Photo of an unidentified animal the Bigfoot Re...

Photo of an unidentified animal the Bigfoot Research Organization claims is a “juvenile Sasquatch” “Jacobs Photos” . . Retrieved 2009-09-16 . (Photo credit: Wikipedia)

Well, urban legend has it that Sasquatch aka American BigFoot, the name given to an ape-like creature apparently inhabits forests, mainly in the Pacific Northwest region of North America and it has been some decades that people have been arguing about its reality. Last year in September 2012, Dr. Melba S. Ketchum announced with some big fanfare that she and her team from DNA Diagnostics Inc. havesequenced the genome (mitochondrial and nuclear) of sasquatchfrom all the alleged samples people have collected from some time. However, instead just verifying that Sasquatch is nothing but an urban legend they issued this press release:

“Our study has sequenced 20 whole mitochondrial genomes and utilized next generation sequencing to obtain 3 whole nuclear genomes from purported Sasquatch samples. The genome sequencing shows that Sasquatch mtDNA is identical to modern Homo sapiens, but Sasquatch nuDNA is a novel, unknown hominin related to Homo sapiens and other primate species. Our data indicate that the North American Sasquatch is a hybrid species, the result of males of an unknown hominin species crossing with female Homo sapiens.

Hominins are members of the taxonomic grouping Hominini, which includes all members of the genus Homo. Genetic testing has already ruled out Homo neanderthalis and the Denisova hominin as contributors to Sasquatch mtDNA or nuDNA. “The male progenitor that contributed the unknown sequence to this hybrid is unique as its DNA is more distantly removed from humans than other recently discovered hominins like the Denisovan individual,” explains Ketchum.

“Sasquatch nuclear DNA is incredibly novel and not at all what we had expected. While it has human nuclear DNA within its genome, there are also distinctly non-human, non-archaic hominin, and non-ape sequences. We describe it as a mosaic of human and novel non-human sequence. Further study is needed and is ongoing to better characterize and understand Sasquatch nuclear DNA.”

So, one would immediately say -Yay science proved it exists, right? The answer however will be a big emphatic NO. The prime reason is that science doen’t work on hearsay but on repeatable, well-designed experiments with no ambiguity in either the way its conducted or how samples are gathered. And this is where this so called genetic evidence fails big time.

One of the biggest red flags to this whole study is: How did she get her samples? After all, if she was working from a well-reliable source, that alone might be a big sensation because no physical evidence of Bigfoot exists on record. As it turns out, Dr. Ketchum says her DNA sample was obtained from a blueberry bagel left in the backyard of a Michigan home that, according to the owner, sees regular visits from Sasquatch creatures.

And if the sample gathering itself is in doubt, then how can anyone believe the results ? Another face-palm statement: Fully human mitochondrial DNA, which is inherited from your mother, so she assumes that all Sasquatches had human women as relatively recent ancestors, but at the same time, the nuclear DNA is some bizarre menagerie that includes non-ape sequences? And frankly speaking, any biology student would tell you its hogwash !!

But all of this was from last year, and ever since then she has been trying to publish it in a scientific journal and recent news suggests that she has been unable to clear the peer-review stage. So, in response to this, she has decided to start over – recollect samples, do the whole sequencing again, and re-interpret the results…..Naaaaaaa, thats what any other scientist would have done. What she has done is to buy a journal !!  The Journal of Cosmology was available  she bought it and renamed it to De Novo.  One glance at the website and you are reminded of your art school classes in grade 8. The icons are mis-matched, the colour is horrid and the overall design is completely unprofessional. PZ Myers in is blog Pharyngula has it better:

Then she came out with a special edition. It’s Volume 1, Issue 1. It contains precisely one paper, hers.

You should be laughing by this point.

The online journal is a mess. The layout is funky-ugly, it’s difficult to figure out how to actually get to the paper, and when you navigate to it, it’s got a wretched little “Buy Now” button imbedded in a couple of intersecting blocks of color in a hideous table-like layout. It reminds be of the esthetics of JoC.

Anyway, it’s $30 to buy a paper so bad they had to build a custom journal around it to get it published. Not interested.

So, seeing all this mess i wish to bid adieu to Sasquatch !! May it continue to relive in our science fiction movies…

More on this:

  1. Sasquatch is ill-served, Pharygula, 2013.
  2. What I really want to see is the DNA sequence of an alien Grey, Pharyngula, 2012.
  3. Bigfoot in popular culture, Wikipedia.
  4. Is this Bigfoot … or is it a bear with bad skin?, Daily Mail, 2007.


It's Darwin Day!

It’s Darwin Day! (Photo credit: Kaptain Kobold)

Darwin Day commerates the birth anniversary of Charles Darwin who was born on February 12, 1809. And on this day, various scientific institutions, agencies and bodies organise lectures and talks to highlight the awesome contributions of Darwin to science. Without his impressive array of work, science would have been quite bare and we quite ignorant about the inner workings of nature.  So, celebrate this day not in the name of Darwin but what science has done for the betterment of humanity in general. Think about all the inventions and discoveries science has brought us and let’s drink to it !!

So, what better way to celebrate this day  than to showcase the Bird-of-Paradise Project of Cornell Ornithology Lab.  The site gives a wonderful description of their project:

The birds-of-paradise are among the most beautiful creatures on earth—and an extraordinary example of evolutionary adaptation. On this site you can find what few have witnessed in the wild: the displays of color, sound, and motion that make these birds so remarkable. Then you can delve deeper, examining the principles that guided their evolution and the epic adventure it took to bring you all 39 species.


Global Warming – The ultimate quibble of this century !! Or should i say the “haute” of this century. Why? Now, common ask yourselves, which single topic apart from the religion/atheism debate, you always hear in any gathering or book reading circles or conferences or on social platforms which is ready to divide people into two opposing camps. Books are being written, movies made, debates fought and what for – “The legitimacy of Global warming”. Despite numerous evidences detractors still love to question it. However, a new paper published this month in PNAS provides genomic evidence forphenotypic responses to climatic warming.

What’s it all about?

Ongoing changes in regional climates, especially the trend of warming winters and blazing summers are pushing many species (both plants and animals) to shift their distribution toward higher latitudes and altitudes. Such a change in the species distribution, with an expansion in previously hostile areas and contraction in their own habitats which are becoming less favorable, can occur rapidly both in plants and animals. However, not all species can migrate to lesser hostile areas, and there are many reasons proposed for it. Primarily among them is the increasing trend of Habitat Fragmentation. Habitat fragmentation can result from human expansion into wilder areas resulting in few phenomena:

  • Reduction in the total area of the habitat
  • Isolation of one habitat fragment from other areas of habitat
  • Breaking up of one patch of habitat into several smaller patches
  • Decrease in the average size of each patch of habitat

As, a result of such human activity many species especially plants can’t migrate into other areas resulting into their dwindling numbers. But some species do survive in such increasingly fragmented habitats and hence have adapted to the climatic warming. Though some previous studies inDrosophila melanogaster have shown adaptive trait variation in relation to climate change in both natural and experimental population, however in some cases, the evolutionary response to climate change may be slow due to genetic constraints causing a time lag between the environmental change and an observed evolutionary response. Hence,understanding how various species track climate warming bygenetically based adaptive trait variation and which traits facilitate the evolution of such adaption is important.

What is the new evidence?

Thymus vulgaris

The authors decided to look at Mediterranean wild thyme (Thymus vulgaris), a low growing herbaceous plant which is native to Southern Europe and is often used as a culinary herb. The plant contains many oils and the chemical composition(phenolic or non-phenolic) of it varies in different regions based on the temperature. These oils make a plant adaptable to freezing and hence different climatic areas have plants with varying composition of oils (chemotypes). So it would be worthwhile to see if the recent trend of gradual warming of extreme winter freezing events, has brought about an evolutionary response in plants i.e, has their chemical composition changed over time? Interestingly, any such change in the respective oil compositions in different climactic areas with different temperatures would have a genetic basis. And this is what the authors looked about.

The study area had a Mediterranean climate with summer drought but also severe winter freezing temperatures within the basin as a result of a dramatic temperature inversion In this area, there are six differentchemotypes that are the expression of a genetically controlled polymorphism in T. vulgaris. Two phenolic chemotypes (carvacrol and thymol) are largely dominant on the slopes above 250-m elevation and four nonphenolic chemotypes (linalool, thuyanol-4, α-terpineol, and geraniol) below 200m elevation, where they experience the winter temperature inversion. Hence, phenolic chemotypes are predominantly winter non-tolerant whereas non-phenolic types are winter tolerant.

There is thus a sharp gradient in the chemotype frequency over only 3–5 km that goes from 100%of either phenolic or nonphenolic chemotypes to 100% of the other form, with a narrow transitional zone. In short, nonphenolic chemotypes show adaptation to habitats, which in the past have experienced extreme freezing temperatures in early winter, whereas phenolic chemotypes are sensitive to intense early-winter freezing and occur in habitats where extreme summer drought can exclude nonphenolic chemotypes.

Hypothesis: Phenolic chemotypes (thymol and carvacrol) now occur in sites where they were previously absent or have increased their frequency in the transitional sites due to a relaxation of selection pressure normally associated with extreme early winter freezing temperatures due to climatic warming.

To do so, they compared the chemotype composition of populations observed in the early 1970s  to that in 2009–2010 for 36 populations sampled along six transects. Each transect was <10 km long, each containing six populations, with two “phenolic,” “mixed,” and “nonphenolic” populations.

They found that the mean percentage of phenolic chemotypes in a population was significantly (df = 35, S = 68.5, P < 0.01) higher in the contemporary samples (overall value of 53.1%) than in those of the initial study (47.7%) of 1970’s. The changes in composition of the initial nonphenolic populations were associated with the appearance of the thymol chemotype in all eight of the populations whose composition changed and the carvacrol chemotype in three of them.

The changes reported involved a reduced intensity of freezing events and changes in frequency of freezing tolerant and nontolerant phenotypes in natural populations of the Mediterranean aromatic plant, Thymus vulgaris. A significant appearance of freezing-sensitive phenolic chemotypes in sites where they were historically absent and an increase in their frequency in previously mixed populations was observed. Such changes have occurred in 17 of the 24 populations where they could potentially occur.

Such studies, illustrate that a rapid evolutionary response to temperature modifications can occur where genetic variation is combined with a change in a previously strong selection pressure, even for a perennial woody plant. Hence, this provides quite a neat example of genetic changes brought about by climatic warming.  I guess, the detractors of global warming would be feeling quite uneasy now !!

More on this:

  1. Genetic consequences of climate change for northern plants, Alson, Proceedings of Royal Society B, 2012.
  2. Climate extremes: Observations, modeling, and impacts, Easterling DR, Science, 2000.
  3. Ecological and evolutionary responses to recent climate change, Parmesan C, Annu Rev Ecol Syst Evol, 2006.
  4. Ecological responses to recent climate change, Walther GR, Nature, 2002.
  5. Rapid shifts in plant distribution with recent climate change, Kelly AE, Goulden ML, Proceedings of National Academy of Sciences, 2008.
  6. The distributions of a wide range of taxonomic groups are expanding polewards, Hickling R,Global Change Biology, 2006.
  7. A globally coherent fingerprint of climate change impacts across natural systems, Parmesan C, Nature, 2003.
  8. Running to stand still: Adaptation and the response of plants to rapid climate change, Jump AS, Ecology Letters, 2005.
  9. Genetic response to rapid climate change: It’s seasonal timing that matters, Bradshaw WE, Molecular Ecology, 2008.
  10. Climate change and evolutionary adaptation, Hoffmann AA, Nature, 2011.


The title of this post – To Quiver, or to Shiver is taken from a new article published this month in Proceedings of Royal Society London B. The paper deals with an interesting question – If a organism is good at one thing, does it mean that its good at all others too? OR Do you have to pay a price for being the best at something?

What is it all about?

Parasemia plantaginis coll. Mus. Zool. Oulu

Parasemia plantaginis coll. Mus. Zool. Oulu (Photo credit: Wikipedia)

Wood Tiger Moths, a species of moth(Parasemia plantaginis) found throughout Europe are widely known for their different wing colourations depending on the place they live.

Now why would this moth have bright colours?

Wouldn’t it attract more predators and hence get eaten up?

It turns out colours are used by various organisms as a predator-defence strategy. There can be two kinds of colouration schemes:

  • Camouflage:It  is one colouration-based predator defence strategy and benefits from variable coloration, which prevents predators from developing a search image for the most abundant phenotype of prey.Because, if the prey have a consistent camouflage colouration then the predator would after a few trials and errors, learn to identify the prey easily and then the prey would be wiped out due to the predation pressure.
  • Aposematism: Situated at the opposite end of the predator aversion strategy spectrum, where prey use conspicuous warning signals to advertise their secondary defences. Warning signals of such organisms are not expected to vary much because predators should learn to avoid a uniform signal more efficiently than a variable signal, leading to greater survival.

Now, Wood Tiger Moth the species in question as seen in the picture above show aposematism and use these conspicuous colours as a warning signal towards predators. But, contrary to the predictions for this warning signal homogeneity,  many such moths possess variable warning signals.

So, if uniform colouration is so important for predator defence, then why does the Wood Tiger Moth show variation in colours?

One reason could be that though different hindwing colours (white or yellow) ,in case of Wood Tiger Moth form the basis of predator defence but as one goes towards the Northern Latitudes, melanization or a general blackening of the hindwing is necessary for maximal absorption of sunlight or thermoregulation.

The general blackening to which i refer is the deposition of melanin, a process called melanization. It is used by many organisms including us !! Its benefits include immune response, thermoregulation etc.

To give you an example, see the below picture of the samples which the authors took from Europe.


So, in general as one can see in the Alpine regions where the sunlight is very rare for the whole year, the moths have  less than 20% colouration !! (see, picture above (b))

But why??

It seems that higher melanization limits the amount of other pigments important in the warning signal, thereby setting the stage for atrade-off between defensive signalling and thermoregulation.

The question which the authors looked upon is something like this:

Do variation in male hindwing melanization is linked to thermoregulation and/or involved in a trade-off with protective benefits of colour ?

What did they find?

The authors started off with a combination of field based studies and predation experiments with artificial moths. Have a look at them:


  • The amount of melanization increased with increasing latitude in Wood Tiger Moth males from Estonia to north Finland.
  • Individuals in the Alps had a significantly greater amount of melanin covering their hindwings than those in central Finland.
  • Melanization also varied more among individuals in the Alpine region compared with central Finland.
  • Greater melanization also increased the average rate for warming up for the moths.
  • Every 10 per cent increase in the amount of melanin resulted in a 16 per cent increase in the odds of being attacked.

Taken together,the results show the likely existence of a trade-off between thermoregulation and predation risk with respect to the amount of melanin present on the hindwing in Wood Tiger Moths. Specifically, what they found was that greater amounts of melanin in both white and yellow males resulted not only in an increased ability to absorb radiation, but also increased the likelihood of attack by avian predators. The results provide evidence that the differences in costs and benefits of melanin in the two locations can drive phenotypic differences in the warning signal of males on broad and local geographical scales.

Take home message:

If an organism is good at having X, then it must come at some cost. And as X is very costly it does not mean that its not a successful strategy, if the benefits of the costly strategy(X) outweighs the high cost  !!

More on this:

  1. The redder the better: wing color predicts flight performance in monarch butterflies, PLoS One, 2012.
  2. Linking color polymorphism maintenance and speciation, Gray SM, McKinnon JS, TREE, 2007.
  3. Insect melanism: the molecules matter, True JR., TREE, 2003.
  4. Visual predators select for crypticity and polymorphism in virtual prey, Bond AB, Kamil AC., Nature, 2002.


Free Speech

I usually write about science, the exciting new papers which come up, and occasionally on philosophy. So, why have i suddenly gravitated to writing on social policies or to say more accurately – Why do i want to question our society and write about it ?

My fellow colleagues (and me included) are all adept at talking about the philosophies of  heaven & earth,  discuss the latest transgressions of our beloved politicians over a mug of hot, steaming coffee. But the moment our coffee mugs are empty, we stop thinking about the world outside our closed walls. We go back in our small cocoons called university where we don’t think about the big, bad world outside but eat and think science.But occasionally something happens in that big, bad world which forces us to look beyond our glass domes.

The Outcry

Such an event happened this year at the Jaipur Literary Fest, considered as the biggest literary event in Asia, held annually in Indian city of Jaipur  since 2006. In a panel discussion on “The Republic of Ideas,” with IBN7 Editor Ashutosh, Tehelka editor Tarun Tejpal, famed historian Patrick French, philosopher Richard Sorabji, and sociologist Ashis Nandy, which was moderated by, Urvashi Butalia. After an interesting discussion on the “promise” of the Indian Republic and Constitution, the exchange turned to the theme of corruption and the importance of the anti-corruption protests led by Anna Hazare.

In trying to deconstruct the sociology of corruption, Tarun Tejpal argued that we need to first understand the – “corruption” of  poor and the marginalised people in the society as an essential strategy to break the shackles of the suppressive nature of our rules, regulations and laws. Further on, he marked the “so-called diverse” Indian society as deeply divided, hierarchical and oppressive, our laws and societal rules, are mostly designed to “keep out” the oppressed from having their say. The corruption of “people like us” — an elitist which has both the resources and power to undermine the politico-judicial system — often goes unnoticed, and if discovered, rarely ever get prosecuted. The crimes of the “others,” in contrast, not only get prosecuted, but also generate outrage, in part because they do not have the necessary skills to successfully cover up their corruption.

“As long as this is the case, the Indian Republic will survive,”  said Prof. Ashish Nandy replying to Tejpal’s comments, citing the example of West Bengal, which he said was the State with the least extent of corruption. “In the last hundred years, nobody from the OBCs, SCs and STs has come to power there. It is an absolutely clean State.”

These remarks led to strong reactions from the audience, and one of the panelists  Mr. Ashutosh, said it was the “most bizarre statement” he had ever heard. Some members of the audience were also quite enraged to the remarks and asked Professor Nandy to retract them. Dalit activists, later on staged a demonstration against the so-called “offensive remarks,” and a First information report was lodged by tribal activist Rajpal Meena against Professor Nandy and Mr. Roy, for which the Section 506 (criminal intimidation) of the Indian Penal Code and Section 3 (1) of the Scheduled Castes & Scheduled Tribes (Prevention of Atrocities) Act was cited . The police have started to investigate the matter.

Later on, despite Prof. Nandy’s clarying remarks saying that he was taken out of context, the media ire against him hasn’t cooled down. In giving a small summary the editor of Tehelka magazine has this to say:

Why does it matter ?

Ashis Nandy’s choice of words, phrases, and examples can certainly be questioned. He is not known as an organised and media-loving public speaker. One can also beg to differ with both his argument and analysis. For example, the way he didn’t clarify his statement by differentiating the “corruption of the poor” and the “corruption of their leaders,”whose pure neglect of rules often results in them looting the very poor who also fall into their constituents. Nevertheless, Nandy’s argument that the “rules of the game” have been fixed by the ruling, elite class to which he too belongs, which remains a highly privileged lot, and hence, the deliberate neglect of those rules is an inevitable strategy for those seeking to survive and also for upward mobility, certainly has a lot of merit especially in India, where the income gap between rich and poor classes have widened. Clamping down on such nuanced utterances and confusing statements of the kind Prof. Nandy made will only make us a poorer democracy and Republic than what we already are.

Free speech is recognized in many western developed countries as the basis of their civilization. To disagree and be offended but still defend it to death. Voltaire famously said “I disapprove of what you say, but I will defend to the death your right to say it” and this is also their basis for democracy. It is on this precarious and precious right does a healthy civil society and political society depend. All societies that engage in preserving ‘sentiments’ of either the oppressor or oppressed by curbing speech have failed and continue to do so. It is shameful for any politician to call for curbs on speech simply on offense, it is further shameful and immoral for a freethought humanist group to call for a curb on free speech of an individual. There has been no compelling logically coherent explanation given other than non-sequitur engaging question begging statements.

Freedom of speech by State is everything to freethought soaked society and to grow rational, humanist thinking. ‘Sunlight is the best disinfectant’ has been said in the American supreme court, which has proven to be true. A society where all ideas are openly talked about and entertained no matter how abhorrent or distatesful, is a society that improves. America has done better than India and Pakistan partially due to this openness. What Ms. Mayawati has proposed is draconian, fascist and anti-humanist. Leaving aside there is a purposeful misunderstanding of a statement taken out of context in Prof. Ashish’s speech, even without context there is no logical and humanist excuse to jail him. It will remain an anti-humanist draconian and oppressive action which will only be of harm in precedent to freethought and freedoms.

The burden of proof lies with those who wish to curb a right. There is good review of free speech and its foundational premise in building civil society in the American court decision supporting Westboro Baptist Church. Idea of anti-racism is also open to criticism, which is the reason why there are racist academics who publicly engage in racist publications such as Satoshi Kanazawa. They are fought by social and academic boycott, not by legal sanction.

ACLU is known for protecting the civil liberties and is traditionally viewed as a liberal group. One of its finest moments came in  1978. I  am quoting that incident from ACLU’s website:

ACLU defended a Nazi group that wanted to march through the Chicago suburb of Skokie, Illinois where many Holocaust survivors lived. The ACLU persuaded a federal court to strike down three ordinances that placed significant restrictions on the Nazis’ First Amendment right to march and express their views. The decision to take the case was a demonstration of the ACLU’s commitment to the principle that constitutional rights must apply to even the most unpopular groups if they’re going to be preserved for everyone. Many now consider this one of the ACLU’s finest hours.

An important matter to take a note of is that this is not the first time when the largest democracy in the world, India has not clamped down free speech, which remains a fundamental right here. A simple look intoWikipedia for free speech violation gives me this huge list:

  • In February 2009, the police filed a complaint against Ravindra Kumar and Anand Sinha, the editor and the publisher respectively of the Kolkata-based English daily The Statesman. The police charged Kumar and Sinha under section 295A because they had reprinted an article from The Independent by its columnist Johann Hari. Titled “Why should I respect oppressive religions?”, the article stated Hari’s belief that the right to criticise any religion was being eroded around the world. Muslim protestors in Kolkata reacted to Hari’s belief by violent demonstrations at the offices ofThe Statesman.
  • In September or October 2007, the police in Pune arrested four Bangalore-based software-engineers for posting on the Internet an obscene profile of Chhatrapati Shivaji, a sixteenth-centuryMaratha warrior king, clad in female underwear.
  • In May 2007, a Buddhist group in Maharashtra’s Amaravati district said their religious sentiments were hurt, and filed a complaint against Rakhi Sawant, an actress, because she posed in a bathtub against a statue of Lord Buddha.
  • In March 2007, a newspaper editor BV Seetharam was arrested under the Sections 153A, 153B, and 295 of the IPC for allegedly promoting religious hatred. He had written articles criticizing the public nudity of the Digambara Jain monks.
  • In 2007, the authorities charged ninety-one-year-old Maqbool Fida Husain with hurting religious sentiments by painting Mother India as a naked woman.
  • In December 2006, a complaint was filed against cricketer Ravi Shastri for hurting the religious feelings of Hindus by his allegedly eating beef during a Test match in Johannesburg.
  • On 2 August 2006, two religious groups in Ahmedabad complained to the police that their religious sentiments were hurt because a garment-maker had printed text from the Hindu and Jain religions on clothing. The police filed the complaint as a matter under section 295.
  • In November 2012, Maharashtra Police arrested Shaheen Dhada (aged 21) for questioning the total shutdown in the city for Bal Thackeray’s funeral in a Facebook post, and also her friend Renu Srinivasan (aged 20) for liking her post. Although no religious issue was involved, the two were charged under Section 295 (A) for hurting religious sentiments, apart from Section 66 (a) of the Information Technology Act 2000.

So, in times like these when the world is considering India to be one of the next superpowers, how can a humble budding scientist like me stay quiet and listen to the regular subversion of free speech in my country. Sometimes its done in the name of religion, caste, political figure, some old archaic customs and what not !! You name it, and India will probably ban it in the name of protecting the cultural diversity and hate speech. What it needs is to define the boundaries, limitations and definitions of hate speech. Make free speech, really FREE.

In the end, i would like to reiterate the words of Shoma Chaudhury, Tehelhka’s editor:

“What is the whole idea of Freedom of Speech, without the idea of discomfort? If we are only going to speak in ways that would make each other feel comfortable, then we might as well give up on the idea of free speech in India.”

More on this:

  1. Two women arrested for Anti-Shiv Sena comments on Facebook, government orders enquiry, Economic Times, 2012.
  2. Mumbai shuts down due to fear, not respect, The Hindu, 2012.
  3. A Forgotten History, Outlook India, 2007.
  4. India’s First Blasphemy Prosecution, International Humanist and Ethical Union, 2002.
  5. Sacred text on clothes: fashion designer booked, Nerve, 2006.
  6. M F Husain loses home over nude ‘Mother India’, Express India, 2007.
  7. Case filed against Ravi Shastri for eating beef, Zee News India, 2007.
  8. Freedom of expression under attack, The Hindu, 2007.
  9. Pune cops book Orkut user, Times of India, 2007.
  10. Editor arrested for ‘outraging Muslims’, The Independent, 2009.
  11. Indian police probe Nandy caste remark (91live.in)



Okay, i agree i am not 60 years old retired chap who has started worrying about the inescapable, insidious start of significant physical–and sometimes mental–decline leading to a sort of death anxiety. Rather, i am in my late 20’s, single chap who recently has had some time to ponder about all things in life-big and small. And among all those one of the biggies is definitely – Death. I know you must be thinking what about the other things in life – Love, relationships, career or kids, don’t they matter at all? I agree with this assessment of yours that there are too many things in life to ponder about other than death. For death, is not a continuation of life  as all the religious books loftily say (brag?) about but death is a sort of full stop  An ending to a life, to all his/her dreams, thoughts, wishes. For nothing progresses after death come knocking at your door. And if i remember correctly, this was indeed the reason i began to think about it.

Death or lets say Mortality (for those people who begin to equate the word death with the ghastly image of a tall hooded chap with a scythe in its hand or the Reaper, as is known in some circles) is indeed one of the neglected things in life. I am reminded of Saul Bellow‘s ruminations about it: Death is the dark backing that a mirror needs if we are able to see anything. 

Despite being so important, we daily run and hide from it seeking shelter in humor, hedge against it with good works, shun reminders of our mortality. Yet we all share the reality of mortality, and we know it, try as we might to throttle our thoughts about it.

The previous evening i had a mild-tempered discussion with a friend who was quite sure that one can live one’s life without even pondering about death if you live by the name of god. His prime argument being you live on this earth as god’s creation, consume god’s gifts ( food, air etc) and then when we die, we simply shift our residences to the A-class facilities called Heaven. And the faithful buy their ticket to heaven by incessantprayers. At this juncture of our conversation, i was reminded of the definition of “prayer” by Ambrose Pierce in his Devils’s Dictionary:

Prayer: A petition that the laws of nature be suspended in favour of the petitioner; himself confessedly unworthy. 

I chuckled and decided to share in the joke hidden here.

“The man who prays is the one who thinks that god has arranged matters all wrong, but also thinks that he can instruct god how to put them right.”

Somewhere in here is the realisation that nobody is in charge, and hence this call to prayer, this call to delay or deny the realisation of mortality is“self-cancelling” as the late Hitchens said.

Now, i understand this faith, but just didn’t see why we should believe in that. So, i decided to put my obliging friend on a test of faith. What about a devout fellow with a life-threatening metastasing  tumour, (or as Hitchens described it “blind, emotionless alien” ) wouldn’t he/she want to prolong his/her life to be with friends, family and kids? Or does he/she decide to give up earth and migrate to heaven? The answer in many cases comes to the fact that everyone appreciates the modern benefits of medicine and hence prolong their own life. So, saying that they don’t think about mortality would be simply wrong and quite a fallacious statement in itself. And invoking the argument that gods awards the appropriate cancers is strange, since you must also account for the numbers of infants who contract leukemia. Hence, both the arguments don’t work – devout people don’t think of mortality and they just want to go heaven. By the way, the evening ended by a toast to our status as a mortal animal and immortal friendships we make while alive

Still are thy pleasant voices, thy nightingales, awake;

For Death, he taketh all away, but them he cannot take.

(From, the ode of Calimachus to his beloved Heraclitus)

I still remember when as a kid living in the riotous aftermath of the bloodyBabri Masjid demolition,  witnessing the terrible shock of bodies lying bruised, some killed. One would think the carnage which men undertook in the name of an invisible, inactive and hypothetical god  might have sensitized me to the effects of our dear friend, death. But alas, in all those sufferings and even when popping up this latest pill to alleviate my debilitating spine, i am constantly reminded of our perilous position. Death or Mortality is our constant companion, whether being brought upon us due to irrational acts of man or the unforgiving nature of blind chance it always strikes a note of fear.

I have seen the moment of my greatness flicker,

And i have seen the eternal Footman hold my coat, and


And in short, I was afraid.

(From, T.S. Eliot, “The Love Song of J.Alfred Prufrock“)

So where does it leave me? I do realise that we are mere mortal animals and cannot avoid death by incessant/irrelevant prayers or even by the ever-mordernisation of medicine. I have seen death dancing in people’s eyes willing to kill for the same god who apparently also gives life to the victim. I have seen death in the faint- heart beats of a dying man. I have seen them all, you would say. And yet in some corner of my mind, i am still afraid of its cold embrace, it’s ever watching eyes and its constant companionship. But at least i am not blind to it and best of all i can count it to be my ever vigilant friend. Ahh don’t worry i am not being drawn into  Nietzsche.

Death has this much to be said for it:

You don’t have to get out of bed for it.

Wherever you happen to be

They bring it to you – free

(Kingsley Amis)

In an ode to the polemical genius, Christopher Hitchens



In one of the biggest funding exercises ever, European Commission has selected Prof. Henry Markrams (pictured above) dream project – The Human Brain Simulation Project for a mammoth grant of € 1 billion over a period of ten years.

The Human Brain Simulation Project or the Blue Brain project has been a center of quite a controversy ever since it started in 2005 at the  École Polytechnique Fédérale de Lausanne (Switzerland). It aims to create a synthetic brain by reverse engineering a human brain down to its molecular details. It uses the famed Blue GENE supercomputer  and uses Michael Hine’s NEURON software to recreate neural connections not just by using Artificial Neural Networks but by a closer approximate model of neurons.

What is it all about?

Neuroscientists have been trying to understand the inner workings of our human brain for some centuries now. First came, the detailed anatomical drawings by Rufus of Ephesus, Galen and Leonardo da VinciThen English physician Thomas Willis published his Anatomy of the Brain which assimilated all its inner structures. The goal of understanding what brain is and how it does work started from these anatomical drawings and has continued on to constructing detailed mathematical models of how each of the cells within it work. Of course, i am talking about the famous Hodgkin-Huxley model which for the first time describes how action potentials in neurons are initiated and propagated.

The quest for understanding how billions of neurons come together in a complex network with millions of feedback loops and yet function so harmoniously without any hint of chaos is considered to be one of the Holy Grails of Science. In this picture comes Prof Markram’s Human Brain Simulation project. With advanced supercomputer at one side, and brilliant electrophysiologists at the other the aim has been to model not just the neural circuits involved in, say, the sense of smell, but to model everything,

“from the genetic level, the molecular level, the neurons andsynapses, how microcircuits are formed, macrocircuits, mesocircuits, brain areas — until we get to understand how to link these levels, all the way up to behaviour and cognition”

Progress until now?

Obviously to even start off this mammoth task, one has to first demonstrate this so-called unified approach on a smaller scale. And that was indeed what he started off with. From 1995 to 2006 he collected data on the simulation of a rat neocortical column, which can be considered the smallest functional unit of the neocortex (the part of the brain thought to be responsible for higher functions such as conscious thought). Such a column is about 2 mm tall, has a diameter of 0.5 mm and contains about 60,000 neurons in humans; rat neocortical columns are very similar in structure but contain only 10,000 neurons (and 108 synapses). By December 2006, Markram was able to map all the types of neurons and their connections in that column.

By 2008, the researchers had linked about 10,000 such models into a simulation of a tube-shaped piece of cortex known as a cortical column. Now, using a more advanced version of Blue Gene, they have simulated 100 interconnected columns.This has indeed proven that  such unifying models can, as promised, serve as repositories for data on cortical structure and function.

All of this has only been possible due to the large-scale advances in supercomputing technology and data storage facilities. The computer power required to run such a grand unified theory of the brain would be roughly an exaflop, or 1018 operations per second, which were quite hopeless in the 1990’s when Markram started off the project. But as available computer power doubles roughly every 18 months, soexascale computers might be available by the 2020’s.


There has been some criticisms to this project, and that has to do with the media hype generated by Markram. His critics argue that he has been making his case through talks, media interviews, well-placed ads, and through the traditional means of publishing articles, reviews etc. The detractors also argue that the Markram’s bottom-up approach might yield such a model  which could be so detailed that it is no easier to understand than the real brain. Also, the progress till now has not been daunting either, as the rat neocortex has no inputs from sensory organs or outputs to other parts of the brain, and produces almost no interesting behaviour.

But despite all the criticism, one hopes that this gargantuan project with its lofty aim would yield interesting results, even if not a complete replica of human brain but at least a shadow simulacrum would be enough. For all the critics, who are too afraid of Markram’s bold new ideas I would reiterate James Russell Lowell:

 “Creativity is not the finding of a thing, but the making something out of it after it is found.”

More on this:

  1. Turing at 100: Legacy of a universal mind, Nature News, 2012.
  2. European researchers chase billion-euro technology prize, Nature News, 2011.
  3. Bioinformatics: Industrializing neuroscience, Markram, Nature, 2007.
  4. The Blue Brain Project, Markram H, Nature, 2006.
  5. Human Brain Project, EU Initiative.
  6. The Blue Brain Project @ EPFL



Well, we have all heard the age-old adage of bigger brains being the better and how humans have the largest brain-to-body ratio among all animals. So, scientists have been asking this question: What would happen if the size of brains continue to increase? Would the organism become more intelligent? Would there be any cost?

Evolutionary biologists in 1990’s proposed the The Expensive Tissue Hypothesis to account for the costs and benefits of brain size. Brains are highly useful organs; more amount of brain cells would allow for more flexibility in doing different behaviours, better control of larger bodies, and, obviously intelligence. But if bigger brains were always better, then every animal would have them. So, the biologists reasoned, there has to be a downside of such increased brain size. Hence, the hypothesis suggests that while having larger brains are awesome, however their extremely high energetic cost limits their size and tempers their growth.

For example in humans, our brains take up just 2% of our bodies, but they take up a whopping 20% of our energy requirements. And one has to wonder: if our brains use up that much energy, which body parts have paid the price? The hypothesis suggested our guts have suffered, but the  extra intelligence gained by having more brain cells made up for more efficient foraging and hunting, hence overcoming the obstacle. Despite over a century of research on the evolution of brain size, empirical support for the trade-off between cognitive ability and energetic costs is based exclusively on correlative evidence and the theory remains controversial.

Source: planetanimalzone.blogspot.com

What they did?

A study published in Current Biology this month, led by Niclas Kolm and others have attempted to solve this question by conducting an empirical study on guppies (Poecilia reticulata, pictured above).  They used artificial selection on relative brain size in the guppy, to provide a direct test of the prediction that increased brain size is genetically associated with increased cognitive ability but that a large brain is also traded off against gut size and results in reduced reproductive performance. Breaking it down, they had four steps:

  1. To test the evolutionary response to divergent selection on relative brain size.
  2. The cognitive ability of large and small-brained individuals was tested using an associative learning assay designed to investigate numerical quantification, a relatively advanced form of cognition.
  3. The correlated evolutionary response of gut size in response to direct selection on brain size was also tested.
  4. Lastly, it was tested whether the important proxies of reproductive fitness (offspring number, offspring size, age at first reproduction) are anyhow affected by brain size evolution.

What they found?

First, the team selected for larger and smaller brains from the available natural variation in guppies. They  then successfully created smart guppies that had brains about 9% larger than their counterparts through artificial selection. Then, they put them to the test. While the males seemed to gain no benefits from possessing the larger brains, thefemales with bigger brains were significantly better at the tasks.What they found was that the evolution of relative brain size in guppies can be a fast process when under strong directional selection as in the study. Also, the relative brain size was found to be highly heritable in both sexes.


What was really remarkable was the cost of these larger brains. Gut size was found to be 20% smaller in large-brained males and 8% smaller in large-brained females. The reduced digestive system seemed to have serious reproductive consequences,  as the smarter fish produced 19% fewer offspring in their first clutch, even though they started breeding at the same age as their lesser bright counterparts. One thing to keep in mind here which the authors also noted, was  that this experiment was conducted in an idealized tank setting with all the guppies receiving plenty of food—So what about the wild, where resources are harder to come by? How much of a cost does a reduced gut have when resources are scarce?

Though, there are still many questions to be answered. For example, the authors aren’t entirely sure why females were the only ones to show cognitive improvement with larger brains. They suggest that, perhaps, the measure of intelligence used (the numerical task presented to the guppies) may be favourable toward female behaviors. As is known from literature, in the guppy, females are more active and innovative while foraging. As females feed more, so they may have had more time to associate the cue with food in the experimental design.

What now?

The clear trade-off which the authors see between brains and guts, is an important finding. By providing an empirical evidence for the physiological costs of brains, this study provides the first direct support for the expensive-tissue hypothesis, and can provide us with insights into how our own big brains evolved. One of the prevailing hypothesis for our own brain growth is that the incorporation of more animal products into our diets, through hunting or cooking or however, allowed us to obtain more energy from less food, thus offsetting the cost of a reduced gut. The less food we needed to eat for the same amount of energy, the more our brains could grow even if our guts suffered for it. The debate, however, is far from over. Comparative analyses in primates don’t support a gut-brain tradeoff, and there are certainly plenty of other hypothesis as to how and why we developed our massive lobes, and what prices our bodies paid for them.


Source: Stephanie Mitchell/Harvard Staff Photographer

A recent paper published by Arvind Subramaniam (pictured above) and co-authors in Proceedings of National Academy of Sciences have attempted to provide a solution to a decades old problem in genetics.

Though the genetic code, the rules by which DNA gets transcribed to RNA and then translated to proteins, is quite well understood, but what has remained puzzling is the degeneracy of the genetic codeunderlying protein synthesis. Now before understanding more about what they did, let me give you a brief primer on the problem itself.

What is it all about ?

Decoding of DNA is accomplished by the ribosome, which links amino acids in an order specified by mRNA (messenger RNA), usingtransfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time.  So mathematically we can calculate that, with four different nucleotides (in RNA), a three nucleotide code  could code for a maximum of 43 or 64 amino acids. However, in the process of translation (RNA to proteins) only 20 kinds of standard amino acids are produced. So, many of these groups of nucleotides, called codons  produce same amino acids i.e, code synonymously.  For example, the amino acid can be produced in six different ways. A cool figure below shows all the 64 codons and the different amino acids they code for.


This apparent degeneracy has been a core problem in genetics, i.e, whether those seemingly synonymous codons truly produced the same amino acids, or whether they represented a second, hidden genetic code. Now Harvard researchers have published a possible solution to this problem, and they hope the solution would lead to developing new methods to fight resistant bacteria.

How did they solve it?

To try and decipher this synonymous coding problem, they decide to use a simple bacterium Escherichia coli. First they considered the synonymous codons for seven amino acids: Leucine, Arginine, Serine, Proline, Isoleucine, Glutamine, and Phenylalanine. This set of seven amino acids is representative of the degeneracy of the genetic code,as it includes six-, four-, three-, and twofold degenerate codon families. Then they constructed a library of 29 yellow fluorescent protein (YFP) gene variants, in such a way that each version of the gene could code for a specific amino acid. Then all these genes were inserted into E.coli. To test whether the codons function similarly or not, they applied environmental perturbations on E.coli. This perturbation was in the form of amino acid availability. They monitored growth and YFP synthesis in these strains during amino acid-rich growth as well as during limitation for each of the seven amino acids.

What they found, was quite startling that under different environmental conditions (amino acid availability) the codons produced proteins at a different rate.  If the bacteria are in an environment where they can grow and thrive (amino acid rich), each synonymous codon produces the same amount of protein, but if they are starved of an amino acid, some codons produce a hundredfold more proteins than others.

The reason for such differences in protein production lie in the nature oftRNA, the Transport RNA which ferries the amino acids to the cellular machinery that manufactures proteins. The authors managed to rule out the usual rules associated with tRNA abundance and codon usage. Rather,it was the competition among tRNA isoacceptors foraminoacylation which was the underlying reason for the robustness of protein synthesis. In plain-speak, what this means that different tRNA molecules have different levels of amino acid carrying efficiency. So, if some tRNA molecules are not able to deliver the amino acid to where it needs to be, the cell would not be able to manufacture the proteins it needs. In an environment where amino acids are in short supply, that ability to hold onto them becomes very important.While the system helps cells to make certain proteins efficiently under stressful conditions, it also acts as a biological fail-safe  allowing the near-complete shutdown in the production of other proteins as a way to preserve limited resources.

What now?

Given the universality of the genetic code, it would very interesting to explore what role (if any) differences in the seemingly synonymous portions of the genetic code may have in other organisms. Also, in diseases like cancer, the cancerous cells deplete amino acids faster than normal cells, so given that environmental perturbations lead to different protein production efficiencies, would it be possible to devise any interventions or treatments to combat them!!

More on this:

  1.  Degeneracy and complexity in biological systems, Edelman GM, Gally JA, Proceedings of National Academy of Sciences, 2001
  2. Cooperation between translating ribosomes and RNA polymerase in transcription elongationProshkin S, Rahmouni AR, Mironov A, Nudler E, Science, 2010
  3. The GCN2-ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivation, Ye J, et al., EMBO J, 2010
  4. High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma, Zhou Y, Goodenbour JM, Godley LA, Wickrema A, Pan T, Biochem Biophys Res Commun, 2009



In a painful yet laughable story, we see a Louisiana senator asking a high school teacher whether E.coli can evolve into people !! This happened during the Senate Education Committee’s hearing on Senator Karen Carter Peterson‘s bill to repeal the odious Louisiana Science Education Act (the “LSEA”). Though the act was repealed by a tiny majority, but this kind of ignorance (in the face of reason) is quite scary.

So, lets come back to the strange quip by the senator. On asking the biology teacher, whether there was any evidence of evolution actually happening in modern world, she decided to put forth one of the best evolution experiments ever – Richard Lenski’s decades long experiment on E.coli adaptation . At this point the senator quipped:“They evolve into a person?”

Now this kind of question, points out to the main arsenal which creationists use in their never-ending, pointless battle against evolutionary biology and i.e, How does the tiny changes in the gene pool of a population translate into giant, morphological changes over time ?

Microevolution which is basically, a change in gene frequency within a population is understandable they say (though, not all of them), but what they vehemently deny is macroevolution. The “creationist skeptics” refuse to be convinced unless, as the senator  points out, they see an example of a bacterium directly transforming into a human being.

For the creationists like the Senator in question, this remains a sort of trump card which they wave every time in a debate about evolution. What they don’t realise is that, if they study a bit more about evolutionary biology then they can answer it themselves. The parsimonious explanation of how mutation, genetic drift, migration and natural selection can bring about  evolution at both levels – micro and macro is something which these creationists still need to understand.

More on this:

  1. How 19-year-old activist Zack Kopplin is making life hell for Louisiana’s creationists, Io9.com,2013
  2. Senator Asks For Proof Of Evolution, Discovers He Doesn’t Actually Understand What It Is