Category Archives: blogrolling

Nothing in Biology Makes Sense: The rationality of science denialism

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Denial Photo by cesarastudillo.

This week at Nothing in Biology Makes Sense!, Sarah Hird delves into the psychology of science denialism to understand why facts alone can’t help a creationist:

Rosenau makes the case that when we (scientists/science supporters) talk to deniers/agnostics, conversations that begin in the scientific realm very quickly turn to religion, personal freedom, morality and even capitalism. The denial stems from how people identify themselves and how they see the world; it can be rooted in fear, anger and distrust of things outside their social group (religious and political affiliations are two major such groups). … The denial is not rooted in scientific facts.

To learn what does help denialists come around, go read the whole thing.◼

The Molecular Ecologist: Which programming languages should I learn for bioinformatics?

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Over at The Molecular Ecologist, Mark Christie runs down the considerations to take into account when you’re thinking about making the effort to learn a programming language — he focuses specifically on bioinformatics, but his points really apply for just about anything you’d do with a script.

Perl and Python programs are (typically) compiled each time before they run and they are often not compiled to the same extent as C and C++ (but see PyPy for Python). This means that C and C++ typically run faster and require less memory after a program has been completed. Like most things in life, however, there is a tradeoff in that C and C++ programs usually require more lines of code because there are more details that have to be specified in each program. Thus there is a tradeoff between time spent developing, writing, and debugging code and the time that the program takes to run through completion.

Planning your first bioinformatics project? You should probably go read the whole thing.◼

Knowing what I know now: Let’s make it a carnival!

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County Fair Photo by Justin in SD.

Cross-posted from The Molecular Ecologist.

So, not long after I posted my advice for grad school, and said I hoped that The Molecular Ecologist ultimately collect similar posts from a whole bunch of people, Scicurious e-mailed to point out that there’s a thing we do in the blogosphere when we want to collect a bunch of posts on a particular topic: we hold a carnival!

So the plan is now that The Molecular Ecologist will host a “Knowing What I Know Now” carnival on Monday, December 10, and if you’re working in science at any career stage, you’re invited! All you need to do is write up a few things you wish you’d known in your previous career stage that would’ve helped you prepare for your current career stage. (i.e., grad students, write about undergrad; postdocs, about grad school; and so on.) In my original post I may have over-emphasized the academic career track — we’d love to hear advice about preparing for work in industry, or with a non-academic nonprofit, or in government, too.

If you have a blog, write up your advice as a post and either e-mail the link to me or post it in the comments below. If you don’t have a blog, we’ll be happy to post your contribution at The Molecular Ecologist — again, e-mail me to set that up. Please send all your links and post contributions by Saturday, December 8, and I’ll pull them together for the carnival post on the 10th.

Ready? Set? Start your advice-ing.◼

The Molecular Ecologist: Knowing what I know now (about grad school)

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2007 - Day 113 - This England Tea. It’s important. Photo by Jonathan_W.

In what I hope will be the start of a whole series of posts about careers in science, I’ve taken a stab at writing down what I wish I’d known to do (and what I’m glad I did) during graduate school, over at The Molecular Ecologist:

I can’t claim to have any blinding new insights — my own career is very much still under construction. But I’ve been interacting with a number of freshly-arrived graduate students this semester, and I’ve found myself thinking, after conversations with them, about what I might have done differently back when I was looking ahead to five (oops, six) years of grad school — and about what I did that worked out pretty well.

And no, I will not apologize for the choice of videos I’ve used to illustrate the complete post.◼

The Molecular Ecologist: Tallying differences between species — across the whole genome

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Muchárik bielokrký (Ficedula albicollis); Collared Flycatcher A collared flycatcher. Photo by Photo Nature.

This week at the Molecular Ecologist, I discuss a new, genome-wide study of genetic differentiation between two closely related species — the collared flycatcher and the pied flycatcher.

Equipped with the core genome sequence, the team collected still more sequence data from ten male flycatchers of each species, and aligned these additional sequences to the genome sequence, identifying millions of sites that vary within the two species, and millions of sites where they share variants. They scanned through all these sites to identify points in the genome where differences between the two small samples of flycatchers were completely fixed — that is, sites where all the collared flycatcher sequences carried one variant, and all the pied flycatcher sequences carried a different variant. The frequency of these fixed differences varied considerably across the genome, but there are dozens of spots where they’re especially concentrated, forming peaks of differentiation.

To learn what all those “islands of divergence” could tell us about how the two flycatchers came to be different species, go read the whole thing.◼

Nothing in Biology Makes Sense: Tuning the molecular clock

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Clock Photo by Earls37a.

Over at Nothing in Biology Makes Sense!, guest poster Gustavo Bravo explains why evolutionary biologists spend a lot of time thinking about how frequently DNA mutations occur.

There are two ways in which we can translate the number of substitutions between a pair of lineages into absolute dates. First, we can calibrate the clock against absolute times resulting from independent evidence such as fossil or geological dates. And secondly, we can measure directly the rate of mutation by comparing DNA or protein sequence data in present day organisms. Because the fossil record for some groups is incomplete and the dating of geological events remains controversial, some of those clocks are likely to produce inaccurate estimates of time.

To learn how re-setting the “molecular clock” has changed our thinking about human evolution, go read the whole thing.◼

Nothing in Biology Makes Sense: Making sense of maternal mammary metagenomics

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Breastfeeding symbol Breastfeeding. Image via Topinambour.

This week at Nothing in Biology Makes Sense!, Sarah Hird digs into a new study of the bacterial diversity in human breast milk.

Cabrera-Rubio et al. (2012) analyzed the bacterial composition of HBM [human breast milk] from 18 women at three time points over 6 months. The mothers in the study varied in weight and delivery method. The researchers were basically exploring what factors influence the microbial composition in breast milk, with an emphasis on weight of the mother. They used next-generation sequencing to produce a library of sequences that were analyzed for what specific bacteria were found in each sample and how the samples relate to one another as whole communities.

Some of the factors that turned out to influence bacterial diversity in HBM are pretty surprising — to find out what they are, go read the whole thing.◼

The Molecular Ecology Online Forum

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Remember the Molecular Ecologist symposium I attended as part of the 2012 Evolution meetings in Ottawa? Well, there’s going to be a sequel, launching Wednesday in convenient online format.

The Molecular Ecologist will be hosting speakers from the Ottawa symposium in a live-chat on the blog, starting at 9 a.m. US Central Time and running until noon (that’s 3-6 p.m. GMT, for those of us located outside North American). We’re trying out a live-chat service called CoverItLive, which will let readers follow the coversation and submit questions and/or comments directly from the blog — test runs have gone pretty smoothly, and I’m excited to see how this works as a medium for scientific discussion.

If you want to review the Ottawa symposium beforehand, check out the archived material at the Molecular Ecology websited. To indicate your interest and submit questions in advance, e-mail Molecular Ecology Managing Editor Tim Vines; otherwise, just join us Wednesday morning at The Molecular Ecologist.◼

Nothing in Biology Makes Sense: The vital importance of genetic variation

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Black Bean Aphid Aphis fabae. Photo by robbersdog.

Over at Nothing in Biology Makes Sense!, Devin Drown describes an interaction between aphids and a species of wasp who lay their eggs in the aphids so their larvae can eat the aphids alive. A new study tests whether the success of a wasp larva infecting an aphid depends on the specific genetics of the wasp, and of a bacterial symbiont the aphid carries:

The Vorburger group studies a crop pest aphid, Aphis fabae, and its common wasp parasitoid, Lysiphlebus fabarum. The adult parasitoids lay their eggs in unsuspecting aphid hosts. As the parasitoids develop they battle the hosts defenses. Some aphid hosts are also infected with a bacterium symbiont, Hamiltonella defensa, which can provide protection against the parasitoid by releasing bacteriophages that target the parasitoid invader (Vorburger et al 2009; Vorburger and Gouskov 2011). If the wasp parasitoid can evade all the host defenses then eventually it develops inside the still living aphid. Eventually, as the authors describe in grisly detail

“metamorphosis takes place within a cocoon spun inside the host’s dried remains, forming a ‘mummy’ from which the adult wasp emerges” (Rouchet and Vorburger 2012).

To learn how Vorburger et al. evaluated the importance of wasp genetics for successfully mummifying aphids, go read the whole thing.◼

Nothing in Biology Makes Sense: God’s AIC score

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The creation of Adam. Image via Web Gallery of Art.

This week at Nothing in Biology Makes Sense! Noah Reid takes a cue from Bill Nye the Science Guy and applies information theory to test whether a model of divine intervention fits a simple phylogenetic dataset.

Without getting into the details, we can think of information theoretic criteria for model selection as formally implementing Occam’s Razor: the simplest model with the most explanatory power is to be preferred. By preferring simple models, you guard against overinterpreting data, a pitfall that can make models poor predictors of new observations.

So, I realized as long as we can formulate any mathematical model of “The Hand of God”, rejectable or not, we can compare it to an evolutionary model in this framework. If, as Nye suggests, evolutionary theory is simple and powerful, and creationism is a model of fantastical complexity that doesn’t much improve our understanding of the data, information theory would help us sort that out.

If you want to settle the whole evolution-versus-creationism thing once and for all (okay, not really), or just learn how biologists use information theory to select models (really!), go read the whole thing.◼