The nano scale, fingernails, and using yourself as a research subject

A nanometer is one billionth of a meter. It’s hard to visualize something that small. To try to put it in understandable terms, Robyn Williams said this on The Science Show (I think).

By the time you finish this sentence, your fingernails will have grown one nanometer.

And for some reason, that little claim stuck with me. I kept wondering, “Is that accurate?”

Last fall, I asked students in my Biological Writing class to estimate how much time it would take for fingernails to grow one nanometer. We had talked about Fermi problems in class, using some examples in the book Guesstimation: Solving the World's Problems on the Back of a Cocktail Napkin (Amazon). Out of 13 estimates, eleven ranged from 0.09 to 1.6 seconds, and I had two outliers of 60 and 600 seconds.

But estimates just weren’t good enough. I wanted real data. When the new year came, the next time I trimmed my fingernails, I opened up a spreadsheet and wrote down the date. When I needed to cut them again a few weeks later, I got out calipers that could measure to 0.01 mm. I measured each fingernail at three points to get an average rate of growth and to even out irregularities from my cutting the nails.

I was going to measure the rate of growth (nanometers per second) five times. I managed to fracture a couple of my nails at one point, making correct measures of length tricky for them, so I went another time. I ended up with five or six measures of growth rate for ten fingers.

The results of my somewhat obsessive self-study:

An average fingernail growth rate of 0.92 nM / sec. My Biological Writing students had come up with quite decent estimates – certainly better than you’d get by just guessing! The mode estimate from the class was that it would take about one second for a fingernail to grow one nanometer.

I was a bit surprised to see that growth isn’t as even as I might have expected. It fit my subjective impressions that the ring fingernails looked like they needed trimming first, though I wouldn't have expected the middle fingernail was growing just as fast.

Getting back to the original claim, we need not only the rate of growth, but the time of the sentence. It took me about 3.77 second to say, “By the time you finish this sentence, your fingernails will have grown one nanometer” (n = 10, timed with stopwatch).

This means that the original claim is quite conservative! By the time you finish saying that sentence out loud, your fingernails will probably have grown something like three and a half nanometers (3.47 nM, if you wanted to be precise), not just one.

The anti-calm poster

This one is Becca’s fault...

More appropriate for those in grad school, tenure track... academia generally.

Comments for first half of March, 2012

Scicurious offers advice on writing a dissertation.

Jason Snyder looks at differences in citation report databases.

What’s the craziest thing you’ve done for science?

io9 reports on science crowdfunding.

The Cellular Scale looks at action potentials in an iconic meat eating... plant.

Calling South Texans!

Have you seen the items in this gentleman’s hands?

Whale shark researcher Dr. Al Dove reports that these GOS tags have been found near Brownsville, Texas. He would like them back!

If you are a local here in South Texas, please help spread the word. If you get them, send him a tweet: he’s @para_sight on Twitter.

Additional, 16 March 2012: This was featured on one local television station’s evening news broadcast. I’m glad the story spread, though we are still looking for these!

The Zen of Presentations, Part 52: Big finish

Two people go in for a rather invasive and somewhat painful surgical procedure. The nature of the procedure means that the can’t be anesthetized. To keep track of their pain, the physicians ask the patients to rate the level of pain they’re experiencing at regular intervals, from one to ten. Imagine this is charted below, with the “0” for the red line being because the procedure was done by them.

Some months later, on a follow-up, the patients are asked to describe their overall experience.

You would expect the patient whose responses that are plotted in blue in the chart above would report the experience being much worse. If you add all the numbers, this person’s average pain was higher, and they were in pain for much longer.

The patient whose responses are in red usually reports the experience being much worse than the patient whose responses are in blue. Why?

Endings matter.

The entire experience is profoundly influenced by that last memory. The patient in red ends in almost excruciating pain; the patient in blue ends with mild discomfort. And that last experience tends to be one that sticks.

This might explain why twist endings in movies and television and other stories are so divisive. They can be spectacularly successful or agonizingly bad. Sometimes a great ending saves an movie or episode and turns the run-of-the-mill into something quite amazing (e.g., The Sixth Sense). How many times have you been going alone, carried along with a story... and the ending ruins it, and you leave with a sour taste in your mouth? (E.g., Jacob’s Ladder.)

This talk - the most popular Ignite! talk to date - could be significantly improved:



This talk is popular because it is so useful. But the ending... a recap? What do you need a recap in a five minute talk for? Peoples’ memories aren’t that bad.

Nancy Duarte nailed what an ending should be in her book Resonate: a vision for a better tomorrow. She calls it, “the new bliss.” The new bliss sets out what could be, if the audience takes the story you have told them and acts on it.

Here’s a great example of an ending that lays out a new bliss. It’s Hans Rosling talking about the magic of washing machines:



A world with washing machines is not just a world with clean laundry. A world with washing machines is a world where machines have freed up time for parents to read books to their children.

In a scientific talk, the new bliss can be something as simple as a more complete understanding of some fine theoretic point that people in your field will appreciate. It could be ruling out an hypothesis. Or it could be a shifted paradigm. Or maybe there are big potential practical spin-offs that could come out of the work.

Put a lot of work into your endings.

Note: I heard the patient story on an online video somewhere; I thought it was on the TED website, but can’t find it gain. If anyone recognizes this and can point me to it, I would be most grateful!

Tuesday Crustie: Headline news

Because really, kids should be getting IACUC training much earlier.

Okay, this is a cheat: there is no actual crustacean in this picture. But I love this headline too much. Better without context.

Photo by Gerry Balding on Flickr; used under a Creative Commons license.

Neuroscientists Talk Shop

When I was at the University of Texas San Antonio last week, I recorded an interview with them for their Neuroscientists Talk Shop podcast. Mine is now up. It’s mostly about nociception, although the connectome post I published last week also came up.

In this interview, my co-author on the nociception paper, Sakshi Puri, talks a bit about getting emails from PETA. When we published our paper, I blogged about my worries that there would be some people who would not like it regardless of what the paper actually says. I was disappointed to learn I was right, after the amount of effort we put into the paper to prevent misunderstandings.

For the record, if any of you have a problem with my research, please include me in that conversation.

There are 80 other interviews in this series. For fellow neuroethologists, some that might be particularly interesting include:

• David Perkel on bird song
• Karen Bales on primate bonding
• Peter Narins on acoustic communication
• Mike Smotherman on bat vocalizations
• Suzana Herculano-Houzel on comparative brain sizes
• Brenton Cooper on bird song development

Mine was so enjoyable and the questions were so good, I plan go back and listen to a lot of episodes in their back catalog.

UTSA talk

On Wednesday, I drove up to San Antonio to give a talk and meet the fine folks in the University of Texas San Antonio neuroscience group. Because I had decided to talk about nociception, Sakshi Puri came along with me. We got to San Antonio early enough Wednesday that we were able to play a little hooky, and decided that it was a lovely day to go to the zoo. We saw this massive guy there:

Biggest snapping turtle I have ever seen. It looked like it was a million years old.

Thursday went very well. We met lots of people who were doing interesting science but who weren’t waaaaay into themselves. My feature talk was well received, had a mini-Tweet-up (one person who was following me from the Ecology meeting last summer!), followed by lunch with students.

We then recorded an interview of Neuroscientists Talk Shop. My interview isn’t up yet; I’ll let you know when it it. But there are plenty of other interviews there for the neurocurious (76, I think). Just the thing to keep your mind working through an exercise routine, say! We talked about nociception and yesterday’s connectome post.

One of the unexpected things I learned on this trip from my host, Todd Troyer: How to catch a zebra finch.

If a zebra finch escapes in your room, wait until it lands. Note where it is. Then turn off the lights, and reach and grab where it was.

These guys completely shut down when the light goes out. In a room full of chattering birds, the silence was so sudden when we flipped the light switch out that it seemed as though the switch was connected to the birds and the lights both. I just couldn’t get over how immediate and complete the silence was, and how quickly they started up again when the lights went back on.

After the visits, we went to The Monterey Restaurant. The website does not at all convey the great, funky feeling of the place. It also features the most... different... desert I think I have ever had: the cheese-plate pop-tart. It’s a slightly surreal combination of sweetness and, well, cheese. I was glad that I had it, because it was a taste unlike any other I can ever remember experiencing. I’m not sure I would order it again.

Thanks to all the students and faculty at UTSA for making it such a fun day for us!

Overselling the connectome

In the last few years, there has been much discussion about the prospect of tracking the neural connections of mammalian, and particularly human, brains at very high levels of detail. Following the concept of a genome – every gene in an organism – a connectome is a map of every anatomical connection between every neuron in an organism.

One of the major proponents of this effort has been Sebastian Seung, who you can see giving a TED talk here. He sells the idea that understanding the human connectome will help us understand human identity. In his talk, Seung encourages his audience to say along with him. “I am my connectome.” He’s written a new book on this subject, Connectome: How the Brain’s Wiring Makes Us Who We Are.

This is an ambitious research project that will no doubt yield highly improved techniques to get anatomical information and analyze it. We will learn a lot from it.

And it will fail.

The allure, promise, and shortcomings of the connectome approach are yesterday’s news to neuroethologists. In the 1960s and 1970s, neuroethologists put in a lot of effort to crack partial connectomes of several species. These were usually referred to as “circuits” or “wiring diagrams.” (“Connectome” only appeared when neuroscientists got genome envy.) We made good progress on these. For example, we can explain escape behaviour in fishes and crayfish by the main synaptic connection between the critical neurons. That said, escape systems were chosen specifically because they were unusual behaviours. they are very sterotyped, very fast, and dedicated to one single task.

As other circuits were cracked, they revealed a much more subtle story.

A new paper by Bargmann details the case histories of a few of the species that neuroethologists have basically cracked the circuit. And contrary to some expectations, getting the complete set of synaptic connections did not solve the problems of understanding behaviour. I’m very glad that Bargmann wrote this paper, because it saves me the trouble of writing a much longer blog post.

For example, the nematode worm Caenorhabditis elegans has 302 neurons, and all the connections between them are known (the first complete connectome in the animal kingdom). Bargmann writes:

At a more profound level, however, the wiring diagram was and remains difficult to read. The neurons are heavily connected with each other, perhaps even overconnected – it is possible to chart a path from virtually any neuron to any other neuron in three synapses. ... Circuit studies suggest a reason for this failure: there is no one way to read the wiring diagram.

One of the major lessons that emerged in the 1990s from the study of these small circuits where we knew all the synaptic connections was the importance of neuromodulation. Neurons’ functions were not set only by their anatomical connections. They were profoundly influenced by a cocktail of neuroactive chemicals that could change the physiological responses of neurons.

Bargmann breaks it down. First, she shows that only rarely can you link single neurons to single behaviours. Then, she shows how one behaviour can result from several circuits, and how one neuromodulator can influence several behaviours. She notes that given how neuromodulation has appeared pretty much in every nervous system where we’ve looked, there’s every reason to expect it’s going to be a major factor in determining human neural activity, and thus, human identity.

In his TED talk, Seung draw an extended metaphor that the connectome is like the bed of a river.

I would like to propose a metaphor for the relationship between neural activity and connectivity. Neural activity is constantly changing. It's like the water of the stream; it never sits still. The connections of the brain's neural network determines the pathways along which neural activity flows. And so the connectome is like bed of the stream; but the metaphor is richer than that, because it's true that the stream bed guides the flow of the water, but over long timescales, the water also reshapes the bed of the stream. And as I told you just now, neural activity can change the connectome. And if you'll allow me to ascend to metaphorical heights, I will remind you that neural activity is the physical basis – or so neuroscientists think – of thoughts, feelings and perceptions. And so we might even speak of the stream of consciousness. Neural activity is its water, and the connectome is its bed.

Knowing the bed of the river still doesn’t tell you everything. The same river bed can have a trickle one day, and a flash flood the next. Neuromodulation is a bit like a dam partway along the river. It can regulate whether you have a torrent or a trickle.

Bargmann and I agree that connectome projects are very useful. But they alone will not solve the question of human identity. But at least when they fail, they will fail in an interesting way.

Reference

Bargmann C. 2012. Beyond the connectome: How neuromodulators shape neural circuits. BioEssays: In press. DOI: 10.1002/bies.201100185