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.

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.