Friday Coffee Break! Jules-likes-the-links Edition.

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Here’s what we’ll be talking about while we wait in line for a latte:

Are you unreasonably paranoid about germs? New proposals by the FDA  may add a lot of stress to your life. The rest of us, however, should be quite happy about them.

A discussion of the ecological “ghosts” of extinct birds in the ecosystems they inhabited.

A pair of videos about urgent environmental issues utilizing very effective visuals, one on road building and deforestation and a second on overfishing.

A NEW TAPIR species has been discovered. When a 100kg mammal flies under science’s radar for so long (local indigenous people knew it was different all along…) you know we have a terrible grasp of earth’s biodiversity.

This week in genetics/popular science controversies: DNA sequence motifs that regulate gene expression are found to overlap with sequences coding for proteins far more frequently than previously thought. This may explain some prominent and heretofore mysterious features of protein coding DNA. An unfortunate attempt at coining a new term (“duon”) and blundering PR campaign about the work inspire some stinging rebukes.

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Friday Coffee Break: You talkin’ to me? You talkin’ to me!?

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Here’s what we’ll be talking about while we wait in line for a latte:

War. War never changes. Argentinian mockingbirds brutally attack brood parasitic cowbirds, but fail to stop them from laying eggs. -From Noah.

ARE THE MEATS AND CHEESES YOU LOVE ALTERING YOUR GUT MICROBIOTA TO MORE CLOSELY RESEMBLE THAT OF LAB MICE WHO ARE SIGNIFICANTLY MORE LIKELY TO SUFFER VARIOUS AILMENTS, AND THEREFORE KILLING YOU?! FOR THE LOVE OF GOD, CLICK THIS LINK TO FIND OUT BEFORE ITS TOO LATE! -From Sarah.

But Wait! There’s More! The jet-propulsion butt-hydraulic system also is a gill.” -From Jeremy, who tells me that Apple and Samsung are currently waging a high-stakes patent battle over the butt-hydraulics to be included in the next generation of smart phones. 

Finally, in keeping with the belligerent theme: David Dobbs writes an adversarial piece on the concept of the selfish gene and Richard Dawkins and Jerry Coyne rebuff it. Meanwhile, Michael Behe [link redacted] says something that makes everyone ask “Must creationist effluvia befoul every. single. google search I do for this blog?”

Should scientists be more subjective?

Peer-Review-Nick-Kim-cartoon3-resizeThough the goal of scientific research is to objectively follow evidence to advance our knowledge of the world we live in, it has become increasing apparent that there are some substantial road blocks in our way.  For example, a number of recent articles have argued that (A) we get the wrong answer – a lot, (B) the hotter the area of research, the more likely we are to get it wrong, and (C) the higher the profile of the journal we published in, the more likely we are to have got it wrong (Ioannidis 2005, Pfeiffer & Hoffmann 2009, Brembs et al. 2013).  Ideally, science is self-correcting process, allowing us to reach the correct answer over time, in spite of such misleading results.  However, the authors of a recent Nature article argue that a phenomena they refer to as “herding” can prevent or severely delay the process of self-correction and their proposed solution is quite surprising: add more subjectivity to the peer review process (Park et al. 2013).

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Friday Coffee Break: Just what is a Denisovan Anyway?

They’ll never believe you.

Here’s what we’ll be talking about while we wait in line for a latte.

From Sarah: Drug cartels and academia share similarly structured labor markets.

…and in that cynical vein, a statistical analysis using professors’ last names that shows nepotism is a significant force in Italian universities.

From Noah: A new record is set in ancient human DNA sequencing: 400 thousand year old hominid DNA has been successfully sequenced. The results suggest previously unknown complexity in human history, and that we don’t really know what, exactly, the Denisovans were. Or at least they suggest that Noah doesn’t know.

It’s an old reference, but it holds up: check out this ten year old David Foster Wallace essay, “Consider the Lobster“. For an article in a food magazine, it sure has a lot of interesting lobster biology in it.

We may be late to the party on this one, but there has been some interesting debate about the role the FDA should have in human genetic testing, particularly as it relates to the company 23andme’s direct-to-consumer model. Here is Michael Eisen’s take. Also, a blog post on the statistical issues associated with large scale screening for disease-associated genotypes has generated some interesting discussion (23andme genotypes are all wrong).

Meanwhile, 23andme has decided to stop offering health-related interpretation of the genotype data they provide.

Ten Rules (Plus Two Cents) For Getting Published

I recently discovered a series of papers from PLOS Computational Biology – the “Ten Simple Rules” collection. These papers by Phillip Bourne (et al.) cover a wide range of topics – including “Ten Simple Rules For Making Good Oral Presentations” to “Ten Simple Rules For Graduate Students” to “Ten Simple Rules For Aspiring Scientists In A Low-Income Country”. There are more than 20 in all and they are definitely worth checking out (especially if you’re interested in a career in Computational Biology or a starting graduate student). “Ten Simple Rules For Getting Published” has some pretty sound advice and although I’m no publishing expert – I’m adding my two cents (the black text) to Bourne’s golden nuggets of advice (the red italic text).

Rule 1: Read many papers and learn from both the good and the bad work of others.

This is important for any Academic – reading papers and noting their strengths and weaknesses will have benefits beyond just getting published. As a figure junky, I have learned a lot by analyzing what makes a visual aid particularly pleasing or confusing – doing this with text and content are just as helpful.

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