Somatopsychic

Ideas

noreply@blogger.com (Mitch) — Tue, 15 Dec 2009 15:08:00 +0000

During the intermission between semesters I have two projects that I'm working on:

1) Finish revisions of my specialty paper. This is the report on the salvia experiment that we will be submitting for publication. I've been through several rounds of drafts and am circulating the paper among authors, and re-writing in perpetuity. I'll keep you posted.

2) I need to propose a dissertation. In a lot of ways you are defined by your dissertation, and so I want to choose something that I'd like to do more of. It is tempting to keep on with Salvia (I have some anxiety data that is interesting) but I don't really want to be 'Salvia guy.' Instead I'm more interested in the Chronic Mild Stress model that we used; I would like to work on some animal model for anxiety. I'm just starting to dip into the literature to see what is out there but if you know of anything exciting, be sure to let me know. :)

I'm Qualified

noreply@blogger.com (Mitch) — Mon, 17 Aug 2009 20:39:00 +0000

Sorry I haven't been posting. Instead of blogging I have been preparing for qualifying exams. I blogged about the first few papers I read for qualifying, but it was taking too much time. THe first step to quals was selecting a committee to evaluate me. I chose, Dr. Taylor (my Mentor; interested in hormones and works with rats), Dr. Griffin (my psycho-pharmacology professor; interested in trauma and recovery) and Dr. Bucur (my cognitive professor; interested in cognitive declines with aging). They assembled reading lists that I rad in preparation this exam. I read 115 journal articles (well maybe a dozen or so were actually book chapters), totaling 1,623 pages. I spent 18 hours across two days working on the written portion of the exam, the longest I spent answering one question was 4.5 hours. My written exam answers were composed of 10,425 words (29 pages). Then there was a terms test, which was a brief vocabulary test (apparently there were problems in the past). Last up was oral exams. Like a supreme court justice's confirmation hearing, oral exams involved a series of questions from my advisory committee. Long story short, I passed!

What do I qualify for? Well I am now qualified to be an official doctoral candidate. Even though I was accepted into grad school, and accepted into the PhD program that doesn't mean you are qualified to be a candidate for a PhD.

I plan to spend the next year blogging about the readings I did for this exam. Most (if not all) of the articles I read were interesting (to me anyway) and I have already taken copious notes. So it is my plan to post up two QUAL notes each week on Tuesday and Thursday for this next year. I plan to leave out most of the textbook chapters but there are a handful that are too good to pass up. I also plan to blog about BBoB (every three weeks) and ABDG (weekly) so that will be a lot of science review on this blog! I'll also be posting about my research, the animal lab here, and my general grad school experience as the thing is born. I've also decided to spin-off blogging about teaching into another blog: College Undergraduate Teaching Of Psychology (CUTOP)

Talk Sex wtih Dr. S

noreply@blogger.com (Mitch) — Fri, 08 May 2009 14:52:00 +0000

A professor at UMSL has begun a YouTube sex advice channel. I had the pleasure to observe her teaching a research methods class and she is excellent in the classroom. While you may bot be able to sit in on her lecture, hopefully this venue proves just as enjoyable:

Award-Winning Science

noreply@blogger.com (Mitch) — Tue, 21 Apr 2009 15:32:00 +0000

Yesterday the Graduate School at UMSL and Sigma Xi hosted the annual Graduate Student Research Fair. My poster took first prize ($750) for social sciences! Thanks to my co-authors, collaborator, and mentor for all of their help and input. If you are interested I'll embed a close digital approximation of my poster.

UPDATE: Some of you were having trouble viewing the poster. Try this link.

Homework from The MacGuffin

noreply@blogger.com (Mitch) — Tue, 24 Mar 2009 14:18:00 +0000

Recently The MacGuffin asked for evidence of peer-review of a 2007 JAMA article showing the efficacy of Topiramate in treating alcohol dependence. I ran down 10 quotes from some papers citing the work.

"Topiramate has demonstrated efficacy in the treatment of alcohol dependence in two placebo-controlled trials." (Garbutt 2009; Johnson et al., 2003; Johnson et al., 2007)
"a 14-week placebo-controlled trial of 300 mg per day of the anticonvulsant topiramate reported up to a 16% reduction in heavy drinking days, although the rate of modest side-effects was high." (Schuckit 2009; Johnson et al., 2007)
"Medications such as methadone, buprenorphine, and naltrexone are beneficial for the treatment of heroin addiction and naltrexone and topiramate for the treatment of alcoholism." (Chandler, Fletcher & Volkow 2009 ; Johnson et al., 2007)
"The results of this study support the efficacy of topiramate in the relapse prevention of alcoholism." (Baltieri, Dar, Riberio & de Andrade 2008 from Abstract)
"Results of published trials are promising, showing efficacy for drinking outcomes and quality of life as well as general safety." (Olmsted & Kockler 2008 from Abstract)
"Topiramate is the best studied of the anticonvulsant medications that have been evaluated for the treatment of alcohol dependence. It has been shown to be effective in reducing a variety of drinking outcomes among alcoholdependent patients (see table 3 for
mechanism of action) in both a singlesite study (Johnson et al. 2003) and in a randomized, placebo-controlled, double-blind, multicenter trial (Johnson et al. 2007)." (Arias & Kranzler 2008)
"Both topiramate and naltrexone were efficacious in the treatment of alcohol dependence, and the treatment costs were similar. There is a trend for topiramate to be superior to naltrexone on critical measures of drinking; however, the study did not have adequate statistical power to establish this fact." (Florenz et al. 2008 from Abstract)
"Topiramate compared with placebo significantly (P <.05 for all comparisons) decreased obsessional thoughts and compulsions about using alcohol, increased subjects psychosocial wellbeing, and improved some aspects of quality of life, thereby diminishing the risk of relapse and longer-term negative outcomes" (Johnson BA 2008)
"Interestingly, topiramate – an anticonvulsant compound that blocks AMPA and kainate receptors, in addition to having other sites of action – reduces relapse rates in alcohol-dependent patients and the harm of excessive drinking (Johnson 2003). Moreover, in a recently published study, continuously drinking alcohol-dependent patients reach their abstinence goal significantly faster when treated with 300 mg/day topiramate compared with placebo (Johnson 2007)." (Spanagel & Kiefer 2008)
Lastly, it's not a direct quote, but in JAMA 299(4) there are three letters to the editor with negative criticism of the Johnson 2007 publication, and two responses to those ciriticisims (one from Johnson).

Johnson, B., Rosenthal, N., Capece, J., Wiegand, F., Mao, L., Beyers, K., McKay, A., Ait-Daoud, N., Anton, R., Ciraulo, D., Kranzler, H., Mann, K., O'Malley, S., Swift, R., & , . (2007). Topiramate for Treating Alcohol Dependence: A Randomized Controlled Trial JAMA: The Journal of the American Medical Association, 298 (14), 1641-1651 DOI: 10.1001/jama.298.14.1641

Reading List: Evolutionary Psychology: The Emperor's New Paradigm

noreply@blogger.com (Mitch) — Sat, 28 Feb 2009 18:06:00 +0000

I've always been suspicious about Evolutionary Psychology, and David Buller is as well. Let me be clear, I don't doubt evolution; I doubt in the methods and results ascribed to evolutionary psychology. So in short this paper is preaching to the choir. Prepare for some rah-rah in this post.

Tangent: I think the title of this article is inflammatory, just as much as "Voodoo Correlations in Social Neuroscience." It comes as no surprise to me that when scientists engage in tearing down other scientists research, we do so with no lack of venom. Criticizing (destructive or otherwise) the science of others is half of what science is (the other 90% is statistical errors), and we need to have a thick skin about it.

"Evolutionary psychology is an approach to psychology, in which knowledge and principles from evolutionary biology are put to use in research on the structure of the human mind. It is not an area of study, like vision, reasoning, or social behavior. It is a way of thinking about psychology that can be applied to any topic within it (Cosmides & Tooby 1997)."

This definition sets up the paradigm of evolutionary psychology (EP) with the goal to analyze human behavior as an adaptation that would have helped our ancient hunter-gatherer kin survive or reproduce. This seems logical enough, but how could this be science? In review of The Method, we see that logical observation is only half of the equation, and that relevant and testable explanations are also required (Copi 1982). In this paper Buller examines three 'discoveries' of EP and suggests that they are not sufficiently supported by evidence.

The Cheater-Detection Module

If altruism is an evolved adaptive behavior (a vampire bat regurgitates excess blood for others to eat so that when times are lean others will recipricate the behavior), then cheating would also be adaptive (vampire bats that do not regurgitate blood), and thus cheater-detection would be required for altriusm to remain an adaptive behavior (vampire bats that don't regurgitate for fat bats hording all the blood).
EP would then like to apply such a logical progression to human altriusm and the evolution of a cheater-detection module, and that this module would focus on social interactions. By manipulating the content of situations (social and otherwise) presented as part of the Wason selection task, EP researchers have shown results that appear to support this idea. Unfortunately, as Buller illustrates, the manipulations used were flawed at least linguistically if not also logically; by making the situation a social interaction researchers also changed the logical type of the situation from indicative (if statements) to deontic (must statments). Results: inconclusive.

Sex Differences in Jealosy

The thoeries from EP are that men are more concerned with sexual infidelity since his offspring would have to compete with another male's offsprings for maternal care. Likewise, women are more concerned with emotional infidelity since her mate might withdraw praternal care from her and her offspring. Thus men respond to sexual cues of infedility while women respond to emotional cues. EP researcher David Buss gathered survey data froma questionaire on infidelity to support this theory. And while it did show that men care more about sexual infidelity than women, it did not show that men cared more about sexual infidelity than emotional infidelity. Additionally female sexual infidelity is more (compared to males) indicative of general relationship dissatisfaction and is more likely to result in abandonment. So the percieved threat of the infidelity may be the cause of the sex-difference, rather than an adaptive behavior. Results: inconclusive.

Discriminative Parental Solicitude

EP suggests that substitute parents are more likely to engage in dangerous parenting than genetic parents. I'll restate that: Step-parents are more likely to abuse their kids than biological parents. This seems to be the best support by the available data (conservatively step-children are 8 times more likely to be physically abused). But the problem is that the data are confounded. Invariably these data come from offical state records, and unfortunately state records only note about half of the fatal maltreatment of children officially. Also, state child-protection workers often use the pressance of a step-parent as a diagnostic indicator of abuse, durther biasing the data. Results: inconclusive. In the interest of full-disclosure: I'm a step-father.

I'll close here with a direct quote from this paper:

"Thus, although the Evolutionary Psychology paradigm is a bold and innovative explanatory framework, I believe it has failed to provide an accurate understanding of human psychology from an evolutionary perspective."

D BULLER (2005). Evolutionary psychology: the emperor's new paradigm Trends in Cognitive Sciences, 9 (6), 277-283 DOI: 10.1016/j.tics.2005.04.003

Reading List: The ontogeny of behaviour in the albino rat

noreply@blogger.com (Mitch) — Tue, 17 Feb 2009 16:30:00 +0000

This article is in the section of classics that I am to reading for qualifying exams. It is certainly well cited, Google Scholar lists the citation count at 213! Indeed this paper was a "Citation Classic" in Current Contents in 1981. At the time Robert Bolles was still living and stated:

"I have always believed in the idea that experimenters should look at their animals...the human eyeball is the instrument of choice if you want to observe a new phenomenon, and particularly if you want to gain a new understanding of it."

In fact this article describes qualitatively the behaviors of infant rats from birth to about 24 days (rats are weened at day 21). In the first experiment, Bolles and Woods observed 13 litters with an average of 9 pups (117 pups) in their "natural" laboratory environment (cages). The animals were of the Sprague-Dawley line, which is still used today. They did use several different methods of observation and schedules of observation to arrive at a comprehensive guide to the ontogeny of lab rats.

They begin with postural observations, describing three postures that develop over time: lying, sitting and standing. Lying being the default resting position of the rat, often using other bodies for support. Sitting began on day 4 when subjects first began to lift their heads, and was fully developed by day 17 when subjects could sit and perform activities such as grooming. Also beginning on day 4 are the first attempts to support weight on the legs, and by day 10 the animals can support themselves. By day 13 they can run, by day 15 they can stand on three legs and scratch with the fourth. They can rear up on two legs with support for the front legs on day 16 and can rear independent of support (for the purpose of play-fighting with siblings) by day 18.

In similiar fashion reflexes are described. Without relating the specific timeline the reflexes are: twitiching, head waving, stretching and yawning, body flexion, righting reaction, freezing, sniffing, auditory orientation, and visual orientation. When describing startle response int he auditory orientation section there is a great footnote on the word "click:"

*The sound used was relatively well-controlled and constant, but, unfortunately rather poorly defined; it was the sound of a Parker T-Ball Jotter pen being retracted at a distance of approximately 1 foot.

Psychologists are hilarious. Also found it interesting that the animals did not freeze in fear until day 26 and they froze for approximately 15 seconds. I've never seen my rats hold still for that long unless they were sleeping.

Following reflexes functional activities are described. Here is the list: sleeping, consumatory behavior, locomotor activity, climbing, grooming, exlporation, manipulation, digging, and defacation. Here the theme of development was similiar as above, with rudimentary non-functional behaviors appearing first (such as scratching motion without making contact with the skin), that later developed into full-fledged adult-like behavior.

Ultimately we get a description of the social behaviors in the observed rats. Social behavior in young rats is evidenced by chasing and fighting. Bolles, and Woods observed rats begin this social play-fighting on day 14 when their eyes began to open.The activity peaks between day 20 and 30 when the whole litter engages in a high level of activity.

In a second experiment Bolles and Woods attempt to quantify the behaviors they observed in the first experiment. Using experimental methods the authors observed 12 rats (2 each from 6 litters) and summarized their behaviors as percentages. Here is Table 1 from their paper. There are many more graphs showing the time course of the development of behaviors and it really is a fascinating reference, but I won't reproduce all of that here.

The first point of discussion and perhaps the most salient is that from these findings we can view rats as a far more social animal that might otherwise be considered. Begining early social interactions are to wrangle for nursing or comfort, and later become play fighting and chasing. AS the authors noted this social behavior likely leads to long lasting changes in the adult organism and "offers interesting possbilities for research in this area." (See the next 45 years of rat studies for more on these possibilities)

R BOLLES, P WOODS (1964). The ontogeny of behaviour in the albino rat Animal Behaviour, 12 (4), 427-441 DOI: 10.1016/0003-3472(64)90062-4

Required Reading for Science Majors Meme

noreply@blogger.com (Mitch) — Tue, 10 Feb 2009 21:34:00 +0000

From: Pleiotropy

Imagine: YOU are asked to assign a half-dozen-or-so books as required reading for ALL science majors at a college as part of their 4-year degree; NOT technical or text books, but other works, old or new, touching upon the nature of science, philosophy, thought, or methodology in a way that a practicing scientist might gain from.

Post your list, and forward the meme to a half-dozen-or-so other science-oriented bloggers of your choosing.

I'll give it a shot:

Soul Made Flesh by Carl Zimmer, this book made me want to study the brain.
The God Delusion by Richard Dawkins, I'm sure any pro-atheism book will do but this is the only one I've read, and really, why do you need to read more than one?
Elegant Universe by Brain Greene, this was required reading in my alchemy class (really) and while I still don't understand physics it is a great example of colliding paradigms in science.
Getting Things Done by David Allen, I hesitate to put this on my list, but managing a research project requires some organizational strategy and having none of my own I adopted GTD.
Bonk by Mary Roach, the science of sex should appeal to any science student regardless of discipline.
Frankenstein by Mary Shelly, I wanted to include at least one work of fiction as I think that to some extent we as scientists are driven by fiction. This book is as good as any for exploring bioethics and the impact of science on the human condition.

The science bloggers whose lists I'd like to see are:

The Loom
Of Two Minds
Science Geek Girl
Urban Science Adventures
Perogative of Harlots

Reading List: Gonadal Hormones Humour the Brain

noreply@blogger.com (Mitch) — Mon, 09 Feb 2009 16:47:00 +0000

Every field of biological research seems to have a development similar to that of European architecture: from classical simplicity to the floridity of high Gothic or Baroque, before resolving back to simplicity." (Altman 2004)

What a brilliant opening sentence. This article is the summary of a conference held in Paris to discuss the endocrinology and the brain. The crux of the matter is that endocrinology is very complicated.

The first complexity examined is that of the multiple molecular pathways by which Activin and Inhibin stimulate and inhibit Follicle-stimulating hormone (FSH) secretion. Inhibin and Activin are peptide hormones produced in the ovaries and pituitary. Activin, binds to a activin receptor (ACTIIR), which conjugates with ALK4 (another type of activin receptor) stimulating a serine kinase activity, which via intracellular Smad proteins regulate the activities of target genes. Ultimately resulting in the release of FSH. Of course, inhibin can bind to ACTIIR to arrest this process, but unfortunately inhibin has a lower affinity than activin for ACTIIR so at best it is a partial-antagonist. Unless of course betaglycan is present on the surface of the cell in which case it will work with inhibin to become a full-antagonist to the ACTIIR, preventing activin from binding at all. In short, this system prevents over-stimulation of FSH secreting cells (which could cause tumors), while providing flexibility as to which cells are inhibited by inhibin (via the presence or lack of betaglycan).

While it is probably infringing for me to reproduce a flowchart from the paper showing the routes by which estrodiol effects various genomic processes in the body, I'll tell you this: the chart has 31 arrows and at least 15 boxes. There are two receptor sub-types for estradiol, ER-alpha and ER-beta. These receptors have a wide distribution throughout the brain and appear to have overlapping regulatory influence, although ER-alpha dominates the pituitary, and ER-beta alone effects cerebral circulation.

Estrodiol aslo has non-genomic effects such as regulating (with testosterone) the production of microtubules that regulate the outgrowth of neuronal branches. It also alters the functionality of enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) altering it's role in the release of dopamine. Also estrodiol changes the flow of sodium and potassium channels in the ventromedial hypothalamus and in the striatum it blocks calcium channels that regulate the release of dopamine.

Not only do gonadal hormones effect neurotransmitter release but the converse is true, and is evidenced in puberty. There is an immensely complicated interaction between neurotransmitters, hormones, glial cells (and their factors), and gonadotropin hormone-releasing hormone (GnRH) during puberty that results in sexual maturity. The flowchart for this interaction has 27 bubbles and 23 arrows (and some non-arrow connecting lines too). The paper does mention a selection of these molecules and how they interact, but the changes the bring about puberty aren't entirely clear as of yet.

Just as the gonadal hormones effect physical sexual development, they are also involved in regulating sexual behavior. Estrogen enhances motor activity, and as the text points out, "when an intact female mates with a male in an arena that has a place for her to escape from the male’s attentions, she slows down the male’s ardour by removing herself from the action at regular intervals." This motor activity stimulates the release of progesterone from the corpus luteum and increases the chance of successful impregnation. And dopamine released just prior to copulation reinforces this behavior. This interaction of estrogen and dopamine may also be implicated in the predisposition for females to become addicted to cocaine (a drug which enhances the dopamine reward circuit in the mid-brain) faster and at lower doses than males.

Estrogen is also implicated in brain health during old age; it stimulates the production of brain-derived neurotopic factors (BDNF) that prevent cell death and protect against free-radical damage. While hormone replacement therapy (HRT) for post-menopausal women may help, part of the problem is cellular insensitivity to estrogen in old age. Apparently this is due to astrocytes no longer reducing glial acidic fibrillar protein (GFAP) levels in response to estrogen.

Lastly the article the article discuses the role corticotropin-releasing hormone (CRH) in the HPA and anxiety. Binding of CRH to type 1 corticotropin receptors (CRHR1) in the limbic system appear to result in increased anxiety. Drugs that are CRHR1 antagonists did result in the reduction of anxiety but also caused liver toxicity, so clinical trails are on hold. But, CRH may also have neuroprotective effects; Alzheimer's Dementia patients show a decreased level of CRH. Stimulating CRH receptors in the cerebellum does appear to release BDNF which may be the mechanism by which mild stress is neuroprotective.

So in sum: it's complicated. But, with our current level of understanding, and the detail at which we can examine these molecular interactions, we might be moving to a more parsimonious understanding of gonadal hormones influence on the brain.

Jennifer Altman (2004). Gonadal Hormones Humour the Brain Neuroendocrinology, 79 (6), 287-295 DOI: 10.1159/000080045

Career Minded: Reading Groups

noreply@blogger.com (Mitch) — Thu, 05 Feb 2009 17:53:00 +0000

Reading groups are a great activity whether you are an undergraduate looking for ways to pad your CV and get good letters of recommendation, or a graduate student wanting to be more involved in your program. Seeking out groups that read, discuss and critique peer-reviewed articles is also a great way to immerse yourself in the literature of your field. In this post I will discuss three of the reading groups that I have participated in, as well as suggest some ways to choose and participate in these types of reading groups.

More...

BBoB: Blood Glucose Levels Before and After Cognitive Testing in Diabetes Mellitus

noreply@blogger.com (Mitch) — Tue, 03 Feb 2009 21:59:00 +0000

This month's BBoB was an article examining the consumption of glucose by diabetics during cognitive testing. Diabetics have difficulty utilizing the glucose in their blood, which might have a cognitive impact The researchers measured glucose levels before and after cognitive testing and subtracted to create a delta score. The researchers hypothesis states that those diabetics that consume glucose (have a large negative delta number) will also perform better on the cognitive tests compared to those diabetics that do not consume glucose (have a low negative, or positive delta number).

The authors used a statistical technique that I think is kind of shady. The first thing the authors did was to throw away 33% of their data. They seperated the partisipants into three groups based on their delta (glucose consumption) score. Low consumers, middle, and High consumers, and then they discarded all the middle consumers from any analysis. I understand why you would do that (to make your comparison groups more extreme) but it is an arbitrary choice and I think it reduces the validity of the results. Ultimately I think the data they have (two scale variables) would be better analyzed with regression. It seemed to me that they were trying to ask the question, "do changes in blood glucose level predict performance on cognitive tasks?" If that is the case then regression could be used to answer that question. Without having to discard the middle portion of data, AND without having to reduce the other cases into two groups.

That said, the study seemed also to deal with a relatively small and homogeneous group and while there may be something to find there, I think they went about it in the wrong way. I would love to see this study replicated in a larger sample with more representation, with regression as the statistical analysis.

They also used a depression inventory as a screening tool that I hadn't heard of before: the Zung depression test. I looked it up and it seems fine as such things go, but there are a lot of physiological questions (are you constipated, etc.) that I thought might possibly be confounded by diabetes (e.g. Constipation interferes with some diabetes treatments). That said the Zung is what a couple of other diabetes studies had used, so I assume that's why it was used here, and it was only a screener anyway.

Natalie Galanina, Vijaya Surampudi, Daniela Ciltea, Sant Singh, Lawrence Perlmuter (2008). Blood Glucose Levels Before and After Cognitive Testing in Diabetes Mellitus Experimental Aging Research, 34 (2), 152-161 DOI: 10.1080/03610730701876979

Qualifying Exams

noreply@blogger.com (Mitch) — Mon, 02 Feb 2009 17:38:00 +0000

This may I will be taking my qualifying exam to become an official doctoral candidate. It is a multi-day exam with both written and oral components. In preparation I have selected three committee members that will evaluate me, and they in turn have given me a reading list that I am responsible for. This reading list is massive (So far I have 72 papers and 12 book chapters), and so it will consume a lot of my time over the coming months.

So I am dropping some semester goals, and instead I will be blogging on these readings for the next few months. Hopefully some of them are interesting to you. I'm dropping my CUT and viscera goals for the semester as well replacing them with QUALS. So expect to see the first post tomorrow or Wednesday.

Final Salvia Preference Chart

noreply@blogger.com (Mitch) — Wed, 07 Jan 2009 16:03:00 +0000

I finally got around to making the final chart for the 1st segment (n=16) of my Salvia experiment:

As you can see, applying Chronic Mild Stress (CMS) to our rats led them to consume less sugar-water (in proportion to regular water) which is our measure of anhedonia (a common feature of depression). After three weeks we began injecting half of the rats with Salvinorin A (the active component of Salvia divinorum), while the other half recieved control injections. As we continued to apply CMS, the rats injected with Salvinorin A showed a renewed interest in sugar-water, while the control rats continued to sink into depression. This supports our hypothesis, and is consistent with the findings presented in Hanes (2001).

Reformatting my PDA

noreply@blogger.com (Mitch) — Tue, 16 Dec 2008 17:34:00 +0000

As I end this semester and prepare for the next, I have been reformatting my PDA. I wanted to be sure I was well organized for this next semester. What I usually do is carry around my data entry devices and take little notes, jot things down, draw pictures and diagrams on them, and whatnot. That way when I get back to my dock I can sync those up and have a good working environment for all my data. Also my Dock is the only place in my office where I get a cell-phone signal so I also integrate my cell-phone with my PDA. Here is a picture of what the Dock looks like now that I've wiped it clean and created some new folders.

This is, of course, a Hipster PDA, and it works great for me!

I carry around a stack of notecards that is bound with a binder clip (I keep another bundle in my lab coat pocket so I'm never without) and I jot things down. Most of the meetings I have with people are brief, and often impromptu, so having the ability to jot has proven very useful. When I get back to my office sometimes those jottings get pinned directly to the bulletin board, sometimes I try to reorganize them on a new notecard before I pin it up.

As you might be able to see my organizational rows (projects) are:

And these are the five areas I intend to put the majority of my effort into this coming semester. These also match up to five folders in on my computer, where all of my digital efforts are organized. The first thing I will do is defie successful completion of the project, and identify milestones that reflect progress toward that goal. That goes on the first note card. Then each week I make a ToDo list that will include a task from each group to move me closer to the next milestone. I'm not an innovator, my process has all been adapted from GTD which has been around for a while and there are plenty of blogs about that.

Salvia Week 5: Almost done

noreply@blogger.com (Mitch) — Fri, 12 Dec 2008 21:36:00 +0000

Well it's the penultimate week for this run of the Salvia study and things are looking good. Salvia rats have showed continued improvement in anhedonia, while control rats keep getting more depressed. The only problem in the data has been that gap between control and salvia at the outset of the experiment. This chart sums it up nicely.

Keeping it Blind

noreply@blogger.com (Mitch) — Fri, 05 Dec 2008 20:37:00 +0000

In any sort of study where drugs are administered you generally want to keep the researchers and the subjects unaware (or blind) of who is getting what. In medical research you often hear of the double-blind study in which neither the researchers or the subjects know if they are getting drug or placebo. In our study keeping the rats blind is easy, since we can assume they don't have conscious expectations of a drug affect We keep the researchers blind by assign rats to color groups (Red and Green for example) where no one who is doing a behavioral measure knows which color is placebo and which is experimental.

This was the first week for injections in our study. This week myself and two other graduate students did all of the injections because I was worried that it might be too obvious which animal was getting salvia based on behavior after injection. So this morning we did a little experiment to work that out. After injection the rats were taken to another room for 1-5 minutes while three other researchers observed the rats and made a guess about which condition (drug or control) the rats were in.

So we start by calculating the odds that they would be correct, which is 1 in 2, or 1/2 or .5
The total number of guesses is 48 (3 observers each made 16 independent guesses)
The average score (or chance score) we might expect is the product of these two numbers (48 * .5(, or 24.
The product of the odds of being right, by the odds of being wrong is (.5 * .5) .25
I'll take that product times the total number of guesses (48 * .25 ) to get 12
Now I'll find the square root of 12, which is 3.46
Now I take the Actual score (24) minus the average score (also 24) to get 0
Then take 0 divided by 3.46 ... Also Zero.

What I've calculated there is the z-score. If this value was greater than 1.96 then we'd have a problem. As it is, the observes were successful exactly at chance. If you are curious they would've had to get more than 31 (or less than 17) correct to have scored significantly better (or worse) than chance.

Short story: Researchers blind to the injection cannot predict which drug was injected based on the rats post-injection behavior. So, next week undergraduate researchers will be performing injections.

Maybe there isn't a problem?

noreply@blogger.com (Mitch) — Mon, 01 Dec 2008 04:04:00 +0000

So as you saw in my last part there is an unusually signifcant difference between the control and the salvia group even though we haven't yet begun administering salvia. There are actually two other divisions in our stress-rats that should have no difference. I thought because the divisions are independant of each other it might help reveal the confound. I didn't do any stats on these, just graphed it out and did a spot check since creating these simple graphs is ... well simple.

In this first graph I've seperated the rats by the undergraduate researcher (3390) to which the rats are assigned. And you can see that while in the first week there seemed to be a difference, this has disappeared in subsequent weeks.

In this next graph we see the rats seperated by their schedule group:

Uhm, so... if there was an over representation of "Group A" in the "Control" rats that could explain things. And there are (There are 5 A rats in Control and only 3 in Salvia)! So, for some reason "Group A" is not as effective at CMS as "Group B." The difference between group A and B is merely scheduling of the pairing and tilting stressors since we don't have enough space or apparatus to do all 16 rats simultaneously. I think this is easy enough to correct, as I can simply switch the schedule each week. Or maybe adjust some other elements of the schedule.

Salvia Week 3: New charts for sad rats

noreply@blogger.com (Mitch) — Sat, 29 Nov 2008 03:57:00 +0000

This week we have clearly established group anhedonia. The difference between 24 hour sucrose preference between week 1 (Mean = 66.35%) and week 3 (Mean = 58.38%) was significant, t(29.99) = 2.06, p = 0.048. So that means that the group of rats is depressed. But there is a strange hitch. The 24 hour sucrose preference averages across all three weeks for the control rats (Mean = 67.90%) was higher than the rats that will be getting salvinorin A (Mean = 57.64%) which is significant, t(40.98) = 3.48, p = 0.001. And it is important to note that neither group has been giving any treatment yet, they are all house in the same area, and no one who is doing anything with the rats knows which is which. So... I guess I suspect it is Type I error, but it is significant at a really low alpha. This next week I'll go through all of our procedures and try to find what is causing this anomaly.

In any event I promised an R chart. You really need to click it to see it correctly. This graph shows the three weeks of 24 hour sucrose preference by group:

Salvia Week 2: Depressing the Rats

noreply@blogger.com (Mitch) — Mon, 24 Nov 2008 16:04:00 +0000

This week we are starting to see the first signs of anhedonia in our rats. Five out of our sixteen rats have shown a clear lack of interest in sucrose this week. For the sake of anonymity I will refer to these rats as John, Pete, Paul, George and ... Ringo. Here is a table summarizing their development of anhedonia:

The average decrease in consumption of sucrose for these five rats is 36.46 mL (S.D. 48.61), so I feel as though their anhedonia is progressing nicely. But of course it isn't really fair to cherry-pick data. The overall group averages are not yet significant:

The average decrease in consumption of sucrose for the group is -6.12 mL (S.D. 34.02). But of course they have another week or two of CMS to go before I would expect the group averages to reflect significant anhedonia, and there is a decrease in both consumption and preference so maybe they are just starting to loose their enjoyment of sweet things. Lastly here is a chart showing these five rats versus the group average:

Salvia: The First Bits of Data

noreply@blogger.com (Mitch) — Mon, 17 Nov 2008 15:40:00 +0000

Our first bit of data is establishing that our rats prefer sucrose to plain water. This seems like an obvious conclusion, but there are important considerations:

What concentration of sucrose should we use?
When should we measure sucrose consumption?
Will the rats be neophobic of the sucrose solution?
Should we use sucrose consumption or sucrose preference?

For the first a quick look at the other CMS papers that we've used to guide our CMS paradigm suggest a 1% sucrose solution. But then, what does 1% mean? One organic chemist suggested that we start with warm, but not boiling, distilled water and then add in sugar until no more will dissolve. This would be a 100% sucrose solution, then just dilute it with a ratio of 1:99 with distilled water to achieve a 1% solution. That sounds good, but then still other organic chemists suggested that we just use 1g per 100mL. Since we don't actually care about the solution except as a hedonic alternative to tap water, this second easier option seemed sufficient.

Several labs used food and water deprivation the night before then a measure of sucrose consumption after one hour of exposure to the sucrose solution (but not yet food). Unfortunately I fear that sucrose consumption might be motivated not only by pleasure-seeking but also by metabolic pressure. Other labs didn't use food deprivation as part of their CMS, and still others used a 24 hour measure of sucrose consumption in the presence of food. We've decided to do both. We will do the food deprivation the night before, then they will have 1 hour with the sucrose solution and tap water. Then we will return their food, and give them an additional 24 hours with the sucrose. This way we can compare the two methods for measuring anhedonia and in future studies make an empirically informed decision about which to use.

Rats, just like my five year old daughter, have neophobia; they don't like to try new foods. In rats this is a survival mechanisms since they can't regurgitate poisons that they might eat. In fact in our lab we have to expose rats to cheerios about a week before using them as a food reward. Fortunately, we have planned all along to use both a 1 hour measure and a 24 hour measure of sucrose consumption. So if our first hour measure shows relatively little consumption of sucrose, we can chalk that up to neophobia, but by the 24 hour measure I would hope they'd be over it. Or at the very least by next week,

Some CMS papers use sucrose consumption as the measure for anhedonia, still others use sucrose preference (ratio of sucrose consumption to water consumption) instead. At first I didn't understand why anyone would choose consumption over preference since the latter seems to capture a better picture of a change in behavior. But when discussing where to put two water bottles into our rats cages I started to understand. You see, if we put the sucrose where the normal water is, I would say that might make them MORE likely to drink from it when thirsty (due to conditioning), and the opposite would be true if we put the bottle on the opposite side. Ultimately we decided to randomize the bottle position to wash out this effect.

Results:

1 Hour:
Sucrose Consumption Mean(SD) = 22.61 mL (6.04)
Sucrose Preference = 51.79%
(Sugar Vs Water) t(25.28) = 0.88, p = 0.39
(Control Vs Treatment) t(12.28) = 1.77, p = 0.10

24 Hour:
Sucrose Consumption Mean(SD) = 90.67 mL (34.28)
Sucrose Preference = 67.06 %
(Sugar Vs Water) t(20.46) = 4.94, p < 0.001
(Control Vs Treatment) t(10.63) = .672, p = 0.52

Interpreting the results:

At 1 hour, there was not a significant preference for sucrose. This could be for a lot of different reasons, but as discussed above our assumption is neophobia. There was nearly a significant difference in sucrose preference between the control group and the treatment group, which would be bad at this point since we won't begin actual treatments on the treatment group for another 3 weeks. This one I'll chalk up to statistical anomaly.

At 24 hour we are looking much better. There was a significant preference for sucrose (67% of all fluids consumed were sucrose, which means they drank twice as much sucrose as water). Also there was no significant difference in preference between the treatment and control group (which is good).

For those who are interested in such things those are Welch's t-tests.

So far, off to a good start. I'll likely continue to post our anhedonia finding here from week to week.

Book Meme

noreply@blogger.com (Mitch) — Wed, 12 Nov 2008 14:06:00 +0000

Grab the nearest book:
Tabachnick & Fidell, Using Multivariate Statistics (5th ed.)
Open it to page 56:
Chapter 3, Review of Univariate and Bivariate Statistics
Find the fifth sentence:
Correlation is used to measure the association between variables; regression is used to predict one variable from the other (or many others).
Post the text of the sentence in your journal along with these instructions.
Don’t dig for your favorite book, the cool book, or the intellectual one: pick the CLOSEST.

No real danger of this being mistaken as the cool book.

HatTip: huayra's blog

IACUC Approved

noreply@blogger.com (Mitch) — Mon, 10 Nov 2008 23:36:00 +0000

My first experimental protocol has been approved by UMSL's Institutional Animal Care and Use Committee (IACUC). Whenever a scientist wants to conduct research ethics boards have to be consulted. Experiments with human subjects are reviewed by the Institutional Review Board (IRB), while research with animal subjects is reviewed by the IACUC. After a one month process, a full-review and two rounds of revisions, my protocol was approved, and we will begin this week!

I'm all for the OpenLab and as such I would like to share with you all the details of my experimental paradigm, but at the same time I have to consider the integrity of the experiment and security of our lab. As such I'll just give you a sketch outline of what we are doing, and I'll sprinkle in details as I continue to post about the progress of the experiment.

History

This all began about a year ago when I started reading up on plant (Salvia divinorum) and it's active ingredient Salvinorin A. In particular I was interested in articles in which this powerful kappa-opioid agonist had anti-noiceptive properties as well as possible anti-depressant effects. Around the same time a potential faculty member was giving a job talk in which she described an interesting model of depression that she used with her rats. And so I thought that this might make an interesting research question that our animal lab could answer.

With encouragement from my mentor, I started a more serious literature search in the spring. By the middle of summer I had put together what I thought was a good idea to blend the too interests into an experimental protocol and started writing on it. After several rounds of internal revision we submitted the protocol to the IACUC in September. They requested a full-review, and met in the middle of October, then requested that we address a dozen or so concerns. We did and now we are approved.

The Experiment

Our plan is to use CMS to model depression in rats as measured by anhedonia. Anhedonia is the inability to experience pleasure from pleasurable stimuli, and a common feature of human depression. In our rats we will operationalize this by measuring the amoung of sugar-water they drink in relation to tap water. Noramlly rats will drink 65-80% sugar water, but anhedonic rats drink only 50% (showing no preference for sugar water).

Once we have anhedonia modeled in our rats, we will begin drug treatment with Salvinorin A. We hope to see that this alleviates the anhedonia and treatment rats once again show a preference for sugar water.

For me there are several exciting things about this experiment above and beyond it being my first authorship of an animal protocol. I'm excited to introduce a new behavioral paradigm (CMS) to our lab. I'm excited to work with a compound that has been relatively under researched until recently. I'm also hoping that this experiment can help me develop a program of research that leads to a dissertation in good time. In any event, keep checking back for progress updates!

¿Dónde está la biblioteca?

noreply@blogger.com (Mitch) — Thu, 09 Oct 2008 01:31:00 +0000

The above is one of the few Spanish phrases I remember from Spanish I. I took the class in 1998 from Senor Hall at Vincennes University. There were 7 students in the summer session and 5 of them were Asian.

Anyway, thanks to DNLee over at Urban Science Adventures for pointing out this challenge:

Can you name 5 (or more) Latin-American Scientist? Latin-American Heritage Month ends October 15th.

Rules
1. Be sure to name their discipline or field.
2. You can't choose people from your own institution or company. (I may go soft on this one, this time)
3. You can't Google or use the internet to aid in your search. (But if you know someone is a scientist, but not sure what disciple, you can look that up).
4. You can consult textbooks, journals, and class notes.
5. You can ask others to help you brainstorm, but they can't use the internet just to get 5 names fast (see #2).
6. Living and deceased scientists are acceptable.
7. Links to or references about the named scientists are greatly appreciated. Let's share the knowledge, and list as many as you can, even if it isn't five.

Okay, here's what I got off the top of my head:

John Garcia -- Described Taste Aversion
Robert Rescorla -- Cognitive Psychologist that studied Classical Conditioning
Maranon -- Early physiologist / physiologist who worked on sympathetic nervous response and emotions
Naranjo -- Did some work with hallucinogens
Tomasello -- Cognitive guy who does language stuff

Unfortunately I'm not very certain about my list. Now that I've named them I did a web-search and found: Garcia was born in California, Rescorla doesn't look at all hispanic, Maranon was a Spaniard, and Tomasello was born in Florida. The only definate Latin-American is Naranjo who was born in Chile. Hey, maybe next year I'll do better.

Career Minded: Developing a Thick-Skin

noreply@blogger.com (Mitch) — Thu, 19 Jun 2008 15:20:00 +0000

Most of you are familiar with the light-side of science; designing empirical experiments, discovering new information, presenting data and crafting theories. But that is only half of the picture. There is also the often ignored dark-side of science; correcting flawed experiments, criticizing inappropriate data analysis, and tearing down the ideas of fellow scientists. Yes, the peer-review process is a harsh mistress but is equally important to the scientific process (some might argue more so) as its light-sided counterpart. As such, developing a thick-skin to the criticism of others, is a vital step for any developing scientist.

Criticism can come from peers, mentors, review-committees, editors, parents, the media, and anyone else who might be privy to your work. First we should begin with an operational definition of criticism, from Merriam-Webster we find: a critical (exercising or involving careful judgment or judicious evaluation) observation or remark. That sounds about right. We usually attach a negative connotation to criticism, but that's not necessarily the case. Criticism can come in many different forms, for example...

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Career Minded: Writing Your Curriculum Vitae

noreply@blogger.com (Mitch) — Fri, 13 Jun 2008 15:24:00 +0000

First time authors of a Curriculum Vitae (CV or Vita) can easily be intimidated by the task. If you've never created a resume' or even if you have, knowing what to write, and how to write, and even in which order to write your vita is a challenge. Hopefully this post can point you in the right direction and by the time you submit your graduate school applications you can have a polished looking vita. Or if you are already in graduate school, dig out the vita you sent with your application and update it with all you've been doing; someday you'll be applying for post-doctoral fellowships or faculty positions and you'll want your vita to look its best.

Absolutely everything goes in your vita and as your academic career unfolds you'll increasingly add to this document. But as an undergraduate (and even as a graduate student), your vita might be a little sparse. Don't worry we can beef it up a bit by including some info that you will eventually prune away. There are many sites about vita-writing, and I'm not sure I could do any better than them. But I can share with you the Vita I enclosed with my grad school applications. This is it. I'm not saying it is the paragon vita that you should strive for; it is more of a cautionary tale, but let's walk through the document and I'll try to explain why it is what it is.

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