Thursday, January 30, 2014

Thoughts on Smuggled Piranhas

Red-belly piranhas at the Muséum Liège (Belgium)
(photo by Luc Viatour)


Piranhas were smuggled into New York City by an importer called Transship Aquatics. The owner of the company Joel Rakower smuggled almost 40,000 piranhas in 2011 and 2012 from a Hong Kong distributor by having them labeled as silver tetras. That's a pretty fun story in and of itself, but I had various other thoughts on the matter.

How can piranhas be confused with silver tetras?
Piranhas do indeed have sharp teeth,
but they are best exposed by pulling back the lips.
Definitely not something to try at home!
Some people pointed out that piranhas and silver tetras aren't all that similar, and questioned how this confusion could've happened. Part of that confusion probably stems from what most people think of as piranhas, these big, tough-looking fish. But I've actually seen piranhas sold (legally) at pretty small sizes, including similar sizes to the tetras you commonly see around. Given the fact that he sold almost 40,000 piranhas over two years, I'd be pretty confident that most of them were less than 3", no bigger than a silver tetra. Piranha teeth aren't necessarily obvious, either; only when the mouth is protruded and the lips pull back do they really become all that obvious, and on small fish such teeth may be missed. To add to the matter, piranhas and tetras are in fact closely related! So you can imagine piranhas as being quite a lot like tetras, but bigger.

Silver tetra (Ctenobrycon spilurus)
Photo from FishBase
One thing that's interesting is, as an aquarist of about 15 years, I can tell you that silver tetras are not very common in the pet trade. You can find some information on the internet on them easily enough, but searching silver tetra usually pulls up the very different silver tip tetra, which is a mainstay in the aquarium industry. So silver tetras aren't exactly a fish that people have a lot of direct experience with, so it might be hard to tell a small piranha from a tetra.

Juvenile Catoprion mento wimple piranha
Full disclosure: This is not the common
red-belly piranha species that was likely involved.
(Photo by Charles & Clint)



Though perhaps piranhas take it even further than rough similarity. Juvenile piranhas and tetras live in the same rivers, and some piranha species have been seen to school with other tetras, feeding off of the unsuspecting school members (Nico & Taphorn 1988). It's been suggested that juvenile piranhas actually mimic the tetras to get away with this! As far as I know, direct mimicry of piranhas with silver tetras has not been reported, but it's not that hard to imagine that juvenile piranhas and tetras might be confused with each other.

That's a long way to go for piranhas!
Piranhas are from tropical rivers in South America, so it's interesting that the fish are from Hong Kong. Hong Kong of course is on the other side of the planet from both South America and New York, so if you wanted a direct source of piranhas you'd think it'd be easier to get them from South America itself. That's not necessarily the cheapest way, though. There are ornamental fish farms in a number of tropical Asian countries. I'd be willing to wager that these piranhas were captive bred on such a farm, shipped to Hong Kong, and then to New York. Crazy how trade of a South American fish doesn't need South America's involvement at all!

There are ornamental fish farms in Florida, but piranhas are illegal to own in Florida too, so they couldn't come from there.

This whole point about piranha legality actually raises another question. Piranhas are illegal in many states, including New York, California, Georgia, Texas, Washington, and Florida (although some of these states allow permits and licenses). These states contain some of the biggest international airports, and thus shouldn't even be able to import piranhas. It's surprising piranhas come in that much at all given that the main pathways in are theoretically limited or cut off, but I have seen them quite often in states where they are legal.

What did he do with them after smuggling them in?
From their website, Transship Aquatics says they supply fishes to wholesalers. But how are the wholesalers supposed to know what they're ordering? I'm going to admit that I have no idea what happened here. Piranhas are illegal in New York so Transship Aquatics probably couldn't put piranhas on their lists, and labeling them as silver tetra on the list would probably lead to some real confusion. Maybe they did it all under the table. Alternatively, since piranha prohibitions are spotty across the states, it might be possible for some sellers in other states ordering piranhas to simply not know they are banned in New York.

At what cost?
This guy smuggled "39,548 piranhas, worth $37,376." I assume these are the cost to Transship Aquatics, since they're really low for anyone that only sees retail prices on fish. Almost no fish in the pet trade is sold under a buck a piece on retail. I'm not sure what these were being sold at, but I'd wager the typical prices could range anywhere between $4-10 if these fish are as small as I think and prices are how I remember them (piranhas are illegal in my current state). So it's potentially big money for anyone involved, although the money has to be divided amongst the various links from exporter, to importer, to wholesaler, and to retailer. Generally, though, the major hike in prices happens at the retail level; many of the more common fish are staggeringly cheaper earlier in the distribution chain. For fish that are wild-caught, fishermen often get paid very little relative to the prices that the fish command in the pet trade.

It's a good thing piranhas are banned in New York, right?
I'd also like to mention that piranhas are typically not all that aggressive, despite the mythology that surrounds them. It's been written on quite a bit but I'll just point you to Prosanta Chakrabarty's commentary on a recent incident where people in Argentina were bitten by a school of piranhas. Piranhas are dangerous, for sure, especially when cornered or captured. They have strong bites and sharp enough teeth that piranha jaws can be used to give haircuts. So like other wild animals, you do have to be careful around piranhas, but they're not man-eating killers.

Even though there are 40,000 extra piranhas in New York (or elsewhere?), there's nothing to worry about. There's little chance piranhas can survive the frozen winter in New York. However, the aquarium trade is definitely a main pathway for invasive species to reach the United States. All aquarists should be urged not to release their fishes into the wild, which is extremely irresponsible. I can see that these bans in some of the more southerly states as more valid. In any case, I hope that the piranhas have found good, legal homes.

Red-belly piranha at the Newport, Kentucky aquarium
(Photo by Greg Hume)
Piranhas are pretty cool fish, though. They are often found at public aquaria, too, so if you ever get the chance, you'll see they can actually be pretty mellow.

Tuesday, October 15, 2013

The PhD-Faculty Gap

Source: Nature Biotechnology. The figure caption said the following:
"Since 1982, almost 800,000 PhDs were awarded in science and engineering (S&E) fields, whereas only about 100,000 academic faculty positions were created in those fields within the same time frame. The number of S&E PhDs awarded annually has also increased over this time frame, from ~19,000 in 1982 to ~36,000 in 2011. The number of faculty positions created each year, however, has not changed, with roughly 3,000 new positions created annually."
The above figure has been making the rounds on the internet. It's from a recent essay in Nature Biotechnology. This isn't even the main focus of the essay, as it's only used to introduce the topic, but it's been getting a lot more attention than the essay's actual content.

The graph does oversimplify things. For example, it includes engineers, who I've heard enjoy more job positions outside of academia than people such as ichthyologists. The graph doesn't show at all if there's an increase in positions outside of academia. Many PhDs are still trained by academics for an academic job, and that this is entrenched in academic culture. Some professors still view academia as the end-all be-all for their students, and if their students want to explore other careers or don't make it into academia, that is the equivalent of failure. Students still unwisely go into academia, not sure what the academic job market is like, myself included. Sure, the academic job is not the only job path, but this is not heavily emphasized, and many PhDs are resigned to trying to go into academia since no other options are made clear to them. This figure shows how the academic job market is getting increasingly competitive.

Of course, this isn't news. Here are three other graphics that people already made to portray the gap between PhDs being awarded and the number that can actually get hired as faculty.

Source: Nature
Nature covered this PhD gap in 2011 in a special on the future of the PhD. In articles like The PhD Factory, Nature showed various graphics that showed that the job market for those targeting an academic life is becoming increasingly competitive. There are lots and lots of PhDs, translating into lots and lots of postdocs, and the faculty job pool isn't increasing enough to keep up with it.

Source: PhD Comics

PhD Comics is well known among academics for its satirical look at life as a graduate student. The above comic really drives it home. Darwin noticed that reproducing organisms would be limited by resources, causing competition. The populations of faculty (and available funding) are also limited, resulting in extreme competition among PhDs to get academic jobs. Quite simply, it's not sustainable for PhD students to expect to be going into academia, as there are only a few jobs out there.

Source: The Royal Society. This figure focuses on the UK. The original caption:
"This diagram illustrates the transition points in typical academic scientific careers following a PhD and shows the flow of scientifically-trained people into other sectors. It is a simplified snapshot based on recent data from HEFCE33, the Research Base Funders Forum and from the Higher Education Statistics Agency’s (HESA) annual Destinations of Leavers from Higher Education’ (DLHE) survey. It also draws on Vitae’s analysis of the DLHE survey. It does not show career breaks or moves back into academic science from other sectors."
This last one shows a particularly bleak picture for those aiming for a faculty position, where less than .5% of PhD students actually become a professor. It's from The Royal Society, but regardless the disparity between PhDs produced and the faculty positions available is not unique to the UK. Needless to say there are many other people that have written about this problem, and other figures out there that neatly display the problem.

If the increasing competition for jobs wasn't enough, there many other reasons not to go to graduate school

The problem has been known for quite a while and people have thought about various ways to fix it, such as slashing the number of students accepted into PhD programs, or by getting schools to better prepare PhD students to do things besides going into academia (which can be hard to expect professors that went into academia to do for their students). You can read many of these suggestions in Nature's special I mentioned earlier. These dismal job prospects prompted the authors, who are graduate students themselves, to take control of their own futures, and most of the article goes into how the authors formed a group (and eventually a company) that provides consulting to start-up companies and their university's Office of Technology Management. It's really interesting and really quite impressive. On the other hand, it's so different from the current system, it's hard to imagine. But that's probably what we need.

I don't know how to fix the PhD. But one day I hope there will be an infographic that shows that the Phd-Faculty gap doesn't matter.

Thursday, October 10, 2013

Can you DDIG it?

I've been spending most of the fall semester so far writing a proposal for the Doctoral Dissertation Improvement Grant (DDIG). The grant was supposed to be due today, but given that the government is shut down, that didn't happen. It's somewhat ironic since the deadline this year is a month earlier than last year's. So in the meantime while we wait for the government to reboot, I thought I'd write down a few thoughts on the DDIG for others, from my perspective. This is not meant to be a comprehensive guide to writing a DDIG. Please refer to the program solicitation to find out everything you need to do.



What is the DDIG?
The DDIG is one of the big grants for graduate students in the sciences, and is funded through the National Science Foundation (NSF). For the DDIG, basically the main qualification you need is to be a PhD candidate (someone who has passed their qualifying exams). The goal of the program is to fund PhD students to build upon their dissertation (ie. improve it, as suggested by the name).

This grant is not for early graduate students, who should really check out the Graduate Research Fellowship, which graduate students can only apply for in their first year (and second, if they have not exceeded a certain number of credits).

Why write a DDIG proposal?
The DDIG is a fantastic opportunity for PhD candidates in the US to get NSF funding for their research. The DDIG will fund research up to $13,000 of direct costs, which is more than almost all grants that graduate students can apply for that I know of, so you can do a lot with it to further your research and do more science. NSF is pretty broad with what it funds for the sciences, so a lot of different kinds of scientists can apply for it; because of this, the DDIG is quite competitive, but it still manages to have a funding rate of about 30% from what I've heard. Of course, because it is competitive, receiving a grant itself boosts your qualifications. I've also noticed that many of the job candidates that come to interview at my school tend to have gotten a DDIG, which almost seems to elevate it to a minimum requirement for tenure-track research positions. And of course, if your aim is to be a research scientist one day, you will need to be applying for grants in such a position anyway, and so if nothing else, writing a DDIG is good practice. Even though I'm lucky enough to be in a lab where my advisor has been positive about funding my research, I don't think that having available money is a good reason not to apply for a DDIG. After all, we're not in graduate school because it's easy.

What does NSF require for their DDIG?
Among other things, a DDIG needs to include what you've done so far for your dissertation and how it provides a context for the proposed work, explicit hypotheses that you will test with your proposed work, and what you propose to do for your research and how you will accomplish your goals. Additionally, like other NSF grants, a DDIG has an "Intellectual Merits" section, which from what I can tell discusses the scientific importance of your work, and a "Broader Impacts" section, where you talk about how you will expand outside of the lab and promote science education, such as to undergraduate students, primary and secondary schoolchildren, and laypeople. Specific to the DDIG, you need to write up a Context for Improvement, which talks about how your work not only improves upon your dissertation, but is also outside of work that your advisor is doing. I think this is to show NSF that you're not just looking for more money, since NSF may be less likely to fund a project if your advisor can already pay for it. There are also various other ancillary things that need to be included as well, such as proof that you are a doctoral candidate in the form of a signed letter from your department chair, letters of collaboration if your proposal includes collaborators, a data management plan, and others. A full list is provided in the solicitation.

Thoughts on how to write a good grant
So finally here are my thoughts. As I'm not a reviewer and I have been unsuccessful at getting a DDIG so far, perhaps my thoughts on how to write a good one may not be realistically helpful. But these are some of the main things I've been thinking about as I've written my DDIG.
  1. Get previously submitted proposals and the reviewers' comments on them, if you can. This will give you an idea of how to write and how not to write, and give you a basis for the organization. Even though the proposals I referenced were successful, the reviewer comments pointed out weaknesses too, not just strengths. This is one of the most important things, since I think having a reference to base your proposal after definitely helps to get you started, even on unrelated topics.
  2. Preliminary data, preliminary data, preliminary data. This grant is supposed to be an improvement grant, so you need to show what you've done so far and how it leads up to the proposed work. It also shows off your abilities as a scientist, which gives you credibility in your claims you can achieve your work. If you want to be submitting a DDIG in a year, then you will want to be working hard now, so you can have preliminary, or even published articles of your own to cite.
  3. You need to demonstrate that the work is feasible for you to do. Preliminary data can be helpful in proving that you can use the tools that you propose to use. If you don't have such data to show you can do the proposed work, despite the fact we're in graduate school to learn how to be scientists, reviewers may be doubtful of your abilities to do difficult tasks. If you lack preliminary data, other ways you can demonstrate that the work is naming collaborators or mentors that can help you do the work. You can also demonstrate your knowledge from the literature, but I'd imagine this isn't going to be as strong as demonstrating you have practical experience.
    Another potential idea that I thought of to demonstrate knowledge of data analysis was to analyze simulated data; since some data is expensive to procure, you may not have data yet to analyze for real. I'm not sure if reviewers will buy it, but I think something is better than nothing.
  4. Organization is important. There should be a logical flow, and you should be clear and concise. I have a bad habit of being too wordy. Reading out loud can help you trim the fat; reviewers need to read a lot of proposals and you don't want to be rejected just because your proposal was hard to read.
  5. Broader Impacts are important. It will help if you are already engaged in doing broader impact-related stuff already, to prove you have a track record of doing this. So like with your dissertation, actively engage in outreach over time so you will have a good track record to expound upon here; this really is the part that makes candidates stick out as not just researchers, but proactive educators.
  6. Explicit hypothesis testing is the framework that science uses. There is a lot of descriptive and exploratory science as well, but I don't think that reviewers tend to think these are the best to fund. Questions, hypotheses, and objectives are the types of things that need to be laid out clearly. This may differ depending on the field that you're working in.
A couple links
I'm not the only one to write about this stuff. Here are a couple links I've been referencing for writing my DDIG, and there are others around as well. The links below highlight certain things I don't mention or emphasize above, so they're worth a look.

Friday, August 16, 2013

Pufferfish Love Nests

Mysterious undersea circles...
Image by Yoji Okata
Male pufferfish Torquigener sp.
Image by Yoji Okata

Last year, images of these strange, undersea geometric structures first appeared on the internet. These rippling structures were discovered in 1995 by Japanese diver and photographer Yoji Okata. They are about 6 feet (2 m) across and are found off the coast of Japan in about 80 feet of water. Although initially mysterious, in 2011 it was found that these structures were built by little male pufferfish of the genus Torquigener, which themselves are no larger than about 5 inches (12 cm).
Male pufferfish at work building the nest.
The scale of the nest in comparison to the fish can be appreciated.
Image by Yoji Okata






It turns out the male pufferfish build these large nests to attract females to mate. Males going out of there way to do things to attract females is a familiar theme across animal life. Male bowerbirds are well known for building intricate nests to attract females. While nest-building is well-known among many species of fish, building the nest with these radial peaks and valleys, as well as decorating it with shells, has never been seen before.

In July, the scientific paper describing these nests and the pufferfish behavior appeared in the journal Scientific Reports, a relatively new journal published by Nature Publishing Group. But even cooler than that, it came with new pictures and videos! The appearance of the paper caused a small resurgence in social media on the discussion of the pufferfish. No one's really mentioned the videos, though, which is a shame because the paper is actually open access and so the videos are free to watch! If a picture is worth a thousand words than video is even better, right?

Male pufferfish building a nest, using his fins and body to dig valleys.
Photo by K. Ito

The only image of a pufferfish in the entire paper isn't anything new compared to the images that were already out there, but yet again demonstrates a male Torquigener hard at work building a nest. You can see how the male pufferfish uses its fins and body to dig the valleys into the sand. The male pufferfish will take seven to nine days to build the entire nest, but when attracting females is the game males across the animal kingdom do some pretty involved things.

The paper also describes the nest-building behavior more specifically, includes the steps for how the nests change over time and how the pufferfish behaves over time, and some video documentation.
Caption from paper: "Changes in the circular structure constructed by male pufferfish. (a) Early stage; (b) middle stage; (c) final stage; and (d) after spawning of the same circular structure of K1 in Figure 2. Photograph by Y. Okata on 23, 27, 29 June, and 6 July 2012, respectively."

The above image shows off the stages of nest-building. The nests start off roughly circular, and the valleys and hills get more pronounced over time (a-c). Not longer after spawning, however, the structure is left alone (d) and fades away.

Several videos are also available in the supplementary information, where you can the various male pufferfish digging behaviors. You can see how it uses its bodies and then waves its fins around, sometime sinking down into a spot and beating its fins to dig deeper pits. You can also see how the male pufferfish nicely fits in the valleys. The pufferfish keeps the center smooth with fine sand particles, and at the end of construction gives it a pattern (c). There's even a shot where it picks up stuff (which the paper says are shells) with its mouth and puts it down on the outer peaks. The last video is of the male attempting to court a female. Definitely very cool behavior to watch!

Sand particles from the nest the day before spawning and the day before hatching.
If the male is successful at courting the female, they will spawn and the eggs are laid in the central portion. Like in many fishes, the male will be the primary caretaker, and the female goes off on her own while the male hangs around for about 6 more days to care for the eggs, during which he stops maintaining the nest structure (d). Lack of maintenance of the nest also reduces the amount of fine sand particles in the center of the nest. Because of this, it's inferred that the complex nest building seems to be important for attractive females, but not so much for actually raising the young.

While the nest is already just pretty neat to look at and impressive to boot, according to the paper, the radial pattern, the central patch of fine sand, and the decoration of the nest with shells are apparently all characteristics never seen in fish nests before. Also, the peaks and valleys of the nest affect the flow of water, and allow for fine sand particles to flow into the valleys, which are then moved to the inner circle by the male. Interestingly enough, the male pufferfish don't re-use their nests. The authors hypothesize that this could be because the fine sand particles get used up, and so they have to find a new site to rebuild.

All in all, this is pretty cool behavior, but plenty of questions remain. The authors note that the specific reasons the nests are designed are unknown; why does the puffer build the nest symmetrically, or with certain numbers of peaks and valleys, certain peak heights and valley depths? How does it choose how to decorate the nest site with shells? There are further questions as well. What's the function of fine sand particles in attracting females? Do other Torquigener species build nests?

These types of discoveries also stress how little we still know about the deep. It was only two years ago when the puffers were finally observed building nests. We can be sure that other secrets remain to discover under the sea.

Wednesday, August 14, 2013

First Post

Photo by Damian Gadal
So here's my blog! Finally. Here it is, done, I've taken the first step.

This blog will be generally a science blog, but I can't promise that I won't dive down unrelated rabbit holes that catch my fancy. After all, it's my blog, I can pretty much do what I want with it.

I'm a graduate student studying fish biology at Auburn University. There are many great reasons for graduate students to blog. An article from Scientific American came out in April titled "Why grad students should be required to blog"; the author Maria Konnikova says that blogging gives quick and regular exercises to research a topic, synthesize it, and write it all down, skills which are useful to graduate students who will be doing just that. Shortly after, C. Titus Brown followed up with a post echoing this benefit, as well as how blogging gets himself thinking. A post even came out just today by Scott Wagers in Nature's Soapbox Science on the topic of how science blogging can help you learn.

And of course, blogging rolls into scientific communication, and there are tons of people saying that scientists need to communicate better. There's an ever growing number of scientists that are fighting the good fight: Steven Hawking, Neil DeGrasse Tyson, Brian Cox, Richard Dawkins, are some particularly notable contemporary scientists who are doing just that. If you think about it, what do these people have in common? They wrote, and not just for other scientists (as we are required to do under the "publish or perish" paradigm). As such, I will write too.

Photo by Tommy Huynh
These benefits and others have been getting me thinking I need to start a blog for quite a while. Of course, as a graduate student I'm fairly busy, but that's not the only thing that was stopping me. When I pursue things I tend to want to do them well. It's a little bit ambition and it's a little bit perfectionism. There is no shortage of good science writing on the internet nowadays. There will be a little more science writing now, and you can be the judge of how good it is.

Every great journey starts with the first step. So whether or not this blog ever becomes great, it won't become anything without a first post. Let's see where it takes me.