A science-y tweet makes my heart skip a beat

When I first heard about Twitter (several years before I actually understood what it was) – I remember thinking it sounded silly. Who cares what celebrities are thinking (Figure 1)? I dismissed everything Twitter-related as irrelevant and continued on my merry way. I think it was during Evolution 2011 that Jeremy (from this blog) suggested I join Twitter because you can follow interesting talks and remain engaged throughout conferences. It took a little while for me to work up a real affection for Twitter but the longer I’ve been a member (and perhaps the longer Science and scientists have had to assimilate it into our work world), the more useful I find it (Figure 2).

Figure 1: An example of the "Why bother?" side of Twitter. Why 103,000 people thought this was worth repeating via "retweeting" is beyond me because it gets dumber each time I read it...

Figure 1: An example of the “Why bother?” side of Twitter. And why 103,000 people bothered repeating this via “retweeting” is beyond me. It gets dumber each time I read it.

Figure 2: Why you actually should bother. Devin's posts include (top to bottom) - passing along a job opportunity, interesting publication, a professional interaction about science spam, a second paper and link to our blog!

Figure 2: Why you actually should bother. Devin’s posts include (top to bottom) – passing along a job opportunity, interesting publication, a professional interaction about science spam, a second paper and link to our blog!

Regarding social media and scientists in general, Bik & Goldstein have written a great introduction. They discuss the pros and cons of several platforms (i.e., blogs, Facebook, Twitter) and how to choose amongst these depending on your interests. For example – are you most interested in communicating science to the “general public”? TO THE FLOW CHART! Perhaps creating your own content in the form of a blog is for you. Alternatively, are you more interested in compiling cool stuff you’ve found from across the world wide web? Consider Facebook.

Despite the ubiquity of social media in our world, many scientists are reluctant to embrace it. That’s somewhat understandable – “Why bother?” is an easy question to ask and get no answer to if you’re “unplugged”. Bik & Goldstein outline four major “research benefits from an online presence”.

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Friday Coffee Break

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.

It’s like the saddest picture book you’ve ever read. True stories about how some species went extinct. (from Jeremy)

The hoatzin becomes an even cooler bird. (from Noah)

Looking for a phylogenetics discussion board? Try phylobabble. Looking for free silhouette pictures of plants and animals? Try phylopic. (from Sarah)

When art and science meet – oh baby – that’s some good stuff. Awesome glass sculptures of viruses. (from CJ)

Are you an aspiring statistician? How to read histograms and use them in R.  (from Amy)

They look like ants, but they’re ain’ts! (from Jeremy)

Need help with the whole peer-review thing? Look no further than this guide from the British Ecological Society. (from Sarah)

Friday Coffee Break

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.

Should we consider poop a drug or a tissue when it’s used to cure the ill? Or – now hear me out – a DIY project?

“Fairness” may have evolved out of spite, not goodness. (That sounds about right, wouldn’t you say, humans?)

Your brain and Fido’s are more similar than you might think.

Ever notice how the “impossible” actually happens sometimes? Why is that?

Friday Coffee Break

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.

Ant larvae only poop ONCE?!?! (From Jeremy)

Sir David Attenborough is losing patience with you people. (From Sarah)

Long-read (and Yong-read) on the endosymbiotic origin of eukaryotes. (From Jeremy)

5 misconceptions about evolution, with very nice graphics. (From CJ)

A nice synopsis on the joy of scientific discovery. (From Bill Nye, from Amy)

Why do stinky animals live alone? Hint: It’s not the reason stinky humans live alone. (From Jeremy)

Some harsh advice on your cover letter. (From Sarah)

Friday Coffee Break

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 Turkish coffee.

Will the puma catch the monkey? Let the pictures tell the story. (From Noah)

What’s the connection between cycling success, birth control and attractiveness? Science. (From Amy)

Can’t get enough of the Bill Nye/Ken Ham debate? We’ve got “the most powerful evidence for evolution that you can imagine” (from Jeremy). Also, and dependent on your blood pressure, the somewhat baffling list of 22 messages from Creationists after the debate.

Boobies are amazing. (I know you want to click this one because you have no idea what’s going to come up. Am I right? From Sarah)

Bee sting, bad. Bee portrait, oh so good. (From Noah)

Better than citations, enter the hypercitation. (From Sarah)

Pssst. Your holobiont is showing.

Here’s a sad story: Species A mates with Species B. They succeed in making a Hybrid Baby but their Hybrid Baby dies before it can fully develop. (I warned you it was sad.) Why did that happen? Sure, sometimes two genomes are just too different to successfully coexist – both the stars and the chromosomes must align to make a baby. Other times, as recently reported by Brucker and Bordenstein, the Hybrid Baby’s microbiota is the problem.

I think (or rather Google thinks) this is a Nasonia wasp.

In Nasonia wasps, there are three closely related species that all diverged less than one million years ago: Nasonia vitripennis (who I’m going to refer to as the V wasp), N. giraulti (the G wasp) and N. longicornis (the L wasp). When L and G mate and their LG offspring are mated to other LG offspring, 8% of the males die. When V and G mate and their VG offspring are mated to other VG offspring, 90% of the males die.

The phylogeny of the three Nasonia wasps (left) and the crosses that result in hybrid male lethality.

The phylogeny of the three Nasonia wasps (left) and the crosses that result in hybrid male lethality.

Brucker and Bordenstein hypothesized that microbes were responsible for the hybrid lethality of the the VG hybrids. Through DNA sequencing, they found that the gut microbes of the VGxVG wasps were unlike either parental type (in abundance or diversity), whereas the LGxLG wasps were. So, when a hybrid’s gut microbiota is like one of the parental species, the hybrid males live. When the gut microbiota is unlike a parent, the hybrid males die. They further found this could be boiled down to a change in the single dominant species: whereas a Providencia bacterium was most abundant in both V and G parents, a Proteus bacterium was most abundant in VGxVG wasps.

But that doesn’t conclusively show that microbes are responsible for the hybrid lethality. Brucker and Bordenstein then compare germ-free hyrbids to conventional hybrids – in other words, if we remove the germs (the microbiota, that is), do the hybrids still die? The short answer is no. Under normal conditions, about 80% of the pure Vs and pure Gs survive, whereas only 10% of the VGxVGs survive. Under the germ-free conditions, about 70% of the pure Vs and pure Gs survive and 60% of the VGxVGs survive. That’s a pretty significant increase in living hybrids! And to strengthen the case even more – when the germ-free wasps were fed a mixture of Providencia and Proteus bacteria, the hybrid survival rates went down to about 30%.

The authors perform other experiments for this study that include analysis of wasp genomic loci that were previously linked to hybrid lethality and a transcriptomic analysis, where they find immune genes to be a significant player. However, I’m going to switch gears a little bit and talk about the context the authors frame their discoveries in: the HOLOGENOME concept.

Most evolutionary biologists probably consider the individual as the fundamental unit of natural selection. We think about the genes of one mother or one father being passed on to one descendant. But is this view too constrained? The “hologenome” is all the genomes that belong to the “holobiont” – an organism and all its microbes. The Hologenome Theory of Evolution posits that the holobiont is the fundamental unit of natural selection, not just “the big organism”. Generally speaking, this makes a lot of intuitive sense, I think: we macros are pretty dependent on micros to get our genes to the next generation. But is the reverse true? To be THE fundamental unit of selection, the holobiont must pass its hologenome to its offspring – and I’m not sure this assumption universally holds. Certainly some macro-organisms always pass specific micro-organisms to their offspring (coprophagy in mammals might be a good example). But in most cases, where our microorganisms come from is a mix of vertical transmission (from our parents) and horizontal transmission (from the environment). I just can’t make this distinction make sense with what I think I know about heredity and selection. Natural selection depends on traits that make an organism more fit being passed on to its offspring and if some – or most? – of our microbiota is randomly acquired from the environment, natural selection can’t act on it. On the other hand, it’s very possible reality doesn’t abide by our definitions: perhaps only a few microbial taxa need to be passed directly from parent to offspring and these “founders” get microbial communities off on the right track and the rest of the communities fall into place from the environment.

Regardless – Brucker and Bordenstein pretty conclusively turned that sad story into a science story by showing that in Nasonia wasps, gut microbes play an integral role in hybrid survival. And if the Hologenome Theory of Evolution applies anywhere, I’d say it does here!

A healthy viable Nasonia holobiont (top) and an unhealthy, inviable Nasonia holobiont (bottom). From Brucker and Bordenstein (2013), figure 1B.

The sad story told in pictures: A healthy, viable Nasonia holobiont (top) and an unhealthy, inviable Nasonia holobiont (bottom). From Brucker and Bordenstein (2013), figure 1B.

Brucker, R. M. & Bordenstein, S. R. 2013. The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia. Science 341: 667-669.

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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Bacteria, Circumcision and HIV. Oh my!

Basically every place on our bodies is loaded with bacteria. All of these communities are important (I’ve written about some of the ways before) and more and more research seems to be finding that our microbes play an active role in fighting (or causing) disease.

So maybe it’s obvious that microbes in our swimsuit areas could be involved in sexually transmitted disease. OK, maybe not “obvious” but it may be the case with HIV and the penis microbiota. Did you know that circumcision reduces the rate of HIV transmission to men by 50 – 60%? That’s a pretty significant reduction (no pun intended). There are two major (and non-mutually exclusive) hypotheses as to how circumcision accomplishes this – morphological and bacterial. [SIDENOTE: if you are unfamiliar with the technical aspects of circumcision, I suggest Wikipedia – which has a lot of information but contains an image or two that may not be safe for work – or this Mayo Clinic site.]   

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Friday Coffee Break

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 - 

Just in time for snot season, scientists discover a ‘blue print’ for a universal flu vaccine. Yay Science!

“The immune system produces these CD8 T cells in response to usual seasonal flu,” Prof Lalvani said. “Unlike antibodies, they target the core of the virus, which doesn’t change, even in new pandemic strains.

If imitation is the sincerest form of flattery, Malaysian orchids must be super flattered by the orchid mantis.

“The orchid mantises we observed were not hiding amongst flowers, but were sitting on their own against a backdrop of green vegetation,” O’Hanlon said. “Thus, it was the body of the mantis itself that was attracting the pollinators, and not any flowers in its vicinity.”

From Sarah - 

Another awesome mimic??? WAHOO! But this time it’s Uropyia meticulodina moths and dead leaves.

And it’s not just brown like a curled up, dead leaf, it depicts a leaf catching the light, with shadows in all the right places and you can even see the veins casting tiny shadows along the curled underside. It’s like one of those optical illusions that still work even when you know it’s a trick.

Science news nexus PopSci is no longer allowing comments on their articles…and for really good reasons!

A politically motivated, decades-long war on expertise has eroded the popular consensus on a wide variety of scientifically validated topics… And because comments sections tend to be a grotesque reflection of the media culture surrounding them, the cynical work of undermining bedrock scientific doctrine is now being done beneath our own stories, within a website devoted to championing science.

Speaking of comments on blogs, we here at Nothing In Biology have posted a very condensed blog commenter and contributor policy. And before you ask – yes, there is a Monty Python reference involved.

From Amy - 

An attractive, simple and delightful motions graphics piece explaining the big concepts in evolution. It’s so fun to watch, you won’t even know you’re learning!

From Noah -

The iconic Darwin’s Finches are being threatened by a parasitic, introduced fly.

“Usually their beak is all messed up,” said George Heimpel, an entomologist at the University of Minnesota who has done research on the fly. “And for Darwin’s finches we know that the beak is an important part of their livelihood.”

From CJ -

The requirements for a perfect colleague (according to one delusional scientist).

I will not work with a colleague that does not have a NIH or NSF career development grant.

I am not looking for any type of colleague that is materialistic or a gold digger or expects a collaborator to pay for everything.

Friday Coffee Break

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 -

Coffee goes really well with information about plant immune responses.

The plant behaves as an integrated organism, but communication from one part of the plant to another is not the same as having a central nervous system.  We might try to imagine what it feels like to be a plant (normally or when under attack), but even if the plant is a unitary creature, its sensory awareness doesn’t have to be ‘conscious’ or centralized for it to be an example of the integration of many parts into a whole.

From CJ -

Oh, the stories that whale’s earwax could tell!

Whale earwax is a fat-rich deposit that stores the same chemical data as blubber. But it also records time — similarly to the rings of a tree, the wax is laid down in light and dark bands, with each band correlating roughly to a six-month period. In baleen, or filter-feeding, whales, earwax forms a solid plug that may be tens of centimetres long and remains intact even after its death.

A nicely timed (although slightly profane) complement to CJ’s post last week on science funding.  Do you really f*&#ing love science?

If you really love science, you’ll start making noise about this issue.  You’ll start asking why the US is shooting itself—and the world—in the foot, by putting science on the back burner.  We can spend as much as we want on other things, but in the end, if we’re not funding science, we’re moving backwards.

From Amy -

Do you ever feel like you just don’t have enough time to understand contemporary genius’ and their theories? It can’t just be me or this really awesome video – Stephen Hawking’s big ideas made simple – would have been sent to me personally. 

From Noah -

It’s like where Neo does that thing with the bullets in the Matrix – except with animals and actual data. Small animals perceive time on a different scale than larger animals and can use that to escape predators with lightning fast reflexes.

“Flies might not be deep thinkers but they can make good decisions very quickly.”

From Sarah -

Did you catch Bill Nye on Dancing With The Stars? Some wonder if his performance was a little counterproductive.

His dance did end with fans cheering his name, and he had the biggest social media buzz of any contestants. But I think his over-the-top performance on “Dancing With The Stars” on Monday night was a disservice to the science community by reinforcing stereotypes that scientists are nerdy, old white men who can’t dance.

And finally – the  top 10 - nay - the top 20 - important questions in science. From “What is the Universe made of?” to “Can we travel in time?” with a little “What’s the deal with prime numbers?” in between. Get ready for some brain bending.