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November 19, 2013

MathCAD and Livescribe Desktop on a Linux Machine

I"ve finally found a version of Linux that meets most of my needs, out of the box, without a lot of fuss. Meeting "all my needs" requires the occasional use of Windows programs, either by dual-booting to Windows or running Windows in a virtual machine. Neither was very difficult; see below.

I've been using WIndows and Microsoft Office for many years, but have been finding them increasingly annoying, with "updates" that were worse than the versions they replaced -- forced on us by their use of new file formats (docx, etc.), GHz computers running slower than MHz computers used to because of all the bloatware, etc. Sticking points in earlier versions of Linux I've tried were:

* Support for two monitors on my desktop PC, one requiring rotation for portrait mode.
* Support for WiFi on my Acer Aspire One netbook.
* Support for a few Windows-only applications, notably MathCAD and Livescribe pens, which record handwritten notes in a proprietary format, which can be exported to PDF bitmap images and text or spreadsheet files, as I've discussed before.

Linux Mint handled both of these with ease.

On my desktop, I decided on a dual-boot configuration, to keep all my old XP programs, settings, and files, for now. I followed these instructions, using a $6 Linux Mint 15 MATE DVD from OSDisc.com.

Linux Mint comes with LibreOffice, which handles some things (e.g., importing from various spreadsheet file formats) better than Microsoft Office. It even imports and exports docx, which I suppose will just enable people to keep using that evil format. I'm not sure .odt is better, though. If I can't edit a document file with a plain-vanilla text editor, it's harder to process it with Python.

I also used Linux Mint's package manager to install VirtualBox, installed Windows XP within VirtualBox, and installed MathCAD (one of the few Windows programs I can't do without) on the XP virtual machine. I couldn't get the VirtualBox version of XP to use my second monitor, but if I need two monitors for a Windows program I can still boot to my old copy of XP. Within Linux Mint itself, setting up the two monitors and rotating one was easier than it had been in XP.

I used the same DVD (and an external drive) to replace the aging operating system on my Acer Aspire One with Linux Mint, encouraged by this video. Mint seems to connect to Wifi faster than Linpus did, though other operations seem slower. Mint found my video camera but not the microphone, so I may have to use an external headset for Skype or Google Hangout -- but I couldn't get either of those to work at all with the previous operating system. Mint doesn't respond to tapping the touchpad either, but the buttons work. The netbook seems to lock up more often than it did with the less-capable older version of Linux, so I may be pushing the limits of what you can do with 500 Mb of RAM.

Maybe these minor problems can be solved, but I'm really impressed by how well Mint worked out of the box on both desktop and netbook.

Getting Livescribe Desktop working was a bit of a challenge:
* Installed VMware (may be possible with VirtualBox, but maybe harder)
* Installed WindowsXP as virtual machine, from original CD.
* Installed .NET framework 2 (otherwise Livescribe Desktop installs, but won't run)
* Downloaded and installed Livescribe Desktop.

Once I did all that, it was able to upload and display pages from my Livescribe Echo smartpen, a very useful tool for lab notes, as I've discussed elsewhere.

September 16, 2013

Meeting size matters

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I usually enjoy smaller meetings (20 to 40 people) more than larger ones (hundreds to thousands). Big meetings often schedule sessions on related topics at the same time, so the person who could point out a fatal flaw in the speaker's argument may be in another room. They usually allow only 2-3 minutes for questions, after which people may disappear into the crowd. At small meetings, in contrast, the whole group typically eats together, so there's plenty of time to pursue arguments.

That was certainly the case at last week's meeting on connections among evolutionary biology, anthropology, and economics. Peter Turchin has some discussion and pictures on his blog. With fewer people, small meetings can be held in more-interesting settings than the typical big-city convention center. Last week's meeting, for example, was held at Ringberg Castle, in the Bavarian Alps. Note that Peter's castle photo is almost identical to one I took, at right -- we must have been prowling the same battlement. In the dinner photo, the bald head at lower right is mine.

The Applied Evolution Summit was another great small meeting, held on an island in the Great Barrier Reef, bringing together people applying evolutionary biology to medicine, agriculture, and conservation.
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Location aside, grad students would really benefit from hearing the vigorous and usually constructive discussions at smaller meetings. Unfortunately, if everyone brought grad students, the meetings wouldn't be small anymore. Fortunately, there are lots of stimulating discussions at big meetings as well. It's just that they don't necessarily happen in the lecture halls. Poster presentations sometimes generate better discussions than oral talks, but it's also important to include grad students in meals where interesting arguments are likely.

May 24, 2013

Put MOOCs to the test

With all the hoopla about whether universities should give academic credit for what students learn in online courses (MOOCs), people seem to be missing the point that we already have a widely-accepted mechanism by which students can get credit for material learned elsewhere: the Advanced Placement (AP) tests. If MOOCs are doing such a great job, why aren't they publicizing AP-test success rates for their students?

No, seriously. I'm open to the hypothesis that a student could learn as much or more in a well-produced MOOC than in a typical large-lecture/computer-graded introductory course. But let's see the data.

Professor Char Weise writes:

"I am also a parent who is going to be paying college tuition for his oldest child in a couple of years. I am being made keenly aware of the cost-quality tradeoff, and I'm seeing a product that sacrifices only a little on the quality end while having major benefits on the cost end. As a parent, I'm intrigued. As a professor at a liberal arts college, I am terrified."
...and suggests...

"Another approach would be to outsource the introductory courses in economics and other disciplines [to MOOCs]. We already do this to some extent by accepting credit for our introductory courses for courses taught at high schools or other institutions including community colleges. A student who gets a score of 5 on the AP economics test gets credit for Econ 103 and 104... I can imagine a time when the standard program of higher education involves a student spending a year (maybe less) accumulating a year's worth of college credit for introductory courses by taking MOOCs and then enrolling in Gettysburg's (or a similar institution's) excellent and prestigious three-year bachelors' program."
Outsourcing introductory classes, which few professors enjoy teaching, would free us to teach more-interesting, advanced classes. Offering credit for MOOCs on advanced topics without a widely-accepted standard test is more problematic than continuing to offer credit for high AP-test scores. If we had data showing that grades in introductory MOOCs were highly predictive of AP-test scores, that would give me some confidence in their grading, but advanced classes typically call for reasoning and analysis skills that are harder to test. Also, advanced classes are more likely to benefit from small-group interactions with the professor. Take Bill Hamilton, for example. (You knew there had to be an evolution angle here somewhere!) According to this excellent biography by Ullica Segerstrale, he was a terrible lecturer in introductory classes, but did a great job on smaller advanced classes.

May 3, 2013

Sampling Daphnia from a canoe, in the snow, May 3...

...for our research on the evolution of aging. Sandra Brovold is sampling, I'm trying to remember the J stroke, and Bob Sterner took the video.

May 1, 2013

Handwritten data to CSV file without typing

Tired of typing data from lab notebooks into spreadsheets?

* Record data using a Livescribe pen, in one of their microdot notebooks.
* Put a comma after each entry, including last entry in each line.
* Use MyScript to convert page to text, using Rich Text option.
* Select (highlight) table data, including comma-separated heading.
* Open a blank Libre-Office Calc (spreadsheet) document.
* Edit / Paste Special, using "Unformatted text'' and comma-separated options.
* Edit if needed.
* Save as .CSV file using defaults.

The result can be opened in Excel, if you insist. When I tried pasting the data directly into Excel, values weren't separated properly, but there may be a way to do it.

I have only tested this with Livescribe 4 GB Echo Smartpen.

I got this idea here.

April 8, 2013

Fake journals and conferences in NYT

Conferences that invite people at random, for money, are bad enough. Those that mimic real conferences are worse. The New York Times reports that people signed up for Entomology-2013, sponsored by "The OMICS Group", mistaking it for the scientific-society-sponsored Entomology 2013. I've discussed this problem before. The NYT article also discusses fake "scientific journals" that publish garbage for money. Since real journals vary in quality, and many charge authors for some of the cost of publication, it may sometimes be hard for people outside the field to tell the difference.

Real scientists publish in journals with scientific-sounding names, but publication in a scientific-sounding journal is no guarantee that the conclusions are correct or that the author is a real expert.


March 18, 2013

More conference spam... from Nature

I've complained in the past about fake scientific conferences organized by BIT Life Sciences and IEEE. Now Nature Publishing Group is getting into the act, with TEDMED:

"meet a Nobel laureate or two, talk informally with the heads of the FDA, NIH..."
If I did medical research, I might be fooled into thinking the invitation had something to do with my expertise. The $4950 registration fee gives the game away, though.

February 27, 2013

More fake-scientific-conference spam from BIT Life Sciences

Would you pay to go to a fake "scientific conference" in China where speakers were invited at random? What if the scientists they list as speakers hadn't actually agreed to speak? That seems to be the business model of BIT Life Sciences. For example, "Knut Buttnase" got invited to chair a session based on an abstract and CV that were obviously fake.

They're getting more sophisticated, though. They're still inviting me to speak on topics I know nothing about -- "Fungal Bioenergy", most recently -- but their software now inserts the title of a recent paper into the email.

"Since we have learnt that you are making valuable contributions to INSERT TITLE HERE, your unique inspirational message will be the perfect way to kick off the congress."

I guess the idea is that, if 5% of the people they email have some connection to the conference topic, some of those people will be fooled into signing up. But that might not work, for people who have already received lots of spam from them. Also, anyone who Googles "BIT Life Sciences" would hesitate to send them money. So I predict that their next move will be to change their name.

They are listing some real scientists as speakers. Apparently they've done that in the past, without bothering to make sure the claimed speakers were in the right field. The speakers they're listing now look OK, but the one I checked with emails that:

"I didn't agree to speak, after they invited me I declined citing lack of funds to justify such a trip and they offered to waive the conference fee [maybe they get kickbacks from the hotel? -- Ford] only so I said no. I guess I should ask them to take my name of their list."
I'll update this post if they actually remove his name. If not, they're not only spammers, but guilty of fraud.

January 29, 2013

A citation a day keeps ideas in play

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I'm always amazed how badly out-of-date many of my colleagues' publication lists are. Spend a few minutes setting up a Google Scholar page, and you'll always be up-to-date with publications and citations. Here's mine.

My first evolution-themed paper, proposing host sanctions as an explanation for the evolutionary persistence of legume-rhizobia cooperation, was published in 2000.

December 4, 2012

Grad school without an undergrad degree?

Update:
It may also be possible to get an undergrad degree through some combination of on-line classes, proctored tests, and evaluation of knowledge and skills gained through nonacademic experience. Thomas Edison College is an example of a college that awards such degrees, as discussed in the NY Times. Some grad schools might have specific requirements for GPA etc. that could create problems for students who are primarily self-taught, though. And you still need to convince a prospective major professor that your unconventional education has prepared you well for research in her lab.

Interesting discussion this week in NY Times, Slashdot, and UnCollege.org about alternatives to a spending an expensive 4 years in college, now that free courses and lots of other educational content are so widely available on the web.

College grads tend to make more money, with some well-known individual exceptions, though the reasons aren't clear:
1) knowledge and skills learned in classes are a good match for high-skill jobs?
2) contacts met while getting drunk?
3) employers assume that people with degrees are smarter or work harder, even if most skills needed will actually be learned on the job?
Note that reasons #2 and #3 would make individuals with college degrees more competitive for the best jobs but wouldn't necessarily imply any benefit to society from greater investment in education, as I've discussed before. But that's not today's topic.

What if your goal isn't to get rich from writing an ap, but to do science? Depending on what kind of science you want to do, you might need access to an electron microscope, a gene sequencer, and dozens or hundreds of journals costing hundreds or thousands of dollars each per year. Having a wide range of experts to talk with would help, too. In other words, you need access to a major research university.

How can you get such access, without running up a lot of debt? Easy. Go to grad school. Grad students in science don't usually need to take on much additional debt, unless they have kids or an expensive life-style. 20 hours a week as a teaching assistant and your tuition is covered, plus (barely) enough to live on. Or, if you're lucky, you get a fellowship or a research assistantship that pays you to work on your thesis research.

But can you go to grad school without getting an undergrad degree first? It's not easy, but is it impossible? Suppose you spent 2-3 years reading lots of scientific papers, working part-time in a lab, and asking interesting questions in department seminars. Then you ace the GRE and get a great letter from your boss. Is that enough to get into a good grad school?

Absolutely, if you did the above while also getting an undergrad degree from the least-expensive accredited school you can find. (Later in life, nobody will care that your undergrad degree is from Southern Nowhere State, if your PhD is from Big-Name University.) Without any undergrad degree, alternative credentials like great GRE scores and a published paper would convince many professors to take you as a grad student. (That's how I got into Cornell, on probation. I did have a degree from Evergreen, but they weren't accredited yet and didn't give grades.) But would the professor's grad school agree? Most would not, at least today. But could that change, if there were significant numbers of such nontraditional students applying?

I think it would be very risky to assume that you can skip college and still go to grad school, even if you can manage to learn more science "on your own" than you would have in college. But on-line learning is starting to shake things up. Who knows what might be possible in the future?

November 9, 2012

Guest post: THE DAVID ATTENBOROUGH STYLE OF SCIENTIFIC PRESENTATION

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Will Ratcliff gives great talks. It helps that his results are so exciting, but here are some of his other secrets. He made a PDF version also: David Attenborough style of scientific speaking.pdf

One of the biggest hurdles to giving a good talk is convincing people that it's worth their mental energy to listen to you. This approach to speaking is designed to get that buy-in from the audience, without them even realizing they are doing so. The key to this is exploitation of a simple fact: people are curious creatures by natureand will pay attention to a cool story as long as that story remains absolutely clear.

In the D.A. style of speaking, you are the narrator of an interesting story. The goal is to have a visually streamlined talk where the audience is so engaged with your presentation that they forget you're standing in front of them speaking. Instead, they're listening to your narrative and seeing the visuals that accompany your story, at no point do they have to stop and try to make sense of what you just said.

Here are the key points:

Continue reading "Guest post: THE DAVID ATTENBOROUGH STYLE OF SCIENTIFIC PRESENTATION" »

September 26, 2012

Two science scams in one day !

I've written about fake scientific conferences, but here's the latest twist on vanity publishing for scientists. A company called Research Media has offered to write about our research in a "special journal" called International Innovation, in exchange for $2930. Needless to say, our library doesn't carry this "journal."

Also, someone offered to write a favorable review of my book on Amazon in exchange for endorsing her Kickstarter project. She wasn't quite that explicit, of course.

Do people really think scientists are stupid?

August 28, 2012

The importance of titles

Years ago, someone reinvented a method I'd published in a journal he regularly read (and published in), without citing my paper. I complained. He pointed out that the title of my article didn't hint at that aspect of the contents.

Since then, I've tried to get the main point of each paper into the title. For example:

When Stress Predicts a Shrinking Gene Pool, Trading Early Reproduction for Longevity Can Increase Fitness, Even with Lower Fecundity

But journal editors don't always cooperate. For example, we wanted to call our recent Perspective in Science (discussed here) "Are Antibiotics Weapons, Signals, Cues, or Manipulation?" The editor insisted on "Alternative Actions for Antibiotics."

We worried that people would glance at the title and think, "Oh, another one of those antibiotics-as-signals articles." A "signal" is information whose transmission benefits sender and receiver. A "cue" is information used in ways that don't necessarily benefit the source. For example, bacteria may respond to low doses of antibiotics by turning on protective mechanisms, by fleeing, or by hiding in a biofilm. I would only call antibiotic production a "signal" if scaring away competitors, rather than killing them, is the main way it increases the producer's fitness.

Just as we feared, a recent paper miscites our work:

"Antibiotics, especially at subinhibitory concentrations, can act as signal molecules aside from their antibacterial effect (Davies et al. 2006; Yim et al. 2007; Ratcliff and Denison 2011)."

Choose your title carefully.

August 3, 2012

ResearchGate, Google Circles, Linked In -- useful or annoying?

Watergate, ClimateGate, ResearchGate?

I keep getting emails saying someone I know has "invited" me to join these "professional networks." In some cases, the person who supposedly sent the "invitation" denies it. So either the networks are outright lying (sending an invitation without any authorization by the "inviter") or they're asking permission to send an invitation, but in a way that it's not clear that's what they're doing. Like they translate "yes, I'm interested in what this person is publishing" into "this person is inviting you to join our network."

In my experience, most scientists are pretty willing to answer email questions (in their area of expertise, beyond what one could learn in 5 minutes on Wikipedia) and to collaborate when it makes sense, whether or not you're a friend of a colleague of a relative. So I don't see the point to these artificial networks. But I haven't used them, so maybe I'm missing out.

Comments?

July 30, 2012

Correcting Science and PNAS, evolution of more-deadly suicide bombers, blind composers, transcending tradeoffs, light-responsive rhizobia

Absence of Detectable Arsenate in DNA from Arsenate-Grown GFAJ-1 Cells
GFAJ-1 Is an Arsenate-Resistant, Phosphate-Dependent Organism
Surprise! They don't use arsenic instead of phosphorus after all.

Unobserved time effects confound the identification of climate change impacts "PNAS reported statistical evidence of a weather-driven causal effect of crop yields on human migration from Mexico to the United States. We show that this conclusion is based on a different statistical model than the one stated in the paper."

Evolution of music by public choice ...as in natural selection, variation is random but selection isn't.

Explosive Backpacks in Old Termite Workers ...they weren't going to reproduce anyway, but I wonder how long these "suicide vests" took to evolve.

Compensatory mechanisms for ameliorating the fundamental trade-off between predator avoidance and foraging "enhanced nutritional physiology allows caterpillars to compensate when threatened. However, we report physiological costs of predation risk, including altered body composition (decreased glycogen) and reductions in assimilation efficiency later in development." Similarly, reducing investments in research may not affect economic development much between now and the next election.

Light regulates attachment, exopolysaccharide production, and nodulation in Rhizobium leguminosarum through a LOV-histidine
"illumination of bacterial cultures before inoculation of pea roots increases the number of nodules per plant and the number of intranodular bacteroids."

July 17, 2012

University of Minnesota UROP Undergraduate Research Opportunity Program

You could have gone to a 4-year college with smaller classes and professors focused mainly on teaching, rather than research. Why did you choose to go to a major research university, like the University of Minnesota? If you answered "football and beer", read no further.
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Alfalfa root nodules containing nitrogen-fixing rhizobia (photo by Alex May).

Maybe you hoped that professors actively involved in research would give more up-to-date lectures. I hope that's true. But to really take advantage of the opportunities at a research university, go to some current-research seminars -- every department has them. Even better, look for an opportunity to do some research yourself, as part of a team of grad students and undergrads working with a professor on a topic that interests you.
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Lab-evolved multicellular yeast showing simple division of labor (photo by Will Ratcliff).

At the University of Minnesota, one of the best ways to do this is to design your own research project in collaboration with a professor, and get it funded by the UROP Undergraduate Research Opportunity Program. You can request up to $300 for supplies -- many professors will supplement that, if needed -- and $1400 (140 hours at $10 per hour, say) as a stipend, so maybe you can afford to quit that pizza delivery job and get paid for doing research instead.

If this sounds like something you might want to do, you need to PLAN AHEAD. To work on a UROP during Spring 2013, you need to submit your proposal by 8 October 2012. That's only a month after classes start. A month isn't a lot of time to:
* find a Faculty Mentor
* discuss general ideas for a project
* find and read some relevant papers
* write a first draft of your proposal
* revise the proposal at least once based on suggestions from your mentor and then...
* submit it October 8.

So smart undergrads will start contacting possible Faculty Mentors during the summer -- what, you thought we were on vacation all summer?

Examples of possible research topics in the Microbial Population Biology group:
* Experimental evolution of multicellularity
* Evolution of cooperation between legume plants and nitrogen-fixing rhizobia bacteria
* Evolution of aging explored using Daphnia
A lab class that included careful note-taking, calculations with units (e.g., molar concentrations) and some microbiology (sterile technique) would be good preparation for any of these.
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July 8, 2012

Evolution 2012, people

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I am having fun at Evolution 2012 in Ottawa. Lots of great talks and poster presentations - see recent posts -- and discussions with interesting people. Last night I had dinner with several well-known bloggers: Larry Moran of Sandwalk, Carl Zimmer of The Loom, and Ryan Gregory of Genomicron. Unfortunately, I got in too late on Friday to join a group that also included Rosie Redfield of RRResearch (making a big splash debunking "the arsenic paper") and Jerry Coyne of Why Evolution is True. Imagine discussing evolution with the authors of two of the first three books cited in my just-published book on Darwinian Agriculture.

Tonight, dinner was with two of my former colleagues (and neighbors) from UC Davis, Rick Grosberg and Sharon Strauss, their new colleague Johanna Schmidt -- we figured out that we had met 40 years ago -- and various associates. Running for the elevator, back at my hotel, I discovered that the helpful couple holding the door for me were Rosemary and Peter Grant. Discussions with younger colleagues, like Maren Friesen (working on legumes and rhizobia) and Jon Sanders (studying bacterial symbionts of ants and deep-sea clams), have also been great. They all seem to be making impressive progress on interesting and important research. Let's keep funding the National Science Foundation, which is supporting much of this work.

May 26, 2012

A current research update and remembering 1970's student-originated undergrad research at Evergreen

Finishing two research projects on rhizobia (interacting with legumes and each other), ending this summer, has been a higher priority than blogging lately. My pre-proposal to NSF for research on neglected phases of the rhizobial life-cycle (root nodule senescence, survival for months or years in soil, and rhizosphere interactions prior to infecting a new host) didn't make the first cut, so I may have to tap into my retirement savings if I want to continue basic research on rhizobia. I'm interesting in some applied problems also, but don't know if I can get funded for that.

I've also been helping plan some long-term research -- long enough that evolution could be an issue -- at our agricultural field stations around the state. And I want to spend more time with our research on the experimental evolution of multicellularity.

My book on Darwinian Agriculture is coming out in July, so I will start discussing additions, corrections, criticisms, and updates. Should I start a new blog, or do it here?

I recently enjoyed the 40th-anniversary reunion of the Evergreen State College, where I earned my undergrad degree in 1975 as "Bob Denison" and did research on how acid rain and other factors might affect nitrogen-fixing lichens in the tops of old-growth trees (see photo below), funded by NSF's long-defunct Student-Originated Studies program. Cindy Swanberg, who worked on that project, was at the reunion, as was Peter Dratch, who co-directed another student-originated project with Cindy, on the prospects for reintroducing wolves to the Olympic Peninsula. Cindy and I and Peter reminisce about our undergrad research projects on a videos Evergreen posted on You-Tube.
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I will discuss "Measuring effects of symbiosis on fitness of legumes and rhizobia" at the upcoming Evolution meetings in Ottawa. This is trickier than many people in the field seem to realize. At the same meeting, Will Ratcliff and Mike Travisano will have exciting presentations on our evolution-of-multicellularity work.

First, though, I'm off to Hawaii, hoping to observe the transit of Venus. These are much rarer than solar eclipses. And yes, I'm so vain I probably do think this blog is about me.

April 17, 2012

Scientific retractions and competition for jobs

According to a recent article in the New York Times:

"the journal Nature reported that published retractions had increased tenfold over the past decade"

The article suggests that this may be partly due to scientists cutting corners (fraud, or sometimes choosing to publish more papers rather than to check results more carefully), due to increased competition for jobs:
"In 1973, more than half of biologists had a tenure-track job within six years of getting a Ph.D. By 2006 the figure was down to 15 percent."

Over the same period, competition for research grants has becoming increasingly fierce. Meanwhile, universities that hired many more faculty and built many more buildings than needed for teaching (anticipating lots of research grants from which university administration takes up to 50%) deny tenure to even excellent teachers and researchers who don't bring in enough grant money.

Some scientists suggest that these problems could be solved by exponentially increasing research funding to match the exponential increase in PhDs, just as some economists suggest that an exponential increase in food production is the solution to exponentially increasing population. But neither of those is going to happen. So, the article suggests, maybe we should:

"move away from the winner-take-all system, in which grants are concentrated among a small fraction of scientists. One way to do that may be to put a cap on the grants any one lab can receive. Such a shift would require scientists to surrender some of their most cherished practices -- the priority rule, for example, which gives all the credit for a scientific discovery to whoever publishes results first."

I don't think the link between winner-take-all and the "priority rule" is so clear. I can only think of two cases, over my whole career, where someone beat me to a specific result I was working on also. But labs with more resources than mine get more total results, which helps them out-compete me for grants, so that they get even bigger. Should we limit this process of cumulative advantage?

We're talking about tax money here, so we should do what's best for society as a whole, not necessarily what's best for individual scientists or aspiring scientists. But there may be societal benefits to making scientific careers more achievable, or at least perceived as more achievable. Kids who aspire to be scientists rather than football players may learn more in school and subsequently make more contributions to society, whether or not they actually become scientists.

Even leaving such role-model benefit aside, data from NIH show that labs with less total funding produce more papers per dollar. So the public might get more research per tax dollar by spreading the wealth around to more labs.

April 5, 2012

Perverse incentives in science

Economist Paula Stephans has a stimulating commentary in Nature this week, arguing that "Counterproductive financial incentives divert time and resources from the scientific enterprise."

For example, she says that cash incentives offered in China, South Korea, and Turkey have led to a 46% increase in submissions to Science, but no increase in publications. Officials in offending countries are presumably indifferent to the workload of Science reviewers, so is this really a perverse incentive, from their point of view? It could be, if papers from their country get such a bad reputation that even good papers suffer guilt by association.

She argues that graduate students should be supported mainly by broad training grants rather than research assistantships tied to specific research projects, because the training grants have lower overhead costs (8% versus 50%). This is nonsense. Unless we somehow reduce the actual costs of educating grad students, which would likely reduce the quality of their education, the money has to come from somewhere. Universities subsidize training-grant students by diverting money from 50%-overhead grants to cover the difference between 8% and the actual cost of those students. Eliminate the 50%-overhead grants, and the whole thing falls apart. On the other hand, she may be right that students in training grants get a better education. If so, maybe we should support more training grants, but we'll have to pay for them.

But is the 50% overhead rate fair? It may be too high. I would argue that the socially optimum overhead rate is the rate at which university administrators would accept a grant iff they thought it would increase the university's (or their own) prestige, not just for the money. At 50%, they would probably accept a grant to study almost anything (the healing power of prayer, say), so long as incremental costs of providing facilities for that research were much less than 50% of the grant amount. On the other hand, an administrator at UC Davis told me not to apply for USDA grants, because they only paid 15% overhead. So the fair overhead rate is probably somewhere between 15% and 50%. 8% isn't enough to cover even the marginal costs of research.

Stephans discusses various perverse incentives that make individual labs grow too big -- smaller labs publish more per dollar -- which she attributes to "bonuses" based on external funding. I don't think eliminating such bonuses would much effect. The real problem is that grants tend to go to those who have published the most, not those who have published the most per dollar. So big grants lead to more big grants, a process known as "cumulative advantage." I discuss this problem in more depth in the "Selection Among Ideas" chapter of my forthcoming book, Darwinian Agriculture.

Stephans also discusses perverse incentives that make universities build too many buildings. If they borrow money for new buildings, they can include the interest on the loans in their overhead costs. In addition to this perverse institutional incentive, there may be perverse individual incentives. The administrator who takes credit for the new building puts it on her CV and uses it to get a higher-paid job, leaving the costs of maintaining the building (as state and federal funding declines) to her successors.

The issue of "training more PhDs than there are jobs" is more complex than Stephans implies. What's best for the millions whose taxes support research universities isn't necessarily best for individual students. Click "careers in science" for my past discussions of this topic.

December 29, 2011

Shrimp on treadmills

Politicians who didn't hesitate to spend a trillion dollars invading and occupying Iraq apparently think they can win a few votes from ignoramuses by ridiculing spending on scientific research. Their latest target is "shrimp on treadmills." Here's a NSFW (National Science Foundation Website) link to the project in question.

Looks worthwhile to me. They're studying how bacterial infection affects respiration and swimming ability in shrimps and crabs. One could argue that the main beneficiaries are the shrimp and crab industries, so they should have paid part of the cost. But work with one species often helps us understand other species. Much of what we know about genetics of humans and crops goes back to research done with fruit flies. I'm glad Thomas Hunt Morgan didn't have to depend on the banana industry to fund his research.

I agree that we should be scrutinizing public spending to make sure we're getting value for money, but NSF is a model of efficiency and transparency. How about starting with the most-expensive programs and working down? And it seems only fair to give those criticized a chance to respond.

December 15, 2011

Fighting back against fake-conference spam

An anonymous scientist apparently figured that if BIT is inviting speakers randomly, he could invite himself, submitting an obviously-fake CV and satirical "abstract." BIT not only failed to spot the obvious joke, they invited him to chair a session. (For an additional fee, maybe?)

December 14, 2011

Thanks, Google Scholar !

Keeping publication lists on web pages up to date is a task that often gets neglected. Now Google has made it easy. Search Google Scholar for "Ford Denison" and you should get this page, which took me about three minutes to set up. The list of publications is updated automatically, supposedly, and it also plots citations over years and provides links to abstracts and sometimes to PDFs.

If you're a published scientist, information on how to set up your own page is here.

December 2, 2011

Exporting Livescribe Smartpen notes as a PDF

I've been using a Livescribe pen for lab and seminar notes. The pen has a little camera that tracks dots on their special paper to record pen-strokes. Various notebooks using this paper are available, at a reasonable price. Their Livescribe Desktop software is amazingly good at searching my handwritten text, so I don't have to spend time paging through notebooks looking for the data or notes I need. Automatic backup of my lab notebooks, plus search capability... who could ask for more?

Well... a nonproprietary file format would be nice.

Continue reading "Exporting Livescribe Smartpen notes as a PDF" »

July 27, 2011

Would IEEE really sponsor a fake scientific conference?

The email was typical fake-scientific-conference-in-China spam: "we courteously invite you to deliver a Plenary Speech" as a "leading authority" in a field where I have no expertise. I've gotten several of these from "BIT Life Sciences."

This time, though, IEEE, a (formerly?) respectable engineering organization, was listed as a sponsor. I assumed the scam was using IEEE's name without permission, but the "6th International Conference on Bioinformatics and Biomedical Engineering " is actually listed on the IEEE web site. Apparently, IEEE has been involved in many fake conferences, which have, for example, accepted papers that are computer-generated garbage. Sad.

Not all conferences in China are fake -- I went to one a few years ago that was excellent, and am scheduled to speak at another -- and fake conferences are presumably held in other countries as well. China does seem to be afflicted with more than its share, though. Maybe it's harder to sue there, or something.

UPDATE -- someone left a comment with links to a blog suggesting that IEEE sponsors many fake conferences. Unfortunately, I had to delete the comment, because it linked to a blog attributing my concerns to "The University of Minnesota." The views presented here are my own, and not official positions of the university.

July 5, 2011

Another fake conference?

My latest invitation to speak at a fake "scientific conference" in China is for the "1st Annual Symposium of Antimicrobial Research."

This one is hosted by Xiaodan Mei, from BIT Life Sciences. I guess they still haven't been able to trick any well-known scientists into forming a puppet "organizing committee."

May 7, 2011

Fake World Congress of Agricultural Biotechnology?

I got an invitation to speak at a "World Congress of Agricultural Biotechnology" in China. I was a bit surprised, because I'm better-known as a critic of biotechnology -- a constructive one, I hope -- than as a biotechnologist. So I did a little web research.

The business model of the organizers, a company called BIT Life Sciences, seems to bear some resemblance to a pyramid scheme, according to information on the website of The Scientist about an earlier conference they sponsored:

Dan Fintel a cardiologist at the Bluhm Cardiovascular Institute at Northwestern University in Chicago, is listed as one of the plenary speakers on both the defunct program and the current program, and already booked a flight for himself, his wife and his son. But he said that BIT has now told him he must pay a $700 registration fee, unless he recruits four other cardiologists to participate in the meeting. In that case, in addition to waiving the fee, "they will give me $500 and pay my hotel," Fintel said.

The web site for the World Congress of Agricultural Biotechnology did nothing to assuage my fears. Their Program Committee, as of May 6, consisted of "Foreign Experts Databank of SAFEA-Dalian Biotechnological and Medical Experts Subdivision, China." A real scientific conference would have a program committee consisting of individually identifiable scientists with strong reputations -- reputations they wouldn't put at risk through association with a low-quality or imaginary conference. Reputations like mine, for example. If my name shows up in the program, against my explicit instructions, you'll know the conference is a complete fake.

April 22, 2011

More on PhD glut

Some religion professor has noticed a population that is growing faster than the resources needed to support its preferred lifestyle.

Yes, more PhD's are produced each year than academic jobs. Few science PhD's are unemployed for long, but going to grad school might sometimes decrease, rather than increase, your lifetime income. I've commented on that before and advised people not to go to grad school unless they think they will find grad school itself worthwhile. But I thought one of the comments (from Igor Litvinyuk) was quite insightful:

Fierce competition for academic positions is the only way to maintain excellence in academia. That's why academia needs more qualified Ph.D.-holding candidates than there are vacancies.... society gains from having an excellent merit-based academic research system. Some measure of frustration and disappointment among the less successful contestants who chose to participate in this competitive system is unavoidable and is not unreasonable price to pay. Is it really all that different from other walks of life where competition is the norm, i.e. sports, literature or show business?

I agree that the optimum ratio of PhD's to jobs (or the optimum funding percentage for grant proposals) should be determined by long-term benefits to societies, not just the short-term interests of PhD's or grant applicants. But I wonder whether, beyond some point, increasing competition may be counter-productive, and not just for the competitors.

April 1, 2011

Transferable skills

Mike the Mad Biologist makes some good points, commenting on the claim that employment options are worse in biology than other scientific fields.

...most of the skills you learn are only useful in...the biomedical sciences. Most don't learn enough 'generalist' skills, such as high level math or serious programming skills, to have other career alternatives if academia doesn't work out.

Jessica Palmer says the key is to develop "transferable skills." I agree. And not just skills that can be applied outside biology, but skills that can be applied to new problems within biology. As Mike the Mad Biologist continues:

Worse, many of the skills they learn become obsolete. A decade ago, sequencing was a Ph.D. activity, or at least, an activity supervised very closely by a Ph.D. Now, it's largely automated...

So, grad students and postdocs should learn skills that will continue to be needed and can't be automated, especially critical reading, writing, and thinking skills. Can you spot flaws in scientific papers, especially flaws that are only evident in light of information from other papers or even other fields? Can you combine information from different fields and come up with new questions and hypotheses? Can you import useful ideas from economics into biology, or vice versa? Can you express complicated ideas clearly, orally and in writing? If so, you have little to fear from automation.

But, Mike continues

one reason that won't happen is the shortage of funding.... It isn't in the career interest of those doing the training to have students do many things that aren't related to the [short-term?] success of their lab's--their PI's--research program.

I agree that 6% funding rates for grants put Principal Investigators under a lot of pressure. But does that really translate into pressure on students and postocs to crank out data with the skills they already know, rather than learning new ones? Maybe in big, multipostdoc labs, only the most creative postdocs are encouraged to develop new ideas, while the rest become glorified technicians. I wouldn't know.

In my own small lab, interactions with grad students and postdocs are motivated by the hypothesis that fierce competition for grants puts a premium on creativity and new ideas, often combining theory and methods from different fields, even if that means having a little less preliminary data. I therefore encourage them to learn a variety of highly transferable critical-thinking skills, in addition to whatever technical skills may be needed for a particular project.

It might help if the career success (in academia or elsewhere) of former grad students and postdocs in a lab (pro-rated by the number of years spent in that lab) was weighed more heavily by grant programs.

March 29, 2011

International collaboration?

The Royal Society just came out with a report on the internationalization (if that's a word) of science. China now produces the second-highest number of papers, but rates last in percent of papers involving international collaboration. Why so little collaboration? Three hypotheses:
1) the rest of the world doesn't realize all the great science they're doing in China, so is missing out on opportunities to collaborate with excellent researchers,
2) Chinese scientists are doing great work, but are reluctant to collaborate with outsiders,
3) the average quality of science in China is less than you would expect from the number of papers.
These aren't mutually exclusive and there could be other possibilities. In any case, increased emphasis on science in China seems like a good thing, for various reasons, while I worry that budget constraints (and politics) may hurt science in the US.

The Royal Society report also shows that papers with authors from more countries get cited more. Three of the six papers I've published so far this year (and one we're submitting this week) have authors from 2 or more countries, but all three were review articles. So collaboration mainly involved emailing manuscripts back and forth. Collaborations involving experiments in two or more countries seem trickier.

Apart from airplanes, parcel express, and email, can any of you recommend tools useful for remote collaboration? Seems like being able to see the same data that's on collaborators' computer screens while talking over an audio connection would be useful. Are there better options for this than Skype's "share screen" mode (which seems to have some limitations)?

March 18, 2011

The problem of pronatalist professors

"I never trust anyone who's more excited about success than about doing the thing they want to be successful at." -XKCD

Suppose there were some cultural group that made more than their share of positive contributions to society. Suppose members of this group overwhelmingly believed in evolution, liberal democracy, and [insert your favorite meme here]. Suppose, for the sake of argument, that they bicycle to work, insulate their homes, etc., making their per-capita consumption of nonrenewable resources less than average for their society. The only thing is, their numbers increase twofold with each generation, so the total consumption of resources by this group increases, despite their low per-capita consumption. Is this group a problem?

Continue reading "The problem of pronatalist professors" »

February 4, 2011

H-index and Erdos number

There must be some mistake here. Professor Smith, of PhD comics has out-performed me by a factor of 3 (papers in Science or Nature) to 17 (PhDs graduated), by every criterion except the H-index of citation impact, where I hold a slight lead, 23 to 19. In other words, 23 of my papers have been cited 23 or more times, so far. And my lead seems to be increasing.
cites.jpg

I don't think my H-index is unusually high, so maybe Smith's is unusually low. Perhaps, if he treated his students better, they'd write better papers together?

Also, where's his Erdos number, the degrees-of-separation formula that inspired this XKCD cartoon? Mine is 5, via T.R. Sinclair, R.H. Rand, H.D. Block, and P.C. Rosenbloom. The first two links are via papers in nonmathematical journals, though. I'd be more interested in my W.D. Hamilton number, anyway. Incidentally, Hamilton's H-index is only 15, so maybe it's not such a reliable measure of scientific impact after all. Other approaches to citation analysis have been developed, including "eigenfactors."

October 20, 2010

Grad school application deadlines in December

If you're thinking about grad school next year, it's time to get serious. Application deadlines for the two grad programs I'm associated with are both in December. You might want to read my thoughts on who should go to grad school first, though.

If that didn't scare you away, I still have some money left to support a student to work on the first of these two grants. Other topics are possible, but it's nice to work on something for which your major professor has a grant. You may be able to support yourself in grad school as a teaching assistant, but what about money for supplies?

Prospective grad students must apply to the grad program. In my case that would be:
Ecology Evolution and Behavior or else Plant Biology. If you want to be taken seriously by any grad program, you also need to identify specific professors you might want to work with and contact them individually -- after reading at least two of their recent papers. If the papers seem boring to you, you will probably hate working in that lab. Look elsewhere!

October 19, 2010

Applied Evolution Summit video (Heron Island)

Many evolutionary biologists do field work in exciting locations, like the Galapagos. I mostly work in the lab these days -- when I'm not at the computer writing or revising papers -- but I often get invited to speak at meetings in interesting places. For example, I'll be talking about Darwinian agriculture in Paris in December, at the EUCARPIA meeting on plant breeding for organic farming.

But it's hard to beat Heron Island, Australia, where I spoke at the Applied Evolution Summit in January. The scientific output from our discussions will be coming out in Evolutionary Applications, but if you like sea turtles, birds, and coral reefs with your science...

Here's a beautiful video about the meeting.

turtle.JPG
Casuarina, a tree that hosts nitrogen-fixing bacteria not closely related to those that form symbioses with legumes, frames a sea turtle laying eggs, on Heron Island. Photo by R. Ford Denison.

June 25, 2010

Evolution meetings in Portland

The Society for the Study of Evolution, the Society of Systematic Biologists, and the American Society of Naturalists are meeting together over the next few days, in Portland, Oregon. I'm not going this year, unfortunately, but my grad students Ryoko Oono and Will Ratcliff will both be speaking.

Once again this year, there are no sessions scheduled on atheism, pornography, abortion, etc., just evolution. It's almost as if evolutionary biology were a science, maybe even a branch of biology! Reminds of a job fair long ago, where they told me "ecology" was too broad a specialty, but "biology" was OK.

June 11, 2010

No evolution this week

Actually, evolution is continuing, but I don't have time to write about it this week. I'm still working on my talk for the North American Symbiotic Nitrogen Fixation Conference next week and I need to read parts of a couple theses before I leave, so my two PhD students can graduate on schedule.

May 19, 2010

Tenure, seniority, and the benefits of incumbency

Retention based on seniority is, in effect, a conspiracy between teachers' unions and people for whom lower taxes are more important than quality education for the kids in their community.

This post is inspired by two recent New York Times stories. One reports the battle between teachers' unions (favoring pay and job retention based on seniority) and educational reformers who want pay and retention to be based on other criteria, such as student test scores (Brill 2010). The other story reports that some incumbent politicians in the US lost primary battles to challengers in their own party (Zeleny and Hulse 2010). This is news because it hardly ever happens.

I want to make two points. First, US teachers and US politicians are in similar situations. Once they've been in the job for awhile, they can be hard to get rid of, even if their performance falls well below average. This is also true of university professors, medical doctors, and business executives, although pay in those occupations may depend more on current or past performance than it does for politicians or teachers.

Second, random changes to the current system could make things worse rather than better, for an economic reason I haven't seen discussed. More-thoughtful changes are another story.

Continue reading "Tenure, seniority, and the benefits of incumbency" »

February 19, 2010

Science fairs versus real scientific meetings

"But there's an invitation to read my paper before the Academy of Science." -- John Steinbeck, Sweet Thursday
This is part of a series on science fairs; click "science fairs" at right for more.

If you're a kid interested in science, people may encourage you to do a science project and enter it in a science fair. I agree with the "science project" part, but I'm not so sure about the "science fair" part. The thing I don't like about science fairs is the idea that someone wins and everyone else loses. That's very different from the way real science works.

We scientists do like to get together and tell other scientists about our projects. Some of us give talks, to audiences of a few other scientists or hundreds. Others put up "poster presentations", which are pretty similar to the displays at science fairs. The posters are typically up for at least a day, as part of a meeting lasting several days, but there are specific times scheduled when scientists will be at their poster to answer questions.

But, with a few exceptions, nobody is in charge of "judging" talks or posters. People ask questions and sometimes make positive or negative comments, but a student can criticize a Nobel-prize winner; there aren't any "judges."

When I was in high school in Oregon, the Oregon Junior Academy of Science put on real scientific meetings like this, where high-school students presented their work and discussed it with other young scientists. If there was any judging going on, it wasn't emphasized enough for me to remember it. It was an honor just to have your talk accepted for presentation, like it was for "Doc", the character (based on real-world scientist Ed Ricketts) speaking in the quote above. Most US states still have a Junior Academy of Science, but I get the impression that many are now infected by judging. Too bad. There's also a national American Junior Academy of Sciences, which meets alongside the grownup version, the American Association for the Advancement of Science or AAAS. Meetings of the AAAS always look interesting; I should go to one some year, but I usually end up spending my meeting-travel budget on more specialized meetings.

Although the Oregon Junior Academy of Science talks weren't judged, the rewards sometimes went beyond the satisfaction of interesting discussions. One year, six of us were offered an expense-paid trip to the national Junior Science and Humanities Symposium. There were only two catches. We had to give our talk at the state symposium, which was easy and fun. And... the state and local symposia are sponsored by the military.

This was the height of the Vietnam War, for which men about our age were being drafted to die propping up a South Vietnamese government that didn't seem to be any more democratic than the rebels -- I guess we would call them "terrorists" now -- trying to overthrow them. Lots of Vietnamese civilians were being killed, too, and the National Guard had just shot several students at Kent State. Nobody in the Oregon group was very enthusiastic about the military, but we agreed to go, anyway....

Continue reading "Science fairs versus real scientific meetings" »

September 18, 2009

How to maybe possibly get a grant

I'm not doing a paper-of-the week (although I'm expecting a guest post) because I'm too busy reading a bunch of proposals for a grant panel. I can't give any details, of course, but here are some general observations that may be of interest to people who apply for or fund grants.

So far, every proposal I've read has seemed worth funding. This was not true the last time I served on a similar panel. Maybe the word has gotten out that grant funding is highly competitive, so few people bother sending weak proposals? This makes it easier to understand why some of my own recent proposals were rejected, often for what seemed like minor problems.

Unfortunately, we can only fund a small fraction of the proposals submitted. Of course, we could fund more proposals if we gave each group less money. There might be some merit in that approach, but I'll leave that topic for another time.

For those who are writing or thinking about proposals, here are some generic tips:

Continue reading "How to maybe possibly get a grant" »

September 11, 2009

Applied Evolution Summit

I've just agreed to give a talk in January at the Applied Evolution Summit: a small group of experts meeting at an island research station near the Great Barrier Reef to apply evolutionary biology to critical problems in human health, agriculture, fisheries, etc. It might surprise some evolution denialists to learn that pornography, abortion, atheism and "death panels" are not on the agenda, just science. Of course, when we talk about how global warming is affecting the coral reefs critical to some fish, we may need to go look!
Heron Island aerial.jpg
I'm going to try really hard to finish my book before the meeting, which will keep me quite busy until then. I don't teach regular classes -- as an adjunct professor, I'm paid only from our grants -- but reading proposals for a grant panel, writing a paper on "spiteful solar tracking" in alfalfa for Evolutionary Applications, and helping my hard-working and brilliant grad students with methods and manuscripts can't wait until my book is done. So I may be posting only sporadically for a while.

September 2, 2009

Effective communication on preserving crop diversity

This talk by Cary Fowler, on the Global Seed Vault at Svalbard, is worth watching both for the content and as a model for effective public speaking. For that reason, I've categorized it under "careers in science" as well as "agriculture." Note the lack of bullet-point slides!

[Note added 9/11: text slides can make presentations boring, but handouts of text slides help students focus on understanding rather than scribbling notes. So I'm going to cut down on text slides in talks at meetings, but not necessarily in guest lectures to undergraduate classes.]

It's worth noting that even dry, frozen seeds may lose viability in storage. (You could probably still recover DNA, but that's only of practical value for the few traits, if any, whose value can be identified from DNA sequence alone.) So it's good to take seeds out of storage and grow fresh seed periodically. Usually, you want to do this in a way that minimizes natural selection in the seed-increase environment, to avoid losing traits that were useful where the crop was grown originally. For example, you want plants far apart enough that tall plants don't shade shorter neighbors enough to keep them from producing seed. And you don't want plants that were particularly prolific in the seed-increase environment to be over-represented in your next stored sample. Preserving crop diversity is a vastly under-funded activity, although that is true of most areas of agricultural research without immediate links to short-term profit.

Although even a few stored seeds can be multiplied enough in a few years to deal with slowly developing problems, such as climate change, if there's a global wheat epidemic you need at least enough disease-resistant seed on hand that one cycle of seed multiplication will meet farmer needs for the next growing season.

July 31, 2009

Grants!

Just as I was starting to dip into retirement savings to keep my lab going, we got word that both of the grant proposals we sent to the NSF in the latest round were funded, one of them with money from Obama's stimulus funding. We won't be paying ourselves any billion-dollar bonuses, but I may be able to get two months salary this year after all. Both proposals are resubmissions, significantly improved based on suggestions and criticisms from past reviewers. Both projects will use rhizobia, bacteria best known for providing legume plants with nitrogen, but the second project may have eventual applications in medicine (e.g., curing persistent infections) rather than agriculture. The summaries below are intended for a nonscientific audience, such as members of Congress.

"Suppression of rhizobial reproduction by legumes:
implications for mutualism"

(with Prof. Michael Sadowsky, largely based on ideas and preliminary results from grad student Ryoko Oono -- see this recent review article we wrote with Toby Kiers)

Rhizobia are bacteria that can live in soil, but also symbiotically, inside root nodules on plants like soybean or alfalfa. Although many rhizobia provide their host plants with nitrogen, saving farmers billions in fertilizer costs, less beneficial strains cause problems in some areas. Some hosts, including alfalfa and pea, make rhizobia swell up as they start to provide nitrogen. Unlike the nonswollen rhizobia from soybean or cowpea nodules, swollen rhizobia apparently lose the ability to reproduce, but does rhizobial swelling somehow benefit the plant?

To find out, the investigators will map this trait on the family tree for crops and wild plants that host rhizobia, to see if causing swelling evolved more than once, suggesting a positive benefit to the plants. Three dual-host rhizobia (plus mutants that differ in their ability to hoard resources) will be used to measure effects of rhizobial swelling on costs and benefits to the plants. Plant defenses against rhizobia that provide little or no nitrogen, already demonstrated in soybean, will be tested in species that impose bacterial swelling.

This research will increase understanding of a symbiosis that supplies nitrogen to agricultural and natural ecosystems, with implications for other important symbioses. Results could guide the development of crops that selectively enrich soils with the best rhizobia, decreasing future fertilizer requirements. Educational opportunities will be provided for undergraduates, at least one graduate student, and a postdoctoral researcher. Two female high school students have already won trips to the International Science Fair for research done in the principal investigator's laboratory, where such mentoring will continue to be a priority.

Evolution of persistence in the model bacterium, Sinorhizobium
(with Prof. Michael Travisano, largely based on ideas, preliminary data, and writing by grad student Will Ratcliff, with some ideas from Andy Gardner and colleagues -- see the second paper discussed in this post -- and possible relevance to our work on evolution of aging.)

Some bacteria can enter a nongrowing "persister" state that allows them to survive antibiotics and other treatments that normally kill them. By suspending growth, they may also free resources for their genetically identical clonemates.

Most species form only a few persisters. This makes persisters hard to study, despite their importance in long-term infections. However, certain harmless bacteria from plant roots can form up to 40% persisters. These will be used to determine whether persisters benefit mainly from enhanced stress resistance or by increasing the growth of their clonemates.

Successful completion of this research will provide two main benefits: First, this research will determine the conditions that favor the spread of persister-forming bacterial strains over nonpersister strains, and the genetic basis of persistence. This can provide direct medical benefits by aiding the development of novel management strategies, drug targets, and eventually treatments for patients infected with persister-forming bacteria. Second, some conclusions may apply to other species that are difficult to eradicate because they, too, form dormant, stress-resistant stages. These include many agricultural weeds and some species of mosquito. One key advantage of the proposed approach is speed: experiments that would take decades with weeds or mosquitoes can be conducted in months with bacteria. This research will provide training opportunities and jobs for undergraduates, high school students, and a post doctoral researcher.

I am planning to accept another grad student for autumn 2010.

July 20, 2009

Join my lab?

I hope to welcome one or possibly two new graduate students in autumn 2010.

As I noted on the Ecology, Evolution and Behavior web page, much of my research can be seen as following up on ideas first discussed by W.D. Hamilton. This includes our work on the evolution of cooperation (Nature 425:78-81) and on longevity-versus-reproduction tradeoffs as a possible explanation for the health benefits of eating low doses of plant toxins (PLoS One 4:e6055). Often, my grad students use crop plants and/or noncharismatic microfauna (bacteria, yeast, etc.), so if aesthetics is more important to you than science, choose a different major professor. I am also interested in agricultural implications of past and ongoing natural selection (Q. Rev. Biol. 2003 and forthcoming book), although I don't currently have any grant funding for this work.

I also accept students in the Plant Biology grad program, which has been unusually generous in financial support for grad students, providing first-year and summer stipends, paying for meeting travel, etc. (Budget cuts could change this.) Also, unlike most Plant Biology programs, their vision extends beyond molecular biology of Arabidopsis, with significant strength in evolution and in legume (especially Medicago) symbiosis. So students interested in plants should consider both programs.

June 2, 2009

Traveling

I will be visiting in-laws in Hawaii and then at the International Congress on Nitrogen Fixation, so may not post again until late June.

Maybe by then I will be able to write something about our recently accepted paper on the evolution of aging.

Or maybe I'll have good news about an NSF grant. One grad student has a little money left in his own small grant, but the other two are also doing interesting and important work and need to pay for supplies, flow cytometer use, etc.

May 23, 2009

Livescribe SmartPen Review and solution to "unable to access your database folders" problem

My wife bought me a Livescribe Smartpen for my birthday. It's an amazing device, but I can't recommend it at this point. First, the positive: as advertised, it records handwritten text (using special notebooks), displays the text on a computer, and recognizes hand-printed text well enough to search through stored pages for keywords. It can also record sound. It doesn't work with Windows 2000, so I switched to Windows XP, something I haven't had to do for any other program. But I thought my planned uses justified the switch:


1) lab notebooks. I often need to refer to something I wrote months or years ago. With Livescribe, it should be possible to find it quickly.
2) taking notes in seminars. The audio recording is good enough I can can just write keywords and make sketches of graphs, knowing that I can refer back to the audio for details I didn't get written down.

But, after only a few days of use, the program suddenly informed me that it was:

"Unable to access your database folders. Please contact customer support."

Reinstalling didn't help. OK, I'll contact customer service and report here (and Amazon.com, etc.) how they respond.

Apparently other people have had the same problem.

Update: I got a reasonably prompt generic ("what operating systems are you using?", etc.) response but no actual help so far. I was able to install on a different computer, but worry that the same problem could arise there at some random time in the future, meaning I would lose any files that weren't still on my pen.

Update2: After a few days, "customer service" sent me another generic request for information. Maybe they figure repeatedly asking for more information and just hoping users will solve the problem themselves can be outsourced, whereas they would have to hire someone competent to actually figure out what was wrong. The reason I suspect this is that they didn't seem to do anything with the information they asked for the first time, and they didn't answer a very specific question I asked when I sent them the first bunch of information they asked for, namely, whether it might help to copy the (hidden) MyLivescribe directory from another computer where I'd gotten it to work. Anyway, I went ahead and tried it and that seems to have fixed the problem. So I guess backing up the MyLivescribe directory periodically would be a good idea. There's apparently some way to back stuff up on the company web site, but what happens to the data when the company goes out of business?

I agree with comments on their website: until there's a way to send Livescribe files to colleagues without going through the Livescribe website, they will lose millions of potential customers. For example, this system would be great for notebooks used to document patentable inventions, but nobody working on a patentable invention is going to trust their notes to an outside company.

April 27, 2009

Abolish tenure?

Mark Taylor, a professor of religion, has observed (in the New York Times) that

"graduate programs in American universities produce a product for which there is no market (candidates for teaching positions that do not exist)…[with] sometimes well over $100,000 in student loans."
This is not really true of the sciences, where the main product is the research that is central to graduate education, research that often leads directly to improvements in healthcare, agriculture, engineering, or environmental quality. Nor do science PhD's usually take on much debt. (If you are applying to grad school in science, and they don't promise you fellowship support or paid teaching opportunities sufficient to meet minimal living expenses, it's either because you are poorly qualified or because the program is poorly funded. Either way, you should reconsider.)

But programs in the sciences do collectively graduate more PhD's than they hire, so a PhD is no guarantee of a faculty position. I have discussed this before.

Taylor's proposed solutions? Several ideas whose effects on the stated problem are hard to predict but probably small (restructuring curriculum, abolishing departments, accepting video games and such as substitutes for traditional written dissertations), one that would make the job shortage worse but might have other benefits (eliminating programs and substituting internet courses), and two that might help new PhD's find jobs (preparing students for nonacademic careers and abolishing tenure). Preparing students for nonacademic careers is something that has been discussed for years and Taylor doesn't offer any new ideas on how to do this. But what about abolishing tenure?

Continue reading "Abolish tenure?" »

January 30, 2009

Research funding and economic stimulus

This is what I sent our Senator:

Please support the higher NSF research grant funding in the House stimulus bill. Scientific research has long-term benefits, but it may also have a higher multiplier effect than generic tax rebates for rapid stimulation of the US economy. Most grant money goes to pay poor graduate students, who will spend it all locally on food and rent. The remainder goes for scientific equipment and supplies which, unlike consumer products, are mostly made in the US.

Even if we get this burst of funding, it won't solve the long-term problem: the supply of well-qualified researchers with good ideas is increasing faster than research funding, and this trend seems likely to continue. I'm not sure this scientist surplus is a problem for society as a whole, though, unless it's causing people with great research potential to waste their lives as doctors (helping only a few people rather than the millions that benefit from each scientific advance) or Wall Street crooks.

January 20, 2009

Making scientific careers family-friendly

Like most US scientists, I have been distressed by how the Bush administration twisted or ignored scientific evidence on global warming, abstinence-only education, etc. and I am optimistic that things will improve with President Obama. But some problems will be difficult to solve. Today's NYT has an article on under-representation of women in science. Relative to their fraction of the population, my impression is that African-Americans are even more under-represented, but that doesn't seem to get as much attention. Or maybe it's just that the perceived or actual reasons for under-representation are different, calling for different remedies.

One problem that may deter some women from pursuing research-university faculty positions is that these jobs are so demanding they make it difficult to also raise children. Many of my female colleagues are doing both well, but it's got to be hard. A proposed solution from the article:

Continue reading "Making scientific careers family-friendly" »

January 19, 2009

Liberal education, basic research, and Neal Stephenson's "Anathem"

In today's NYT, Stanley Fish laments the demise of liberal education, which, he says

"is distinguished by the absence of a direct and designed relationship between its activities and measurable effects in the world..."
This could perhaps also be a criterion by which basic research is distinguished from applied research. Another characteristic that basic research shares with liberal education is that each offers fewer career opportunities than there are people who want to pursue it as a career. This led me to suggest, in a previous post, that the only people who should consider grad school in science are:

Continue reading "Liberal education, basic research, and Neal Stephenson's "Anathem"" »

January 2, 2009

Ford Denison, amateur scientist

My NSF grant will run out soon, so I get to spend the year in which we celebrate the 200th anniversary of Darwin's birth and the 150th anniversary of The Origin of Species as an amateur scientist, like Darwin himself. I'm not as smart or as rich as he was, but I do have imaginative and hard-working students and much better equipment.

I'm working on two grant proposals and several papers while dreaming of getting back to writing my book, so no detailed paper analysis this week. But Nature is highlighting 15 major papers on evolution they have published in the last few years.

August 28, 2008

Bias in science vs. honest errors

Some comments attached to the previous post discuss cases where scientists made statements or drew conclusions that turned out to be wrong. When should we suspect bias, as opposed to honest errors? Some scientists, of course, may have financial conflicts of interest, such as stock in tobacco or biotech companies. But strong opinions can be a source of bias even without a direct conflict of interest.

Here's an example from my own past research. For ten years, I directed the Long-Term Research on Agricultural Systems project at UC Davis. This huge field experiment included comparisons of organic and conventional farming methods. (LTRAS also compared irrigated and nonirrigated systems, which you might think would generate more interest, given how much of California's limited water supply is used by agriculture. But these comparisons never generated as much controversy, for some reason.)

The simplest way to compare conventional and organic systems would be to have the organic system exactly like the conventional one, only without the synthetic fertilizers and pesticides. But no serious organic farmer would farm that way.

So, for example, we substituted compost and nitrogen-fixing cover crops for fertilizers in the organic system (and in several alternative systems that were not strictly organic). OK, but which cover crops? A scientist biased against organic methods could tilt the balance in favor of the conventional system just be choosing a bad cover crop. A lazy scientist, or one pressed for time or money, could choose a cover crop based on published data (trying to match local conditions) or by asking a nearby organic farmer for a recommendation. Ideally, one would start with such sources but then test various alternatives before making a final decision. At LTRAS, Martha Jimenez tested four cover crop species, each at two seeding rates, and two combinations. Woollypod vetch or a mixture of vetch and peas did best in her one-year experiment, so Dennis Bryant and his crew tested these options over three years before deciding. (Vetch+peas proved to be the least risky, even though vetch-only did slightly better under ideal conditions.) Similarly, we tested Farm Advisor Tom Kearney's suggestion that we should use a different corn cultivar in systems without nitrogen fertilizer. (These tests and other results for the first nine years of this 100-year experiment have been published: see Field Crops Research 86:267; email me if you want a PDF). Without this "tuning", the organic system would have done worse than it did. Similarly, we tried to optimize each of the nine other systems at LTRAS within its particular system-specific constraints. For example, irrigating the nonirrigated system was not an option, but we did choose a wheat cultivar suited to nonirrigated conditions.

Here's where concerns about bias come in. For each system, someone who suspected us of bias could claim that we should have done more to optimize their favorite system. For example, if timing of cultivation is important in all systems, but especially in organic ones, should we always have given the organic systems priority when scheduling, even if that meant neglecting conventional ones in ways no conventional farmer would do? I know that we were committed to finding out which methods are best, rather than trying to prove preconceived ideas. But that doesn't mean we always made perfect decisions. And why should you believe me? After all, my brother Tom Denison is an organic farmer; I could be biased by that or by a graduate education and postdoctoral work in Crop Science that those not familiar with my advisers Tom Sinclair and Bob Loomis might assume was "brainwashing." (It would be more accurate to call their efforts "brain-building.")

If individual scientists or groups of scientists have conscious or unconscious biases, that may influence their conclusions and even their results. Fortunately, two solutions to this problem are built right into the fabric of science today. The first is peer review. Before a paper is published in any reputable scientific journal, it is reviewed by at least two experts with no direct connection to the authors of the paper. (We may know each other, however.) These reviewers look for problems such as unreliable methods, inconsistency between results and conclusions, and inconsistency with previously published results. The latter should not lead to rejection, but reviewers should insist the discrepancy be discussed. Note that most books, web sites, pamphlets, popular magazines, television program, and even certain "junk journals" (low citation impact is a clue) have little or no peer review. As I result, I have usually found reading such sources to be a waste of time. For example, critical details needed to assess the reliability of results are often left out.

Second, and more important, any really important conclusions need to be based on results confirmed by at least two independent groups. This is the best way to detect fraudulent or biased results: do other research groups, who may have different biases, nonetheless get the same results? This is one reason society would benefit from investing more in research. When research money is scarce, studies needed to confirm or refute important results may not get done.

With peer review and independent testing of important results, the biases and errors of individual scientists do not prevent the scientific community from reaching reliable conclusions, sooner or later.

July 9, 2008

Busy

I'm busy this week. Our last two grant proposals were rejected by NSF -- funding rates are down around 10% -- and my lab is almost out of money. (Some other time, I may address the question of whether there are too many good proposals, not enough money, or nonoptimum distribution of grants.) So I'm working on revised versions of those two proposals this week, with help from the grad students they would support. Then I have an overdue book chapter to revise before I can take time to blog, probably discussing more interesting talks at Evolution 2008. After that I have two interesting manuscripts sitting on my computer waiting for my input, one from a grad student in my lab and one from an Australian colleague I haven't met yet, before I can get into the lab and start some long-delayed experiments.

For those considering a faculty position at a research university, you do know that you will spend summers writing papers and grant proposals and (if you're lucky) doing research, not vacationing, right? On the other hand, I am rarely bored.

June 29, 2008

Evolution 2008: sexy plants, battling bacteria, durable cooperation

About 1500 scientists attended Evolution 2008 here last week. The four-day meeting was filled with 15-minute talks (usually ten at once, in different rooms), plus two evening poster sessions (like a science fair, for grownups, with discussions rather than judging), scenically located on a pedestrian bridge over the Mississippi. Reports that “scientists are abandoning evolution�? appear to be exaggerated.

Here are summaries of some of the talks I enjoyed.

Continue reading "Evolution 2008: sexy plants, battling bacteria, durable cooperation" »

June 13, 2008

There are none so blind...

A tiny little box labeled "correction" in the latest issue of Nature alerted me to a re-examination of data supposedly showing discrimination against female authors by manuscript reviewers. This claim, echoed in a Nature editorial (now retracted), was based on data showing that the fraction of papers with female first authors increased in one ecology journal when that journal started withholding the names of authors from reviewers, a procedure known as double-blind review. It turns out that other journals in the same field showed a statistically indistinguishable trend (more female authors over time), even though they still provide author names to reviewers. Thomas Webb and coauthors of this re-examination, published in Trends in Ecology and Evolution, note that a larger study published in American Economic Review reinforced their conclusions: double-blind review does not increase relative acceptance rates for papers with female authors.

Continue reading "There are none so blind..." »

May 7, 2008

Real vs. fake controversy

I liked this essay comparing areas in evolutionary biology where there is genuine controversy -- i.e., where people who are actually collecting data and publishing on a topic disagree -- vs. the phony controversies imagined by creationists. Group selection may still almost qualify as a controversy, a question I may address in a later post, but age of the earth, common ancestry of all species (at least those studied so far!), and the power of natural selection to solve difficult problems are not at all controversial among those actively publishing on related topics.

The question of how much exposure high school students should have to genuine scientific controversies seems a bit more complex to me. I agree that helping students get enough of the basics to understand active controversies in any depth is a big challenge. On the other hand, I've been amazed how many high school students (and their parents) think that the only definition of "research" is looking up information in a library or on the web. If we want students to understand that scientific research is an exciting, ongoing activity, some kind of exposure to areas where scientists disagree seems essential. Areas of research that are easier to understand, like the mindless screening of drugs, don't convey the intellectual excitement of real science.

Here's a seminar class I've thought about for either high school seniors or first-year college students. First, let's set the minimum standard for a scientific controversy as: at least two conflicting points of view, each represented by data-containing papers from at least two nonoverlapping groups, in journals with an impact factor of at least 1.0. Each week we consider one question, such as:
1) What causes AIDS?
2) What is killing amphibians around the world?
3) How old is the earth (within 10%, say)?
4) What living species is the closest relative of chimpanzees?
Students get points for showing that each topic was controversial, at least at one time, with a big bonus for whoever shows controversy most recently. Then we could make a time-line, showing when each question was settled (pending new data, of course!).

March 14, 2008

Why we need peer review

Most scientists also volunteer their time as "peer reviewers" for scientific journals, checking submitted papers for serious flaws, such as lack of appropriate controls. Reviewers also make good papers better by, for example, suggesting alternative interpretations of results. My own papers have been greatly improved by this process, which makes up for the few times I've thought a paper was rejected unfairly. (Fortunately, there are plenty of good journals, and the odds are against getting the same incompetent or biased reviewer twice.)

As a minimum, reviewers try to make sure that the paper describes what was done and what the results were, clearly and unambiguously. Which brings me to two recent sentences from the New York Times that probably wouldn't have made it through peer review:

And now add to the lengthening list Gov. Eliot Spitzer, husband, father of three teenage daughters, who authorities on Monday said had been involved with a ring of prostitutes.

Police found the soldier, who was still in the vicinity, shortly after 11 p.m., using a helicopter with a thermal camera.

February 19, 2008

Career vs. beer?

If you get a position where promotion (or even continued employment) depends on how much research you publish, how hard should you work? Morgan Giddings writes in PLoS Computational Biology that:

Enough work is exactly the amount at which one can maintain enjoyment of the process of work, without burning out (which is not enjoyable) or becoming socially isolated (which is not enjoyable). If that amount of work is not enough to maintain a scientific career, then a different career may need to be considered, where such enjoyment can be found.

But there may be a negative correlation between drinking beer and publishing.

December 20, 2007

MPen is mightier than MSword

You know how, whenever you edit an MS Word document, your neatly positioned figures and captions fly off in opposite directions? Someday, MPen will solve these and other problems. Meanwhile, here's a work-around I just figured out:

Layout graphs and captions you want to stay together on a single Power Point "slide." Make slide width equal the width of your printed lines, so Word won't try to squeeze text on either side. Save individual slides as WMF files. Import each WMF file into Word about where you want the slide. Slides may still jump around when you edit the document, but at least slide(s) and caption(s) will stay together.

I'm still working on grant proposals, but thought those of you who don't use LaTeX might find this useful.

October 2, 2007

Grad school as an epic quest

I thought this analogy between grad school and Lord of the Rings was pretty funny, but what about Monty Python and the Holy Grail? I'm really tempted to start my next oral exam with:

What is your name?
What is your quest?
What is the long-range dispersal mechanism of Cocos nucifera?

Continue reading "Grad school as an epic quest" »

August 23, 2007

Scientist glut as a tragedy of the commons

Lots of discussion on Pharyngula today on a Nature story on the PhD glut. 7000 new biomedical PhDs per year and only 20,000 tenured positions. I remember looking at all the grad students and postdocs at the Ecology meetings and thinking "there aren't nearly enough job openings for this many ecologists", at least not at major research universities. Comstock commented

I see the universities as eager players, ready to get their share of the grant money, and not worrying that much of it relies on the labor of a servant class who will never be made master of the house.
I tend to see tragedies of the commons everywhere, but is this one?

Continue reading "Scientist glut as a tragedy of the commons" »

August 15, 2007

Defining "transformative research" for NSF

According to a National Science Foundation survey, 30% of grant panel members say that they often recommended "transformative research" projects for funding, but only 10% of other panel members (who also, presumably, answered the same question) did. This seems like a mathematical impossibility, like men having had more girlfriends, on average, than women have had boyfriends. But, just as the definition of "girlfriend" (or "sex", for that matter) may vary, so may the definition of "transformative research."

Can we do better than "the projects I like are transformative; those you like aren't"?

Continue reading "Defining "transformative research" for NSF" »

July 17, 2007

Farewell and funding

Rob Knop is leaving academia, essentially because it's so hard to get grants to support his research.

I'm all for increasing research funding, because I think benefits to society exceed the costs, on average. But increased funding might not help individual assistant professors as much as you would think. One problem, at least in the US, is that those who already have grants will usually have more publications and more preliminary data, so they (we) will also tend to be more competitive for any new money. So some professors have multiple postdocs working for them (not me!), generating yet more publications and preliminary data, while others can't get a grant.

Also, universities (which take half of each grant) would (and do) respond to increased research funding by hiring more professors than they need for teaching. This increased hiring would make it easier for new PhDs to get a job, at least in the short run, but it would then increase competition for grants, until the "tenure misery index" comes back into equilibrium.

My impression is that the Canadian system is more egalitarian and maybe less stressful. Anyone know if this is true? If so, how does this affect overall scientific productivity and quality (citations per dollar, say)?

Yes, I will be discussing an evolution paper this week.

June 21, 2007

Opportunity cost of grad school, etc.

Rob Knop liked my previous post. The comments on his post are well worth reading. For example, someone pointed out that, even if you don't go into debt to finance grad school, there's still usually an economic opportunity cost. During the years you spent in grad school and as a postdoc, you might otherwise be paying down a home mortgage, saving for retirement, etc., not to mention nonfinancial opportunities, like starting a family.

Terence Tao also has some good career advice,. It's aimed mainly at mathematicians, but much of it is relevant to science in general.

Continue reading "Opportunity cost of grad school, etc." »

June 19, 2007

Who should consider grad school in science?

This entry is inspired by "Why I got out of research" at http://vwxynot.blogspot.com/ and Rob Knop's blog entry Get out; you're not good enough , and is addressed to readers considering grad school in science.

There are more people qualified for faculty positions at research universities than there are openings. By "qualified" I mean having earned a PhD, done a postdoc, and published at least one senior-authored peer-reviewed journal article from each. By this definition, one can be qualified without necessarily being competitive in today's academic job market.

Those of us lucky enough to get such a research university position find that (as vwxynot put it):

"Even if you do make it big and get your own lab, you're suddenly responsible for your whole team's job security as well as your own. Grants depend on the quality of the researcher and their work, yes, but also on trends, fads, luck, nepotism, reputation, political interference and geography."

The importance of nepotism, politics, and geography probably varies among countries, but there's no doubt that only a fraction of good proposals get funded. And yet, getting grants is often an expectation for tenure.

So, if most PhD's won't get a research university faculty position (RUFP), then who should consider going to grad school in science?

Continue reading "Who should consider grad school in science?" »