Frustrations with Jenoptik, and a better photomicrography solution

In my lab, I have a nice, inexpensive setup for capturing microscope images. About 10 years ago, I bought a dedicated photomicrography system from Jenoptik, a cooled CCD camera with a software package called ProgRes. It did what I needed, which was basically to provide an easy way for students to see on the computer screen what they were looking at on the microscope, and also to capture time lapse recordings of developing embryos. It had other useful features, like being able to calibrate the images, automatically annotate them with scale bars, etc. I had quite a few students learning how to easily get scientific-grade images out of this thing.

“Had”. The system has a few huge flaws: like most of the companies making these gadgets, the scientific side feels like a low-profit sideline for them, and most of the money is coming out of industrial imaging applications. That means poor support for us people who are on a tight budget who aren’t going to buy a hundred cameras for our factory, and that means you’re screwed when something doesn’t work. The software for this system breaks every time there’s an update to the MacOS. Like, it runs, but it doesn’t connect to the camera, so all I see is a blank screen. And the software hasn’t seen an update since 2010.

The last time this happened, they sent me a camera firmware patch that had to be run from a PC, not a Mac, and a slightly patched version of the application. It got it working again, but I can see the writing on the wall: as far as Jenoptik is concerned, they are done, they’ll continue to sell off their inventory as long as suckers are willing to buy it, but it’s not as if they’re going to invest any further resources into maintenance and development for mere biologists. It’s frustrating. The system is currently dead and useless.

So I’ve been exploring alternatives…on a tight budget. I’ve come to the conclusion that simple consumer grade cameras are far better bang for the buck. They won’t work if you’ve got some specific, narrow application, like low-light fluorescence imaging, but for the kind of general transmitted light microscopy I do, they’re better: higher resolution, more control, more imaging options. The only thing they lack is that one touch of a button capture of an annotated image.

I was tinkering this morning. Canon Rebel cameras come with something called the EOS Utility, which allows you to connect the camera with a USB cable (or in some models, over wifi) and control everything — aperture, exposure, focus, ISO, I mean everything, and take pictures with a click of a button. You can also set it up to do time lapse with intervals as short as 5 seconds (my usual is one image every 60 seconds, so no problem), and it was impressive to watch. It takes a photo, downloads it to the computer, and shows a preview image, and you end up with a folder of 30mbyte RAW images, which is just what my camera is set to take, I could go to a lower resolution. I’ve got tools to convert those to mp4s, and I also have tools to do bulk processing.

It’s somewhat more complex than a dedicated software solution, but I have smart students. They can master this easily. And the output is much nicer.

Now the next step: paying for this. Anybody want to buy a Jenoptik C3 camera? I can’t use it anymore, but maybe they’ll be better about keeping it updated for Windows machines. Otherwise, it’s going to get stuffed in a drawer and forgotten.

I can get a Canon t5i body (I don’t need lenses) for a few hundred dollars, and even the nice t7i for a bit more, and I’m happy with used cameras, too. It’s about a fifth of the cost of my Jenoptik! I may have to write an in-house grant proposal to scrape up that much, or if there’s anybody out there that has an old Canon sitting in a closet, I’ll take it off your hands. I’ll even put a label on it naming it after you: the [your name] Spider Cam! What an honor! I know some companies would dream of this promotional opportunity, but I’m sorry, I won’t accept the Exxon Spider Cam or the Facebook Spider Cam. I do have limits.

Until I can set up a dedicated lab camera, though, I’ll make do with my personal camera. If anyone out there is setting up a lab and need a low-cost camera system, I’ll offer a word of advice: steer clear of Jenoptik.

What’s with these MFing spiders in this MFing lab?

There hasn’t been much fertility in this lab, and I don’t know what’s going on. The spiders are getting weird and lazy. Here’s Yara (last seen here), who has been building thick clumpy cobwebs and also assembling debris into a nest — she’s partly obscured by a wood shaving here. The strange thing is above her, and to the left.

Those are unhappy looking eggs enclosed in a thin web, not an egg sac. I can say with some confidence that they’re not going to develop.

This is awkward and annoying. Next week I’m going to sterilize cages with alcohol and set up new frames and repopulate, hoping this problem will go away. Maybe they’re stressed? Maybe they’re just old and lapsing into decrepitude?

Is this how an innocent man responds?

I already wrote about the data-faking scandal with Jonathan Pruitt, but the one thing I was missing was any explanation from Pruitt himself. Science just covered the matter, and got a statement from him.

At first, he was in the fray tweeting—but no longer. “There are so many voices and they are so loud and diverse, there’s no way to address it.” Instead, he says he’s focusing on his fieldwork, setting insect traps across the South Pacific before and after cyclones hit to learn how different species are affected by these tremendous storms. Last year, he reported on work in which he collected data on spiders before and after a U.S. hurricane. It’s one of the papers now being scrutinized.

That’s right, there are more papers under investigation, and he’s collecting more data that will have to be carefully scrutinized. What he ought to be doing, if he’s innocent, is working to validate his previous work, not flying off to the South Pacific. His career is in dire peril, and he knows it. Instead, he seems to have resigned himself to being caught and his future is bleak.

Pruitt says he has no expectations that he will be able to continue in behavioral ecology, saying he knows he has lost the trust of his colleagues about his data. But these cyclone data will be useful no matter what happens, he says. “If I’m on fire and my longevity is [short], I will bequeath them to another researcher.” He is concerned, however, that as each retraction happens, even innocuous mistakes in his data or experiments will be cause for more retractions. It’s a worry that Dingemanse shares. Such careful inspection of data will often turn up something, no matter how well collected and compiled, he says. “If you looked at my data [this way], you might also come up with causes for concern,” Dingemanse says.

What? No. I’ve got a pile of data I’m sorting through right now, and I’d happily let anyone look at it. It’s just tables of counts of spider species in various locations, but I’ve got a paper trail — all the on-site notes for each site — and the numbers are honestly recorded. I have no fear that it can be misinterpreted.

Also, the colleagues who made this discovery have a vested interest in not seeing causes for concern, since they’ve had to retract published work. It has cost them to report the problems. You know they tested the heck out of the data set before making that difficult decision.

Also, there’s this little tell.

Simmons has spent the past 3 days poring over the 11 papers Pruitt has written for his journal, going back to a data repository now mandated by his journal and others to check raw data. Yet he laments that the initial hashtag—#Pruittgate—is too damming and thinks “we need to, as much as we can, avoid a witch hunt.”

Jeez. The “witch hunt” accusation has become as predictable and useless as the “-gate” suffix.

Scallops aren’t animals? Is the author not a journalist?

Oh, man. This is bad. An article on Vice asks, Are Scallops Vegan?, and if you know the rule of questions in headlines, the answer should be “NO”, but this article actually plumps down on the side of “maybe?”

In the case of bivalves—that is, sea creatures with a hinged shell, such as oysters, clams, mussels, and scallops—the line between plant and animal, especially in regards to cooking and eating, remains unclear. “But, they’re alive,” someone may say who has seen the pulse of oyster flesh or the slow opening and closing of a scallop shell. But so are plants—every carrot you slice and every apple you bite into was once alive, and begins to die as it’s removed from its stem or roots. And while some bivalves, like scallops, open and close their shells by using an adductor muscle, plenty of plants can also independently move.

Being alive is not an adequate criterion — it doesn’t distinguish anything in biology. By definition, “life” is “alive”. But whether molluscs of any kind are animals or not is unambiguous — yes, they are animals. They are triploblastic, bilaterian protostomes, members of the lophotrochozoan clade in this diagram.

It’s always a good idea, O Journalist, that when you have a biology question you should ask a biologist, and not just a random layperson you meet at Whole Foods. Or at a local seafood restaurant.

I, a lapsed vegetarian, first heard the argument that scallops could be considered vegan during a recent lunch at Greenpoint Fish & Lobster Co., a Brooklyn seafood restaurant dedicated to sustainability. Though a spot with fish tacos and daily oyster selections may not seem like a vegan’s first pick for dinner, co-owner Vinny Milburn told me that the restaurant has numerous vegan regulars who visit to eat scallops and other bivalves, justifying their consumption, ethically and environmentally, with science. “They feel okay about it because it doesn’t have a central nervous system,” Peter Juusola, general manager at Greenpoint Fish told me.

Uh, they’re not vegans. They’re not even vegetarians. They’re pescatarians. Which is perfectly OK, I’m more of a pescatarian myself, because while I’ve been cutting back, I do eat seafood now and then. I’m not judging them, except to point out that mislabeling yourself because you’re pretending to be more ethical and environmentally sensitive than you actually are is dishonest and a bit yucky.

See that diagram above, with the colored bits labeled protostomes and deuterostomes? All of the members of those groups have nervous systems, every one. So do the ctenophores and cnidarians, although they tend to be more diffuse and lacking in specialized regions. Sponges do not have a nervous system, although their cells do communicate with one another using protein networks that have evolved into our nervous system. Arguing that vegans get to eat anything lacking a nervous system, a dubious claim, would mean you only get to eat sponges. If having localized collections of neurons that function as a kind of primitive “brain” qualifies as an exclusion, you also get to eat jellyfish.

Molluscs do have a central nervous system in the form of a couple of ganglia. Those count.

The killer counterargument, as far as I’m concerned, is that scallops have eyes. You’re not a vegan if you eat something that can look back at you. They’re even pretty blue eyes!

This does not seem to persuade some people, who ignore the physical evidence.

Conclusive evidence on whether bivalves, or even crustaceans, for that matter, feel pain, has yet to surface, but for starters, they “do not have a brain,” Juusola says, demonstrating with his fingers that when a scallop opens and closes, that’s a reaction due to a nervous system, not their nervous system calling out pain or danger.

They have multiple ganglia, which can be demonstrated anatomically, but apparently the argument from “opening and closing fingers” refutes the observable existence of coordinated, interacting sets of neurons.

I’m going to have to remember that one. When someone questions me on whether Trump has a brain, I’ll just wiggle my fingers and say, “Obviously, no. See my fingers?” In other good news, we can also legitimize the claim that the rich are brainless non-animals, allowing vegans to eat them.

So what are you waiting for, vegans of the world? Dig in!

When leadership matters

There are legitimate fears of a coronavirus pandemic — don’t panic, it’s an emerging threat, not a full blown emergency — and that’s when it’s a good idea to prepare. We should have a strong medical infrastructure, plans in place, people organizing now, just in case. In the US, however, our plan to respond to potential medical threats is a shambles.

For the United States, the answers are especially worrying because the government has intentionally rendered itself incapable. In 2018, the Trump administration fired the government’s entire pandemic response chain of command, including the White House management infrastructure. In numerous phone calls and emails with key agencies across the U.S. government, the only consistent response I encountered was distressed confusion. If the United States still has a clear chain of command for pandemic response, the White House urgently needs to clarify what it is—not just for the public but for the government itself, which largely finds itself in the dark.

Who is to blame for the chaos? It seems Obama had a thorough, if flawed, response team in place. One man and one party have been actively working to dismantle the entire system.

In the spring of 2018, the White House pushed Congress to cut funding for Obama-era disease security programs, proposing to eliminate $252 million in previously committed resources for rebuilding health systems in Ebola-ravaged Liberia, Sierra Leone, and Guinea. Under fire from both sides of the aisle, President Donald Trump dropped the proposal to eliminate Ebola funds a month later. But other White House efforts included reducing $15 billion in national health spending and cutting the global disease-fighting operational budgets of the CDC, NSC, DHS, and HHS. And the government’s $30 million Complex Crises Fund was eliminated.

In May 2018, Trump ordered the NSC’s entire global health security unit shut down, calling for reassignment of Rear Adm. Timothy Ziemer and dissolution of his team inside the agency. The month before, then-White House National Security Advisor John Bolton pressured Ziemer’s DHS counterpart, Tom Bossert, to resign along with his team. Neither the NSC nor DHS epidemic teams have been replaced. The global health section of the CDC was so drastically cut in 2018 that much of its staff was laid off and the number of countries it was working in was reduced from 49 to merely 10. Meanwhile, throughout 2018, the U.S. Agency for International Development and its director, Mark Green, came repeatedly under fire from both the White House and Secretary of State Mike Pompeo. And though Congress has so far managed to block Trump administration plans to cut the U.S. Public Health Service Commissioned Corps by 40 percent, the disease-fighting cadres have steadily eroded as retiring officers go unreplaced.

But here’s what worries me most: the systemic incentive to continue to wreck what system we have. There is no price the Republicans will have to pay. People will die, the country could be thoroughly disrupted, and the demagogues will just blame it all on the Democrats, or the Chinese, or Islamic terrorists, or filthy disease-ridden immigrants, and people will want to believe them, and everything will just get worse. In fact, catastrophe will strengthen their grip on the country.

Heckuva job, Trumpy.

It’s an anniversary!

Ten years ago today, the Lancet issued a formal retraction of Andrew Wakefield’s notorious bogus paper claiming a link between MMR vaccinations and autism. The paper was wrong, it was shoddily done, and the work hasn’t been replicated.

Ever since, Wakefield has been living in shame, no one treats him as an authority anymore, and of course no one would claim that vaccines cause autism anymore.

Why do scientists cheat?

I am dismayed at this emerging story about fraud in science. It stars Jonathan Pruitt, a professor at McMaster University who studies variation in individual behavior and how it affects group behavior. I’d heard of him since he’s doing a lot of work in social spiders.

He built up several productive collaborations, in particular with Kate Laskowski at UC Davis, sharing data with her that she used in several publications. That’s where the story turns dark, because Laskowski later examined the data in more detail and found multiple examples of blocks of data having been duplicated, padding the data set with more replicates than were actually done. He’d actually passed her a poison pill that tainted all the work they’ve done together; her papers are no longer trustworthy, and she has retracted them.

Laskowski is being heroically restrained in her reaction to this betrayal — I’d probably be throwing things and saying lots of not-nice words. Pruitt also seems to be peculiarly blasé and detached from the problem, conceding that there are serious problems in the data set, but not offering any explanations about how this has happened (again, if some of my data were found to be bogus, I’d either be furious and trying to track down the source of the bad data, or, if I were guilty of doing the duplications, I guess I’d be trying hard to deflect.)

There’s a lot of discussion and dissection of this issue going on, and most of it seems to be rightly concerned with making sure Pruitt’s coauthors aren’t hit with serious splash damage. At some point, though, there has to be a reckoning, and the source of the contamination tainting so much work will have to be dealt with. So far, everyone seems to be strangely cautious and circumspect.

I will not say Jonathan Pruitt is a victim, but he is part of the tragedy. Will we ever really know what motivated him? I decline to guess. He burst on the animal behavior scene with his first paper in 2008 and immediately began publishing at such a prolific rate that in another year or two he would have overtaken my own 41 year career in numbers of publications. This output got him a lot of academic success leading to his current position (current as I write anyway) of Canada 150 chair at McMaster University.

What Jonathan Pruitt produced was so far beyond average, it is hard to believe anyone would feel pushed to that level. But others feel pressure to produce in academia.

Fine. I’m not involved in any of this concern, so it’s not my place to say how the victims ought to respond. But I would say that the slower the build-up, the bigger the explosion, and so far this is looking to be a truly ugly meltdown at some point in the near future. Keep an eye on Jonathan Pruitt, there will be a supernova at some point soon, and not the good, pretty kind.

I’m mainly dismayed at the failure of scientific ethics. You don’t make up data! Ever! Every year I’m in student labs, explaining to students that “your data is your data” (I literally say that a lot, I’m afraid), and if your experiment didn’t come out the way you expected, or the data are ambiguous about what the one true Answer is, your job isn’t to make the data fit, it’s to rethink your work, track down sources of confusion, repeat the work, analyze the results appropriately, and if it doesn’t support your expected answer, revise your expectations.

That’s easy for me, though. The students don’t have a publication in Nature or a tenure decision in their favor, so they’re lacking all that unscientific pressure to get the neat, tidy, snazzy answer with beautiful p values.