Pruning the family tree, chance & inevitability | Gene Expression

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I picked up Clive Finlayson’s The Humans Who Went Extinct: Why Neanderthals Died Out and We Survived mostly for its alternative history value. By this, I mean that it was published in the fall of 2009, less than a year before research which suggests that not all Neanderthals went extinct, in that ~2.5% of the genomes of non-Africans derive from this human lineage. Going by the subtitle I’d assumed that Finlayson’s treatment would be useful, despite its likely false premise. Of course the author was no fool, he was channeling the consensus of his time, even citing the mitochondrial DNA studies which indicated no admixture between between the Neanderthal and modern human lineages. But to my surprise the overturning of a central presupposition of the book did little to alter the theses of Finlayson’s narrative.

In many ways the subtitle was something of a bait & switch. The author clearly was only reluctantly working within the “Out of Africa” framework, which he believed fostered sloppy and incoherent thinking. From what I can tell this seems to be a function of Finlayson’s background in paleontology and ecology, rather than genetics. ...

The Postmodern Consequences of “He Said, She Said” Journalism | The Intersection

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Way back in 2003/2004, I wrote a kind of classic piece in Columbia Journalism Review about the problems with “he said, she said, we’re clueless” coverage of scientific topics. You can read it here.

There was much evidence back then that this was a problem, but we certainly lacked this–a new study showing that “he said, she said” coverage leaves readers less certain that they are able to discern the truth about politics. In other words, such “passive” journalism contributes to a postmodern state of affairs in which nobody thinks they can pin down what reality actually is. It is therefore damaging and detrimental to our efforts to achieve consensus in contested areas, and sound policy solutions.

I have much more to say about this at DeSmogBlog:

The study, conducted by The Ohio State University communications professor Raymond Pingree, did not focus on climate change but rather the U.S. healthcare debate—but the same lesson would seem to apply. Study subjects were asked to read fake news stories in which two disputes about the contents of a healthcare bill were either left unresolved, or factually adjudicated. In other words, sometimes the subjects were exposed to “he said, she said” coverage, and sometimes they were exposed to a breed of journalism that unflinchingly examines where the truth lies.

Then the study subjects answered survey questions about their confidence in whether it was possible to discern the truth in politics. For instance, they were asked how much they agreed that “If I wanted to, I could figure out the facts behind most political disputes.” What kind of article they’d read had a significant effect: Those who’d read the “passive” story were more, er, postmodern in outlook. They were less sure they could discern the truth (if it existed).

You can read the study here; and continue reading my DeSmogBlog analysis here.


NCBI ROFL: And the most racist study of the year award goes to… | Discoblog

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Associations between climate and IQ in the United States of America.

“Relations between average temperature of each of the 48 contiguous states and estimates of state IQ were inspected. Additional state variables were controlled in the correlational analyses, namely gross state product, percent Hispanic, Black, and Asian in the state population, and the pupil-to-teacher ratio for each state. A significant correlation between average temperature and state IQ was found (r = -.70, p < .001). Possible explanations are discussed.”

Bonus excerpt from the text:
“Significant negative relationships were found between state IQ and both winter (r = ?.73, p < .001) and summer (r = ?.53, p < .001) temperatures. Moreover, a significant negative association was found between state IQs and year-round temperatures (r = ?.70, p < .001). Thus, as environmental temperature decreases, the state IQ tended to increase, congruent with the hypothesis and the findings of Templer and Arikawa (2006). While expected, these results are difficult to explain. Previous research has attributed the relationship between climate and IQ to the evolutionary process. Lynn (1991) posited that early humans who migrated from tropical climates to colder ones, were forced to undertake challenging cognitive ...


Daily Roundup: Robotic Moths, Cancer Battles, Electricity Vending Machines | 80beats

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All bats aren’t created equal: Using robotic moths, scientists discovered that bats emitting non-stop radar-like calls catch more insects than their intermittent-emitting brethren—and they do this by hearing the “siren-like” echoes of flying bugs. This suggest that bats evolved their echolocation abilities to increase their nightly catch.
Scientists reported that ovarian cancer survival rates have doubled in the UK in the past 30 years, a change they attribute to better treatments, such as broader access to chemotherapy.
Cheetos, Snickers, and electricity: Japanese companies are rolling out the first vending machines capable of charging electric cars, with plans of installing at least 10,000 by the end of the year.

Laugh your leg ulcers away: After a five-year study discovered that ultrasound—commonly used to treat leg ulcers—was ineffective, lead researcher Andrea Nelson told the BBC, Instead, lead researcher Professor Andrea Nelson said: “The key to care with this group of patients is to stimulate blood flow back up the legs to the hear….[and] “believe it or not, having a really hearty chuckle can help… This is because laughing gets the ...


Cooler-Than-Steam Brown Dwarf Blurs The Line Between Star & Planet | 80beats

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Planetar. Substar. Failed star. Sub-stellar object. Astronomers have pinned each of these monikers on brown dwarfs, a category that has always perplexed scientists because it raises questions about what it means to be a star or a planet. And if that wasn’t enough, now they’ve discovered the coldest brown dwarf yet, blurring the line between planet and star even further.

It’s name is CFBDSIR J1458+1013B, and may be cooler than the boiling point of water (at the pressure of Earth’s atmosphere). This strange body is about 75 light-years from us, where it orbits its binary partner, another brown dwarf. Using the infrared capabilities of the 10-meter Keck II Telescope on Mauna Kea, University of Hawaii researcher Michael Liu and his team estimated the brown dwarf’s temperature, and have a ballpark range for its mass: between 6 and 15 times the mass of Jupiter.

It’s special because it may be a class Y dwarf (temperature less than 225 degrees Celsius (440 F)), a type of object whose existence astronomers had predicted but never actually found. Before this candidate arose, the coolest known brown dwarf was in the T spectral class; while ...


Researchers Use Avatar Camera Technology to Try to Understand Kangaroo’s Hop | 80beats

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At first glance, biologists slapping motion capture gear onto kangaroos sounds like a scientific foray into the 3-D-movie craze. But James Cameron can rest assured: The scientists are merely performing their day jobs, studying kangaroos—and using a nifty new camera to do it.

As kangaroos mosey along at low speeds, they walk, using their tail as a fifth limb. But as they speed up, they slip into their signature bounce. The mystery for scientists is why such large animals—some being over six feet tall—are so darn springy, and as Alexis Wiktorowicz-Conroy, a researcher at the Royal Veterinary College, told the BBC, “We can’t really explain … why their bones don’t break at high speeds.”So the question here isn’t only why and how roos hop, but also why they don’t fall apart when they do. To tackle these questions anew, a team of international scientists is trying out a new gadget on kangaroos at Australia’s Alma Park Zoo, in Brisbane: an outdoor motion-capture camera that uses infrared light—much like how a sonar uses sound—to study the kangaroos’ bodies movements in detail. After the scientists place several plastic-ball markers on the joints of kangaroos (a ...


A question for you: what should I do with my lectures? | The Loom

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I just got back from San Francisco, where I gave a keynote lecture about how our bodies are like ponds, and why doctors need to think like ecologists. It takes a lot of time for me to put these talks together, and so I like to share them afterwards with more people than those who were physically in the room with me. Sometimes the people who invite me videotape the lectures and put them online. (Example: A talk I gave about science and the media.)

Other times, I make an audio recording and merge it with the slides to create a video. (Example: A talk about Neanderthals.) Still other times, I turn my lecture notes into an essay, illustrated with some of my slides. (Example: a piece on why we get old.) Either way, it takes a fair amount of time and so I want to make sure I’m actually making something people want to watch or read. But it occurred to me that I don’t know audience psychology well enough to know what the best course of action is.

So, if you don’t mind, let me foist this quick little poll on you. I’d really appreciate your answers, ...


Skeptic Exchange | Bad Astronomy

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You know, I was going to write a post about how Skeptic Exchange is a really cool way for skeptics and critical thinkers to talk about various topics and get expert answers for questions, how it encourages thoughtful answers using community-based awards, and what a great resource it could be, but then Tim Farley went and wrote a very thorough discussion of it.

So I’m off the hook. Go read Tim’s write-up, then head over to Skeptic Exchange and contribute! Make the world more reality-based!


The Fourth Annual Clinton Global Initiative University Meeting | The Intersection

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One of the most inspiring events I’ve attended in past years was the 2010 Clinton Global Initiative meeting. It’s a unique environment where heads of state, government and business leaders, scholars, and NGO directors come together “to analyze pressing global challenges, discuss the most effective solutions, and build lasting partnerships that enable them to create positive social change.” Members at last years meeting made close to 300 new commitments on issues involving economic empowerment, energy and the environment, education, global health, and more. Since launching CGI, they have put $63 billion toward improving nearly 300 million lives in over 170 countries. In other words, CGI demonstrates that we are truly becoming a global community.

Today President Clinton announced the Fourth Annual Clinton Global Initiative University Meeting, which will take place at the UC San Diego from April 1-3. Approximately 1,000 students will come together from all over the world to meet with non-profit leaders, entrepreneurs, and celebrities engaged in efforts to create positive change. Each student will make a Commitment to Action – a detailed plan for improving lives within one of CGI U’s focus areas: education, environment & climate change, peace & human rights, poverty alleviation, and public health. Since 2008, this university event has brought together more than 2,500 students from 575 schools in 99 countries. As Clinton explains:

“Their work has improved the lives of thousands of people around the world. I am looking forward to convening the next generation of global leaders once again, so they can learn from each other and gain practical skills that will help them turn their ideas into real change.”

What comes out of CGI U? So far, students have:

· Over $1.3 million in infrastructure improvements to schools and libraries in countries including the U.S., Rwanda, Nigeria, and Laos;
· Reached more than 74,000 students, faculty, and staff with educational efforts and outreach about clean energy and sustainability;
· Placed more than 3,800 new recycling containers on college campuses and in surrounding communities;
· Engaged 2,700 people in workshops on conflict resolution, diplomacy, and peace;
· Established and maintained more than 90,000 square feet of community gardens;
· Introduced more than 3,000 bicycles on college campuses in the U.S., Ghana, Uganda, Kenya, Cameroon, and China;
· and much more

CGI U will be webcast live at http://www.cgiu.org. You can read the full agenda here and follow updates on Twitter @cgiu and @ClintonGlobal and Facebook.


Modal Logic and the Ontological Proof | Cosmic Variance

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The ontological proof for the existence of God (really “proofs” or perhaps “arguments,” as there are various versions) has popped up in the blogs a few times recently: e.g. Ophelia Benson, Josh Rosenau, Jerry Coyne. You’ve probably heard this one; it was most famously formulated by Saint Anselm, and most famously trashed by Immanuel “Existence is not a predicate” Kant. A cartoon version of it would be something like

  1. God is by definition a perfect being.
  2. It is more perfect to exist than to not exist.
  3. Therefore, God exists.

Now, this is a really cartoonish version of the argument — it’s not meant to be taken seriously. This kind of ontological proof is a favorite whipping-argument for atheists, just because it seems so prima facie silly. Just ask Jesus and Mo.

This kind of mockery is a little unfair (although only a little). What’s important to realize is that the ontological proof is perfectly logical — that is, the conclusions follow inevitably from the premises. It’s the premises that are a bit loopy.

It’s instructive and fun to see this in terms of formal logic, especially because the proof requires modal logic — an extension of standard logic that classifies propositions not only as “true” or “false,” but also as “necessarily true/false” and “possibly true/false.” That is, it’s a logic of hypotheticals.

So here is one formalization of the ontological argument, taken from a very nice exposition by Peter Suber. First we have to define some notation to deal with our modalities. We denote possibility and necessity via:

Just given these simple ideas, a few axioms, and a fondness for pushing around abstract symbols, we’re ready to go. Remember that “~” means “not,” a “v” means “or,” and the sideways U means “implies.” Take “p” to be the proposition “something perfect exists,” and we’re off:

There is something beautiful here, even if it’s somewhat silly as a proof for the existence of God. It’s silly in an illuminating way!

As Suber says, the argument is “valid but unsound.” He pinpoints three premises with which reasonable people might disagree: 1 (“if perfection exists, it necessarily exists”), 2 (“perfection possibly exists”), and 5 (“if something is necessarily true, then it is necessarily necessarily true”). That last one is not a typo.

For me, the crucial mistake is some mixture of 1 and 2, mostly 2. The basic problem is that our vague notion of “perfection” isn’t really coherent. Anselm assumes that perfection is possible, and that to exist necessarily is more perfect than to exist contingently. While superficially reasonable, these assumptions don’t really hold up to scrutiny. What exactly is this “perfection” whose existence and necessity we are debating? For example, is perfection blue? You might think not, since perfection doesn’t have any particular color. But aren’t colors good, and therefore the property of being colorless is an imperfection? Likewise, and somewhat more seriously, for questions about whether perfection is timeless, or unchanging, or symmetrical, and so on. Any good-sounding quality that we might be tempted to attribute to “perfection” requires the denial of some other good-sounding quality. At some point a Zen monk will come along and suggest that not existing is a higher perfection than existing.

We have an informal notion of one thing being “better” than another, and so we unthinkingly extrapolate to believe in something that is “the best,” or “perfect.” That’s about as logical as using the fact that there exist larger and larger real numbers to conclude that there must be some largest possible number. In fact the case of perfection is much worse, since there is not single ordering on the set of all possible qualities that might culminate in “perfection.” (Is perfection sweet, or savory?) The very first step in the ontological argument rests on a naive construal of ordinary language, and the chain is no stronger than its weakest link.


Puny Banner and tip jar | Not Exactly Rocket Science

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A couple of house-keeping things.

Firstly, if you cast your eyes a few pixels upwards, you’ll notice the snazzy new banner. All the Discover blogs now have them to give us a bit more of an individual feel. I love mine/them. The designer’s done a great job with reconciling the “rocket science” bit with the fact that I write almost entirely about biology. You can see the rest of the logos on the sidebar, and I’ll probably be doing a Cafepress store at some point.

Secondly, you might have noticed that there’s also a “Support Science Writers” box in the sidebar. I’ve added this in light of my new initiative to voluntarily pay for the best science writing that I read. In the comments, people suggested various ways that these micropayments could be done easily, but all the best suggestions involve adding some sort of code to one’s site.

While a simple solution may take some more work, I’ve implemented these Paypal buttons as a temporary fix. The top one goes to the writers I pick every month, distributed equally (any donations this month will go to February’s picks, and so on). The bottom one goes to me and I’ll match a third of the donations and send that to the chosen writers too.

Both go to my Paypal account but they’re tagged differently so I can sort through all the donations and distribute them easily. This isn’t ideal by any means, but like many things on the Internet, I thought I’d give it a go and see what happens. So if any of you would like to support NERS or any of the other great blogs that I link to, please feel free to contribute. There is, of course, no expectation to do this.

For reference, here are the people who I’ve donated to this month:

Reminder: NECSS in April! | Bad Astronomy

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The critical thinking meeting season is about to kick off, and the first big one in the US is NECSS: The Northeast Conference for Science and Skepticism. It’s from April 9 – 10 in New York City, and has a pretty cool list of speakers. I’m honored to be giving the keynote address, and there are lots of fun extracurricular activities planned as well.

Still not convinced? Then listen to the smooth basso of my pal George Hrab in this promo he put together for NECSS. He’ll be there too, and I bet we can convince him to do a song or two from his latest album.

Registration is now open, and there’s an event page on Facebook if you’re into that sort of thing too.

UPDATE: George just let the cat out of the bag on this, too: we’ll be doing a live performance of his song "Death from the Skies!" Saturday night at the reception. Here’s a taste of what you’ll get:


A banner day | Bad Astronomy

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Sharp-eyed viewers may have noticed that the BA blog has a new banner! If you didn’t notice, then look up a few centimeters. See it?

All the Discover blogs got spiffy new banners to help individualize them, yet have a design theme to tie them together. If you look over on the right, at the sidebar, you’ll see the blogs linked by their banners. That’ll make it easier for you to read all the other science blogs enthralled to the Hive Overmind. If you haven’t checked them out, you should. We have quite a variety here, and they’re all really good.


Mentos Is to Diet Coke as Coffee Filter Is to Guinness?! | Discoblog

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The SATs might have made you hate analogy problems, but this one sure is tasty.

That clangy thing taking up space in the bottom of your Guinness or Tetley’s can might soon be done away with and replaced by a coffee filter.

The ball inside the Guinness can, called a widget, contains a pocket of nitrogen gas held under pressure. When some lucky person opens the can, the pressure is released and the gas shoots out into the beer through a small hole and creates the foam.

You may now be thinking, Wait a minute—most beers seem to have plenty of gas bubbles even without some fancy widget. The thing is that Guinness and similar brews need the widget because nitrogen bubbles are smaller than those filled with carbon dioxide, the bubbling gas in other fizzy drinks. The small nitrogen bubbles make Guinness’ foam deliciously thick and creamy, but it’s harder to get the gas to come out of solution. The widget forces lots of excess nitrogen into the beer, setting off a well-timed bubble eruption.

But the widget is not the only way to send nitrogen bubbles cascading upward. In normal ...


NCBI ROFL: The scent of a woman. | Discoblog

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Masculinity/femininity of fine fragrances affects color-odor correspondences: a case for cognitions influencing cross-modal correspondences.

“Four experiments found that the colors people choose as corresponding to the odors of fine fragrances are influenced by the perceived masculinity/femininity of those fragrances. Experiment 1 examined the colors chosen for 3 male and 3 female fragrances. The pattern of colors chosen for female fragrances differed from that for male fragrances. Experiments 2 and 3 found that colors assigned to 2 unisex fragrances depend on whether subjects thought that the fragrances were male or female fragrances. Experiment 4, by labeling unisex fragrances as male or female, showed that this difference in color selection was the result of subjects’ thinking that a fragrance is a male or female fragrance. Thinking of the masculinity/femininity of a fragrance influences the selection of colors that corresponds to these odors.”

Photo: flickr/fruity monkey

Related content:
Discoblog: NCBI ROFL: I’m a lumberjack, and I’m OK, I smell like pine and get chicks all day!
Discoblog: NCBI ROFL: Oral malodor and related factors in Japanese senior high school students.
Discoblog: NCBI ROFL: Smelly Week: ...


Hungry for solutions: science and feeding the world | The Intersection

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This is a guest post composed at the NSF Science: Becoming the Messenger Workshop at the University of Nebraska, Lincoln (UNL) by Vicki Miller, Office of Research and Economic Development, University of Nebraska-Lincoln.

I grew up in rural Nebraska amid friends and family who tilled the soil, grew crops and raised livestock. Low farm prices and over production were the pressing issues. Food was abundant and cheap. No one thought much about the whys and hows of this abundance and there was much talk on the farm about America’s so-called “cheap food policy.”

We didn’t think much about it at the time but, it turns out, this abundance was fueled by science. Agricultural research spawned improved crops and technologies that spawned the “green revolution” and expanded ag production worldwide. University of Nebraska-Lincoln agronomist Ken Cassman says that, by the late 20th century, food was plentiful and inexpensive partly because of scientific advancements made decades earlier.

Those days of plenty could become a thing of the past. Food security – producing enough food to feed a rapidly expanding population – is shaping up as one of the 21st century’s most critical challenges. Scientific research will again be at the heart of the solution.

The stakes are high and the issues are complex. As an agronomist, Cassman has spent his career working on issues related to food security. These days he keenly focused on what kinds of agricultural research will produce the most bang for the investment of time and money. He chairs a council of scientists that advises an international ag research centers – the Consultative Group on International Agricultural Research, known as CGIAR – on global agricultural research projects.

While Cassman doesn’t buy the doomsday predictions that a global food crisis is inevitable, he says science must play a leading role. And researchers must make wise choices about the most critical issues to address.

The stakes have never been higher for the next green revolution. As a former farm kid and a science communicator, I’m betting on the power of science and the ingenuity of farmers to find ways to keep food on the global table.


Is Pond Scum the New Sexy? | The Intersection

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Fuels derived from biological sources, biofuels, are currently receiving a fair amount of press.One of the biggest concerns is always, are biofuels a viable option? With rising oil prices and instability in the Middle East, biofuels, especially those derived from non-food energy sources, are becoming more and more attractive possibilities.As part of an NSF-supported program, we are attempting to enhance lipid production and quantity in algae used for this purpose.These algae can be grown commercially without competition for crop land mass used for food.A beneficial side effect of this process is the inception of new start-up companies to produce these fuels.One example of this is Sapphire Energy Inc.

In a March 8, 2011, news release, Sapphire announced a strategic collaboration with the giant Monsanto Co. In crop development and crop chemical production, Monsanto is at the forefront.Monsanto has been integral in the development new crop plants and chemistry that have made billions of dollars of profit.With an investment from this company, Sapphire is obviously being taken seriously by the business community.In addition, the United States Department of Agriculture and Federal Aviation Administration have teamed up to invest in the production of renewable jet fuels.In two separate tests in January 2009, Continental and Japan Airlines flew pilot missions powered at least partially by jet fuel derived from algae.Mounting evidence attests to the viability of these fuels.

Companies like Sapphire and other new start-ups such as these will require the biological and chemical expertise of new young scientists.It is essential that we now support the education and training of bright enthusiastic students.We can invest in these students future and be at the forefront of this new technology industry or we can be left on the sidelines.It’s our choice.

Guest post by Paul Twigg


The Brain in Action: Windows into the Mysteries of Language Disorders | The Intersection

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This is a guest post composed at the NSF Science: Becoming the Messenger Workshop at the University of Nebraska, Lincoln (UNL) by Autumn McIlraith.

The field of communication disorders is full of unanswered questions. We want to know why some children struggle to speak fluently, and why others have difficulty learning to read. Why are some treatments effective, but others aren’t? Research in the field of speech and language disorders has traditionally used behavioral testing to evaluate the abilities of individuals with impairments, and to measure the effectiveness of interventions. However, behavioral testing has some limitations. Often, we can see the problem, but not where in the chain the breakdown occurred. For the child struggling to speak, was it planning the motor movements that was the issue, or was it putting together the words themselves?

Brain imaging can help to answer these questions. It gives us a window into the hidden world of the brain, without actually opening up the skull and poking it. Techniques like functional Magnetic Resonance Imaging (fMRI), event-related brain potentials (ERP) and magnetoencephalography (MEG) allow us to look at brain activity, by measuring blood flow, or electrical or magnetic activity from neurons. These imaging techniques are completely noninvasive, and can be used with young children and in some cases even infants.

Through brain imaging, we can observe the brain in action. When we look at the brain scan of a child struggling to speak, we hope to be able to see whether the issues lie in areas associated with motor speech planning, language processing, or maybe somewhere else entirely. If the child underwent treatment for his or her issues and seemed to show improvement, we could compare the brain activity before or after treatment, to evaluate its effectiveness.

Speech and language researchers can benefit greatly from the expertise of brain imaging scientists. Collaboration between these areas in the future will help researchers to answer some exciting questions about the nature of speech and language impairments, and give us further insight into the marvelous complexity of the human brain.

(For more information about a language lab involved in brain imaging research, visit the here and here)


Can you hear me now? Advancing hearing loss prevention and treatment | The Intersection

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This is a guest post from Dr. Heather CJ Smith of Creighton University, composed while attending the NSF Science: Becoming the Messenger workshop in Lincoln, Ne.

Hearing loss is a widely-preventable public health dilemma costing the US economy $56 billion annually. In the US alone, oral antibiotics cause approximately 120,000 people to suffer from some form of irreversible-hearing loss. Since antibiotics are essential for treating life-threatening infections, it is critically important to develop new hearing loss prevention and treatment strategies. 

With the advent of new imaging technologies, my research group has been able to make the first real-time measurements of inner ear metabolism (energy production and use). This novel technique allowed us to ‘see’ how inner ear energy production is rapidly and dramatically inhibited by specific antibiotics. Unfortunately, such decreases in metabolism lead to the production of cell-damaging free radicals which, when generated at high-rates, permanently damage cells and the inner ear. This damage leads to irreversible-hearing loss. 

I am working on expanding these novel findings by researching how and why antibiotics interfere with energy production and cause free radical generation in the inner ear. Once we understand the mechanisms controlling the production free radicals during antibiotic treatment, optimized hearing loss prevention strategies can be developed and implemented to preserve the hearing of thousands of people every year.


House Appropriators Preview New CR

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Appropriations Committee Introduces Three Week Continuing Resolution - Bill will Prevent Government Shutdown, Cut $6 Billion in Spending

"House Appropriations Chairman Hal Rogers today introduced a Continuing Resolution (CR) to fund the federal government at current rates for three weeks -until April 8 - while cutting $6 billion in spending. The legislation (H.J. Res 48) is the second short-term funding extension to prevent a government shutdown while Congressional negotiations continue on a long-term plan to keep the government running through the end of the fiscal year. ... - $63 million - NASA - Cross Agency Support".