Action Potential

The next installment of the Nature Network Neuroscience group journal club is now live. The paper is attempting to understand the neural mechanisms that distinguish between conscious and unconscious processing, and is from a collaborative group in Paris.

The contributor discussing this paper for the neuroscience group is Alfredo Pereira, Jr, an adjunct professor at São Paulo State University. I want to thank Alfredo for his participation.

Posted by Noah Gray at 01:29 PMon February 28, 2008 | Permalink | Comments (0) | TrackBacks (0)
Categories: Noah Gray, Interesting Neuroscience, Journal Clubs

By now, you've likely read a shocking headline questioning the effectiveness of the latest generation of antidepressants. Kirsch et al. report that selective serotonin reuptake inhibitors (SSRIs) are only slightly more effective than placebos at reducing depression in a meta-analysis of US Food and Drug Administration (FDA) data. Are these data really worth all the fuss?

As Nicola Jones points out in the Great Beyond, drug companies are not required to publish negative data. Suspicious that published data on SSRI effectiveness were biased, the authors obtained FDA data via the US Freedom of Information Act. Researchers use the Hamilton Rating Scale of Depression (HRSD) to rate depression severity. Antidepressant treatment should reduce depression scores. Placebos often also reduce HRSD scores. A meta-analysis of FDA data showed that most SSRIs significantly (in the scientific sense) reduced HRSD scores relative to placebo, but the relative reduction was less than the effective criterion established by the UK National Institute for Health and Clinical Excellence (NICE). Thus, by NICE criteria, SSRIs would not benefit most people (Note: I am unaware whether the FDA has a similar effectiveness criterion).

By NICE standards, does anyone benefit from SSRIs? The authors found that people with high HRSD scores (people with severe depression) showed SSRI-induced HRSD reductions that passed by NICE criteria, suggesting that SSRIs effectively combat severe depression. However, placebos were less effective at reducing HRSD scores in people with severe relative to mild depression, which may explain the relative increase in SSRI effectiveness, according to the authors.

I'm not a physician, nor am I a policy maker, so I can't comment on NICE's effectiveness criteria. However, based on this study, it is inaccurate scientifically to describe SSRIs as 'ineffective'. That does not suggest that I have feelings about whether they should or should not be prescribed. Are antidepressants overprescribed? Probably. Should people stop taking their SSRIs. NO! It is never safe to reduce, change or stop antidepressant treatment without the supervision of a physician. Perhaps, in the end, effectiveness is in the eye of the patient and his or her prescribing physician.

Posted by Debra Speert at 11:14 AMon February 26, 2008 | Permalink | Comments (3) | TrackBacks (0)
Categories: Debra Speert, Breaking News

A woman in the US has decided that she loved her pit bull (named Booger) so much, that having him all over again is definitely worth the $150,000 price tag. I saw this story in the BBC, reporting how a Korean company, RNL Bio, has taken its initial order for pet dog cloning, the first such venture of commercial scientific canine cloning (a pet cat was first cloned in 2004). The lead scientist at RNL Bio, Dr Lee Byeong-chun, had previously worked with disgraced stem cell scientist Dr Hwang Woo-suk, whose fraudulent publications created quite a stir (we referred to that scandal on Action potential here.)

The client, Bernann McKunney, gave RNL Bio ear tissue from "Booger", preserved by an American biotech firm before the dog died 18 months ago. Ms. McKunney had become quite devoted to her dog after she claimed it saved her life, coming to her aid while she was being attacked by another dog, an encounter that cost her an arm. For those of you wishing you had the six figures required to re-create your close canine companion, never fear, RNL Bio's marketing director, Cho Seong-ryul believes that the cloning costs should come down to be under $50,000, as the industry begins to "take-off".

These pet cloning ventures are fun tests of nature vs. nurture. Although subjective, who better to determine whether the personality, physical characteristics, and other identifying traits of a cloned organism are the same as those of the original than the doting owner? Although I think that paying that kind of money for a dog is a bit ridiculous, I am quite intrigued by what the results will bring. Dogs are very interactive creatures, providing a rich and broad spectrum of repeatable behaviors that can easily be assessed by humans. Although Dolly the sheep was indeed a clone, it must have been a bit of a challenge to determine whether she had he same demeanor as her genetically-identical donor (sister? mother? What was the verdict on that one??) No offense to Dr. Wilmut and his team, but I think that humans have a bit harder time dissecting complicated sheep behaviors as compared to what we are able to observe in dogs. And as any cat owner will attest, feline behavior is erratic, at best, making it difficult to determine personality differences. Comparing the personalities of Booger and "Booger II" will, at least. provide for some interesting discussion fodder.

Even more interesting, a better opportunity to quantify behavior and provide a more objective assessment of original/clone similarity could lie with RNL Bio's other potential clients. Besides cloning loved pets that families cannot live without, the South Korean firm is also going after a different market: those employing dogs for various complicated tasks. Whether as a seeing-eye dog, a drug-sniffer, or a search-and-rescue team member, dogs can learn to complete challenging jobs with discipline and precision. The training process provides many opportunities to evaluate trainee performance, providing the trainers with feedback tracking an individual's progress, and predict which animals are most likely to rise to an elite level. These evaluations involve quantifiable tests. So now we have a decent experiment here. We can compare the performance numbers of the original and the cloned beasts, in an attempt to determine how much of the ability to learn and absorb these tasks is genetic.

But until RNL Bio lands a windfall contract from some major guide dog farm, I'll have to settle for assessing Ms. McKunney's satisfaction with her new Booger.

Posted by Noah Gray at 04:55 PMon February 21, 2008 | Permalink | Comments (2) | TrackBacks (0)
Categories: Noah Gray, Random Thoughts

If a disease affects men and women differently, does the disease's mechanism differ by sex? My guess would be no. However, a recent article has me wondering. Schizophrenia symptoms, age of onset, and disease course differ in men and women, and some researchers report increased risk of schizophrenia in men relative to women. Now Shifman et al. report a single nucleotide polymorphism (SNP) associated with schizophrenia in women but not men in a recent article in PLoS Genetics.

Although schizophrenia is highly heritable, both genetic and environmental factors impact disease risk, so candidate genes have been difficult to identify. The authors analyzed 500,000 SNPs located throughout the genome. A variant of Reelin associated with increased schizophrenia risk in women but not men.

Reelin is a serine protease important in neuronal development. The identification of a Reelin variant associated with schizophrenia is consistent with previous research suggesting that schizophrenia affects neuronal development. What does its sex-specific identification say about the etiology of schizophrenia in men and women? I'm frankly a bit befuddled.

Posted by Debra Speert at 03:43 PMon February 20, 2008 | Permalink | Comments (1) | TrackBacks (0)
Categories: Debra Speert, Interesting Neuroscience, Neuroinformatics

The next installment of the Nature Network Neuroscience group journal club is now live. The paper is on selective nociceptor inhibition, from the lab of Clifford Woolf at Harvard.

The contributor discussing this paper for the neuroscience group is Damien Samways, a post-doctoral fellow at St. Louis University in the lab of Terrance Egan. I want to thank Damien for his participation.

Posted by Noah Gray at 06:28 PMon February 19, 2008 | Permalink | Comments (0) | TrackBacks (0)
Categories: Noah Gray, Interesting Neuroscience, Journal Clubs

The Faculty of Arts and Sciences (FAS) at Harvard University voted Tuesday to adopt an open-access policy, providing a free repository for finished papers, according to a recent press release. This move will allow for greater dissemination of scholarly work conducted at Harvard, says Stuart Shieber, a professor at FAS. Shieber states that a combination of a restrictive publishing system and the “astronomical” cost of journals have led the Harvard professors to support such a venture. An official description of the proposal that was actually discussed by the FAS on Tuesday is here.

As my colleague from Nature Precedings, Hilary Spencer, points out in a recent Nature Network forum, this entire policy is very vague with regards to what is meant by the scholarly article or the "final version." Is that the final, journal-produced PDF? The peer-reviewed, unpublished, non-copy-edited version? The non-peer-reviewed pre-print? According to an analysis written up on TheScientist.com, this mandate would require that published articles be submitted. However, go back and re-read the original proposal and tell me where it says that explicitly.

That brings us to the main point. Harvard is extremely vague about exactly what this proposal covers. A smart move, if you ask me, because now they can stress any position or interpretation that they want, based on the response they receive. If they feel too much pressure from younger faculty concerned that for-profit journals may not consider papers from Harvard because of a potential conflict with journal policies, they are free to say “Don’t worry, we just meant the pre-print.” If the public sentiment is in full support of their repository, they may feel emboldened to say “Of course this means published papers!!” But frankly, any legal hair-splitting that may have to be done regarding the exact wording of this proposal becomes moot because of the opt-out clause that is available to the faculty. Although “required” to make the research available immediately for the repository, researchers can acquire a waiver to maintain exclusive rights, allowing them the freedom to proceed as they wish with publication, without worrying about whether policies at their institution and their chosen journal are in legal synchrony.

So what do we really have here? Of course this is a victory for open access, because of Harvard’s clout. But it seems hollow to me. Harvard now gets the great PR, without the danger of backlash because of their vague wording and inclusion of an opt-out policy. If Harvard (or any other institution considering the same type of proposal; see this, this and this) really wants to promote the free and open worldwide dissemination of their research, the next policy should be a little more specific about their ground rules and intentions. If the intention is really to change the way that publications are handled and distributed, then providing multiple backdoor exits and loopholes is probably not the most efficient way to bring about said change.

P.S. For the record - Nature Publishing Group encourages authors to self-archive the submitted version of their manuscript 6 months after the publication date, a policy that complies with recently passed legislation from the NIH stipulating that work supported by NIH grants must be publicly self-archived within 12 months of publication.

Posted by Noah Gray at 02:03 PMon February 14, 2008 | Permalink | Comments (2) | TrackBacks (0)
Categories: Noah Gray, Breaking News, Scientific Publishing

The next installment of the Nature Network Neuroscience group journal club is now live. The paper focuses on the generation of new hair cells from avian mesenchymal tissue.

The contributor discussing this paper for the neuroscience group is Shelley Batts, a graduate student at the University of Michigan. I want to thank Shelley for her participation.

Posted by Noah Gray at 01:05 PMon February 12, 2008 | Permalink | Comments (0) | TrackBacks (0)
Categories: Noah Gray, Interesting Neuroscience, Journal Clubs

The Darwin Day celebration was initiated by Dr. Robert Stephens and was held at Stanford University on April 22, 1995 to celebrate the scientific accomplishments of Charles Darwin. In subsequent years, the event was changed to be on or around the birthday of Darwin (February 12, 1809) and has had many illustrious speakers take part, including Richard Dawkins and Donald Johanson. The celebration has become a global one, with museums, academic institutes, private foundations, and others sponsoring some form of a tribute to this famous scientist.

A consolidated list of this year's events, held around the world, is here. Tell us what you plan to do on Darwin day, and if you take part, report back here on what you learned, disagreed with, or experienced. If we get a nice response here, perhaps we can prepare an event synopsis for ARJ, in case their readers miss out on the celebration.

Posted by Noah Gray at 05:04 PMon February 08, 2008 | Permalink | Comments (1) | TrackBacks (0)
Categories: Noah Gray, Random Thoughts

In mid-January, the Science and Engineering Indicators 2008 was released by the National Science Board. The goal of this report is to provide quantitative information about US science for private and public policymakers, as mandated by law.

This study is full of interesting information, and feel free to point out any gems that you dig up. For now, let's focus on a couple of sections, namely science education and the section entitled "Public Attitudes and Understanding." In science education, there are both reasons to cheer and be alarmed; as for the public understanding of science....be afraid...be very afraid.

From 1990 to 2005, US students (regardless of gender, race or class) seem to have been improving in both math and science in the earlier primary school years of school. But in the upper grade levels, they are actually doing worse, particularly in science, with test scores declining. Why is this? Since the scientific subject matter becomes more complex and diverse in high school, do we begin to lose students due to both a lack of interest and/or ability? It is not due to less-qualified teachers, since in high school, close to 90% of science and math teachers have at least a college degree in the field they are teaching, while in the lower to middle school grades, that proportion drops to 30-50%.

Unfortunately, the race/class gap in the "quality' of teachers is bigger than ever, with a good inverse correlation between the number of science/math teachers holding an advanced degree and the proportion of minority and low-income students in a particular school. These same schools lacking MS or PhD-holding teachers also had a much higher number of educators working "out-of-field" and/or who had three or less years of experience. Obviously these differences mostly boil down to the money that is available to the school district, and finding ways to increase funds for fiscally-challenged schools, although far from trivial, is a straight-forward strategy or solution to the problem (I'm not saying that it is easy to find money for schools, but just that implementing a solution is a different problem from not having one.)

In my opinion, much more work and investigation needs to go into why the gains made early-on in science education (which are blind to class/gender/race) not only do not translate, but get worse at the education stages that are the most influential in leading students to their secondary education. How can we better examine this disparity between grade level performance so as to understand it and reverse it? What policy changes can be made nationally and locally to address this important problem?

Moving on to the public's basic science knowledge, one could think that we have no science education at all in out schools, based on some of these answers. Let me provide you with my shockers:

Those facts I was shocked that the public did not know:

1. Lasers work by focusing sound waves. (This one was answered "False" correctly by 60% of men and only 30% of women; it is the women that disappointed me here.)

2. It is the father’s gene that decides whether the baby is a boy or a girl. (Answered "True" correctly by only 55% of men and 75% of women; hello guys, this is one you should know!!)

3. The universe began with a huge explosion. (Answered "True" correctly by 40% of men and 27% of women; must have asked this question in the Bible belt...)

Those facts with which the public impressed me with their knowledge:

1. The continents have been moving their location for millions of years and will continue to move. (Answered "True" correctly by 85% of men and 75% of women.)

2. A doctor tells a couple that their genetic makeup means that they’ve got one in four chances
of having a child with an inherited illness. Does this mean that if their first child has the illness,
the next three will not? (Answered "No" correctly by 90% of men and 84% of women.)

3. A doctor tells a couple that their genetic makeup means that they’ve got one in four chances of having a
child with an inherited illness. Does this mean that each of the couple’s children will have the same risk
of suffering from the illness? (Answered "Yes" correctly by 75% of both genders).

The last two are obviously related, and even address a bit of mathematics knowledge in there too! With the popularity of "doctor dramas", these genetics questions are becoming a breeze, aren't they?

Real head-scratcher:

1. Does the Earth go around the Sun, or does the Sun go around the Earth? (Answered "Earth around Sun" correctly by 66% of men and 46% of women; come on, why is this one not over 90%???? Where's Copernicus, Kepler and Galileo when you need them!)

However, I want to focus on one in particular that really goes to the heart of an issue that has concerned me for a while. A question about experimental design was confirmatory for me, revealing that only a minority of Americans really understand the scientific process:

Two scientists want to know if a certain drug is effective against high blood pressure. The first scientist
wants to give the drug to 1,000 people with high blood pressure and see how many of them experience
lower blood pressure levels. The second scientist wants to give the drug to 500 people with high blood
pressure and not give the drug to another 500 people with high blood pressure, and see how many in
both groups experience lower blood pressure levels. Which is the better way to test this drug??

Only 40% of respondents, regardless of gender, answered correctly that the second strategy would be more effective due to the inclusion of a control group. If the scientific process is not understood on a basic level, then scientists, and those who report on science in the popular press, need to be very careful with how results are disseminated, since they cannot count on the average person to understand the difference between results acquired appropriately (following the scientific process) and peer-reviewed, and those that are not. These pieces of information need to be spelled out explicitly for them.

Perhaps I'll call Fox and see if I can get a pilot started for a new primetime drama about grad students and post-docs conducting research at the bench. If there are enough good-looking people, sex and emotional outbursts in it, I bet I could teach the public the scientific process!

Posted by Noah Gray at 05:08 PMon February 05, 2008 | Permalink | Comments (2) | TrackBacks (0)
Categories: Noah Gray, Science Policy