Tuesday, September 12, 2017

Current sea surface temperatures

Seeing this, it seems somehow unsurprising that we got three simultaneous Atlantic Hurricanes, including two that repeatedly made landfall as Major hurricanes. That many millions of square miles of high-energy water are not natural, and not good news.

Friday, August 04, 2017

Meiosis kills! (Now in print, and video)

Scientists are rarely dispassionate about their research. Why spend years trying to figure out the fine details of something you have no interest in? Before my wife and I lost two pregnancies, I had thought abstractly about the question of why developmental failure is so common across plants and animals, but it wasn't personal. I was interested in the fact that dying before reproductive age means an individual does not get to pass on whatever traits caused it to die. In other words, natural selection should quickly remove any heritable trait that commonly causes developmental failure. At the same time, pretty much any organism loses some of its offspring, implying some broad based mechanism WAS commonly causing developmental failure. I even went so far as to publish a review article focusing on what this mechanism might be.

But once developmental failure became personal, I wasn't just interested, I needed to know.  

The result of that impulse was just published by Proceedings B, one of my favorite scientific journals. 

In addition, I worked with Sarah Friedrich, the extremely talented Graphics Specialist in my department, to make this video explaining the science in public-friendly ways:

Wednesday, July 26, 2017

I, lichen.

This fungal individual makes lots of complex structures, on which microbes live. So do you.
A lichen is an ecosystem. It consists of a multicellular fungus that provides the gross structure of the lichen, and a community of microbes that live in and on that structure, including photosynthesizers.

A human is an ecosystem. It consists of a multicellular animal that that provides the gross structure of the human, and a community of microbes that live in and on that structure. A human, unlike a lichen, generally cannot photosynthesize. 

We usually see humans as individuals, but lichens as ecosystems. In the last few years some scientists have advocating deep thought about humans as ecosystems. There has been very little deep thought about lichens as individuals.

Friday, May 19, 2017

Me as a peer reviwer

I find it painful to read a very critical peer review, even if it clearly intended to be constructive. This is somehow especially true when I am the reviewer. That I've just written a rejection-worthy critical review, and seem to do so fairly often (always accompanied by specific suggestions for improvements) is part of my job, but not one I relish.

Friday, March 24, 2017

My brother and the failure of TrumpCare

Why, please ask yourself, do the Republicans, after years of wishing to replace the Affordable Care Act, have no replacement even they can support? One clear answer is illustrated by my brother, Jason Levitis, an unsung American hero. I've mostly kept quiet about this, because he has, but the cat is out of the bag, Jason is out of government, and the time has come. In his recent article in Vox, his byline reads, "Jason A. Levitis is a senior fellow at the Solomon Center for Health Law and Policy at Yale Law School. He led ACA implementation at the Treasury Department during the Obama administration." That's all true, but Jason was on this long before the ACA was law. He was the single most frequent visitor to the White House throughout the entire Obama administration, and he wasn't there for the tour. I feel safe in saying that no one in the world knows the Affordable Care Act better than my brother, or has thought more deeply about why each part of it functions as it does. When President Trump said, "Nobody knew health care could be so complicated," my response was, "actually, my brother knows exactly how complicated."

I can clearly remember Jason telling me that he was going to reform the U.S. healthcare system in the year 2000. He and I were both recovering from injuries, limping through the newly reopened Hayden Planetarium at the American Museum of Natural History. Both of us, as patients, had been screwed by the healthcare system. Our parents, both physicians, had recently retired early because they just couldn't stand being part of that system anymore. As we crept along, two very similar looking young men on canes, to an evening planetarium show, he explained matter-of-factly that he had decide that the most important thing he could do was fix American Healthcare. This, he explained, would require years of work to understand the system, probably a law degree, the building of connections in the policy world, and an activist White House brave enough to succeed where "HillaryCare" had failed. His younger brother, I had to admit he was talented enough to carry out each step, and still found it improbable.  As we watched billions of years of galactic evolution whiz around us, I wondered how long my always swirling brother could focus on this very long-term plan.

Seventeen years later, he is still following his plan. He built his detailed understanding of the system as a Senior Analyst in the health economics department at the Greater New York Hospital Association. Then he got his law degree at Yale. Then he built connections and expertise in health law at Connecticut Voices for Children. He moved from there to being a Senior Analyst and Counsel at the Center on Budget and Policy Priorities, a DC think tank that is just as wonkish and unflashy as its name implies. He testified before various state legislatures about earned income tax credits and other stuff that I only understand because he explains it well, and I thought his singular focus on health policy had melted. I was wrong. He had become a respected part of DC health policy wonkdom, and with his co-wonks was working up a national policy resembling Massachusetts’s health reforms, aka RomneyCare. By 2008, when Obama ran for president, their framework was far better developed than the final TrumpCare bill that failed today.

President Obama appointed Jason as Senior Advisor to the Assistant Secretary for Tax Policy, Department of the Treasury. In practice, Jason worked day and night, often over 100 hours a week, writing the text of the bill that would come to be known as the Affordable Care Act. He would come to an important family event and would pull out two Blackberries, communicating on both simultaneously with the half dozen other people writing the bill with him. He would go into the bathroom and be arguing with somebody about the wording and punctuation of some sentence that was likely to be challenged in court.  He fought for fine policy details that his training in both law and economics told him would actually help the American people, not just make good TV. He sat next to Obama's people as they testified before Congress, feeding them the details they needed to give full answers. He undertook endless last-minute rewrites to try to meet the demands of that one last wavering Democratic Senator. Once the bill became law, he spent years writing the regulations needed to implement it. He, with a few close colleagues, is the policy brain of the Affordable Care Act.

I tell you all of this not only to praise my brother, although he clearly deserves it. The Affordable Care Act has brought health coverage to millions of Americans, slowed the increase in healthcare costs, spurred needed innovation and raised standards across the American healthcare system, and in the process saved countless lives. My purpose here is not to litigate the merits of the law, but to point out the intellectual rigor at the heart of the Affordable Care Act, and contrast it with the mushy sloganeering and flailing demagoguery that is the Republican approach to health legislation. The entire Republican machine spent years scheming to replace the ACA, made that their mantra, and have utterly failed to find any solution that isn't demonstrably, disastrously worse. There is no Republican reflection of my brother, no Nosaj Sitivel, because one can't take the details and ramifications as seriously as Jason does without rejecting conservative "principles." There is no health policy wonk taken seriously by Republican leaders who saw these problems  two decades ago and resolved, without ideological baggage, to learn how to increase healthcare access and quality. There is no one in the Republican establishment willing to fight for effective policy that is hard to explain and harder to sell. So as many years as they spent railing against Obamacare's imagined failings, and promising to replace it with bottled heaven, they remain incapable of offering any substance. TrumpCare failed because nobody involved in writing it actually cares.

You want to know how to improve on the ACA? Ask my brother. He, of course, has detailed, well researched, carefully considered lists of fixes. Will our current all facade, no building, leaders implement any of that? Of course not, they want the ACA to fail so they can blame Democrats. But with the defeat of the American Health Care Act of 2017, it seems much more likely that government with an honest interest in good policy will be back. Facts matter, logic matters, policy matters, even in politics. And that is reason for hope.

Thursday, February 02, 2017

Friendly Advice for Your First NSF Pre-proposal

It is going to be okay. Very okay.

Let's start with the important information that until last month I, like anyone who needs to read this post, had never applied for, let alone received, US National Science Foundation research funding. Having been out of the US for most of my time since earning my Ph.D., and other extenuating circumstances, kept me from applying to this extremely important source of funds. As with my posts on applying for NIH and ERC funding (which I didn't get), I'm writing this not as an expert, but because most people who write advice on applying for NSF funding are to varying degrees experts, and have been doing it for so long that they have no idea what us newbies might not know. I've never been on an NSF panel, I've never been to NSF, and all my attempts to talk to NSF employees have been unsuccessful. I am, like you, an outsider. So I learned a lot along the way, much of it later than I should have, and I'd like to share some key points. Before we begin, let's take a moment to contemplate this bodacious caterpillar I found in the University of Wisconsin Arboretum last summer:


Alright, now that you remember that you love science, and brim with important and exciting questions about the world, let's delve.

1. NSF, we can agree, does not have the funds to support more than a small fraction of the grant applications they receive. Other huge governmental funders of science, like NIH, are in a similar situation. (I am assuming here, perhaps in vain, that the US government under El Presidentisimo continues to invest in funding basic research at some meaningful level.) This is a problem not only in terms of almost-everybody-doesn't-get-funded, but in terms of the phenomenal amount of time that scientists squander writing unsuccessful grant applications. In many cases, months of each year are spent applying for funding that is not available. On the flip side, NSF has to harness huge amounts of scientists' time to serve on committees, wading through the reams of applications finding reasons to reject as many of them as possible.

NSF has attempted a partial solution to this problem: the preliminary application. Basically, one starts by writing a short (four pages of text, plus many ancillary documents, including a one page Project Summary) version that has to be approved by a committee before one is invited to submit a full application. Most applicants (about 75%, in the program I'm applying to) only have to write the short version before being rejected, and the committees mostly have to read piles of short applications, with relatively few longer ones coming after that.

2. Writing the preliminary application was honestly not that bad. Several reasons: No budget is required, and many of the ancillary documents that NSF needs before they can fund anyone don't get submitted until your preliminary proposal is approved. More importantly, I have good collaborators, who are in practice writing these things. There is a huge amount to know about NSF specific 'grantsmanship.' When the committee gets to our application, after having already scanned scores of others, they will be both eager to find something really interesting that keeps them awake, and eager to find some reason that the thing can be rejected, so that they can get it over with. They will be looking for key phrases that everyone should have, and possible pitfalls indicated by things only people who have served on these committees (or maybe only that particular committee) know about. In short, it would be tremendously surprising if someone who just had phenomenal scientific ideas but no insider guidance as to the evaluation process ever got funding. I am lucky to have had that guidance; while it means I did a lot of rewriting to try to conform to a culture I've never encountered, it also, hopefully, means we have some chance of being invited to submit a full proposal. If so, that's what I'll be doing this summer, again with about a 20-25% chance of success.

3. As with any funding application, reading past successful applications to the same program is important. Notice not only the language used, the level of methodological detail given, and the structure of the proposal, but also the scope and scale of the proposed science.

4. Write, and revise, the one page Project Summary, and make sure everyone in the project agrees on it, before bothering with the longer Project Description. I made the mistake of drafting the Project Summary, receiving only minimal feedback on it from one of my collaborators, then writing the rest of the grant. By the time I got more extensive feedback from this collaborator, I had only a few days to reconsider the scope of the work being proposed and extensively rewrite. The proposal ended up much better for it, but I could have gotten a lot more sleep if I'd pushed for more feedback after writing just the summary.

5. The whole thing really isn't that much writing. Given that one knows what one is doing, and has good communication with collaborators, a good draft can be banged out in a couple of solid days.

6. In most cases, the one page Summary has to be uploaded as unformatted text, and it takes up more space the way NSF automatically formats it than it would if you or I formatted it according to their rules. I, and a few people I've talked to, ended up hacking down the one page summary very shortly before the deadline when we figured this out.

7. In order to apply, you need an "NSF ID." Looking on the NSF web page, you will find lots of information on retrieving your NSF ID, what to do if you have two NSF IDs, whether NSF ID is the same thing as various other identifiers NSF has used in the past, and so on. You will not find any information about how to get an NSF ID if you don't already have one. If you call NSF to ask how to get one, they will be so confused by you that they won't be able to help you, as if you had called to ask how to breath in before speaking. You just do it, and you must already know how. So I will tell you the secret: somewhere in your university or other approved research organization, there is some individual with the official power to communicate with NSF to get you your very own NSF ID. You will have to find out who that person is and request the NSF ID several days before the application deadline. My collaborator at another university didn't get a reply to his request until a few hours before we submitted, and we were actively discussing what would happen if we had to leave him off the PI list. Don't let that happen to you.

8. Which reminds me of another important point. I was advised to contact the NSF Program Officer for my application when I had a nearly final Project Summary worked up. As mentioned above, that didn't happen until less than a week before the grant deadline, at which point the Project Officers were all swamped by others trying to meet the same deadline. I emailed the Program Officer, and got back a very short email, but never got to talk with her. Finishing your Project Summary early will allow you to get input from your Project Officer.

9. Be smart, work very hard, and have extremely good luck.

Thursday, January 19, 2017

Large Alligators, explained.

I've now seen several reactions to this video shouting questions like, "Why aren't they all dead?!", "Why aren't they running for their lives!?"

Well, sit yerself down my friend, I'm going to be brief.

1. Telephoto lens makes that ol' gator look bigger and closer than it is.
2. Gators rarely attack people unless fed by people, or defending nests. Average is less than one fatal attack a year in the US.
3. Gators are aquatic ambush predators. They don't run down large prey on land.
4.  Florida has well over a million gators. Spend time there, you learn not to worry about them.
5. I stepped on a live, submerged gator while working in the Everglades. It moved away. So did I.
6. Florida,  outside Miami Beach, is the deep South. Somebody, possibly everybody, in that crowd is armed.
7. If they had all run away there would be no video of it.

 "Video: Large Gator Spotted in Florida" isn't quite fake news, but it certainly isn't news.

Friday, January 13, 2017

Adventitious knowledge

Joseph Grinnell, eminent ecologist and zoologist of the early 20th century, and founding Director of the Museum of Vertebrate Zoology, where I was a graduate student, wrote some hilarious stuff. Google Scholar lists 376 publications in his name, most of which are actually by him, including foundational papers in niche ecology, bio-geography, museum science, and so forth. He took so many thousands of pages of detailed, elegant, highly legible, informative, rigorous, lyrical, systematic field notes that if I told you how many, I'd have to look it up again, and it is getting late here. And he is rightly revered as a founder and role model in the MVZ. But perhaps my favorite thing of all about Joseph Grinnell is his nearly forgotten, mildly disturbing, profoundly droll paper, "A Striking Case of Adventitious Coloration." I have no memory of how I first encountered this paper, other than that it was in my former life as an ornithologist at the MVZ. I have never come across another paper that cited it, and Google Scholar lists none. It is, at core, a mystery.

The whole story is available here. The first two sentences:
On February 8, 1920, I spent the afternoon with my family at a point in Moraga Valley, Contra Costa County, California, some five miles, airline, northeast of Berkeley. My son Willard undertook to exercise the shotgun for the purpose of securing some specimens of local birds such as happened to be needed at the Museum.
So ornately informal, so precisely vague, so informatively not-to-the-point, I am in love with this opening. No reputable journal would publish it these days, and that is a shame. He's storytelling, and quite well. The story strides on: Willard blasts a mated pair of Oak Titmice, both of whom have bright yellow breasts. Why bright yellow? Oak Titmice are grey, never yellow.  Grinnell rushes the five airline miles back to Berkeley, marches into the botany department with his dead birds, and tells them to figure out what kind of yellow pollen these birds have got on them. Not pollen, say the botanists. Grinnell marches into a mycology lab and tells them to figure out what kind of yellow spores his birds have on their breasts. Maybe slime molds, hard to tell, say the mycologists. Grinnell concludes that possibly bird feathers could be an important means of dispersal in slime molds! He finishes by pointedly mentioning that if anyone is interested, these two birds "and their loads of spores, constitute Nos. 40,391 and 40,392 in the bird collection of the Museum of Vertebrate Zoology." He publishes the whole thing in The Auk, and that is the end of that, for almost a century. A century, by the way, is how long Grinnell said some of the MVZ's specimens might have to wait before they would be put to some as yet un-imagined use. It has been 97 years.

Which brings me to that wonderful word in Grinnell's title, "adventitious." It means something on the order of "acquired by chance" which is how those titmice presumably got their yellow, and how I came to the knowledge that in a drawer in Berkeley two spore laden titmice waited.  What did I intend to do with this knowledge? Keep it in a drawer, until, perhaps after one hundred years, it proved valuable.

Now, I unexpectedly find myself with colleagues interested in spore dispersal ecology, and somebody mentioned spore dispersal via bird feathers. Which started me rummaging around in my dusty rusty musty gusty fusty drawers of ornithology, hunting for memory of birds with spores on them. All I remembered clearly was Willard undertaking to exercise the shotgun, but eventually (this morning) I found first memory, then paper, and shared both. And by afternoon my new mycology colleagues had requested access to Nos. 40,391 and 40,392 from my old ornithology colleagues at the MVZ, so that we can collect some of the long faded yellow dust. A little bit of molecular genetics wizardry (our lab is set up for sequencing DNA from dried fungal museum specimens) and we may finally be able to discover what made Grinnell's birds so yellow. If it is a new species of anything, we must surely name it after Willard.