Friday Coffee Break, Easter/April Fools edition

black coffee with chocolate easter eggs

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

To get this weeks coffee break started, Amy brings us a post about the Paleo diet.  A new book by Marlene Zuk aims to show that the Paleo diet is a misinterpretation of evolution.

Jeremy takes the time this week to wonder about the effect on sea level if all the ships in the ocean were removed.  Alternatively, XKCD also wondered what would happen if you removed all the sponges.

Sarah stumbled upon this gem of a PDF book which will hopefully prove useful as she transitions from student to post doc.  She also brings up the potentially scary idea that you may not own your own DNA.  At least if the current patent situation remains upheld.  What happens if a company can own a 15-base pair fragment of DNA?

CJ continues the discussion on DNA with an article on the recent sequencing of the HeLa genome and the continued controversy regarding the ownership and publication of an individuals genome.  We continue to venture on into a strange new world with these issues.

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Which came first: The obese chicken or its obese microbiota?

Historically, medical research has focused on pathogenic bacteria when trying to understand the relationship between human health and microorganisms. This makes intuitive sense – since pathogens make us sick – but our bodies host way more nonpathogenic bacteria than pathogens and they function in keeping us healthy. Our gastrointestinal tract has trillions of bacteria in it and much recent work has been trying to understand these complex communities. Mice are a common model for understanding human gut microbes and health. Enter Obie, the obese mouse (Figure 1, left) and Lenny, the lean mouse (right).

Figure 1: Obie and Lenny

Obie and Lenny are genetically different at a locus in their genomes that codes for leptin – a hormone that inhibits appetite. Mice that can’t make this hormone become very hungry and morbidly obese. These two mice also differ in the composition of their gut microbiota – obese individuals (both mice and human) have different amounts of the main bacterial phyla in their gut and as a result, are able to more efficiently extract calories from food. In other words, if you give both of them the exact same amount of food, Obie is going to get more calories from it than Lenny, contributing to Obie’s weight problem. In humans, where the status of our “leptin locus” is not normally known and probably not as straightforward as the case of Obie and Lenny– it’s been hard to tell whether this shift in gut microbiota is the CAUSE of obesity or the EFFECT of obesity. That brings me to today’s paper: a short communication in The ISME Journal (that’s open access!) by Fei and Zhao that addresses this exact problem.

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Friday Coffee Break, Official Springtime Edition

springcoffee

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

With the official start of Spring this week, at least depending on where you are.  For me, I’m currently sitting in Ithaca, NY where the high for the day is still only squeaking into the above freezing range which only makes me miss Richmond, VA right now all the more.  So without further adieu, which is apparently my new catch phrase, your links for the week.

To start things off on a light and happy note.  Sarah has some wonderful news that she passed her dissertation defense!!  She is so excited, as she should be, that her link this week is a ton of dancing GIFs.  Of note, she things either Carlton or Ace Ventura match her mood best.  Congrats Sarah!

This week CJ wonders about the possibility of a gender gap in pain perception as discussed in the NYTimes article.  She also thought this article gave a good break down of the process of becoming tenured and is indeed quite helpful (and makes me glad to be in the field that I am in).  And finally, an opinion piece on why De-extinction would not work.

From Jeremy, a piece from the blog Why Evolution is True on why science writing is tedious and often boring and what it takes to write good science.

From Amy, a depressing story on the passage of an amendment limiting the funding for NSF research regarding political science and the letter from Senator Tom Coburn justifying this measure.

Finally, I’d like to end things with a video.  I’m a big fan of TED talks and also of U2, so when I saw that Bono gave a TED talk about his passion of helping to fight to end poverty I thought it was worth a look.  I loved his analogy of how poverty could end in as short a time period as about 3 more Rolling Stones farewell tours.

Natural History in the -omics era

This post is a guest contribution by Michael Harvey, graduate student in Robb Brumfield‘s lab at the Museum of Natural Science at Louisiana State University. Mike studies avian evolution, phylogenomics, and Neotropical ornithology. 

Blackwater river…approximate Bayesian computation…dawn song…genomic islands…wing chord…target DNA enrichment…

My life as an evolutionary biologist straddles two worlds. I study the comparative phylogeography of Amazonian birds, and on the one hand my research involves laboratory and computational methods that push the limits of new technologies and analytical techniques, and on the other, expeditions to the tropics that are nearly indistinguishable from the natural history work conducted by Victorian era biologists. I am a PhD student at Louisiana State University, and for most of the year my work is in the lab and at my desk. For several months of the year, however, my work is general ornithological collecting expeditions to the Amazon Basin.

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Friday Coffee Break, St. Patty’s Style

Irish Coffee

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

First of all, my deepest apologies for the lateness of this post.  As you may know I am a 4th year medical student and today was Match Day and I was deep in the throws of celebrating the completion of 4 years of medical education as well as learning where I will be training for the next three years in Family Medicine.   So, without further adieu, your links for this week.

CJ decided to that there were too many good links and had to share several.  First, as a skater herself she found an article relating to transmission of skin flora between close team mates and those competing in roller derby.  Next she decided to share how the sequester is going to affect science jobs and the next few years could be difficult.  But finally, a cool post on five animals that could possibly take over the world, which makes me look at spiders a little closer now.

Next, Jeremy likes the fact that new evidence from the Mars rover is favorable to the possibility of conditions that could have sustained life on the red planet.

From Sarah, some very cool slow mo predator vs. prey footage.  Gotta say this is pretty awesome!  She also found some up close and personal pics of jumping spiders.

From Noah, a video documenting several scientists as they inventory one of the worlds most biodiverse locations, the Yasuni Biosphere Reserve.

Finally, in the spirit of March Madness, from Devin comes a battle of the Mammals. “Mammal March Madness from the Mammal’s Suck blog. Although the tournament is purely fictional, the facts and natural history information given out during the extended live tweet rounds are amazing. The first rounds are already complete, but tune in for the exciting finals. Live action via twitter: @Mammals_Suck and general info via the website:”

How many phylogenies are there in a genome? Lots!

One candidate for the original “evolutionary tree”—the only figure illustrating the first edition of The Origin of Species. Image via Wikimedia Commons.

Biologists have been constructing trees since before we knew why tree-shapes made such convenient organizing structures for living things. Since Charles Darwin (and Alfred Russel Wallace) first made the case that diverse groups of living species arise from common ancestors, we understand that tree-like relationships reflect this common descent, so that if we can infer the specific structure of those relationship-trees, or phylogenies, we can begin to draw conclusions about how individual species evolved to be what they are today.

Back in the day, we had to estimate phylogenies using directly observable characteristics—measurements of particular parts of particular bones (for mammals), or the shape of the antennae (for butterflies), or the capacity to synthesize lysine (for paramecia). If species that are more recently related tend, on average, to look more similar than each other, this kind of morphological data can be useful. But! When you’re setting out to reconstruct a phylogeny from a whole pile of morphological measurements—dietary preferences, tooth counts, fur color, wing length—what do you do when different traits support different relationship structures? Different traits will naturally change at different rates over evolutionary time, and it’s rarely obvious what those rates are.

Starting in about the 1970s, though, it became increasingly straightforward to directly compare the genetic codes of differnt species. That’s appealing for several reasons: first, because DNA is as direct a marker of inheritance as you can find, it provides a record that’s independent of potentially misleading, morphological similiarities. Second, because DNA sequences have only four character states—the good old “bases” adenine, guainine, thiamine, and cytosine—it’s more tractable to estimate how they change over time.

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Friday Coffee Break, Spring Break Style

Every Friday at Nothing in Biology Makes Sense! our contributors pass around links to new scientific results, or science-y news, or videos of adorable wildlife, that they’re most likely to bring up while waiting in line for a latte.

beachcoffee

To get things started, CJ found a depressing study (depending on your perspective anyway) about how your attitude can affect your health.  It’s not what you would expect a study to find, but there are additional conflicting studies so take it as you will.  However, she follows it up with another article about how the privatization of space flight has a long way to go before we can all reach for the stars.

From Amy, a new variant in the African-American Y-chromosome leads to the speculation on how long ago the common ancestor of modern humans existed and/or whether there was potential interbreeding between Neanderthals and modern humans.

To follow that up, Jeremy found an interesting video that shows a morphing of the faces of human ancestry.

From Sarah, a rather fun blog post on Scientific American on how one individual looked for answers to questions and found lots of information, but failed to answer the original question.

Finally, to return to the spring break theme, the CDC reports in its weekly grand rounds about multi-drug resistant gonorrhea.