Unrelated to all that, 8/30 edition

Humanity’s Longest Lasting Legacy May Be The Miles Of Holes We’ve Dug

The distance to the center of the Earth is roughly 3,960 miles (6,373 kilometers). Animal life stops 1.2 miles (2 km) below the surface — the depth where miners discovered deep-dwelling worms in South African gold mines. All known microbial life stops at a depth of around 1.7 miles (2.7 km). But humans have left a permanent mark well beyond those depths, geologists say.

Humans’ first underground foray came during the Bronze Age, when people began digging shallow mines in search of flint and metals. The Industrial Revolution of the 1800s sent humans even deeper below the surface. Still, many of the disturbances, like water wells, sewage systems and subway lines, were relatively shallow and extended less than 330 feet (100 m) below the surface. Only after 1950, a period referred to as the “Great Acceleration” by some geologists, did humans really plunge below 330 feet, Zalasiewicz and his colleagues explained.

A Unified Theory

For the last half-century we’ve had a popular notion that our intellectual culture is sundered in two — the literary and the scientific. “The two cultures” is the bumper-sticker phrase for this view. It dates back to a hugely influential 1959 lecture, also published in book form that year, by C. P. Snow — “a moderately able research chemist who had become a successful novelist,” in the historian Lisa Jardine’s not very adulatory description. According to Snow, on one side were the humanists, on the other the scientists, and between them lay a shameful “gulf of mutual incomprehension.”

In the 21st century, the two cultures are still with us, but the fault lines have shifted. Plenty of people can talk about thermodynamics and Shakespeare with equal facility; for that matter, no one has ever explained the second law better than Tom Stoppard in “Arcadia” (“You cannot stir things apart”). You’re probably comfortable with scientific expressions like “litmus test.” The question now is, can you explain a hash table? A linked list? A bubble sort? Maybe you can write — but can you code?


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Trapjaw ants, filmed at 600 frames per second

By Adrian Smith; taken from Myrmecos.

The smell of rain: what is petrichor?

  1. a pleasant smell that frequently accompanies the first rain after a long period of warm, dry weather.
    “other than the petrichor emanating from the rapidly drying grass, there was not a trace of evidence that it had rained at all”

After the goofy first 40 seconds, this video lists two things that make up the ‘smell of rain’: ozone and petrichor.

Petrichor is the decomposing plant matter that rain causes to erupt from the soil. This same substance is – supposedly – a signal to plants that the soil has been dry and will prevent seeds from sprouting.

But when I went looking for more scholarly information on petrichor I found it…practically non-existent. There were no articles that mentioned it in the 2000s. There was one article that mentioned it in the 1990s. There were a few articles that mentioned referred to a specific article from the 70s. In fact, the were only two original research articles that I could find investigating petrichor as a scientific concept, both by the same two authors: IJ Bear and RG Thomas. These are “Petrichor and Plant Growth” and “Genesis of Petrichor“. As far as I can tell, none of the research was followed up on or replicated though the idea has occasionally been taken up in other contexts.

Petrichor clearly exists as a smell, but it turns out that there is precious little knowledge of what it actually is.

[via Ed Yong]

The sound of silence

Sensory neurons receive input from the outside world and send these signals on to the rest of the nervous system. This makes the concept of ‘silence’ fairly intriguing: what happens when there is very little sensory signal for the rest of the brain to process? It is well known that, after a while, no sensory stimulation means massive hallucinations. But quiet – brief periods of weak or no relevant stimulus – is different:

In the mid 20th century, epidemiologists discovered correlations between high blood pressure and chronic noise sources like highways and airports. Later research seemed to link noise to increased rates of sleep loss, heart disease, and tinnitus. (It’s this line of research that hatched the 1960s-era notion of “noise pollution,” a name that implicitly refashions transitory noises as toxic and long-lasting.)

Sound waves vibrate the bones of the ear, which transmit movement to the snail-shaped cochlea. The cochlea converts physical vibrations into electrical signals that the brain receives. The body reacts immediately and powerfully to these signals, even in the middle of deep sleep. Neurophysiological research suggests that noises first activate the amygdalae, clusters of neurons located in the temporal lobes of the brain, associated with memory formation and emotion. The activation prompts an immediate release of stress hormones like cortisol. [neuroecology: really? all noises?]

…He found that the impacts of music could be read directly in the bloodstream, via changes in blood pressure, carbon dioxide, and circulation in the brain. (Bernardi and his son are both amateur musicians, and they wanted to explore a shared interest.) “During almost all sorts of music, there was a physiological change compatible with a condition of arousal,” he explains…But the more striking finding appeared between musical tracks. Bernardi and his colleagues discovered that randomly inserted stretches of silence also had a drastic effect, but in the opposite direction. In fact, two-minute silent pauses proved far more relaxing than either “relaxing” music or a longer silence played before the experiment started.

In light of this, I found the experiences of a hermit who has been living alone since the 1980s fascinating:

He explained about the lack of eye contact. “I’m not used to seeing people’s faces,” he said. “There’s too much information there. Aren’t you aware of it? Too much, too fast.” (Note: he may have asperger’s)

“But you must have thought about things,” I said. “About your life, about the human condition.”

Chris became surprisingly introspective. “I did examine myself,” he said. “Solitude did increase my perception. But here’s the tricky thing—when I applied my increased perception to myself, I lost my identity. With no audience, no one to perform for, I was just there. There was no need to define myself; I became irrelevant. The moon was the minute hand, the seasons the hour hand. I didn’t even have a name. I never felt lonely. To put it romantically: I was completely free.”

…”What I miss most,” he eventually continued, “is somewhere between quiet and solitude. What I miss most is stillness.” He said he’d watched for years as a shelf mushroom grew on the trunk of a Douglas fir in his camp. I’d noticed the mushroom when I visited—it was enormous—and he asked me with evident concern if anyone had knocked it down. I assured him it was still there. In the height of summer, he said, he’d sometimes sneak down to the lake at night. “I’d stretch out in the water, float on my back, and look at the stars.”

3quarksdaily nominates best science writing

3quarksdaily has their nominations up for the year’s Best Science Writing. You should go read, and vote.

I started to aggregate the list of articles but it looks like the majority are related to neuroscience or ecology! That’s a crazy large number. Sorry chemistry and physics and economics and sociology and anthropology and molecular biology and biochemistry and meteorology and geology and oceanography.

Birds being bros


Who knew birds were such good friends to other animals?

cockatoo with treats crow with snacks 2 crow with snacks bird with snacks cockatoo with noodles duck feeding fishbird being a dick

via reddit

Greetings from Portland, OR

I’m currently visiting the Greatest City on Earth which is interfering with my science blogging. But here is some personal photoblogging.

(to be updated, if anyone cares)

waterfall number 4 multnomah falls line to the bridge how to buy a fish

sun above the waterfall the gorge mystery pipe froggy friend

The first scientist…or natural philosopher

Nature has a review of a book on Aristotle:

Aristotle is considered by many to be the first scientist, although the term postdates him by more than two millennia. In Greece in the fourth century BC, he pioneered the techniques of logic, observation, inquiry and demonstration. These would shape Western philosophical and scientific culture through the Middle Ages and the early modern era, and would influence some aspects of the natural sciences even up to the eighteenth century…

Leroi, an evolutionary developmental biologist, visits the Greek island of Lesvos — where Aristotle made observations of natural phenomena and anatomical structures — and puts his own observations in dialogue with those of the philosopher. It was in the island’s lagoon of Kolpos Kalloni that Aristotle was struck by the anatomy of fish and molluscs, and started trying to account for the function of their parts. Leroi’s vivid descriptions of the elements that inspired Aristotle’s biological doctrines — places, colours, smells, marine landscapes and animals, and local lore — enjoin the reader to grasp them viscerally as well as intellectually.

But it is important to distinguish between natural philosophy and science. I have always thought Francis Bacon was the first scientist due to his, y’know, inventing much of what we consider scientific method. I don’t know the extent to which he codified existing ideas versus creating some sort of novel synthesis?

The history of the scientific method is of course a long gradient. Perhaps it began with another early innovator in scientific methodology was Ibn al-Haytham:

The prevailing wisdom at the time was that we saw what our eyes, themselves, illuminated. Supported by revered thinkers like Euclid and Ptolemy, emission theory stated that sight worked because our eyes emitted rays of light — like flashlights. But this didn’t make sense to Ibn al-Haytham. If light comes from our eyes, why, he wondered, is it painful to look at the sun? This simple realization catapulted him into researching the behavior and properties of light: optics…

But Ibn al-Haytham wasn’t satisfied with elucidating these theories only to himself, he wanted others to see what he had done. The years of solitary work culminated in his Book of Optics, which expounded just as much upon his methods as it did his actual ideas. Anyone who read the book would have instructions on how to repeat every single one of Ibn al-Haytham’s experiments.

Become an SfN official blogger! #sfn14

The annual Neuroscience meeting (SfN) is coming up soon and SfN has announced that they are once again seeking official bloggers:

Social media allows for the widespread sharing of scientific information and increased interaction with colleagues. Twitter, Facebook, and personal blogs allow up-to-the-minute scientific exchanges and experiences to be shared virtually.
The call for applications is now open and ends September 5, 2014.

I don’t have a particular reason to go to SfN this year, so I was wondering if SfN was willing to fund the travel – at least, the SfN Membership and conference fee. If anyone else was wondering the same thing, here is the response I got from SfN:

Thank you for contacting the Society for Neuroscience (SfN). SfN accepts blogger applications with the understanding that applicants have secured membership, and are registered to attend the annual. SfN offers bloggers the prestige of being an official blogger for the annual meeting, and an opportunity to increase their blog’s audience. Bloggers do not receive compensation for expenses associated with attending the annual meeting (ie. housing, travel, registration, etc).

Please let us know if you have any questions.

Membership costs $65 for grad students, $140 for postdocs, and $185 for ‘regular members’. Registration is another $100+…so they’re asking you to pay hundreds of dollars to be an ‘official blogger’ (in addition to housing and food, if you feel like eating or sleeping.)

Sure, you could probably relate this to the broader problems in academia such as the emphasis on cheap labor and expectation of overwork for the sake of ambition. But what do I know?

Announcing the NeuroRumblr: Crowd-sourcing information in neuroscience

When it comes to providing information about jobs, Neuroscience is behind the times. Other fields have systems set up to allow faculty applicants to share information with each other about the job market. Economics has econjobrumors while ecology has this awesome wiki. Even undergrads applying to grad school are better at sharing information about jobs than us professional neuroscientists!

Inspired – especially by the ecology wiki – I decided to set up a central site to host a wiki for job applicants, as well as other useful information for neuroscientists: the NeuroRumblr. So far, I only have upcoming conferences but if anyone has ideas for anything else I’d be open to adding them.

It’s currently in what I’ll term “major beta”, but if people are finding it useful I’d be happy to spend a bit more time on updating it.

I’ve started seeding it with information but if you are applying to a faculty job, please share your information (anonymously)! Post your gossip about who said what, what offers you are getting, anything that would be helpful to other people.