The Corpus Callosum

New Role for Karrikins

Mon, 05 Apr 2010 01:35:36 -0500

This is a nice little study in PNAS. It is nice for a few reasons. For one, it is the sort of thing that drives conservatives crazy, for it seems to be a highly detailed study of something useless. Two, it could turn out to be pretty useful. Three, when I searched ScienceBlogs for "karrikin," I got zero hits. Fourth, when I search Wikipedia for "karrikin," I got zero hits. So it is about time someone started talking about these chemicals. Plus, "karrikin" is a cool word.

"Karrikin" is the Noongan word for "smoke." Karrikins comprise a class of chemicals found in smoke from burning plant matter. It has been known for a long time that smoke from brush fires can stimulate the germination of some kinds of seeds. In fact, persons who are trying to germinate difficult-to-start seeds, will sometimes use products derived from smoke, in an effort to get the seeds to germinate.

Figure 1. Partial structural similarity between the karrikin family of plant growth regulators and strigolactones.

Researchers in Australia have been studying this for a few years, at least:

Ground-breaking research into the link between seed growth and smoke

Dr Nelson, a researcher at the Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, at The University of Western Australia, is investigating how it is that some plant seeds are triggered to germinate after exposure to smoke...

Dr Nelson said fires played a major role in shaping the Australian bush.

"Even though the landscape looks devastated to us after a bushfire, it is quickly covered by a flush of new growth," he said.

"For the seeds of many native Australian species, the smoke from a fire is the trigger to wake up and take advantage of the newly available resources. Understanding this phenomenon could have major impacts on conservation efforts and agriculture."

Although smoke is a complex mixture of thousands of different compounds, recent work at UWA and Perth's Kings Park laboratories was able to identify a single 'smoke alarm' component that snaps seeds out of dormancy...

Now, it turns out that karrikins have an additional role:

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Happy Easter

Sun, 04 Apr 2010 17:48:54 -0500

Well, it is not the traditional flower, but it happens to be what is blooming right now. The crocuses and daffodils are pretty much spent; the lilies and allium haven't blossomed yet.

These are blossoms on a claretcup cactus (Echinocereus triglochidiatus).

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In Which Hannity Demonstrates Nothing

Fri, 26 Mar 2010 08:58:26 -0500

I guess Fox News is starting a series of vignettes, hoping to show that stimulus money is being wasted. In an early attempt, Hannity and Carlson track down an entomologist, at Michigan State University, who got a $200,000 grant from stimulus funds. The scientist is Dr. Anthony Cognato, Associate Professor in the Department of Entomology.

I will let the viewers judge for themselves if the Fox crew managed to demonstrate anything at all. One thing that is clear: they do not understand basic science, or anything about science. They also fail to appreciate how foolish it is to confront experts, without having done some serious preparation.

If you are trying to make a point, you should not ask questions to experts, unless you have a pretty good idea of what they are going to say.

It this video, it appears as though they expected to find that the grant did not produce any jobs. But it did produce jobs: four students for two years, at 8-10 dollars per hour, plus the manufacturing jobs for those who made the supplies. They expected to find that the project has no value, but it does have value. Scientists need data, and for entomologists, some of that data comes from collections. At an agricultural university, the study of insects happens to be rather important.

While there is no guarantee that this particular collection will lead to important discoveries, that is always the case with basic research.

They may be skeptical of the value of basic science. Indeed, there are valid arguments to be made about how much funding should go to pure vs. applied research. However, they did not address that at all. They merely dismissed it out of hand, with no attempt at analysis.

The only value in a vignette such as this, is if you are attempting to incite the passions of those who already have a particular belief, and who are susceptible to confirmation bias. Such persons see evidence that appears to confirm what they already believe, so they do not examine the evidence (or the issue) any further.

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Ghost Chile Update #2

Tue, 23 Mar 2010 23:55:19 -0500

I've written before about the world's hotter chle pepper: the bhut jolokia, rated at over 1 million scoville units. (Sauce available here.) Now, India has a new use for the infernal things: combatting terrorism.

India deploys world's hottest chilli to fight terrorism
Bhut jolokia, or 'ghost chilli', to be used for teargas-like grenades to immobilise suspects, defence officials say

Ever since the Trojan Horse - and probably long before - men have bent their minds to developing the ultimate secret weapon. Now, at last, the Indian army just might have discovered it: the world's hottest chilli pepper.

The Indian army believes that the pungency of its ground seeds of the bhut jolokia - a capsicum hybrid, growing around the banks of the Brahmaputra river, that is reputed to be 100 times hotter than a jalapeño - could be harnessed in smoke grenades against rioters or to flush out terrorists in confined spaces...

These peppers are two orders of magnitude hotter than the jalapeño. Mother nature always wins, in the end.

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WSJ: Incompetent Ranting

Mon, 15 Mar 2010 08:27:12 -0500

At first, I was going to title this post WSJ: Incompetent Ranting. Then I decided that was too strong. Then I read the article again, and went back to the original title. Mind you, this is not intended to be an ad hominem attack. The author, Edward Shorter, has been the Hannah Professor in the History of Medicine since 1991, and in 1996 was cross-appointed as Professor of Psychiatry (at the University of Toronto). He has written some good books, including A History of Psychiatry: From the Era of the Asylum to the Age of Prozac. The book was reviewed favorably in an APA journal.

The WSJ article is so fraught with problems, that I thought it must have been written by a Scientologist, or someone like that. No, Dr. Shorter is a serious academician. Perhaps his perspective has been distorted by some unstated agenda. I don't know.

(Note: the WSJ has a dorky semi-permeable paywall, so the link below might not work. If it does not, perhaps the Google cache version will, or a link taken from a Google search.)

Why Psychiatry Needs Therapy
A manual's draft reflects how diagnoses have grown foggier, drugs more ineffective
By EDWARD SHORTER
LIFE & STYLE
FEBRUARY 27, 2010

To flip through the latest draft of the American Psychiatric Association's Diagnostic and Statistical Manual, in the works for seven years now, is to see the discipline's floundering writ large. Psychiatry seems to have lost its way in a forest of poorly verified diagnoses and ineffectual medications. Patients who seek psychiatric help today for mood disorders stand a good chance of being diagnosed with a disease that doesn't exist and treated with a medication little more effective than a placebo...

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Yeah, We're Calling Obama Socialist

Mon, 08 Mar 2010 09:18:51 -0500

A few days ago, there was a minor ripple in the political world, when a media person tried to get John McCain to say that Obama is a socialist. Even though McCain had hinted at that several times during the campaign, he would never state directly that Obama is a socialist. Well, he still won't (as reported by Fox):

DAVID GREGORY, HOST, "MEET THE PRESS": Do you think that goes too far? Is it a socialist agenda from the president?

SEN. JOHN MCCAIN, R-ARIZ.: There is no doubt in my mind America's a right-of-center nation, and this administration is governing from the left. That's why the president's approval ratings continue to decline.

GREGORY: But my question was, do you think that kind of -- because have you heard that description before. Not just from J.D. Hayworth, but others. Does it go too far to say the president's agenda is a socialist agenda?

MCCAIN: I think I gave my description. I think they're governing from the left on a broad variety of issues, but I'll let others speak for themselves. I have enough time taking care of my own misstatements.

McCain is someone I try to like, although I did not vote for him.

Now, the issue is picking up steam, without McCain on board:

Top Republicans: Yeah, We're Calling Obama Socialist
by Liz Halloran
March 5, 2010

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Early Spring

Sun, 07 Mar 2010 19:31:58 -0500

We had little squall clouds today, such that there was interesting light and shadow in the yard. This made for a nice opportunity to photograph the nectarine tree blossoms.

Emotionally uplifting, I would say. The only problem is that we now have to watch for frost warnings, then run out and cover the tree if it might freeze.

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Dietary Practices, Depression and Anxiety

Tue, 02 Mar 2010 07:22:28 -0500

The January 2010 American Journal of Psychiatry has two articles pertaining to the relationship between dietary practices and mental health. One article presents the results of a study; the other is an editorial.

Association of Western and Traditional Diets With Depression and Anxiety in Women
Jacka et al.
Am J Psychiatry 2010; 167:305-311 (published online January 4, 2010; doi: 10.1176/appi.ajp.2009.09060881) © 2010 American Psychiatric Association

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Evolution Messed Up?

Sun, 21 Feb 2010 21:03:06 -0500

James Gunn, the director for the movie Slither, seems to be enthralled by creepy crawly things. He also has a blog-like website, on which he posted Evolution Fucked Your Shit Up: The World's 50 Freakiest Animals. (HT: Interesting Pile.)

The creature pictured above, by the way, is an ajolote. The term ajolote can refer to either the Axolotl an (aquatic salamander (genus Ambystoma), or it can refer to the Mexican mole lizard (Bipes biporus). The one in the picture is the lizard, Bipes biporus.

I am not going to say any more about the vexations of taxonomy, or even about Mr. Gunn. The photos are kind of neat, but they speak for themselves. What I am going to address is the notion that evolution messed these creatures up. I suspect that Mr. Gunn was not intending to make a scientifically verifiable statement. But it is way off base, and it illustrates a fundamental misconception about evolution.

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Zen and the Art of Dracaena Growing

Sun, 14 Feb 2010 07:54:43 -0500

Sometimes I see sad-looking plants on clearance, buy them, and try to heal them. This activity provides me with a gratification that is similar to that which comes from healing sad-looking people, but without the tribulations that occur if it does not work as well as we had hoped.

I even have some of these plants in my office (although none of the worse cases go there). At stressful times, I may go and look at the parts of the plants that are growing well: apical meristems, leaf primodia, and axillary buds -- or green shoots, in the vernacular of our time. I just look at them. I don't actually do anything, at least anything that is outwardly visible, most of the time.

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Proposed Diagnostic Criteria Revisions

Wed, 10 Feb 2010 07:46:41 -0500

The American Psychiatric Association has gone public with the details of their proposed revisions to their Diagnostic and Statistical Manual. As expected, most of this is bland and not worthy of attention from the general public.

Unfortunately, as Benedict Carey points out, the book often is used for purposes other than those for which it is intended, which can lead to unintended consequences. It remains to be seen what these will be.

I'm just going to make some quick, admittedly superficial comments.

First, I wince at the new category for autism: Autism Spectrum Disorder:

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Objective Diagnosis Of PTSD Using Magnetoencephalography

Mon, 01 Feb 2010 09:08:41 -0500

Objective diagnosis is in some ways the holy grail of medicine. It has been maddeningly elusive in psychiatry. Now comes a paper in which the authors suggest that they may have found this treasure.

The paper details a method of using magnetoencephalography to assess human brain function. They claim that, in a select population, it can correctly identify patients with PTSD with 90% accuracy.

The synchronous neural interactions test as a functional neuromarker for post-traumatic stress disorder (PTSD): a robust classification method based on the bootstrap
A P Georgopoulos et al 2010 J. Neural Eng. 7 016011

Abstract. Traumatic experiences can produce post-traumatic stress disorder (PTSD) which is a debilitating condition and for which no biomarker currently exists (Institute of Medicine (US) 2006 Posttraumatic Stress Disorder: Diagnosis and Assessment (Washington, DC: National Academies)). Here we show that the synchronous neural interactions (SNI) test which assesses the functional interactions among neural populations derived from magnetoencephalographic (MEG) recordings (Georgopoulos A P et al 2007 J. Neural Eng. 4 349-55) can successfully differentiate PTSD patients from healthy control subjects. Externally cross-validated, bootstrap-based analyses yielded >90% overall accuracy of classification. In addition, all but one of 18 patients who were not receiving medications for their disease were correctly classified. Altogether, these findings document robust differences in brain function between the PTSD and control groups that can be used for differential diagnosis and which possess the potential for assessing and monitoring disease progression and effects of therapy.

The synchronous neural interactions test is a test that is done by having persons perform a simple task, while the magnetic signals from their brain are being measured. The process is called magnetoencephalography. The resulting record is called a magnetoencephalogram (MEG). It is similar to an electroencephalogram (EEG). The difference is that the EEG measures small electric currents. The MEG measures magnetic impulses. These impulses are only slightly affected by the intervening tissue (skull, skin, etc). Therefore, it is possible to get readings that are more precise. The downside is that it requires a more elaborate device, and a special, magnetically-shielded, room. Very few of these devices exist.

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Google Chrome on Opensuse 11.2

Sat, 30 Jan 2010 07:31:27 -0500

I decided to try using Google Chrome as a web browser. The reason is that it is supposed to be faster, particularly for sites that make heavy use of Flash. It turns out that installing it is a hassle if you do it the obvious way, because Flash does not work without fiddling around. That sort of defeats the purpose.

The easier way is to use the one-click install at:
http://software.opensuse.org/ymp/ope...2/chromium.ymp.

This adds the necessary repositories, downloads the application, and configures it so that flash works right away.

It seems to work pretty well. It remains to be seen, however, if Chrome has any chance of becoming my main browser. After all, the first browser I used was NCSA Mosaic, which morphed into Netscape Navigator, which went through several iterations, then became the basis for Firefox. I just followed along. After 17 years, it might be hard to change.

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Glaxo Patent Giveaway: Charity or "Theft"?

Mon, 25 Jan 2010 08:23:02 -0500

I saw this headline on Google Fast Flip, and had to read it. I'm always game for an anti-big-pharma story: even though I appreciate their efforts to relieve suffering, I do like to take notice of their shadier practices.

Is Glaxo's Charity Really Theft?
Jan 20 2010, 5:30 pm
by Daniel Indiviglio

Is there a fine line? Corporations have a duty to shareholders to maximize profits. But when they donate to charity -- which is regularly done these days, often through foundations -- this takes money out of shareholders' hands or stifles future growth. It instead provides that money to some cause that management deems appropriate. But Glaxo-SmithKline's recent decision to put thousands of chemical compounds which may cure malaria into the public domain gives this question a new dimension, adding additional complexity...

The story does not go where I expected. It is not talking about some kind of charity scam, in which they get PR karma for doing something that really only benefits themselves. Rather, the story is about the fact that Glaxo is releasing some of the compounds it has developed, into the public domain.

Indiviglio's story is posted on the Atlantic business blog. It is based upon an article in the (UK) Guardian. The Guardian version is reasonably thoughtful, whereas the Atlantic version is frankly offensive.

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Why should the city be a concrete desert?

Tue, 19 Jan 2010 09:17:02 -0500

Susanne Sternthal, a writer based in Moscow, has published an article about the ecology of stray dogs. The article is in Financial Times, of all places. Why is that?

Moscow's stray dogs
By Susanne Sternthal
January 16 2010 00:04

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