Cortical Confusion.

Hair today-gone tommorow

2007-02-25T07:46:00.000-08:00

Below is a lift-off from an abstract from Behavioural Brain Research Journal, except of course for my enthusiastic cheering in blue.

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Group-housed laboratory mice are frequently found with their whiskers and facial hair removed. It has been proposed that dominant mice are responsible for barbering the hair of the recipient and early studies suggest that the hair is removed by nibbling.

In the present study, pairs of mice, composed of a barber and recipient, were separated to allow hair to regrow. The animals were then placed together in an observation box and their social behavior was videorecorded.

During grooming, one member of a mouse pair removed the vibrissae of the conspecific and did so by grasping individual whiskers with the incisors and plucking them out.

ouch ouch ouch

Although plucking appeared ‘painful’, recipients were passive in accepting barbering, and even pursued conspecifics for further grooming.

Pluck me baby one more time

Other measures indicated that barbers were heavier than recipients and brain weights were not different.

Like you need brains to do that

The results are discussed in relation to the hypothesis that barbering is an expression of social dominance, the origins of the barbering behavior, and the consequences of barbering on brain function.

Thats a post-doc option- Effect of barbering on brain function.

Reading this abstract I was reminded by the salon my sister goes to get her eyebrows plucked by a fat auntie....ummm ...why...

Scientist finds hunger strike effective

2007-01-15T09:22:00.000-08:00

In an example of reverse technology transfer, a leading stem cell researcher from MIT has used our very own indigenous techinque of hunger strike to further his own cause. Experts from India point out that this technique, when used in right concentration and with close physiological monitoring could be a sure shot success.

They also caution that it could cause serious adverse health effects in case of prolonged exposure. Many activist protest that an governmental ethics committe has to be formed to regulate and restrict these activities. Experts in the field say that this move is radical and is a double-edged sword (experts are not very creative and tend to use cliches a lot).

This scientist is suspected to have collaborative links with Trimul congress, which might have trained scientists in kundalini yoga, gemology and breath control technique, all very potent weapons for aural MRI, astral urology and to cure all cancers and the burning sensation one gets the morning after a very spicy meal.

Below is an article from TheScientist.com

An African-American associate professor of Biological Engineering at the Massachusetts Institute of Technology (MIT) has vowed to go on hunger strike if he does not receive tenure, alleging that it was denied because of his race.

James Sherley has been appealing the school's decision for nearly two years, and plans to camp outside the Provost's office starting on February 5 until he receives tenure.

"I will die defiantly," he said in an Email to colleagues, when asked about his plans if his protest becomes futile.

This is the first ever hunger strike in a tenure controversy.

Do you drive a big car ?

2006-11-23T04:09:00.000-08:00

Advertised with spray cans on abandoned buildings and government property is the wisdom that larger the car one owns the small is their reproductive organ. Initially intended to scare people off buying fuel guzzling SUVs by environmentalists (it used to be the best way until Bush fucked up Iraq, now they must be printing anti-SUV posters with massacred Iraqi children) this catchy has Darwinian undertones and supports an sperm competition theory.

All one has to do is make a small assumption that cars are analogous to horns on the head of the beetles, as in they serve the purpose of attracting mates. I don’t think this is such a great stretch. But just for skeptics, I would like to point to prevailing wisdom that the men with successful career get to mate more than unsuccessful ones, and a killer cars costs more which only successful men can afford. Also since in our society one can’t know a person if someone is actually successful by looking at his bank balance (OK. lets be materialist for a while, its easier to defend in evolutionary theory) one has to look at ‘markers’ for success. And that would be a fancy car or Armani suits. So these objects can be ‘weapons’ that help in attracting mates and securing a mating session.

Evolutionary theory predicts that organisms have limited resources that they can decide to use between having betters weapons of mate attraction and having better testis size. This was experimentally proved by group of scientists working on a genus of horned beetle. By cauterizing a group of cells in the larval stage, which would later become horns, they engineered beetles without horns. They found that they cauterized males has disproportionately large testes.

It doesn’t sound very intuitive to think that resources that can be used to further the genetic cause (sperm production) are diverted to make better weapons, which are for attracting mates. But one can argue that attracting a mate is the logical first step in furthering ones genes, but why does it have to be done at the expense of all important sperm production?

To think of this in terms of probabilities, what is the probability that an organism will be able to have an offspring with average attracting capabilities and very large amount of ejaculate? Is this probability lower than the probability of having offspring when an organism has lower sperm count and very large attraction capabilities?May be the weapons can influence the frequency of mating encounters and make up for the lower sperm count from lower resource allocation for testis. We dont know for sure if having bigger horns is better or bigger testis is.

The resource allocation conundrum that these organisms face seem to be a developmental phenomenon, where body parts that were closer in the larval stage have more competition for the same resources and resulting trade-off in their morphology. According to this theory the authors have predicted that the trade off effect would be more pronounced in species that have horns from their thorax rather than the head, as its farther way in the developing tissue.

But surveying the natural population of 25 species for this trade off between horns and testes, the authors did not find any significant relationship between the two. But other observations like evolution of an extra thoracic horn in species, which have less mating competition show that sperm competition constrains origin of new horns.

This paper gives a fascinating insight into development of secondary sexual characters and the important role it plays in sperm competition and evolutionary success. Also the perplexing thought that evolution has to choose between male investment in gaining matings and fertilizations.

Got Milk? They make good fire bombs.

2006-10-30T23:29:00.000-08:00

Mystery of the exploding custard factories explained.

Science experiments in school have always been boring. Uninspiring teachers and rude attenders make it real hell. I have always felt lost, bored, clueless, an intense desire to burn the place down etc etc...But in a quest to make experiments a little entertaining in school, a teacher demonstrated the hidden explosive power of innocuous looking milk powder(see pics in link). He sprinkled milk power on an open flame which made the powder explode into a big fireball several meters high.

Apart from the entertainment value and the noble agenda of attracting bright kids into science, this demonstration also explains the risk of storing of powdered material in large scale and the fact that reactivity of materials is related to its surface area. Milk (custard powder also) is not combustible in liquid form, but when dried and powdered more of its area is exposed to air making it combustible.

See the explosive experiment in the series of pics in this link

http://observer.guardian.co.uk/flash/page/0,,1927850,00.html

Vervet monkey and George Bush

2006-10-16T13:28:00.000-07:00

An eariler post discussed the intricacies of the blue-balls of vervet monkeys. These monkeys have a lot more in common with humans; hypertension, anxiety and alchoholism. Their alcoholic behavior has a startling parallels to human behaviour and is being studied as an animal model for alcoholism. Some of the similarities are....

1. They don’t have to be trained to drink alcohol.

2. They drink only alcohol when they have access and won’t stop till they have are intoxicated or in comatose state.

3. When a social drinker they prefer their drink with sweetened liquid.

4. Once heavy drinkers they prefer to drink with water and drink more during the day.

5. After a period of alcohol deprivation, they come back to the bottle with a vengeance and drink in 4 hours what they drink in 24 hours.

6. They drink local rum without any pairing or with sweet taste (yeah cocktails are for wussies).

7. They prefer to drink between 4 PM to 8 AM.

8. They drink to the point of heart, liver and intestinal damage.

Watch this clip, its pretty funny.

http://www.youtube.com/watch?v=ZYuIYNaKynI

Fold me baby one more time

2006-10-16T13:01:00.000-07:00

I washed and hung my full-sleeved shirt to dry. The toughest part of washing ones clothes is to get them folded after the afternoon sun crisps them. I labor at it every week to get those unwieldy clothes into order, but I never get better at it. That’s when I realized that I have a folding problem.

It turns out that it’s not that uncommon at all. Proteins that run the cellular household have to be folded into intricate shape to make them active.. If they aren’t folded properly the result can be disease like Alzheimers. Likewise DNA has to be folded into a helix, so folding is that trivial afterall.

In everyday life, airbags have to be folded, large lenses have to be folded, fit into spacecrafts and sent to space. Stents have to folded and sent into arteries and unfolded at the right places to remove a clot. Parachutes have to be folded. Basically these are design problems; things have to be folded into smaller dimensions.

This is what the ancient Japanese time pass, origami does. I used to think it was a useless pursuit folding neat sheets of papers into shapes, but one physicist, Robert J. Lang formerly with Caltech has made Origami into a precise science. He has written a program, which will generate complex folding patterns and give the exact location of the folds on paper. His work puts mathematical foundations to origami, in the patterns and locations of folds, spawning new disciplines like Computational origami and Origami mathematics. His algorithm gives efficient and the best way to fold complicated shapes like a dinasaur.

Now he is a full time origami artist and also works as a consultant for many companies and research organizations on their folding problem.

Check out his website

http://www.langorigami.com/

Now I have to go and fold my starched white full sleeve monster.

Neuroscience and Sex

2006-09-27T10:55:00.000-07:00

Faculty position: Neuroscience and Sex. at Kinsey Institute, Indiana University.

These people want someone who is proficient in both neuroscience and sex. I am afraid I am short in experience and training:-)

http://www.kinseyinstitute.org/research/facultyannouncement.htm

I almost got fooled by the heading:-)

Check out the video collection in their library. This might be the only library where they have to regulate large enthusiastic crowds of graduate students coming for 'research'.

Ranulfo Romo

2006-09-27T10:02:00.000-07:00

The recent issue of PNAS (Sept 2006) has a profile of Dr. Ranulfo Romo. He has made some exciting advances in the understanding in the area of neural basis of perception, decision making and sensory representation working on the somatosensory system.

This profile follows his induction in the prestigious National Academy of Sciences. Its rare to find scientists working on perception and decision making the somatosensory system, as most of the information about such basic attributes of the brain come from studies in the visual system. Somehow information about him was difficult to find in the web (apart from his HHMI page) so this profile would be useful for people interested in his work.

Here is the link
http://www.pnas.org/cgi/content/full/103/39/14263

Guilt Laundry

2006-09-16T11:17:00.000-07:00

Grandmothers have a keen insight into human nature, accumulated by years if idleness and general whining. My grand mother firmly believes that taking a dip in the holy river of Ganges absolves one of all wrong doings. Her conviction is similarly strong for the south Indian ritual of tonsuring one’s head. Many of my relatives have made that trip to a church leaving them unfashionably bald for a week and even more unfashionably stubble-headed for a longer time. People who go through this act of cleansing/tonsuring vouch for the feeling of a their guilt being reduced.

In the realization of a ‘wrong-doing’ a strong desire to correct the wrong deed arises. In the event of it being irreparable, despair and guilt arises. This guilt can affect the behavior of the person and can also lead to depression. So one turns to religious/cleaning rituals to deal with the guilt and go back to a morally sound self-image.

And God thrives on guilt, in a completely helpless situation; religious rituals, however irrational they are give a feeling of relief and forgiveness from the wrong deed. This belief is so deep rooted that the very act of cleansing like washing or tonsuring can give a feeling of relief to the person, although the wrong doing has not been undone. This psychological pairing of the physical act of cleansing and mental state of being morally pure was investigated in a study reported in Science.

In one of the studies the authors wanted to connect the morally compromised mental state with the need for physical cleaning. Subjects were asked to hand copy a story, either an ethical one or an unethical one, and later asked to evaluate the desirability of objects, some of which were cleaning products and others were neutral products. The subjects who copied an unethical story rated cleansing products as more desirable consistently than the other objects. These subjects also preferred to take cleaning products like an antiseptic wipe as free gifts over other gifts like pencils.

Does physical cleaning restore the self-image of moral purity of the subjects? A guilt-ridden person is likely to compensate for his wrong doing by doing altruistic and penitential acts, like volunteering. Have the people who have undergone the physical act of cleansing recovered their morally pure mental state, would that make them less likely to volunteer for an altruistic job? It seems from this study that it did. Subjects were asked to describe an unethical deed from the past and only one group was given an antiseptic hand. Both groups were then asked if they liked to volunteer a student in need of help. Less number of subjects in the group that has washed their hands volunteered than the other group.

For the reasons and importance of this study, I will quote the authors

Would adherence to a rigorous hygiene regimen facilitate ethical behavior? Or, would cleansing ironically license unethical behavior? It remains to be seen whether clean hands really do make a pure heart, but our studies indicate that they at least provide a clean conscience after moral trespasses.

On a personal note, I have never trusted anyone who exhibit excessing cleaning behavior. May be they are subconsciously trying to clean their guilt of some super sin that they have commited. By the same (flawed) logic, I live like a slob, I feel no need for cleaning, hence I have commited no sins:-)

Link to Gordon Sheperd interview

2006-09-07T02:32:00.000-07:00

I found an interview of Prof. Gordon Sheperd at the IBRO website. GS is a special man, as he is one of the few who has a brilliant scientific career and has written an influential basic textbook. His 'Neurobiology' was the first neuroscience text book I read (and thoroughly enjoyed) in the dusty Loyola College library.

Click on this link for a scientific and personal interview.

If the hyperlink doesnt work here is the URL http://www.ibro.info/Pub_Main_Display.asp?Main_ID=550

Manesar Premier League

2006-09-04T12:59:00.000-07:00

Oh the red, that many fight for. That tastes better to some than others.

The winning captain with the coveted bottle of wine.

The winning team. The Theoretical Thunders. OK. I admit its a lame name. But they didn't look very lame when they pumped in 5 goals on the favourites.

The three captains Leslee (systems ,white), Buddha (theoretical, black) and Sandy (Molbio, Red) with the referee, Manoj Uncle of stem cells fame(Grey T). Without his no-nonsense and professional approach this tournament would have lost all decency and would have become a kickboxing convention.

(I wonder what Sandy is all cheerfull about. Atleast I had the weekend to forget my pain).

Two (of the three) things that rock my fucking world. I will give away one free inflatable sheep to anyone who comments with the correct answer to what's the third.

Who're you trying to scare. Bitch.

Pepsi helps bring in the crowds.

Practice. Untill November comes.

Port wine on wet grass. Buddha Laughs his way to help himself to some more chicken

2006-09-04T12:57:00.000-07:00

It became clear when the Buddha laughed on the green grass with a bottle of port wine that the battle was won, convincingly, leaving the opponents search for excuses and ice to numb their pain. Sprays and creams didn’t work, because the pain was somewhere deeper. This battle had gone awfully wrong for a group with vociferous supporters, for the other this was the end of a roller coaster ride, a ride that took them to the depths of despair, kicks on the shins inflicted by their own boots, and ultimately the sweet and poetic victory of the underdogs, the written-offs over the over-confident and the under-smarts (is that a fucking word, but that’s how I can describe my team in mild terms).

So it all started in a rather dull mood before the ball was kicked, with murmurs that the weekend break cooled down the insanity of football supporters. It was like having foreplay and taking the weekend off to have sex. But people who know what I am talking about will know that this break can make one mad and change the normal course that was indicated before the break. OK I will leave the sex analogy alone. I don’t want people to falsely accuse me of talking about sex all the time.

But when the ball was moved from the central spot, there was something different in the way the game was defining itself. The Molbios were lacking in something, passes were awry, strikers came to the spot seconds after the ball passed by, defenders gave away passes. Everyone seemed like they had just woken up after partying with the Rolling stones the previous night.

Whatever the Molbios were lacking, the computationals excelled, their trio of Buddha, Jyoti and Vishnu make great short passes, held the ball and passed it around and found the net they did, not once but five fucking times. There was nothing but silence and awe, apart from the munching of chips and samosas in the audience who came to see another routing of the computational dudes by the Molbios, like the opening 3-0 drubbing.

It was raining goals, everyone made merry, Buddha, Jyoti, Vishnu and Venkat on the once infallible opponents. When the first goal was scored by computational, the molbios conceded that they were in trouble, shoulders were drooping, basic trapping went wrong and passes missed by miles. By half time there was no cohesion in their game, just anger and disbelief. It was then easy for the computationals with experienced and intelligent players to capitalize on this lack of confidence to dominate the game completely. Only a late resurgence saw some kind of fight back, which resulted in a late Sandy goal. Just once did Sanjay let the ball go past him and especially on wet grass, this was a tough job.

All is well that ends in a flurry of goals, so the first tournament in the Manesar Premier League was a roaring success. Until the next one comes along to whip some enthusiasm in the rural hinterlands of Haryana, this 5-1 unlikely victory by the Computational Biologists will be talked and deconstructed many many times.

So long…until November.

The ‘sour-less’ mouse that solved a tasty mystery.

2006-09-03T13:40:00.000-07:00

Our brain constructs a perception of taste from the food we eat. Foods that taste similarly also have some chemical commonality. Actually they taste similar because they have a common chemical group. For example sugars have a glucose moiety, which will be sensed by specialized cells in the tongue, which fire electrical impulses to the brain, which in turn constructs a percept of ‘sweetness’. We perceive many different tastes of which the main basic types are sweet, bitter, sour, salty and umami (taste of monosodium glutamate).

We are able to digest far more chemical groups than the number of tastes we perceive. Why evolution gave us only these five basic tastes is debatable. (I would have liked finer taste discrimination for humans, sometimes Old Monk and Old Cask tastes similar, although I know in my heart of hearts I know they are not). Actually biochemists get into a philosophical argument with psychologists about taste classification, the latter don’t believe in such a classification casting doubts on the physiological basis of such a classification.

The five main basic tastes are thought to signals important information about the food we ingest. Sweet taste is an indicator of how ripe a fruit, which contains more nutrients that raw fruits. Bitter is a good indicator of whether a fruit or plant is poisonous. It makes good sense to evolve a mechanism to know ripe fruits from raw ones and poisonous from non-poisonous. Salty taste evolved probably as an indicator of salt intake since animals have to maintain salts levels to maintain homeostasis and sour taste is elicited by acidic pH, which is abundant in rotten and unripe fruits, which has to be avoided by animals.

Most of the tastes have been well studied in terms of the cell types that sense the molecules and the mechanism that senses these chemicals and makes the cells fire electrical impulses. But the mechanism behind the sour taste was speculative till last week. Some believed that sour and salty taste shared a common mechanism of detection. Many hypotheses were put forward, but there was no proof for anything.

With the Human Genome Project available to fish for genes that could have specific properties, a group at UCSD did just that, fishing out an ion-channel gene that would sense pH (and hence acidity). They found one a gene called PKD2L1. They found that this gene was present in subset of cells in the tongue, which were not sweet, salt or bitter sensors, making it a prime candidate for acid sensing in the tongue.

Now that the cells are found in the tongue, the next question is, what do these cells do? (They could be cells that produce bad language for all we know). So these scientists selectively killed the cells that expressed this gene in mice and tested these animals for their ability to taste. These animals were unable to taste sour taste, although their capacity to detect other tastes was intact, including salty taste. This showed that these cell types were exclusively responsible to the detecting sour taste only. (Wow so neat.)

Adding further feathers to their hats, the group found that these ion-channel genes were also expressed in the central canal of the spinal cord (the small hole that runs through the middle of the spinal cord, where the cerebrospinal fluid runs through). This fits into an even older story. The acid sensing mechanism is important in many ways to an organism, to maintain the functional state of body fluids. For example pH is the way to detect the carbon-di-oxide levels in blood and CSF. The cellular basis of pH sensing mechanism is not known in the CSF. This ion-channel PKD2L1 could be the mechanism that senses pH in CSF being expressed in the edge of the central canal and also firing action potentials for minor changes in pH.

Ten Simple Rules for Getting Published

2006-08-23T02:30:00.000-07:00

Philip E. Bourne, a computational biologist at the department of Pharmacology at UCSD published 'Ten Simple Rules for Getting Published' in PLOS computational biology. I think the list is also relevent to Neuroscience too. This list is intended for young grad students who are mostly first time publishers, so here it is..

Rule 1: Read many papers, and learn from both the good and the bad work of others.
It is never too early to become a critic. Journal clubs, where you critique a paper as a group, are excellent for having this kind of dialogue. Reading at least two papers a day in detail (not just in your area of research) and thinking about their quality will also help. Being well read has another potential major benefit—it facilitates a more objective view of one's own work. It is too easy after many late nights spent in front of a computer screen and/or laboratory bench to convince yourself that your work is the best invention since sliced bread. More than likely it is not, and your mentor is prone to falling into the same trap, hence rule 2.

Rule 2: The more objective you can be about your work, the better that work will ultimately become.
Alas, some scientists will never be objective about their own work, and will never make the best scientists—learn objectivity early, the editors and reviewers have.

Rule 3: Good editors and reviewers will be objective about your work.
The quality of the editorial board is an early indicator of the review process. Look at the masthead of the journal in which you plan to publish. Outstanding editors demand and get outstanding reviews. Put your energy into improving the quality of the manuscript before submission. Ideally, the reviews will improve your paper. But they will not get to imparting that advice if there are fundamental flaws.

Rule 4: If you do not write well in the English language, take lessons early; it will be invaluable later.
This is not just about grammar, but more importantly comprehension. The best papers are those in which complex ideas are expressed in a way that those who are less than immersed in the field can understand. Have you noticed that the most renowned scientists often give the most logical and simply stated yet stimulating lectures? This extends to their written work as well. Note that writing clearly is valuable, even if your ultimate career does not hinge on producing good scientific papers in English language journals. Submitted papers that are not clearly written in good English, unless the science is truly outstanding, are often rejected or at best slow to publish since they require extensive copyediting.

Rule 5: Learn to live with rejection.
A failure to be objective can make rejection harder to take, and you will be rejected. Scientific careers are full of rejection, even for the best scientists. The correct response to a paper being rejected or requiring major revision is to listen to the reviewers and respond in an objective, not subjective, manner. Reviews reflect how your paper is being judged—learn to live with it. If reviewers are unanimous about the poor quality of the paper, move on—in virtually all cases, they are right. If they request a major revision, do it and address every point they raise both in your cover letter and through obvious revisions to the text. Multiple rounds of revision are painful for all those concerned and slow the publishing process.

Rule 6: The ingredients of good science are obvious—novelty of research topic, comprehensive coverage of the relevant literature, good data, good analysis including strong statistical support, and a thought-provoking discussion. The ingredients of good science reporting are obvious—good organization, the appropriate use of tables and figures, the right length, writing to the intended audience—do not ignore the obvious.
Be objective about these ingredients when you review the first draft, and do not rely on your mentor. Get a candid opinion by having the paper read by colleagues without a vested interest in the work, including those not directly involved in the topic area.

Rule 7: Start writing the paper the day you have the idea of what questions to pursue.
Some would argue that this places too much emphasis on publishing, but it could also be argued that it helps define scope and facilitates hypothesis-driven science. The temptation of novice authors is to try to include everything they know in a paper. Your thesis is/was your kitchen sink. Your papers should be concise, and impart as much information as possible in the least number of words. Be familiar with the guide to authors and follow it, the editors and reviewers do. Maintain a good bibliographic database as you go, and read the papers in it.

Rule 8: Become a reviewer early in your career.
Reviewing other papers will help you write better papers. To start, work with your mentors; have them give you papers they are reviewing and do the first cut at the review (most mentors will be happy to do this). Then, go through the final review that gets sent in by your mentor, and where allowed, as is true of this journal, look at the reviews others have written. This will provide an important perspective on the quality of your reviews and, hopefully, allow you to see your own work in a more objective way. You will also come to understand the review process and the quality of reviews, which is an important ingredient in deciding where to send your paper.

Rule 9: Decide early on where to try to publish your paper.
This will define the form and level of detail and assumed novelty of the work you are doing. Many journals have a presubmission enquiry system available—use it. Even before the paper is written, get a sense of the novelty of the work, and whether a specific journal will be interested.

Rule 10: Quality is everything.
It is better to publish one paper in a quality journal than multiple papers in lesser journals. Increasingly, it is harder to hide the impact of your papers; tools like Google Scholar and the ISI Web of Science are being used by tenure committees and employers to define metrics for the quality of your work. It used to be that just the journal name was used as a metric. In the digital world, everyone knows if a paper has little impact. Try to publish in journals that have high impact factors; chances are your paper will have high impact, too, if accepted.
When you are long gone, your scientific legacy is, in large part, the literature you left behind and the impact it represents. I hope these ten simple rules can help you leave behind something future generations of scientists will admire.

I work with models

2006-07-30T03:27:00.000-07:00

I work with models. I have to get close to them, get personal and intimate with them. That’s part of my job. Sometimes my boss asks me to go slow or else I might scare them away, so I spend a few hours each day touching them, playing with them, stroking them, letting them get used to my body and odors (I don’t smell btw, I smell like Old Spice). I have also given nicknames to them; they eat out of my hand, literally. I have complete control over them. I control their sleep cycle, feeding. I have them under my wand; they do what I tell them. Sometimes I get emotionally attached (I am human after all), but my job demands me to be a cool-detached-objective guy. And I do it. For the greater good of mankind. I am selfless. I use my models with a cold-blooded planning and clarity. I choose them according to their attributes, some for their eyes, some for their inability to put on weight, some for their bodies, some for their heart. After I get what I want with them, I dispose them, carefully with love and tenderness with the most stress-free method available to me.

I want to share some info and photos of the more exotic models with whom my colleagues around the world work with.

Armadillo
Researchers have found that the core body temperature of the armadillo is low enough to favour the growth of the leprosy-causing bacterium Mycobacterium leprae. Using the armadillo, scientists have been able to develop a vaccine against leprosy, and one day these unusual South American mammals could help to provide a cure for the disease.

Bee
The natural products of bees, such as royal jelly, honey and even their venom, have been found to have significant effects in cancer treatment and prevention. The application of these products inhibited tumour growth and increased survival of the animals they were tested on. These results may lead to human clinical trials using royal jelly or honey, combined with chemotherapeutic agents

Hamster
An interesting use of hamsters in medical research is the study of the neural basis of our internal daily (circadian) rhythms – in humans this controls our sleep-wake cycle over a 24h period. The control centre for these rhythms was found in the hypothalamus of the brain, and the use of hamsters clearly demonstrated the role of the hormone melatonin in this daily cycle

Jelly Fish

These ocean creatures may have a painful and sometimes deadly sting, but they have proved to be very useful in scientific and medical research. Some researchers have used jellyfish to search for an effective anti-venom to save victims of Sea Wasp stings, whilst others are studying the chemicals in jellyfish for possible use in treating cancer. A bioluminescent chemical found in a type of jellyfish from the Pacific has already allowed doctors to trace the movement of specific chemicals through the body and could help reveal ways to inactivate defective genes, such as those in Huntington's disease.

Octopus
The Animals (Scientific Procedures) Act 1986 regulates scientific procedures which may cause pain, suffering, distress or lasting harm to "protected animals"; it refers to these as "regulated procedures". Protected animals are defined in the Act as all living vertebrate animals, except man, as well as one invertebrate species, the common octopus. The octopus was added 12 years ago after extensive discussion concluded that its well developed nervous system may make it capable of feeling pain. However, no regulated procedures have been carried out using the octopus since its inclusion

Quail
Research into head and facial development is an important use of quails. In one study, the embryos from both quails and ducks were used to implant neural crest cells (simple cells that arise very early in development) from one species into the other. The result was quails with duckbills or "duails", and ducks with quail beaks or "qucks". This suggests that head and facial diversification is due to neural crest cells, and further work should help to unravel the underlying causes of craniofacial defects, which are among the most common birth defects. Quails are also used to test the safety of agrochemicals in the environment.

Tamarin
Cotton-top tamarin monkeys have a high rate of spontaneous colon cancer. They develop colon cancer in a very similar way to humans, so investigations of whether colon cancer is heritable – as it can be in humans – are now a focus of research. Other monkeys used in research include macaques and marmosets, mostly in brain research and in safety testing of new medicines.

Vole
Voles are commonly used in studying social traits. A particular gene that produces a protein called vasopressin in their brains contributes to these behaviours. Adult male offspring with the long version of the gene have more of the protein in brain areas involved in social behaviour and parenting. These males tend to investigate female odours, greet strangers more readily and nurture their young. So variability in the length of the gene could help account for differences in normal human personality traits, such as shyness, and could perhaps influence conditions like autism and social anxiety disorders

I stole all info from

http://www.rds-online.org.uk/pages/page.asp?i_PageID=2096&i_ToolbarID=2

…go there for a complete list.

Magic mushrooms. - A tool to study the neurobiology of human consciousness?

2006-07-26T13:07:00.000-07:00

Back in the 60’s when Hendrix was setting fire to his amplifiers, people were really happy. Not just because he played some kick-ass rock and roll but they also had drugs, lots of it. Psychedelic drugs like mescaline (from cacti), LSD (synthetically produced) and psilocybin (from mushrooms) were freely used. Then the government had to clamp them down, they just can’t stand any part of the society have some fun. (Actually these happy unemployed music lovers with drug induced world view started turning in large numbers to anti-war rallies). Unfortunately this also meant an end to research on these substances which were regarded as a promising candidate for treating chronic pain and depression in terminally ill patients.

Quick jump to the beginning of the next millennium, when boy-bands are tearing up the scene, sending 15 year old girls into a crying frenzy every time they are seen in public and at the same time propelling sales of atrocious giant sized posters with their baby faces on them. People are sad, not because they don’t have good drugs (some genius boiled powder cocaine with baking soda to give the world crack) but the music truly sucks. But there is hope for the people who really need new drugs. No, not the aging ex-rock stars, (even David Bowie has gone clean and is the CEO of his own internet company), but the chronically ill and depressed thanks to a renewed interest in psychedelic drugs by the scientists.

In a double-blinded study, the effects on psilocybin administration was studied by Roland Griffiths of Johns Hopkins University and his colleagues on several volunteers and published in Psychopharmacology. The subjects reported their experience after taking the drug(below).

Twenty-two out of the 36 volunteers described a so-called mystical experience, or one that included feelings of unity with all things, transcendence of time and space as well as deep and abiding joy

Two months later 67 percent of the volunteers rated the psilocybin experience as among the most meaningful of their lives, comparing it to the birth of a first child or the death of a parent.

The long term effects and mechanism of the drug is not known completely. According to Charles Schuster, a neuroscientist at Wayne State University, this drug should be further investigated as to how they can be used to treat diseases like "the ennui and anguish of impending death" as well as "alcoholism and other forms of drug addiction."

Pheww… a long journey for the simple magic mushrooms.

Machines Maketh Us.

2006-07-17T13:41:00.000-07:00

The list of the most outrageous/exciting/pushing the frontiers of science/fantastical/I-am-running-out-of-adjective kind of scientific discoveries has just got a little smaller. A feat accomplished by a multi-disciplinary group of neurosurgeons, computer scientists, and electrophysiologists have struck off ‘bionic man’ from the list of impossible dreams.

In the latest issue of Nature, John Donoghue a neuroscientist from Brown University and a pioneer in this field along with other colleagues have reported a successful control of a computer cursor by a paralyzed man by the just his ‘thoughts’.

Matt Nagle who was paralyzed neck below after a knifing incident, has a microchip implanted in his brain and a wire coming out of his head connecting him to a computer. He is able to move the cursor with just his intention to do so. He is able to send emails, play basic games, control his TV and draw a circle with modified painting software. He was able to do this with minimal training.

Technically known as NMP (Neuroprosthetic Motor Prostheses), these interfaces uses signals from the brain to drive prosthetic devises. They come under a large category of BCI (Brain Computer Interface), which interfaces any part of the brain to machines. The NMPs uses signals from a specific area of the brain which controls all movements of our body called motor cortex.

How does this work?
legend for pic is given below
It starts with implantation of a chip in the area of the brain that controls movement and recording activity when he is asked to ‘move the cursor’ on the screen in front of him. The cursor is actually being moved by someone else, he traces the movement mentally, that is his brain is sending the required information to the muscles for the particular movement of the cursor. Although he can’t move any of his muscles, there will be activity in the motor cortex which has information for the movement, like direction. Then this pattern of activity will be fed to an algorithm that separates these signals into intentions - for example- assigning the pattern of activity of ‘move left’ into instructions for the cursor to ‘move left’. Then another algorithm has to detect these patterns and changes them into coordinates for the position of the cursor on the screen.

This work is a culmination of animal studies done earlier by many groups. An exhaustive list will look like a review for IEEE, and so I will just refer to a couple of experiments done by Nicolelis and group at Duke University who is well known in this field.

In a paper published in PLOS in 2004, Nicolelis trained monkeys to use a cursor to reach a target on the computer screen by moving a joystick. They were also trained to grip the joystick with varying force according to size of a cursor in the screen. The monkey had to vary the force and velocity to reach to do the task. They then recorded from various parts of the motor, premotor (required for planning for movement) and somatosensory area (where perceptions of touch arises, this is needed because touch feedback is essential for movement) while the monkey was doing this task. They used an Artificial Neural Network to extract information about hand grip force and velocity of hand trajectory from the brain recording. They then moved the cursors with these signals alone. The monkeys soon realized that they don’t have to move their hand to move the cursor, all they had to do was to think of doing it and they stopped using their hands. The brain signals were also used to drive a robotic arm which used parameters derived from the recorded activity alone. This study showed the possibility of using brain signals from paralyzed patients to drive bionic arms.

In earlier work published in Nature Neuroscience the same group trained rats to press a lever with their paws to obtain a water reward from a spout (the authors call it robotic arm). Simultaneously neuronal activity patterns from motor cortex (and other areas in thalamus) were recorded. These neuronal activity patterns were put through mathematical transformations to convert them into signals to control the spout. Rats then had a choice to press the lever or just ‘think’ of pressing the lever and the program would convert those signals to move the spout to give them water. After repeated trials the rats reduced or stopped pressing the lever. They got water by just ‘thought’.(Lazy rats).

Although this is exciting the situation is akin to the prototype Hondas one sees in Motor expos. There is a long way to go before it is implemented in patients routinely. There are a handful of groups around the world (and we are one) working on developing BCIs for the paralyzed, what separates them is the area in the nervous system where they choose to record neuronal activity from and the kind of algorithm they use to extract signals that can be used to control.

But whatever it is now, its exciting times ahead.

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a- chip on the penny and connector which will be fixed to the skull

b- chip under electron microscope

c-MRI of Matt's brain, red square shows area where the chip is implanted

d-Matt connected to the setup

Donoghue has started a company ..this is their URL http://www.cyberkineticsinc.com/

The experiment videos are available on the website, so is the original paper for free and some news item about it.

http://www.nature.com/nature/focus/brain/experiments/videopage1.html

Are we patenting nonsense?

2006-07-14T12:43:00.000-07:00

A recent news article in Nature has asked some uncomfortable questions about India’s patenting plans. Council of Scientific Industrial Research (CSIR) is India’s largest research organization funding 38 national laboratories across the country. For many years they did nothing. Traditional Indian natural products like turmeric and neem were patented by US firms which woke up Indian scientists to harsh reality. Eventually they fought and got the patents revoked.

When Ragunath Mashelkar took over as its head, he also brought a culture of patenting with him. He encouraged patenting anything that the CSIR laboratories invented that passed the basic criteria without considering whether the discovery has any economic value.

This drive has resulted in a large amount of patents, between 2002 and 2006 there were 542 US patents — more than the total number granted to CSIR’s counterparts in France, Japan and Germany combined. It seems like a good idea to patent everything and then think about which ones can make money for us, but the costs involved are high. Each US patent costs $25,000 for filing and $4000 annually for maintenance and many patents are not worth that much money like a US patent in 2002 by CSIR of cow urine extract claiming to enhance activity of antibiotics. This has not been proved by any peer reviewed study till now.

This smells dangerously of our country’s inclination to parcel pseudo-scientific/religious ideas as science. Remember the college degree courses in Astrology by UGC started by Dr. Murli Manohar Joshi and the general acceptance of Vedic mathematics?

This patenting overdrive is also seen in the Indian Patent Office also. In the fast moving field of biotechnology, CSIR filed more patents that any other companies. In the year 2004, CSIR filed 202 patents while BASF has filed 88 patents, Novo Nordisk 79 and Procter and Gamble 55.

But Mashelkar has a different take on things. He says "There is a clear sign that the reverse flow in technologies has begun from India to the West. In the new IPR regime, the country will not be found lacking in the field of frontier technologies. We have been doing great research work thus far at our labs, but we had lacked the industry-institutions networking. That is happening now." referring to the fact that CSIR was in top 50 US patent applicants in 2002.

But there are good points also, Masheklar points out to a cluster of three US patents on a potential anticancer molecule has been licensed out to an Indian entrepreneur in the United States for around $100,000.

“Considering that only about 3% of US patents are ever licensed, it is too early for the CSIR to expect big returns” he says.

All this costs money, and the strategy of ‘patent first and think later’ approach my Mr. Mashelkar seems like we will end up spending a lot of money patenting utter nonsense. The IPO should have tighter regulation and someone should tell Mr. Mashelkar that no one is giving prizes for number of patents but it’s the quality and promise of licensing or application that matters.

Bigger..hotter.

2006-07-14T11:37:00.000-07:00

I am not rambling about my sexual preferences; I am referring to an obsession of the masses whose only scientific exposure is to read some kind of digested scientific stuff in bad blogs run by depressed grad students like this one or in fancy magazines which make technical complications that took the best part of a few post docs look as simple as opening a can of coke.

The obsession I am talking about is dinosaurs; I am not talking about the sex life of dinosaurs either. (I have to pay the price of having a fancy title and get the point in such a round about way).

The topic is about temperature regulation in dinosaurs. Dinosaurs are large animals reaching up to 42 feet in height and 90 tonnes in weight. They were arguably the most successful tetrapods ever to have lived on this planet. But not a lot is known about their physiology, obviously. (Sigma doesn’t sell knock-out dinosaurs. I wish they did). How did they maintain their body temperature (homeothermy) is a big issue in biology for a long time.

The initial controversy was whether to slot dinosaurs into warm blooded (like birds and mammals) or cold blooded (reptiles, amphibians and fishes). Warm blooded animals, also known as endotherms maintain high body temperature supplied by large amount of internal metabolic heat and keep a constant body temperature in different thermal environments. They also have elevated rates of lung ventilation, oxygen consumption which allows them to thrive in many environmental niches unlike the cold blooded animals also called ectotherms.

The problem with slotting dinosaurs under endothermic animals is that endothermy or warm blooded animals evolved later and are found in birds and mammals. Slotting the dinosaurs under ectoderms is that they were thought to have lower metabolic rate and would depend on the sun to increase their body temperature which would make them sluggish.

But ‘Inertial homeothermy hypothesis’ carves a new category. This shows how being cold blooded doesn’t mean that they can’t maintain constant high body temperature (homeothermy). Many large reptiles bask in the sun and are able to maintain high temperatures all year long because of minimal surface-to-volume ratio and minimal heat loss. The commodore dragons, Galapagos tortoises and alligators are examples of large reptiles who maintain homeothermy in this way. Thus it was possible for the large dinosaurs to have large homes, pursue, hunt large prey and defend themselves fiercely.

A recent modeling study has shown direct evidence that dinosaurs maintained high body temperature by the ‘inertial homeothermy hypothesis’ which predicts the body temperatures to increase with body size. Their model based on growth curves of dinosaurs show that the body temperature of dinosaurs increased from 25.8 C at 12 Kg to 41.8 C at 13000 kg. To validate the model it was used to predict body temperature of crocodiles with different body masses which when tested empirically and was shown to be an accurate.

Blue balls

2006-07-11T01:56:00.000-07:00

Blue balls

Here is a fun experiment. Catch a vervet monkey, paints its balls bright blue and let him back into a cage with other members of his troupe. Your fine brushwork would have elevated his status in the troupe and the other monkeys with paler blue balls are behaving as his subordinates.

This was an experiment performed to understand the relationship between secondary sexual skin color and the status of the monkey in its troupe. Many primate species have colored sexual skin (pads in its bottom) and the face also. In rhesus macaques reddening signals readiness for mating, but in vervet monkeys they signal the position of the monkey in the social hierarchy. Male monkeys with brightest blue testicles in a troupe get to mate with his choice and boss the other males who have paler shade of blue testicles.

So blue balls are not always a bad thing….at least for the vervet monkeys.

Mating Madness

2006-07-01T08:46:00.000-07:00

Joe is a good man, average looking, caring, sensitive, supportive, has a good job, car, savings and makes the safe and sensible choice in life. But he can never get a date and none of his classmates from school remember him. Fonzi on the other hand, drives a motorbike, sports a killer leather jacket, which makes him dashingly good looking. He doesn’t have a job, drinks in the morning, and eats off his mother’s savings, but is charming as the devil.

If you were a woman looking for a date, whom would you fall for? The sensible Joe or Fonzi?

Fonzi right. Why would women want to make the risky decision and choose Fonzi?

Evolutionary biologists working on cockroaches have given us proof for a theory that explains this kind of behavior. The reason we have to drag in evolutionary biologists to explain this behavior is that this is an evolutionary conundrum, because mate choice is believed to bring about better fitness (survival of genes) to the female and male. But in such behavior it’s the opposite effect for the females. Imagine Fonzi’s girlfriend bringing up a kid with no support from Fonzi. This is detrimental to the fitness of the woman. This has been reported in other animals also. (So we are not the only superficial animals who make stupid decisions).

So how does the organism reconcile with the loss of fitness when it goes for the hot guy? Scientists have found out that this direct cost of choosing the hot guy is exceeded by the fitness that offsprings enjoy when mating with the hot guy. In other words offsprings from mating with a hot guy has more chance of survival and passing on his genes than when mated with Joe.

Although this theory has been around for some time, recent experiments with cockroaches have proved this idea. Cockroaches were separated into ‘attractive’ and ‘unattractive’ (believe me, there are attractive cockroaches). They did this by letting males have sex with females in two different ‘mating tournaments’, the males that were able to get laid twice were ‘attractive’ and ones that couldn’t even once was ‘unattractive’. The fitness of the offsprings from random females mated with attractive and unattractive males were measured. For offsprings from mating with attractive males, both offsprings had better fitness than offsrings of females that mated with unattractive males. Males were more attractive and females produced larger number and size of eggs.

So all you angry dads. Be Calm; your daughter has made the right choice. Your grandkids gonna rock!

Better Acoustics with Sake

2006-06-22T10:28:00.000-07:00

Behind every seemingly unsolvable problem lies a simple solution, attainable only to the mildly alcoholic. After trying 20 years to press birch wood into speakers without splitting them (apparently birch wood has brilliant acoustics) JVC has stumbled upon a rather simple solution. Soak in Sake. Yes they soaked the wood in tubs of sake. This process has made the wood malleable so they can be pressed into cone shaped speakers.

The result, Sake not only brings happiness but crystal clear sound in JVC's EX-A10 with "sake-soaked" wood cone speakers.

"Sake makes me bright."

Coke® or Pepsi®?

2006-06-22T10:06:00.000-07:00

Ask this question to a caveman; living without aggressive marketing campaigns, larger-than-life billboards and catchy ad jingles, he will say “I don’t care, they taste the bloody same”. It’s true. They are chemically very identical drinks. But what makes people choose one over the other?

Neuroscientists at Tuft’s university in a paper in Neuron investigated the influence of the brand image on behavioral choice and brain response when they exercised their choice between Coke® and Pepsi®.

Now. It will be wrong to assume that the cavemen didn’t have any food or drink preference (I am sure they hated broccoli as well) but they were based on biological reasons like - gives more energy or strengthens the immune systems. But in the modern world factors like social context, mental state, expectation, cultural influence etc play a role in choosing ones food or drink, apart from the sensory aspects of taste and smell.

Scientists have used fMRI (functional Magnetic Resonance Imaging, a technique that detects which area of the brain is being used when the subject is performing a particular task.) to study which region of the brain is activated when the subjects prefer one drink to another, with or without a brand cue (like the Coke logo).

They found that a part of the brain called Ventro Medial Prefrontal Cortex (VMPFC) was responsible when the subjects chose the drink based only on sensory information that is, when the subjects were asked to choose drinks on unmarked cups. This brain area is known to be responsible for basic appetitive aspect of reward.

In the next task the subjects were asked to choose between Coke® or Pepsi®, but this time one of the cups indicated what drink there was (with a large bottle of Coke or Pepsi with the prominent logo next to the cup). This biased their preference. Subjects chose Coke more often than Pepsi!! (The marketing department of Coke has a scientific reason to feel superior to their counterparts in Pepsi).

Also, different brain areas were activated, like hippocampus, Dorso-Lateral Pre Frontal Cortex (DLPFC) and midbrain. The DLPFC is hypothesized to employ affective information in biasing behavior and the hippocampus is used to recall cultural information to bias our judgment. (which fits nicely into our story).

Scientists say that there are two separate neural pathways in the brain for food preference. One pathway determines preference by the sensory aspect of the food like smell and taste, and the other is determined by cultural information which has a strong component of memory attached to it. And when it comes to a preference that has a strong cultural aspect also, both the pathways interact and result in bias in preference.