The Biology Refugia

Creationism in Hong Kong schools?

2009-06-19T05:48:00.003+08:00

Earlier in the year, a number of scientists in Hong Kong complained to the territory's Education Bureau about the new biology syllabus for schools, which included a clause stating that "in addition to Darwin's theory, students are encouraged to explore other explanations for evolution and the origins of life, to help illustrate the dynamic nature of scientific knowledge" (the latest version of the document on the bureau's website lacks this statement). Such wording has been used by advocates of creationism and Intelligent Design (ID) in the United States to legitimate the teaching of these so-called 'alternatives' to evolutionary theory in classrooms.

In May, a group of 62 people including education professionals replied to this criticism saying that there was no problem with the above wording and continued to impute that ID was a valid alternative to evolution. As a result, a group called the Concern Group for Hong Kong Science Education has set up an online petition calling on the Education Bureau to clarify its position on the teaching of evolution and to refute the claims of ID supporters in Hong Kong.

It's interesting how these hot-ticket issues have somehow become transplanted wholesale into a society which until lately has not seen such a polarized opposition between the secular and religious. Lacking the social and historical context (or baggage) of the ID debate in the US, the position of the pro-ID supporters in Hong Kong would seem very mild and entirely reasonable to an unsuspecting public. After all, what's wrong with teaching 'both sides' of the issue? To those who are aware of former creationist arguments against evolution, however, the sort of evidence and explanation used by the pro-ID camp seem uncannily familiar. They are not so much in favor of scientific even-handedness (suppose one wanted to teach 'both sides' of the Newtonian theory of gravitation...) but specifically wish to discredit evolution. As such it is quite disingenuous for the issue to be framed as merely giving voice to 'alternatives'.

As a social phenomenon, I'm quite curious to see how this plays out. Why is it that the ID or creationist movement has only started gaining prominence beyond the US around this decade? Reports have surfaced in the news about similar problems plaguing science educators in the UK and other European countries. In Turkey, the creationist movement is largely driven by one man, who goes by the pen name Harun Yahya, who although framing his opposition to evolution from an Islamic perspective, simply reuses the arguments of the Christian anti-evolutionists. So, future intellectual historians of our times: why is this happening now? And why simultaneously in societies so different from each other and from the US, where all this started?

Update: Simon Singh libel case

2009-06-11T07:32:00.002+08:00

Nature magazine has just published an editorial calling for libel laws in Britain to be changed. The editor observes that it is not that science should be given a position of privilege within the law, but that the law itself is wrong-minded.

Mon 22 Jun 2009: 6.30pm - "Darwin, Wallace, and Evolution: Celebrating a major paradigm shift in science"

2009-06-05T11:50:00.001+08:00

As part of our 60th anniversary celebrations, the Department of Biological Sciences presents:

"Darwin, Wallace, and Evolution:
Celebrating a major paradigm shift in science"

Monday, 22nd June 2009: 6:30pm

Lecture Theatre 31
Science Drive 1
Faculty of Science NUS
A buffet dinner will be served at 8.30pm.

Registration is open:
Sign up at darwinwallace.rafflesmuseum.net

The year 2009 is the bicentennial of Darwin's birthday, and 150th anniversary of the publication of his book "The Origin of Species". Darwin's theory of evolution is one of the major breakthroughs in the history of science and it is now generally accepted that "nothing in biology makes sense except in the light of evolution" (Dobzhansky).

Unfortunately, the contributions of another important British scientist, Alfred Russel Wallace, are less appreciated. Wallace had independently of Darwin developed a theory of natural selection and described his findings in a letter to Darwin in 1858. It was this letter that initiated the publication of "The Origin of Species" in 1859. Wallace conducted much of his research in Southeast Asia and collected biodiversity specimens throughout the region (including Bukit Timah Hill).

In celebration of these contributions, the Department of Biological Sciences will host this "Darwin, Wallace, and Evolution" public event and invite two prominent speakers - Dr. John van Wyhe from Cambridge University and Prof. Naomi Pierce from Harvard University will cover the historical aspects and illustrate how evolutionary theory is used in modern research.

[1] "Darwin and Wallace 150 years on,"
by John van Wyhe

About the talk - The theories of Charles Darwin and Alfred Russell Wallace have changed science, and the world, forever. Yet much of what is often written about these two men, their similarities and differences, and their debts to one another, is wrong. It has recently been claimed, for example, that Darwin stole many of his ideas from Wallace. For many years it has also been claimed that if Wallace had not sent his essay on evolution to Darwin in 1858 that Darwin never would have published his theory. This presentation will revisit the true story of Darwin and Wallace and rebut several common myths.

About the speaker - John van Wyhe is a historian of science, currently based at the University of Cambridge. He is the founder and Director of Darwin Online, a website that presents the complete works of Charles Darwin with more than 90 million views since 2006. A Bye-Fellow of Christ's College (Darwin's own college), he is also a member of the British Society for the History of Science and author of "Charles Darwin: The Story of the Man and His Theories of Evolution" (2008). Van Wyhe led the restoration of Darwin's Christ's College rooms and contributing to a proposed iconography of Darwin.

His recent research has challenged "Darwin's delay" - the long-held view that Darwin held back or kept his theory secret for 20 years. In 2009, he publishes three books and numerous shorter items on Darwin. Committed to sharing Darwin's work, scholarship and the history of science with the wider public, Van Whye lectures and broadcasts on Darwin, evolution and the history of science around the world and has written for The Guardian, New Scientist, USA Today and The Independent.

John's webpage.

[2] "From Darwin to DNA: Evolution of blue butterflies and ants," by By Naomi Pierce

About the talk - Modern evolutionary research is still thriving on Darwin's seminal ideas about adaptation, natural selection, and the Tree of Life. Blue butterflies in the family Lycaenidae provide a model system for understanding how adaptation and natural selection have shaped organisms and generated the biodiversity we see today. This talk will focus on the complex life histories of Lycaenidae, a group whose caterpillars associate symbiotically with ants, and whose feeding preferences range from herbivory to highly specialized forms of carnivory. Reconstruction of the evolutionary history of the family using characters from both morphology and DNA reveals how interactions with ants have shaped the diversification of this group.

About the speaker - Naomi Pierce is one of the most prominent living evolutionary biologists and is an expert in the ecology and evolution of species interactions. Her research has ranged from field studies measuring the costs and benefits of symbioses between ants and other organisms, to genetic analyses of biochemical signaling pathways underlying interactions between plants, pathogens and insects. She has also been involved in reconstructing the evolutionary "Tree of life" of insects such as ants, bees, and butterflies, and in using molecular phylogenies to make comparative studies of life history evolution and biogeographical distributions.

Pierce was awarded a Macarthur Fellowship for her research on insect/ plant interactions, and has held positions at Griffith University in Australia, Oxford University in the UK, and Princeton University in the US. She is currently the Hessel Professor of Biology in the Department of Organismic and Evolutionary Biology at Harvard University, and Curator of Lepidoptera in the Museum of Comparative Zoology. She lives in Cambridge with her husband and their two daughters.

Naomi's webpage

chiropracters sue for libel

2009-06-02T06:24:00.003+08:00

The science writer Simon Singh, best known for his popular science books on code breaking and Fermat's Last Theorem, has been sued by the British Chiropractic Association for writing in his co-authored new book on alternative medicine, Trick or Treated, that chiropractic is a 'bogus' form of medicine.

Chiropractic is quite uncommon in Singapore but widely practiced in countries like the US (where it started) and the UK. Its central tenet is that diseases are caused by misalignments of the spine, and so can be cured by the appropriate manipulations of the spine and other joints to bring them back to the proper position (Medline article, Wikipedia page). While it might actually have some help with back pain, which is the most common reason that people visit chiropracters, practitioners also claim that it can help with diseases like colic and asthma, claims which Singh's co-author, Edzard Ernst, had found to be unsupported by published clinical trials.

Nick Cohen writing in the Observer has details on the case and some important observations, foremost among them being that if the criteria of libel laws are being used to settle scientific (or in this case, pseudoscientific) matters in court, then it is impossible to defend oneself against pseudoscientists (or conspiracy theorists, etc.) who claim that one has defamed them by accusing them of being dishonest, which is implied by the word 'bogus', because "the worst thing about the deluded is that they sincerely believe every word they say." Furthermore, the legal costs associated with defending oneself are also crippling and may force capitulation even if there is a good chance of a successful defence.

This matters to us who are involved in science, whether as researchers or educators or even as members of the public curious about scientific matters, because there's no telling who would take offence at scientific commentary in the public sphere. The evolution/creationism issue (I'm not going to call it a 'debate' because it's hardly an equal match) is one, but also climate change, alternative medicine, and even UFOs. Defamation is a notoriously dicey aspect of law, and I have the feeling that there is still a fair degree of deference to 'expert' authority among the public in this country, such that pseudoscientists are unlikely to choose legal avenues to press their opinions. But as alternative views become more common (in the UK, for example, alternative therapies like homeopathy and acupuncture enjoy public funding and even royal patronage), we will certainly have more members of the public questioning the 'scientific establishment' and its pronouncements. I would actually welcome such a dialogue because it would mean that people are actually thinking critically about issues in the news and not simply accepting what they are told as-is. Those of us who work in science then have to do our part to communicate what we know in a robust and effective way. After all, there's no point in doing science if it's just for ourselves and a small circle of specialists. The public has a right to know what their tax dollars are funding.

----

P/S: There's a Facebook group for those who would like to find out more or support Singh's cause.

Cenchrus brownii

2009-05-13T19:53:00.001+08:00

Before I forget again and have to hunt the web for the scientific name!

Its quite common along the beach forest and it was first recorded in Singapore in 1950. I browsed the www and realised that the plant is in some flickr sets in Singapore without the name (I commented on them).. so here's the name so that the next time someone gets poked by it, at least can curse it properly.

Here's a nice picture of it courtesy of Ria from wildsingapore

It belongs to the grass family and not the sedge family.

Cenchrus brownii!

As you can see, I am pretty invigorated by the fieldtrip I had this morning...

Nudibranchs and the power of the sun in their tentacles

2009-05-13T19:44:00.001+08:00

Saw this cutie at Sentosa today - Polka-dot nudibranch (Jorunna funebris)

Besides nudibranchs, there were a few other people from the seashore groups that were there brought in by the low tide today.

Then I happened to see this slug or is it a nudibranch (could it be Phyllodesmium briareum? asks Ria from the blur photo I sent her) and this dude who happened to be there mentioned that it was a slug that could photosynthesize. I can't verify the species but the nugget about slugs photosynthesizing brought to mind an article I read. But first the pictures of this fair creature... I hope this is really a slug of some sort! I thought they were a cluster of mollusc eggs. I am not sure if this slug really photosynthesizes though.

But anyway, more about photosynthesizing slugs! Well they don't really but they do collect the plastids (chloroplasts basically) by feeding on the algae (they one that this slug is feeding on is presumably Bryopsis). Collecting the plastids is already quite amazing since the slugs selectively do not digest this organelle. Another most profound aspect of this ability to harness photosynthetic machinery is a gene that is co-opted by the slug in its co-evolutionary history... so baby slugs are born with one photosynthetic gene that helps maintain the ingested plastids for at least 9 months... cool.

Solar-powered Sea-slugs Live Like Plants

ScienceDaily (Dec. 3, 2008) — The lowly sea slug, “Elysia chlorotica,” may not seem like the most exciting of creatures, but don’t be fooled

“Photosynthesis needs around 2,000 to 3,000 genes, and animals do not have many of the critical genes,” says Manhart. So Manhart and his co-workers looked into how the plastids consumed by the slug can continue photosynthesizing.

“We found that the slug has at least one gene required for photosynthesis in its nuclear genome, which has never been found in any animal,” says Manhart. “The critical thing is the plastids come from the alga, but the slug nucleus contains at least one, and probably more of the genes required for plastid functioning,” he adds.

California says biofuels aren't so green

2009-04-30T09:55:00.002+08:00

California has approved a new clean-fuel rule requiring fuel providers to cut greenhouse-gas emissions from fuels by 10% in 2020 compared to 2010 levels. The rule to calculate emissions, however, takes into account all aspects of fuel production, hence biofuels will face a penalty:

"Despite intense opposition from the US corn (maize) ethanol industry, the rule takes into account agricultural expansion abroad caused by rising grain prices as food crops are diverted for biofuels. This 'indirect' effect boosts the estimated emissions for various categories of corn ethanol by 50% or more, meaning that ethanol often results in higher greenhouse-gas emissions than gasoline." (from the Nature news article)

The formula that California uses to calculate the greenhouse gas cost of biofuel, however, is fairly conservative, and some analysts argue that it should be even higher.

Communicating the Swine influenza A (H1N1) crisis

2009-04-30T01:26:00.001+08:00

Informed or misinformed?

With the emergence of Swine influenza A (H1N1), a phenomenal amount of news is available via the internet. There are numerous webpages, blogs (and their rss feeds), facebook walls, notes and pages and these days, tweets as well.

The chatter is welcome instead of silence, but with any communication medium, the undiscerning reader runs the chance of being misinformed almost as easily. This ability of people to be misinformed and pass on incorrect news was discussed last week regarding Twitter. Agencies are doing their best to fight back. e.g. CDC Emergency's latest tweet when I was writing this said, "CDC reminds you that you can NOT get swine flu from eating pork...." and follows with a link to their FAQ.

The chance of being misinformed increases when a reader engages in multi-tasking activities or lays claim to "reading" hundreds of sources - in a crisis I am reluctant to rely on rss-skimming friends for specific facts, but rather, use their pointers as potential sources of information pending investigation before further forwards. And beware that one time you relax your guard - it will be the occasion in which you contribute to the problem of misinformation!

Be a source of reliable information

Avid web-readers can be a resource to friends and family in such trying times by being a source of reliable and updated information. In addition to television news from international and local news sites, I find reading just a few reliable sources on the net thoroughly and reviewing the information for specific lessons helpful - I find it useful in responding with practical applications including communication and myth-busting in daily conversation!

During the SARS outbreak in 2003, I found the face to face conversations with like-minded friends (they happen to helpfully also be biology grads) to be extremely helpful. These conversations were supplemented by email discussions, and all of it helped me in decision making and preparations for a large meeting of about 300 people at the university (Biodiversity of Singapore Symposium). This pattern was employed during the 2004 Indian Ocean Tsunami - the information completely transformed my approach about how to help.

The need to communicate

Will large, global agencies tell it like it is? I was quite surprised by the aggressive updates of the the World Health Organisation (WHO) during the SARS outbreak - I felt information was served up as soon as it was acquired, and this was later expressed as a critical strategy in the WHO Outbreak Communcation Guidelines [pdf], which advocate "Trust, Early warning, Transparency, An understanding of the public, suggesting mitigation measures and an aggressive Communications plan."

For the H1N1, I find these same (as in SARS) international and local sources useful:

WHO Disease Outbreak News

Center for Disease Control and Prevention: Swine Influenza (Flu): cdc.gov/swineflu/

CDC has a twitter account, @CDCemergency! Hat tip - Kevin

Ministry of Health, Singapore: Update on Global Human Swine Influenza - helpfully this URL: moh.gov.sg, brings you right there.

New sites I refer to include:

Channel News Asia special on the Swine Flu Outbreak - note the useful, simple URL: channelnewsasia.com/swineflu/

CNN Health: Swine Flu

BBC: Swine Flu Special Report
News aggregators (search term = "swine flu"): Google and Yahoo

Besides the very helpful graphics and background pieces, archive stories and supplemental news on social, economic and other aspects, the mainstream media is important for its opinion pieces, especially by experienced medical journalists. And alternative views of seasoned writers help keep a perspective at times, e.g. see Simon Jenkins' "Swine flu? A panic stoked in order to posture and spend." The Guardian, 29 April 2009.

Singapore - see the Ministry of Health's webpage

In Singapore, where the WHO Outbreak Communcation Guidelines meeting was held, the reliable source of updated information about status and core health issues is available at the Ministry of Health. The "Highlights page" now carries the "Update on Global Human Swine Influenza" - there is text and video of the minister's media update which is useful. The site could profit from a dedicated section, a useful rss feeds for this developing situation and perhaps, twitter as nudged by @acroamatic.

Too much information - a summary?

All this reliable information poses another problem - it is A LOT of information. A summary would be helpful but run the risk of sacrificing accuracy. Also with news updates and changes almost every day during such incidents, these would need to be regularly updated.

Well information dissemination is critical to limiting the further spread of infections and a "lack of information and knowledge about a global outbreak ... makes all affected people vulnerable, especially health professionals who need accurate and up-to-date information to care for patients and undertake crucial research."

However "... health information can [now] be rapidly accumulated and disseminated through the internet to the global medical community. .. Just-in-time (JIT) lectures, which target educators, can help to improve the dissemination of information in a health crisis." (Chotania, R. A., R. E. LaPorte, F. Linkov, S. Dodanic, D. Ahmed & K. M Ibrahim, 2003. Just-in-time lectures: SARS. The Lancet, 361 (9373): 1996. [7 June 2003: doi:10.1016/S0140-6736(03)13586-6])

Their paper recounts this approach during SARS which apparently borrowed a term from a manufacturing concept: just-in-time lectures (JIT) - these were rapidly assembled presentations that informed users could adopt, incorporated the brevity of a slideshow, distributed rapidly electronically, updated frequently and from what I see properly labelled to reflect the specific version.

The Just-in-time Swine influenza lecture

As a result, here it is: "Just-in-Time Lecture: Swine influenza A (H1N1) Outbreak in US & Mexico: Potential for a Pandemic," by Rashid A. Chotani. Uniformed Services University of the Health Sciences (USUHS). Updated daily. The html and powerpoint versions are available at the Supercourse site at the WHO Collaborating Center, University of Pittsburgh.

Pointing to the latest update

In response to an email query, he said, "Please use, post and circulate as widely as possible. .. I update the presentation everyday (some time twice)."

In light of his statement and the awareness of the potential of rapidly changing information, I abandoned any thought of using a slideshare embed of Version 3 (28 Apr 2009), but simply point back directly to the Supercourse site, for the reader to obtain the most updated version.

The slideshow is simple and clear for clinicians and biology teachers to use directly for briefings. The explanation of terms that are broached before diving in further is critical in clarifying the use of specific terms and the different sections are clearly spelled out.

Likewise in Singapore, despite the web2.0 shortcomings, the MOH webpage page includes a pdf slideshow which teachers and organisation communication teams will find useful for briefing or disseminating to students and staff. THe MOH slideshow reviews details of the local status with a breakdown of cases and types and sort of control measures that are being adopted and enforced.

Teachers like Cheng Puay who are primary communicators, are using such information to educate and prepare students. They are certainly armed with more effective tools these days!

Are heart cells and mammal eggs regenerated?

2009-04-18T08:07:00.003+08:00

Two of the dogmas that most biology students learn in school are that cardiac muscle is not renewed, and that women (and almost all female mammals) are born with their full complement of eggs - they can't make new ones. Two recent studies have shown that these dogmas may not be as clear cut as they originally seem to be.

The first of these studies (New York Times article) was carried out by a team at the Karolinska Instituet in Sweden. They wanted to see if any of the cardiac muscle cells in humans were formed after the person's birth. In biology, the classic method to do such a tracing experiment in animals is to feed the animals some sort of radioactive tracer, which would then become incorporated into the DNA of cells that are being formed during the period that the the radioactive tracer was being fed to the individual. Cells formed after that period would not have radioactive tracer in their DNA. Obviously there are ethical implications of feeding humans radioactive tracers, but the experiment has already been done on unwitting subjects at a global scale.

During the 1950s, Cold War powers tested nuclear bombs above ground, releasing significant and measurable quantities of carbon 14 into the atmosphere. Individuals born during that time would have incorporated this carbon 14 signal into their tissue. After the test ban treaty in 1963, carbon 14 levels gradually diminished, and this changed isotope ratio can be detected in DNA synthesized after that date. The team applied their method to heart muscle cells, and found that for individuals born before the test ban, some of their heart muscle cells had a lower carbon 14 isotope ratio, meaning that those cells were produced after that date - evidence for regeneration.

The second study was carried out at the Shanghai Jiaotong University, and involved mice and not humans (NY Times article, Science feature). They also used a really cool technique, but one which operates on a less grandiose scale. Before this study, the debate in the field was whether supposed female germline stem cells (FGSCs) in mouse ovaries thought to be responsible for generating new oöcytes were in fact capable of doing so. The method used to isolate the FGSCs is called immunomagnetic isolation. Antibodies to a protein found only on FGSC surfaces were raised, and coated onto magnetic particles. Therefore, a magnetic filter would be able to isolate the supposed FGSCs. After isolation, they were transformed with green fluorescent protein, and introduced into the ovaries of sterile mice. The sterile mice were then mated with normal males, and offspring, expressing green fluorescent protein, were produced. This demonstrates that ovaries possess stem cells that are capable of regenerating oöcytes. Given the similarity of mouse and human reproduction, it is possible that humans have similar capabilities.

In both cases, therapeutic applications are a long way off, but it is still intellectually exciting to be aware that what has long been "known" as fact is still open to reassessment by pure empirical work, showing that biology is still a young and growing field.

John Maddox Dies

2009-04-16T10:53:00.002+08:00

Longtime editor of the journal Nature, John Maddox, has passed away at the age of 83. Aside from ushering in major changes to the journal's format, he famously was a member of the team that investigated a claim made by a French laboratory to have demonstrated efficacy of antibodies in aqueous 'high dilution', widely thought to be evidence in support of homeopathic medicine. Together with magician James Randi and expert in scientific misconduct Walter Stewart, he wrote a comprehensive contradiction (Nature 334: 287-290, 28 Jul 1988) of the original claims.

The journal itself has also put out a special feature in commemoration of him. Although his background was in physics, he made substantial contributions to science journalism in general. Let's hope those standards will be maintained as we enter the age of science blogging.

The Evils of biofuels

2009-04-04T20:50:00.002+08:00

One of the biggest reasons for forest clearance in Southeast Asia is the expansion of oil palm plantations. Oil palm, Elaeis guineensis, has superseded rubber as the major cash crop of this region. Its oily fruit is pressed and processed to make palm oil, which is ubiquitously used in processed food (have a look at your instant noodle packet). The panic over climate change and high oil prices not too long ago led to an interest in biofuels, plant-derived alternatives to traditional petroleum-derived fuels, such as corn-derived ethanol and, that's right, palm oil.

Ironically, or insidiously, the opportunity to make even more profit from using crops for fuel than using crops for food has persuaded many agricultural corporations to convert many of their fields to biofuels production, putting pressure on food systems and increasing the rate of land conversion - because people are still as hungry as they were before biofuels. Therefore, biofuels, far from being the savior of our carbon-emitting economy, is making the problem worse, by giving people incentives to eliminate biodiversity, and actually causing a net carbon dioxide release into the atmosphere, because the cheapest way to clear forest is to burn it.

In Indonesia, clearance of forest is not only impacting the monkeys, trees, and elephants. It is a direct injustice to indigenous peoples who rely on the rainforest for their sustenance. (The opening paragraph of this article does have a slightly misleading vignette: pumpkin and cassava are natively South American crops that were only introduced to Southeast Asia probably in the 16th century, while rubber, a native of Brazil, only arrived in the 19th. But this does not affect the rest of the story, which is set very much in the present day.)

All the ills that characterize business in the tropical frontier are present: corrupt officials both civil and military, legal protection on paper but not in fact, large multinationals more interested in profit than social conscience. Perhaps one may accuse the author of this article as being sentimental in trying to portray the Dayak villagers whom she visits as being a heroic underdog up against the heartless corporations and corrupt officials - is the reality really this black and white? But to those who complain of soppy sentimentality, I say that cynicism easily blinds us to caring about the real human costs of what people usually see as an environmental problem. Forests are not only where the plants and animals live: they are important to people, too, who are just as vulnerable when the forest is gone.

I reflect on this issue because one of the major customers of the company seizing ancestral Dayak lands to clear cut for oil palm is a Singapore-based firm. Doubtless they have their reasons and excuses, but I feel that the problems of oil palm agriculture have been underappreciated in Singapore. I recall being brought on school field trips to Malaysia where we would tour different kinds of farms and plantations, and learn about how oil palm and rubber were produced and processed, how they were made into such a wonderful variety of goods. Silence, however, on what was lost to make that possible. The environmental rhetoric surrounding biofuels has also papered over the true cost of biofuel production - basically trading the tropics for the myopic carbon conscience of consumers in the industrialized nations. Most end-of-the-chain consumers, people like you and me, of course are decent people who would be aghast if their purchasing habits were the direct cause of why the Dayak were being driven forcibly from their homes. But the sheer indirectness of modern supply and production chains absolves anyone of direct responsibility, and makes it easier for unscrupulous acts to be obscured.

A recent letter in Trends in Ecology and Evolution (vol. 24, no. 2, pp. 67-68) by Koh Lian Pin (an associate of the RMBR) and David Wilcove (of Princeton) point out how deliberate misinformation in the media is used by the oil palm industry to justify themselves. For example:

Claim: Oil palm is grown on former rubber and other plantations, so little new forest is being cleared.

Fact: Untrue. From 1990 to 2005, more than half of oil palm expansion in Malaysia and Indonesia was on old growth and secondary forest.

Claim: Oil palm plantations are 'planted forests' that green the landscape and harbor biodiversity too

Fact: Quite clearly false. This banks on the urban public's ignorance of what life is like in the forest and plantation. Any casual observer walking through can tell that they are qualitatively different. Oil palm also uses massive quantities of pesticides, that often drain into adjacent forests.

Claim: Developed nations have no right to interfere with how the developing world uses its land, because they have been polluters and deforesters in the past

Fact: This is like saying that I should have the opportunity to smoke cigarettes and ignore the advice of a sick old smoker, because he's had the chance to smoke and I haven't. This is reminiscent of the simplistic moralizing of the Asian-values debate.

Claim: The Malaysian government claims that it will protect places zoned as protected forest and forest reserve from oil palm land conversion.

Fact: Unprotected forest will be cleared regardless. Also, Malaysia has bought hundreds of thousands of hectares of land in Indonesia, Papua New Guinea, and Brazil for oil palm development. It is effectively exporting its problem to other places which care less, something like the NIMBY mentality in the developed world.

I close with a picture of an oil palm plantation, what huge swathes of the region now looks like. The sad thing is that this picture was taken by me just outside of the Pasoh forest reserve in Negri Sembilan. Pasoh is a protected area, because it contains a long-term ecological study plot established by Peter Ashton half a century ago, that is part of a world-wide network of long term forest 'observatories' run by the Center for Tropical Forest Science. Hundreds of scientific publications have been written on this 50 hectares of forest. But contrary to what one might assume when reading these papers, this is not a sample of 'pristine' forest at all. It is surrounded on three sides by oil palm, coming right up to its gates, with very little by way of a buffer zone. If this is the best we have, then forest ecology will soon be a museum science.

Is science journalism scaling back?

2009-03-19T05:21:00.003+08:00

Newspapers and traditional journalism is taking a big hit from declining circulation and revenues: likewise, science journalism is suffering. Can science blogging by scientist-bloggers make up for the shortfall? A recent article in Nature looks at the situation now.

To my mind, science blogging will not be able to 'replace' traditional journalism, for the following reasons: 1. blogs tend to be personal and immediate, focused on the blogger's experience and so may leave out perspectives beyond those most familiar, 2. they are not necessarily written for a wide audience - the lay public will find most science blogs a bit too specialized or 'geeky', 3. unless they go looking for them actively, most people will not ever have the occasion to read a science blog, whereas newspaper science and technology reporting is there with all the other news, and finally 4. how are we going to know the reliability of the blogger? It's all well and good when the blogger is someone familiar and trustworthy (like this blog!) blogging on fairly innocuous topics but what about issues of biomedicine where there are many ethical conflicts of interest? Journalists, at least in theory, are supposed to weigh the facts and present both sides of the story as fairly as they can - but what are we to make of a blogging biomedical researcher presenting his supposedly candid opinion of a drug under review?

These conundrums aside, I think the field is a healthy one and it certainly is growing. Many institutions are using the web to reach out to the public, going beyond the traditional press release. Even professional societies and academies are offering podcasts about new research, job opportunities, and member profiles. All I can say for now is 'watch this space'!

Why Autumn leaves are red (part II)

2009-03-14T06:21:00.004+08:00

One of the hypotheses to explain the investment of anthocyanins in plants during autumn was very well detailed here previously (see the 14 Nov 2008 post). A recent TRENDS review by Archetti himself, with Doring and other experts in diverse fields lists the abiotic (photoprotection, osmotic regulation and warming) and other biotic factors (coevolution, fruit flag, direct defence, camouflage, anticamouflage and tritrophic mutualism). Here's a short note on the photoprotection hypothesis, as reviewed by Archetti et al., to complement the anti-herbivory theory.

As protection against photo-oxidative stress in autumn, the red anthocyanins may do one, two or all of three things:

(1) Directly shield leaf tissues from the sun's rays. There is some support for such a function in aging, young and evergreen leaves, as red leaves are less light stressed than non-red leaves in high light conditions.

(2) Indirectly protecting tissues from reactive oxygen species (ROS; i.e., antioxidant effect), hydrogen peroxide being the most likely as it is the only one known to penetrate both chloroplast (ROS produced) and vacuole (ROS stored).

(3) Enhancing nutrient (nitrogen) absorption through maintenance of light absorption function by anthocyanins.

The photoprotection hypothesis is significant due to the increased risk of damage in autumn as a result of: (i) lower photosynthetic capacity in the cold; (ii) increased light from thinning canopy, and (iii) decreased self-shading by chlorophyll due to its breakdown.

Some other untested hypotheses include:
-anthocyanins help decrease leaf osmotic potential, i.e., retain water to prevent drought stress when leaves start to be lost
-anthocyanins convert light to heat, protecting against cold temperatures
-anthocyanins make leaves unpalatable to herbivores
-anthocyanins inhibit fungal growth
-colours attract birds for seed dispersal
-colours expose camouflaged herbivorous insects
-colours attract aphids + ants (those that are symbiotic to each other) to defend the plant

Indonesia to sell carbon credits to conserve forests

2009-03-12T06:25:00.000+08:00

(From Nature magazine, 11 Mar 2009)

Indonesia has applied to join a World Bank programme intended to help developing nations fight deforestation by selling tradeable carbon credits.

International climate negotiators are working to allow developing nations the right to sell some carbon credits if they clamp down on deforestation, which is responsible for roughly 20% of global greenhouse-gas emissions. The World Bank's US$300-million Forest Carbon Partnership Facility is designed to lay the groundwork for such an international agreement.

The programme already includes 25 countries, but Indonesia, the world's third-largest greenhouse-gas emitter, had remained on the sidelines until it applied in Feburary. The bank estimates that the country could earn between US$400 million and $2 billion selling credits for protecting forests.

Happy 200th birthday, Charles Darwin!

2009-02-12T21:15:00.001+08:00

Today is Charles Darwin's 200th birthday (thanks to the reminder via twitter @gracechua). Lots is happening around the globe, just see the Darwin Day webpage.

To commemorate the 200th anniversary of Darwin's birth and the 150th anniversary of the publication of On the Origin of Species, Stanford University initiated a Stanford Continuing Studies course called Darwin's Legacy (DAR 200) in September 2008. Part of the motivation of this was to increase literacy in the theory of evolution, inescapable in the environment of what Time magazine called "The Evolution Wars."

Stanford video-recorded this series that included many speakers from around the country who explore Darwin's legacy in fields as diverse as anthropology, religion, medicine, psychology, philosophy, literature, and biology.

The Darwin's Legacy series is available on iTunes and on YouTube as well:

iTunes: http://tinyurl.com/stanford-DL-itunes
YouTube: http://tinyurl.com/stanford-DL-youtube

Have fun watching, downloading and listening to these entertaining lectures on some of those long bus journeys!

Thanks to Dan Colman, editor of Open Culture.

"The Tree of Life" narrated by David Attenborough

2009-02-10T13:48:00.001+08:00

Sir David Attenborough narrates the Tree of Life, a six-minute video that was broadcast on BBC One. Formore on the tree of life, see: wellcometreeoflife.org.

Hunting Evolution

2009-01-06T10:28:00.001+08:00

An interesting article about how hunting is driving evolution in reverse appears in Newsweek this week ["It’s Survival of the Weak and Scrawny," by Lily Huang. Newsweek, 03 Jan 2009].

It does makes sense when you think about it in light of evolutionary theory since hunting removes all the strong alpha male specimens which provide the best trophies, leaving behind "losers" to breed!

The 'Passive House' and the Seal's Flipper

2008-12-31T01:46:00.010+08:00

It's wintertime in the Northern Hemisphere and word of something snug, warm, and money-saving will certainly receive a lot of attention or a lot of envy. Therefore it is no surprise that the Passive House concept (Passivhaus in German) is being widely reported in the American news (the New York Times's most-emailed article for the past day or two) as a great European invention that could potentially help Americans cut their considerable expenditure on heating. One happy German family reports that they get "all the heat and hot water they need from the amount of energy that would be needed to run a hair dryer." How does it work? Wikipedia helpfully explains the following points of design that contribute to a warm house (though the diagram is still in German...):

Very efficient insulation (including super airtight windows)

Orientation to pick up solar energy

Using passive heat sources like body heat and appliances

Shunting ventilation through a heat exchanger

The last element is also known as a heat recovery ventilation system (description) and works by having incoming fresh cold air be in thermal contact with outgoing stale warm air, so as to transfer some of the heat from the outgoing air to the incoming air, and reducing the heat loss through the ventilation system. The air is not being mixed, rather they are fed through closely interlaced tubing that maximize heat transfer between the two streams. How does such a simple system achieve such high efficiency? The New York Times article describes an exchanger that retains up to 90% of the heat. This would seem incredible if not for the fact that animals of cold environments have been using the same passivhaus design for a long time.

Like a passivhaus, the seal has a superb insulation system of blubber and fur. On top of that, it has its own heat exchanger system to minimize heat loss from the body's interior to the external environment. This heat exchanger is the counter-current exchange system, found in the seal's flipper and in the limbs of many other animals. The problem that it solves is how to keep the extremities supplied with blood while losing as little heat as possible (because arterial blood coming from the heart is essentially at core body temperature - as anyone who has been disconcerted by the warmth of his own blood in the tubing at a blood donation drive can attest). In a counter-current system, the arteries (carrying warm, oxygenated blood from the heart) run parallel to and in contact with the veins (carrying cool, deoxygenated blood back to the heart), but with the blood flow in opposite directions, i.e. in a loop. At the steady-state, this will result in a temperature gradient in both vessels will be such that the innermost end is warmest, and the outermost end is the coolest.

This serves two purposes: (1) the blood returning in the vein at the base of the limb is warmer than the venal blood at the tip of the limb, hence the core body warmth of the animal is protected, and (2) the average temperature of the limb is reduced, which is desirable. After all, a high average temperature in the limb means that there is a higher temperature gradient between the limb and the environment, hence a higher rate of heat loss, by Newton's law of cooling.

So a simple arrangement of tubing can lead to dramatic improvement in function. Countercurrent exchangers are also found in other organs and body parts. For example, tuna use a countercurrent system in its body wall to keep its active swimming muscles warmer than the surrounding water. Fish also use a countercurrent system to maximize yield of oxygenation in their gills. A countercurrent arrangement can also be used actively (rather than passively), e.g. in the loops of Henle in the kidney, to actively concentrate the urine, and in the rete mirabile of fishes, to actively concentrate gas in the swim bladder. Doubtlessly there are many points of similarity between German houses and seals (or tuna, or kidneys) but the use of a countercurrent exchanger is probably one of the more ingenious among them!

'Gender-bending' chemicals in the environment

2008-12-15T10:04:00.000+08:00

Males of wildlife vertebrate species are becoming more female, yikes!

Chemicals from common household products that enter the environment are feminising male wildlife from fish to mammals and suggests potential harm to human beings as well.

See the Chem Trust report, "Effects of pollutants on the reproductive health of male vertebrate wildlife - Males under threat," 07 Dec 2008.

This was widely reported in the media in articles such as: "It's official: Men really are the weaker sex," by Geoffrey Lean. The Independent, 07 Dec 2008:

"Wildlife and people have been exposed to more than 100,000 new chemicals in recent years, and the European Commission has admitted that 99 per cent of them are not adequately regulated. There is not even proper safety information on 85 per cent of them.

Many have been identified as "endocrine disrupters" - or gender-benders - because they interfere with hormones. These include phthalates, used in food wrapping, cosmetics and baby powders among other applications; flame retardants in furniture and electrical goods; PCBs, a now banned group of substances still widespread in food and the environment; and many pesticides."

From the report highlights:

"All vertebrates have similar sex hormone receptors, which have been conserved in evolution. Therefore, observations in one vertebrate wildlife species, may serve to highlight pollution issues of concern for other vertebrates, including humans.

Indeed, given the widespread presence of endocrine disrupting chemicals in the environment, effects are likely to be occurring in more species than those currently reported."

For a local flavour, see Bayen et al., 2005. Persistent organic pollutants in mangrove food webs in Singapore. Chemosphere 61(3). doi:10.1016/j.chemosphere.2005.02.097

Pygmy tarsiers re-discovered in Sulawesi

2008-11-19T15:42:00.002+08:00

First time this species was seen alive in 80 years!

I love to see the tarsiers at our Night Safari. the little google-eyed munchkins zip around so fast that they disappear in a flash like ninjas!

Why Autumn leaves are red

2008-11-14T08:55:00.005+08:00

It's autumn now in New England (or as the Americans call it, fall), and the leaves are turning beautiful shades of yellow and red. While cycling down a leafy avenue in Boston, I was struck by how perfectly the autumn foliage complemented the stately brownstone town houses—checking the property prices, an apartment in each of them in Boston's Back Bay area is typically priced upwards of $1.5 million, so I quickly abandoned my dream of moving into the neighborhood.

But what use, biologically speaking, is it for trees to produce such beautiful colors before they shed their leaves? Many plant physiologists will say that it is simply an effect of chlorophyll resorption by the plant. Chlorophyll is metabolically expensive, so plants will want to save on further investment by resorbing it before shedding their leaves. Yellow to orange colored carotenoid secondary pigments, normally present in leaves alongside chlorophyll, will be unmasked when chlorophyll is gone, exposing their yellow colors. That explains yellow leaves in fall, but what about red leaves? It turns out that red leaves get their color from anthocyanins, and these are produced and shunted into the leaves before they are shed, so they are not usually present. Hence there must be some explanation for why the plants make this additional investment.

Autumn leaves (Wikimedia).

One hypothesis, originally proposed by William Hamilton (of kin selection fame) and Sam Brown, but also independently by Marco Archetti, is that the red coloration acts as an 'honest signal' to aphids. Aphids are major herbivorous pests and can inflict potentially significant damage to a plant's health and hence reproductive fitness. Plants with red autumn leaves (not all temperate trees turn red, contrary to what we in the tropics think) tend to be correlated with high phenolic content. Phenolics are secondary metabolites that are commonly used by plants to deter herbivores. Therefore, red colors are a signal to deter aphids from settling and laying eggs on the trees before winter (eggs that would hatch come springtime), but this signal is no empty threat but also carries the force of anti-herbivory defenses behind it. This idea of honest signals originally came from economics, where a whole field of signaling theory has been built up.

Recently, however, this nice adaptationist story has come under criticism. You may have seen this review in PLoS Biology by Chitka and Doring that essentially says aphids (and insects in general) can't see red, so how could they perceive this signal? Insects with three color receptors (trichromatic) have maximal sensitivities at ultraviolet, blue-violet, and yellow. Aphids are trichromatic, and have pretty much the same maximal sensitivities. This is unlike human photoreceptors, which are maximally sensitive at blue, green, and red. So humans are able to see red, but unable to see ultraviolet like insects do. Does this deal a fatal blow to the 'too good to be true' story of Hamilton, Brown, and Archetti?

On Tuesday I had the privilege of attending a talk by Archetti himself. He's presently come to Harvard from Oxford, and was invited to present his work to the Cambridge Entomological Club at its monthly meeting. It turns out that he is acquainted with Chitka and Doring and soon after their review came out in PLoS, he went to see Doring with the argument that aphids actually can see red. His theoretical argument is that spectral sensitivities reflect sensitivities to monochromatic light (i.e. light at a single wavelength). So a monochromatic beam at say far red will be indistinguishable from another beam at near red or yellow to an insect. But the pigments in leaves do not have monochromatic reflectances - they reflect light across a band of wavelengths. If one plots out reflectance against wavelength for leaf pigments, they resemble step functions, instead of being narrow single-color bands. Overlaying the reflectance data for green leaves and red leaves against the sensitivity spectra of insect eyes, it shows that it is possible for them to distinguish between say green, yellow, and red.

That shows at least that it is possible for insects to distinguish between red and other colors despite not having a dedicated red photoreceptor. But do they actually do so in nature? Archetti then did a very simple experiment, painting petri dishes in various hues and setting them out in a field experimental station in England. He found that insects preferred to land in yellow dishes most of all (an unusual affinity that field entomologists have long known as a trick for luring insects into traps more effectively), followed by green, then least of all red. So they are able to distinguish between these colors, a trend that is supported even when corrected for the different brightnesses of these colors.

Archetti also examined the relative distribution of hues in autumn foliage in different regions, in the wild and in cultivation. It turns out that New England has the highest proportion of red/yellow foliage in autumn (ca. 70%), compared to an average for all temperate zones of about 15% though the reason for this disparity is unclear. Furthermore, within a single species in different regions, there is often variation in what proportion of the local population turns red, showing that it is a variable trait subject to selection. To support his hypothesis, he examined the relative proportion of red against green autumn foliage in wild versus cultivated fruit trees. Cultivated fruit trees show a smaller proportion of red leaves compared to their wild counterparts, suggesting that the selective pressures on the leaf color trait has changed upon domestication.

The evidence he has mustered is mostly indirect. We still do not know what is the direct influence of aphid herbivory upon temperate trees. But at least he has shown that the theory, that red autumn coloration could be a warning signal to aphids or other herbivores, is still a plausible one. More work obviously has to be done to tease apart the various interactions that are going on. In the tropics, one related question is the bright coloration of young and immature foliage. What function does this coloration serve? Perhaps a similar process might be going on, and it would be interesting to see how immature foliage coloration in tropical plants correlates with secondary metabolite content (anti-herbivory agents) and actual rates of herbivory.

"What our Biology students are learning" - a 2008 update

2008-11-12T21:01:00.001+08:00

Warren Tan of The Warren, recently provided an update on his biology experience in JC (= "high school") in the comments section of Brandon's 2007 post, "What our Biology students are learning". He was responding to Brandon's query, "What do you find most interesting about biology, and do you find that what you learned in school fulfills that?"

I reproduce his comment here to highlight his update on the 'A' level biology scene:

"Me personally, i like microbiology/cell biology. I was also very fortunate that in my secondary school(and later JC1), i was chosen to participate in research programme in that field.

So at least for me, i do find H2 biology interesting. (most of classmates don't however)

Our batch was the "transition of syllabus" batch. We barely touched on molecular biology in secondary school, and many of my us found it hard to adapt to the new focus in H2 biology. (it was better for me, due to my research exposure, but i do empathise with my classmates)

I fully agree that system biology and ecology is important, and the lack of coverage in the current H2 biology could be a liability. The syllabus assumes we had covered sufficiently in sec/pri school. Nevertheless, i think keeping in touch and expanding existing knowledge is important.

SPA was the greatest complain me and my classmates had. Because, each assessment is important, the college had no choice but to chose experiments we can do well in, over anything else. We end up memorising standard answers 99% of the time.

Also, our teachers explained that experiments can be expensive and tedious to prepare. As Junior College, funds are limited.

Until funds specially are set aside for "Poly/Uni level" experiments, and until they would be duly recognised for assesment, it may be hard to move beyond osmosis experiments. (at least for the mainstream students). Research and H3 students had more opportunities and exposure.

In conclusion, it may not be that the syllabus is too skewed. But that, opportunities for an expansive biology education are too few and far in between. Not many people can qualify for H3 subjects. The idea of SPA may need to be revised.

The situation may be better for the the next few batches, since they are under the new syllabus since secondary school (unlike us whom are the transition batch)"

Link: "What our Biology students are learning," by Brandon Seah. The Biology Refugia, 01 Apr 2007.

Singapore so hot - Its people ought to be very warm?

2008-10-27T12:41:00.007+08:00

"Experiencing Physical Warmth Promotes Interpersonal Warmth" - Williams & Bargh 2008 (Science, 322: 606-607)

"'Warmth' is the most powerful personality trait in social judgment, and attachment theorists have stressed the importance of warm physical contact with caregivers during infancy for healthy relationships in adulthood. ... we hypothesized that experiences of physical warmth (or coldness) would increase feelings of interpersonal warmth (or coldness), without the person’s awareness of this influence. In study 1, participants who briefly held a cup of hot (versus iced) coffee judged a target person as having a 'warmer' personality (generous, caring); in study 2, participants holding a hot (versus cold) therapeutic pad were more likely to choose a gift for a friend instead of for themselves."

See also "Warm Coffee, Warms The Heart Some Say".

Don't jump to conclusions yet though, there may be confounders!

Where is the Toddycat!?

2008-08-13T22:05:00.004+08:00

The evolutionary relationships among Asian palm civets were recently reconstructed using DNA sequences of four genes.

Patou, M.L., Debruyne, R., Jennings, A.P., Zubaid, A., Rovie-Ryan, J.J., Veron, G., 2008. Phylogenetic relationships of the Asian palm civets (Hemigalinae & Paradoxurinae, Viverridae, Carnivora). Molecular Phylogenetics and Evolution 47, 883-892.

Here is the trimmed down tree to show where the palm civet that inhabits Singapore and the logo of RMBR stands phylogenetically.

It is in fact most closely related (in this sampling) to the brown palm civet that is endemic to Western Ghats... And has the binturong and masked palm civet (implicated in SARS) at the base of the lineage.

The study also shows some interesting stuff:

(i) the Asian palm civets (Hemigalinae + Paradoxurinae) have a single origin, in other words monophyletic, the gold standard in systematics
(ii) Paradoxurinae, containing the Toddycat, is also monophyletic
(iii) the Asian palm civets (Hemigalinae + Paradoxurinae) apparently diverged from the rest of the Viverridae family in the Late Oligocene/Early Miocene (~20-25 million years ago)
(iv) the Toddycat, as a species, is probably between 5-10 million years old, one of the younger ones in this group of mammals.

David Attenborough's 1973 Royal Institution Christmas Lectures

2008-08-13T16:01:00.001+08:00

"The Royal Institution Christmas Lectures have been held in London annually since 1825." [see Wikipedia] Michael Faraday (who is quite the man) is the star of the series which continues to this day. He lectured a record of 19 times between 1827 - 1860! The scene of one of his lectures is depicted on a UK 20-pound note and is a depiction I remember from my childhood.

In 1973, Sir David Attenborough, who has inspired many a naturalists' career in Singapore and elsewhere, participated in this grand event by giving a series of five lectures over five days, on "The Language of Animals":

"Beware" (Wed 26 Dec 1973)
"Be mine" (Thu 27 Dec 1973)
"Parents and children" (Fri 28 Dec 1973)
"Foreign languages" (Sat 29 Dec 1973)
"Animal language, human language" (Sun 30 Dec 1973).

The videos are available at the Royal Institution of Great Britain's webcast archive (you have to “shop” and “checkout” but can watch the webcast for free).

This excellent series of videos (and a dashing David) are available on YouTube courtesy of threespeed. Due to YouTube's 10 minute limitation, the series of five hour-long lectures are in 30 parts!

Besides highlighting these clips to the biodiversity and animal behaviour students, they serve as appropriate inspiration just before my module-heavy semester begins. I'll soak in ol'David to stoke those flames of passion and hope some fire is evident during the 8am ecology lecture!