Friday action item: An awful budget, now with detail

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!

There’s a detailed Federal budget proposal out this week, covering the Trump administration’s plans for the 2018 fiscal year. Have you called Congress about it? You should.

Detailed breakdowns have identified cruel cuts to the social safety net and a multi-trillion-dollar arithmetic error that make excellent reasons to oppose the plan all on their own. But there’s also piles of bad news for science:

We’ve also, for the first time, got a concrete proposal for the National Science Foundation’s budget — more than 11% lower than what it had in 2016 — to the lowest it’s been, in inflation un-adjusted dollars, since 2008. The spending plan NSF has prepared with that number in mind would reduce funding for graduate research fellowships, EPSCoR support for institutions in states that otherwise receive less NSF funding, and the research at undergraduate institutions (RUI) program, among others.

As we saw with the Trump proposal for continuing funding in 2017, this will almost certainly not pass Congress in its current state; but Congress can use every bit of encouragement we give it. Call!

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Molecular adaptation in a deep-sea alien…*ahem* amphipod

Space: the final frontier…or is it? I was inspired Jeremy’s post yesterday to talk about that deep dark abyss that takes up the vast majority of our mostly blue planet. For the record, I’m in agreement with the assessments for the marine (micro)biologists. After perusing images of the critters down there, you might wonder if it’s not more interesting (or at least equally interesting) to dive deep under the ocean to see what might be the closest to aliens we can currently get (discussed recently here). One glimpse of a goblin shark (maybe kinda scary for some kids) or anglerfish, should convince you.

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Posted in adaptation, evolution, genomics, Molecular Ecology, the journal, next generation sequencing | Tagged , , | Leave a comment

The last of us, Ph.D.

(Prometheus, Twentieth Century Fox)

I hear tell that there’s another movie in the Alien franchise in theaters, which makes this a fine opportunity to revisit the beauty and stupidity of the last one, Prometheus. In that previous instalment, we watched people who were, allegedly, some of Earth’s greatest scientific minds blunder their way into an alien bio-weapon storage facility only to get eaten by and/or mutated into horrific H.R. Geiger-designed monstrosities. The behavior of the Prometheus team’s biologist Rafe Millburn is a regular joke on Science Twitter even without millions of dollars of studio marketing to remind us about it — he infamously reaches out to a hissing alien snake-thing that promptly breaches his spacesuit and kills him. Recently, though, that regular discussion landed on an important question arising from poor Rafe’s bad example: what kind of field scientist would do better than the Prometheus team?

So here’s my rundown of the survival strengths and weaknesses of people with experience in some fieldwork-intensive STEM disciplines, specifically in the context of an expedition to a hostile alien planet. Note that I’m trying to focus on skills and personality types that distinguish each area of expertise — so, for instance, I assume that everyone would be about equally likely to have wilderness first-aid training, or the physical conditioning for a long hike with a pack. I’m sure these assessments are going to be off, and biased or distorted by my membership in #TeamAutotroph — feel free to make counterarguments in the comments or on Twitter. Without further ado, the list, in no particular order:

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Posted in fieldwork, just for fun, modest proposals | Tagged | 1 Comment

Relatively rare tropical trees all agree: avoiding the ‘rain of death’ seems like a good call

When you think of a tropical jungle, what’s the first thing that comes to mind? Probably a lush green landscape with trees, vines, flowers, and let’s be real, at least one toucan. Tropical forests are made up of diverse groups of tree species, in contrast to other more temperate forests, that might only have one dominant type of tree, something you might see in Yosemite, perhaps.

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Posted in genomics, Molecular Ecology, the journal, next generation sequencing, plants, transcriptomics | Tagged , | Leave a comment

Friday action item: What comes next?

The March for Science approaches the Capitol. (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!

It’s been just about two weeks, now, since many of us Marched for Science, and just about a week since even more people filled up the same streets with the People’s Climate March. We’ve had a little good news since then — Congress reached a deal to fund the government through September, which mostly leaves research funding unchanged and actually boosts the NIH budget. But that ray of sunshine is pretty faint — the EPA still saw a funding cut, just not a catastrophic one – and it’s already clouded over with the passage, by the House of Representatives, of a healthcare plan that would gut the provisions and protections of the Affordable Care Act, and the Trump Administration’s contemplation of a withdrawal from the Paris Accord plan to fight climate change. We’re in a marathon, not a sprint, and this feels like the point — usually about mile 6 of 26, for me — where the excitement of a big race gives way to the realization of just how long it’s going to be. What’s your plan for the long term?

Keeping in touch with your Members of Congress is important, but at the end of the day, the best prospect to change the priorities of the Federal government is going to get some new Members of Congress. The health care repeal vote and historically low presidential approval have made that more do-able than ever, but now is the time to start planning. If you’re in a district represented by a Republican, get on board with their opponent’s campaign right now, and prepare for the work of getting out the vote in a non-presidential election year. If your reps are Democrats, check out SwingLeft to pick a vulnerable Republican close by and find out how you can help defeat them. You can also pitch in to one or more of SwingLeft’s District Funds to support opposition candidates. The general midterm election is 550 days away on November 6, 2018, but make sure you’re ready for primaries beforehand, and for special elections in Montana’s 4th district on May 25, and in Georgia’s 6th, on June 20.

The only route to restoring a functioning government any time soon is through the ballot box. Pick a lane and pace yourself, and we’ll get there yet.

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N50 for transcriptome assemblies

This is the sixth in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies.

Transcriptome assemblies are inherently different from genome assemblies. With genome assemblies most people strive to achieve an optimal contig length equaling an entire chromosome. Meaning that, if you have an organism with four chromosomes, your optimal (dream) genome assembly would consist of four long contigs. This is in stark contrast to transcriptome assemblies where contigs represent transcripts. An optimal transcriptome assembly will vary depending on your question, but would likely consist of all possible transcripts from all expressed genes, including alternatively spliced variants (isoforms).

Using the normal N50 metric for transcriptome assemblies can therefore be highly misleading, as transcriptomes do not strive to achieve long contig lengths and high N50, but instead one contig for each transcript. Furthermore, the most highly expressed transcripts do not necessarily constitute the longest ones and the majority of transcripts in a transcriptome assembly will normally have relatively low expression levels.

Fig 7. Example of a typical transcriptome assembly with a high number of short contigs and few contigs of intermediate length (from Senatore et al. 2015).

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(Un)usual sources of ancient DNA

Working with ancient DNA can be quite painful at times, but hard work pays off (or so they say) and scientists are starting to reap great benefits from their effort by exploring more and more things to extract DNA from.

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Posted in evolution, genomics, methods, Paleogenomics | Tagged , , , | 1 Comment