A field that is about to go public in a big way

John Hawks has a nice post pointing to the falling costs of genome sequencing services and how that is going to change the nature of the industry; towards the end of the post, he has some advice too:

I expect that the company that advances the fastest will be the one that gathers in the coolest stable of young scientists to do association work and population history.

It’s a very good time to get into this field and set yourself apart, because it’s about to go public in a big way.

Sounds very exciting!

Zen meditation, William James on PhD thesis and Darwin’s London

Here are a few links via Coturnix at A blog around the clock:

Zen meditation

Science daily reports (via):

Experienced Zen meditators can clear their minds of distractions more quickly than novices, according to a new brain imaging study.

The paper in question is published in PLoS ONE (via); here is the abstract:

Recent neuroimaging studies have identified a set of brain regions that are metabolically active during wakeful rest and consistently deactivate in a variety the performance of demanding tasks. This “default network” has been functionally linked to the stream of thoughts occurring automatically in the absence of goal-directed activity and which constitutes an aspect of mental behavior specifically addressed by many meditative practices. Zen meditation, in particular, is traditionally associated with a mental state of full awareness but reduced conceptual content, to be attained via a disciplined regulation of attention and bodily posture. Using fMRI and a simplified meditative condition interspersed with a lexical decision task, we investigated the neural correlates of conceptual processing during meditation in regular Zen practitioners and matched control subjects. While behavioral performance did not differ between groups, Zen practitioners displayed a reduced duration of the neural response linked to conceptual processing in regions of the default network, suggesting that meditative training may foster the ability to control the automatic cascade of semantic associations triggered by a stimulus and, by extension, to voluntarily regulate the flow of spontaneous mentation.

William James on PhD theses and PhDs

William James, more than a century ago (via):

When the thesis came to be read by our committee, we could not pass it. Brilliancy and originality by themselves won’t save a thesis for the doctorate; it must also exhibit a heavy technical apparatus of learning; and this our candidate had neglected to bring to bear. So, telling him that he was temporarily rejected, we advised him to pad out the thesis properly, and return with it next year, at the same time informing his new President that this signified nothing as to his merits, that he was of ultra-Ph.D. quality, and one of the strongest men with whom we had ever had to deal.

To our surprise we were given to understand in reply that the quality per se of the man signified nothing in this connection, and that the three magical letters were the thing seriously required. The College had always gloried in a list of faculty members who bore the doctor’s title, and to make a gap in the galaxy, and admit a common fox without a tail, would be a degradation impossible to be thought of. We wrote again, pointing out that a Ph.D. in philosophy would prove little anyhow as to one’s ability to teach literature; we sent separate letters in which we outdid each other in eulogy of our candidate’s powers, for indeed they were great; and at last, mirabile dictu, our eloquence prevailed. He was allowed to retain his appointment provisionally, on condition that one year later at the farthest his miserably naked name should be prolonged by the sacred appendage the lack of which had given so much trouble to all concerned.

Getting the sense of Darwin as a young man

Richard Conniff at the Atlantic (via):

In paintings and sculptures from the last years of his life, Charles Darwin gives the impression of a man deeply wishing he could be somewhere else. At the National Portrait Gallery in London, he keeps his rumpled hat clutched in one hand, ready to bolt for the door. At the Natural History Museum, he has his coat folded across his lap, as if yearning to shed the burden of fame and slip quietly into oblivion. On the £10 note, his eyes are haunted beneath a vast furrowed brow, and there’s dismay behind that biblical white beard.

This image of Darwin is everywhere, and that seemed to me, on a recent trip to London, to be a pity. Even the founding father of evolutionary theory was not born a gloomy old man. I began to wonder if it might be possible to walk Darwin’s London and get a sense of him as a young man caught up in the fray. The landmarks of his life turned out to be all around. One day, for instance, I ducked into the Burlington Arcade—a handsome 1819 predecessor of the enclosed luxury shopping mall, where the bon ton of Darwin’s day shopped—and then, via another arcade, out onto Albemarle Street. To the right was the Royal Institution, where Darwin attended lectures. Brown’s Hotel, where a pro-Darwin group called the X Club used to meet in the 1860s, stood in mid-block. And though Darwin’s publishing company was sold off a few years ago to a conglomerate, the seventh generation of John Murrays still presides over the company’s old house just down the street. Murray told me he was already being inundated with visitors anticipating next year’s big anniversaries of Darwin’s birth (1809) and of the publication of his book On the Origin of Species by Means of Natural Selection (1859).

Happy reading!

Micro-microscope or a scope on a chip!

An interesting news item:

Researchers have developed a micro-microscope. Writing in the journal Proceedings of the National Academy of Sciences, scientists at Caltech describe the creation of an on-chip, lens-free microscope that they say could be built for about ten dollars. The device uses a screen of tiny holes mounted above a CCD sensor to image liquids flowing through microscopic channels in the chip. Such a microscope chip could provide high-resolution microscopic images in field instruments for taks such as blood screening and water testing.

Link via Seed’s Daily Zeitgeist.

Here is the PNAS article in question, Lensless high-resolution on-chip optofluidic microscopes for and cell imaging:

Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (≈0.9 μm for the first and ≈0.8 μm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as ; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications.

Have fun!

Role of brain in perception

Atul Gawande has a very interesting piece in the latest New Yorker titled The Itch; as part of the essay, Gawande explains the role of mind in our perceptions thus:

The images in our mind are extraordinarily rich. We can tell if something is liquid or solid, heavy or light, dead or alive. But the information we work from is poor—a distorted, two-dimensional transmission with entire spots missing. So the mind fills in most of the picture. You can get a sense of this from brain-anatomy studies. If visual sensations were primarily received rather than constructed by the brain, you’d expect that most of the fibres going to the brain’s primary visual cortex would come from the retina. Instead, scientists have found that only twenty per cent do; eighty per cent come downward from regions of the brain governing functions like memory. Richard Gregory, a prominent British neuropsychologist, estimates that visual perception is more than ninety per cent memory and less than ten per cent sensory nerve signals. When Oaklander theorized that M.’s itch was endogenous, rather than generated by peripheral nerve signals, she was onto something important.

The fallacy of reducing perception to reception is especially clear when it comes to phantom limbs. Doctors have often explained such sensations as a matter of inflamed or frayed nerve endings in the stump sending aberrant signals to the brain. But this explanation should long ago have been suspect. Efforts by surgeons to cut back on the nerve typically produce the same results that M. had when they cut the sensory nerve to her forehead: a brief period of relief followed by a return of the sensation.

Moreover, the feelings people experience in their phantom limbs are far too varied and rich to be explained by the random firings of a bruised nerve. People report not just pain but also sensations of sweatiness, heat, texture, and movement in a missing limb. There is no experience people have with real limbs that they do not experience with phantom limbs. They feel their phantom leg swinging, water trickling down a phantom arm, a phantom ring becoming too tight for a phantom digit. Children have used phantom fingers to count and solve arithmetic problems. V. S. Ramachandran, an eminent neuroscientist at the University of California, San Diego, has written up the case of a woman who was born with only stumps at her shoulders, and yet, as far back as she could remember, felt herself to have arms and hands; she even feels herself gesticulating when she speaks. And phantoms do not occur just in limbs. Around half of women who have undergone a mastectomy experience a phantom breast, with the nipple being the most vivid part. You’ve likely had an experience of phantom sensation yourself. When the dentist gives you a local anesthetic, and your lip goes numb, the nerves go dead. Yet you don’t feel your lip disappear. Quite the opposite: it feels larger and plumper than normal, even though you can see in a mirror that the size hasn’t changed.

Gawande goes on to describe the “brain’s-best-guess” theory of perception.

For those of you who have read V S Ramachandran, Oliver Sacks and, more recently, Jonah Lehrer, some  of these thoughts might not be new. But, the sensation of itch, and its origins in our minds is something that I am learning for the first time.

Some parts of the essay (like the description of a lady who scratched her scalp, bones and into her brains) does not make a pleasant reading; however, it is one of those un-put-down-able pieces. Take a look!

The polio vaccination controversy

This time around, it is being played in The Hindu.

Dr. Pushpa M Bhargava argues for IPV as against OPV, and forwards some conspiracy theories too:

As already mentioned, by this time the West had decided to replace OPV with M-IPV. Therefore, market had to be found for OPV. WHO advised that developed countries use IPV, while developing countries use OPV. For us to oblige WHO, two steps were necessary: (1) that BIBCOL produces no OPV of its own; and (2) India reverses its decision to gradually shift to IPV. Both the steps were taken. BIBCOL has not produced a single dose of OPV till today, and the Ministry of Health decided soon after the March 1988 meeting, without any further consultations, to shift permanently to OPV. Consequently IVCOL was closed down after incurring substantial expenditure, and a number of senior officers of the above Ministry got plum U.N. jobs with tax-free dollar salaries, after retirement.

It is particularly interesting that at a conference jointly organised by the International Comparative Virology Organisation and the WHO in New Delhi, in January 1992, experts from all over the world indicated the preference of IPV over OPV for any plans of eradication of polio in developing countries.

An interesting question that one may, therefore, ask is: if we really felt that there was a strong scientific case for using OPV (which there wasn’t), why did we not make it ourselves. The answer is that this wouldn’t have served the foreign interests to whom we had sold ourselves, ignoring the interests of our own people and the sane advice of our own experts based on incontrovertible evidence. It is amusing in this context that even the appropriate WHO document clearly states that there is evidence that OPV has not worked in developing countries.

The 64,000-rupee question now is: would the government wake up and get out of the clutches of WHO so that it may serve our interests and not the interest of powers that be outside India? And if it needs endorsement from a foreign channel, it may read the article by V.K. Bhasin in January 2008 issue of Nature Biotechnology, Nature being perhaps the world’s best-known and most respected scientific periodical. The article says that, in 2006, there were 1,600 cases of OPV–induced polio plus a large number of cases of AFP from which virus was not cultured.

So, the problem continues. But who cares! Polio is not a disease of billionaires.

However, in the Letters to the Editor section of the Hindu, at least one letter of Dr Santhosh Rajagopal brings the other view point to the discussions:

Several developing countries have eliminated polio using OPV. The U.S. switched over to IPV only recently when the number of vaccine-induced cases, while minuscule, exceeded cases of natural infection (which was near zero).

If, as the author states, OPV is so ineffective, how and why did a majority in India eliminate polio without a single shot of IPV? Any scientific explanation for the OPV-is-a- failure statement needs to explain why a large section of India, particularly in the south, is relatively free of the disease. While IPV might be theoretically as good as, or even better than, OPV, one has to contend with harsh ground realities.

While OPV can be administered by a trained volunteer, IPV requires a trained medical person with possibly stand-by arrangements to respond to an emergency. With poor health infrastructure in most of north India, implementation of an IPV plan would be a logistical nightmare.

India is currently having the lowest incidence of Polio Virus Type 1, the most dreaded variety-5 cases. Type 3 is what is adding to the numbers and this was expected as the emphasis has been on Type 1 in the past two years.

Dr. Santhosh Rajagopal,

Madurai

Personally, I find that the arguments of Dr. Rajagopal makes sense (and, I have heard similar reasoning given by Dr. Balasubramanian (as I noted in one of my earlier posts) as well as by our paediatrician in US).

The question of why we did not decide to make the OPV ourselves is an entirely different issue that does not seem to have anything to do with the efficacy or non-efficacy of the vaccine in spite of what Dr. Bhargava has to say.

On the ethics of clinical trials

Dr. Balasubramanian, in his Speaking of Science column in the Hindu, writes about the need to stick to Helsinki declaration and not follow FDA:

Take the case of the trial, in 2001, of a drug that acts against sudden lung collapse in children and thus saves lives. Initiated by the U.S. firm Discovery Labs, this wanted to try the drug on children in a Latin American country.

Rather than compare their drug with one of the several effective drugs already in use, the company wanted to give inactive placebos to 325 children in the control group.

The Food and Drug Administration (FDA) of the U.S., which clears such trials, warned them that this was unethical, since effective treatments were available in the U.S. and Europe (even if not in the Latin American country).

The company then had to change the protocol and gave the control group the alternative active treatment. This was in keeping with the Declaration of Helsinki.

Yet, with increasing pressures from companies and sponsors, FDA is starting to buckle.

It has announced that starting October 2008, it will shelve the Helsinki Declaration, and adopt a new standard called Good Clinical Practice (GCP).

This is a document prepared by drug regulators and drug companies from the US, European Union and Japan.

As the journal Nature notes in its 22 May 2008 issue: ‘Although GCP deals with subject protection, it is in essence a manual on how to conduct rigorous clinical trials, not a human rights document…. If FDA jettisons Helsinki, it risks sending a message that ethical considerations are expendable when research subjects live half a world away’.

Indian agencies such as the Drug Controller General of India, Indian Council of Medical Research (ICMR), and contract research organizations that conduct and oversee human trials, and also the institutional ethics committees should take note.

Overall, the Helsinki Declaration argues for ethical universalism. Let us not follow FDA and change our guidelines. After all, it cannot be that some humans are more equal than others.

Short and long-term impact of meditation on mind and brain

Vaughan at Mind Hacks collects and comments on couple of review articles on the neuroscience of meditation:

This month’s Trends in Cognitive Sciences has a fantastic review article on the neuroscience of meditation – focusing on how the contemplative practice alters and sharpens the brain’s attention systems.

The full article is available online as a pdf, and discusses what cognitive science studies have told us about the short and long-term impact of meditation on the mind and brain.

…

A recent review of ‘mindfulness’ meditation-based therapy found that although research is in its early stages and not all possibilities have been ruled out, there’s good evidence from the existing RCTs that it’s particularly good in preventing relapse in severe depression.

Though Vaughan notes that some of the meditational techniques used in these studies are taken from Buddhist meditation practices (and the role that the interest that the science-savvy Dalai Lama have shown on such scientific studies), such practices are also used in several of the Indian meditational practices and schools — though, to be fair to Buddhists, I think, they are the first ones to secularise meditational practices by noting that any word can be used for meditation and that there is no special power associated with any mantra or special word.

Take a look!

Anti-(polio)vaccine lobby in India

I often come across posts in some of the scienceblogs (like aetiology for example), about anti-vaccination lobby in the US. However I did not know about such groups which are active in India till I saw this post in Mutiny today.

While I am thankful to Mutiny for drawing my attention to such lobbies, I still am pained not only by the timing of the post at Mutiny (when a tragedy in Tamilnadu is already wreaking havoc on public morale with respect to vaccination), but also by some of the claims made in the post which are irrational and unscientific (and, border strongly on sensationalism, fear-mongering and conspiracy theories). Here is an example:

Do you think the government medical agencies/programmes are aware of the dangers of vaccination? If so, do you think there is some kind of hidden agenda in running this programme continuously?

There is no doubt that they are aware of the side effects. It is the WHO (World Health Organization) that develops such programme and implement it in third-world countries. And no such countries (like India) are conducting any quality check or screening test of these medicines. The multi-national pharma companies import the medicines with a certification and they pack and label the medicines in their units here in India.

The pharmaceutical companies already have a negative reputation all over the world for their political and financial connections. Are they exporting these medicines only to the under-developed nations?

Yes, they export it mainly to under-developed and poor nations. That is their best market. Only seven countries in the world conduct such vaccination programmes. All these eradication programmes are purely based on the business interests. No disease can be controlled with vaccines.

There has been a terrible incident today in Tamil Nadu today. Four little kids died due to an anti-measles vaccination programme and fifteen more are hospitalized. What do you say about that?

I haven’t learnt the exact details of the incident. But I see this in two ways. There is an initiative being done under the leadership of WHO and our government to shut down the vaccine producing factories in India saying that they do not meet the standards of WHO. They have decided to build a vaccine park in Chennai with participation of the private sector. This decision has invited protests from the people who watch the medical scene in India. So in the first reading of the news of Tamil Nadu incident, I doubt if it was contaminated vaccine distributed in this case to weaken the protests against the vaccine park.

Even if we ignore this thought, it is possible that the children died because of the side effects of vaccines (and it has happened before). As per the information that I received, it is not anti-measles, but chicken pox vaccine. But some evening newspapers reported that it is polio vaccine. We are in touch with Chennai and hope to get the right information by tomorrow morning (25th April).

Apparently the Dr. Hari, who is being interviewed, is a homeopathic doctor, and he claims, that no disease can be controlled with vaccines, and the interviewer at Mutiny is willing to publish, blithely, everything that the doctor has to say, without ever even mentioning that there might be other opinions, and even prompts some of the answers with his questions (like the ones about reputation of pharmaceutical companies and the hidden agenda of the government etc).

I was once a member of Mutiny, and have lots of respect for several of the contributors there; however, this kind of stupid (and, worse — wrongly timed) posts need to be condemned in the strongest possible terms.

By the way, the wiki page on polio vaccination discusses some of the science — why oral vaccines are used, in which places they are used, what are the problems associated with such viruses, why oral vaccines are administered the number of times they are administered etc. The short answer: in places where polio is not completely eradicated, oral vaccine is the way to go — but, if the immunization rate is very low, then such oral vaccines can cause outbreaks; when polio is completely eradicated, then it is possible to switch to IPV. This piece by Dr. Balasubramanian in the Speaking of Science in the Hindu published a couple of years ago is also relevant in the present context.

Music practise and noise level maintenance

They had rehearsed the piece only once, but already the musicians at the Bavarian Radio Symphony Orchestra were suffering. Their ears were ringing. Heads throbbed.

Tests showed that the average noise level in the orchestra during the piece, “State of Siege,” by the composer Dror Feiler, was 97.4 decibels, just below the level of a pneumatic drill and a violation of new European noise-at-work limits. Playing more softly or wearing noise-muffling headphones were rejected as unworkable.

So instead of having its world premiere on April 4, the piece was dropped. “I had no choice,” said Trygve Nordwall, the orchestra’s manager. “The decision was not made artistically; it was made for the protection of the players.”

The cancellation is, so far, probably the most extreme consequence of the new law, which requires employers in Europe to limit workers’ exposure to potentially damaging noise and which took effect for the entertainment industry this month.

This time around, it is no report from Onion but from NYTimes. Of course, there is also a mention of computer program devised to tackle the problem:

At the Royal Opera House, the management has devised a computer program that calculates individual weekly noise exposure by cross-referencing such factors as the member’s schedule and the pieces being played.

Musicians are spacing out rehearsals and playing more softly when they can. As the Welsh National Opera prepared for the premiere of James MacMillan’s loud opera, “The Sacrifice,” last year, the brass and percussion sections were told to take it easy at times in rehearsal to protect the ears of themselves and their colleagues, said Peter Harrap, the orchestra and chorus director.

And, then there is the mention of a stand-off between a conductor and musicians too:

Although Switzerland is outside the European Union, an extraordinary noise-related argument between the conductor and the Bern Symphony Orchestra disrupted the opening night of Alban Berg’s “Wozzeck” in March.

The piece called for 30 string players and 30 wind and percussion players, all crammed into a too-small pit. When the stage director complained in rehearsals that the music was too loud, the conductor didn’t order the orchestra to play more softly, but instead asked for a cover over the orchestral pit to contain the noise, said Marianne Käch, the orchestra’s executive director.

That meant the noise bounced back at the musicians, bringing the level to 120 decibels in the brass section, similar to the levels in front of a speaker in a rock concert. The musicians complained. The conductor held firm. But when the piece began, “the orchestra decided to play softer anyway in order to protect themselves,” Ms. Käch said.

That made the conductor so angry that he walked off after 10 minutes or so, Ms. Käch said. Told that there had been “musical differences” between the conductor and the orchestra, the perplexed audience had to wait for the two sides to hash it out.

In the end, the orchestra agreed to return and finish the performance at the loud levels. For subsequent performances, a foam cover that absorbed instead of reflecting the sound was placed above the pit, and the conductor agreed to tone things down.

“This is the problem you find in many places, that the conductors are conducting more and more loudly,” Ms. Käch said. “I know conductors who have hundreds of shades of fortissimo, but not many in the lower levels. Maybe the whole world is just becoming louder.”

Take a look!

A film I would love to see

Vaughan’s description (at Mind Hack) itself is so rivetting, leave alone the movie:

Although Marsh normally works at St George’s, one of London’s most established hospitals, he has regularly travelled to the Ukraine for 15 years to assist the development of neurosurgery in this still struggling country.

The contrast itself is striking. One scene sees Marsh and Kurilets looking through street market hardware stalls for screws, rivets and power tools to use in their operations.

One of the most gripping scenes is where the two surgeons open a patient’s skull using a Bosch power drill only to find the battery is going flat as they proceed.

The man has been only given local anaesthetic as the Ukrainian hospital doesn’t have the facilities to safely put someone under and wake them up after initial part of the procedure.

Some of the most moving moments concern the tension between the shortcoming of medicine and the hope of the patients. There are many profound moments that aren’t well captured by brief summaries, and I’m sure each viewer takes something different away from them, so you’ll need to experience them for yourselves.

Take a look!