Coprolites and Paleofeces: The Importance of Knowing Your Shit

As research on microbial diversity – or as it’s now been rebranded, microbiomics – continues, microbiologists are studying more environments, often overlapping with other fields. One interesting tendril of this new expansion extends into archaeology, where biologists armed with the latest DNA sequencing tools are exploring the microbiomes of lost tribes and cultures. It’s fascinating work.

One of the most abundant and informative sources of new data is ancient feces. For most of human history, people crapped wherever it was convenient, dumping generous samples of their microbiomes in privvies, trash heaps, or communal piles. In many cases, these deposits got buried and ignored until archaeologists unearthed them centuries later. The result is a globally distributed trove of paleofeces (or paleofaeces if you’re writing for Nature), encoding the microbial, dietary, and genetic history of past cultures. For scientists, paleofeces are more informative and likely better preserved than pottery shards, building foundations, or even corpses. All glory is fleeting, but shit remembers.

Unfortunately, the microbiologists now flocking to study ancient feces seem to have missed a crucial lesson on terminology: many of their papers now refer to these samples as coprolites, rather than paleofeces. Stay with me, this isn’t as pedantic a distinction as it sounds.

Coprolite cufflinks.

Coprolite cufflinks. Don’t try this with paleofeces. Image courtesy Jessa Dow-Anderson.

A coprolite is a piece of fossilized feces. Fossilization is a chemical process that replaces most of the original sample with minerals, generally over a period of millions of years. It’s exceedingly unlikely that anyone could recover useful DNA samples from a coprolite. That’s why we don’t have the Apatosaurus microbiome already done, despite the abundant coprolites left by that enormous herbivore. Conversely, we don’t have many (if any) human coprolites around. We’re too new as a species.

Paleofeces are not fossils. They’re just old poop. As feces dry, sugars form a protective coating on their surface through the Maillard reaction. That’s the same chemical process that browns a steak, but it takes a bit longer for feces because they’re (hopefully) not being grilled. Thus protected, the fecal material inside the paleofeces can remain essentially unchanged for centuries. There’s no mineralization.

This matters for two reasons. First, scientists entering a new field should try to respect the terminology that field has already established. Archaeologists and paleontologists have good reasons for distinguishing paleofeces from coprolites – the two terms aren’t interchangeable, and they describe samples of radically different ages. Second, if we start conflating fossilization with other, faster forms of preservation, we’ll inevitably muddy an already confused discussion with the general public. We’re saying “fossil feces” formed in just a few centuries, but then turning around and telling young-earth creationists that dinosaur fossils must be millions of years old, because fossilization takes so long. Which is it?

So, fellow microbiologists: please get your shit straight. Thank you.

Pricing Freedom in Science Publishing

There’s been another dustup between advocates of open access science publishing and the world of traditional subscription-based scientific journals. That’s pretty much like having my old friends shouting at my boss, so yes, I’ve paid attention.

In case you missed it, the American Association for the Advancement of Science (AAAS), which publishes a very traditional journal called Science, is launching a new open access publication, Science Advances. AAAS also just hired a new publisher to oversee its journals, a fellow named Kent Anderson. Anderson has been a vocal critic of open access publishing. Perhaps you see where this is headed.

Sure enough, when Science Advances finally started up and outlined its requirements and fees, open access advocates began screaming. In the most prevalent open access business model, scientists pay the journal a fee to publish a paper, and in exchange the journal makes the paper available freely to the public rather than requiring an expensive subscription. Apparently, the page fees at Science Advances are higher than open access advocates feel is appropriate. They outlined this and other concerns in an open letter to the AAAS.

The letter makes four recommendations to AAAS. I have some problems with the first one, and it will take some unpacking:

1. [Offer] CC BY as standard for no additional cost, in line with leading open access publishers, so authors are able to comply with respective funding mandates;

The CC-BY license is the least restrictive Creative Commons copyright, allowing anyone to reuse, remix, resell, and otherwise adapt a piece of work however they want, so long as they cite the original author. That’s very attractive to grant-funded academics, whose careers depend on publishing highly-cited work. For academic scientists, it doesn’t matter who uses the work or how, so long as it’s been published and cited.

For publishers, it matters immensely. The ability to control commercial reuse of content is at the core of the traditional publishing business. Consequently, Science Advances uses a CC-BY-NC license by default, allowing people to reuse the work only if it’s for noncommercial purposes. If you want to reuse it commercially, you have to get permission from the AAAS. Authors who want their papers published under the less restrictive CC-BY license have to pay a higher page fee. The AAAS has determined what they think the commercial reuse of a scientific paper is worth, and attached a price to it.

This is where at least some of the open access advocates start to go astray. Much of the advocacy against the CC-BY-NC license is along the lines of “scientific ideas should be free” and “people have to be able to reuse data without restrictions.” Those arguments misrepresent what copyrights do. No copyright prevents anyone from reusing ideas or data. You can’t copyright ideas. It doesn’t matter if a research article is CC-BY or CC-BY-NC or All Rights Reserved, the only thing that’s protected is the presentation of the content. In other words, you can just put it in other words. I can write a book about a short guy who goes on a hike across a war zone to dispose of a piece of jewelry, and the Tolkien estate can’t sue me for it – unless I call him Frodo and give him a buddy named Samwise. This is why science operated just fine even when all the journals used maximally restrictive copyrights. The ideas and data have never been copyrighted, and can’t be.

Ultimately, the only coherent argument I’ve been able to get from open access proponents on this is that the CC-BY license will allow commercial indexing services to compile literature databases. Of course, they could also do that under the CC-BY-NC license, they’d just have to ask permission first, so that’s not exactly a strong argument. To be clear, I have no problem with scientists wanting to publish their work under CC-BY licenses. I do have a problem with scientists trying to dictate to publishers what such licenses are worth.

The “in line with leading open access publishers” bit refers to the apparent success of Public Library of Science (PLoS). PLoS finally broke even in 2010, and has turned a nice profit in the past four years, all while using the CC-BY license by default. That’s great, but it’s not the whole story. What finally made PLoS profitable was the PLoS ONE paper mill. Unlike a traditional journal, PLoS ONE doesn’t require that papers be groundbreaking or interesting, just technically valid. With the bar thus lowered, PLoS ONE cranks out out tens of thousands of papers a year. The page charges from that avalanche of papers catapulted the whole PLoS operation into the black. Saying that PLoS proves the sustainability of open access publishing is like saying proves the sustainability of the corner bookstore.

Now back to the open letter, the rest of which is easier to annotate:

2. [Provide] a transparent calculation of its APCs based on the publishing practices of the AAAS and [explain] how additional value created by the journal will measure against the significantly high prices paid by the authors;

Read: Disclose proprietary business information so your competitors can see.

3. [Remove] the surcharges associated with increased page number;

Read: Eat the extra costs when we want to blather on for twenty pages.

4. [Release] all data files under CC0 (with CC BY optional), which has emerged as the community standard for data and is used by leading databases such as Figshare and DataDryad.

I’m less familiar with data release standards than text copyrights, but I think this is another version of the same demand made in (1).

At this point, it probably sounds like I oppose open access. I don’t. It’s wonderful to be able to read the latest papers without having to jump over paywalls or pester the authors for PDFs, and it’s great that I can link to papers and know that readers can access them. But all of those things are possible without an absolutist insistence on a CC-BY license.

As someone who has run a small but consistently profitable business for the past sixteen years, I also find it galling to see a crowd of academics acting as if they’re qualified to tell a publisher how to price a publication.

I have a dog in this fight. As I implied in the first paragraph, I work for some traditional publishers, including the AAAS. This blog is completely independent of them, so don’t interpret this as any kind of official statement; they’re quite capable of speaking for themselves. I’ll just raise a few questions for researchers to ponder.

When you pick up a copy of Science or Nature, and see a cool graphic on the cover, then news articles in the front, then perhaps a special section of additional coverage on some issue related to science, and then finally the research papers, what parts do you enjoy? Do you know who paid the artist for the cover? Any idea what it costs to put together a regular magazine news section? Would you like those parts to go away? How about the whole print edition – can we chuck that too, and go exclusively online?

The reason I ask is that so far, that’s been exactly what most open access journals have offered: research articles, served online, hold the extras. Everyone I’ve spoken to in the open access movement has said that they appreciate science journalism and would love to support it. To date, none have done so.

I don’t believe open access advocates are trying to undercut science journalists and illustrators, any more than the developers of Craigslist set out to kill newspapers. But if researchers continue to make ideologically-driven demands on publishers without understanding how those demands might affect the business, that could be the result we get.

Colony Collapse Disorder: More Dead Bees, More Sloppy Science

I’ve gotten some requests to revisit a blog post from a couple of years ago, as the authors of the paper I eviscerated in that essay have published again on the same subject. If you don’t have time to re-read that post, the upshot was that some researchers did a poorly-controlled experiment with beehives and insecticide-laced artificial nectar, then made lots of wild headline-grabbing claims about how they’d found the cause of colony collapse disorder (CCD).

Having been stung by my withering criticism – or perhaps having simply completed a high school-level course in experimental design – the same team is back again with the same argument. Their new paper appears in the same highly sketchy journal, but it’s a bit better than the previous one. That’s not to say the data come anywhere near proving what they’re trying to claim. However, they did at least do a couple of additional controls.

For example, they used two different artificial nectars, high fructose corn syrup (HFCS) and a sucrose solution, and analyzed both beforehand to see if they were already contaminated with neonicitinoid insecticides. They weren’t. That was one of the things I had called for in my previous criticism. The lack of detectable insecticide residues in the HFCS actually undercuts the theory they put forth in their previous study, but let’s let that slide for now.

The investigators also tracked the outdoor temperature throughout the study, accounting for the extreme weather variability we get here in Massachusetts. The 2012-2013 winter was considerably milder than the 2010-2011 season in which the previous study occurred. Otherwise the protocol was pretty similar, with experimental hives getting artificial nectar laced with various quantities of insecticide and controls getting unadulterated nectar. The experimental hives fared worse.

So that’s the smoking gun, right? Well, that’s certainly what Lu et al. seem to think:

The results from this study not only replicate findings from the previous study on imidacloprid and extend to clothianidin, but also reinforce the conclusion that sub-lethal exposure to neonicotinoids is likely the main culprit for the occurrence of CCD.

But the experimental hives didn’t develop CCD. They had fewer bees in them at the end of the winter and produced less brood, and six of the twelve treated colonies died compared to only one of the six controls, so the treated colonies do seem sicker. However, the dead hives contained many dead bees, and the surviving insecticide-treated hives had little or no brood and/or no queens. In CCD, the bees abandon the hive, leaving behind brood and a queen but no dead bees. What Lu et al. are doing here is equivalent to looking at a heart attack and calling it cancer. Insecticide-laced nectar may indeed make beehives sick, but there’s no evidence in this paper that insecticides cause CCD.

The new work also suffers from one of the other major flaws of the previous study; the entire project took place in New England. Yes, this is a lovely part of the country, but the commercial hives that seem to be most susceptible to CCD don’t stay in one place. They get loaded onto trucks and driven thousands of miles north and south to provide pollination services to crops along the way. They experience a sort of eternal summer, and all of the hives in the Lu et al. study did just fine in the summer – it was winter that killed them. The experiment just isn’t a very good model of reality.

There are other groups publishing papers on this subject, though. Many of them are even doing good science. Most are much more circumspect about their claims than Lu et al., which is appropriate: the whole CCD story is clear as mud right now. Does sub-lethal insecticide exposure cause CCD? Nobody knows. But we can be certain that making bold claims from shoddy data won’t get us any closer to an answer.

How to Identify a Labor Shortage (Hint: It’s Probably Bullshit)

A little while ago, I saw a news story about the major pilot shortage now facing the airline industry. No, it wasn’t a tasteless (and premature) MH370 joke. It was a serious argument advanced by straight-faced industry representatives at a Congressional hearing. According to these experts, a wave of pilots recruited decades ago is now retiring, and airline routes are simultaneously expanding, making it impossible to fill all the cockpits. The punchline, which you probably see coming, is that they want Congress to relax some “burdensome” regulations to make it easier for the industry to hire more pilots.

It’s total bullshit. In fact, there are tens of thousands of fully qualified pilots who aren’t currently working for the airlines. The labor pool is huge. Considering that “airline pilot” is about the most glamorous job this side of “movie star,” why aren’t these folks jumping at the chance to strut through the terminal in leather jackets? You probably see this coming, too: the pay and working conditions at airlines these days suck. There’s no shortage of pilots. There’s a shortage of pilots willing to work for cheap. This is Economics 101: raise the pay and improve the working conditions and the “shortage” will evaporate.

I was reminded of that story when I saw Michael Teitelbaum’s thorough and well-written exploration of the “shortage” of scientists and engineers. You’ve definitely heard the official line, espoused by everyone from the President down, that America is facing a crisis in scientific leadership. With a generation of Sputnik-era researchers retiring, we must start training replacements and developing new government initiatives to keep our airline transportation system scientific research enterprise running. See where this is headed?

As Teitelbaum points out, it’s hard to square this account with the reality of scientific employment trends. He’s not the first to notice the discrepancy, either. Beryl Benderly penned a nice summary and history of the same argument two years ago for the Columbia Journalism Review, and within the research community the sorry state of the job market has been a running joke for over a decade.

The scientist and pilot “shortages” share the same dissonance between employers’ claims and employees’ reality, but they have different causes . We have plenty of scientists willing to work under labor conditions that would make a Foxconn executive drool. They’re called postdocs. You can’t swing a dead cat in a research lab without knocking over a dozen of them, all of whom are qualified to run their own labs. The problem is that there’s nowhere near enough money flowing into science to employ that many researchers. We lack science, not scientists

It’s as if the airlines decided to have only a single flight each day from New York to Chicago, and then claimed that they needed more pilots to improve the service. There would indeed be a shortage of flights on that route, but throwing more pilots at the problem wouldn’t fix it. We’d need more planes.

Unfortunately, the “labor shortage” story never seems to outlive its welcome. Over the years we’ve heard about a lack of nurses, doctors, teachers, and even lawyers. All of these scarcities have been completely fictional. As a public service, I now offer this simple guide for reporters who are about to write another “shortage of x” story:

1. Ask who’s promoting the story. If an industry, sector, or employer is the main source, then you should presume that the labor shortage is false until clearly proven otherwise. It’s overwhelmingly more likely that the industry or employer just isn’t willing to pay market wages for the workforce they want. According to Economics 101, any job can be filled if you set the price high enough. This question would have immediately spiked the pilot, nurse, engineer, and doctor shortage stories, for example.

2. If you’ve established with certainty that there really are highly desirable jobs in the labor-starved industry, ask how many of those positions have gone unfilled in the past year solely because of a lack of qualified applicants. This spikes the scientist story and probably the lawyer one.

3. If the source answers (2) by saying “well, the positions are filling now, but we’re about to have a huge wave of retirements that will lead to a massive crisis,” tell them to call you back when that happens. Don’t expect to hear from them again.

4. In the event your story survives steps 1-3, and you’ve confirmed that awesome jobs with great pay and benefits are begging for workers, apply immediately. It’ll beat the hell out of what you’re doing now.

Public Outreach: Results and Discussion

Three videos and a month after I threw down a gauntlet, in front of my fellow science bloggers, let’s look at how it went.

The first video is the most watched. It’s approaching 300 views, which is about 299 more than I expected it to get but still pretty close to obscurity. Based on the data YouTube provides in my account dashboard, most of the viewers seem to have reached it through this blog, my Twitter feed, or TWiV. The other two videos have over 100 views each, mostly coming from the same referrers. Lots of people have told me they like these videos. All of those people either live here inside the science ghetto or visit it regularly.

Studio setup.

Production shot from Turbid Plaque Studios.

I’ve failed to reach the audience I was aiming for, at least so far. That doesn’t surprise or upset me. Internet media success is a lottery system, where a few entries win big and most lose. Internet success or failure is not a measure of value, utility, or technical quality. If you’ve paid any attention to the sorts of things that “go viral” online, you understand that.

As I said in the original post, my other goal was to spur others to try to explain science to a broader audience as well. That challenge still stands. You don’t have to copy what I did. The only rules are that you should try to explain how science works, and do it at a level that’s understandable by people who don’t read science blogs or follow science news. A comic strip, a catchy song, or even a poem might work.

Consider this: if you ask an American of my generation to describe our legislative process, there’s a good chance we’ll sing you a song. Ask a typical American how science works, though, and odds are you’ll get a fumbling ramble that tapers off into an excuse. But the fundamental process of science is more important and actually easier to understand than the workings of Congress.

Sure, specific scientific findings can get ridiculously complex, but that’s not what people really need to appreciate. I couldn’t care less whether the average person can explain how Sanger DNA sequencing works, but being able to articulate what’s special about science and how to evaluate factual claims is a basic life skill. Our educational institutions have apparently failed to teach it adequately, so let’s pick up the slack.

Even if the online media system is a lottery, tickets are cheap and someone will eventually win. As my videos illustrate, you don’t need fancy equipment, a big payroll, or even any special talent to play this game. If you have any of those things you should certainly deploy them, but they’re not required. All you really need is a bit of persistence and the ability to suppress your fear of failure. Any science blogger is automatically qualified.

If you pick video as your medium, put a little effort into learning how to shoot it. I’m no expert, but given the feedback I’ve gotten I gather my videos aren’t completely awful, so here’s my advice for other aspiring science filmmakers.

Start by reading this book. It teaches exactly what the title says, quickly and effectively.

Next, write a script. If it’s longer than 1,000 words, trim it or plan to break it into parts. You’ll want to speak at 100-150 words per minute, perhaps with brief gusts to 200, and any video over 10 minutes (1,000 words at 100 wpm) is pretty much doomed online. Edit the script. Edit the script again. Obsess over the script. Don’t worry too much about how you’re going to illustrate the concepts at this point, just try to explain them as succinctly as possible. Imagine someone will be listening to the audio by itself, and focus on making the narration the best it can be.

Now plan the shots. The simplest shooting plan is to memorize the script or use a teleprompter, and speak directly into the camera in a single take. That’s been the standard format for the evening news for half a century, and you probably have all of the necessary equipment already. The most important thing about a monologue video is to establish a connection with the audience. Look at the lens, not your notes, and dress like someone you’d want to talk to at a party. And please, please pay attention to the lighting. A cheap hardware store clip-on reflector lamp with a high-wattage “warm white” CFL bulb, mounted about 45 degrees above and to one side of your face, will improve your image quality enormously. If the direct light seems too harsh, try aiming the lamp at a white ceiling or wall to bounce it in a more diffuse pattern. If you use a visual aid or a whiteboard, be sure it’s easy to see and properly focused.

My strategy was obviously a bit different, but it still wasn’t very complicated. My total expenditure for the three videos was less than $100. I already had the tripod, webcam and laptop, so I just picked up iStopMotion, a reasonably priced and very capable animation program. The “infinity” background is a roll of sketch paper taped to the wall, the lighting is a pair of clip-ons I found kicking around the back of the basement, and most of the cast and props arrived in a Lego minifigure package. Additional players appeared courtesy of my daughter.

Whatever approach you use, learn from my error and have someone you trust take a look at your work before you put it online. That’s especially important if you’re working in a medium other than your usual one; I’m now keenly aware that what works fine in writing may set the wrong tone in a video.

So there go all of your excuses. Use what you have and give it your best shot. When you’re done – whatever medium you’ve used – please drop me a line through this site or on Twitter, and I’ll do what I can to help promote your work. The hashtag for this little challenge is #thinklikeascientist.

Sorry About That

Yes, I deleted the video that appeared in the previous post. Sorry about that. After re-watching the final version and getting some objective feedback, I realized that it missed the mark. I tried to cram too much into too little time, and didn’t quite hit the right tone for the target audience.

If you enjoyed it anyway, thanks, but as I explained initially I’m not really aiming these videos at regular readers of this blog. This is my attempt to reach the rest of the crowd – the folks who don’t understand why science is different from other ways of knowing things, or how it really works. I want to reach people whose last contact with “science” was a pile of seemingly unconnected facts they had to memorize for a standardized test in high school. I’m not optimistic about my chances, but I do intend to give it my best shot.

So stay tuned. We’ll be right back.