oregon to start regulating birdseed. With all these unregulated pathways still existing -- despite the spread of significantly destructive invaders such as sudden oak death and the Asian longhorned beetle caused by free-trade-trumps-all thinking -- the fight for the conservation of biodiversity and habitat diversity truly seems an uphill climb.

Labels: invasive species

An excellent article by Michael Pollan in this week's Times magazine has relevance to the subject I had already picked for my next post: how bad science and standard journalism practices contribute to a raft of contradictory, misleading, and often worse-than-useless nutritional and medical advice. He explains how another important facet of the problem is purely political, but touches more briefly on the issues to do with bad science. I will leave the politics to him and focus on the science. The media's role should be fairly obvious already.

What is the bad science? For an example I will use a paper whose topic has been publicized recently by the media: Corrada, et al. 2005. Reduced risk of Alzheimer's disease with high folate intake: the Baltimore longitudinal study of aging. Alzheimer's & Dementia 1:11-18.

This paper is first a perfect example of the reductionist approach to nutrition that Pollan discusses in his article. How do the authors identify folate as a nutrient associated with Alzheimer's? They first use self-reported diet and supplement data, which is notoriously bad in the first place (I can't help but add, probably even worse in a study which assumes a certain proportion of the participants will be having dementia during the study). Then, one author estimates the level of each of 6 nutrients of interest (vitamins C,E,B6,B12, folate and carotenoids). For some reason I can't yet figure out, they then decide whether each person took more or less than the U.S. R.D.A. for each nutrient. The relative risk for Alzheimer's is then calculated with a particular type of regression that I have not used, but let's assume that part's fine.

This procedure provides the following summary of results: the calculated relative risk (RR) for folate is .41, supposedly meaning that if you imbibe more than the RDA of folate over a number of years, your risk for Alzheimer's is only 41% of that of someone who takes less than the RDA.

Both vitamins E and B6 showed a tendency to reduce risk as well, so the authors reran the data in a test using these nutrients only, designed to confirm the importance of these vitamins and find out if RR was correlated among these three. They found some correlations but decided it didn't matter, and determined that folate was the nutrient they were looking for.

There are (at least) two major statistical problems with the paper. The first is common to a lot of scientific papers, especially medical ones, which doesn't make it any more wrong: using the wrong significance level. The scientific standard is to find two different groups of data different if there the chance they came from the same population is less than 5%. This is a completely arbitrary standard, but considered conservative enough to be accepted by the scientific community. Trouble is, every time you run a statistical test, there is a 5% chance that data that look different really aren't. Simply, this means that if you run 20 statistical tests as part of your analysis, then on average one of them is a false positive. This is why I do not panic when I do a free blood workup every other year offered by our insurance, and it always says that one of the things it is testing for (cholesterol, iron, etc.) is out of the "normal" range - if you test over 20 things and use 95% confidence intervals for where they should be, then that's what happens.

The paper does 6 initial analyses so at a minimum, the significance level should be set to 5%/6 = .833%. By this standard only folate shows any activity in the orginal test. But then they do a whole lot of other comparisons - they take each vitamin and break it into smaller groups and compare different levels of each to see what levels are associated with Alzheimer's. In the first table alone, there are a total of 18 statistical comparisons. Bottom line: if you fish for enough stuff for a long time, you're bound to catch something. (This also explains why all these "breakthrough" studies are so ridiculously contradictory when you put them all together - which the authors of this paper themselves admit in their discussion - and why all these nutrition fads come and go with such rapidity.)

The next statistical problem is that when they find 3 nutrients of interest, they reuse the same data set to confirm the suggestion that one or more of these are actually having an effect. This breaks a cardinal rule of statistics. If a data set gives you the idea that there is a certain effect, using the same data set to confirm the effect is basically self-confiming prophecy. How do you deal with this problem when the data are from a long-term study? You don't want to have to wait 20 years to confirm your suspicions. Fortunately, you don't have to. Before the study begins, you arbitrarily break your group into two. Then when doing the analysis, you use one group to hunt for any nutrients that might be doing something, and you use the second group to test your (now formulated) hypothesis that a particular nutrient is significant.

And by the way - the actual numbers of the study show that those taking more than the RDA of folate had a 7% chance of getting Alzheimer's, while those taking less had an 11% chance. Not exactly earth-shattering.

None of this touches on the idiotic notion that single nutrients are somehow acting in a vacuum to prevent or cause disease. But the media is just as in love with this idea as "nutritionists" are. Read Pollan's article. It will be obvious how this all fits together to create a multibillion-dollar supplements industry for stuff we feel we need because we are eating so much crap produced by the multibillion-dollar processed food industry.

These studies are a waste of time and money.

Labels: brain, health, humans, statistics, vitamins

I hope to continue this more regularly after a long hiatus. Heck, it's unclear whether anyone will ever read Bioblog anyhow, but then again, blogs are all about narcissism and self-deception anyway.

This article about "gay sheep" research in the New York Times has the ironic purpose of describing how the mainstream media distort science.

In this example, a quote by the researcher was taken completely out of its scientific context:

"The release quoted Dr. Roselli as saying that the research "also has broader implications for understanding the development and control of sexual motivation and mate selection across mammalian species, including humans.""

"Control," in Dr. Roselli's context, refers to how the brain controls behavior, given its anatomy and physiology. Yet of course media reports implied that the scientists were for some reason interested in "controlling" gay behavior - i.e. somehow figuring out how to "turn" gays into heterosexuals. According to the original paper referred to by the Times and presumably other articles, their interest is purely in the interaction of brain anatomy and animal behavior [ROSELLI et al, 2004. The Volume of a Sexually Dimorphic Nucleus in the Ovine Medial Preoptic Area/Anterior Hypothalamus Varies with Sexual Partner Preference. Endocrinology 145(2):478-483]:

__________

Similar to the results in humans, the variability in oSDN measurements
within each group of sheep was large compared with the differences
between groups, and it is impossible to predict the sexual
partner preference of any individual on the basis of a single
brain measurement. Nor do the present data allow us to
determine whether the observed differences in the size of the
oSDN are the cause or consequence of an animal's sexual
partner preference, or whether the size of the oSDN is influenced
by other unidentified variables. However, experiments
in several species (11) have shown that the development
of sexually dimorphic nuclei within MPOA/AH is the
direct result of exposure to testosterone or its metabolites
during a critical period in prenatal or early neonatal life.
Although it seems likely that the size of the SDN in sheep is
also established by testosterone exposure early, this relationship
has not yet been established.

_____


In other words, the authors are careful to point out the chicken-and-egg problem of correlating brain structure with behavior: innate structural differences can affect behavior, but lifetime experience can alter brain structure itself (how else would we be able to store memories?). This is why media accounts of gender studies showing "genetic" differences between males and females get my hackles up - by the time a baby is born, its environment (starting day 1 in the womb) has already affected its development.

Why study "gay" animal behavior if you don't have some sort of political agenda? I can give one good reason, off the top of my head. Many behavioral traits are very difficult to quantify and correlate with brain structure. Homosexual behavior is easy to study as a clear either-or behavior (at least in this case). Why not go for the slam-dunk of really being able to correlate specific behavior with a brain structure? Because it's cool. That's why scientists do their research - because it's cool. I guarantee you it isn't for the money. But of course a brush with fame is tempting, and we all want the world to know that our research is cool. Unfortunately many scientists, not really aware of life outside their ivory lab, get excited about the media attention without realizing how it can get out of control when a hotbed topic is concerned. I had a friend in grad school who studied sex in nematodes. When he discovered that male nematodes that never had sex lived longer than male nematodes that did, it wasn't just in the Science Times, it hit the front page (which was OK with him). What does nematode biology have to do with humans? Absolutely nothing. But sex sells.

In my own case, a Science paper on a topic less sexy but of burgeoning importance to environmentalists, nontarget attacks by biological control agents, led to an NPR interview, and I discovered how that works: all the intelligent things you say during the interview come out of the interviewer's mouth in the finished piece, and all the dorky things are when you are actually talking.

Labels: brain, evolution, health