The Plants Are Talking to Themselves…

Updates will be sparse for awhile owing to a hectic field work schedule, but fear not!  More updates are on their way soon!

Rick Karban of the University of California-Davis and his colleagues have discovered that plants the plants are talking to themselves.

Sagebrush_bloomsThese researchers discovered that when a sagebrush plant is cut (as when it has been bitten by a herbivore), it releases chemical compounds that communicate with other branches that are genetically identical. By communicating with itself in this way, the plant is able to coordinate a counter-attack to decrease its likelihood of being further damaged by herbivores.   The article can be found here.

Knowing that even plants are talking to themselves makes me feel a bit better about doing it myself.


How Should One Design Their Dissertation Topic?

Awhile back I had a debate with some of my PhD friends over the type of dissertation project that was most likely to land you in a position at a Research I institution. We fell into 2 main camps.


Off to get some data!

The first group thought it best to pick a series of “safe projects”.  Our definition of safe project was one that had a high probability of yielding results that would meet your predictions and would build upon an existing framework.  Despite the fact that your results wouldn’t be super sexy or surprising, these experiments would show that you understand how to conduct sound science and contribute to an existing body of work.

The second group thought it best to pick a risky project that, should it be successful, would dramatically change our understanding of a particular phenomenon. Should it prove unsuccessful, however, you’re left with pretty much nothing.

At the heart of the debate was our desire to be attractive candidates for the precious few positions in academia that open up each year. Of course, an even smaller subset of these academic positions are at Research I institutions, where a number of the individuals in the debate are striving to end up.

Completing a safe project will likely land you at an institution with a heavy emphasis on teaching. After years of publishing sound science and establishing your name, then you may be able to make the jump to a Research I institution eventually.

The problem with being at a school with a less strong emphasis on teaching is that they usually can’t afford to give as much money to start up a new lab as a school with a stronger research emphasis might. Additionally, heavy teaching loads mean less time in the lab or in the field and less time to write papers. So we decided that a safe project could land you in a Research I institution eventually, but it might be a pretty long journey before you make it there.

A risky project that works out and results in a number of publications in big name journals will certainly boost your chances of getting into a good research institution early in your career. The monetary and facility support that you receive here will be much better than at a teaching institution, making it easier for you to conduct lots of great experiments and acquire high quality students to work in your lab. What researcher could ask for more?

On the other hand, if your project idea doesn’t work out, then you’re worse-off than you would have been had you done a safe project.  A series of post-doc positions can fix this mistake, but you’re once again years away from the coveted Research I position.

So what project do you choose?  Well, like so many things in science, we’ve probably set up more of a dichotomy than actually exists.  I think that the best solution is to set up a big project with one sexy, but risky experiment and a series of safe experiments.  You need 3 chapters for your dissertation anyway, right? I think that taking a risk on at least one of the chapters is worth it for the potentially big pay-off.

I’d be interested in hearing feedback from other graduate students on how they are choosing their dissertation or post-doc projects.  Additionally, I’d love to hear feedback from post-docs or professors on what they think makes a successful dissertation project (where success is defined as ending up at a Research I institution).

(NOTE: I do understand that outstanding research is conducted at non-Research I institutions.  Also, I think teaching is vitally needed and noble pursuit. I did not mean to downplay the importance of either of these points, I just personally have my heart set on a position at a Research I institution.)

The Seafood Consumption Debate

On the front page of this weekend is a series of posts by blogger Jennifer Jacquet (of Guilty Planet) on the debate raging over seafood consumption. Although I applaud her willingness to take a strong stance and to provide a wider spectrum of voices on the issue, her stance that people need to cease consuming seafood entirely is, in my mind, counterproductive.

Fish_on_TrawlerIt’s becoming clear that we are on the road to the collapse of the fisheries industry due to intense and unsustainable overfishing. Individuals concerned with this trend have been making informed decisions about their seafood consumption with the help of sites such as Seafood Watch run by the Monterey Bay Aquarium. This site provides information about which fisheries are implementing sustainable techniques as well as information on fisheries that are being overexploited. Seafood eaters can make informed decisions about the types of practices that they want to support based on this information.

The blog Guilty Planet argues that it is not enough for people to switch to eating only particular seafood species as an increased demand on these species would result in their decline due to overexploitation. The blog proposes that the solution is to cease eating seafood altogether.  This stance isn’t going to make an appreciable dent in seafood consumption and is likely to alienate the very people that we need to be working with in order to bring about effective change.

An extreme stance such as this is likely to appeal to only a narrow range of supporters, limiting its overall effectiveness.  The vast majority of seafood consumers do not even abide by the guidelines for sustainable fish consumption, suggesting that an even smaller handful will be willing to give it up entirely.

To be fair, Guilty Planet concedes that few people will likely adopt a no-seafood policy.  She hopes that by providing a more extreme position newcomers to the debate will find other solutions (such as eating fish from sustainable fisheries or cutting down their consumption) more palatable. I worry that publicity for the “Stop Eating Seafood Movement” will scare away the newcomers who are starting to become concerned with the decline of overexploited species and are looking for an easy way to make some positive changes. When they see the sacrifices that we’re asking them to make by cutting seafood out entirely, I worry that they’ll give up on making changes altogether. Let’s be honest, we’re not going to get the majority of Americans onboard unless you make conservation seem easy (although it clearly isn’t).

Essaouira,_Fish_MarketBut the real problem lies in the message that this stance sends to the seafood industry and, in particular, the message that it sends to individuals in the industry that have been working hard to implement sustainable techniques. They were once “rewarded” for their sustainable behavior by the increased patronage of sustainability-savy individuals (with the help of sites like Seafood Watch).  The new message that we’re sending with a call for a boycott of seafood is that we’re abandoning the industry altogether (including those working on making positive changes) and we’re unconcerned with their situation. After all, the fishermen would also prefer that marine species were not in decline as this business feeds their families.

The small decline in consumption that this stance may generate will certainly put a bad taste in the mouths of the industry with which we need to cooperate. They need to feed their families and we need them to change the way that they do their job. Without collaboration and wide-scale changes in practice, the overfishing problem will not be resolved.

There are people all over the world who rely on seafood as an important protein source. To me this implies that the solution can not be reached by pleas for a removal of seafood from one’s diet. As long as there are fish to catch, there will always be fishermen. Coming to terms with this fact necesitates that we keep lines of communication open with the seafood industry so that they will be open to our suggestions and technologies in the years to come.

To reiterate, Guilty Planet and I on the same side.  We both want to see major reforms in the way seafood species are collected and consumed so we can reverse the trends of decline. I also agree individuals should think carefully about the diet choices they make as well. I personally limit my seafood consumption and consult Seafood Watch before making a purchase.  Jennifer and I simply differ in the method in which we think is the most effective in bringing about change.

The Worst Advertisement I’ve Ever Seen

I was browsing Science Daily today and noticed the following advertisement:

HarrisonFordI spent awhile trying to figure out if it was a joke or not and have come to the conclusion that this group actually believes that people will sign their petition just because a haggard looking Harrison Ford thinks that they should.

Does this sort of advertising actually work on people? I personally don’t know anything about what Harrison Ford stands for.  Why would I blindly follow a man about whose belief system I know nothing?  I know he made a darn good Indiana Jones, but I don’t even know which political party he generally identifies with.

Too bad they didn’t use a picture of Harrison Ford from 20 or so years ago.  Maybe then I would have signed their petition. Or maybe if Hugh Jackman thought I should sign it…..

More Scientist Humor

In an earlier post I listed species and gene names that were clearly conceived of by scientists who had a sense of humor.  I have another one to add to the list.

Phallus_drewesiiA newly discovered mushroom species found in West Africa has recently been named Phallus drewesii (Latin translation: Drewes’ penis).  It was named by a colleague after a California Academy of Science curator named Bob Drewes who explains, “I am utterly delighted. The funny thing is that it is the second smallest known mushroom in this genus and it grows sideways, almost limp.”  Clearly, this is a man with a good sense of humor.

Check out this article for the original story.

Below is a video of the man himself discussing the function of snake venom:


I recently received the following message from Adam:

Hi Kelly. I was thinking about your post about the responsibility of scientists to explain things to the public. Recently, there’s been a renewed bout of global warming skepticism, and I’m not really sure how to get about the truth. The point is I’m a big fan of science. It works. But there’s a problem. Not with science itself. But with what we do after we’ve done the science. There’s a problem with information. I may be a big fan of science, but I’m not a scientist. I can understand basic principles, and I know that if I were to go and do enough research on physics, and pay attention, and work my way through stuff, I could understand it. But that’s mainly because people agree on stuff now. All the really hard work – slogging through experimental reports, searching for bias, ensuring people weren’t selective with their evidence – all that stuff’s been done for me. If I want to go and do that kind of stuff for myself, it’s a lot harder.

EarthSay I want to evaluate this climate change stuff, and get a better opinion about how important solar cycles and stuff are. It’s not that easy. I don’t know where to find the data, I don’t know where to find the experiments. Even if I do, it’s pretty hard for me to recognise where someone might have ignored previous research, or only used certain evidence. If I want to see that, my best bet is to find what other people have said about that paper or experiment. So there’s a lot of needless searching and taking other people’s opinions for granted. There’s no central place where I can go and search through documents, and compare conclusions, and judge stuff for myself. And I think that’s a problem. Because I read about global warming, and I take that for granted because “scientists say so”. And then I read some anti-global-warming thing, and I think, “Oh, well, these scientists say the first ones were wrong. So I guess they could be right.” And then the other group makes counter-claims.

There are only two solutions. The first is to get one group to make a report, the other group to have a counter-report objecting to the first one, the originals to counter-counter report, and so on until we figure out who has a better grip on the facts. The second is for me to go and try and do that by myself, comparing their data and reports and positions. The first would be better, but it’s unlikely, because the job of scientists is to research science, not necessarily explain it to me or explain why the other people are wrong. And the second is more likely to happen/doable, but it’s really hard, because I just don’t have access to the kinds of materials I need. So I’m kind of stuck.

How do you suggest not-scientists like me figure out the truth about science?

That’s a tough one.  Even for scientists it can take months to years to become totally acquainted with the literature in one’s field. Perhaps more importantly, there are often many more than just 2 sides of an issue.  Global climate change (I prefer this more accurate term for global warming) is a great example. I don’t think that too many scientists are currently arguing that global climate change is a non-issue, but a healthy debate is definitely raging over the predictions that we can make about patterns of global climate change – for example, how far we predict that sea level will rise as the polar ice caps melt. It would be easy if the debate were polarized, but it’s far more nuanced than that.

Baby_ginger_monkeySo unfortunately, you’re going to have to do a lot of work to get complete information on topics such as global warming.  Sometimes you’ll get lucky and a handful of prominent writers will have published their view on a topic, which will cut out some of the work that you’ll have to do to track down references. Blog writters can also be useful resources if you’re lucky enough to find one who is well-informed and willing to consider multiple sides of an argument.

Other times you’ll get a lucky break when a review paper has been published in the scientific literature. Finding a review paper is often better than finding a book on the topic as books can be biased by personal opinions and have not undergone the same peer review process that a review paper goes through.

Review papers can be found through sites such as Google Scholar, but readers who aren’t associated with research institutions may not have access to anything more than the article’s abstract (an abstract is a short summary). Fortunately, more and more open access journals are popping up (PLoS One, for example) which allow all readers access to the entire article.  If you find a review paper that you’d really like to read and it isn’t available in its entirety online, e-mail the main author and ask for a reprint.  If they’re able to, they’ll probably send you the article.

To determine how well an article is accepted by the scientific community, check to see how many times the article has been cited and read a few of the articles that have cited it.  You can find this information by clicking the link in Google Scholar that says “Cited by: XX” which appears underneath the article’s title. If a paper has been written which refutes the claims made by the article in question, it should be listed here.

Another good indicator that the researchers in question used sound methods and made reasonable conclusions is to check the impact factor of the journal in which the article was published. Better journals are more critical of the work that passes through their doors and more often than not are publishing high quality work.

Finally, you can browse the Internet to find researchers who study the topic that you’re interested in and shoot them an e-mail.  Ask them if they know of any laymen literature on the topic.  They should be able to direct you to popular science books, news articles, documentaries, blogs, etc.  If one professor doesn’t write you back, just try another one. It’s been my experience that busy professors forget to reply to e-mails such as these when their to-do list gets exceedingly long.  Don’t get angry, just try someone else.

I hope that helps a bit, Adam!

Why We Should Clone Woolly Mammoths

Adult_Woolly_MammothIt’s entirely possible that the ability to clone a woolly mammoth will become a reality in the not-so-distant future. Scientists have already sequenced 70% of the woolly mammoth genome (find the Nature article here) and the remaining 30% will surely be sequenced soon owing to the discovery of new, well-preserved mammoth specimens. After patching up the missing DNA chunks with DNA from African elephants, we’ll be able to use African elephants as surrogate mothers to bring woolly mammoths back a planet that hasn’t known them for ten thousand years.

There is a lot of debate over whether or not we should bring woolly mammoths back.  In my opinion, bringing these and other extinct animals back to life could do a lot of good.

Cloning a woolly mammoth will require an extensive amount of funding.  I don’t suspect that the National Science Foundation (NSF) or the National Institute of Health (NIH) will be chomping at the bit to fund this sort of research, so private investors will have to step up to the plate.

Such a high profile project  is sure to attract the attention of private investors, who will undoubtedly identify the one could monetize the hell out of a cloned woolly mammoth. Imagine how much people would pay to see such a thing! Surely investors will see dollar signs and fund the cloning research.

A woolly mammoth preserved in permafrost

A woolly mammoth preserved in permafrost

Investors would mainly be interested in the production of clones, but their money would have to be spent on basic research as well. Previous cloning attempts have produced short-lived animals that quickly succumb to tumors, diseases, etc.  In order to solve this major problem, part of the money that investor’s provide would necessarily fund basic research in fields as diverse as development biology, genetics, epigenetics, immunology, and microbiology. The results of these studies would be applicable to numerous species, not just woolly mammoths.

The percentage of submitted projects that are funded by NSF and NIH is pretty darn low. A sexy and exciting project like cloning woolly mammoths would undoubtedly tap into previously unexploited private funding resources, bringing millions of dollars into biology labs across the country.