Friday Action Item: Tell Congress to protect environmental science funding

Posted on 10 Mar, 2017 by Jeremy Yoder

“Mary Workman Holds A Jar of Undrinkable Water That Comes from Her Well, and Has Filed A Damage Suit Against the Hanna Coal Company.” — a photo taken by Erik Calonius as part of an early EPA project to document the country before modern environmental regulations took effect, highlighted by the Discover EPA Twitter feed. (Flickr: US National Archives)


*On Fridays [while the current administration is in office](http://www.molecularecologist.com/2016/11/road-ahead/) we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? [E-mail us](jbyoder+tme_action@gmail.com)!*
In the last week, supporters of science have seen some of our worst fears about the election of Donald Trump become a lot more concrete. The Trump administration released a budget outline proposing to boost military spending by $54 billion, paid for by cuts to virtually every other element of discretionary domestic spending. Specifics are still trickling out, but they already include big proposed cuts to crucial scientific work.
Under the proposals seen so far, the climate- and weather-monitoring National Oceanic and Atmospheric Administration will lose [17% of its budget](https://www.washingtonpost.com/news/energy-environment/wp/2017/03/03/white-house-proposes-steep-budget-cut-to-leading-climate-science-agency/), including to its satellite network. There’s also proposed cuts accounting for [up to 30%](https://qz.com/925729/leaked-document-details-trumps-epa-budget-cut-plan/) of the budget of the Environmental Protection Agency, [including](http://www.oregonlive.com/environment/index.ssf/2017/03/here_are_42_of_president_donal.html) thousands of staff jobs, air and water monitoring, research funding, and education. Thursday a twenty-four-year veteran EPA administrator, who helped start the agency’s environmental justice work under the President Bush, [resigned](https://insideclimatenews.org/news/09032017/epa-environmental-justice-mustafa-ali-flint-water-crisis-dakota-access-pipeline-trump-scott-pruitt) in protest over the proposed elimination of that program.
The good news, for now, is that all of this is proposed — it has to go through Congress, and Congress is [already raising objections](https://www.theatlantic.com/politics/archive/2017/03/trump-is-headed-for-a-budget-battle/518454/). So this is a great time to [call up your Representative and Senators](http://www.molecularecologist.com/2017/01/friday-action-item-put-your-members-of-congress-on-speed-dial/) and tell them how you feel about the loss of research funding, environmental monitoring, and protection against pollution. A lot of the points you might have used to protest the earlier [freeze on EPA research funding will apply here](http://www.molecularecologist.com/2017/01/tuesday-action-item-help-thaw-the-epa-freeze/):
– Call a local office if you can, rather than Washington, DC and identify yourself as a constituent.
– If you’re a scientist, say so, and if your research relies on EPA or NOAA funding or data, say that too.
– Identify work by the agencies that impacts your local community, which could be anything from environmental cleanup to hurricane monitoring.
As ever, calling a Member of Congress is helpful *even if you think you already know the Member’s position*. If they’re on the wrong side, it’s good for them to hear directly from constituents who disagree. It [*does*](http://www.slate.com/blogs/the_slatest/2017/01/03/reps_say_phone_calls_prompted_ethics_reversal.html) make a [difference](http://www.newyorker.com/magazine/2017/03/06/what-calling-congress-achieves).

Posted in Action Item, funding, politics, United States | Tagged , | Leave a comment

Have we got the power?

Posted on 9 Mar, 2017 by Stacy Krueger-Hadfield

Sabrina Heiser wrote this post as a final project for Stacy Krueger-Hadfield’s Science Communication course at the University of Alabama at Birmingham. Sabrina grew up in Germany, completed a BSc (Hons) in Marine Biology at Plymouth University (UK) and then lived in Antarctica for 2.5 years working for the British Antarctic Survey. Now, as a PhD student in Dr. Chuck Amsler’s lab at UAB, she is finally able to combine her love for macroalgae and the Frozen Continent, where she is investigating algal population structure and how gene flow shapes the distribution of geographic patterns in physiological traits. Sabrina tweets at @sabrinaheiser.

Genetic diversity is something we all worry about — especially in our rapidly changing climate. We care about species when trying to conserve biodiversity, but that inherently means we also need to care about the historical and contemporary processes that have resulted in the patterns of genetic diversity within that species. Hoban (2014) predicted that simulation software would be increasingly used to address these issues, but is it?
Simulations can help us calculate and maximize the statistical power of a given sampling strategy. We can optimize power by balancing the amount of populations, genetic markers and individuals that are being sampled (Hoban, 2014). Increasing the number of markers used, can drastically decrease the amount of individuals required, for example. This is especially important when studying organisms with limited access due to location or abundance.
But, what about more complicated organisms, like haploid-diploid species?

Continue reading →

Posted in blogging, community ecology, evolution, haploid-diploid, natural history, NSF, population genetics | Tagged , , , , , , , | 1 Comment

I think we’re NOT alone now

Posted on 7 Mar, 2017 by Stacy Krueger-Hadfield

Finding new and engaging ways to communicate science is of paramount importance. But, how many opportunities are there to practice the art of communication?
When can we try out different methods of distilling science?
It seems that these chances are relatively rare considering clear communication is something for which we all strive.
I was given carte blanche to develop my first course at the University of Alabama at Birmingham.I decided to fill a gap in the grad student curriculum and test run a scicomm course. As I was developing and teaching the course, I wondered how many other science communication courses were out there.
It’s not to say there aren’t opportunities. There’s fellowships, such as workshops at AAAS, but they seemed somewhat out of reach to the regular undergrad or grad student working on their degree.
Books, such as Nancy Baron’s Escape from the Ivory Tower, are also available, but when can you practice what these books preach, regardless of your career stage?
In the fall of 2016, my students and I would either sink or swim together.
Continue reading →

Posted in blogging, career, community, interview, science publishing | Tagged , , , , , | 4 Comments

Why science cannot help but be political

Posted on 3 Mar, 2017 by Jeremy Yoder

The Smithsonian Institution’s “castle” in Washington, DC. (Flickr: Robert Lyle Bolton)


What does it mean to say that science is political?
I’ve been contemplating that question since long before November 9, 2016, but it’s gained a great deal more urgency in the light of the current U.S. presidential administration. It’s also been a surprising focus of conversations around the March for Science. It’s mildly astonishing, to me, that serious people think scientific work could be separate from politics in the best of times, and the idea that it might still be is absurd. Science as we know it could not exist apart from politics, and scientific work is inextricably important for political discourse.
Continue reading →

Posted in politics | Tagged | 1 Comment

An Update on the Great BAMM Controversy

Posted on 1 Mar, 2017 by Ethan Linck

Update, 01 August 2016, 2:50PM. This post has been updated to include information contained in the supplemental material of Rabosky et al. 2017, and clarify the difference between branch-specific and tree-wide rate variation.
Back in August, I summarized the main points of a debate over the
reliability of the popular macroevolutionary modeling program BAMM. At the time,
critics Moore et al. (hereafter “MEA”) had published a high profile paper in PNAS arguing that several
crucial aspects of BAMM’s implementation and theoretical underpinnings
hindered its ability to accurately estimate diversification rates. Though the paper stimulated a vigorous online debate, a formal rebuttal from the program’s developers Rabosky et al. (hereafter “REA”) did not appear until this week, published early access in Systematic Biology.
Before getting to the major takeaways of REA’s response, a quick cautionary note: like many scientific discussions that blossom over the internet, the debate over BAMM has involved both peer reviewed and non-peer reviewed dimensions. While blog posts from both MEA and REA are useful to understand different perspectives on the issue at hand, it’s important to understand that these dialogues are on essentially parallel tracks — and so the failure to discuss a particular online critique in a published paper should not be taken to mean that the authors have nothing to say on the topic if the argument has not yet been made in the peer reviewed literature. (REA have themselves stated they will only respond to peer reviewed critiques going forward.) For the purposes of this update, I’ve focused only what has been presented in the PNAS and Systematic Biology papers, but I would encourage users of the program to read both REA’s initial rebuttal on the BAMM website and MEA’s in-depth posts on the Treethinkers blog.
With that out of the way, here’s where things stand.
Continue reading →

Posted in blogging, evolution, methods, phylogenetics, science publishing, software, speciation | Tagged , , , | Leave a comment

How much wood would a termite chuck…if it was missing its microbial symbionts

Posted on 24 Feb, 2017 by Kelle Freel

Termites get a pretty bad rap, probably because we think of our houses disintegrating when they move in. Ironically, we have a lot to learn from these critters, and their mounds have served as an inspiration for modern architecture. Either way… maybe, just maybe, after learning more about them, you will appreciate how interesting they are.
Continue reading →

Posted in Coevolution, evolution, genomics, microbiology | Tagged , , , , | 1 Comment

Friday Action Item: Visit a natural history museum

Posted on 24 Feb, 2017 by Jeremy Yoder

The great hall of the Field Museum, in Chicago. (Flickr: jby)


On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!
This weekend, take a break from the news, if you can, and get out of the house. In a lot of the U.S., it’s still not a time of the year when the best way to get out of the house is just to go outdoors. Let me suggest, instead, that you visit the nearest natural history museum.
I don’t think I have to convince our readers of the scientific value of natural history collections — see here and here for some examples — but they’re also, of course, incredibly important local institutions of public science. Natural history museums remain highly trusted by the public, even as other institutions have lost standing, and they can provide both “big-picture” overviews of the diversity of life and windows into ongoing research. Some, like the Field Museum in Chicago, include “fishbowl” laboratories where museum scientists work in public view, and many others have exhibits drawn from the current work of affiliated researchers. Most curate exhibits out of collections of specimens assembled for research purposes; the Beatty Biodiversity Museum at UBC, my current institutional affiliation, takes that idea to its limit with collections cabinets that double as display cases.
So mosey over to the campus museum after work today, or spend a weekend afternoon touring a city landmark. Leave your phone in your pocket. Except maybe if you want to take pictures.

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What's left of the black rhino's genetic diversity?

Posted on 22 Feb, 2017 by Patrícia Chrzanová Pečnerová

With the current poaching epidemic we might lose rhinos before we even have time to get to know them. Luckily, the day has come and thanks to Yoshan Moodley, Mike Bruford and their team we know have a pretty good idea about the genetic diversity of one rhino species, the black rhinoceros.
In ”the largest and most geographically representative sample of black rhinoceroses ever assembled” (as they boldly but appropriately state in the abstract) Moodley et al. compared 19th and 20th century museum specimens with modern samples from universities, zoos, private hunters, and faecal samples collected in the field. Their dataset stretched in time, between 1775 and 2008, as well as in space, covering 20 countries of the black rhino’s historical range. Just so that you know, now we are down to 5 countries.
Probably the most striking result of the study is the 69% loss of mitochondrial diversity, as only 20 out of 64 historical haplotypes were found in present populations.
Continue reading →

Posted in conservation, evolution, Paleogenomics, phylogeography, population genetics | Tagged , , | 1 Comment

Population genomics in the "melting pot"

Posted on 21 Feb, 2017 by Jeremy Yoder

(Flickr: Amanda)


North America is full of new arrivals. Europeans colonized the continent starting half a millennium ago, displaced and eradicated native populations, and brought enslaved workers from Africa with them — and further immigrants have followed ever since. This mass movement of people is a huge complication for studies of human population genetics, but it’s also an opportunity to study how that movement is reflected in the diversity of the people who now live in North America. One study of people in the Caribbean, for instance, found the effects of colonization and the slave trade, but also evidence of migration across the region that pre-dated both.
An important tool for studying the complex human history of North America is emerging from a consumer trend you’ve probably heard about on a couple thousand podcast sponsorship messages — personalized genetic analysis. Services like 23andMe and Ancestry.com offer genome-wide genotyping and comparison to geographically-specific samples to identify your ancestors’ origins, and both companies ask customers to volunteer their data for research. Data collected by 23andMe allowed comparison of genetic ancestry to racial and ethnic identity that reveals how slippery the relationship between race and biology really can be. Now, a study of AncestryDNA customers helps link the history of colonization and migration across North America to individual Americans’ family histories.
Continue reading →

Posted in genomics, pedigree | Tagged , , | 1 Comment

Friday Action Item: Remind your Senators to vote against Scott Pruitt

Posted on 17 Feb, 2017 by Jeremy Yoder

“‘Teepee’ burner incinerates lumber mill’s waste, 05/1972.” — a photo taken by Boyd Norton as part of an early EPA project to document the country, before modern environmental regulations took effect, highlighted by the Discover EPA Twitter feed. (Flickr: US National Archives)


On Fridays while the current administration is in office we’re posting small, concrete things you can do to help make things better. Got a suggestion for an Action Item? E-mail us!
It’s been almost a full month since the inauguration (good heavens) and it’s hard to keep track of the scandals and outrages, more or less as expected. But if you’ve got it in you to make one call to Congress this week (and we hope you do), let us suggest you spend it on reinforcing the resistance to the nominee for head of the Environmental Protection Agency.
Scott Pruitt has built a political career working against the very concept of evidence-based regulation — not just rules to reduce carbon emissions, but regulation of mercury and particulate pollution as well. The Senate is scheduled to vote on his confirmation today, even as Democrats have been requesting a delay while Pruitt’s office complies with a court order to release e-mails that could illuminate his ties to the fossil fuel industry, and EPA employees themselves are, extraordinarily, lobbying the Senate against a prospective boss who opposes the very mission of the agency.
So: Call your Senators. Tell them to vote against Pruitt.

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