Wendy Doniger & fungi

The best stories are those that help us give new meanings to old objects, accustomed ideas and known tales. This notion applies both to articles in a newspaper and a work of fantasy fiction. It’s why I think I enjoyed The Immortals of Meluha despite its predictable plot and the familiar mythos. The author, Amish Tripathi, reinterpreted gods as human champions, paving the way for them to be judged by the same standards that mortals were.

However, the plot element I enjoyed following the most was that of the Somras, a purported “drink of the Gods” that granted its consumers immortality, and its evolution over the course of three books from being a panacea to a blight. If he had to carefully negotiate his characters between the guiding rails of Hindu values and rituals, Tripathi might have had that extra freedom, on the other hand, to manipulate the origins of Somras as a plot device of his own making. This because the drink, which finds mention in the Vedas as well as Zoroastrian lore, is of unknown origins.

A short detour through Wikipedia tells us that Somras, or the soma plant (the “ras” suffix meaning “essence”), is considered an entheogen: a chemical substance, such as but not limited to psychedelic drugs, used for religious purposes. And among entheogens, debate over the last century has almost invariably centered on two candidates. In 1968, Robert Gordon Wasson and another person proposed that soma could be Amanita muscaria, the fly-agaric mushroom. Only three years later, a vedic scholar named John Brough suggested the stimulant called ephedrine, particularly when extracted from the plant Ephedra sinica.

What I found remarkable is the combination of exegesis and botany/mycology, where experts worked with the scientific knowledge of the chemical properties of plants/fungi and the critical interpretation of historical texts to deduce what soma could be. Wasson was such an expert, an ethno-mycologist. He was assisted furthermore by a vedic scholar named Wendy Doniger O’Flaherty. It was slightly surprising to learn of Doniger’s involvement with Wasson’s work. Thanks to my ignorance, I hadn’t heard of Doniger’s name before early 2014, when her book The Hindus: An Alternative History was recalled in India by its publisher Penguin after a frivolous lawsuit alleging that it was outraging religious feelings. She appears to have dropped the O’Flaherty from her name on books by the late-1990s.

A cursory glance of her bibliography reveals themes like eroticism, asceticism, gender issues and religious politics. Add to that helping curious minds figure out the identity of prominent fungi in Hindu mythology – the breadth of her knowledge is inspiring. Then again, I do feel like I’m admitting Doniger’s knowledge of Indian history is more fascinating than Indian history itself, but I’m okay with that.

Toll of Jure landslide mounts

On August 2, a landslide in Nepal’s Sindhupalchowk district resulted in 33 deaths, with more than 120 missing and 400 displaced. A preliminary survey by the local District Disaster Relief Committee (DDRC) revealed 115 houses had been completely destroyed. The Nepali government has since declared all missing persons dead, bringing the total death toll to 150+. Other damages include a two-km section of a highway, the reconstruction of which, according to the International Centre for Integrated Mountain Development (ICIMOD), is “nearly impossible”, and two gates of the Sun Koshi Hydropower Project.

People and households affected by the Jure landslide, by village. Source: DDRC
People and households affected by the Jure landslide, by village (link to chart and data). Source: DDRC

Satellite images of the area have shown that it’s been landslide-prone since at least 2011. Given the damage to the hydroelectric power project, the incident is another reminder that the Himalayan region presents significant geological threats to hydroelectric projects being planned in the region. GPS investigations in the past have revealed that the Lesser Himalayas, which the country of Nepal straddles, are rising at ≤ 3 mm/year due to movements on active faults, landslides being one symptom of this. As this article in Current Science argues, “If the idea is to have environment-friendly power projects, then the planners and dam builders must not ignore the geological reality of the geodynamically sensitive region”.

Following up on the DBT/DST OA policy

Earlier in July, a group of people working with the Departments of Biotechnology and Science & Technology (DBT/DST) of the Government of India had drafted an open access policy covering research funded by federal grants, and mandating their availability in a national repository.

The move was lauded because it meant Indian academia was finally making an attempt to embrace open access publishing, as well as making research labs more tractable and accountable about how they spent the people’s money. However, there was some ambiguity about whether the policy would address the issue of scientists typically preferring to publish their work in high impact factor journals, and the tendency to evaluate them on the basis of that number.

There were also questions about who would pay for maintaining the national OA repository as well as the institutional repositories, how it would address institutional reluctance, and if “glamorous” journals like Nature, Cell and Science – which prohibit self-archiving of published papers – would support DBT/DST.

Last week, I met Prof. Subbiah Arunachalam, one of the people on the committee that drafted the policy, and asked him about the policy’s exact goals. He then spoke at length about the its origins and what it would and wouldn’t do.

For starters, he said that the policy will negate institutional reluctance by requiring all scientists applying for federal grants to submit the ID of their previous papers in the OA repository. It will also allow only the Government of India to keep track of and evaluate the research and the scientists it funds.

On the other hand, it won’t address scientists’ preference for high impact factor journals (such as Nature, Cell and Science), and it definitely won’t interfere with how institutions choose to evaluate their scientists – at least for now. In effect, the policy is a purely people-facing gesture and not a solution to any of the other problems facing the Indian research community, and it’s doubtful what it will do to check institutional nepotism.

The drafting committee is now looking for comments, suggestions and other feedback on the document, while waiting for a go-ahead from a government that is likely to take its time.

The policy draft does mention that the DBT/DST will maintain the repository, but Prof. Arunachalam couldn’t speak about the institutional repositories. In fact, he said that concern was farther in the future than getting those journals prohibiting self-archiving to make an exception for India’s scientists, and if they don’t, to allow pre-prints of the respective papers.

The eventual goal would be to set up a queriable database of citations, along the lines of PubMed but encompassing not just medical or biological literature but also for physics, he added.

Some research misconduct trends by the numbers

A study published in eLIFE on August 14, 2014, looked at data pertaining to some papers published between 1992 and 2012 that the Office of Research Integrity had determined contained research misconduct. From the abstract:

Data relating to retracted manuscripts and authors found by the Office of Research Integrity (ORI) to have committed misconduct were reviewed from public databases. Attributable costs of retracted manuscripts, and publication output and funding of researchers found to have committed misconduct were determined. We found that papers retracted due to misconduct accounted for approximately $58 million in direct funding by the NIH between 1992 and 2012, less than 1% of the NIH budget over this period. Each of these articles accounted for a mean of $392,582 in direct costs (SD $423,256). Researchers experienced a median 91.8% decrease in publication output and large declines in funding after censure by the ORI.

While the number of retractions worldwide is on the rise – also because the numbers of papers being published and of journals are on the rise – the study addresses a subset of these papers and only those drawn up by researchers who received funding from the National Institutes of Health (NIH).

pubsfreq

Among them, there is no discernible trend in terms of impact factors and attributable losses. In the chart below, the size of each datapoint corresponds to the direct attributable loss and its color, to the impact factor of the journal that published the paper.

tabpublic 15-08-2014 100128

However, is the time to retraction dropping?

The maximum time to retraction has been on the decline since 1997. However, on average, the time to retraction is still fluctuating, influenced as it is by the number of papers retracted and the nature of misconduct.

trendTimeToRetr

No matter the time to retraction or the impact factors of the journals, most scientists experience a significant difference in funding before and after the ORI report comes through, as the chart below shows, sorted by quanta of funds. The right axis displays total funding pre-ORI and the left, total funding post-ORI.

prepostfund

As the study’s authors summarize in their abstract: “Researchers experienced a median 91.8% decrease in publication output and large declines in funding after censure by the ORI,” while total funding toward all implicated researchers went from $131 million to $74.5 million.

There could be some correlation between the type of misconduct and decline in funding, but there’s not enough data to determine that. Nonetheless, there are eight instances in 1992-2012 when the amount of funding increased after the ORI report, of which the lowest rise as such as is seen for John Ho, who committed fraud, and the highest for Alan Landay, implicated for plagiarism, a ‘lesser’ charge.

incfundFrom the paper:

The personal consequences for individuals found to have committed research misconduct are considerable. When a researcher is found by the ORI to have committed misconduct, the outcome typically involves a voluntary agreement in which the scientist agrees not to contract with the United States government for a period of time ranging from a few years to, in rare cases, a lifetime. Recent studies of faculty and postdoctoral fellows indicate that research productivity declines after censure by the ORI, sometimes to zero, but that many of those who commit misconduct are able to find new jobs within academia (Redman and Merz, 2008, 2013). Our study has found similar results. Censure by the ORI usually results in a severe decrease in productivity, in many cases causing a permanent cessation of publication. However the exceptions are instructive.

Retraction Watch reported the findings with especial focus on the cost of research misconduct. They spoke to Daniele Fanelli, one part of whose quote is notable – albeit no less than the rest.

The question of collateral damage, by which I mean the added costs caused by other research being misled, is controversial. It still has to be conclusively shown, in other words, that much research actually goes wasted directly because of fabricated findings. Waste is everywhere in science, but the role played by frauds in generating it is far from established and is likely to be minor.

References

Stern, A.M., Casadevall, A., Steen, R.G. and Fang, F.C., Financial costs and personal consequences of research misconduct resulting in retracted publications, eLIFE. August 14, 2014;3:e02956.

Life on Titan’s world of goo

In the August 8 issue of Science, an international team of scientists has a paper that submits evidence of life in an asphalt lake in Trinidad. Despite having a low water content of 13.5%, it still possesses methane-digesting microbes huddled up in tiny water droplets. One of the authors, Dirk Schulze-Makuch, speculates in an Air & Space Magazine article that the find could have important implications for Saturn’s moon Titan, which is wrapped in chemistries similar to what was found in the lake minus the presence of liquid water.

In fact, its atmosphere is mainly nitrogen, with lakes of liquid methane and ethane on its surface. So, that there are extremophiles living in a world of goo means not all hope is lost for alien life to form on Titan, no matter that such hopes are still too far beyond the ambit of scientific conservatism inspired by how little we know about life’s origins. Nevertheless, the Science paper isn’t the first to demonstrate that life can exist in such extreme conditions similar to those spotted on planetary bodies in the Solar System; in fact, going by previous reports, it isn’t likely to be the last either.

In a 2011 study published in Microbial Biotechnology, South American researchers reported the presence of a fungus, Neosartorya fischeri, that could metabolize asphaltene, “which is considered the most recalcitrant petroleum fraction”. Their work in turn draws from a 1993 study that proved asphalt is susceptible to reacting with certain extracellular enzymes.

However, Schulze-Makuch’s article makes many assumptions. For example, Titan is much colder than Trinidad’s Pitch Lake, a tropical deposition of oil rising up from a tectonic fault at its bed. For another, it is not known if Titan harbors liquid water, which – at least on Earth – is known to decisively encourage the formation of life, just as it did in the lake.

7770_18601_1

Image: Two pairs of moons make a rare joint appearance. The F ring’s shepherd moons, Prometheus and Pandora, appear just inside and outside of the F ring. Meanwhile, farther from Saturn the co-orbital moons Janus (near the bottom) and Epimetheus (near the top) also are captured. This view looks toward the sunlit side of the rings from about 47 degrees above the ringplane. Credit: NASA/JPL-Caltech/Space Science Institute

Fortunately – rather, optimistically – astrobiologists have been able to rationalize how life could form on Titan. In 2005, Chris McKay and Heather Smith, both astrobiologists at NASA Ames Research Center, were able to come up with a mechanism by which methanogenic microbes in Titan’s troposphere could be metabolizing acetylene, ethane and some other organic compounds – of which the moon has plenty – to release 54-334 kJ/mol, an amount of energy that similar extremophile critters on Earth have been known to get by on.

They also think it’s possible that the microbes could be catalyzing biochemical reactions despite the low temperature, around -180 degrees Celsius. In either case, their calculations are dependent on the microbes consuming hydrocarbons along with atmospheric hydrogen – an adjustment for convenience. Being a gas with no other sources or sinks in Titan’s atmosphere, any dip in its concentration could be a sign of life, albeit a distant one. McKay had said in a NASA press release in 2010 that “We suggested hydrogen consumption because it’s the obvious gas for life to consume on Titan, similar to the way we consume oxygen on Earth.”

His and Smith’s hypothesis found some validation in that year – 2010 – when the Cassini space probe found anomalous deficiencies of hydrogen and acetylene, which should be evenly distributed around the moon but weren’t, meaning they were disappearing into somewhere or something, like being consumed. “If these signs do turn out to be a sign of life, it would be doubly exciting because it would represent a second form of life independent from water-based life on Earth,” McKay had said.

Just as well, some other astrobiolgists think the cosmic rays bombarding Titan’s atmosphere could be transforming acetylene into more complex hydrocarbons, constituting the non-biological explanation that scientists would like to have out of the way first. Even today, this attitude hasn’t changed because the basis of methanogenic life is still very theoretical, a possibility hinged on chemical reactions worked out by supercomputers. Yet, it’s a tantalizing possibility.

In a 2004 paper by Steven Benner, University of Florida, et al, the authors discuss how life could form without liquid water if only a few other conditions are met: a thermodynamic disequilibrium (a natural mechanism to maintain periodically varying temperatures), “temperatures consistent with chemical bonding” and the presence of a solvent system. The paper itself begins by questioning not how life originated but, in deference to its great adaptability, why life on Earth is what it is.

I reproduce a paragraph from it that I find provides a fitting explanation to why the search for life on Titan (and perhaps also Io and Enceladus) is worth keeping up:

The universe of chemical possibilities is huge. For example, the number of different proteins 100 amino acids long, built from combinations of the natural 20 amino acids, is larger than the number of atoms in the cosmos. Life on Earth certainly did not have time to sample all possible sequences to find the best. What exists in modern Terran [i.e. Earth-bound] life must therefore reflect some contingencies, chance events in history that led to one choice over another, whether or not the choice was optimal.

It’s also after 2004 – in 2013, actually – that we also discovered that Titan might be running out of methane soon. Studies conducted since around 2005 showed that the moon’s source of methane could be less from photochemical reactions in its atmosphere and more from subsurface pockets where the gas could have been trapped. According to a NASA statement, “the current load of methane at Titan may have come from some kind of gigantic outburst from the interior eons ago possibly after a huge impact,” and could run out in tens of millions of years, a short span on the geological timescale.

If so, then, if methanogenic life hasn’t already formed but is likely to, it better do so quickly. If our models have an as yet undetected or undetectable flaw, then, as always, time will tell. If, ultimately, life is already present on Solar System’s second-largest moon, then one can only hope it’s as versatile as the world that hosts it.

~

References

  1. Scientists Find Life in a Lake of Oil, Air & Space Magazine. Accessed August 10, 2014.
  2. Meckenstock, R.U. et al, Water droplets in oil are microhabitats for microbial life. Science, 8 August 2014: 345 (6197), 673-676. doi: 10.1126/science.1252215
  3. Uribe-Alvarez, C., Ayala, M., Perezgasga, L., Naranjo, L., Urbina, H. and Vazquez-Duhalt, R. (2011), First evidence of mineralization of petroleum asphaltenes by a strain of Neosartorya fischeri. Microbial Biotechnology, 4: 663–672. doi: 10.1111/j.1751-7915.2011.00269.x
  4. Fedorak, P.M, Semple, K.M., Vazquez-Duhalt, R., Westlake, D.W.S., Chloroperoxidase-mediated modifications of petroporphyrins and asphaltenes. Enzyme and Microbial Technology, Volume 15, Issue 5, May 1993, Pages 429–437. doi: 10.1016/0141-0229(93)90131-K
  5. Tobie, G., Lunine, J.I. and Sotin, C., Episodic outgassing as the origin of atmospheric methane on Titan. 28 November 2005, Nature 440, 61-64. doi:10.1038/nature04497
  6. Benner, S.A., Alonso Ricardo, A. and Carrigan, M.A., Is there a common chemical model for life in the universe?. Current Opinion in Chemical Biology, 2004, 8:672–689. doi: 10.1016/j.cbpa.2004.10.003

Curious Bends – Indian Luddites, an academic career, the great forgetting and more

Curious Bends is a weekly newsletter about science, tech., data and India. Akshat Rathi and I curate it. You can subscribe to it here. If have feedback, suggestions, or would just generally like to get in touch, just email us.

1. Say with pride that we’re Luddites

Science is often confused with technology in India. The consequences range in flavour from amusing to dire – for example, we celebrate rockets, not rocket scientists. So we fund rockets, not rocket scientists. This piece explores the history of this perception with interesting and insightful episodes from the past. Beware, though: some of them have evolved many grey areas. (8 min read)

2. India’s hopes for development rely on its public health strategies

That India is neither a middling nor a superpower nation comes down to how good access to health, water, sanitation and education in it are. Health, in particular, needs special attention because of two reasons. First: India shares a disproportionate fraction of the world’s disease burden – especially among non-communicable diseases. Second: the skill and capital needed to resolve the problem is controlled by private interests operating only at state-wide levels. (10 min read)

3. Forgoing a fat pay cheque is totally worth it to become an academic

“The placement season is just starting for the 2015 graduates. And newspapers are already talking about crore+ salaries this year. That it would be for a very small number of graduates is lost on most people. And in this race to get the biggest package, one career that is often forgotten is that of an academic.” (6 min read)

+ The author, Dheeraj Sanghi, is a professor of computer science at the Indian Institute of Technology, Kanpur.

4. China’s JUNO launches international collaboration while India’s INO looks on

The Jiangmen Underground Neutrino Observatory is expected to be completed by 2020, and will search for answers to unsolved problems in neutrino physics. More importantly, it will be China’s second big neutrino experiment and second also to feature an international collaboration of scientists and institutions. The India-based Neutrino Observatory, also foreseeing completion by 2020, is yet to find similar interest. As has frustratingly been the case, it’s the scientists who lose out. (3 min read)

5. Indian universities ban dissections

A campaign led by People for the Ethical Treatment of Animals has borne its fruits: a central body that sets standards for university education in India has banned dissections in zoology and life sciences courses. This move solves some legitimate problems but exacerbates some silly others. For one, removing endangered animals from the table doesn’t mean non-endangered ones can’t be put there. For another, assuming “most zoology students do not use the knowledge gained from dissections after they graduate” excludes those who do, and education is for everybody. (3 min read)

Featured longread: What happened to each one of us before the age of seven?

“… if the memory was a very emotional one, children were three times more likely to retain it two years later. Dense memories – if they understood the who, what, when, where and why – were five times more likely to be retained than disconnected fragments. Still, oddball and inconsequential memories such as the bounty of cookies will hang on, frustrating the person who wants a more penetrating look at their early past.” (18 min read)

Chart of the week

Gone are the days when Britain built most of the world’s ships and ruled the seas. By the end of the Second World War, the US was producing 90% of all the world’s ships by weight. By the 1990s, though, Japan and South Korea had in turns acquired the title. Now this decisive distinction could belong to China. Today, it produces around 35% of the world’s ships. The Economist has more.

World shipbuilding  of total in gross tonnage

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Wealth and religiosity disagree while some Hindus look the other way

My extended family’s annual trip to Tirupati is coming up. Because a more indecisive bunch doth not exist, my relatives have been planning the trip for the last week. One creepy fact their discussions threw up is that, in 2013, the temple earned Rs. 220 crore from its sale of human hair. Pilgrims shave their heads at Tirupati as a token offering, and about 40 million people visit it annually. Although not all of them offer their hair, Rs. 220-crore’s worth must be a lot.

According to this PDF detailing the temple’s finances, the biggest chunk of its income comes from cash offerings from devotees, listed as ‘Kanuka’.

pie1

(All figures in Rs. crore)

Its other revenue receipts, including hair, are listed as such:

pie2

(All figures in Rs. crore)

Many of the world’s richest temples are in India. Some of the richest include the shrine at Shirdi, Maharashtra, for Sai Baba; the Padmanabhaswamy Temple, Thiruvananthapuram, Kerala; the Mahabodhi temple in Bodh Gaya, Bihar; and the Vaishno Devi temple in Jammu and Kashmir. Besides boasting overwhelming attendances, they’re also proof that Hinduism is a very materialistic religion when it comes to offerings despite its abstemious philosophies.

No matter this hypocrisy – the world at large rejects it anyway because religion and wealth share a negative relationship. Specifically, countries with higher GDP have lower religiosity. This document, wherefrom the religiosity numbers were pulled, defines religiosity as simply the fraction of people who identified themselves as religious in a survey.

gdprel