The Molecular Ecologist: Storing and protecting your NGS data

Data Barnacles. Photo by UWW ResNet.

This week at The Molecular Ecologist, Mark Christie shares some tips for how to take care of that massive genetic dataset that’s just come off the high-throughput sequencer:

Congratulations! You have recently received a file path to retrieve your hard-earned next-generation sequencing data. You quickly transfer the files to the computing cluster you work on or perhaps, if you only have a few lanes of data, to your own computer. But before you begin messing around with your data, you quickly realize that you should come up with a plan to back up and store unadulterated versions of your files.

For a nice set of recommendations with some step-by-step instructions, go read the whole thing.◼

Science online, cocoa and Congressional whiplash edition

  • Okay, now this is bad. Humans’ supply of chocolate is in trouble because of bug-tending ants.
  • A history of modern lawns, and the alternatives.
  • And with a funding cut. House Republicans unilaterally decide that NASA should ditch its asteroid-capture plans in favor of a moon base.
  • Because mutation happens during mitosis, too. When it comes to genotypes, we each contain multitudes.
  • Not good! The feedback between climate change and wildfires.
  • It’s about deciding. And also not deciding. On starting up a lab.
  • Good news. The next weapon against one group of drug-resistant bacteria might be a fungicide.

Science online, warp speed edition

2010.07.15 - Bumblebee Lose the best pollinator, and the others are less effective. Photo by jby.

Nothing in Biology Makes Sense: Making sense of the missing human baculum

Walruses on the corner If you think those tusks are impressive, you ain’t seen nothing yet. Photo by Joe King.

Over at Nothing in Biology Makes Sense! Sarah Hird discovers a case in which Creationists are willing to cite phylogenetic context to make a point, and that point is that God made Eve from the bone in Adam’s penis. What, you didn’t know that most mammals have a penis bone?

Baculum is the technical term for the penis bone. Many mammals have one – presumably to aid in sexual intercourse. For mammals that mate infrequently, prolonged intercourse ups the chances that a particular male sires some babies. For mammals that must mate quickly, the baculum provides immediate rigidity. And for all mammals, keeping the urethra straight while copulating is imperative, so maybe it’s there to prevent a kink in the works, so to speak.

To see the full phylogenetic context of the baculum, and learn some possible reasons why a male walrus has a two-footer but humans have none at all, go read the whole thing.◼

Science online, sleep deprivation and sugar edition

Sugar Cubes Sure, it’s not good for you, but is sugar toxic? Photo by howzey.
  • This week, at Nothing in Biology Makes Sense! A guest post calls for escalation in the “arms race” against aggressive mimics in scholarly publishing. And I picked a fight with a Canadian nerd-rapper.
  • Which is more relentless? A new study projects climate change will happen way too fast for vertebrate animals to adapt; but see my take at The Molecular Ecologist.
  • In evolution, and in scientific thought. Reflections on the importance of founder effects.
  • Satisfying the grasshopper and the ant? Cities that plan to prevent—and mitigate—climate change reap short-term benefits, too.
  • Depends what you mean by “toxin,” of course. Is it appropriate to call sugar a toxin?
  • For future reference. The WEIRDness of evolutionary psychology, quantified.
  • I mean, really. Preferring non-science over science for aesthetic reasons is just kind of embarrassing.
  • Let me get back to you on that. Does the self-correcting paradigm of science move too slowly?
  • Vicious cycle. If you lose sleep because you’re worried about something, sleep deprivation will make the axiety worse.
  • Men can still wear whatever they were wearing when they rolled out of bed. How women can dress for success in academia.
  • And it’s not getting better. Handgun safety is a public health problem.
  • Proof-of-concept, anyway. Silencing an entire extra chromosome to cure Down’s Syndrome.

The Molecular Ecologist: Climate’s a-changin’. Will the living world evolve to cope?

Warm Fire It’s getting hot out there. Photo by Kaibab National Forest.

Over at The Molecular Ecologist, I discuss a new study that uses phylogenetic estimates for 17 families of vertebrates to estimate how rapidly those animals have evolved in response to past climate change, and compares those estimates to how fast they’ll need to evolve to keep up with projected climate change. Spoiler alert: past rates of adaptation to climate aren’t anywhere near fast enough.

To keep up with projected climate change, Quintero and Wiens estimated that the species in their dataset would have to undergo adaptive change at from 10,000 to 100,000 times faster than the rates estimated in their evolutionary past.

Well, but maybe. To learn whether the data are telling us what the study’s authors say they’re telling us, go read the whole thing.◼

Nothing in Biology Makes Sense: Pseudoscience in scientific clothing

A snake in the literature? Photo via Wikimedia Commons.

This week at Nothing in Biology Makes Sense!, guest contributor Chris Smith finds something a bit odd in his Google Scholar results:

I recently gave a lecture on the Miller-Urey experiment, and I wanted to pull up the original citation. So, glancing at the clock to make sure I still had five minutes before showtime, I headed over to Google Scholar and entered in the search terms “Miller Urey.” When I started browsing the results I was surprised to find, on the first page, a link to an article titled “Why the Miller–Urey research argues against abiogenesis” published in The Journal of Creation, a product of Creation Ministries International.

To learn what Chris thinks is going on—and how it resembles a phenomenon in evolutionary biology—go read the whole thing.◼

Science online, electrostatic bollocks edition

fog 5 - spiderweb spiral Some web? Photo by feral godmother.

Science online: Glorious Fifth edition

2013.06.24 - Wildflower IV Photo by jby.
  • Again. In which bad science in the service of sexism gets its comeuppance.
  • There is a whole blog about corvids. And they know how to pull tails.
  • Guys, there are taste receptors on your balls. And also on a lot of other parts of your body, apparently.
  • “Wait … these lionfish are overweight?” The invasion of lionfish is so bad that the fish are obese.
  • Leprosy is, evolutionarily, mighty stable. What was discovered by sequencing bacterial DNA from the bones of 14th-century lepers.
  • Mendel v. Fisher. Why scientists screw up, and why the solution is more science.
  • The dot’s barely even blue. Earth, photographed in extreme not-close-up.
  • ““To do science is to search for repeated patterns, not simply to accumulate facts …” Reading Robert MacArthur’s Geographical Ecology.
  • New bird species discovered! In the suburbs of Phnom Penh, Cambodia.
  • Like burning down the forest and replanting it to kill off some weeds, but still. Bone marrow transplants appear to have eliminated HIV infections in two more patients.
  • This’ll come in handy. Teaching evolution through the lens of infectious disease.
  • Sure, the paper’s retracted … but who’s got the movie rights? The story of a retracted Nature paper involves break-ins, tampering with experimental material, and hidden cameras.

Carnival of Evolution, July 2013

2013.06.24 - Spruce bud Photo by jby.

It’s fresh and online at Teaching Biology.◼