Category: Link Love

Ben Goldacre on more bad data: this time from drug companies

By Carl Zimmer | September 30, 2012 10:47 am

This morning I was accused of writing “corporate sponsored blogs whoring themselves out to all and sundry.” Actually, I was arguing that science writers have a duty to call out weak science and press manipulation rather than cave into it. That applies to any kind of research. I happened to be talking about research on genetically modified foods and their health risks. But it applies just as well to pharmaceutical corporations that deep-six drug trials that don’t support their drugs. The most eloquent critic of this bad behavior is Ben Goldacre. You can watch this video of a TED talk he recently gave on the subject, read this essay in the Guardian, or pre-order his new book, Bad Pharma.

If highlighting Goldacre’s vital work means I have to return my gold-plated corporate-whore Corvette, so be it.

[Update: Guardian link fixed, book title fixed]

CATEGORIZED UNDER: Link Love, Meta

Retraction Watch in the Boston Globe: Make Science More Transparent

By Carl Zimmer | April 17, 2012 10:08 am

As I blogged yesterday, I have a story in the New York Times today about some scientists who are calling for a reformation of science, pointing to troubling indicators such as the rise in retractions of scientific papers.

As any sane journalist would do, I consulted the fantastic Retraction Watch, written by Adam Marcus (left) and Ivan Oransky, while working on my own piece. I also called Oransky for his thoughts on the argument I was describing, championed by, among others, Ferric Fang of the University of Washington and Arturo Casadevall of Albert Einstein College of Medicine.

Oransky was a huge help. But by the time my editor and I had shaped the story to fit in the paper, only a brief mention and a link to Retraction remained. Oransky’s own opinions were left behind on the cutting room floor. Fortunately, he knows that floor very well, having swung the journalism scimitar plenty of times himself as the executive editor at Reuters Health.

Even more fortunately, the Boston Globe has published some extended reflections from Oransky and Marcus on what retractions mean for the state of science. Check it out.

[Image: Retraction Watch]

A Smithsonian Q & A with E. O. Wilson: complete with outtakes

By Carl Zimmer | March 23, 2012 2:29 pm

Smithsonian recently asked me to interview Harvard biologist E.O. Wilson about his new book, The Social Conquest of Earth. You can read the Q & A on their web site. 

Wilson and I spoke for quite a while, covering wide range of subjects. One particularly interest part of the talk addressed his ongoing attack on a major aspect of modern evolutionary theory, known as inclusive fitness. I reported on his attacks–and the response of his critics–in the New York Times in 2010.

Basically, most evolutionary biologists believe that a great deal of behavior–including altruistic behavior–can be explained by the way genes get passed down among relatives. If you help your cousins, some of your genes will get transmitted even if you have no kids of your own. Wilson and his colleagues at Harvard, Martin Nowak and Corina Tarnita, argue instead that inclusive fitness doesn’t make mathematical sense and is unnecessary. Wilson holds that good old natural selection on individuals can explain a lot, and he also argues for selection on higher levels. Groups of organisms–human tribes, for example–can be selected for their group-level traits.

In the year and a half since my article, his critics have counterattacked. If you want to see why they think he’s wrong, I’d recommend reading five fiery posts by University of Chicago evolutionary biologist Jerry Coyne at his web site Why Evolution Is True: 1, 2, 34, 5.

For those who have been following this scrum, I thought I would include a portion of the conversation that did not end up in the final version, focusing on Wilson’s response to critics. It goes pretty deep in the biological weeds, and it doesn’t read smoothly, because both of us would stop in mid-sentence to make ourselves clear to each other. (I’ve trimmed a few really incomprehensible dead ends.) But if you just can’t enough of the Hamilton Inequality, enjoy:

Q:  When you presented your ideas in that Nature paper in 2010 with Novak and Tarnita, a number of scientists responded–over 150 scientists responded both in Nature and then in some other journals as well, taking issue with your argument. They said that inclusive fitness was, in fact, a very powerful and legitimate explanation. Had you anticipated that kind of response?

A:  Yes. (Laughter) It’s just that the inclusive fitness theory had persisted as the correct and prevailing theory for almost four decades. And the ones who were animated most of course were those who were working in the field, trying to perfect it and using it to explain social behavior.

But there were two things wrong, and this is what I was pointing out over a period of four years, and finally came to a more definitive form in the Nature paper. First, as the mathematicians showed, the basic foundations of the inclusive fitness theory are unsound. The Hamilton Inequality does not work except in extreme conditions that scarcely exist on earth. And inclusive fitness is a phantom measure which seems intuitively right but which simply doesn’t exist in any form that could ever be measured.

And that being the case, then we should look more carefully at just what has been accomplished with inclusive fitness theory. Extremely little, in quantitative terms. And most of the applications that have been made–and they’re made over and over again to make up the main corpus of literature on inclusive fitness theory–applies to degrees of conflicts of societies, which vary inversely with the degree of relatedness among individuals. I’ve been able to show that there is a perfectly good set of alternative biological hypotheses to explain that. That’s in my part of this article, in Nature, but I went into much more detail in an earlier paper in Bioscience.

Even the applications of inclusive fitness theory are not necessarily the only ones that can be made. I have argued that ones from an individual-level or group-level selection–or the interaction between the two–provide superior fits. And further, the multi-level selection model allows us to explore and explain a great deal more phenomena. And I expect that to be shown as work goes on. I think it’s particularly relevant to the explanation of the social behavior in humans.

Q:  Just to take one example that the critics raised, they talked about how inclusive fitness theory makes a prediction about sex allocation, about the investment in different sexes in the offspring. And they say this is something that inclusive fitness predicts and we’ve gone out and we’ve done a lot of tests to see if that’s true and they find these ratios in lots of animals as predicted by that theory. When they make that sort of argument, what’s your response?

A: It’s a little bit like Ptolemaic astronomy: epicycles will always give the exact results if you’re willing to add them. And in this case–I have pointed this out as well–there’s a flaw in the reasoning about the studies of investment, particularly in whether you invest more in males or females in the social insect societies.

If you have only one female who is queen in the colony, and if that queen has mated only once so that her offspring are that close, then you should see because of the implications of haploid/diploid, the way sex is determined in ants, bees, wasps. You should see a favoring of investment in new queens, over investment in males as measured by the amount of biomass. And that inequality does exist and it should be three to one investment in the weight. And that has been what is thought to be a very powerful argument.

However, this I believe has a major flaw in the reasoning. The colony wishes to make an investment in males versus females in numbers that would be most advantageous in having a female successfully mated, when they leave the nest to get mated, bees, ants, wasps. And therefore, the colony should be trying to get something closer to a one-to-one investment.

And since females are much bigger–they have to have all that fats and ovary and so on–and males are much smaller because in most of these social insects. All they have to do is find a female, deliver their sperm, and die. So the males are much smaller.

This means then that getting a one-to-one ratio in sex that is the same as you see throughout the rest of the animal kingdom, means that you will be having to invest much more in the females when you invest in males. And actually when you make that hypothesis, use that principle, which is the obvious one, then that comes closer to the actual figures we have in the biomass investment.

They [Wilson’s critics] may dispute that, but my point is that they did not by any means find a testing ground on which the old theory could stand or fall. It’s in my view a much simpler and more precise explanation to use the argument of one to one ratios of male and female.

Q:  One other thing that critics have brought up is they claim that there are no new predictions in the argument that you and your colleagues set forth. Are there predictions that you can make from this different view of social evolution?

A:  My book, The Social Conquest of Earth, is filled with them.

Q:  What would be a couple predictions?

A:  You mean in terms of group versus individual level selection? Yeah. What it is, is more of a…Rather than an a-prioristic application of group selection as it is the use of group selection to explain what actually happened. And that is, you piece together only by the close examination of the biology of the various stages leading up to advanced social behavior. That’s the best I can say right now.

Multi-level selection theory is undeveloped, essentially, most undeveloped because it has been almost abandoned due to the dominance of inclusive fitness theory. I think inclusive fitness theory has been rejected and now we have every reason to return to a multi level selection theory and develop it. And Martin Novak is beginning to do that to some extent and to develop a rejuvenated, multilevel selection theory.

So I think at this point multi-level selection now is open to development without the inhibition of inclusive fitness theory–may I use the expression the deadweight of inclusive fitness theory?—will, I believe, from this point on be developed and tested in a proper way.

Photo by On Being via Creative Commons

Gutenberg, the Solar System, and Biological Cities: New Reviews at Download the Universe

By Carl Zimmer | March 17, 2012 10:39 am

Here’s the latest batch of reviews from Download the Universe. Check out these science ebooks:

Living Architecture: How Synthetic Biology Can Remake Our Cities: A contemplation of how tinkering with cells can change civilization.

The Solar System: An interactive guide to the planets.

Gutenberg the Geek: How the explosion of the Internet today mirrors the birth of movable type.

Natural History: Mammals – Carnivores: Lions and tigers and bears, oh my!

The Stir of Waters: Radiation, Risk, and the Radon Spa of Jáchymov. A journey to a bizarre resort where people bathe in radioactive waters.

CATEGORIZED UNDER: Download the Universe, Link Love

Take the Flame Challenge

By Carl Zimmer | March 4, 2012 12:36 pm

Alan Alda has come up with an excellent contest for scientists:

Answer the question, “What is a flame?”

Here’s the catch. The audience for the answer is 11-year-olds. Writing this week in Science (free pdf), Alda recalls how he asked this question to his science teacher when he was 11. The answer he got was, “It’s oxidation.”

Accurate, but not enlightening. This, of course, is a challenge that science writers face every day–how to use everyday language to convey insights that scientists describe to each other and students with precise, but often obscure, terminology.

It’s not easy for experienced writers to do this, and it can be even harder for scientists who are just starting to communicate to a broad audience. When I teach workshops for science graduate students, I force them to do without a long list of jargon. (The Index of Banned Words) I want them to think of plain-English alternatives and mind-lifting metaphors instead.

It can be a struggle for them to resist those words. The most vivid way I can illustrate the struggle is to pick someone at random at a workshop and ask, “What do you  do?”

Simple enough to ask, but remarkably hard to answer. All the people I’ve picked have been investigating fascinating stuff, from subconscious priming to nanotechnology to coral reefs. And yet they manage to give me answers that are both boring and vague–and peppered with those banned words. So I just keep asking them to try again until we get to the heart of things–an answer that’s accurate, but also conveys to a non-scientist why their research is interesting, important, and inspiring enough to keep them working insane hours on it.

Alda has thought a lot about these issues as well; he’s on the advisory board of the Center for Science Communication at Stony Brook University. And he hopes, through his “Flame Challenge” to get more scientists to think about them as well. Here are the rules for his contest:

1. Answer the question — “What is a flame?” — in a way an 11-year-old will find intelligible and maybe even fun.

2. Answers will be screened for accuracy by scientists, then judged by a panel of 11-year-olds.

3. Answers can be submitted through April 2, 2012. [Click here for the entry form.]

4. The winning entry will be unveiled at a special event at the World Science Festival in New York in June. The winner will get VIP tickets to the Festival, along with a Flame Challenge T-shirt, and the gratitude of a nation of 11-year-olds.

5. Finalist entries, as well as the winning entry, will be posted on the Flame Challenge website:www.flamechallenge.org

6. Entries can be written, spoken (on video), or told through graphics.

7. There is no limit on length, but remember – brevity is the soul of wit, particularly when the 11-year-old has a cell phone, an X-Box, a Facebook habit, etc.

May the best explanation win…

[Image: Photo by qisur on Flickr, via Creative Commons]

 

 

CATEGORIZED UNDER: Link Love, Meta

Introducing Download the Universe: A new science ebook review

By Carl Zimmer | February 21, 2012 11:06 am

I’d like to draw your attention to a new project some colleagues and I have built: a science ebook review.

For over a year now, ebooks about science have been published at a remarkable clip, but there’s been a serious gap in this growing ecosystem: a way for people who want to read new ebooks about science to find out about new projects. Because science ebooks are so new, they have a way of falling between the cracks. Conventional book reviews aren’t very interested; blogs only sporadically pay attention.

At this year’s Science Online conference, some colleagues and I decided that this was a problem easily solved. So we set out to solve it, with a new site: Download the Universe.

We are fifteen writers and scientists who want to explore this new form. On a regular basis, we’ll be delivering new reviews of ebooks about technology, medicine, natural history, neuroscience, astronomy, and anything else that fits under the comfortably large rubric of science. We also define ebooks generously–everything from a plain-vanilla pdf on an author’s web site to a Kindle Single to an elaborate iPad app. (We will not be reviewing ebooks that are simply digitized versions of print books.) We welcome tips about titles to review–from readers, authors, or publishers.

We already have an inventory of reviews that we’ll be publishing over the next few days, and we’re at work on more. There’s a lot to cover, we’re happy to report.

CATEGORIZED UNDER: Ebooks, Link Love, Writing Elsewhere

A Hot Young Earth: My Answer to the Annual Edge Question

By Carl Zimmer | January 15, 2012 12:47 pm

Each year, literary agent and science salonista John Brockman poses a question about science and gets a slew of answers from scientists, writers, and other folks. This year’s question is

WHAT IS YOUR FAVORITE DEEP, ELEGANT, OR BEAUTIFUL EXPLANATION?

Brockman got 187 responses, totaling some 126,700 words. A book, you say! Well, if this year is like previous ones, this year’s answers will indeed become a book. But in the meantime, you can browse the answers for yourself, perhaps plucking out those of your favorite people. (Fellow Discover blogger cosmologist Sean Carroll chooses Einstein’s explanation of gravity, for example.)

I found this year’s question particularly thought-provoking. Why is it that we call an equation or a theory “beautiful”? They don’t have pretty hazel eyes. They aren’t desert landscapes. I’m not sure of the answer. Scientific explanations seem to be beautiful if they give sense to confusing complexity in a very short space. Or maybe we just like the feeling we get when we consider how our puny human brains can interpret the universe.

For a lot of physicists, the beauty of an equation seems to be a good hint that it’s probably true. But I’m always a bit suspicious of beauty as a guide to the natural world. A number of contributors selected Darwin’s theory of evolution as their favorite explanation, and there’s no doubt that’s both beautiful and true. But there have been some wonderfully beautiful accounts of the natural world that have proven awesomely wrong. I was reminded of this fact while working on a new version of my evolution textbook (this one’s for biology majors). I was re-researching how scientists first came to appreciate the vast age of our planet, and realized it was a bit more complicated than I had previously appreciated. So that’s what I chose as my answer, which I’m reprinting here in full:

A Hot Young Earth: Unquestionably Beautiful and Stunningly Wrong

Around 4.567 billion years ago, a giant cloud of dust collapsed in on itself. At the center of the cloud our Sun began to burn, while the outlying dust grains began to stick together as they orbited the new star. Within a million years, those clumps of dust had become protoplanets. Within about 50 million years, our own planet had already reached about half its current size. As more protoplanets crashed into Earth, it continued to grow. All told, it may have taken another fifty million years to reach its full size—a time during which a Mars-sized planet crashed into it, leaving behind a token of its visit: our Moon.

The formation of the Earth commands our greatest powers of imagination. It is primordially magnificent. But elegant is not the word I’d use to describe the explanation I just sketched out. Scientists did not derive it from first principles. There is no equivalent of E=mc2 that predicts how the complex violence of the early Solar System produced a watery planet that could support life.

In fact, the only reason that we now know so much about how the Earth formed is because geologists freed themselves from a seductively elegant explanation that was foisted on them 150 years ago. It was unquestionably beautiful, and stunningly wrong.

The explanation was the work of one of the greatest physicists of the nineteenth century, William Thompson (a k a Lord Kelvin). Kelvin’s accomplishments ranged from the concrete (figuring out how to lay a telegraph cable from Europe to America) to the abstract (the first and second laws of thermodynamics). Kelvin spent much of his career writing equations that could let him calculate how fast hot things got cold. Kelvin realized that he could use these equations to estimate how old the Earth is. “The mathematical theory on which these estimates are founded is very simple,” Kelvin declared when he unveiled it in 1862.

At the time, scientists generally agreed that the Earth had started out as a ball of molten rock and had been cooling ever since. Such a birth would explain why rocks are hot at the bottom of mine shafts: the surface of the Earth was the first part to cool, and ever since, the remaining heat inside the planet has been flowing out into space. Kelvin reasoned that over time, the planet should steadily grow cooler. He used his equations to calculate how long it should take for a molten sphere of rock to cool to Earth’s current temperature, with its observed rate of heat flow. His verdict was a brief 98 million years.

Geologists howled in protest. They didn’t know how old the Earth was, but they thought in billions of years, not millions. Charles Darwin—who was a geologist first and then a biologist later—estimated that it had taken 300 million years for a valley in England to erode into its current shape. The Earth itself, Darwin argued, was far older. And later, when Darwin published his theory of evolution, he took it for granted that the Earth was inconceivably old. That luxury of time provided room for evolution to work slowly and imperceptibly.

Kelvin didn’t care. His explanation was so elegant, so beautiful, so simple that it had to be right. It didn’t matter how much trouble it caused for other scientists who would ignore thermodynamics. In fact, Kelvin made even more trouble for geologists when he took another look at his equations. He decided his first estimate had been too generous. The Earth might be only 10 million years old.

It turned out that Kelvin was wrong, but not because his equations were ugly or inelegant. They were flawless. The problem lay in the model of the Earth to which Kelvins applied his equations.

The story of Kelvin’s refutation got a bit garbled in later years. Many people (myself included) have mistakenly claimed that his error stemmed from his ignorance of radioactivity. Radioactivity was only discovered in the early 1900s as physicists worked out quantum physics. The physicist Ernst Rutherford declared that the heat released as radioactive atom broke down inside the Earth kept it warmer than it would be otherwise. Thus a hot Earth did not have to be a young Earth.

It’s true that radioactivity does give off heat, but there isn’t enough inside the planet is to account for the heat flowing out of it. Instead, Kelvin’s real mistake was assuming that the Earth was just a solid ball of rock. In reality, the rock flows like syrup, its heat lifting it up towards the crust, where it cools and then sinks back into the depths once more. This stirring of the Earth is what causes earthquakes, drives old crust down into the depths of the planet, and creates fresh crust at ocean ridges. It also drives heat up into the crust at a much greater rate than Kelvin envisioned.

That’s not to say that radioactivity didn’t have its own part to play in showing that Kelvin was wrong. Physicists realized that the tick-tock of radioactive decay created a clock that they could use to estimate the age of rocks with exquisite precision. Thus we can now say that the Earth is not just billions of years old, but 4.567 billion.

Elegance unquestionably plays a big part in the advancement of science. The mathematical simplicity of quantum physics is lovely to behold. But in the hands of geologists, quantum physics has brought to light the glorious, messy, and very inelegant history of our planet.

[Post-script: Thanks to responses from readers, I can see how this essay is confusing. I added some passages from the papers I cite below down in the comment thread, which I hope can clear things up a bit.]

[Update: For an up-to-date review of the age and formation of the Earth, see this paper [abstract, free pdf] For a great look at Kelvin’s work, see this piece in American Scientist or the more technical paper on which it was based (free pdf).]

[Image: Photo by Hawaiian Sea - http://flic.kr/p/8AyKnC via Creative Commons]

Words bring life to life

By Carl Zimmer | January 13, 2012 8:58 am

Drew Berry is one of the great movie-makers of the molecular world. He makes gorgeous computer visualizations of DNA, proteins, and the various goings-on inside the cell. Last night I spent a little time watching a new TEDx talk of his just posted online. My first thought was, “Why didn’t I get to see these movies when I was learning about biology as a kid? Life is unfair.” Compared to the flat cartoons of textbooks, or even the crude animations in documentaries of yore, Berry’s work seems to come from some advanced alien civilization.

In case you haven’t seen Berry’s work before, I’ve embedded his lecture here. (You may have heard about him when he got a recent Macarthur “genius” grant.) If you have seen his stuff before, I’d suggest you watch this anyway. And this time, don’t just watch. Listen.

When I first saw Berry’s work a while back, I was immediately gob-smacked. But as I watched his synchronized swimming of molecules a while longer, I realized after a while that I didn’t understand a lot of what was going on. I didn’t know the names of the molecules I was looking at, and, more importantly, I couldn’t tell what a lot of them were doing. The only sense I could make of it all derived from what I already knew.

Berry’s TEDx talk is more satisfying because it’s a talk. You look at the mesmerizing images, and Berry explains what you’re seeing. What’s really interesting is how he–no doubt unconsciously–uses words that switch on the mental eye. When he zooms in on a chromosome, he points out structures passing through it that look “like whiskers,” which act as the “scaffolding” for the cell (the microtubules). He then zooms into the place where the chromosome and microtubule meet, the kinetochore. What you see looks like a supercomputer’s acid trip. But you can make sense of what you see because Berry uses metaphors. He calls it a “signal broadcasting system.” Now all the molecules jittering around aren’t totally random. We can see how molecules come together to make life possible.

There’s no question that people like Berry are going to be making the movies that fill our heads in our future when we think about what’s going on in our bodies. But those movies will need good soundtracks.

CATEGORIZED UNDER: Link Love, Top posts

XMRV takes another step to de-discovery?

By Carl Zimmer | December 22, 2011 12:01 pm

I’ve written a few times here about the battle over a virus called XMRV, and its supposed link to chronic fatigue system. I just wanted to point this morning to a few articles by some fine writers about the latest twist: the paper that first claimed a link has been completely retracted.

Ivan Oransky in Reuters

Jon Cohen in Science

Ewen Callaway in Nature

[Image: Wikipedia]

Melville and microbes: An interview about science writing with Eric Michael Johnson

By Carl Zimmer | December 20, 2011 5:02 pm

Eric Michael Johnson, an historian of science, is also the writer behind an excellent blog, “The Primate Diaries.” The other day he gave me a call to talk about science writing. He put together a two-part Q&A that he published today (part one and part two) that ranges from the science writing in Moby Dick to the microscopic virtues of Twitter. I was particularly flattered to get a portrait done by Nathaniel Gold. Check it out!

CATEGORIZED UNDER: Link Love, Meta
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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.
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