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?

When mummies attack! Why specificity matters for coevolution

Evolutionary change by means of Natural Selection needs a couple of things in order to happen: heritability and variation in fitness. That is, offspring need to resemble their parents at least a little (heritability) and individuals need to differ in their survival and offspring production (fitness). WORDLE Rouchet Vorburger 2012We’ll worry about heritability in another post, but variation is something that seems like it might be hard to maintain. Some forms of Natural Selection will reduce variation as more fit individuals become frequent and all the different kinds of less fit individuals are eliminated from the population. However, there is a force, common in nature, which may maintain variation, parasites.

Interactions between hosts and parasites can generate strong selective pressures on each player, especially if your life depends on infecting a host. Often, biologists make an analogy to an arms race where players are developing bigger and better defenses or weapons. Antagonistic interactions may also generate negative frequency dependence where a rare host type is favored because the parasites are adapted to a common type. You can learn more by checking out CJ’s post on the Red Queen Hypothesis or Jeremy’s post on a different coevolutionary puzzle. A key component for maintaining variation via negative frequency dependent selection is specificity. There must variation in the interaction among different host genotypes and parasite genotypes. This is sometimes referred to as a GxG interaction. If parasites can infect all the hosts, there is no specificity. Specificity allows different hosts to be favored over time depending on the composition of the parasite population.

Theoreticians love to use different models of interactions between hosts and parasites, but without empirical evidence, there seems little point. In a recent paper by Rouchet and Vorburger (2012), the authors looked for evidence of just the kind of genetic specificity would result in the maintenance of genetic variation.

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Friday Coffee Break, Vienna 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 Devin:

The future of online learning. PLOS Computational Biology puts together a great set of online resources for biologists or more specially a bioinformatics Curriculum. “…in an exhaustive meta-analysis of 51 published head-to-head trials, found that ‘on average, students in online learning conditions performed better than those receiving face-to-face instruction’” 

From Sarah:

Even “living fossils” have evolved over time.  The term debunked in this piece on the Wired Science Blog. “The new fossil described by Briggs and colleagues records a critical transformation in horseshoe crab history. Discovered at an exceptional site in the 425 million year old rock of Herefordshire, England, the new genus is justly called Dibasterium durgae – a tribute to the invertebrate’s mysterious limbs and to Durga, ‘the Hindu goddess with many arms.’”

From Jeremy:

Which professions do you think drink the most coffee?  If you guessed Scientists you’d be right.  Learn more here from a poll by Dunkin Donuts and CareerBuilder to determine the most caffeinated workers. “Scientists today are spending much more time working than initially intended. They are deprioritizing their hobbies, leisure activities, and regular exercises, which negatively influenced their mental and physical health.”

From Noah:

Native Inuit of Canada face new challenges with increased climate change and rapid retreat of sea ice along with encroaching industry. “Some Inuit feel they are losing control of a homeland whose ice-covered expanses had acted as a barrier to the outside world. A growing number of interests — mining and oil companies, scientists and conservationists, military vessels from Canada and other Arctic nations — are appearing in the Inuit’s traditional homeland…”

Finally From Jon:

The trend of Doctors turning away from insurance and moving to cash only concierge service could pose a problem for the future of access to care for uninsured and underinsured patients. “a new survey of 13,575 doctors from around the country by The Physicians Foundation found that over the next one to three years, more than 50 percent plan to take steps that reduce patient access to their services, and nearly 7 percent plan to switch to cash-only or concierge practices, in which patients pay an annual fee or retainer in addition to other fees.”

Evolution vs. Creationism: A completely unambiguous, logically unassailable scientific test. Now we can all stop arguing on the internet about it.

Bill Nye the Science Guy.

Bill Nye (the Science Guy!) has recently thrust himself into the public eye with some commentary on the implications of the persistent fights over the teaching of evolutionary theory in the United States. One of the soundbytes that emerged from the whole thing really jumped out at me:

Your world just becomes fantastically complicated when you don’t believe in evolution.

As an evolutionary biologist, my first defense against any religious impingement on science is often to say that appeals to divine intervention are not rejectable. Therefore they cannot be addressed using in the hypothetico-deductive method and so should be excluded from scientific inquiry. I often add when talking to undergraduates that if any of them came up with a rigorous, falsifiable model of divinity, they would certainly be famous for it.

But when I read this quote, I realized I’d been selling science short. Bill Nye’s statement suggests that we don’t HAVE to view religious hypotheses as untestable simply because they are unrejectable. In many cases in science, we are interested in finding a useful working model of some phenomenon. In those cases we regularly view the issue as one of choosing the best model from among a set of candidates rather than one of rejecting all models that are wrong. In at least one case I can think of, we apply a complex, unrejectable model in a test of the adequacy of a much simpler model (about which, more below).

When we engage in this process, we often employ Information Theory to guide our selection. 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.

So why not give it a whirl?

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