June 2011 Archives

I collect fountain pens, not stamps, but I may have to buy a set of these. The U.S. Postal Service has just issued a new set of Forever stamps honoring four American scientists:

• Melvin Calvin, Chemist
• Asa Gray, Botanist
• Maria Goeppert Mayer, Physicist
  
• Severo Ochoa, Biochemist

Calvin worked out the chemistry of photosynthesis, Gray was the premier American botanist of the 19th century and corresponded extensively with Charles Darwin, Mayer helped explain the structure of the atomic nucleus,¹ and Ochoa was the first to synthesize RNA.

Les Mehrhoff would have loaded up on the Asa Gray stamps.

Some readers of this blog are good with numbers and statistics. If you're one of those people, if you have a little spare time, and you'd like to put your quantitative skills to good use, please check out Data Without Borders. Here's the blurb from their website:

Data Without Borders seeks to match non-profits in need of data analysis with freelance and pro bono data scientists who can work to help them with data collection, analysis, visualization, or decision support.

Big companies like Google and Amazon recognize the importance of dedicated data science teams and can support fulltime analysts, but non-profits, though they may have rich and interesting datasets, don't have the resources to capitalize on their data or may not even know the value of the data they already collect.

Data Without Borders aims to close that gap through a data scientist exchange, bringing exciting new problems to the data community and helping to solve social, environmental, and community problems alongside non-profits and NGOs.

March 14th is Pi Day (3/14), but did you know that today is Tau Day (6/28). In case you've forgotten what tau is

τ = 2π
In honor of this great occasion, New Scientist features a musical presentation that I've embedded here. Enjoy



How geeky is it to get a kick out of things like this?¹

You may recall that in April, Congress voted to remove Endangered Species Act protections from the northern Rockies population of the gray wolf. It was a rider attached to the budget bill that allowed the federal government to keep operating for the rest of 2011. Rep. Mike Simpson (R-ID) and Sen. Jon Tester (D-MT) took credit for the rider, although Sen. Max Baucus (D-MT) tried to get in on the act.

As I wrote in April:

This is a very bad precedent. I don't know enough about the settlement that was proposed or Judge Molloy's decision to know whether (a) the settlement was a good one or (b) whether Molloy's rejection was reasonable. I do know that decisions about whether to list or de-list plants or animals should be based on scientific assessments of population status, not by riders attached to budget bills in congress.

And why did I know that? Because I knew that the next time an endangered species designation looked inconvenient, there would be someone who proposes to ensure that the species is never listed in the first place or is removed immediately if it's already on the list.

Enter Sen. John Cornyn (R-TX) and Rep. Steve Pearce (R-NM) who want to stop listing of the dunes sagebrush lizard. That's the lizard you may have heard of whose protection is claimed to threaten the livelihood of west Texas and eastern New Mexico by placing unreasonable restrictions on oil exploration and drilling.

And what does Mike Simpson think of this?

I sometimes forget how lucky I am and how deeply repressive other societies can be. Then I read something like this and give thanks for the many opportunities I have had.

A University of British Columbia student has been blinded after being savagely attacked while visiting her family in Bangladesh.

Rumana Monzur's eyes were gouged and part of her nose was bitten off. Her husband, Hassan Syeed, was arrested 10 days later. ("Vicious attack in Bangladesh leaves UBC student blind; husband arested," by Jill Mahoney and Stephanie Nolen, The Globe and Mail, 23 June 2011)

What could cause a husband to attack his wife so viciously?

At UBC, Ms. Monzur is taking a master's degree in political science - specializing in climate change - and holds a post as assistant professor in Dhaka University's international relations department. Students describe her as happy, brilliant, studious and devout, but the shocking June 5 assault has shattered that life.

...

Ms. Monzur expected to return to defend her thesis in Vancouver, but close family members told Ms. Akter that Mr. Syeed vehemently opposed her leaving again. (Akter is a relative who lives in Vancouver; "Women's-education advocates rally behind UBC scholar blinded in Bangladesh," by James Bradshaw, Jill Mahoney, and Stephanie Nolen, The Globe and Mail, 23 June 2011)

UBC has set up a website where donations for Ms. Monzur's family can be made for the next few days. For more information on the UBC response to this horrific attack, visit this website.

Related articles

• UBC scholar's blinding in Bangladesh firms resolve of women's education advocates (theglobeandmail.com)
• The scourge of violence that claimed Rumana Monzur (theglobeandmail.com)
• UBC community to rally for blinded student (ctv.ca)

Non-scientists often see science as boring and geeky. They think of test tubes and white lab coats, whiteboards filled with inscrutable equations, or massive machines that crash invisible particles into one another to reveal strange properties of matter. What most non-scientists never see is the fantastically beautiful world these instruments can reveal to us. The American Museum of Natural History is out to give its visitors an opportunity to share in that world.

Whether Museum scientists are studying parasites, people, or planets in other solarsystems, cutting-edge imaging technologies such as infrared photography, scanning electron microscopes, and CT scanners now make it possible to examine details that were previously unobservable. This exhibition, curated by Mark Siddall, curator in the Division of Invertebrate Zoology, features more than 20 sets of large-format images that showcase the wide range of research being conducted at the Museum as well as how various optical tools are used in scientific studies

Picturing Science: Museum Scientists and Imaging Technologies opened in New York yesterday and runs through 24 June 2012. That gives you nearly a year to stop by and see it. Please do.

How many times have you read a piece of environmental news only to turn away shaking your head at how depressing the world is? How many times have you seen photos (or worse seen in person) a river filled with waste and pollution? How many times have you followed a poorly maintained truck belching black smoke into the air? How do you feel after that? Are you inspired? Do you have a dream? Or do you have a nightmare?

It's not easy living in this world when you care about the environment and the plants and animals we share it with. And it not being easy isn't just a problem because it makes it hard to inspire people when we constantly tell them how bad things are. It's a problem because it's not good for us.

Environmentalists ... often aren't aware of the emotional toll of their work. "Talking to environmentalists can be like talking to a bunch of macho cowboys," he says. "A lot of people will say, 'I'm fine, I'm fine,' and I'll say, 'I don't know how to tell you this, but you're really not looking healthy.'" The result, he says, is that many environmentalists unconsciously express their stress in meetings or classrooms -- sometimes sabotaging their own mission. (source)

The "he" in that paragraph is John Fraser, a psychologist with the Insitute for Learning innovation. There's an interview with him over at Grist that's well worth reading. Breathe deeply. Click on the link. And read slowly.

For the small number of readers who are interested in F-statistics (the kind we use in population genetics, not those used in analysis of variance or regression analyses), I just realized that I forgot to mention a paper that appeared online-early in Biometrics last fall. Here's the information, the abstract, and a link. You (or your library) will need a subscription for access to the full text.

A Beta-Mixture Model for Assessing Genetic Population Structure

1. Rongwei Fu
2. Dipak K. Dey
3. Kent E. Holsinger

An important fraction of recently generated molecular data is dominant markers. They contain substantial information about genetic variation but dominance makes it impossible to apply standard techniques to calculate measures of genetic differentiation, such as F-statistics. In this article, we propose a new Bayesian beta-mixture model that more accurately describes the genetic structure from dominant markers and estimates multiple F_STs from the sample. The model also has important application for codominant markers and single-nucleotide polymorphism (SNP) data. The number of F_ST is assumed unknown beforehand and follows a random distribution. The reversible jump algorithm is used to estimate the unknown number of multiple F_STs. We evaluate the performance of three split proposals and the overall performance of the proposed model based on simulated dominant marker data. The model could reliably identify and estimate a spectrum of degrees of genetic differentiation present in multiple loci. The estimates of F_STs also incorporate uncertainty about the magnitude of within-population inbreeding coefficient. We illustrate the method with two examples, one using dominant marker data from a rare orchid and the other using codominant marker data from human populations.

http://dx.doi.org./10.1111/j.1541-0420.2010.01506.x

If GFAJ-1 doesn't ring a bell, maybe the #arseniclife hashtag will. And no, GFAJ-1 hasn't arrived here. It's arrived at the University of British Columbia, Rosie Redfield's lab in particular.

Maybe now things are starting to click. Let's see. Rosie Redfield, she was among the first to criticize the paper by Felisa Wolfe-Simon and colleagues¹ claiming discovery of a bacterium that can substitute arsenic for phosphorous in biomolecules, including DNA. GFAJ-1 is the strain of bacteria claimed to have this ability. Now Rosie has cells of GFAJ-1 growing in her lab and can run her own experiments.

Leave aside whether or not Felisa Wolfe-Simon and her co-authors are shown to be wrong, as seems likely given my reading of the critiques,² the #arseniclife episode illustrates something important about how science works, something that intelligent design proponents ignore. I pointed out last December that

Wolfe-Simon and her colleagues will give other scientists samples of the bacterium that is claimed to have these extraordinary properties and those scientists will have a chance to verify Wolfe-Simon's claims. If Wolfe-Simon's claims turn out to be right, textbooks will be rewritten, and all of us will have to think differently about the chemistry of life. If her claims turn out to be wrong, only a few specialists will remember that the paper was ever published.

Now those samples are in the hands of Wolfe-Simon's critics. Experiments, data, and analysis will now vindicate either Wolfe-Simon or her critics

Compare that lengthy, tortuous process of debate and review among experts to the "debate" that intelligent design creationists want to have in high school textbooks. Which process do you think is most likely to help kids understand their world?

Related articles

• Starting to work with GFAJ-1! (rrresearch.blogspot.com)
• From the shadows to the spotlight to the dustbin - the rise and fall of GFAJ-1 (scientificamerican.com)
• Critics weigh in on arsenic life (nature.com)

While I was out of town, our corpse flower bloomed.


That's Clint Morse, our greenhouse manager, providing the narration.

"Martin Luther King did not say 'I have a nightmare'." If you are concerned about the future -- whether because of climate change, the loss of biodiversity, the pollution of lands and waters, or anything else -- you should follow his example. Share your dream and get people to follow. Nic Marks says it much better than I can.



The video comes from a recent post on Dot Earth where Andy Revkin is arguing that we should adopt the approach of a "despairing optimist" -- René Dubos.

Even as he recognized the environmental costs attending human development in the 20^th century, he expressed relentless confidence that a shift to a deeper, more durable, definition of progress could be melded with the power of innovation to produce better outcomes.

I mentioned last month that Yale made many materials from its museums available for open access over the web. I didn't mention that there are also a variety of courses available on the web through Open Yale Courses. Bravo, Yale! I'm delighted that you are making your museums and courses available to a wide audience.

But Shaanxi Normal University is behaving badly.

Shaanxi Normal University, which describes itself as "the cradle of teachers in Northwest China," has published a book based on several of the most popular Open Yale Courses, including economist Robert Shiller's "Financial Markets" and philosophy professor Shelly Kagan's "Death." ("China ♥ Yale -- maybe too much?", by Carole Bass, 06250: the news blog of the Yale Alumni Magazine)

Yale's lawyers are in on the act, as they should be. It is abundantly clear that Shaanxi Normal University is violating the terms of use.

Open Yale Courses is owned and operated by Yale. Yale is the owner of the compilation of data, images, software, documentation, text, audio and audio-visual materials and other intellectual property (the "Materials") hosted on this site. Materials within Open Yale Courses are protected by copyright laws and may be subject to other legal restrictions as well.

For open access to work, those who benefit must respect the rights of those who provide the material. I hope Yale's lawyers win their case, and that they win it decisively.

I've never linked to Uncommon Descent before. In fact, I've only visited the site once or twice, but this is too good to pass along. (When reading it remember that Uncommon Descent is a blog that "serves the intelligent design community".)

At UD we have many brilliant ID apologists, and they continue to mount what I perceive as increasingly indefensible assaults on the creative powers of the Darwinian mechanism of random errors filtered by natural selection. In addition, they present overwhelming positive evidence that the only known source of functionally specified, highly integrated information-processing systems, with such sophisticated technology as error detection and repair, is intelligent design. (emphasis added)

As Joe Felsenstein says in the post at Panda's Thumb that pointed me to that paragraph,

I really can't think of anything to add to that.

Thanks, Joe.

I know next to nothing about non-academic careers. I went straight from college to graduate school, from graduate school to a post-doc, and from a post-doc to here as an assistant professor. In fact, once I entered school in kindergarten, I never left.

Since I know so little about non-academic careers, I was pleased to run across a list of resources at Bad Astronomy that includes links to blogs, discussion forums, specific opportunities, personal stories, alternative careers, books, and job finders.

The first complication is that scientists - all of us really - have to accept that the decisions we make are not entirely determined by data and reason. They are, or should be, influenced by data and reason, but our decisions are inescapably bound up with the representation of the world that we carry in our head. So if we want to influence public opinion and public policy, we have to hire professionals to help us make sure we construct the right representation of the world.

But what is the "right" representation? That's the second complication.

Science is really good at data, evidence, and reasoning. That's the reflective thinking embodied in "Data rule!" It's not good at distinguishing right from wrong or good from evil. Philosophers argue about whether David Hume was right. Some argue that it is possible to develop a purely naturalistic ethics derived from empirical facts about the world. Others argue that ethical principles derive from other sources. Regardless of which side is right, it's safe to say that it isn't easy or straightforward to go directly from a scientific statement - "The global average temperature will be 2°C higher in 2050 than it is now." - to an ethical or policy statement - "We ought to reduce global emissions of carbon dioxide to 1990 levels or below by 2020".

That puts the IPCC into a real bind. As scientists, the IPCC can provide a solid assessment of the likely trajectory of future changes in climate and of the likely impacts associated with those changes. It can even identify the technologies that might be needed to adapt to future climate change and the costs associated with different strategies for adapting to climate change or to reducing the magnitude of climate change or both. What it can't do is to determine which of those strategies is preferable or ought to be adopted. Those choices will involve questions of value - What kind of a world do we want to live in? What responsibility do developed countries have, given that they are responsible for most of the greenhouse gases in the atmosphere? What responsibility do emerging economies have, given that they will be the source of most future emissions?

Unlike an advocacy organization, the IPCC can't identify a preferred policy outcome and organize a campaign around that, including a representation of the world that supports that policy outcome. Instead, its objective must be something more nebulous and less definite. Its objective must be to provide the public and policy makers with an intuitive grasp of the earth's climate system and with tools to guide their reasoning that are consistent with the scientific details in the 5th assessment report. And because climate science has become so deeply politicized, they must find a way to do so that is open and transparent - a daunting, but vital task.

If I had good ideas on how to accomplish it, I'd offer them. Right now, I can diagnose the problem. I can't suggest a cure.

I'll be visiting family and friends in Idaho and lecturing in Module 3, Population genetic data analysis, of the 16th Summer Institute in Statistical Genetics at the University of Washington in Seattle. Blogging will be light (or non-existent) until I return.

Yesterday I argued that the IPCC should hire some professionals to help it communicate its findings to the public and policy makers. There are two complications: (1) Many scientists regard a communications strategy as "fluff" and "spin". (2) Effective communication requires a coherent message.

Let's talk about "fluff" and "spin".

As scientists, we're trained to collect and analyze data. We use those data to evaluate hypotheses and to refine our understanding of the world. If the data we collect are inconsistent with what we thought we understood, we modify our understanding. This approach can be summed up in two words: Data rule.

If data rule, then how they're communicated don't matter. It's the data that determine whether our ideas are right, not how flashy our PowerPoint is or how cool our graphics are. If the extent of Arctic sea ice is decreasing faster than expected, it doesn't make any difference if I draw a pretty picture or simply print a big table of numbers. What matters is what the data say. In fact, you could argue that the table of numbers is better, because it allows you to make quantitative rather than qualitative comparisons of the data and what's expected.

Daniel Kahneman, Dan Lovallo, and Olivier Sibany would point out¹ that this reflects only one of two modes of human thinking, what cognitive scientists call "reflective thinking". The other mode of thinking, "intuitive thinking" mostly determines our thoughts. It "produces a constant representation of the world around us". It's that representation of the world that determines how we respond.²

That's where the communications professionals come in. They live and breathe in a world that's focused on affecting our intuitive thinking, not our reflective thinking. And there's a science, or at least an art, to doing that well.

Most people, even most policy makers, don't have the time to study the data and findings of the IPCC in detail.³ Their opinions and decisions about policy will be based on intuitive thinking, on the "representation of the world" that has been formed in their mind.

Which brings us (tomorrow) to the second complication.

Andy Revkin has been arguing for a long time that climate scientists need to take communication more seriously, and Chris Mooney has made the same point. Revkin has an especially thoughtful piece, The new communications climate, on some of the challenges in the WMO Bulletin. In that piece he argures that

[t]he gap between information and impact can also be substantially reduced (without a large financial cost) simply if more scientists and scholars, and their institutions, think creatively about ways to expand their communication circles and pathways.

The crux of his argument is that traditional media are shrinking in importance as blogs, Twitter, and YouTube play a larger and larger role.¹ The explosion of new media means that "distributing a press release and waiting for journalists to call back to fill in the gaps" won't work any more - if it ever worked at all. Reading further, though, Revkin emphasizes that expanding communication circles and pathways will cost money.

As the IPCC prepares its Fifth Assessment Report, it does so with what, to my eye, appears to be an utterly inadequate budget for communicating its findings and responding in an agile way to nonstop public scrutiny facilitated by the Internet. I would love to think that the countries that created the climate panel could also contribute to boosting the panel's capacity for transparency, responsiveness and outreach.

As Ed Carr writes in his blog about Revkin's WMO Bulletin piece:

I'm not convinced that the IPCC (or much of the global change community more broadly) yet understands how desperately we need to engage with professionals on this front. (emphasis added)

Exactly. The IPCC engages experts to analyze the science, because it needs people who understand the details of the earth-atmosphere system and can reliably project the consequences of projected changes in climate. It also needs to engage experts in marketing and communication so that it can ensure that its conclusions are effectively communicated to the public and policy makers.

But there are some complications. Stay tuned.

We lost Les Mehrhoff last December. Every time I've been outdoors this spring and saw another plant whose name I should know but have forgotten, I've remembered how gently Les would remind me: "Prunella vulgaris", "Lychnis vulgaris", "Galium aparine".¹

We had a wonderful symposium celebrating Les' life and contributions in late May. His wife and daughter were there, and Les would have loved it.

A little earlier in May, Region I of the Environmental Protection Agency recognized Les with a lifetime achievement award. Here's what they had to say:

Leslie J. Mehrhoff (posthumous)
The late Leslie J. Mehrhoff of Willington, Conn. was an outstanding botanist who was well known in Connecticut, New England and the nation. He was an accomplished and enthusiastic naturalist and received his graduate training at the University of Connecticut. He worked for many years with Connecticut's Department of Environmental Protection before becoming the manager of the Torrey Herbarium at the University of Connecticut. During his career, Les inspired, encouraged, mentored and educated many people, influencing botanists, biologists, legislators, students and gardeners young and old. His innumerable presentations on biodiversity and the importance of protecting species and their natural communities included his renowned high-quality photographs. He worked tirelessly to protect endangered species and to prevent the negative impacts from invasive species. In recent years, he traveled to China to promote control of invasive species. He had a spirited sense of humor, and his sense of wonder about the natural world gave him a childlike innocence. Les' life work made incalculable contributions to the protection of biodiversity and ecosystems throughout Connecticut and New England. He was instrumental in gaining passage of Connecticut's Endangered Species statutes, in publishing The Connecticut Butterfly Atlas and in development of The Atlas of Breeding Birds of Connecticut, and The Atlas of Ground Beetles of Connecticut (Coleoptera: Carabidae, excluding Cicindelini). He retired in 2009 and passed away in 2010.

There's a short news piece in UConn Today about the award.

Houstonia caerulea, photograph by Daniel Mosquin. Licensed for noncommercial use: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License

---

Or at least it's eye candy if you're a botanist. I just discovered that the Botanical Garden at the University of British Columbia has a botany photo of the day. Not only are the photos nice, but they are accompanied by brief posts providing information about the plants that are featured.

And the definition of "plant" is broad. I saw at least one fungus when I was paging through the entries. Unfortunately, nearly all of the images have copyright restrictions. The image above is the only one I found that had a Creative Commons license.

It may be worth your time to investigate RExcel. I watched only the first few minutes of the video demonstrating its use, but it looks as if it could come in handy for some types of applications. I'm not sure I'd use it much, even if I spent most of my time on Windoze, but your mileage may vary.

90 second podcast
8 minute podcast

You may have heard the report a couple of weeks ago that cellphones harm honeybees. If you were skeptical of that report, you were in good company. In the podcasts above, May Berenbaum explains that there is no reliable evidence that cell phones contributed to honeybee declines. And she tells EarthSky that in the U.S., the most recent survey of colony numbers showed an increase.¹ Listen to the podcast or head over to EarthSky for details.

Related articles

• Bees, cell phones and sensationalist media (abbotlab.wordpress.com)

Wikipedia can be very useful. When I need to remember how a Dirichlet process works, Wikipedia has a very helpful page to remind me. It's page on genetic drift is pretty good, too.¹ Still, it pays to be careful.

Several years ago, for example, The Telegraph reported that one of Wikipedia's most prolific contributors, "a professor of religion with advanced degrees in theology and canon law", was a community college dropout.

But the American Psychological Association has decided to take things into its own hands.

The call to action was all over the Association for Psychological Science's annual meeting here this past weekend. "Attention APS Members. Take Charge of Your Science," fliers shout. Promotional ads in the conference programs urge the society's 25,000 members to join the APS Wikipedia Initiative and "make sure Wikipedia--the world's No. 1 online encyclopedia--represents psychology fully and accurately." And the Wikimedia Foundation, which backs the encyclopedia, was holding editing demonstrations in the middle of the conference exhibit hall. "Academics, in New Move, Begin to Work With Wikipedia", by Josh Fischman, 28 May 2011, The Chronicle of Higher Education

The President of the APS, Mahzarin R. Banaji of Harvard, is quoted as saying "I'm hearing nothing but enthusiasm, and I really think this is going to work." From the Wikipedia Initiative website:

The broad goals of the APS Wikipedia Initiative (APSWI) are:

• Ensure that articles about psychological research and theory are accurate, up-to-date, complete and written in a style appropriate for the general public
• Ensure that articles are based on independent reliable secondary sources
• To represent scientific controversies and scientific consensus fairly, writing articles in a neutral style
• Improve and review articles to Good Article and Featured Article quality
• Assess psychology-related articles and tag them appropriately when there are problems

It will be interesting to see how this works out.

Carbon dioxide emissions declined in 2009, thanks to the global financial crisis. They went up again in 2010, and they didn't just go up a little. They were 5 percent higher in 2010 than they were in 2008, and the 30.6 gigatonnes released in 2010 is the largest amount ever released in a single year.¹

"This significant increase in CO2 emissions and the locking in of future emissions due to infrastructure investments represent a serious setback to our hopes of limiting the global rise in temperature to no more than 2°C," said Dr Fatih Birol, Chief Economist at the IEA who oversees the annual World Energy Outlook, the Agency's flagship publication.

...

The IEA's 2010 World Energy Outlook set out the 450 Scenario, an energy pathway consistent with achieving this goal, based on the emissions targets countries have agreed to reach by 2020. For this pathway to be achieved, global energy-related emissions in 2020 must not be greater than 32 Gt.This means that over the next ten years, emissions must rise less in total than they did between 2009 and 2010. (emphasis added)

The Guardian quotes Sir David King, a former chief scientific adviser to the UK government: "The only people who will be surprised by this are people who have not been reading the situation properly." According to The Guardian, Sir David will soon release research showing that carbon dioxide emissions in the West decreased only because we have relied on imports from countries like China.

Related articles

• Carbon emissions hit record: energy agency (cbc.ca)
• CO2 emission hits record level, energy agency says (cnn.com)
• CO2 emissions climb to all-time high (blogs.nature.com)
• Record gas emissions 'puts drive to halt temperature rise at risk' (telegraph.co.uk)