Stephen Asma on Body Worlds and the macabre

Humans have always been fascinated by death and the macabre. Long before Body Worlds brought plastinated human bodies on display around the world, people were jostling to see mummies dug out of dusty crypts, or executed murderers freshly cut down from the gallows. Stephen Asma, whose interest in death, decay, and decrepitude has been marked by books on monsters (On Monsters) and natural history museums (Stuffed Animals and Pickled Heads), writes about our shared predilection to gawp at death. I cannot deny being one of the gawpers myself, either!

Google Earth and Science

Google Earth and its cousin, Google Maps, are really useful. I don't think I've used a street directory or road map since I learned how convenient it was to just google it. Aside from just being a tool for finding out how to get from point A to point B, or for businesses to promote themselves, it's also a great tool for crowdsourcing, as memorably happened after the Haiti earthquake two years ago.

It's really useful for scientists too. I'm sure many of us have used Google Maps to check out field sites before going there, and also afterwards to plot localities and routes. The terms "virtual globe" or "Digital Earth" refers generally to such tools, which represent geographical features in digital form. A recent paper in PNAS looks at how current virtual globe tools have been used to help science and make it accessible to the public, and what the prospects are for the future.

One way to get more out of Google Maps is to use KML, a standard markup language for displaying geographical data in virtual globe software (tutorial). If you already use the "My Maps" feature, you can download your maps as KML to share with others. Alternatively, if you want to plot known coordinates and annotate them, you can mark up your data as KML and import into Google Earth to visualize it. 

How to foster good science in Singapore?

The institute in Germany where I'm studying was recently subject to an external review. Our staff and students got to mingle with the reviewers at a dinner in-house one evening, and while waiting in line at the buffet I started talking to someone who turned out to be a senior official in our research organization and also a practicing biologist.

I mentioned that I was from Singapore, and there was a look of recognition in his face. He asked me "ah, A-Star?" Like many others around the world who work in science, he knew about Singapore's big investment in research and technology, and of course also knew about Philip Yeo ("a very smart man"). But he also felt that the Singapore model had a few serious shortcomings, and after our conversation I thought it would be useful to share some of these observations, especially because they are held by someone who is himself a senior scientist and is responsible for administering a large scientific organization.

Singapore has been very successful at setting up the physical infrastructure for research, mobilizing plenty of money and political will to build new institutes and stock them with equipment and supplies. In terms of talent, which is the perennial Singaporean question, we've gone for a top-down approach: recruiting the "big names" in various fields, giving them very good salaries (the few scientists in the US whom I've talked about this before have all mentioned the attractive remuneration) and more importantly the funding to continue their projects in Singapore.

The official said that he didn't think this was the best way to build up a scientific community. What about the students? As he put it, if you're a senior scientist wanting to set up a lab in another institution, the first question you're going to ask is whether you're going to have good students (who of course do all the actual lab work). Unfortunately, Singapore seems to do a very good job of exporting its best students. They're sent overseas on fully-funded, prestigious scholarships to foreign institutions. In the case of A-Star's PhD scholarships, the recipients only make their way back to Singapore after about a decade of study abroad, and maybe even longer if they do a post-doctoral fellowship or two to gain additional experience. While they are overseas, they're not just learning but actively contributing to science. I think that most graduate students would agree that graduate school is not about learning at the feet of your professors, but is instead about finding one's own way in science, while being guided to independence. As a research student, you are actively making science while learning it.

My own experiences appear to bear this out. When I was studying in the US, it was (and is) common for undergrads to do active scientific research, usually mentored by graduate students or post-docs; this was something that was actively encouraged. When asked about undergraduate research opportunities, many professors would comment on how fortunate they themselves were to be in an institution where bright and motivated young people would come and ask to work with them. The professors are undoubtedly good at what they do, but they need good students to keep the research going at a high level, and they recognize this fact.

I explained to him that such scholarships are not limited to the sciences, but are also the most culturally prestigious means for recruitment to careers in public service. At that point I saw the general relevance of what he had said to this entire system of talent recruitment. It's not just about the money that's being spent on having these students shipped abroad and tutored far away from home. Prestige matters too. If the best students do not stay in the country, then it is difficult to develop local institutions to higher levels. Worse still, we are not building confidence in our own institutions.

The foregoing isn't meant to say that the research and graduate students in Singapore are not up to par. Several of my friends are doing science in Singapore, and they certainly have motivation and ability. The matter is whether, for the amount of resources we have poured into the project, we can build up a human infrastructure to match the physical infrastructure.

It's not about how many citations or high-impact papers we can garner. It's about whether we can build a self-sustaining research community that will renew itself by training new scientists. Instead of importing "big names" (the top-down model), let's find a better way to nurture the talent we already have (the bottom-up model).

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Some other comments:

I myself am a participant in the (I hope, temporary) brain-drain, although I'm not on a state-funded scholarship. As I want to return home to work in Singapore in the future, I feel that I have to keep an eye on how science and research are developing there. I've also decided not to name the official that I talked to because I don't want it to seem like these are the official views of our organization, neither did I think at the time to ask him for his permission to share them publicly.

Also, the model for scientific training that I've described -- senior scientists leading labs training graduate students who also generate the scientific results and publications -- is causing serious problems in other developed countries, especially the US. Supply of newly-minted PhDs seriously outstrips demand, in terms of the number of new faculty positions opening up for them in academia. This is a well-recognized problem (see the careers pages of many recent issues of Nature and Science), and according to this perspective article in Science, the seeds for the current situation were sown in the 1940s with the recommendations of Vannevar Bush that led to the establishment of the National Science Foundation in the US. That's another unpleasant outcome that we have to avoid.

Afterword on "arsenic-life" affair

Popular Science magazine has recently published a profile by Tom Clynes on the scientist in the middle of the "arsenic life" controversy, Felisa Wolfe-Simon (see previous Biology Refugia post). This comes after the Science finally published her paper in its 3 June 2011 print issue, along with a selection of responses from her critics (see the editor's note for links).

The magazine feature is sympathetic to her, and notes how much of the initial criticism started by criticizing the science then moved into questioning the scientists' motivations. Many accusations were made at the time, including that they were motivated by fame as a result doing "bad science". But Science didn't publish her paper without peer-review. In fact, additional evidence was gathered as a result of peer review. Were the results inadequate for the claims which were made in the media ("new form of life", "proof that extraterrestrial life is possible", etc.)? Yes, certainly.

My opinion is that this was a "perfect storm" caused by the confluence of mass media and science. Without making any assumptions about anyone's motivations, Wolfe-Simon's team or their critics, we can say that (i) the hyped-up press conference organized by NASA was a mistake, and the oversimplified media kit only led to a proliferation of misinformed headlines, (ii) the quick criticisms by scientists posted to their blogs and websites appeared much faster than any research team could possibly respond to carefully, (iii) the media attention on Wolfe-Simon made it difficult to respond to technical criticisms and also increased their defensive posture (reading the Pop Sci article, I'm struck by how overwhelming it must have been for her) – simply finding the time to do it would have been difficult. I quote Clynes's article:

I find it hard not to feel sympathy for her. In a matter of weeks she was catapulted to fame, then singled out and assaulted with professional and personal criticism, some of which resulted from missteps beyond her control. Wolfe-Simon is an early-career researcher in a field dominated by older men. Few scientists, no matter how established, would have the skills to navigate the situation that she found herself in. What made the level of criticism so extraordinary is that the paper, in itself, is not so flawed that it should not have been published. The argument was compelling, the conclusions were measured, the data was thorough, and the paper made it through the same peer-review process as other articles in Science. 

Some who initially blasted Wolfe-Simon have since changed their mind. Blogger Alan Townsend, who directs the environmental studies program at the University of Colorado, says he was guilty of rash judgment, and that his preliminary opinions—expressed in writing and conversations with his colleagues—contributed to a response from the scientific community that was “often unprofessional, and at times became downright shameful.” He says, “Absent major ethical violations, no junior scientist full of passion for an idea deserves crucifixion for a professional failure or two. If a paper is flawed, it should be dismissed. The scientist should not.”

Learning to deal with the media is not typically part of a scientist's education. After all, most could only wish they were so lucky. If the need should arise at all, it's probably handled by PR departments of their institutions or employers, or from the agencies that fund them, like NASA in this case. Perhaps it's time for scientists to come together and figure out what a code of conduct for publicizing their work should be like. For example, is it a conflict of interest to write a newspaper column that trumpets your own work while raising criticism of your competitors, especially if this is unpublished research? How far should we go in "jazzing up" the science in order to sell it to the public? Some degree of spin and oversimplification is unavoidable, but a technical audience would know where to look when reading a scientific paper to judge for themselves whether a specific claim is justifiable (typically buried somewhere in the Materials and Methods). Should we always be cautious and measured in our pronouncements? What if the issue is something politically-charged like climate change, where climate change "deniers" seize upon caution and use it as supposed evidence of falsehood? Difficult questions for difficult times, and scientists should take the lead in trying to figure them out.

MacClade at 25, now available free

MacClade is one of the most popular computer tools for phylogenetics today. It's commonly used for editing data sets and analyzing phylogenetic trees, though it can't be used itself for inferring trees. It recently celebrated its 25th birthday, and has been available for free online since 1 May. It will no longer be supported on the upcoming version of MacOS ("Lion") so the Maddison brothers, who authored the program, suggest using Mesquite instead, which is also developed by them.

Transparent animals as art

The technique of 'clearing and staining' is used to prepare anatomical specimens of small animals to show their bones and cartilage in situ. It involves digesting away the protein in a preserved animal body with enzymes, and rendering them transparent with other chemicals. The skeleton is then colored with brightly colored stains, creating specimens that look almost like stained glass and definitely as beautiful (if somewhat macabre).

Japanese artist Iori Tomita has been making cleared and stained specimens since 2007. His project, called New World Transparent Specimen, is his effort to "help people feel closer to the wonders of life." Much of the appeal of his works, he points out, is because "they appear as if they were beautifully sculpted from minerals."

(Source: New World Transparent Specimen website.)

The website is definitely worth a look. I've always found anatomy to be oddly compelling. Quite a few of them are invertebrates (like the shrimp in the picture above), which I've not seen before as cleared specimens. The technique is typically used to prepare fish, amphibians, and other small vertebrates.

(via sarzha)

Big Bad Science

If you talk to some people, you might walk away thinking that science is medicine's poor cousin. "Oh you study biology! That means you'll be working in the pharmaceutical industry, right?"

No, but you just can't convince some people.

Not being able to make money might be a good thing, in so far as science is concerned, though. A damning article by Harriet Washington (probably to promote her forthcoming book) recently published in The American Scholar has a familiar moral to its story: commercial concerns can get in the way of doing good science. But boy is it one heck of a story. (A similar sad tale is told in the context of psychiatric drugs in a recent book review by Marcia Angell.)

Medical research suffers from severe conflict-of-interest issues,

"Today, medical-journal editors estimate that 95 percent of the academic-medicine specialists who assess patented treatments have financial relationships with pharmaceutical companies, and even the prestigious NEJM gave up its search for objective reviewers in June 1992, announcing that it could find no reviewers that did not accept industry funds."

... from the seedy plague of ghostwriting,

"Many biased medical-journal articles are the work not of physicians or scientists, but of ghostwriters who script them in accordance with the drugmakers’ marketing messages. A medical expert is found who, for a few thousand dollars, is willing to append his or her signature, and then the piece is published without any disclosure of the ghostwriter’s role."

... advertisements passed off as genuine research journals,

"Elsevier, the Dutch publisher of both The Lancet and Gray’s Anatomy, sullied its pristine reputation by publishing an entire sham medical journal devoted solely to promoting Merck products. ... its Australasian Journal of Bone and Joint Medicine, which looks just like a medical journal, and was described as such, was not a peer-reviewed medical journal but rather a collection of reprinted articles that Merck paid Elsevier to publish. At least some of the articles were ghostwritten, and all lavished unalloyed praise on Merck drugs, such as its troubled painkiller Vioxx. There was no disclosure of Merck’s sponsorship."

... and much, much more.

Washington cites a satirical 2003 article published in the British Medical Journal, titled "HARLOT plc: an amalgamation of the world’s two oldest professions" (free registration required to see the full article). HARLOT stands for "How to Achieve positive Results without actually Lying to Overcome the Truth", and was the brainchild of two doctors who effectively catalogued the various ways that one might distort the truth to present a favorable outcome in clinical trials.

Here's where I think the relevance is, for us regular basic science people. It's also a quick tutorial in bad science - what we know we should not do (by commonsense or otherwise) but may be tempted to do, in the interest of making our results look nicer or getting a paper published faster. Some tips from HARLOT, if you want to go down that path:

• Cherry-pick your data - Selectively ignore negative results.
• Shifting the goalposts - Use one set of standards for your experiments and another for your controls or comparisons.
• "Munchausen's statistical grid" - Slice your data in as many ways as you can until you find a statistically significant result.
• Overinterpreting positive results

And that's just what you can do with your data and experimental design. The human element is important too: hiring 'experts' to sell your snake oil, celebrity endorsements, and behind-the-scenes moves like lobbying government agencies, using litigation as a tactical weapon....

Ultimately the lesson we should take from all this is the one lesson that formal education cannot really teach: critical thinking and appraisal. Should I trust a certain research finding, even if it's been published in a big-name journal?

This affirms my thinking on how one should read a scientific paper. One of my tutors told me something offhandedly that has stuck with me since freshman year of college: the materials and methods are the most interesting part of a paper. Get to know how an experiment was really done, and look at the actual data as much as possible, instead of just buying the conclusions and interpretations that the authors try to feed you. Many students make the mistake of jumping straight from the Introduction to the Results and Discussion, but these are precisely the parts where the authors are trying to spin their research as being 'relevant' and 'important'. Also: discussion is cheap. It is the data which are the hardest-won; perhaps our attention should be proportional to the effort put into producing it.

Otherwise we might eventually end up buying that snake oil.

German nuclear shut-down - what next?

Germany has recently announced that it will shut down all its nuclear power plants by 2022. This comes in the wake of the disaster at Japan's Fukushima nuclear power plant, and election gains by the German Green Party in the key state of Baden-Württemburg. The Green Party is a major player in German politics, and supports the cause of denuclearization.

What does this mean for the politics of energy production in Europe and beyond? On the one hand, we want to reduce our dependence on fossil fuels. Existing sources will eventually run out, and the carbon dioxide released by burning them is believed to be the key factor driving climate change. On the other, are nuclear power and renewable energy may be inadequate to meet the shortfall. Nuclear power, in particular, is fraught with difficulties. Not only are people fearful of potential disastrous accidents ('Fukushima' may eventually become a cultural keyword in the same way that 'Chernobyl' is now), but there are practical concerns regarding the disposal of nuclear waste. If we forgo the nuclear option, will wind, solar, wave, and other so-called 'renewables' be enough?

This seems like a good time to introduce an important book on the issue, Sustainable Energy - Without the Hot Air, written by David McKay, a physicist at Cambridge University. The whole book is available for free online, in addition to a 10-page synopsis for those who want to get the gist of it quickly. An even shorter summary has been written by him for the BBC website.

McKay's analysis, which is essentially a straightforward, but necessary, accounting of the relevant figures and facts, shows that relying exclusively or heavily on renewable energy sources would be hugely disruptive and intrusive to both our existing way of life and, ironically, to the environment. The main fact is that wind farms, solar farms, and the like are not energy 'dense' - they require large tracts of land to produce the same amount of power as a conventional or nuclear power plant. Given existing levels of energy consumption (the book focuses on the UK but other industrialized nations are comparable), there would be hardly any land left for other purposes!

Wind farming projects around the world, for example, are already running into opposition from local citizens who find the windmills, and the electrical pylons required to connect them to the grid, hugely unsightly. Their constant whir is also a form of noise pollution. Biofuels and solar energy harvesting, two commonly-proposed alternatives, would possibly squeeze out farming and natural woodland. Even so, they would not yield very much. The figure below, from Without the Hot Air, shows to scale the quantity of land required for biofuels, wood harvesting, and other forms of renewable energy, required to meet the UK's current demand (the last five symbols in the legend are not to scale, but the rest are).

Therefore, if nuclear were out of the question entirely, it seems unlikely that renewable energy, in the state of technology that is available now, would be able to carry the day. Realistically speaking, it is likely that the Germans will find that after the closure of their nuclear plants, the supply of energy from renewables will not be able to keep up and they will be forced to revert in some degree to fossil fuel, or to importing energy from neighboring countries.

Nuclear energy is something even Singapore has to take into account. Even if our country decides that the risks are simply too high for our island-state, we still have to consider the possibility that neighboring countries will adopt nuclear power. It is important to have a frank discussion of the risks and realities now, than to be enveloped in doubt and fear later. 

Rebirth of Bird Watching

"Bird watching" sounds like such a back-to-nature pursuit: just me and my binoculars, hiding behind a bush and waiting for the birds to come out. But with digital cameras making high-quality photography cheap and accessible, and the Internet making sharing those pictures and swapping tips so much easier, birding has become a hobby for the technologically savvy too.

Today, there are crowd-sourced bird-mapping tools, birding packages that double as vacation getaways, birding blogs, birding iPhone apps, and remote-birding Web sites that don't require watchers to be present in the landscape at all. A few old-fashioned birders may still practice their hobby in isolation with binoculars and field guides, but the birding community, these days, has moved on to gather, check, and share sightings across great distances using the fruits of technological industry and the jumbo jet. 

This is from an amusing article about the different kinds of birders and the kinds of communities that they form. What the writer calls "privileged aloneness"–getting up to go birding before other people are even awake–seems like a good way to describe the attitude that many birders have.

The way I see it, it's as much about the birds as it is about immersing yourself in the community and its special culture. Just like hardcore runners (or cyclists, or computer geeks) have their own magazines, fashions, gear fads, the same with birders.

Those birds don't stand a chance.

'Avatar' Director Plans Deep Ocean Dive for Next Movie

Director James Cameron has commissioned a deep-diving submersible, being built in Australia, to dive to the deepest point in the world's oceans, the Mariana Trench of the Pacific, in order to film undersea footage for his upcoming sequel to 2009's blockbuster movie Avatar.

The article linked to above has a great summary of the last (and only) successful dive into Challenger Deep, the deepest part of the Trench, which was the Trieste dive of 1960. The Trieste was a custom-built submersible, comprising a spherical capsule in which the two crew sat with their instruments, suspended underneath a giant container of gasoline. It functioned like an underwater blimp: the gasoline acted as the buoyant balloon, and they carried ballast to bring them down, which was jettisoned for the ascent. It's a great story of engineering and derring-do, unfortunately not much was learned about the biology of the deep sea from that expedition.

I particularly liked the writer's description of how life can survive at such high pressures in the deep:

One oceanographer described how as follows: a human is like a party balloon – taken down to great depths it will be crushed to nothing; but a deep-sea fish is like an untied balloon – take that down to the bottom of the ocean and the pressure has little effect. Perhaps the greatest difficulty is that intense pressure causes nerves to stop working, a problem that deep-sea life has side-stepped by evolving a more robust physiology at molecular level.

Cameron's quest is not really a scientific expedition, but is still an exciting opportunity for observation of life in the deep sea. The director is also known for his underwater documentary film-making, such as Volcanoes of the Deep Sea featuring the submersible Alvin). Given that the marine realm has inspired many of Cameron's cinematic works (Aliens, The Abyss, Avatar, and of course Titanic) it's only natural that he returns to it for inspiration, like marine enthusiasts all over the world, except with deeper pockets!

How to be a Famous Scientist

Can you aspire to be as famous a scientist as Charles Darwin?

"Darwin's full name is invoked at least once in more than 2% of books published in the English language. (I know that is hard to believe, but we have carefully verified it. And it is on the rise. "Charles Darwin" appears in about 4% of English books published in the year 2000.)"

Science magazine feature The Gonzo Scientist teamed up with one of the team that gave us the recent culturomics study (pdf) and Google Ngrams, to assess the nature of scientific fame. Among the advice for making a name for yourself? Don't be a mathematician, and consider blogging....

Bizzare/Funny Science Blog

A friend told me about this, and it's too good not to share.

Two graduate students at UC Berkeley have a blog called NCBI ROFL where they post weird or humorous papers dredged up from the PubMed database.

Some recent gems include:
Unsuccessful treatment of writer's block
Doctor reinvents the calculus, names it after herself

They also have a Twitter feed.

Happy New Year!

Is Nature 'Good'?

What is 'natural' and 'organic' may not necessarily be good for you:

"Nonetheless, in resisting many things that I view as "unnatural"—nuclear weapons, global warming, chemical pollution, habitat destruction—while also honoring, respecting, defending, admiring, and nearly worshiping many things that are natural (sometimes just because they are natural), it is all too easy to get carried away, to forget that much in the world of nature is unpleasant, indeed odious. Consider typhoid, cholera, polio, plague, and HIV: What can be more natural than viruses or bacteria, composed as they are of proteins, nucleic acids, carbohydrates, and the like? Do you object to vaccination? You'd probably object even more to smallpox."

Read more

"Natural Security" in a world of scarcity

The US military is starting to plan for potential future conflicts based on scarcity of natural resources such as water, arable land, mineral resources, and environmental degradation due to climate change. Policy makers have coined the term "natural security", and warn that these future scarcities can represent "triggers for conflict".

One would assume that the military would not have an ideological stance for or against acknowledging climate change, because there's no inherent reason to do so, if their mission is simply to protect their country's security interests. So it's interesting to watch the military essentially taking climate change into account in their plans, while some civilian politicians can still win votes by refusing to even consider the possibility that human activity can have global impact on the physical world that we live in.

Sungei Buloh bird makes Guardian's Week in Wildlife

The Guardian newspaper's website runs a regular feature called Week in Wildlife, featuring wildlife photos from around the world. It's one of the more popular features they have, and one usually expects to see creatures rare and exotic, but in this week's collection there is a snap of an ashy tailorbird from Sungie Buloh, taken by the KL-based photographer Rahman Roslan. Hidden treasures in our backyard, indeed!

Like maps? Help map IUCN Red List data

Distribution of the Spanish Ibex, drawn from IUCN data. (Source: By Nrg800 [CC-BY-SA-3.0 or GFDL], from Wikimedia Commons)

If you've always wanted to do something with GIS (geographic information systems) but needed data to make pretty maps with, why not help draw species distribution maps for Wikimedia Commons? The International Union for the Conservation of Nature (IUCN) has partnered with Wikimedia to put the species distribution data from its Red List of threatened and endangered species in the public domain. Wikimedia is looking for volunteers to map this data onto a world map background, to produce distribution maps for species with available data (about 25 000 of them). An example is shown above.

Zombie ants update

The zombie ants story, while not really a new thing as far as biology is concerned, has found its way to gossip news site Gawker. I suppose stories about science can be filed from stranger places. It's part of the zombie fashion afflicting Western pop culture today; previous appearances of the undead brain-eaters include the august pages of Foreign Affairs....