The racket of academic publishing

September 1, 2011 • 9:22 am

I’ve always thought that two of the most overpriced things in the world are lattes at places like Starbucks, and the prices of some academic journals.  Most laypeople, whose taxes go to fund scientific research through institutions like the National Institutes of Health or the National Science Foundation, aren’t aware that if they want to have access to the results of their largesse—the scientific articles that emanate from that research—they have to pay huge amounts of money.  And some of those journals turn huge profits from the bloated subscription fees and prices for journal articles (the latter can reach more than $50 US to buy and read a single article online!).

In Monday’s Guardian, author George Monbiot reveals the sordid and grasping capitalism of academic publishing in a piece called “Academic publishers make Murdoch look like a socialist.”

If you’re a scientist, read and weep: Elsevier, one of the most notorious offenders, turned a profit of 36% last year.  As Monbiot shows, the journals claim that these exorbitant profits reflect the value added by the journal, but that’s hogwash.  Remember that virtually all of the scientific vetting of the papers published is done for free: as a public service by other scientists!  We get nothing for our close scrutiny that decides which papers get published and which are put in the cylindrical file. 

Further, the subscription rates to libraries are often equally exorbitant (though cheaper online): Monbiot notes that a paper library subscription to Biochimica et Biophysica Acta is an astonishing $20,930 per year.  Of course, if you belong to a university that can afford such a subscription, you can get the papers for free, either in the library stacks or online, but that still leaves the layperson—and scholars at the many institutions that can’t afford these subscriptions—out of luck.

Open-access publishing, free for everyone, is a better deal, but it’s still somewhat of a scam, for in many such journals the authors have to pay thousands of dollars in “publication fees” just to get their articles to appear.  Where does that money come from? From taxpayers, for it’s simply taken out of the part of research grants devoted to “publication.” The taxpayer gets the results online free, but also unknowingly foots the bill.

Monbiot’s solution, at least the first part, is eminently sensible.

In the short term, governments should refer the academic publishers to their competition watchdogs, and insist that all papers arising from publicly funded research are placed in a free public database. In the longer term, they should work with researchers to cut out the middleman altogether, creating – along the lines proposed by Björn Brembs of Berlin’s Freie Universität – a single global archive of academic literature and data. Peer-review would be overseen by an independent body. It could be funded by the library budgets which are currently being diverted into the hands of privateers.

It outrages me as a scientist that I review papers for free (and this often takes an enormous amount of time), while the journals for which I review rake in huge gobbets of cash.  It’s unfair to scientists, and it’s unfair to the taxpayers.  I’m not sure how good a suggestion a single global “publication,” is, though—it would be nearly impossible for a scientist to winnow for good research, for we often direct our attention to those journals known to have stringent quality control and a history of publishing good papers. But at the very least, the public should have low-cost or free access to the research it funds.

Academic publishing is the Starbuck’s latte of science, and the scam has to stop.

h/t: Matthew Cobb

Robot theology

August 31, 2011 • 9:37 am

According to the description of this YouTube video, three researchers at the Cornell Creative Machines Lab hooked together two “chatbots” (chatterbots), each of which is programmed to respond to humans by engaging in conversation. What happens when they give each other input?

They produce theology!  Check out what happens 50 seconds into this short video:

Bot 1:  What is God to you?

Bot 2:  Not everything.

Bot 1:  Not everything could also be something.  For example, not everything could be half of something, which is still something, and therefore not nothing.

Bot 2:  Very true.

Bot 2:  I would like to imagine it is.

This comes perilously close to the ontological argument for God’s existence.

For a small expenditure on computer software, theologians could generate material for generations to come.

h/t:  “Just Al”

Eagleman vs. Harris: debate on atheism peters out

August 31, 2011 • 6:55 am

I was looking forward to a lively online debate about religion between Sam Harris and David Eagleman, which seemed to be in the offing but now has apparently fizzled out.

We all know Sam, and maybe you’ll know Eagleman, a young, ambitious, and polymath-ic neuroscientist at Baylor University. Eagleman was recently the subject of an admiring profile in the New Yorker, and I’ve mentioned him on this website  (see here and here). Eagleman is also an advocate of a philosophy (or stance) called “possibilianism,” which he originated, and defines on the Possibilianism website:

Asked whether he was an atheist or a religious person on a National Public Radio interview in February, 2009, he replied “I call myself a Possibilian: I’m open to ideas that we don’t have any way of testing right now.” In a subsequent interview with the New York Times, Eagleman expanded on the definition:

“Our ignorance of the cosmos is too vast to commit to atheism, and yet we know too much to commit to a particular religion. A third position, agnosticism, is often an uninteresting stance in which a person simply questions whether his traditional religious story (say, a man with a beard on a cloud) is true or not true. But with Possibilianism I’m hoping to define a new position — one that emphasizes the exploration of new, unconsidered possibilities. Possibilianism is comfortable holding multiple ideas in mind; it is not interested in committing to any particular story.”

Irritated at the last sentence? I sure was. What if those multiple ideas you hold in your mind are incompatible, like God versus no God? Wouldn’t you want to find a way to figure out which notion, if any, was true?

Here’s a video in which Eagleman explained his position in a TEDx talk in Houston.

At 3:17: Eagleman discusses the books of the “neo-atheists,” accusing them of not having the intellectual courage to go beyond the available data.  He argues, as he did above, that we know too little to commit to a position of strict atheism. . . and way too much to commit to a particular religious position.” He adds later that “certainty is an absurd position.”

I found the video irritating and a bit smug, as if Eagleman were saying, “I’m better than both ends of the belief spectrum.”  If he can’t dismiss the idea of God, than neither can he dismiss the ideas of fairies, leprechauns, and fire-breathing dragons whose habitat has simply remained elusive. So possibilianism turns our brains into big Halloween bags full of appealing but unhealthy notions.

Yes, we should keep an open mind about things that may be possible, but those things don’t include God.  For although there could have been evidence for a deity, none has surfaced.  And, contra Eagleman, few prominent atheists have asserted flatly that there is absolutely no God. Rather, nearly all of them say that there is strong evidence against a god’s existence and, like Laplace, feel that invoking a god adds nothing to our understanding of the universe. Certainty may be an absurd position, but few atheists are 100% certain.  Near-certainty, on the other hand, is certainly not absurd.  Is it absurd to be nearly certain that a water molecule has two atoms of hydrogen and one of oxygen? Or that the Earth orbits the sun?

Harris responded to Eagleman’s talk, with the URL of his response slyly calling Eagleman “the world’s nicest accommodationist.” Sam invited Eagleman to discuss the issues in an online debate, similar to the one he had with Andrew Sullivan. From Sam’s initial response:

Unfortunately, on the subject of religion he appears to make a conscious effort to play the good cop to the bad cop of “the new atheism.” This posture will win him many friends, but it is intellectually dishonest. When one reads between the lines—or even when one just reads the lines—it becomes clear that what Eagleman is saying is every bit as deflationary as anything Dawkins, Dennett, Hitchens or I say about the cherished doctrines of the faithful.

I don’t know Eagleman, but I’ve invited him to discuss these and other issues with me on this blog.

Eagleman accepted Sam’s invitation on Twitter, and, over at PuffHo, Steve Volk, a staff writer at Philadelphia magazine, reported this upcoming debate in a piece called “New allies in the theist/atheist debate.” Volk breathlessly predicted that the atheist (Harris) would lie down with the accommodationist (Eagleman).

Sadly, Harris’s invitation, although accepted, has produced. . . nothing. Eagleman has not been forthcoming.  In his latest post, “Whither Eagleman?”, Sam reproduces the letter he sent to Eagleman, explaining what he meant when he called him “intellectually dishonest,” and setting out his (Harris’s) position. You’ll want to read the whole letter (it’s not long), but here’s a snippet:

In your talk, you repeatedly convict Richard Dawkins et al. of false certainty. You say that we have “left the public with a misconception that scientists don’t have the capacity to gamble (gambol?) beyond the available data—that scientists are acting as though we have it all figured out.” But Dawkins, Dennett, Hitchens, and I have never claimed that we can establish the nonexistence of God. We simply observe, as you do, that the God of Abraham has the same empirical status as Poseidon and that the books attesting to His existence bear every sign of having been cobbled together by ignorant mortals. This is all one needs to judge Judaism, Christianity, and Islam to be incorrigible cults peddling ancient mythology. No “possibilian” apologies necessary . .

. . . But there are no serious arguments to be summoned in defense of Judaism, Christianity, or Islam (despite the hopes of their apologists). How can I be sure? Well, for one, these faiths are embraced for the same reasons, and yet are mutually canceling. Worse still, each rests on the premise that its holy book contains the transcribed thoughts of an omniscient Deity. A glance at the books reveals this claim to be manifestly insane, as each is barren of scientific insights and bursting with logical, factual, and moral errors. You know this to be true—you say as much in your talk—and yet this knowledge constitutes nothing more, nor less, than atheism . . .

. . . I do not intend to cut our dialogue short, as I think we have many interesting things to talk about (consciousness, free will, “neurolaw,” etc.). But it seems to me that now might be a good time for you to admit that “possibilianism,” this middle position of yours, is just a piece of performance art, rather than a serious thesis.

Given Sam’s letter, I’m not surprised that Eagleman has fled the scene. I wouldn’t necessarily call Eagleman intellectually dishonest, but he is without doubt an intellectual coward.

The ultimate in camouflage?

August 31, 2011 • 3:08 am

by Matthew Cobb

Over at Myrmecos, Alex Wild has published this picture by William Piel and Antonia Monteiro of this amazing moth, Macrocilix maia, which lives in Malaysia and Borneo. This is a kind of Rorschach test. What do you see?

photo: William Piel & Antonia Monteiro

On his Flickr stream, Allan Lee published another photo and writes: “The pattern looks like 2 flies approaching some bird dung. As my friend have highlighted, we notice that there’s a bad smell emitted by this moth. This is really an interesting moth trying to fool it’s predators by both sight and smell.”

You can find other Flickr pictures of M. maia here.

On Twitter, Alex (@Myrmecos) and Ed Yong (@edyong209)  had a discussion about whether this pattern is indeed ‘meant’ to show a pair of flies. Ed wondered whether Alex was reading too much into it, to which Alex replied “The full flickr collection of this species won me over”.

It certainly looks to me like a fly – what species?! 😉  – and presumably there are a pair of flies here because the genetics of butterfly wings makes it very difficult not to be symmetrical.

However, there is a much bigger issue here. What is the adaptive value of looking like something else that could be eaten, like a fly? Or even worse, a pair of flies? OK, if the “flies” were attacked, then the moth might only get its wings damaged, rather than its body. But that would still be a substantial cost. And surely the added smell would attract either real flies, or predators on flies… It’s an odd story. As Alex says, this is a PhD project just crying out for funding, a bold supervisor and an intrepid student.

[EDIT: Try walking away from your computer screen (not yet, you ninny) and looking at the image from a few metres away. Now it most definitely looks like flies (especially the left hand one). But why?]

[EDIT 2: Antonia Monteiro mailed me, giving me permission to reproduce the photo and saying: “Yes, this moth is quite extraordinary. Bill and I also wrote a small note in a Yale internal magazine about it. It contains precise coordinates as well as the names of the people that helped us identify this moth.”]

Radio 4 on epigenetics and health

August 31, 2011 • 2:25 am

by Matthew Cobb

We’ve discussed epigenetics and the occasionally (generally?) overblown claims about it a number of times (most recently here). BBC Radio 4 obviously loves it, as after their ‘A revolution in evolution’ programme back in July (which we discussed on WEIT), the third episode in a new series on human development and how early experience affects later health (‘The First 1000 Days: A Legacy for Life’), looks at epigenetics.

I haven’t heard this, but looking at the blurb on the BBC website, it seems to be eminently sensible. After all, the genome is NOT a blueprint. It’s more like a recipe (but it isn’t that, either!) – if you change the ingredients (or in the case of a soufflé, the utensils), you change the outcome. Anyone, anywhere in the world can listen to the programme here. Post your comments below.

h/t Dom

Republicans’ science problem

August 30, 2011 • 12:08 pm

by Greg Mayer

Although it’s a problem that’s been around for years, the perception of the Republican party as anti-science is growing in response to presidential contender Gov. Rick Perry’s forceful embrace of climate denialism and creationism (see, e.g., pieces by Jonathan Chait, Kevin Drum, and Paul Krugman). Even a fellow Republican, presidential-contender-without-a-chance  Gov. John Huntsman, tweeted “To be clear. I believe in evolution and trust scientists on global warming. Call me crazy.” Huntsman elaborated on ABC News:

The minute that the Republican Party becomes the party – the anti-science party, we have a huge problem. We lose a whole lot of people who would otherwise allow us to win the election in 2012. When we take a position that isn’t willing to embrace evolution, when we take a position that basically runs counter to what 98 of 100 climate scientists have said, what the National Academy of Science – Sciences has said about what is causing climate change and man’s contribution to it, I think we find ourselves on the wrong side of science, and, therefore, in a losing position.

Republicans have tried to counter this, but Zack Beauchamp at The Dish is having none of it:

When someone like Rick Perry – an avowed anthropogenic climate change and evolution denialist – is accused of rejecting science, it’s an attack on Perry’s epistemological beliefs rather than moral values. Even though the scientific consensus is clear on both questions, Perry refuses to accept both. By rejecting well-supported scientific truths on, say, theological grounds, he is implicitly denying that the scientific method (rather than, say, theological reasoning) is the best way to determine truths about the natural world. That’s what being “anti-science” is. Given that basically everything we know about the natural world comes from natural science, we can’t tell how Perry will evaluate basic scientific truths on a whole host of important issues. That’s a big deal.

[Yuval Levin] is using obscure conceptual arguments to shield genuinely ignorant people like Perry from criticism. …flat-0ut denying the theory of evolution or anthropogenic climate change. ..involves denying the fundamental epistemological values that undergird the scientific project. Little things like “science tells us more about physical and biological truths than theology.”

Although there’s much to disagree with Huntsman about on all sorts of issues (he’s very conservative), it’s a sign of how bad the Republican party has become that their pro-science candidate has next to no chance of winning the nomination, and being pro-science is part of why his chances are so slim. As Republican strategist Nick Walters put it, “That talk won’t fly in the south.”

How many species? I’m still not sure.

August 30, 2011 • 8:59 am

by Greg Mayer

Jerry recently discussed an article in Plos Biology which tried to estimate the number of species on Earth by extrapolating from more or less known relationships between higher and lower level taxonomic diversity. Carl Zimmer has a piece in today’s Science Times, and records some dissent from the method used:

But Terry Erwin, an entomologist at the Smithsonian Institution, think there’s a big flaw in the study. There’s no reason to assume that the diversity in little-studied groups will follow the rules of well-studied ones. “They’re measuring human activity, not biodiversity,” he said.

Terry Erwin initiated quantitative efforts to estimate the number of species in 1982, when, in a brief paper, he estimated there might be 30,000,000 species of tropical arthropods. Erwin’s criticism of the Plos paper is the same as one that I and WEIT reader Mickey Mortimer registered in the comments on Jerry’s piece: taxonomic ranking is conventional (i.e. an agreement among workers on a particular taxon), and too variable among taxa to be used to reliably produce quantitative estimates like this.

Carl Zimmer used a pyramid analogy to explain the method used in the Plos paper: If you know the shape of the top of a pyramid, you can estimate the area of the base. And that’s true. But it depends on knowing how high the pyramid is, what the slope of the faces are, and that the slope is constant (at least at a suitable scale) all the way to the bottom. In the taxonomic case, the height of the pyramid is the number of ranks– this is wholly conventional, and varies among groups; the slope is the relationship between higher and lower level diversity– which we can know for well-known groups, but not poorly known groups; and that this relationship is constant (or at least functionally known) all the way down to species– which may be true in some groups, but not others. And, crucially, the height, the slope, and its constancy may differ among taxa.

The only fact of nature here is the area of the base of the pyramid (i.e. the number of species); the shape and height of the pyramid above are human constructs.

I don’t want to be too hard on Mora et al., because any method of estimating total species diversity is subject to great uncertainty. Discussing Erwin’s estimate for tropical arthropods, E.O.Wilson wrote:

Erwin’s calculations were an important step forward in the study of biodiversity. The explicit figure he arrived at initially, however, is somewhat like an upside-down pyramid balance on its point. At any step on the road to the final total of 30 millian tropical-forest arthropods, the number of species can be shifted drastically up or down by changing assumptions. If the true total is within 10 million of that number either way, it will be sheer luck.

For quite some time, I’ve told classes that the number of species on Earth is somewhere from 3 million to 30 million. I’m going to stick with that range.

______________________________________________________________

Erwin, T.L. (1982) Tropical forests: Their richness in Coleoptera and other arthropod species. The Coleopterists Bulletin, 36, 74-75. pdf

Mora, C., D.P. Tittensor, S. Adl, A.G.B. Simpson, and B. Worm. 2011. How many species are there on earth and in the ocean? Plos Biology 9(8): e1001127. pdf

Wilson, E.O. 1992. The Diversity of Life. Harvard University Press, Cambridge, Mass.

San Diego State has new course on atheism

August 30, 2011 • 8:45 am

KPBS radio in San Diego, California, has a 15-minute interview with Professor Roy Whitaker, who’s going to teach a new course at SDSU called “Atheism, humanism, and secularism.” Whitaker is described as a “religious studies professor and expert in the history of religion and irreligion; and African American religious thought.”

You can hear the show at the link above. Whitaker thinks that atheism properly belongs in academic programs on religious studies, citing the rise of secularism in the United States as well as the popularity of New Atheist books and the effort of sociologist Phil Zuckerman, who has designed an entire secular studies major at Pitzer College.

Whitaker hasten to adds that the course doesn’t have an “anti-religious bent,” but that’s the way it should be. No proselytizing should be necessary. Whitaker describes the course content, with particular emphasis on atheism in marginalized groups (blacks, gays, etc.), a special section on Islam.  I just wonder how hard-hitting a case for atheism the students will be allowed to read: will they be assigned books by Hitchens, Harris, and Dawkins?  Yes, there shouldn’t be any proselytizing, but there’s no need to turn the strong arguments for atheism into pablum.

The KPKS site also adds this:

Southern California colleges are leading the country in the field of secular studies. Claremont college recently announced their latest bachelor’s program devoted to secular studies, UC Irvine now offers courses on Atheism and Secularism, and San Diego State University is debuting its first course on Atheism, Humanism and Secularism this Fall. We will be speaking with the SDSU professor who is instructing the course to discuss this recent trend in higher education and the field of religious studies.

h/t:  Chris