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 which 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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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

A solution to the N50 misassembly problem

This is the fifth 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.

The misassembly problem of N50 that we described in post #3 relates to erroneous joining of small contigs into larger ones. This problem is a bit more complicated and difficult to solve than the filtering problem. Various solutions have been proposed in the early 2010’s:

  • corrected Nx (Salzberg et al. 2011)
  • contig path Nx over alignment graph (Earl et al. 2011)
  • normalized N50 (Mäkinen et al. 2012)
  • NAx (where A stands for Aligned) (Gurevich et al. 2013)

All these approaches are pretty similar and require a high quality reference genome of the sequenced organism. We will here take a look at the definition of NAx.

To compute NA50 of an assembly in respect to the reference genome, we perform sequence alignment of contigs to the genome. Contigs containing erroneous joints (misassemblies) are split into aligned blocks and are subsequently aligned independently to distinct fragments of the genome. If we compute the N50 statistic for the set of aligned blocks (rather than initial set of contigs), we obtain the NA50 value. Note that even if some of the contigs fail to align, NA50 is still computed with respect to 50% of the total assembly length (which includes both aligned and unaligned contigs) to be compatible with N50.

Let’s try the NA50 approach using our hypothetical assembly from post #3. We had a Correct Assembly consisting of four contigs 1 Mbp each (Fig. 6a), and an Incorrect Assembly where these four contigs had been misassembled into a single one (Fig. 6b). N50 are 1 Mbp and 4 Mbp, respectively. Since the N50 of the Incorrect Assembly is four times larger, one can easily be fooled to think it’s better, but we will now evaluate this using NA50 instead.

Fig 6a. Correct Assembly with N50 = 1 Mbp and 0 misassemblies.

Fig 6b. Incorrect Assembly obtained by contig merging of the correct Assembly. N50 = 4 Mbp, 3 misassemblies.

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Friday Action Item: Your #MarchForScience checklist

Sign at the Boston Rally for Science, back in February. (Flickr: AnubisAbyss)

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!

Tomorrow, scientists and science supporters around the world will rally in support of science’s role in society. The flagship March for Science in Washington, D.C. has been plagued by confused messaging and failures to include the full diversity of people working in and interested in science — many of our readers may be going to other Earth Day events or to better-organized satellite marches. Still, I’m hopeful that tomorrow can be the start of a scientific community that is better engaged with the rest of society. Several of us at TME, including me, will be on the National Mall for the march in Washington, and others will be at their local satellite marches. If you’re planning to participate, here’s a few things you’ll want to think about before tomorrow morning:

  • Check the event details at the March (or satellite/alternative event) website — what’s the march route and the start time? What will you be able to bring with you?
  • Check the weather forecast, and dress accordingly. Wear comfortable shoes!
  • Organize to meet up with like-minded folks within larger events — for instance, members of the American Society of Naturalists, Society of Systematic Biology, and Society for the Study of Evolution are going to try to meet before the D.C. march, at Federal Triangle.
  • Make your sign. There’s lots of scope for clever, science-y slogans. “Science not Silence” looks like it’s popular, but I also like “Everybody needs science/ Science needs everybody”, and “We’re here, we’re peer-reviewed, get used to it” — there’s more inspiration in this Twitter thread and this Flickr album from the Boston Rally for Science in February. Bonus points if you can tie your slogan into your own research.
  • Speaking of your own research, have an elevator-pitch version of it ready to go — you will (hopefully) be meeting members of the science-supporting public, and maybe even talking to journalists covering the event, so be prepared to explain what your role in science is, and why it’s important for society.

See you in the streets!

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