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Tag: Science
Managing the sea of data: Mendeley and PubChase
Every few months someone asks me what I use to manage my papers. Stupidly, I don’t use anything. Or I haven’t. Over the past few weeks I’ve been playing around with PubChase and Mendeley. You probably know of the latter, and the fact that it’s been purchased Elsevier. Elsevier is what it is. Mendeley on the other hand is a firm that I have a positive view of, in part because of their culture of openness and support for the free flow of information, but also due to the fact that I’ve known their head of outreach for ten years. You trust people, not things. Mendeley‘s not a charity, and I don’t begrudge them their new resources now that they are under the corporate wing of Elsevier. Whether you’re pessimistic or optimistic about their future, I think caution is warranted.
Michael Eisen wants peer review comments on his paper
This is great, Please review our new paper: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression:
It’s no secret to people who read this blog that I hate the way scientific publishing works today. Most of my efforts in this domain have focused on removing barriers to the access and reuse of published papers. But there are other things that are broken with the way scientists communicate with each other, and chief amongst them is pre-publication peer review. I’ve written about this before, and won’t rehash the arguments here, save to say that I think we should publish first, and then review. But one could argue that I haven’t really practiced what I preach, as all of my lab’s papers have gone through peer review before they were published.
No more. From now on we are going to post all of our papers online when we feel they’re ready to share – before they go to a journal. We’ll then solicit comments from our colleagues and use them to improve the work prior to formal publication. Physicists and mathematicians have been doing this for decades, as have an increasing number of biologists. It’s time for this to become standard practice.
Some ground rules. I will not filter comments except to remove obvious spam. You are welcome to post comments under your name or under a pseudonym – I will not reveal anyone’s identity – but I urge you to use your real name as I think we should have fully open peer review in science.
OK. Now for the paper, which is posted on arxiv and can be linked to, cited there. We also have a copy here, in case you’re having trouble with figures on arXiv.
Peter A. Combs and Michael B. Eisen (2013). Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.
Please leave comments on Eisen’s post.
Via Haldane’s Sieve.
Adding more color to science the wrong way
Over at ScienceDaily there is a report on a new paper on affirmative action and academia, Understanding the Impact of Affirmative Action Bans in Different Graduate Fields of Study. The paper is gated, but the regression model used really doesn’t seem to do much more than confirm intuition. The descriptive details are more interesting and straightforward.
Why so few Asians in ecology? Not all groups have similar preferences
A week ago Keith Kloor had a post up, What Science, Environmentalism and the GOP Have in Common, where he bemoaned the lack of representation of non-whites in these categories. As a matter of fact I think Keith is wrong about science. Even constraining the data set to American citizens and permanent residents people of Asian ancestry are well represented in many areas of science. But not all sciences are created equal. In 2011 there were 158 doctorates which were awarded within the category of ‘evolutionary biology’ for American citizens or permanent residents. Of these 135 were non-Hispanic white, and 5 were Asian. In ‘neuroscience’ the respective figures were 742, 535, and 96. In ‘zoology’ 55, 49, and 0. In ‘bioinformatics’ they were 80, 51, and 17. Finally, in ‘ecology’ the breakdown was 330, 300, and 11. If you are involved in academic biology I’m rather sure that these numbers won’t surprise you too much, even if you’d never thought about it. You can even infer these by walking through the posters at ASHG 2012, and seeing how the demographics of the crowds shift.
We can look at this issue another way. In 2010 US News & World Report listed the top 10 ecology & evolution graduate programs. I went to the faculty websites after typing the university and ‘ecology,’ and then ‘neuroscience.’ Looking at names, and sometimes head shots, I classified everyone as ‘Asian’ (as defined by the US Census) and ‘Not Asian.’ You can find the data here. Please note that the left columns are ecology faculty, and the right are neuroscience.
Iterating science, supercharged
Science is about “updating” with new information. But people are attached to their propositions, and shifts in paradigms can take a very long time, often dependent more on human lifespans than the constellation of the data. But please see this post by Luke Jostins’ over at Genomes Unzipped. He has “updated” his own view of his recent Nature paper on inflammatory bowel disease. This is rather awesome, because yes, there was some talk about the balancing selection aspect of the paper at ASHG, and now Luke has gone and amended his own position.
The reality is that emotions are a big deal in science. But in theory we simply look at the evidence. Bridging that gap, and shifting the balance to the latter, is very important in keeping the enterprise honest, fruitful, and attractive to young scholars. I’m hoping that the more rapid dissemination of information via projects like Haldane’s Sieve will aid in the rate of iteration.
Richard Lewontin against the age
Richard Lewontin’s fame rests in part on his pioneering role in the development of the field of molecular evolution, and secondarily due to his trenchant Left-wing politics. Several readers have already pointed me to his rather strange review of two new works in The New York Review of Books. The prose strikes me as viscous and meandering, but some of the assertions are rather peculiar. For example:
The other exception to random inheritance is not in the chromosomes, but in cellular particles called ribosomes that contain not DNA but a related molecule, RNA, which has heritable variation and is of basic importance to cell metabolism and the synthesis of proteins. Although the cells of both sexes have ribosomes, they are inherited exclusively through their incorporation in the mother’s egg cell rather than through the father’s sperm. Our ribosomes, then, provide us, both male and female, with a record of our maternal ancestry, uncontaminated by their male partners.
Harry Ostrer, who is a professor of genetics at Albert Einstein College of Medicine, and Raphael Falk, who is one of Israel’s most prominent geneticists, depend heavily on our ability to trace ancestry by looking at the DNA of Y chromosomes and ribosomes….
There is no mention of ribosomes in Legacy: A Genetic History of the Jewish People. I know, because I used Amazon’s ‘search inside’ feature. Rather, there’s a lot of reference to mitochondrial DNA and mtDNA, which is what Lewontin truly meant. Or at least I hope that’s what he meant. Because Lewontin is an eminent evolutionary biologist I assume they felt like they didn’t need a science editor, but perhaps they need to reconsider that.
The real end of science
Fifteen years ago John Horgan wrote The End Of Science: Facing The Limits Of Knowledge In The Twilight Of The Scientific Age. I remain skeptical as to the specific details of this book, but Carl’s write-up in The New York Times of a new paper in PNAS on the relative commonness of scientific misconduct in cases of retraction makes me mull over the genuine possibility of the end of science as we know it. This sounds ridiculous on the face of it, but you have to understand my model of and framework for what science is. In short: science is people. I accept the reality that science existed in some form among strands of pre-Socratic thought, or among late antique and medieval Muslims and Christians (not to mention among some Chinese as well). Additionally, I can accept the cognitive model whereby science and scientific curiosity is rooted in our psychology in a very deep sense, so that even small children engage in theory-building.
A social science of the obvious
I’m reading Jim Manzi’s Uncontrolled: The Surprising Payoff of Trial-and-Error for Business, Politics, and Society right now. No complaints, though that’s no surprise, as I’m familiar with the broad outline’s of Manzi’s work, and have found much to agree with him on in the past (though there are issues where we differ, never fear). That being said, I did ponder one aspect of Manzi’s characterization of science: that it makes non-obvious predictions. This is not controversial, and I don’t want to really quibble with it too much. But in the context of social science in particular I think one of the gains of ‘science’ is the clarification of obvious predictions.
Peer of myself
Dr. Joe Pickrell has a follow up to his widely discussed post on updating scientific publication for the 21st century. One section jumped out at me, not because it was revolutionary, but because it made explicit a complaint that I had often heard:
The solution to this problem relies on a simple observation–in my field, I am completely indifferent to whether a paper has been “peer-reviewed” for the basic reason that I consider myself a “peer”. I do not think it extremely hubristic to say that I am reasonably capable of evaluating whether a paper in my field is worth reading, and then if so, of judging its merits. The opinions of other people in the field are of course important, but in no way does the fact that two or three nameless people thought a paper worth publishing influence my opinion of it. This immediately suggests a system in which papers are posted online as soon as the authors think they are ready (on so-called pre-print servers). This system is the default in many physics, math, and economics communities, among others, and as far as I can tell it’s been quite successful.
The reality is that often the “peers” are not peers. How else to explain the publication of the longevity study in Science, now retracted? Or the non-canonical RNA editing? (presumably this is less common of a problem in specialized journals). And sometimes the feedback of peers can indicate that they don’t really know what they’re talking about. For example, I was once told that the authors of a phylogenetics paper which used Bayesian methods were asked to reanalyze their data with a max likelihood framework (jump to the last sentence of this section to see why this is peculiar).
The theory of classical peer review made sense in the pre-internet age. But now there are a plenty of reasons why we might need to revisit this.*
* Not to mention that “peer review” is a somewhat subjective concept. Richard A. Muller has gotten into a back & forth on this issue whether his latest work has undergone peer review. He claims it has, others claim not. I suspect most traditional biologists would be skeptical of Muller’s claim, but physicists would accept it.
How to get beyond bias in science?
Here’s a comment which is interesting, if hard to actually engage with because of the difficulty of the subject matter:
You’re obviously aware of the arguments employed by feminists in the critique of the philosophy of science; that cultural values, in their view patriarchy, could unintentionally contaminate science by affecting how evidence is interpreted and what hypothesises are formed from it. This argument is usually combined with the more fundamental problem of using inductive logic in science, especially biology, and how any cultural norms could be mistaken for biological facts.
My question is how do you separate out the biases from the facts?
What makes you think that the lefts reservations about the studies into sex and race are the result of their own bias and not a legitimate acusation of bias within science? It is obviously not a totally improbable claim considering the long history of racist science in the two previous centuaries.
From my own lay mans knowledge of the subject I’ve got the impression the jury is still out on both innate sex difference and the genetic realities of race.
The art of science
Over at Scientific American Blogs Maria Konnikova posts Humanities aren’t a science. Stop treating them like one. The whole write-up leaves me scratching my head, because I don’t really get what the whole point of all the prose is. This is a thesis that is as old as 19th century romantics, and not all too complicated. The author herself has an academic webpage which indicates she works within an analytic framework that’s anything but “soft.” There are huge confusions with terminology, and Jerry Coyne has a response which addresses many of my questions (e.g., what exactly is the alternative to doing statistical tests in psychology? Rely on the impressions and intuition of the researchers and just trust them?). But let me highlight one section:
… Societal conventions change. And is today’s real-world social network really comparable on any number of levels to one, say, a thousand, or even five or one hundred years ago?
Yes, today’s real-world social network probably is comparable to those of the past. There is some science on this issue. Not even rocket science with abstruse statistics. Science which is highly relevant today. Question science, and it may surprise you with what it has discovered!
The punch first culture
Dr. Daniel MacArthur has a nice write-up in Nature, Methods: Face up to false positives:
Few principles are more depressingly familiar to the veteran scientist: the more surprising a result seems to be, the less likely it is to be true. We cannot know whether, or why, this principle was overlooked in any specific study. However, more generally, in a world in which unexpected results can lead to high-impact publication, acclaim and headlines in The New York Times, it is easy to understand how there might be an overwhelming temptation to move from discovery to manuscript submission without performing the necessary data checks.
This is not just an issue in genomics. I’ve discussed it before as being a major problem in psychology. Though the infamous centenarian study will do nothing for the careers of the scientists involved, I do wonder what the effects of publishing large numbers of false positive results in science are on an individuals’ career when it isn’t so inexpertly executed (i.e., in this particular case the technical errors were so glaring that the authors should never have submitted their findings). I wonder because apparently major newspapers are now running with stories which they know are highly likely to be exaggerations or misrepresentation to induce pageviews, and then subsequently ‘correcting’ them. More specifically, the number of corrections has been rising rapidly.
You can't scoop someone else's brain
I, and I’m sure other people, have worried about being scooped and beaten to publication due our arXived papers. But really this is silly as we’ve usually given talks, posters, etc on them at big conferences, so the idea that people somehow don’t know about our work before it appears in print is ridiculous. It is far better to get work out, once you consider it worthy of publication, so it can be read and cited by others.
This is in reference to the paper The Geography of Recent Genetic Ancestry across Europe. Go and read the materials and methods. I’m sure that a substantial minority of the readers of this weblog have used every single piece of software listed therein. Phasing and such requires a little bit of computational muscle, but that’s not an impossible hurdle. Additionally, many readers with academic affiliations could get their hands on the POPRES data set. But the generation of a paper, from methods to results to discussion, is not simply a robotic sequence of running data through software or algorithms. You need a first-rate statistical geneticist (e.g., the authors) to actually assemble the pieces together together coherently and with insight even granting the fundamental units of the whole.
Then there are sections of the methods with explication such as this:
More on jobs & Ph.D.s
First, I’m sure that the blue-collar readers of this weblog are thinking “cry me a river.” Yes, American scientists (perhaps excluding engineers, and to a lesser extent pharmaceutical researchers) are generally Left-liberal, but the collapse of the American working class due to globalization is something that they fixate on only as part of a broader political vision, along with other concerns. But when it comes to tenure-track jobs, the end is nigh! Consider that the woman who seems to have “wasted” a neuroscience Ph.D. in yesterday’s Washington Post article now has a job in academic administration. This is the sort of failure that manual laborers and factory workers alike would probably kill for.
But in any case, some more posts for you. Reader Miko reflects on searching for a job, Mike the Mad Biologist keeps doing his thing, and fellow Discover blogger Julianne on Subtleties of the Crappy Job Market for Scientists:
No comments please, we've made it through peer review (?)
Recently Daniel MacArthur pointed to the vibrant discussion over at Genomes Unzipped on a moderately infamous paper from Science last year, Widespread RNA and DNA Sequence Differences in the Human Transcriptome, asserting that it is “exactly what open peer review should be like.” This made me wonder, it’s been over five years since Chris Surridge asked why there was so much more commentary on a PLoS ONE paper, By Hook or by Crook? Morphometry, Competition and Cooperation in Rodent Sperm, on blogs than on the paper itself. Has anything changed? The most viewed paper on PLoS Biology, How Many Species Are There on Earth and in the Ocean?, has 9 comments for 45,000 article views. In contrast, Genomes Unzipped has 14 comments for likely far fewer page views. Additionally, if you find the post on the weblog the comments automatically load. Not so with the PLoS Biology paper, you have to click through (yes, I see how this can be a feature, not a bug, but in that case why even bother with comments if you provide an email address for correspondence?)
Mike Snyder profile in Science
Examining His Own Body, Stanford Geneticist Stops Diabetes in Its Tracks:
Over a 14-month period, the molecular geneticist at Stanford University in Palo Alto, California, analyzed his blood 20 different times to pluck out a wide variety of biochemical data depicting the status of his body’s immune system, metabolism, and gene activity. In today’s issue ofCell, Snyder and a team of 40 other researchers present the results of this extraordinarily detailed look at his body, which they call an integrative personal omics profile (iPOP) because it combines cutting-edge scientific fields such as genomics (study of one’s DNA), metabolomics (study of metabolism), and proteomics (study of proteins). Instead of seeing a snapshot of the body taken during the typical visit to a doctor’s office, iPOP effectively offers an IMAX movie, which in Snyder’s case had the added drama of charting his response to two viral infections and the emergence of type 2 diabetes.
Hopefully in about 10 years this will be the norm, not cutting edge science.
"Doctors don't cure nothing"
NSFW
As I observed before, modern medicine is subject to some of the same statistical issues as social science in its tendency to put unwarranted spotlight on preferred false positive results. Trials and Errors – Why Science Is Failing Us:
This doesn’t mean that nothing can be known or that every causal story is equally problematic. Some explanations clearly work better than others, which is why, thanks largely to improvements in public health, the average lifespan in the developed world continues to increase. (According to the Centers for Disease Control and Prevention, things like clean water and improved sanitation—and not necessarily advances in medical technology—accounted for at least 25 of the more than 30 years added to the lifespan of Americans during the 20th century.) Although our reliance on statistical correlations has strict constraints—which limit modern research—those correlations have still managed to identify many essential risk factors, such as smoking and bad diets.
The downsides of grassroots science funding
Grassroot funding for science: A good idea?
Summary: Crowdfunding science is a good idea to add additional support to underfunded missions or to enable small projects. It is not a good idea to draw upon the public opinion to fund research projects from scratch. It might appear as if public money is put to good use, but that use is likely to be very inefficient and misdirected and doesn’t actually solve any systemic problem. If you must, go occupy Wall Street, vote, and make sure your taxes are put to good use.
I have a few of the same questions as Sabine overall. This despite the fact that I solicited funds in a genotyping project. The key is that if you’re going to do crowdfunding/crowdsourcing you have to be clear and precise about the aims. In the abstract I think most people understand that most science fails, but I think it will be hard to get funds if you continue to fail because you’re aiming for “home-runs.” Rather, the best option if you want to go in this direction is to be modest, and aim toward a low reward/risk project. This will minimize the disappointment on the part of your numerous funders, who are going to be more engaged and curious as to the specific result than the NSF or NIH would be.
Though one issue that does need to be pointed out is that at the early stage the people donating to these projects are not the typical citizen. I know the identities of the people who donated to the Malagasy genotyping project, and well over half of them were faculty, postdocs, or grad students. In other words scientists were funding science.
But I think the bigger issue here in terms of the “crowd” isn’t going to be in the area of funds. Rather, I suspect it will be collaboration and labor input. Something analogous to the open source movement. And just like open source software doesn’t mean that firms like Google and Microsoft aren’t eminently profitable, open source science isn’t going to replace “traditional” science. Rather, it’s going to complement.
Think right, not deep
Over the past few weeks I’ve been observing the response to Rick Scott’s suggestion that Florida public universities focus on STEM, rather than disciplines such as anthropology. You can start with John Hawks, and follow his links. More recently I notice a piece in Slate, America Needs Broadly Educated Citizens, Even Anthropologists. There several separate issues here. Superficial concerns of money going to your political antagonists, commonsense considerations of the best utilization of public educational resources, and broader reflections upon the nature of a ‘liberal’ education.
Ingenuity's flight toward rents
Andrew Oh-Willeke, Esq., observes:
One example of cyclicality that continues to today is the practice of law. The basic principles of Roman private law and the complaints that people made about lawyers and litigation were remarkably similar in the 300s to what they are today.
In the 6th century Justinian the Great sponsored a compilation of the body of law which was being widely practiced in the Roman Empire at the time, what is now known as the Corpus Juris Civilis. This is not an abstract or obscure point in the history of modern law:
The present name of Justinian’s codification was only adopted in the 16th century, when it was printed in 1583 by Dionysius Gothofredus under the title “Corpus Juris Civilis”. The legal thinking behind the Corpus Juris Civilis served as the backbone of the single largest law reform of the modern age, the Napoleonic Code, which marked the abolition of feudalism.
Imagine that the astronomical models of Ptolemy served as a basis for modern astrophysics! There’s only a vague family resemblance in this case. The difference is that law is fundamentally a regulation of human interaction, and the broad outlines of human nature remain the same as they were during the time of Justinian and Theodora. In this way law resembles many humanities, which don’t seem to exhibit the same progressivity of science. Our cultures may evolve, but there are constraints imposed by our nature as human beings. Human universals in humanistic enterprises speak to us across the ages. The story of Joseph and his brothers in in Genesis speaks to us because it is not too unfamiliar from our own. The meditations of Arjuna are not incomprehensible to the modern, even if they come from the imagination of Indians living thousands of years in the past. The questions and concerns of the good life are fundamentally invariant because of the preconditions of our biology.
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