How common is dishonesty and misconduct in science?

In the media recently was a revealling story on ‘dubious’ practices in research, describing how the well-known science publisher Elsevier had published a series of  ‘fake’ journals that were dedicated entirely to publishing results from drug company research (such as the ‘Australasian Journal of Bone and Joint Medicine, dedicated to Merck). On similair lines, a classic paper came out a few years ago showing  that ~1% of papers submitted to  The Journal of Cell Biology had digital images that had been ‘improperly manipulated’ prior to publication. Combine with this with the now infamous case of the ‘fake’ human stem cell lines from the Korean scientist Hwang Woo-suk. and it does little to re-assure the public that scientists are keeping science ‘honest’.

To find out how common these habits really are, a recent publication in the journal PLoS ONE attempted to exam the proportion of scientists who  fabricate and falsify research. The results, based upon a meta-analysis of anonymous surveys from scientists from many disciplines, are surprising to say the least. An average of 1.97% of scientists admit to have fabricated, falsified or modified their results on at least one occasion, and upto 33.7% admitted to other ‘questionable’ research practices.

Intriguingly, when scientists were asked about their colleagues, the numbers increased dramatically – upto 14.2% for falsification, and upto 72% for other ‘questionable’ research practices. What seems slightly more alarming is that misconduct was apparently reported more frequently by medical & pharmacological researchers than other fields!Reassured yet? The article concludes with the following

‘Considering that these surveys ask sensitive questions and have other limitations, it appears likely that this is a conservative estimate of the true prevalence of scientific misconduct,’

‘It is likely that, if on average 2% of scientists admit to have falsified research at least once and up to 34% admit other questionable research practices, the actual frequencies of misconduct could be higher than this.'”

Click here to read the article in full at PloS ONE.

Coral almost as genetically complex as humans’

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CNN News, May 29th 2009:

Advances in the study of coral in the last few years has led a group of scientists to conclude that corals almost rival humans in their genetic complexity and their relationship to algae is key to their survival.

“We’ve known for some time the general functioning of corals and the problems they are facing from climate change,” said Virginia Weis, a professor of zoology at Oregon State University and an author of a report published in the journal Science.

“But until just recently, much less has been known about their fundamental biology, genome structure and internal communication. Only when we really understand how their physiology works will we know if they can adapt to climate changes, or ways that we might help.”

The study found that corals have sophisticated systems of biological communication that are being stressed by global change. Disruptions to these communication systems, particularly between coral and the algae that live within their bodies are the underlying cause of the coral bleaching and collapse of coral reef ecosystems around the world, say the report’s authors. (Read the full story at CNN News)

Climate ‘whitewash’ to the rescue

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You might think that this idea sounds a little crazy but I urge you to read on.   Here’s the idea:  Everyone paints the roof of their house white and the rate of global warming will be radically reduced!

Insane?  Well, this idea does have some sense and logic to it.  I recently discussed this with my friend Ken Caldeira at Stanford University.  Over some monstrously huge American sandwiches, our discussions eventually came round to the amazing impact that losing the reflectivity of Arctic summer ice would have on the rate of global warming.  A few back of the envelope calculations by Ken soon convinced the people around the lunch table that changing the reflectivity of an even 1% of the Earth’s surface could have a major impact on the amount of trapped radiation solar.  Flip side?  Essentially, losing the albedo of the Artic sea ice is like piling massive amounts of CO2 into the atmosphere.  

Back at Ken’s lab, discussions with Long Cao (one of Ken’s postdoctoral fellows) turned to whether or not one could influence this effect by manipulating the reflectivity of the earth through other means – What about doing a Christo? What about covering large areas with white chalk or mirrors?  What about inventing a highly reflective plant that would spread out across arid areas and change the reflectivity of desert regions?   Interestingly, the quick search of the literature revealed that this latter idea is being actively explored by scientists:

Andy Ridgwell and colleagues at the University of Bristol in England have another idea, one they call bio-geoengineering. Rather than developing infrastructure to help cool the planet, they propose using an existing one: agriculture. Their calculations, published in Current Biology, suggest that by planting crop varieties that reflect more sunlight, summertime cooling of about 2 degrees Fahrenheit could be obtained across central North America and a wide band of Europe and Asia. Plants reflect slightly different amounts of light depending on factors like how waxy the leaves are. Even differences in growth patterns between two varieties of a crop — the way leaves are arranged — can affect reflectivity.  (Read More)

Now, Steven Chu, the Nobel prize-winning physicist appointed by President Obama as Energy Secretary, has proposed that we seriously explore this idea.  Rather than use the rather challenging (from all aspects!) idea of engineering plants, Steven would like to whitewash the world – to initiate a global initiative to change the colour of roofs, roads and pavements so that they reflect more sun?

As a weapon against global warming, it sounds so simple and low-tech that it could not possibly work. But the idea of using millions of buckets of whitewash to avert climate catastrophe has won the backing of one of the world’s most influential scientists.

Steven Chu, the Nobel prize-winning physicist appointed by President Obama as Energy Secretary, wants to paint the world white. A global initiative to change the colour of roofs, roads and pavements so that they reflect more sunlight and heat could play a big part in containing global warming, he said yesterday. By lightening paved surfaces and roofs to the colour of cement, it would be possible to cut carbon emissions by as much as taking all the world’s cars off the roads for 11 years, he said. (Read More)

Not a bad idea at all – and one that would be achievable in a short-period of time. It would work like this: basically, governments would institute the painting of the tops of roofs and buildings (traditionally black tar, slate, or grey colours) white, this would alter the albedo (surface reflectivity of the sun’s radiation), effectively reducing the amount of heat trapped by the Earth’s surface to offset projected increases from global warming.

As a weapon against global warming, this idea sounds so simple and low-tech that it just might work.  It could be used to reduce warming associated risks and buy some important time as we struggle to bring emissions down. As with all of these ideas, however, we must also be cautious not to use them as an excuse for not dealing with the problem of rising atmospheric CO2.  These measures will only offset part of the problem and certainly will be exceeded in time. And, clearly, reducing global temperature in this way will do nothing for problems like those assoociated with ocean acidification.

Disease-hunting scientist: Dr Laurie Richardson and black band disease in coral

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Just finished reading a great excerpt from a book called ‘Disease-hunting scientist’ by a Canadian author called Edward Willett. The scientist in question is Dr Laurie Richardson from Florida International University, who is well known for her work on ‘black band disease’ (see image above) on Caribbean coral reefs. I’ve never read Willett’s work before (and can’t vouch for the book itself), but I’ve long respected Dr Richardson’s research into black band microbial communities, and the ‘interview’ offered a few intriguing insights. More below:

At 287,231 square kilometers, coral reefs are less than a tenth of a percent of the total ocean floor. But they support more than a million species of marine life. They are also dying, from pollution, overfishing—and black-band disease, among others.

Dr. Richardson started her career researching “microbial mats,” communities of microbes that live in the sulfur-rich water of hot springs. She then worked in Wisconsin on a NASA project that used satellite data in the study of aquatic ecosystems. That led to three years at NASA’s Ames Research Centre in California learning remote sensing and image processing, which in turn landed her in Florida with a NASA-funded grant to work on algal pigments and remote sensing.

One day, while she was diving for fun on a coral reef, somebody showed her an example of black-band disease-and she immediately recognized it as similar to the microbial communities she’d studied in hot-spring outflows.

She looked in the scientific literature, and no one else had made that connection. And that was how the research she’s now been doing for more than 15 years began. (Read more)

“Oyster reefs among hardest-hit ecosystems”

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‘Oyster reefs among hardest-hit ecosystems’ – Washington Post, May 21st 2009

Overfishing and unchecked coastal development have resulted in the disappearance of 85 percent of all oyster reefs, making the ecosystem one of the most severely affected marine habitats in the world, according to a study released Thursday.

The Nature Conservancy study found that several reefs in China have seen drastic declines over the past 30 years, while those in Europe have almost entirely disappeared. Half of the shellfish populations in South America are under threat, while flat oysters have been virtually wiped out in Australia.

Native oyster reefs _ essentially mountains of the bivalves cemented together _ were once dominant features of many temperate estuaries around the world. Much as coral reefs are critical to marine habitats, the bivalve shellfish are vital to bays and estuaries, creating habitats for a variety of plants and animals, the study said.

Oyster reefs provide important benefits by filtering water, providing food and habitat for fish, crabs and birds, and serving as natural coastal buffers from boat wakes, sea level rise and storms, it said.

If you’re sucking down a wild oyster, it most likely came from one of only five regions on the east coast of North America, and in most of these regions, oyster reefs are in poor condition, the study said.

(Read more at the Washington Post)

US ‘global warming bill’ one step closer?

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“House Panel Passes Limit on Greenhouse-Gas Emissions” – Washington Post, 22nd May 2009
A bill to create the first national limit on greenhouse-gas emissions was approved by a House committee yesterday after a week of late-night debates that cemented the shift of climate change from rhetorical jousting to a subject of serious, if messy, Washington policymaking.

The legislation would create a cap-and-trade system: Over the next decades, power plants, oil refineries and manufacturers would be required to obtain allowances for the pollution they emit. Those who need more or less could turn to a Wall-Street-like market in the allowances. The 33 to 25 vote was a major victory for House Democrats, who had softened and jury-rigged the bill to reassure manufacturers and utilities — and members of their own party from the South and Midwest — that they would not suffer greatly.

The vote gives this bill more momentum than any previous legislation to reduce greenhouse gases, but it faces hurdles. In the House, Rep. Collin C. Peterson (D-Minn.) has said he wants to take up the bill in his Agriculture Committee, seeking to change rules for those who raise corn for ethanol. The Senate has shot down previous cap-and-trade plans.

President Obama supports the bill, an aide said yesterday, though some provisions are weaker than what he advocated during the presidential campaign. In particular, Obama called for all pollution credits to be auctioned off by the government, but the House bill would give away about 85 percent of them.
(Read more at Washington Post)

Why the existence of ‘heat tolerant’ corals does not mean that coral reefs will be able to resist climate change.

ofuA recent study published by Tom Oliver and Stephen Palumbi from Stanford University in the journal ‘Marine Ecology Progress Series‘ seems to suggest yet another miraculous and novel mechanism by which corals will ‘escape’ the pressures of global warming. In a nutshell, the researchers found that corals from ‘warm pools’ at Ofu Island (American Samoa) hosted ‘heat tolerant’ types of symbiotic algae, whereas corals from cooler lagoons hosted more ‘heat sensitive’ types of algae. When combined with regional data, Oliver & Palumbi suggest that in regions where annual maximum temperatures reached 29 – 31C, coral ‘avoided bleaching’ by hosting higher proportions of ‘heat tolerant’ algal symbionts.  Whilst these findings are interesting, the study is a long way from the suggestion in the paper and accompanying press release that coral reefs are ‘adapting’ and ‘may survive global warming’, and relies mainly on over interpreting their results. There are several issues at hand:

  1. Whilst these results highlight both the diversity of bleaching responses at a community level and the array of algal symbionts, the finding of heat tolerant corals has been shown throughout the Indo-Pacific and Great Barrier Reef on a number of previous occasions. The suggestion that this pattern results from a correlation in local scale heating based upon a limited sampling regime is far from proving causality
  2. The identification of a few remnant tough (‘heat resistant’) corals does not equate to these corals spreading out and maintaining coral reef ecosystems under rapid climate change.  Such coral types are rare, and are likely to have minimal impacts in sustaining reef populations under future climate change scenarios.  In making this argument, the authors are leaping across a myriad of issues that would need to be proven before we could pin our hopes on a few odd-ball corals for building and maintaining functional reef ecosystems into the future.
  3. Although corals have been shown to be able to ‘shuffle’ symbionts (change the proportion of ‘heat sensitive’ to ‘heat tolerant’ types), to date it has never been shown that corals can uptake ‘novel’ symbiont types from external sources. So, corals that are ‘heat sensitive’ can’t acquire ‘heat tolerant’ types from the environment. In light of rapid increases in sea surface temperatures under future climate scenarios, these ‘heat sensitive’ corals will undergo mass mortality, as they are unable to simply ‘adapt’ or switch to more resistant types.
  4. Any successful proliferation of these heat resistant genotypes will depend on a stabilised climate. Continual increases in temperatures means that these genotypes will have a harder time proliferating and stabilising, given that selection pressures will continue to intensify. This is akin to the bar in a high jump competition being placed ever higher.  As time goes on, fewer and fewer ecotypes from the population will be able to pass beyond the barrier.
  5. The authors seem to imply that functional reef ecosystems (and countless ecosystem services) will be ‘saved’, based upon a specific niche of ‘heat resistant’ corals.  The issue here is not the survival of corals species – many of whom will be resistant to extinction under global climate change (albeit as rare organisms) – but the destruction of functional coral reef ecosystems that millions of people depend on. Unfortunately, a few corals in a warm rock pool in Samoa will not save the day or the planet.
  6. These results do not address ocean acidification – the ‘other CO2’ issue along with temperature that threatens all calcifying organisms. To somehow imply that coral reefs are not facing problems from climate change because Oliver and Palumbi found a few tough coral genotypes in a rock pool, verges on the incredible.

These points aside, the study is an interesting one in terms of exploring heat stress in corals. My main issue is that Oliver & Palumbi have massively overextended their conclusions, which is particularly apparent in the associated press release.  Needless to say, these sorts of overblown claims are less than useful in the lead-up to the critically important COP15 negotiations in Copenhagen at the end of year.

Update, 25th May

And here is a classic example of why such media releases are less than useful, courtesy of the detractor Andrew Bolt:

http://blogs.news.com.au/heraldsun/andrewbolt/index.php/heraldsun/comments/shock_news_reef_not_dying#55023

Endangered shark found. Eaten.

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The megamouth shark (Megachasma pelagios) is one of the worlds rarest sharks – spotted only 43 times since its discovery back in 1976 off Oahu, Hawaii. These sharks are huge and bizzare creatures, capable of growing upwards of 5m in length, with luminescent light organs surrounding the mouth to attract plankton and small fish. So rare is the megamouth shark, that apparently scientists were surprised to find the 44th megamouth shark (caught by mackeral fishers in the Phillipines) had been cooked and eaten by local villagers before anyone could take a closer look. I wonder which part of the 500 kilogram shark was considered the delicacy? Read more at the National Geographic – thanks to Brian for the tip!

World Ocean Conference (Part III): Climate change to cause wave of refugees

picture-392ABC Radio,  May 12th 2009: Australian scientists are warning there could be a wave of economic refugees from South-East Asia and the Pacific if climate change is allowed to devastate the Coral Triangle, north of the Australia. Representatives from 70 countries are meeting in Indonesia today to discuss the health of the world’s oceans. Researchers from the University of Queensland will tell them that unchecked global warming could take a terrible toll. From Indonesia in the west to Solomon Islands in the east and the Philippines in the north, this marine environment is one of the most biodiverse regions in the world. More than three quarters of the world’s reef-building coral species and a third of the world’s coral reef fish can be found within these waters.

[audio:http://www.climateshifts.org/media/ABC.mp3%5D

(Photograph ‘Dawn Rip-Wave No.2, Atlantic Ocean’ courtesy of Flickr)

Poseidon Controls the Iron Hypothesis

picture-389An article in press at Global Biogeochemical Cycles has shown that iron fertilisation can actually decrease the amount of carbon sinking to the ocean floor due to complex ecosystem processes.The iron fertilisation hypothesis was originally proposed as a rapid solution to climate change by increasing the photosynthetic uptake of CO2 by phytoplankton otherwise limited by their source of iron. Unfortunately, one of these climate change experiments was eaten by hungry crustaceans (see “Hungry Crustaceans Eat Climate Change Experiment”).

However, in another experiment, the scientists at the University of California at Berkeley continued to monitor the phytoplankton bloom and changes over an annual cycle with “Carbon Explorers”, floats that recorded data down to depths of 800 meters after the iron fertilisation experiment. These floats were placed both near and away from the iron induced phytoplankton blooms. Initially, these researchers discovered evidence in support of the Iron Hypothesis with a phytoplankton bloom leading to movement of carbon particles to at least 100m below the surface and this was reported in Science in April 2004.

Over the longer term the Carbon Explorers observed a different pattern which may be related to complex ecosystem processes that occurred during the following annual cycle. Despite the demise of the phytoplankton bloom the following winter, there was no carbon rain to match. In fact, there was greater particulate carbon falling at the site away from the original iron fertilisation. It turns out that the zooplankton survive the winter at depths below where the phytoplankton live due mixing of the oceans. Storms that cause this mixing create a conveyer belt of phytoplankton to the deeper dwelling zooplankton.

Larvae (zoea) of the spider crab (left) and the mitten crab (right) between 1 and 10 days old.

Larvae (zoea) of the spider crab (left) and the mitten crab (right) between 1 and 10 days old form part of the zooplankton ( 'hungry crustaceans').

If the water is continually mixed to depths with low light, then the phytoplankton do recuperate and the zooplankton eventually starve. At the site away from the iron fertilisation, the ocean mixing was intermittent and the phytoplankton were able to survive at the surface. The following spring, a bloom in phytoplankton fed the hungry zooplankton and led to increased carbon rain.

It seems that creating the right conditions for increasing oceanic carbon capture is in the hands of Poseidon and not something that can be easily predicted.

(Photograph courtesy of Flickr, zoea drawings from New Quay and UCSD)