Morals and the ethics of collaboration

Why can't scientists stick to science at conferences? I find it hard enough to speak to strangers, and to be welcomed by racist comments that I don't know I can address if I am in the perpetrator's country makes it much harder. Racism and sexism are trashy. You shouldn't have to hide racist/sexist/other-ist thoughts. They shouldn't even come to your mind. Yes - the ideal world. 

But are we too sensitive? Do we rush to conclusions too early? Perhaps. The only time I can remember being called explicitly racist was in fourth grade, after I said I didn't want to watch riverdance for the third day straight and said that Irish people drink beer on St. Patrick's Day (apparently saying that Irish people eat boiled dinner isn't racist though). It seemed (and still seems) ridiculous that my teacher should assume I was discriminating against Irish culture, but it made complete sense to her. 

So am I ridiculous in crying racism after some conference attendees told me that Chinese students are lazy, sleep in the lab and only ever pretend to do work, playing video games all the time instead? Maybe. But it is just another reminder that we need to think about what comes out of our mouths and how, because after that comment, I couldn't bring myself to talk science with them. Or talk to them full stop, for that matter. 

Conferences and face-to-face interactions are vital for the spread of scientific knowledge and forging collaborations, but if these are going to be shrouded in ideals that one party vehemently opposes, then once again ideals have shaped the path of science. Human rights and environmental charities are constantly scorning universities and companies for investing in morally grey areas, so why do scientists think it is OK to collaborate with scientists who hold grey morals? 

I think this is probably because we like to think of science and society as separate when convenient. And it is hard to hold a firm stance against poor morals because so many technological improvements have emerged from dark times and/or dark minds (SONAR, RADAR, and the Haber-Bosch process to name a few). 

But where do we draw the line in collaborations? If we ignore the discriminatory tendencies of our collaborators and work with them to advance science, are we also subtly advancing their ideals? What if we cite papers written by people with questionable morals (James Watson comes to mind here)?

Ultimately, are we not guilty by association if we knowingly collaborate with discriminatory colleagues? Is this how the closed-minded norms perpetuate in fields that like to consider themselves open, in the heads of people who like to think of themselves as educated and/or liberals?

Has the sun set on societies?

My mum asked me to write a post on how society publishers could keep young scientists involved, as this is something that many scholarly publishers, libraries, and societies are thinking about. Her comments were something along the lines of "We oldies, who are the ones making decisions about the future of our organizations, are worried about keeping early career scientists involved. For example, most societies are run by the older generation, and although some (eg. AGU, ESA) do have a good group of early career scientists, these appear to be exceptions to the rule. How can we get more of you involved?"

One factor could be the cliqueyness of conferences. The primary incentive of society memberships I can see are 1. access to jobs boards/listservs and 2. going to conferences (for societies that require membership to attend conferences). But how do you break into a group of scientists who are talking to one another if they are all friends? Would you rather not stick with your own kind? It is kind of like the first day of school all over again, only you probably don't have quite as much courage to ask to join someone else's game (conversation), or the brazen spirit to get over rejection. Then again, later career scientists may feel the same way about talking to earlier career scientists. People are just awkward.

Perhaps the best way to get all age groups is to create intergenerational labs. While as a grad student I may be able to relate to my pre-tenure advisor, I look at many later stage professors and they seem a world away. And since many of them got tenure in a different era, they really are. There are certain full professors I can relate to, but the initial interactions and courage to talk to one another is contingent upon our daily bumping into each other rather than any intellectual exchanges. Of course, deciding who shares which lab space isn’t really within the powers of societies, but holding workshops specifically designed to bridge the generational gap is (so offering miniseminars or discussion groups at conferences where the organizers put together a small group of scientists at different stages in their careers and from different institutions to talk).*

From a publishers perspective, keeping early career scientists involved with the societies they work with is seen as vital for maintaining readership. I can’t really say how to keep up readership in the early career sector, but I know what I want. I want those pesky career services adverts to go away – or at least to not compromise job post quality and relevance in the name of money (do I really seem like the kind to want a job in pharmaceuticals if I am reading a paper on theoretical ecology?).  I don’t need a society’s calculator tools; labs have already developed plenty enough of those, which are high quality so don't waste your resources trying to compete with them. A publisher’s website does not need to be a one-stop shop, and should stop wasting its energy trying to be. Remove that banner stuff and those sidebar links and fill as much of the page as possible with actual content– the screen on my laptop is quite small and I want to see the figures as I read.  Just give me the papers I want to read, please. This isn’t the superbowl.

But perhaps ultimately what societies and publishers can do to involve a younger audience is to stop assuming everyone is going into academia (and in a few instances, perhaps industry). Develop resources that don't immediately exclude the majority of young scientists that aren't in or aspire to be in tenure track positions. 

What do you want from societies and publishers (besides free access to all the journals in the world)? Is there something you think that societies could provide to entice you to participate more, or are societies a lost cause in your mind?

* I would like to point out that there are of course numerous exceptions to my sweeping generalizations about societies, publishers, and conferences and/or organizations doing the things I suggest are good here. The purpose of these statements are to demonstrate instances of where I think these organizations are headed in the right direction.

What makes a paper mind-alteringly good?

Sorry about the overly-dramatic title, but after reading what I think is a very well planned and executed paper on the phylogenetic and geographical dispersion of drought tolerance in plants earlier, I have been thinking about the power that single articles can have over our outlook on our work.

If the world's journal archives were about to be obliterated, the one article I would grab would be Davidsson and Janssens' 2006 paper in Nature on how climate-induced changes in decomposition may feed back. Actually, this is the only paper I kept from my undergraduate, and I have been reading the same dog-eared, scribbled-on copy for the past five years. It is also the only paper for which I have gone through and read every paper cited in it.

But why did this article appeal to me initially? I didn't understand most of it the first time I read it. Or the second. It took a week of staring at Box 1 to understand what it was talking about, and some of the other arguments in the paper seemed flawed to me because the lines of logic they were following weren't laid out, and disagreed with the facts I was aware of the time. But from what I could decode, I knew this paper would be really important for my understanding of the carbon cycle under climate change. And in my young inexperienced state, I thought that it must be good and right, because it was published in Nature.

Despite my interest in the paper's important topic, it was the dense challenge of the paper, working through the hidden complexities of the carbon cycle, that got me. Every time I read it, I get something new out of it, and it helps me frame my work in the bigger picture and remind my why I love my work.

But what article do you keep returning to?

Basic psychology would tell us that for most of us, our most powerful article will be one of the first we read on a topic; our experiences early in life (whether research or real) shape how we perceive subsequent events, and therefore we will find ourselves returning to the point (paper) which established our mindsets. I would think that review articles would also be favored over primary research articles, because they put the research in context and are generally written by people with respected views. Of course, regurgitating what is known doesn't help, but putting a new spin we hadn't thought of (for example pulling in information from other disciplines) would make an influential article in my books.

I think this would mean that journals that want to be cited lots should favor interdisciplinary reviews. I believe I read somewhere that this already happens - does it? That seems like it would be a much too simple key to "success"!

What to do when you're wrong...

Sorry for the delay in posts. I've been busy being wrong.

As we know, one of the first tenets of "good" science is reproducibility. If I follow someone else's protocol, using the same starting material, I should get the same results. But if you do that, and you get a different result, how do you know whether the alternate result is because you didn't quite replicate the protocol, or because the original conclusions were wrong? Or what if you interpreted the same results differently?

I can imagine this is an especially large problem when you are new to a protocol (or at least that is my excuse), as you lack a sense of the range of possible outcomes. For example, a labmate was trying to interpret a catalase test earlier, and would have said that all our results were negative compared to the plate of mixed soil bacteria I had, where adding a drop of hydrogen peroxide caused a baking soda and vinegar type volcano effect. Two of the bacteria were supposed to be catalase positive, and if we added tons of hydrogen peroxide directly to a plate with a high density of bacteria and looked really really close for a few minutes and imagined a positive result, we got one or two small bubbles. This is exactly the same as if I drop a drop of the hydrogen peroxide on uninoculated media. So did the authors who stated these organisms were catalase positive actually mean it, or did some nervous inexperienced student  who was told to look for any sign of bubbling squirt a bubble onto the slide and say there was a positive result? Who decides where the boundaries of a positive or a negative result are - would it not depend on "how" positive or negative your control organisms are? Do people publish the organisms they used as controls alongside their determination of whether something shows a positive or a negative result? No evidence for these yet.

Maybe we should just mandate that all standards in genomics tables be replaced by full-colour pictures. Voluptuously bubbling hydrogen peroxide. Stunning Gram stains. Replace someone else's interpretation of ambiguous data with informative eye candy.

In another instance, I have been working (a bit too long) on trying to get well-published qpcr primers to work, and finding that the conditions as close to the original ones I can reproduce in my lab just don't work. I was afraid I had contaminated the freezer stock of my organism, or put too much or too little template, or used the wrong temperature...something that was my fault. I tried to come up with an answer and a solution for my PI for when I told her that things weren't really working. But apparently, however, what I thought was close enough to the original conditions probably is not; the primers were tested against a sequence placed in a purified plasmid, and I am using genomic DNA.

Which brings us to another class of issues with reproducing an experiment - what if you purposefully are not exactly reproducing an experiment, because you don't believe the methods used are valid and/or reliable and/or result in biologically meaningful conclusions? Why waste time and money trying to reproduce an experiment that was invalid when it was made, and still invalid now, just to try and compare your results to ones you cannot trust? At my stage, I think it is so you can fit in; the ability to reproduce something invalid is a valuable skill for perpetuating some of the falsehoods of science, which you have to be able to do in order to prove your worth in breaking the (methodological) status quo.

So why use a plasmid template for qPCR, even if it does a poor job representing the kinds of templates you will be comparing with from the environment? Because it is one of the standards for this kind of data collection; we can hide behind completely non-reproducible data, uncertain whether it is due to the methods, or because we are dealing with "complex" environmental samples that nobody else is likely to exactly mimic.

But no matter what I may do to try and convince myself I wasn't wrong, I was. I tried to reproduce results under the conditions I thought they should be done, not those in which they were intended.

So if you are wrong, either make sure you do it reproducibly so you can challenge what is deemed right, or do so using conditions nobody expects ever to exactly reproduce. But know when to accept that it is you, not science, not the protocol, that is wrong.

Science on the Free Market?

My mum's friend sent me this article discussing how science is moving away from fundamental research, and towards translational work, and asked for my opinion.

The article is titled "Should Science be for Sale?", which immediately made me think of some kind of sinister plan to buy people out of presenting the whole truth.  

Although faking science is not limited to the former Soviet Republics, the author points out that it has been getting worse there. I agree this is bad; when people build science on bad science, it may take years for its consequences on scientific theory to emerge. However, the author tries to blame this "evil" on the fact that people increasingly see science as a means to an end, rather than for its own holy sake. Yes money can lead to greed and cheating the system, but it can also lead to healthy competition - a bit of a free market with the tax-paying public as customers - for doing the research that matters, and so the author's implied sentiment that applied research is filthy compared to basic science is a bit simple-minded and snooty to me.* 

But by no means do I think science is a holy palace either. Science has its traditions about what should and should not be published which don't always coincide with simple rules of following the scientific method. It is true that scientific knowledge is financially-driven - science journals are after all really just glorified tabloids looking for the biggest and best (fact-checked) stories to boost readership - and researchers need to do the work that will get them money from the governmental funding agencies that decide the country's research agenda. 

While applied research may be more explicitly designed to facilitate progress towards these goals, and to fit in with where the government is funding, by no means does this mean that basic research is excluded from these funding calls. You just have to spin it a bit harder to make it sexy, and ultimately I think this is better for the researchers. Any taxpayer is entitled to know what areas of science his or her money is going to, and to ask scientists how they are attempting to make the world a better place. Taxpayers don't always have to understand exactly how this research will get to that end-point, but by forcing research proposals to consider broader impacts, it better prepares scientists to legitimize their work to their funders, and to think about how their work will ultimately contribute to society. It gives people a goal, and making coherent progress is difficult without one (not to mention checking the boxes on annual reports!)

I think that if this country is going to continue to succeed in science, ALL scientists will have to promote their research and give it credibility in the eyes of the public, who, whether as taxpayers or as private donors, determine its future. We absolutely need more basic research, but if you are up on your high, unapplied horse and refuse to even distantly relate it to a topic of public or private interest, don't whine when funding dries up.

* This attitude towards applied sciences apparently is even worse in maths than in (other?) science. Last year I lived with a mathematician who was complaining about lack of funding for his field, so I asked him what the end goal of his work was - how could it eventually be applied to physics or economics to improve knowledge of the world. He said that application was a no-go word, and even thinking about it would lead to ostracization, so he couldn't tell me what he did or where his research was headed. It was like he was bitter that he had to reduce or filthy himself with applied work, even though the taxpayer had funded grad school for him. 

Fighting foreigners with foreigners: aphid vs. vine

Apparently the NYC Department of Parks and Recreation is releasing thousands of weevils originally from Asia to fight mile-a-minute, an invasive vine also native to Asia, which has taken over parts of the city.

I want your MAM(my)! 

(http://www.hort.uconn.edu/mam/Mile_A_Minute_Poster.jpg)

 

When I first read this, it immediately triggered alarm bells to go off in my head. I don't know if it is the combination of quasi-hippie environmentalist and old-school naturalist professors I had during my undergraduate, which insisted on letting things be, or my mother's insistence that two wrongs don't make a right, but I thought this would be yet another human manipulation destined for failure. Think cane toads, native to central America and introduced to sugar cane fields in the Caribbean and Australia to keep down pests, but now spreading well beyond its range and killing off many of its would-be predators with its poisonous skin. Or, the story (for which I can find absolutely no evidence for now) that rats were introduced to an island, then snakes were introduced to eliminate the rats, and the plan backfired and the snakes have taken over the island, killing much of the native wildlife (it almost sounds like the story of Guam and brown tree snakes, but isn't).

However, I am glad to learn that we have learned from our mistakes, and when we say that extensive research was done to evaluate both safety and efficacy of the aphids in targeting mile-a-minute, hopefully we mean it (see references here). As with most pest invasion studies, potential control mechanisms were identified by looking for the herbivores which keep the plant in check in its native environment. Researchers identified Rhinoncomimus latipes aphids (they really need a good common name - can we nickname them munch-a-minutes?) as good potential targets for further research, and their breeding began in controlled environments in the US.

The potential heroes of the story...

(https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi8s6JkviDmsmBMSknSZKMG6Pb4Lsch98BBhrMIzRfCdjh8OtnmAPidiM0p3tVcRzvTyyhNDKT9PjCQFMEFtP0EZiqou0jCzIn3u4USR-gUeEgHgBNRMLeXzO8mny-JiI-zNCIayUYSs5s/s320/IMG_9297.fix.w.jpg)

Of course, organisms don't always behave the same in a new environment as they did in their original environment (this is why things may be minor members of a diverse community in their native habitat, and invade in another), so the next step was to evaluate whether they still feed primarily (or ideally uniquely) on mile-a-minute. Researchers at the University of Delaware dusted these aphids red, and placed them at the base of non-target plants, or yellow, and placed them at the base of mile-a-minute, and followed them through time to see where they ended up. The researchers found that aphids which originally started on mile-a-minute did not stray onto non-host plants, and those on non-host plants found their way onto mile-a-minute more and more as time went on. This is all good.

However, there are still other questions which remain unanswered. For example, do the aphids have natural predators? If mile-a-minute declines, or is in low density in some places, will the aphids switch to other food sources (like us and previously disregarded fish)? Will they reproduce with native mites and make new, super cabbage-eating mites which will upset community gardeners? And, as far as I can tell, although we know it munches on the weed, we don't know whether the mite occurs in sufficient density to have a noticeable impact on mile-a-minute population.

While some of these worries may seem a little far-fetched, all have previously emerged as problems. That said, we cannot be frozen by fear; we live in a dynamic world we change for better or worse.  We don't have enough knowledge to predict the future, so we should try and balance gathering enough information to make an informed decision, and making a decision in a timely manner. After all, researchers need results for grant applications or to appease investors, and some are willing to release their experimental creatures into the wild without full ecological impact assessments in order to undercut scientists with possibly more ethical methods.

The chemistry of decomposition - what is really going on down there?

I recently visited Jerry Melillo's warming plots at the Harvard Forest, and I don't know why, but I was amazed by how much the leaf litter had decomposed over the past few months. This got me thinking about the structure of carbon of the remaining litter. The historic view has been that labile sugars go first, then cellulose, then lignin, but what about the waxes and other compounds which don't fit into these categories? To a certain extent, our understanding of litter decomposition has been limited by our ability to detect and distinguish these other compounds, but tools like NMR are changing that.

The husband-wife duo of Nishanth Tharayil and Vidya Suseela at Clemson have once again teamed up with Baoshan Xing at UMass to study the fine chemistry of litter. In one of their previous papers, the authors noted that reducing precipitation increased the relative abundance of tannins in red maple litter; in this paper they looked at how the chemistry of Japanese knotweed litter, that horrible invasive which is actually quite delectable when young, changes through time in litter subject to different warming and precipitation treatments at the Boston Area Climate Experiment.

In this experiment, the authors made "old" and "new" litter bags by harvesting Japanese knotweed which had either been decomposing upright following senescence the previous year, or just-senesced stems. They were placed at the edges of the high (~+3C) and ambient temperature plots, under drought (50% of precipitation removed year-round), ambient, or wet (an extra 50% of rain applied during the growing season) treatment, and harvested at four time points over a period of three years. By pulling peaks from various methods I don't understand (DRIFT Spectroscopy, and ¹³C cross-polarization magic angle spinning NMR spectroscopy), they confirmed that decomposition of recalcitrant litter is generally more temperature sensitive than more labile stuff. Again, as previously noted, decomposition is greatest when supplemental precipitation is applied in conjunction with warming. But perhaps the most interesting point was that while the effect of climate treatment on overall decomposition rate did not differ between new and old litter, specific (recalcitrant) compounds did decompose more fully in the older litter, which the authors cite as evidence that initial litter chemistry does matter.

As my PI pointed out, there are a few problems with the way in which this experiment was designed. First, the authors used litter from a plant not found in the warming experiment, collected at a site a hundred miles away. The authors state that this litter was chosen because all litter is clonal, and therefore should have been initially identical, but wouldn't litter taken from one of the trees at or near the experimental site not be adequate? Perhaps the problem would be that litter allowed to decompose in-situ for a year would start with clearly different microbial communities than the litter which had just-fallen from a tree. That said, we know that there is often microbial succession during decomposition, and therefore the litter going in old probably had a different microbial community associated with it than the "new" litter, whether or not it was harvested from immediately adjacent stems from a clonal population. In this instance, differences in decomposition with litter starting chemistry could be due to the presence of a microbe at the litter source site initiating decomposition of compounds that microbial populations are not as well-suited to break down. For instance, there could be fungi at the source litter site which are much less abundant at the experimental warming site because it is a well-trodden former agricultural field with relatively low organic matter content.

My PI also pointed out that using litter which starts from the same plant but is in different stages of decay is not a particularly biologically informative way to answer a question. She said that using various kinds of leaf litters which naturally differ in their starting chemistry, as occurs in ecosystems today and potentially exacerbated by climate-induced shifts in species composition and litter chemistry, would make the results of the experiment more useful in ecosystem carbon models. I believe the litter bags for that experiment are decomposing in-situ as I type.

As I alluded to above, my main beef with the paper was, of course, that they didn't talk about whether the microbial community differed between warming treatments. I am interested in knowing whether the differences in decomposition are due to purely physical effects, or whether changes in the microbial community also played a role. I would also like to know if succession of microbes on the different litter ages and in the different plots followed the same pattern, just being accelerated in some instances, or whether the communities were completely different.

This is a kind of chronic problem with ecologists; they generally ignore microbes (or suppose what is happening without validating the assumption). Almost every paper I read, I hope with all my heart that they have soil cared for nicely and kept in an ultra-low freezer somewhere. But anytime I inquire, the answer is no. If they want to really understand what happened in their system, it is their loss.

But please, if you are doing anything involving soil, or are doing a study in which you expect soil or litter-degrading microbes to be adhered to your object of interest, please flash freeze that soil/litter at collection and place in a -80C freezer. If you don't have access to one, contact me before you collect your samples and I will send a self-addressed cooler with dry ice, and I will fill my PI's freezer with random samples as long as I can without her noticing.