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 Science has its traditions about what should and should not be published which don't always coincide with simple rules of following the scientific method.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.
Sunday, September 1, 2013
Wednesday, August 21, 2013
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.
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.
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.
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.
Sunday, August 11, 2013
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.
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.
Monday, July 29, 2013
The Science OR
Today I got an email via Ecolog, informing me of the birth of a new way for scientists to disseminate their research. Launched by Queens University a couple of weeks ago, one of SciOR's main objectives is to place accountability in the article review process.
The idea that reviewers can say whatever they want and reject papers that conflict with their own beliefs, all behind a veil of anonymity, is not new. Nor is the idea that journal editors select what knowledge is published, and therefore the sphere of knowledge that scientists have. So how does SciOR (or Science Open Reviewed) claim to offer a way around this?
I don't really have enough experience with the peer review process to know if this will work, but the idea of paying reviewers seems a little weird. I don't like the assumption that the SciOR people make that many reviewers don't offer their services "because they are nice people wanting to help advance science", but rather imply that people enjoy the power the position gives them. Wouldn't money take it the other way? If people are interested in power, not the advancement of science, then wouldn't this hold true for authors too, meaning that a reviewer powered by money could become a popularist, letting things slip through? Sure there is a second round of editing before complete acceptance, but editors are not specialists in the subject and therefore may not catch mistakes. Meanwhile, the reviewer has cash in hand and the author another publication to his/her name.
Furthermore, is this really any better and more open than the traditional publication model? First, if journals are going to send the paper out for review again, why bother marketing a reviewed product? Won't this retard the publication timeline? Second, external journals are still picking and choosing the articles it thinks are interesting, while the editor of the Proceedings of SciOR has his/her say on the remainders. Editors are still controlling what we know. Foucault lives on.
What do you think - can ScienceOR resuscitate science communication?
The idea that reviewers can say whatever they want and reject papers that conflict with their own beliefs, all behind a veil of anonymity, is not new. Nor is the idea that journal editors select what knowledge is published, and therefore the sphere of knowledge that scientists have. So how does SciOR (or Science Open Reviewed) claim to offer a way around this?
1. Reviewers register with the website and advertise their reviewing experience and offer a list of topics they feel qualified to review papers on.
2. Authors post paper titles and abstracts as a sales pitch for their papers; SciOR provides a platform for potential reviewers to contact the author's and offer their reviewing services.
3. Authors pick from the list of offers (or invite new ones), and both author and reviewer complete a No-Conflict-of-Interest (NCOI) declaration.
4. Authors pay the reviewers, if that was part of the agreement, and SciOR facilitate the transaction.
5. The authors revise and re-upload the paper, asking for more reviews if they so wish.
6. SciOR serves as a kind of marketer for these articles; journal editors from other journals (or the in-house Proceedings of Science Open Reviewed) pick from the rack of finished reviewed products. They then contact the authors and the authors unpost the paper.
I don't really have enough experience with the peer review process to know if this will work, but the idea of paying reviewers seems a little weird. I don't like the assumption that the SciOR people make that many reviewers don't offer their services "because they are nice people wanting to help advance science", but rather imply that people enjoy the power the position gives them. Wouldn't money take it the other way? If people are interested in power, not the advancement of science, then wouldn't this hold true for authors too, meaning that a reviewer powered by money could become a popularist, letting things slip through? Sure there is a second round of editing before complete acceptance, but editors are not specialists in the subject and therefore may not catch mistakes. Meanwhile, the reviewer has cash in hand and the author another publication to his/her name.
Furthermore, is this really any better and more open than the traditional publication model? First, if journals are going to send the paper out for review again, why bother marketing a reviewed product? Won't this retard the publication timeline? Second, external journals are still picking and choosing the articles it thinks are interesting, while the editor of the Proceedings of SciOR has his/her say on the remainders. Editors are still controlling what we know. Foucault lives on.
What do you think - can ScienceOR resuscitate science communication?
Thursday, July 25, 2013
X, Y, (and Z?)
Since it is my lab tech Rebecca's last full day tomorrow before she leaves for grad school in Florida, I thought I would write about one of her favorite topics: sex determination.
Let's start with us humans - as you know, humans with two copies of the X chromosome are female, and those with two different ones (XY) are males. But what if you are missing an X or a Y chromosome? What if you have an extra sex chromosome? XYY individuals aren't "super men", but XXYY (or XXXY or XXY) individuals are sterile males. Women with an extra X chromosome (XXX - trisomy X) are developmentally delayed, so there is such a thing as being "too much woman". But missing an X chromosome results in Turner's syndrome for women (XO), and spontaneous abortion for males (OY).
So what does this tell us about these chromosomes and sex determination? Well, you HAVE to have the Y chromosome to be male, and an X chromosome to live, but having more X chromosomes doesn't make you more of a woman - it just makes you sicker. This is because the X chromosome actually carries a lot of important information - including sperm production - while the Y chromosome has been shrinking for the past millions of years and pretty much just carries a single important gene. This gene, SRY (pronounced "sorry"), is a regulator for testis development early on, but all the genes controlled by this are on other chromosomes. Thus came the (in)famous statement that y chromosome shrinkage may be driving men extinct - although this has been disproved. One reason for this is because the SRY gene alone can determine maleness, and it is possible for it to insert into the X chromosome (XX males).
But what about other organisms. That fly buzzing over your half-rotten bowl of fruit you haven't quite managed to finish? Femaleness is decided based on having two X chromosomes, rather than maleness being on the presence or absence of a Y chromosome. Those cockroaches crawling out of your walls? They only have X chromosomes, with males having a single copy and females having two. And that sparrow outside your window? It is like the opposite of humans - men have two chromosomes the same while females have two different ones.
But perhaps the most intriguing method of sex determination is found in sea turtles (and alligators), whose sex is determined by egg incubation temperature. Hot eggs are female, and cooler eggs become male; the temperature difference is very slight, and therefore a mother can somewhat control the sex ratio of her offspring by rearranging eggs. However, some researchers worry that this temperature differential will not be possible under a future climate, and so the reptilian world will be run by females. Of course, females are generally better at spacing sexual encounters than males, so a female-shifted population may not be all bad and could mean more sea turtles.
Or what about organisms which can reproduce without sex (an administrator at creation.com denies Jesus was conceived this way). Or those which switch sex at some point in the lifecycle (think Nemo). Or earthworms, which just serve as whatever sex they feel like, and usually have sex with another worm, but can also just fertilize their own eggs.
There are so many more organisms - like sharks (thanks Rebecca!)- that we know nothing about. Understanding sex determination is more than just an intellectual question - it has important implications for managing wildlife, whether it be on the endangered species list, our menu, or a novel invasive species.
Let's start with us humans - as you know, humans with two copies of the X chromosome are female, and those with two different ones (XY) are males. But what if you are missing an X or a Y chromosome? What if you have an extra sex chromosome? XYY individuals aren't "super men", but XXYY (or XXXY or XXY) individuals are sterile males. Women with an extra X chromosome (XXX - trisomy X) are developmentally delayed, so there is such a thing as being "too much woman". But missing an X chromosome results in Turner's syndrome for women (XO), and spontaneous abortion for males (OY).
So what does this tell us about these chromosomes and sex determination? Well, you HAVE to have the Y chromosome to be male, and an X chromosome to live, but having more X chromosomes doesn't make you more of a woman - it just makes you sicker. This is because the X chromosome actually carries a lot of important information - including sperm production - while the Y chromosome has been shrinking for the past millions of years and pretty much just carries a single important gene. This gene, SRY (pronounced "sorry"), is a regulator for testis development early on, but all the genes controlled by this are on other chromosomes. Thus came the (in)famous statement that y chromosome shrinkage may be driving men extinct - although this has been disproved. One reason for this is because the SRY gene alone can determine maleness, and it is possible for it to insert into the X chromosome (XX males).
Look how tiny the Y chromosome is compared to the X chromosome! Image from: fairbanksirl.com
But what about other organisms. That fly buzzing over your half-rotten bowl of fruit you haven't quite managed to finish? Femaleness is decided based on having two X chromosomes, rather than maleness being on the presence or absence of a Y chromosome. Those cockroaches crawling out of your walls? They only have X chromosomes, with males having a single copy and females having two. And that sparrow outside your window? It is like the opposite of humans - men have two chromosomes the same while females have two different ones.
But perhaps the most intriguing method of sex determination is found in sea turtles (and alligators), whose sex is determined by egg incubation temperature. Hot eggs are female, and cooler eggs become male; the temperature difference is very slight, and therefore a mother can somewhat control the sex ratio of her offspring by rearranging eggs. However, some researchers worry that this temperature differential will not be possible under a future climate, and so the reptilian world will be run by females. Of course, females are generally better at spacing sexual encounters than males, so a female-shifted population may not be all bad and could mean more sea turtles.
How many methods of sex determination can you count? From https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcSARbq3hpD6h4wLG7fTv7Z_wRnGZBIr1ttjUeX0qeoTjz1u9aW7Fw
Or what about organisms which can reproduce without sex (an administrator at creation.com denies Jesus was conceived this way). Or those which switch sex at some point in the lifecycle (think Nemo). Or earthworms, which just serve as whatever sex they feel like, and usually have sex with another worm, but can also just fertilize their own eggs.
There are so many more organisms - like sharks (thanks Rebecca!)- that we know nothing about. Understanding sex determination is more than just an intellectual question - it has important implications for managing wildlife, whether it be on the endangered species list, our menu, or a novel invasive species.
Sunday, July 21, 2013
Now, now...share nicely!
In lab meeting a couple of years ago, we
discussed whether making government-funded ecology research publicly available
would actually benefit science. The general consensus was that while the public
should have the right to access research its tax dollars have paid for, making
data open would not really benefit them or science. My labmates argued that there is already
too much data and too few people with the knowledge necessary to make meaning from the data. Furthermore, they argued, the frequency with which some grants require data to be made publicly available would require researchers to take time away from science during peak field season in order to enter and upload the data. And I followed along.
However, attitudes are shifting. Recently there has been a
flurry of papers and blog posts on open data and what it means for ecology. For
example, in a really nice article in Frontiers in Ecology and the
Environment, Hampton and colleagues argue that if ecologists are to survive,
they must both share and use shared data.
Yet in a survey, the authors found that less than half of the papers produced
using NSF funds had also published some or all of the data used to write the
paper. As another incentive to "open" data, the authors argue that there are instances - such as when rapid responses to environmental crises are needed - when open data is used more extensively
than what they refer to as "dark data". Thus worries about data
overload and lack of relevance appear to be unfounded; the government needs
bang for its buck, not tree-hugging.
Joern Fischer, a professor at Leuphana
University responded to this paper on his blog, stating that while he believes sharing
is a nice idea, in practice there is no shortage of data, and allowing other
people not intimate with the sites from which the data was collected is
dangerous. Ecology is apparently a touchy-feely science which cannot be reduced
to data points that can be used to look for larger global patterns, a point
which the Hampton paper also brings up.
But I would argue that 1. getting too intimate
with your site is dangerous (you start seeing patterns which aren't there, so
you MAKE them there when you do statistical analyses), and 2. we really just
need more complete metadata, including many pictures of research sites
throughout the seasons. For example, there have been fires in various plots at the Boston Area Climate Experiment, and they have been logged in the online shared lab notebook. However, to my knowledge, this information is only accessible to people working at the site. "Hidden" metadata like this must be made
available to anyone reading papers and using the associated data to
complete a meta-analysis of climate warming effects themselves.
Another point that Joern brings up is that field
ecologists will do the hard work collecting data and have to publish in
smaller, regional, less-prestigious journals while the modelers sit at their
desks, distant from the field, and compile all this data into articles the top
journals are begging for. I have a number of gripes with this statement. First, if you are doing ecology to get
publicity, you are in the wrong field. That applies for all desk-, lab-, and field-bound types. Second, this separation between writers and doers
is ancient - how many techs do biomedical labs have, and yet PIs write the
paper with no input from the technicians about what funky things happened along
the way? Third, having gone from an almost exclusively field-based position to
an almost exclusively computer-based one, I would do anything to be spending my
summer outside looking at nature's pixels; working at a computer is not some
lazy-ass bliss. Nothing is. Fourth, most ecological data collection can be done
by minimally-trained volunteers (Earthwatch actually requires that projects it funds use
volunteer data collectors extensively); I reckon the future of ecology will be
a PI with some model or question they want to ask, going to public data,
identifying a hole, and involving the public to collect that data, and possibly
analyze it. It seems like a grant-writers dream given the current funding
requirements.
So what are we really worried about? The idea of
more work? Being responsible for a broader array of literature? Isn't it our
job to understand the world? Ecologists don't write grants which say "I
want to understand exactly what happens in the four 6m*6m plots I will be
studying", but rather "I will design a study using four 6m*6m plots
superficially representative of the broader environment with the hope of understanding
patterns and processes in ecology which can be extended to larger spatial
scales".
But to scale up in this day and age, we have a responsibility to
not just conjecture, but actually test it. If nobody is asking the same
question (or if it has been asked, but the data has been
analyzed inappropriately), and we only have published results to go on,
how will we do this? We can ask people for their raw data, but emailing busy
professors who have to dig up datasets not necessarily formatted for
sharing is a time-consuming process.
It's time to go beyond the costs of taking the
time now to put your data in a clear format for others (and you a few years
down the line) to access, and to think long-term. That is not to say that I
think all data should be analyzed blindly without respect to site intricacies;
we don't know what factors are important in ecological data, and how they may
differ with time and space. However, looking over larger landscapes allows us
to examine broader patterns and identify best practices for land management in
the absence of finer resolution data, and if the metadata we have does not
predict responses of interest at a broader scale, we have a reason to apply for
more funding to do field work and ask why.
For a field so obsessed with statistics, such
aversion to testing the effect of increasing sample size
seems ridiculous.
For a more positive spin on open data, Chris Lortie of York University has made a pre-print available on the role of open data in meta-analyses which is available here.
Saturday, July 13, 2013
Cows can fly!
At the Gordon Conference last week, I was introduced to flying cows (aka Hoatzin, or stinkbirds), which, like happy cows, feed almost exclusively on leaves. Because a diet composed exclusively of leaves is incredibly poor in nutrients and hard to digest, like cows, hoatzins use microbes to ferment the food they eat.
Both animals have a wide array of bacteria which make cellulase and lignase enzymes the host animal cannot. These enzymes break down leaf components such as cellulose (long strings of glucose linked together) and lignin (the irregular, phenolic (or ringed) compounds which give the leaf structure), which the microbes ferment into short-chain fatty acids such as butyric acid (which gives Parmesan its "distinctive" smell), propionic acid (which smells like really bad sweat), and acetic acid (as in vinegar). Because this process is relatively slow, the animals must eat a lot of food and have a large fermentation chamber; hoatzins are poor flyers and have to have an extra bump on their chest to help balance on branches so their full gut doesn't topple them, and the cow rumen is so big you could probably fit an adult human in it, though I don't think anyone has tried it.
Compare how much space the crop - the pouch birds use to store food if it over-gorges itself - takes up in the hoatzin (left) compared to the chicken (right). This is where the "pre-digestion" of vegetation occurs in the hoatzin. Small amounts of fermented fluid are released into the small intestine where the short chain fatty acids can be absorbed. Pictures from schaechter.asmblog.org and keep-hens-raise-chickens.com
Cows and hoatzins aren't the only animals which depend on microbes to break down their food. We too depend on microbes, except the majority of our microbes live in our large intestine and feed on our "leftovers" because most of our nutrients are absorbed in the small intestine. Research indicates that some other organisms, such as the giant panda, have lost some of the ability to degrade complex plant matter, and their genomes contain fewer genes encoding enzymes involved in this process than their nearest omnivorous relatives. This might explain why there have been reports of mother panda's feeding offspring their feces - populating your gut with the right microbes is obviously important if you cannot digest your food yourself.
Of course, pandas aren't the only animals to practice coprophagy (poo-eating). Babies do it. Dogs do it. And rodents like rabbits and guinea pigs do it. The last two animals are relatively easy to explain...they are hindgut fermenters, which means the majority of the microbes responsible for breaking down the plants they eat live in a part of the gut which comes after where the majority of absorption occurs. Therefore, in order to get all of the nutrients out of the food they have taken in, the food has to pass through the gut a second time. But babies and dogs...let's just say I don't kiss them.
If you want to learn more about poo, Wikipedia has your a** covered
 |
A hoatzin. Hoatzins are awesome not only because they
are "flying bioreactors", but also because they are a bit like
modern-day versions of Archeopteryx, the ancient gliding bird ancestor
which had claws on its wings which enabled it to climb up trees. Hoatzins live in the Amazon basin. Image courtesy of www.birdsofseabrookisland.org.
|
Both animals have a wide array of bacteria which make cellulase and lignase enzymes the host animal cannot. These enzymes break down leaf components such as cellulose (long strings of glucose linked together) and lignin (the irregular, phenolic (or ringed) compounds which give the leaf structure), which the microbes ferment into short-chain fatty acids such as butyric acid (which gives Parmesan its "distinctive" smell), propionic acid (which smells like really bad sweat), and acetic acid (as in vinegar). Because this process is relatively slow, the animals must eat a lot of food and have a large fermentation chamber; hoatzins are poor flyers and have to have an extra bump on their chest to help balance on branches so their full gut doesn't topple them, and the cow rumen is so big you could probably fit an adult human in it, though I don't think anyone has tried it.
Compare how much space the crop - the pouch birds use to store food if it over-gorges itself - takes up in the hoatzin (left) compared to the chicken (right). This is where the "pre-digestion" of vegetation occurs in the hoatzin. Small amounts of fermented fluid are released into the small intestine where the short chain fatty acids can be absorbed. Pictures from schaechter.asmblog.org and keep-hens-raise-chickens.com
Cows and hoatzins aren't the only animals which depend on microbes to break down their food. We too depend on microbes, except the majority of our microbes live in our large intestine and feed on our "leftovers" because most of our nutrients are absorbed in the small intestine. Research indicates that some other organisms, such as the giant panda, have lost some of the ability to degrade complex plant matter, and their genomes contain fewer genes encoding enzymes involved in this process than their nearest omnivorous relatives. This might explain why there have been reports of mother panda's feeding offspring their feces - populating your gut with the right microbes is obviously important if you cannot digest your food yourself.
Of course, pandas aren't the only animals to practice coprophagy (poo-eating). Babies do it. Dogs do it. And rodents like rabbits and guinea pigs do it. The last two animals are relatively easy to explain...they are hindgut fermenters, which means the majority of the microbes responsible for breaking down the plants they eat live in a part of the gut which comes after where the majority of absorption occurs. Therefore, in order to get all of the nutrients out of the food they have taken in, the food has to pass through the gut a second time. But babies and dogs...let's just say I don't kiss them.
If you want to learn more about poo, Wikipedia has your a** covered
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