Is our clock ticking at the right pace?

This week’s post is a guest contribution by Gustavo Bravo, who recently finished his Ph.D. at the Louisiana State University Museum of Natural Science , working on the systematics and diversification of the Neotropical bird family Thamnophilidae. 

A pervasive goal in evolutionary biology is to elucidate the history of living organisms on Earth. Because we are often interested in knowing when different lineages might have originated, we use different resources to date speciation events as accurately as possible. One of these tools is the “molecular clock”, which is a technique that relies on the rates of nucleotide (DNA) or amino acid (protein) change to infer the timing of events in the distant past. The idea behind the molecular clock is that over time a DNA fragment may accumulate mutations at a constant rate, or in “clock-like” fashion as it is commonly referred to. Therefore, the number of substitutions in a DNA fragment between two different organisms might be proportional to the amount of time since they diverged from each other.

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.

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Friday Coffee Break, Gangnam 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.

My apologies for the lateness of this Korean version of the Friday Coffee Break!

From Sarah:

Starting off on a light note this article describes how dogs can “catch” yawns from humans but only after they are old enough to understand empathy and emotion.  Also from Sarah, has anybody wondered why no mention of the dreaded “C” word (aka Climate Change) has come up at any of the presidential debates?  This blog post from the NYTimes discusses that issue.

From Noah:

Rogue scientist and entrepreneur Russ George dumped tons of iron dust in the Pacific Ocean off the west coast of Canada, “calling it a “state-of-the-art study,” said his team scattered iron dust several hundred miles west of the islands of Haida Gwaii, in northern British Columbia, in exchange for $2.5 million from a native Canadian group. The iron spawned the growth of enormous amounts of plankton, which Mr. George, a former fisheries and forestry worker, said might allow the project to meet one of its goals: aiding the recovery of the local salmon fishery for the native Haida. “

From Jeremy:

Does taking Ritalin increase individuals enhance desire for social conformity?  This study here postulates that there may be some element of connection between increased dopamine levels brought on by taking Ritalin and conforming to social norms.

From Devin:

This link (which at the time of publishing this story appeared to be broken) is a tumblr page dedicated to “things I learned as a field biologist.”  Hopefully the link gets fixed soon.

From Jon:

Given the overabundance of awesome links and a couple medically related ones, I’m going to end this post with a fun video!  Did you know that the lyrics to Gangnam Style is a satire poking fun at the wealthy Gangnam district in Seoul and also discusses how the singer likes the kind of lady who enjoys the freedom of a cup of coffee. I figured given this connection it was only perfect to end the month of October with the Gangnam Style theme!

I’m a total science fiction geek and couldn’t help myself.  There are quite a few other well done parodies of the original video as well such as Obama Style, Mitt Romney Style and even Gunman Style.  Enjoy!

C is for colostrum; C is for cool

Colostrum |cuh-laas-trum| (noun): the first secretion from the mammary glands after giving birth, rich in antibodies 

The amount of research happening right now on microbes and human health is enormous. Think multi-hundred-million dollar, international-collaboration enormous. I’m sure the interest has been building for a long time, but the game changer I’m aware of is Ley et al. (2005), which showed that bacterial communities in obese mice were statistically similar to those from other obese mice and statistically different from normal-weight mice. Turnbaugh et al. (2006) showed that the shift that occurs from normal to obese* microbial communities favors microbes that are more efficient at extracting energy from a given amount of food. I’ll repeat that part: obese individuals extract more calories from a given piece of food than normal-weight individuals extract. The obese individuals have lower bacterial diversity, a trait that has also been linked to allergies. The childhood obesity epidemic is of particular concern to us all – up to a third of American children are obese and the detrimental health effects of this disease are well documented. Having a well-functioning gut microbiota may be a key to healthy weight.

That brings me to today’s topic: human breast milk (which I’ll refer to as HBM for the rest of the post). Cabrera-Rubio et al. (2012) analyzed the bacterial composition of HBM 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.

I couldn’t bring myself to Google image search “human breast milk” so instead I searched “babies”. Note1: there were over a billion hits (click the image to see the little text above it). Note2: the third “Related Searches” term was “black babies” which made me think – why ARE all the Google babies the same color? Curious.

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The Molecular Ecology Online Forum

Cross-posted from Denim and Tweed.

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.◼

Friday Coffee Break, Turkish 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.

From Jeremy and Noah:

Apparently this particular link is so impressive it gets two recommendations!  “OneZoom is committed to heightening awareness about the diversity of life on earth, its evolutionary history and the threats of extinction. This website allows you to explore the tree of life in a completely new way.”

From Sarah:

The quintessential list of items every graduate student should have (at least something similar in each category).  And also, in this story on NPR global warming could have a very detrimental effect on one particular species of  lizard the Tautara as egg temperature determines gender.

From Devin:

Australian scientists respond to massive government budget cuts for funding here and also here.

From Amy:

The evolution of drug resistent strains of gonorrhea or how the clap came back.

And finally from Jon:

Healthcare is very slow to adopt new technology but the flood of mobile technology might help make trips to the doctors office less painful with real time updates on when the doctor is available and to help patients check in.

Many genes, but two major roads to adaptation

Cross-posted at Denim and Tweed.

In the course of adaptive evolution — evolutionary change via natural selection — gene variants that increase the odds of survival and reproduction become more common in a population as a whole. When we’re only talking about a single gene variant with a strong beneficial effect, that makes for a pretty simple picture: the beneficial variant becomes more and more common with each generation, until everyone in the population carries it, and it’s “fixed.” But when many genes are involved in adaptation, the picture isn’t so simple.

This is because the more genes there are contributing to a trait, the more the trait behaves like a quantitative, not a Mendelian, feature. That is, instead of being a simple question of whether or not an individual has the more useful variant, or allele, at a single gene — like a light switch turned on or off — it becomes possible to add up to the same trait value with different combinations of variants at completely different genes. As a result, advantageous alleles may never become completely fixed in the course of an adaptive evolutionary response to, say, changing environmental conditions.

That principle is uniquely well illustrated by a paper published in the most recent issue of Molecular Ecology, which pairs classic experimental evolution of the fruitfly Drosophila melanogaster with modern high-throughput sequencing to directly observe changes in gene variant frequencies during the course of adaptive evolution. It clearly demonstrates that when many genes contribute to adaptation, fixation is no longer inevitable, or even necessary.

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Friday Coffee Break, Irish 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.

From Jeremy:

Antifeminist piece penned by guest editor of Canadian Journal of Physics, Gordon Freeman, gets only mild retraction.  Read synopsis of incident here.  Also, mice may be able to mimic vocalizations that actually could be classified as singing.  Read more at Scientific American.

From Noah:

Oops, lemurs in South America turn out to be misidentified fish.  Find out how this mistake was made on the wired science blog here.

From Devin:

Given the current condition of the economy it never hurts to go back and review tips for nailing that next job.  Here are some tips for writing your next cover letter.

Finally some lighthearted reads from Sarah:

The first is a NY Times piece about an adorable baby walrus orphan found off the coast of Alaska finds a new home in NYC.  The second is perhaps proper justification for owning a dog instead of a cat.  Just how many creatures does the average domesticated house cat kill?