Curious!

Focusbird EP

2011-08-15T22:02:00.000-07:00

Announcing the new Focusbird EP! Alex and I recorded these quiet ukulele/glockenspiel/flute/other sounds for listening over a year ago with the help of Dory Bavarsky. (College graduation and life kept us from getting them up until now.) Check 'em out here: http://focusbird.bandcamp.com/

Lovely art by Julia Kostreva

Edit: Alex has written a nice little review over on Giraffe Kingdom.

What I'm Up To, Where I've been

2011-07-27T08:56:00.000-07:00

I haven’t posted in some time, so I thought I’d just write a little note about what I’ve been up to instead. I had an awesome internship at Discover magazine in NYC, then one at Psychology Today. In the meantime, I’ve been learning mandolin. Not sure what’s next, or if/when I’ll post again, but for now I’ll leave you with this link to new songs I’m working on:

http://soundcloud.com/focusbird

Seeing the Beat

2010-11-11T07:01:00.000-08:00

What makes you “feel” a beat? Music, most likely; or any sound that occurs at regular intervals. Of course, one can also infer a beat from seeing a flashing light, or feeling the pulse in one’s wrist. Perhaps a beat could even be perceived in finely regulated pulses of flavor or scent… But numerous studies have shown that most people are best at perceiving a beat when they can hear it.

What's less understood is how perception of a beat through one medium affects its subsequent perception through another. For example, if you hear a rhythm implying a certain beat, will you be better at perceiving the same beat when it's later presented visually? And what about the other way around? A Neuroimage paper published in September answers, respectively, yes and no.

Jessica A. Grahn and her colleagues created auditory rhythms and visual sequences meant to imply a beat. The rhythms were composed of short sine tones, and the visual sequences consisted of black squares flashing on a white background. They were constructed such that one could infer a slower (implied) beat broken up by sequence elements, or a faster (explicit) beat based on consecutive sequence elements. Control sequences had tempo changes, but all elements fell on the implied beat.

Participants were presented with various sequences in various orders. The scientists asked them to judge whether each sequence was speeding up or slowing down, indicating both ability to sense tempo changes and whether they perceived either the implied or the explicit beat. Perception of the implied beat rather than the explicit one was interpreted as a sign of greater beat sensitivity.

As the authors expected, participants had better tempo judgments and beat sensitivity when presented with the auditory rhythms than with the visual sequences. This supports other studies showing that people are better at detecting tempo changes, distinguishing between different sequences, reproducing them, and synchronizing with the rhythms of auditory sequences than visual ones.

But there were some interesting results when the scientists noted the order in which sequences were presented. Participants exhibited greater beat sensitivity for a given visual sequence if they watched it after hearing the same sequence presented as an auditory rhythm. It doesn't seem to work the other way around; when a rhythm was presented after its corresponding visual sequence, there was no improvement in beat sensitivity.

Why did the audio-visual order improve visual beat sensitivity, while the visual-audio order left auditory beat sensitivity unchanged? Neither order led to increased ability to judge tempo changes, so the scientists ruled out the possibility that hearing the rhythm first made visual tempo judgment easier, somehow resulting in better beat sensitivity. Instead, the scientists propose, hearing a rhythm primes an internal representation of a beat. This representation is then used to promote visual beat perception during the subsequent visual sequence.

Grahn and colleagues linked their behavioral results with fMRI data gathered during a separate session involving the same tasks. Brain activity during the visual sequence was measured with and without auditory priming. Certain regions exhibited significantly greater activity with auditory priming than without, corresponding to an increase in beat sensitivity.

One region that showed increased activity related directly to increased beat sensitivity was the putamen. The putamen is part of the basal ganglia, which are known to play a role in both imagery and auditory beat-based timing. The authors suggest that the basal ganglia might lead to enhanced visual beat sensitivity after auditory priming by allowing for creation of an internal representation.

What could be the nature of such an internal representation? Perhaps the auditory sequence allowed the listeners to imagine still hearing the beat during the visual sequence. In fact, some participants said they did exactly that. Or, maybe listeners created an internal representation of the beat that was neither auditory nor visual. To test this, one could see if beat sensitivity is improved when a visual sequence is preceded by the same sequence presented in a tactile manner, such as through tapping.

I thought this study was interesting because I've only ever considered the relationship between sight and sound when presented simultaneously, such as in films or light shows at concerts. As the authors of this paper mention, there are lots of studies concerning the relationship between concurrent audio and visual stimuli. For example, in the temporal ventriloquism effect, flashing lights and auditory clicks in close succession are perceived as being simultaneous, even if they're not. And the perceived beat is biased toward the clicks.

It will be interesting to see the results of any follow-up studies exploring how tactile sequences affect visual beat perception. For now, to help you feel the beat, here's a track off the recently released album Ardour by Teebs, who is also a visual artist. I wish it were about 5 times as long, but luckily the beat stays in my head long after it's over:

Grahn JA, Henry MJ, & McAuley JD (2010). FMRI investigation of cross-modal interactions in beat perception: Audition primes vision, but not vice versa. NeuroImage PMID: 20858544

image source: dublab

Problems with Pitch: Congenital Amusia and Tone Languages

2010-08-29T20:12:00.000-07:00

What, exactly, is tone deafness? We've all known someone who claimed he or she was tone deaf or "couldn't carry a tune." However, congenital amusia, which seems to be true "deafness" to tone, affects only about 4% of the general population - that is, 4% of the almost exclusively Western populations that have been studied.

Congenital amusia is one of several different types of music perception impairments. A person with the disorder is born with a variety of symptoms, including an inability to recognize a familiar song without hearing the lyrics, an inability to discern the difference between two melodies, and difficulty perceiving when he or she is singing or hearing music performed out of tune. In the video below, Oliver Sacks, author of Musicophilia, shares the story of a woman who lived for decades before being diagnosed with congenital amusia:

Congenital amusia has only been studied in populations lacking tone languages - languages in which the meaning of a word can vary depending on small changes in pitch. In the tone language Mandarin, for example, the syllable "ma" has four different meanings, each associated with certain pitch (frequency) changes over the course of utterance:

Speakers of Mandarin must perceive and produce much smaller pitch changes than those used for expressive speech in English and French. Given the linguistic pitch requirements of the language, the authors of a recent study hypothesized that congenital amusia would be very rare in native speakers of Mandarin.

Yun Nan, Yanan Sun, and Isabelle Peretz recruited 117 normal and 22 amusic participants from a university in Beijing. All participants were evaluated with the Montreal Battery of Evaluation of Amusia (MBEA), a series of musical perception tests that is used to diagnose amusia. The MBEA looks at several different aspects of music perception, including pitch and rhythm. (Interestingly, only 22 of the 96 self-reported amusic individuals were actually scored as having congenital amusia.)

The MBEA scores of the 117 normal participants were compared with scores of 190 normal Canadian subjects. Contrary to the authors' expectations, the scores indicated that the Mandarin speakers did not possess superior pitch processing skills, despite fine pitch processing being more essential for their tone language. Also, four of the normal participants' MBEA scores indicated they had congenital amusia, though the subjects seemed to be unaware of their condition. The authors conclude that congenital amusia may be more prevalent in Mandarin speakers than they thought; perhaps affecting 3% of that population.

Let's take a closer look at the 22 amusic participants. Their ability to correctly evaluate pitch changes in Mandarin was compared with that of 22 control subjects. In a tone identification task, each participant listened to a recording of a one-syllable, two-syllable, or nonsense word, and was asked to identify which of the four tone shapes (see image above) was used for each syllable. In a tone discrimination task, the participants listened to recordings of pairs of one-syllable words, and were asked to discern the difference (if any) in tones used for each word. Sometimes a pair would include two different words, and sometimes both words in a pair would be identical.

The only one of the above tasks that all participants performed well on was the tone discrimination task in which both words in the pair were the same. Each participant was adept at discerning whether the two words were pronounced with the same tone or two different tones.

On average, the amusic subjects performed worse than the control subjects on the other tasks, though some stayed within the normal range. However, six amusic participants performed significantly worse in both the tone identification and different-word tone discrimination tasks. Interestingly, these six participants, identified as having "tone agnosia," did not have significantly different MBEA scores from the other amusic subjects.

Lastly, the 22 amusic and control subjects were evaluated on their ability to correctly produce two-syllable words and nonsense words. The words were either read aloud by the participants, or repeated after listening to a recording. All participants, including the six with tone agnosia, performed very well on this task, indicating that subjects had problems only with tone perception, not production.

There appears to be some connection between linguistic and melodic tone perception in the tone agnosia subjects, but it is difficult to say what that is. Given the ability of the subjects to correctly produce different tones and score well on the same-word tone discrimination task, the issue might not be directly related to pitch processing. Rather, the authors speculate, these participants may have underlying difficulty with attention control.

This paper is not only the first to show that congenital amusia is, indeed, found in speakers of tone languages, but is also, apparently, the first to show a dissociation between impaired tone perception and normal tone production in language. I think it's a fascinating step toward the many further studies that should be done on the neuroscience of music and language in speakers of different, non-Western languages. Clearly, congenital agnosia is not just a problem with fine pitch discrimination. I wonder what other neuro-linguisitc and neuro-musical assumptions would be shattered by extending scientific study to populations without non-tone languages...

For this post's musical dessert, I bring you the work of a scientist who (unlike Darwin, J.B.S. Haldane, and William Lawrence Braggs, apparently) was decidedly not tone deaf: Alexander Borodin, Russian chemist and composer of several major works, including the famous Polovetsian Dances from his opera Prince Igor:

Reference:

Nan Y, Sun Y, & Peretz I (2010). Congenital amusia in speakers of a tone language: association with lexical tone agnosia. Brain : a journal of neurology, 133 (9), 2635-42 PMID: 20685803

Unraveling the Ocean Methane Paradox

2010-08-19T21:18:00.000-07:00

Mention methane production, and cows or oil companies usually come to mind. But much of the methane in the atmosphere (1-4%) actually escapes from the oceans, some of it produced by microbes known as methanogens (like Methanosarcina acetivorans, above). Some methanogens live in anaerobic – oxygen-free – sediments on the seafloor. Others make their homes in anaerobic fish intestines, the guts of some plankton, or fish and plankton fecal matter.

Methanogens live in anaerobic environments. However, measurements of oceanic methane consistently show a high concentration of methane in shallow, oxygenated waters. Thus, we have the “ocean methane paradox:” How are large amounts of methane being produced in an environment with plentiful oxygen?

In the image below, the connected, closed circles represent methane concentrations at different water depths at a seawater sampling site in the Pacific Ocean. Note the spike in concentration around 150 meters, representing the high methane concentrations leading to the ocean methane paradox:

Explaining the paradox is important for scientists' understanding of how the oceans contribute to global climate change. Methane is a powerful greenhouse gas, and high surface concentrations of marine methane result in more of it entering the atmosphere. The high methane concentrations giving rise to the ocean methane paradox are too widespread to be due to non-living sources of marine methane – like geochemical sources partly responsible for natural methane seeps in the Gulf of Mexico and offshore Santa Barbara, CA. So, in working out the paradox, scientists have focused on methanogens.

In 1994, David Karl of University of Hawaii, Honolulu, and Bronte Tilbrook of Australia's Commonwealth Scientific and Industrial Research Organization (CSIRO), measured the flow of methane out of sinking “particulate matter.” This matter included some plankton, plankton fecal material (see image below), some fish fecal material, and marine snow – small pieces of dead organic matter, dust, and other particles that constantly sink through the ocean.

Karl and Tilbrook found that the amount of methane released by the sinking materials is enough to account for the elevated methane levels leading to the ocean methane paradox. They hypothesized that methanogens produce methane in the guts of some plankton and, for a brief period of time, in the anaerobic “microenvironments” of plankton feces. The methane is then released into the ocean from the droppings. Karl and Tilbrook’s results were supported by both previous and subsequent studies that found methanogens living in plankton and fish fecal pellets, as well as other particulate matter.

Karl and Tilbrook’s study - and related research - seemed to provide a straightforward solution to the ocean methane paradox: marine creatures, their feces, and other particles provide anaerobic microenvironments in which methanogens produce methane, which is then released into the ocean.

But it turns out the solution may not be so simple. A 2008 paper by Karl and colleagues provided evidence for the possibility of aerobic (in the presence of oxygen) methane production by marine microbes.

Using seawater samples, the scientists determined that some marine bacteria can use the compound methylphosphonate (MPn, see image below) as a source of phosphorous – an element necessary for synthesis of many important biological compounds. As MPn is broken down, methane is produced as a byproduct. Karl and his colleagues point out that the results obtained in his 1994 paper with Tilbrook could actually be explained by MPn breakdown by free-living microbes or those residing in sinking particles or the guts of animals.

The hypothesis that aerobic methane production could contribute to elevated ocean methane concentrations was further supported by a 2010 paper by Ellen Damm of the Alfred Wegener Institute for Polar and Marine Research and her colleagues. They compared aerobic methane production in two different ocean regions and found an association between increased methane production and a low seawater nitrate to phosphate ratio. Since such a ratio occurs during certain seasonal ecological shifts, aerobic marine methane production by bacteria could be a seasonal occurrence.

While scientists have made good progress in resolving the ocean methane paradox, the mystery still stands. Are both aerobic and anaerobic microbes contributing to the high shallow marine methane concentration? What are the mechanisms and locations of methane production for the organisms? Are there seasons and geographic regions with more methane production by the creatures responsible for the paradox? For now, I'll leave these questions to the scientists and move on to this post's suggested musical accompaniment, a beautiful, ocean-evoking track called Waves by Chihei Hatakeyama:

References:

Damm, E., Helmke, E., Thoms, S., Schauer, U., Nöthig, E., Bakker, K., & Kiene, R. (2010). Methane production in aerobic oligotrophic surface water in the central Arctic OceanBiogeosciences, 7 (3), 1099-1108 DOI: 10.5194/bg-7-1099-2010

Karl, D., & Tilbrook, B. (1994). Production and transport of methane in oceanic particulate organic matter Nature, 368 (6473), 732-734 DOI: 10.1038/368732a0

Karl, D., Beversdorf, L., Björkman, K., Church, M., Martinez, A., & Delong, E. (2008). Aerobic production of methane in the sea Nature Geoscience, 1 (7), 473-478 DOI: 10.1038/ngeo234

Reeburgh, W. (2007). Oceanic Methane Biogeochemistry Chemical Reviews, 107 (2), 486-513 DOI: 10.1021/cr050362v

Image Sources:

Top image: Genome News Network
Methane Maximum plot: Reeburgh, 2007 (see above reference)
Zooplankton fecal material: Sam Wilson, Scottish Association for Marine Science
Methylphosphonate: PubChem

An Arterial Scaffold for the Lymphatic System

2010-08-06T08:43:00.000-07:00

I always forget about the lymphatic system. For me, it seems to lurk quietly behind the dramatic cardiovascular system. But lymph matters, too! The lymphatic system is a network of vessels, nodes, and organs that transport the clear fluid lymph. When blood components leave blood vessels to enter other tissue, they first pass through an intercellular space as "interstitial fluid". A certain amount of interstitial fluid is taken up by lymph vessels to maintain fluid balance and recycle blood components back into the cardiovascular system. The lymphatic system also contains lymph nodes and other organs like the thymus, which play important roles in the immune system. And, some lymph vessels are responsible for transporting lipids after food digestion.

While much is known about what the lymphatic system does, not much is known about how it forms. A recent paper in Development takes some big steps in solving the mystery by focusing on the development of lymph vessels in zebrafish embryos (see zebrafish in the top image).

Jeroen Bussmann, of the Hubrecht Institute, and his colleagues found that developing lymph vessels are closely associated with developing arterial vessels, which carry blood away from the heart. The developing lymph vessels are not associated with developing veins, which carry blood towards the heart. To figure this out, the scientists created transgenic zebrafish in which a red fluorescent protein labelled developing arteries and veins, and a green fluorescent protein labelled developing lymph vessels. Arteries displayed higher red fluroescent protein, so developing arteries and veins could be easily distinguished. 97% of developing lymph vessels were found directly adjacent to developing arteries. This was true for 418/430 developing lymph vessels, in a total of 30 zebrafish embryos.

In this figure from the paper, the developing lymph vessel is the vertical green branch. Note that it is closely apposed to the developing artery (aISV) and not the developing vein (vISV):

To follow up on the observed correlation, the researchers used time lapse microscopy to determine whether developing lymph vessels are attracted to developing arterial vessels from the beginning of their development, or whether they gain the preference later on. It was found that they form along the arterial precursors, indicating an important guiding role for the arterial vessels in lymph vessel development. Further experimentation in embryos engineered to form vein precursors but not arterial precursors indicated a requirement for arterial precursors in lymph vessel development.

But what is the nature of the relationship between developing arteries and developing lymph vessels? Perhaps they both rely on the same developmental cues. Or, perhaps the lymph vessels rely on a cue from the arterial vessels. And, though zebrafish were used in this research, perhaps human lymph vessels develop along human arterial precursors in a similar fashion.

But enough about lymph, I want to talk about music! All this talk of branching vessels is making me think of trees, which is a perfect excuse to listen to Baby Birch off of Joanna Newsom's most recent release, Have One on Me:

References:

zebrafish image: Wikimedia

lymphatic system image: Wikimedia

Bussmann, J., Bos, F., Urasaki, A., Kawakami, K., Duckers, H., & Schulte-Merker, S. (2010). Arteries provide essential guidance cues for lymphatic endothelial cells in the zebrafish trunk Development, 137 (16), 2653-2657 DOI: 10.1242/dev.048207

Super Treehouse

2010-07-25T19:50:00.001-07:00

My musical internet friend Super Treehouse makes delightful glitchy sounds, taking inspiration from life forms, biological processes, video games, and artists like Bibio and Shuttle358. Check him out on myspace and bandcamp. He's also a great artist, and designed the cover art for his recent release Bioluminescens. Go Super Treehouse!

Puppet Science

2010-07-16T07:16:00.000-07:00

This is a goofy talk, but a fun insight into how a taxonomist approaches his work.

(Also, it's a good excuse to post one of my all-time favorite Sesame Street clips:)

I'd like to see an astrobiologist analyze the yip yips.

Worst Opening Line for a Novel

2010-06-30T20:21:00.001-07:00

This isn't necessarily science or music related, but I always find the results of this contest entertaining: http://www.bulwer-lytton.com/.

The idea is to come up with the worst possible opening line for a novel. Just to keep things scienc-y, here's one of the "Dishonorable Mentions:"

Faintly silhouetted against the shadowy murk of a nameless Devonian sea, the Megalodont shark was unaware of trilobites foraging in the primordial ooze not far below, trilobites that unlike the shark’s cartilaginous being would become part of the fossil record of an ancient seabed that would in time heave up, dry out and go through the crusher at the Marulan Cement Works somewhere north of Sydney, Australia.

John Mackesy

A Leap Across A Chasm

2010-06-26T10:26:00.000-07:00

A will probably get many more listeners through his own online connections, but anyone who stumbles upon my little blog should go check out his wonderful new album A Leap Across A Chasm, which he released yesterday under the name Fennel. (Full disclosure: I provided some of the sound samples for the album, though the artistry is all A's.)

A Leap Across A Chasm combines carefully processed instrumental recordings with field recordings of lagoon birds, college students, train stations, frogs, dining halls, roadways, the ocean at night, the ocean during the day, crickets, and more. It's a thoughtful, beautiful, and genuine first album that hints at many more to come.

I love the dialogue that begins the first track; it acts as an invitation into a Luc Ferrari-esque envelopment of field sounds. The addition of instrumentals has the potential to be abrupt, but they are expertly introduced, intertwining with and emerging from friendly dialogue and outdoor sounds. Fluid Boundary/Radiant Yellow, Humid Green (the title a reference to the wonderful opening scene of Gravity's Rainbow), is nicely built upon by the next few tracks. In Fabricating Memories, the listener sinks into a moody, haunting soundscape, only to emerge into the icy, blizzard-brightness of the ethereal last track, Zona Glacialis.

The care with which A Leap Across A Chasm was made is evident, and its honesty and feeling are palpable.

Graduation Gift...To Myself

2010-06-22T18:41:00.000-07:00

Just acquired one of these:

It'll definitely take me a while to figure it out, but I've made some test recordings, and I'm beginning to get the hang of it. In addition to music, it should be useful for recording interviews, field recordings of East Coast beaches and birds, and Focusbird ideas. Now what to do about all that loud traffic outside my house...

I am employed!

2010-06-17T13:35:00.001-07:00

So, after a frantic few months of trying to figure out what would happen to me after graduation (and attempting to avoid, at all costs, having to go home and sit around), I am well into my first week as a science writing intern at the MBL. I'm sure there are rules about blogging about my work on a personal site, so I will just advise you to check out the MBL blog periodically, as I will begin posting on it soon.

I fear I am to be spoiled; my office has a nice view of the Woods Hole harbor.

Dancing Parrot

2010-06-02T22:22:00.000-07:00

Parrots and humans are the only animals currently known to be able to synchronize their movements to an external beat, according to a New York Times interview with Dr. Aniruddh D. Patel.

A while ago, I made a few posts on Dr. Patel's groundbreaking book, Music, Language, and the Brain. One of the fascinating issues explored in the book is the question of whether the human brain is uniquely adapted for music cognition. The seemingly unique ability of humans to synchronize their movements to an external beat is cited as an important piece of evidence in answering this question.

But, about a year ago, Patel published a paper reporting on the ability of Snowball, the cockatoo in the above video, to dance in time with the rhythm of the Backstreet Boys song Everybody (never thought I'd see that boy band in a serious piece of biological literature - love it!). The bird adjusted its movements according to manipulations in the song's tempo. In the New York Times article, Patel says:

What do humans have in common with parrots? Both species are vocal learners, with the ability to imitate sounds. We share that rare skill with parrots. In that one respect, our brains are more like those of parrots than chimpanzees. Since vocal learning creates links between the hearing and movement centers of the brain, I hypothesized that this is what you need to be able to move to beat of music.

Measure Methane, Measure Oil Spill Extent

2010-05-27T11:54:00.000-07:00

Dave Valentine, the head of the lab I've worked at at UCSB, has an interesting opinion piece in Nature today proposing an alternative method to measure the extent of the Deepwater Horizon oil spill. You need a subscription to read the full article, but it's pretty straightforward and makes a lot of sense.

Methane gas actually makes up 40% of the leaking petroleum. Since methane is soluble, we can hypothesize that much of it will end up uniformly dissolved in the seawater surrounding the well. Scientists already have the knowledge and tools to precisely measure methane concentrations, and can look at characteristics such as isotope composition and oxidation rates to account for methane that may have escaped into the air or been eaten by microbes.

The strength of this method lies in the fact that methane gas is soluble while the oil content of the spill is not. Thus, surface slick measurements and visual assessments of the leak could give highly variable results depending on the time and place of analysis. The solubility of methane should make its presence uniform in the area, thus requiring far fewer measurements to approach an accurate quantification of the spill.

image source: Wikimedia Commons

Mammalian Digit Regeneration

2010-05-21T00:43:00.000-07:00

Earlier this year an interesting paper came out discussing new findings in the induction of mammalian limb tip regeneration. You may already know that human fingertips can naturally regenerate if amputation isn't too severe. Similarly, mouse digit tips can regenerate to form near-normal digits (endogenous regeneration), but amputations past a certain threshold merely heal over without elongation.

In the February 15, 2010, issue of Development, Ling Yu et al. present evidence that the mouse endogenous regeneration response involves growth factors (signaling proteins that stimulate cell growth) called BMPs. They then found that amputations past the regeneration threshold could be induced to regenerate when treated with BMPs. This is the first instance of post-embryonic mammalian limb regeneration induced by growth factor treatment.

Interestingly, the induced regeneration response appears to be a reactivation of limb development, as opposed to the more direct endogenous regeneration response. In limb development, newly formed bone develops from a cartilage precursor. In endogenous regeneration, however, there is no cartilage intermediate. Genes associated with bone formation using a cartilaginous precursor were found in the BMP-induced regeneration response. This indicates that the mechanism involves reactivation of developmental pathways, instead of an extension of effectiveness for the endogenous response.

Further studies should be done to elucidate the precise role BMPs play in this induced response. Nonetheless, the work of Yu et al. is a solid foundation on which to build further studies of growth factor-induced mammalian limb regeneration. Scientists hope that, by pursuing these lines of evidence, we will one day be able to persuade human wounds to regenerate, rather than simply heal over.

primary article:

Yu, Ling; et al. BMP signaling induces limb regeneration in neonatal mice. Development, 137: 551-559.

image source: Wikimedia Commons

Bill Nye the Science Guy!

2010-05-12T23:04:00.000-07:00

As I mentioned in my last post, Bill Nye was a big part of my childhood. Well, tonight I got to revisit those days by seeing him in the flesh at UCSB! He gave a very fun (and funny) talk on planetary science and climate change, urging the audience to go out and solve the world's problems. This was followed by a Q&A session, in which only about a third of the people who wanted to ask questions got a chance to. I've been to a lot of performances and events at Campbell Hall, and this was, by far, the fullest I've ever seen it. Bill Nye is important to people my age! And not just to science majors.

I was interested to hear what he had to say about how to make science education effective: Blow things up first! Then give explanations. And science writing: People like to hear stories; tell them stories. (Also a line from another childhood favorite, The Amber Spyglass!)

I really liked that Bill Nye distinguished between being an environmentalist by doing less (e.g. biking instead of driving), and being an environmentalist by doing more, with less (e.g. making energy efficient cars). I feel this is sometimes overlooked, and that the components making up a global environmentalist approach must allow those accustomed to a certain lifestyle to continue to live it, as well as provide for those who aspire to live better. (Of course, we also need to keep trying to change global attitudes toward energy use. But, on its own, attitude adjustment probably won't help enough, especially with skyrocketing populations.)

I also liked that he presented a variety of possible solutions, since I believe that there is no single solution to climate change. Different solutions will work in different situations. That being said, some of the ideas he presented seemed very strange, such as attaching bubble-makers to ships so they leave white trails behind them, reflecting more sunlight back into space. But it's that kind of creative thinking that leads to bigger breakthroughs, even if only by inspiring creative thinking in other people.

Before the talk, I spent way too much time re-watching memorable Bill Nye the Science Guy clips on Youtube. Here are a few:

Richie, Eat Your Crust! (My parents loved this one. I wonder why...):

A World Without Wood:

Quicksand! (love the old film clip):

Crying (I thought this was the funniest thing when I was 10 years old.):

Okay, I'd better stop posting these or I'll be up all night. Here's one of my absolute favorites:

top image source: UCSB Arts and Lectures

Chicken Foot Constellation

2010-05-09T14:07:00.001-07:00

Here's a piece I've been working on for my creative nonfiction class:

Chicken Foot Constellation

I don’t remember what prompted me, but in fifth grade I once raised my hand and announced to the class that in every glass of water we drank, there was probably a miniscule amount of dinosaur spit. I thought this was awesome. It only made sense. There’s pretty much the same amount of water on Earth as there ever has been, and since it just gets recycled over and over, we’ve probably all drunk dinosaur spit, whale pee, baboon sweat. Yuck, I know. Sorry. But it’s true! (Mrs. Claypool and the rest of the class gave me a collective blank stare before returning to whatever the actual lesson plan was.)

I blame my weird childhood thoughts on my parents. Both geologists and lovers of nature, they made sure I grew up with a sound appreciation and understanding of science. I was enrolled in an infant/toddler day care center that organized regular camping trips in the Santa Cruz Mountains. I was given my grandparents’ old copies of National Geographic and all the Magic School Bus books. My dad helped me start a rock collection and made sure I knew the official names of all the minerals in the box I kept on my dresser. When I had trouble falling asleep, we didn’t count sheep; we named off the original 18^th century names of geological time periods (“Primary! Secondary! Tertiary! Quaternary!”). I was regularly quizzed on the names of nearby mountains and the types of rocks, flowers, and trees we encountered on countless weekend hikes. My parents also taught me to identify major constellations: the Big and Little Dippers, Orion, Cassiopeia.

The summer before fifth grade, I went to Space Camp. I got to go for free because I wrote an essay about all the useful Earth products that were originally invented for space travel. (Did you know that TV satellite dishes, medical imaging techniques, fire alarms, vision test charts, ski boots, nontoxic toothpaste, invisible braces, and joystick controllers for computer games were all invented as a direct result of NASA’s space program?)

My friend Emily accompanied me to Space Camp, which was a whirlwind week of NASA tours and (mostly) failed attempts at building cardboard rocket ships. A month after we got back, we were lying on the roof of her family’s houseboat in the Sierra, looking at constellations. We discovered the Chicken Foot constellation, which consists of two stars of the Little Dipper plus three extra “toe” stars (Can you find it in the gif above? hint: it's close to the middle, with toes pointing to the upper right corner). We saw a red shooting star that broke into five smaller ones. Then, as could only be expected from two ten-year-old best friends forced to live together for a week, we got into an argument. I insisted that stars were much bigger than planets, and quite a bit farther away, but Emily wasn’t having it. The stars, she maintained, were smaller than planets and floated among them within the solar system. I was fuming mad and didn’t speak to her again until breakfast the next morning.

That tiff was only one episode in a childhood characterized by intense emotional attachments to scientific facts. Not long after, I wrote a terrible poem about erosion (for the record, this is an exact reproduction):

As I sit here on this rock

Looking out over the ocean

I think about the wind and rain

And other kinds of erosion.

Once this rock was big and tall

As anyone could see

Now it’s eroded down to a spot

Just right and just for me.

In my defense, I was eleven and was missing school to be on a geology field trip near Point Reyes with my dad. All the geologists were scattered along the beach, poking sandstone with their pickaxes and arguing about faults, their beards bobbing emphatically. I was in a reflective mood, and thought I’d put my thoughts on paper.

Science also made me emotional in more predictable settings. I think my current love for certain ambient electronic music evolved directly from hearing aquarium soundtracks. How could I avoid being touched by the unique nervous systems of jellyfish when their lazy drifting was transformed into a graceful ballet by synthesized, soothing new-age music? And the triumphant symphonic arrangements accompanying video footage of migrant birds finally reaching home was sometimes too much to bear.

I was already known to be a huge nerd at school, so I kept quiet about how my love for science was almost spiritual. At home though, I religiously recorded and watched every single episode of Bill Nye the Science Guy, repeatedly. I went to the library and checked out books on time travel and relativity, hoping one day I could understand what the heck they were saying. I had a crystal-growing kit, my dad’s old chemistry set, a simple circuit board kit, and my own geology field kit, consisting of a pickaxe, a magnifying glass, white canvas bags for samples, and a vial of weak acid for identifying certain minerals. I wanted to be able to scrape off rock samples just like my parents did, and once alarmed a mall Santa by requesting a pocketknife for Christmas.

It wasn’t until my junior year of high school that I found out what it actually means to do real science. For AP Biology, we had to pair up with a local scientist and do a yearlong research project at his or her lab. I wanted to learn about microbes living in extreme environments, so my parents introduced me to a colleague at the U.S. Geological Survey who studies arsenic-eating microbes. After struggling through my first primary research paper, I apparently sufficiently impressed the head of the lab, and he allowed me to join his scientists.

I found out that science actually involves a lot of dishwashing. Seriously, the dishes never end. And there’s a lot of waiting, and sterilizing of surfaces and needles, and measuring, and being indoors with no windows for hours at a time. It involves counting hundreds of cells under a microscope and entering numbers into hundreds of cells in Microsoft Excel. Sometimes I slaved away for several hours at the lab, only to find out things hadn’t worked for some inexplicable reason, and I’d have to do it all over again. But at the end of the year, I left the lab armed with charts and graphs and real data. Best of all, I came away feeling like I could actually – finally – call myself a scientist.

image source: Wikimedia Commons

Organic Art

2010-05-03T23:31:00.001-07:00

Here's an interesting New York Times article on biology-inspired art: Of Compost, Molecules and Insects, Art Is Born. The article links to a slide show, which includes this work by Levi van Veluw (Landscape I, 2008):

Focus(bird)ing on Packaging

2010-05-03T15:50:00.000-07:00

I've been brainstorming with Megan of Nutmeg Press about album packaging for Focusbird's upcoming EP. We've got some great ideas, and she's going to be doing some nice illustrations. The packaging will be printed by hand, and, judging by Megan's other work, will be beautiful!

Focusbird goes to band camp

2010-04-26T20:01:00.000-07:00

We started a Focusbird page on Bandcamp! I think it looks a lot better than Myspace pages, and we might consider using it as a place to sell new material in a month or so. For now there are only two songs, but you can download them for free: http://focusbird.bandcamp.com/

A pretty, unrelated picture from a walk to a picnic by the beach:

Focsubird Update

2010-04-25T18:35:00.000-07:00

A. and I have been going back and forth to a friend's studio in LA to make better recordings of our songs, including some that have not yet been recorded. We're playing a show on May 27, and we're hoping to have EPs to sell! (If they're not ready then, we'll have a "release show" when they are.) Still brainstorming packaging/distribution ideas. It's hard doing a project like this on a budget of basically $0!

Our friend M. does a mean Focusbird shadow puppet.

My Lab: Asphalt Volcanoes

2010-04-25T18:12:00.000-07:00

Giant mounds of asphalt were recently discovered on the sea floor off of Santa Barbara. The above diagram shows the formation of these asphalt volcanoes.

Last summer I got to go on an Alvin dive to take samples from two of these features. The head of my lab, Dave Valentine, and his colleagues have just published a paper on them and their formation! Check out the NSF press release here, and an interview with Dave Valentine and colleague Chris Reddy here.

image source: http://www.whoi.edu/oceanus/viewImage.do?id=107898&aid=73026

Denying Science

2010-04-24T15:50:00.000-07:00

Interesting TED Talk by Michael Specter. I wish he'd covered more ground in terms of solutions, but I guess there's only so much you can fit into 16 minutes!

Feeling Music in the Brain

2010-04-06T16:54:00.000-07:00

Lately, I've got the brain on my mind. I've had few courses that touched on neuroscience and cognitive science, so it's very interesting to learn about various approaches used to explore the brain.

One approach is to use neuroimaging techniques to map brain regions (and their responses) to specific functions. Neural processing of emotions is an area of particular interest because of its implications in a variety of clinical settings, including depression. Studies looking at the brain's emotional responses to music have a lot to contribute to our understanding of emotional responses in general, according to a February article in Trends in Cognitive Sciences (Cell Press), called Towards a neural basis of music-evoked emotions.

The author, Stefan Koelsch, presents a variety of studies demonstrating music's emotional effects on different parts of the brain. Apparently, a common view is that emotional responses to music are purely aesthetic, and are removed from "real" emotions. Koelsch argues against this, pointing out that responses to music can be found in the very same structures considered to house the fundamental neural circuitry of "normal" emotions - the limbic and paralimbic structures.

Limbic and paralimbic responses to music

The amygdala, which processes emotions thought to be essential for survival, is a limbic structure. Studies have demonstrated that the amygdala responds a certain way to strong music-evoked emotions (chills). Even when chills aren't experienced, different specific changes in amygdala activity (and activity of associated structures) are observed in response to joyful versus dissonant music. Other studies have shown that certain limbic and paralimbic structures exhibit increased activity in response to videos shown with music, as compared to videos presented alone. Video/music studies have shown different neural responses depending on whether the music played was joyful or fearful.

These limbic/paralimbic structure studies provide support for Koelsch's assertion that music-evoked emotions are just as real as everyday ones, since they activate the same structures.

Music and pleasure

Several of the limbic/paralimbic studies mentioned above also reported activity in brain regions associated with reward and pleasure in response to pleasant music. These and other studies cite activation of the nucleus accumbens, a limbic structure that contains dopamine receptors and is implicated in reward and pleasure. Increased dopamine binding in the ventral striatum has been linked with pleasurable emotional responses to music.

Interestingly, the nucleus accumbens is also associated with behavioral responses to stimuli associated with pleasure or reward. Koelsch speculates this could be why a natural response to hearing pleasurable music is to move, dance, or join in the music-making.

Music and joy

Joy and happiness in response to music are thought to be mediated by separate neural circuits than those involved in pleasure and fun. Specifically, the hippocampus may be responsible for such emotions. The hippocampus plays a very well known role in learning and memory, but studies show that its activity in response to music may also have powerful emotional components.

The hippocampus has connections with many other structures, including the amygdala, the nucleus accumbens, a variety of other limbic/paralimbic structures, and structures involved in hormonal and immune system activity. Evidence, some from music studies, supports the role of the hippocampus in positive and tender emotions, thought to give rise to feelings of happiness (as opposed to those of pleasure and fun).

Implications

Koelsch emphasizes that studies like the ones he presents could have a great impact on our understanding of emotion and the brain. While there is much to be learned, such studies could lead to improvements in music therapy practices for treating emotional disorders like depression and PTSD.

source: Koelsch, Stefan. "Towards a neural basis of music-evoked emotions." Trends in Cognitive Sciences, Volume 14, Issue 3, 131-137, 11 February 2010. doi:10.1016/j.tics.2010.01.002

image source: Wikimedia Commons

LHC!

2010-03-30T18:22:00.001-07:00

The Large Hadron Collider is finally up and running today, and has already begun to set new particle-smashing records. Let the search for the Higgs boson begin!

image source: link

Altered recordings of music could be used to treat tinnitus

2010-03-24T12:26:00.000-07:00

Check out my new JYI article on a promising new treatment for certain types of tinnitus! I actually did a brief post a while back on the same study, but this article is more extensive, and, therefore, much more interesting. :)

image source: Wikimedia Commons

Focusbird on the Radio Tonight, 10pm!

2010-03-18T07:38:00.000-07:00

Hi all, we'll be playing on KCSB's show 5...4...3...2...fun!! tonight at 10pm. You can check it out live at kcsb.org. In addition to his heavy involvement in the diy music scene in the Santa Barbara area, Josh Redman, who does the show, is an awesome musician himself. Check out Watercolor Paintings, a project he has with his equally awesome sister, Rebecca.

Dietary Supplements: The Wild West of Health Care Products

2010-03-14T08:01:00.000-07:00

If you can buy dietary supplements promising great health benefits at your local Safeway or insert-regionally-appropriate-grocery-store-here, you generally assume they're safe and good for you, right? In fact, safety and effectiveness regulations of these products are more akin to those governing food manufacturers than medical drug makers.

Don't get me wrong, most of the dietary supplements you can find in your local grocery store are, at best, healthful, and at worst, harmless (though a recent lawsuit suggests otherwise for fish oil; also, spending a fortune on mega-doses of vitamin C, most of which will flush straight through the body and be disposed of in urine, seems harmful to financial health). But a quick google search will reveal that the world of dietary supplements is vast, especially for products aimed at consumers interested in bodybuilding, weight loss, or natural medicine.

These products include a fascinating array of amino acid supplements, "meal replacements," and "longevity pills." The packaging information for one product, human growth hormone spray for adults, provides an extensive scientific description of the hormone's role in biology and claims to lower body fat, increase energy, improve sexual performance, and raise IGF-1 levels. Human growth hormone (HGH) remains a popular supplement despite several studies showing a lack of evidence for its usefulness. (A 2007 paper said that, based on the authors' findings, it "cannot be recommended as an antiaging therapy.")

Oh, and one of this product's selling points is that it "contains actual HGH." Imagine having to read the fine print of your prescription medications to make sure the pills actually contained the drug you needed.

Dietary supplements like this HGH spray are the basis of a multi-billion dollar industry in the US. According to a Feb. 2010 Nature Network paper, about 20% of the US population uses the products for improved health. There are thousands of products on the market, and a thousand more are introduced each year.

Supplement Regulation

The huge dietary supplement market is made possible by FDA regulations outlined in the 1994 Dietary Supplement Health and Education Act (DSHEA), as well as several changes made since 2005. Unlike medical drugs, dietary supplements do not need to be approved by the FDA before they are manufactured and marketed. In fact, before the DSHEA, supplements were treated no differently from food products in the US.

The DSHEA includes packaging and safety regulations. However, it puts manufacturers in charge of making sure all packaging claims are true and all products are safe. The FDA can only request that a product be taken off the market if it can prove a supplement is unsafe. Moreover, a manufacturer does not have to disclose any evidence it may have that a product is safe and/or effective. Until recently, manufacturers were not required to inform the FDA of serious adverse effects reported by their consumers.

To many, the DSHEA regulations seem overly lax, citing safety concerns. Critics also worry that consumers are getting tricked into paying heaps of money for supplements that haven't even been shown to be effective (very expensive placebos?). Writers of marketing materials are highly skilled at selling their products, often incorporating scientific language and actual facts, and implying without ever quite lying.

Proposals for Better Regulation

The authors of the Nature Network paper mentioned above have some great ideas for improving the safety of dietary supplements. One idea I particularly liked was a "carrot on a stick" approach. In addition to requiring basic safety research before manufacturing a product, the FDA could hand out "seals of approval" for those products on which more extensive testing has been done. This might create an incentive for supplement makers to increase funding on safety and efficacy research, potentially leading to higher quality products.

The authors of that paper also propose the development of a central database of all dietary supplements on the market, allowing for easy access to information on the products. Such a list would be especially useful for clinicians concerned about the effects of dietary supplements on prescribed medications (another area in which there is a dearth of research).

Recently, a proposed bill increasing the FDA's role in monitoring supplements has been receiving a lot of press (probably due in large part to its potential financial effects on the industry). After his initial support of this bill, Senator John McCain withdrew his approval, then proposed compromises limiting the extent to which the bill would affect supplement manufacturers.

While most of the opposition to McCain's bill comes, predictably, from the supplement industry, it is somewhat surprising that many critics are actually the very population the bill hopes to protect - consumers of supplements. These consumers worry about increased prices reflecting the new regulations, and feel that such regulations are ridiculous given the fact that many supplement ingredients have been used for years with no apparent ill effect.

Even with the new regulations proposed by the bill, the supplement industry will maintain a huge amount of freedom. It is disturbing to me that products viewed to be in the same category as prescription medications by many consumers are not subject to nearly as strict regulations. As Peter Lipson, a blogger for Forbes.com, puts it, the DSHEA basically says to supplement manufacturers, "sell whatever you want, just don't let us catch you."

image: Wikimedia Commons

A Science Soundtrack

2010-03-02T13:08:00.000-08:00

In 1979, the history of evolution was presented by David Attenborough in the BBC series Life on Earth. I've never seen the series, but A. recently introduced me to the soundtrack from the show. Composed by Edward Williams, the soundtrack wasn't available to the public until November of 2009. Its current availability is thanks to the efforts of Jonny Trunk, who obtained an original LP recording and subsequently released the soundtrack on his record label.

The album is a compelling avant-garde mix of familiar impressionistic influences and electronic distortions and sounds. After the first listen, I'm particularly enchanted by "Gymnopedie for Jellyfish," which is very obviously inspired by Satie, but done beautifully.

The album is available in the Trunk Records online shop.

image source: http://www.djfood.org/djfood/page/3

Have One on Me

2010-02-23T11:21:00.000-08:00

Forgive me if I descend into fangirl mode several times during this post; Joanna Newsom is quite possibly my very favorite musician, and I’ve been awfully excited for her new release. Have One on Me is a 2-hour, triple album. It comes after Newsom’s rise to fame on the grand, swelling epic that was Ys, and her debut album of enthralling folk songs, The Milk-Eyed Mender.

Have One on Me incorporates all the elements that made Newsom’s previous recordings so wonderful – her signature voice and harp-playing (of course), superbly-crafted instrumental accompaniment, and lyrics that would be poetry by themselves – and adds even more. From the very first track, Easy, one can hear that the “bank” of notes Newsom chooses from for Have One on Me is noticeably different from the wider, more delicate intervals of Ys. Newsom’s new, soulful sound is evident even in quieter songs on the album.

Many tracks, including Easy and In California, build up from sparse accompaniment to beautifully orchestrated, invigorating arrangements, incorporating strings, brass, woodwinds, and percussion. In California’s occasional electric guitar strums and exotic, fluttering flute lines are contrastive, but work nicely. Go Long combines Newsom’s harp with the sounds of (what I'm pretty sure is) a kora for a shimmering interplay of two already enchanting instruments.

’81, an airy, luminous song about the Garden of Eden, is a delicate duet between Newsom and her harp. This is an amazing little song; one of my favorites after the first listen. It is the second shortest track on the album, and stands out in its brevity and simple structure. The song ends with Newsom’s voice suspended over the harp line – breathtaking.

The element of soul is more apparent on some tracks than others, especially in the piano-driven song Good Intentions Paving Company. A driving percussion and piano line accompany energetic vocals, featuring Newsom’s characteristic image-inducing lyrics: “Like a bump on a bump on a log, baby; like I’m in a fist fight with the fog, baby.” The chorus is particularly compelling; Joanna self-harmonizes with an impressively (almost uncannily) synchronized, pulsating vibrato.

Throughout the album, it’s evident that Newsom’s voice has improved; it’s clearer, more flexible, and more controlled. Two thirds of the way through the second-to-last track, Kingfisher, Newsom eases into an exquisitely haunting vocal line that sounds eerily like a theremin. This builds up into one of the most beautifully composed endings of all of the songs on the album.

The final track reinforces the soul element in its quiet nostalgia and bluesy piano chords. Listing different types of fabric, Newsom reminds us of her increasing involvement in the world of fashion: “I’ll buy my silks in shapeless bales; wrap it on up in reams of tissue, and I’ll kiss you sweet farewell.” The song ends with a deep, pulsating electronic fuzz; a surprising texture, but fitting for an innovative album.

I admit I was afraid to begin listening to this new album; everyone knows what it’s like to be disappointed eventually by a favorite artist’s latest work. But, before I was halfway through all of the tracks, I could very safely say that this is so much more than a solid follow-up; it’s an ingeniously crafted new approach to a familiar sound, and I don’t think anyone could have asked for anything more. At the risk of sounding ridiculous, I will say that I’m not sure anyone could have even conceived of what she has delivered to us. Newsom is a truly great musician, and Have One on Me is a truly great album.

image source: http://loki23.blogspot.com/

What I'm Reading: Rhythm and Melody in Speech and Music

2010-02-19T17:28:00.000-08:00

Music, Language, and the Brain, by Aniruddh Patel, is making me wish I had taken more psychology and linguistics courses. This week, I read about comparisons of rhythm and melody in speech and music. I was surprised to read that, despite our intuitions about rhythm, speech rhythm actually involves no periodicity (unlike music, which usually depends heavily on a beat).

You may be familiar with the idea that languages can be divided into two groups: stress- and syllable-timed languages. Speakers of stress-timed languages are thought to spend an equal amount of time between each consecutive stressed syllable. In syllable-timed languages, an equal amount of time is expected to be spent on each syllable. In a third group of languages, including Japanese, timing is thought to be based on regular temporal relations of morae, another type of sound unit.

Despite the widespread acceptance of these language groupings, no empirical evidence supports the idea that any languages are stress-, syllable-, or mora-timed. Thus, linguists must search elsewhere for speech characteristics that give rise to rhythm. Patel discusses a few of these characteristics, and shows how they can be used to compare music and speech rhythm within and among different languages.

Interestingly, in a study on French and English speech and music, Patel did find rhythmic correlations between the two domains, which differed between the languages. Patel attributes this to "statistical learning," whereby a composer has at his/her disposal a language-specific library of rhythms familiar from speech. (Of course, the composer could choose not to use these, but may do so consciously or subconsciously.)

The melody section also spent a lot of time discussing speech, and focused on the melodic contours of speech and music. A melodic contour can be thought of as a graph with time on the x-axis and pitch frequency on the y-axis; it is the "shape" of the melody through time, based on whatever frequency is being used at each moment.

While musical melodic contours involve sitting on the same pitch for some time, speech contours often consist of constant movement between pitches. Linguists have devised two main ways to simplify speech contours. In AM theory, important pitches in the contour are identified, and movement between them is dismissed as perceptually meaningless. In IPO theory, it's the movements between pitches that are viewed as important.

In a prosogram (shown above for a French phrase), a particular pitch is assigned to each syllable. Patel used prosograms to compare French and English speech and music. As with rhythm, he found that linguistic differences in speech melody were echoed by similar differences in musical melody.

Patel finishes up the melody section with a discussion of how asmusia and musical tone-deafness indicate the speech and musical melody processing in the brain overlap to a greater extent than previously thought. I'm going to devote a separate post to this later, as I find it particularly fascinating!

Musical notation source: Wikimedia Commons
Prossogram source: http://bach.arts.kuleuven.be/pmertens/prosogram/

Focsubird with Mirah and Rey tomorrow!

2010-02-19T17:22:00.000-08:00

Be there, or be...not there. But be there!! We'll do our best to put nice sounds in your ears.

Sound Garden

2010-02-18T02:35:00.000-08:00

Here's a fascinating idea by David Benqué: a garden of genetically engineered flora and fauna, designed to provide visitors with a carefully orchestrated aural experience. In addition to the "popping pod fruit" below, imaginary creations include a "sonic termite mound" and a "giant speaker lily."

Via a recent post on We Make Money Not Art. Check out the article for some descriptions of how specific hypothetical garden elements would work. (Images from we make money not art post.)

How to Be a Science Writer, Part 2

2010-02-16T23:45:00.000-08:00

As I mentioned last week, one of my classes was treated to a guest visit from stem cell Ph.D. student/science writer Teisha Rowland. She works very hard to stay on top of her research, blog (All Things Stem Cell), and science column for the Santa Barbara Independent.

Telling a Good Story in Favor of Breaking News

Many of the topics Teisha covered in our class will definitely affect my own writing. For one thing, she emphasized her passion for history and her belief that a science "story" is much better told and understood when a bit of historical background is included. This just makes sense, since the impact of a particular study is only clear when the context of the research is understood.

Teisha also mentioned her dislike of reporting breaking news research, and preference for approaching older news with a new angle. This preference relates to originality and readership. For one thing, reporting on brand new research is going to result in articles that sound a whole lot like many, many other people's articles. Also, it's nearly impossible to be the first to cover breaking news; big news sites will almost always be the major source for such stories.

Instead, Teisha prefers to choose topics her readers may not be familiar with, and present them in an interesting way. For example, her most recent article for the Santa Barbara Independent is on Archaea. As she told our class, many of the readers of her column may not be aware that this third domain of life even exists, since it was only recently recognized. By writing an article on the topic, Teisha is informing her readers in a unique way about a relevant topic, even though it's not breaking news.

Not only are such "story" articles more fun to write and more interesting to read (in my opinion); they can also be a great way to complement breaking news. For example, science news columnists can explore the background and potential impact of recent studies in their columns, helping readers place breaking news in a clear context.

Blog Audiences

Teisha was kind enough to answer a lot of questions from the class. One thing I was very curious about was what she envisioned as the audience for her blog. She said that she began by considering her parents to be the audience, but found that difficult since she wanted to blog about more complex ideas. She says she now tries to write in a style that is accessible to both experts and non-experts by making sure technical passages include explanations and links to explanatory sites.

I've been thinking a lot about the audience for my own blog. I began it with the intention of "reporting" breaking news science stories I found on other websites. The idea was purely practical: I wanted a way to get some practice writing about science for my own improvement.

That got boring pretty fast. So I began writing about things that were more personally important to me, such as topics I was covering in class or in my own research. I also began including writings on music, since it is also very important to me. Now, I choose my topics and writing style as though I were writing for my friends. My audience is anyone who is also interested in science (mostly biology) and music. It's a lot more fun and satisfying to keep up a blog when you write about what you're interested in (more advice from Teisha)!

image source: Wikimedia Commons

Medical Risks of Missions to Mars

2010-02-16T11:44:00.000-08:00

Another article I wrote is also now up on the JYI website. Take a look!

Image: Astronauts during weightlessness training. Source: Wikimedia Commons

A New Way to Fight Mosquito Borne Illness?

2010-02-15T19:45:00.000-08:00

Check out my article on a possible new way to combat mosquito borne illness on the Journal of Young Investigators (JYI) website!
Image: Aedes aegypti mosquito. Source: Wikimedia Commons.

Type 2 Diabetes Video

2010-02-15T18:06:00.000-08:00

One of my classes will be discussing new type 2 diabetes drugs this coming week. It's been a while since I learned about type 2 diabetes, so I found this video useful in brushing up on my knowledge:

We'll be discussing liraglutide, a drug that mimics glucagon-like peptide-1 (GLP-1). GLP-1 is a natural human protein that plays several important roles in glucose metabolism, including stimulation of the pancreas to release insulin into the blood.

The FDA recently approved liraglutide for use in the U.S. under the name Victoza, although concerns remain about its side effects. These include fears that thyroid tumors seen in animal testing of the drug could appear in humans. Due to the caveats, much of the media coverage of the FDA's approval makes rather pessimistic predictions regarding the financial benefits of the drug for Novo Nordisk, the manufacturer. Victoza also faces tough competition from Byetta, a similar drug already taken by many type 2 diabetes patients.

Diagramming Music: Marco Fusinato

2010-02-14T00:20:00.000-08:00

Found these music- and science-inspired artworks while exploring the interwebs. (I'd like to see bigger versions and read the artist's statement, but unfortunately Marco Fusinato's website appears to be down at the moment.)

Update: The artist's website is back up again!

Focusbird: Concert Today!

2010-02-12T02:31:00.001-08:00

Come see Focusbird open for Mirah! (poster)

2010-02-10T02:18:00.000-08:00

Rey Villalobos posted this image on the 'spooce. So excited/nervous!

How to Be a Science Writer

2010-02-08T21:59:00.001-08:00

I'm really excited for my seminar class tomorrow because Teisha Rowland, a grad student at UCSB, will be our special guest science writer. I'll post more after the class, but for now, I wanted to link to an interesting post she made about attending the Science Writers 2009 Conference.

Her coverage of the conference provides a lot of insight into the challenges facing science writers today. I think I'll definitely be referring back to the post in the future. Among all the useful info, a quote from one of the speakers she heard, Dan Gillmor, caught my attention. He said that "Wikipedia is 'the best place to start, [but the] worst place to stop.' "

Though I certainly don't consider my science posts on this blog to be science "journalism" (I think of them more as personal explorations of things that catch my attention), I try hard to be thorough in linking to all my sources and sites that may provide some extra background info. I do often link to Wikipedia for my "further information" links, so maybe this would be a good time to say that I agree with Dan Gillmor's opinion on the site.

Wikipedia can be a great place to start because it gathers a lot of information about very specific topics into one place. While a Wikipedia page should never be cited as a source, the source material for the article (listed at the bottom of the page) can provide a wealth of information.

For example, in preparation for our discussion tomorrow, I read some articles discussing the Woo Suk Hwang cloning scandal. I only had articles from 2005, and was curious about subsequent developments in the controversy, so I checked it out on Wikipedia. The Wikipedia article mentioned something the papers hadn't: that Hwang's research may have actually provided a major breakthrough for stem cell research, just not the one he claimed it did.

But I didn't stop there. I checked the sources cited for that specific piece of information, and found links to two articles confirming it, one of which was an article in Scientific American.

Wikipedia can be misleading (see my post from last Wednesday), but it can be extremely useful when approached as a starting point, with the ultimate goal of discovering information from more reputable sources.

top image source
bottom image source

Imminent Release: Joanna Newsom

2010-02-08T03:23:00.000-08:00

I am so excited for this release! I love the cover art; with her surrounded by various curios, it seems like a 20s-ish, more sumptuous version of her last album's cover art:

You can hear a song off of Joanna's new record (to be released Feb. 23) here.

The Long Lost: A Fanciful Duo

2010-02-08T03:19:00.000-08:00

THE LONG LOST "Colour" (dublab VisionVersion) from dublab on Vimeo.

This is such an enchantingly odd, whimsical, and pretty video of Daedalus (see post below) and his wife.

Concert: Nosaj Thing, Daedalus, Teebs, Jogger

2010-02-08T02:03:00.000-08:00

After a rainy, somewhat harrowing drive down 101 in LA on Friday night, A. and I saw a really fun concert at the Echoplex. With interludes by D.J. Frosty (featuring what sounded like Vietnamese pop), Jogger, Nosaj Thing, and Daedalus kicked off their Magical Properties tour, with a guest appearance by Teebs.

Magical Properties Tour from The Service Company on Vimeo.

We arrived a bit early and had a chance to speak briefly with Daedalus, who was manning the merch table with his beautiful wife. He was extremely friendly, and mentioned that he's uncomfortable with releasing his material in cd and vinyl format because of the environmental impact. I don't think I've ever heard a musician show any reservations about vinyl! By the way, Daedalus and his wife have their own group, the enchanting The Long Lost. I was going to post just a picture of Daedalus, but he and his wife are so charming, I also have to post a picture from their Myspace.

Teebs (below) played first, his set consisting of slower, heavy beats. He was all dreadlocks and smiles. There's something really wonderful about a musician who smiles while they play; Flying Lotus does it too, and it just makes the live performance so much more special. (The smiling-est performer I've ever seen was a set by the jazz guitarist Julian Lage at Stanford Jazz Camp. He looked out over the audience with a big, sincere grin the entire time, and I don't even remember what he played, but I came away being a fan.)

Jogger, a duo (below), was up next. I'd never heard or seen them before, and I wasn't so sure how I felt about them. They had some really interesting, even beautiful passages, but some parts weren't really what I was in the mood for. I'm not much of a hardcore rock person, and they seem to have been influenced a lot by that. I came to the concert more for the glitchy beats than for the noise. Also, their guitarist didn't really look like he was having much fun (advice: smile!). But the other half of the duo was quite entertaining to watch with his big gestures and long hair. A lot of people in the audience seemed to be really into Jogger, so the energy was still there even if they weren't my favorite.

What was my favorite was Nosaj Thing's set. He played some tracks I recognized from his album Drift, as well as his remix of Flying Lotus' song Camel. Then he moved on to some pop remixes, including Lil' Wayne and Drake. Nosaj Thing is another DJ who's really fun to watch. The way he dances while he plays syncs so perfectly with what he's doing, and during his set, I kept finding myself mimicking his movements.

While Nosaj Thing was playing, a man slowly walked onstage, hiding behind an umbrella he was twirling like some dapper, golden-age movie star. He threw it aside, grabbed the mic, and started rapping. With brief bits of dramatic, minor (Tim Burton-esque?) melodies, accompanied by gestures I can only describe as "jazz hands," Busdriver gave an impressive, one-song performance before grabbing his umbrella, and backing offstage behind the twirling prop. It was hilarious, charming, and really cool all at once. Here's a video of that performance:

Daedalus finally appeared on stage in his usual anachronistic attire (he's in the habit of dressing in a sort of Victorian gentleman's style, with impressive sideburns, a tailcoat, and a thick tie around an upturned collar). He uses a monome, which he tilts toward the audience for a very effective display. Daedalus' set was definitely the most dancy; unfortunately, we were pretty tired from standing in the 2nd row on our feet the entire time, so our "dancing" consisted more of head bobbing. Still a great performance, though. The video below is from a different concert, but it gives a great idea of Daedalus' style:

Both times I've seen him, Daedalus has sampled some of my very, very favorite songs. The first time I saw him, he played Gang Gang Dance's Vacuum, which A. can tell you I am fairly obsessed with. At this concert, Daedalus ended his set with a sample of The Flamingos' I Only Have Eyes For You, which is not only (I think) the best doo wop song, but one of my favorite songs of all time.

(Question: Do you think, as I suspect, that Daedalus' "pointing" gestures after he hits buttons on his monome could be moments when he aims for the beat, so as to account for a slight delay in sound production after the buttons are hit? It could just be a stylistic thing...I wish I had thought to ask him!)

After a Daedalus encore, A. and I talked to Nosaj Thing, and, like Daedalus, he was very sincere and friendly. As LA is the "home base" for these artists, there was a really great community atmosphere to the concert, and the artists were very gracious and supportive of each other. I'm excited to see them back in LA after their tour!

Teebs image source.
Daedalus image source.
The Long Lost image source.
Jogger image source.
Nosaj Thing image source.

Focusbird: Opening for Mirah on Feb. 20!!

2010-02-06T21:27:00.000-08:00

Okay, trying not to get too excited...but I'm really excited! We are opening for Mirah's Feb. 20 show at the Hard to Find in Goleta, which will also feature Rey Villalobos. This will be our first non-garage/living room performance! I'm pretty nervous, but really happy and grateful to have this opportunity. Here are the details:

Club Mercy & KCSB present:
Saturday February 20
MIRAH
+ Rey Villalobos + Focusbird
@ The Hard to Find Showspace in Goleta
7190 Hollister Ave.
All Ages, 8PM
Tickets at clubmercy.com

Hope to see you there!

What I'm Reading: M,L&B; Sound Elements

2010-02-04T23:30:00.000-08:00

So I just finished the first section, Sound Elements, of Music, Language, and the Brain, by Aniruddh D. Patel, and I have to say that this is one well-written book. There are not many authors who can master the scholarly, yet crystal clear and compelling style Patel employs.

Sound Elements explores the idea of music and speech perception as two separate learned sound systems that are unique to different cultures. Patel argues that, while these sound systems are definitely separate, they may be acquired through very similar developmental mechanisms. There are so many interesting ideas covered in the section, but listing them all here would make this a very long post, so I'll just focus on a few things I found particularly interesting.

Scales, and the universality of the fifth

Patel talks a bit about how musical scales vary between different cultures. I was taught that the Western scale system is the way it is because intervals with simple, small-number frequency ratios are somehow inherently more pleasing to the brain (Thank you, Pythagoras!). However, a little exploration of other cultures' scales makes it clear that such ratios are not universally admired. Many cultures have scale systems involving intervals with far more complex frequency ratios. In fact, the only intervals that seem to be (almost) universally important are the octave and the fifth.

An appendix at the end of this chapter provides some hypotheses as to why the fifth is so universally appealing. One idea is that the interval interacts with our auditory systems in a way that minimizes "roughness." When a complex tone is played, there is one fundamental frequency, and integer multiples of that frequency determine the tone's harmonics. When an interval consisting of two complex tones is played, harmonics that are very close in frequency but not identical will create a beating sound, or roughness, because of the way the basilar membrane in the ear is excited. An octave interval will minimize roughness because all frequency pairs match up perfectly. A fifth is the next most "smooth" interval, because many of the frequency pairs match up, and the ones that don't are far enough away from each other that they do not cause roughness.

Another hypothesis suggests that it is not the absence of roughness of the fifth that makes it appealing, but the particular neural patterns it produces. Research suggests that the brain, "hears" a fundamental frequency an octave lower than the frequency of the lower pitch, as well as other harmonically related notes. (This is in addition to the actual frequencies of the pitches composing the fifth.) Other intervals do not suggest any other clear pitches in the neural patterns they produce.

The third hypothesis for the universality of the fifth is that it is an important interval in human speech. Data shows that the second most energetic frequency in speech is a fifth above the frequency with the most energy. Perhaps all humans are attracted to the fifth as a musically important interval because it invokes the human voice.

"Speaking" with musical instruments

In discussing pitch in a linguistic context, Patel explores fixed-pitch tonal languages, where the pitch in which a word is uttered is central to its meaning. Some cultures with fixed pitch tonal languages have developed instruments that can be used to convey linguistic messages by imitating the pitches and syllable rhythms of the spoken language.

The West African talking drum is one such instrument. It can be used to convey messages over long distances. In West African drum ensembles, a player in the midst of a musical passage might quickly send a linguistic message using his drum. Listeners familiar with the drum language will immediately be able to separate the musical sounds from the linguistic ones. Other cultures are known to have whistling languages for long-distance communication, and a stringed instrument called the krar (see image above) is used to convey linguistic messages in Ethiopia.

Well, this post is turning out to be a lot longer than I meant for it to be! I'll finish off by mentioning one more thing I really like about Patel's writing. In addition to always providing the experimental basis for the claims he makes, he frequently gives suggestions for how unanswered questions could be specifically addressed experimentally. I really like that Patel isn't just explaining an "end story," but actively engages the reader in the ongoing exploratory process of research.

krar image source.

Portrait of a(n) (ill?) Young Man

2010-02-03T02:23:00.001-08:00

Can doctors spot illness in centuries-old paintings? Some friends and I (none of us experts when it comes to the visual arts) were talking about the significance of the subject's hand gesture in Botticelli's painting Portrait of a Young Man the other day, so I looked it up online. I found this paper from a 1983 issue of the journal Arthritis and Rheumatism. The article claims that the swelling in the joints of the hand is characteristic of juvenile rheumatoid arthritis, and that the painting may document one of the earliest cases of the illness. The authors base their claims on their studies of Botticelli's other works, concluding that the swelling is not a stylistic trait, nor is it a mistake, as Botticelli is well known for his superb technique.

As for the actual positioning of the fingers, the paper notes that the third and fourth finger were often painted together for aesthetic reasons by many artists of the Renaissance, and the fifth finger was often bent as well. (The Wikipedia article is a bit misleading on this subject, as its wording suggests the hand gesture itself is considered to be a symptom of arthritis.) For example, a similar gesture can be seen in the left hand of the subject of Botticelli's painting Fortitude, which represents one of the seven virtues:
The 1983 paper reminded me of a recent claim made by pathologist Vito Franco of University of Palermo that an examination of Mona Lisa's face indicates she had high cholesterol when she was painted. Franco has studied other paintings of the Renaissance and made several other conclusions about illnesses afflicting the subjects. (Unfortunately, I couldn't find a link to his formal findings, which he presented at a human pathology conference in Florence last fall.)

In going back to the Time article on these claims, I found that Franco actually has a different diagnosis for Botticelli's Young Man. According to him, the subject suffers from Marfan syndrome, a genetic disorder that affects connective tissue and generally results in tallness and elongation of limbs. As evidence, Franco presents the "unusually long, thin fingers" of the young man.

Personally, I am skeptical of diagnoses of diseases based on analysis of paintings of patients, but I think it's fascinating that beloved art can be approached from all sorts of angles, even medical ones.

What I'm Reading: Music, Language, and the Brain

2010-02-02T01:16:00.000-08:00

Just started this book by Aniruddh D. Patel for an independent reading project I'm doing on music cognition with a music professor. So far, I'm really enjoying it; fascinating concepts are well-organized and explained in a scholarly, yet clear manner. I plan on updating Curious! periodically with interesting tidbits from the book. For now, here's Amazon.com's description:

In the first comprehensive study of the relationship between music and language from the standpoint of cognitive neuroscience, Aniruddh D. Patel challenges the widespread belief that music and language are processed independently. Since Plato's time, the relationship between music and language has attracted interest and debate from a wide range of thinkers. Recently, scientific research on this topic has been growing rapidly, as scholars from diverse disciplines, including linguistics, cognitive science, music cognition, and neuroscience are drawn to the music-language interface as one way to explore the extent to which different mental abilities are processed by separate brain mechanisms. Accordingly, the relevant data and theories have been spread across a range of disciplines. This volume provides the first synthesis, arguing that music and language share deep and critical connections, and that comparative research provides a powerful way to study the cognitive and neural mechanisms underlying these uniquely human abilities.

image source

The "Breast" Age to Begin Regular Mammograms (sorry...)

2010-01-25T18:43:00.000-08:00

...I can never resist an awful pun!

One of my classes is discussing the mammogram guidelines controversy that shook up doctors, patients, and policy makers toward the end of 2009. In November, The U.S. Preventative Service Task Force released a study with updated guidelines about when women should begin receiving regular mammography screening for breast cancer. (ABC News has a pretty well written article on the issue.)

The study states that "The USPSTF recommends against routine screening mammography in women aged 40 to 49 years." The recommendation, based on eight separate clinical studies, several databases, and other studies, was reached after the authors concluded that the risks of mammograms in women aged 40 to 49 outweigh the benefits.

The Controversy

This finding raised immediate outcries from all directions because previous guidelines recommended beginning routine screening at the age of 40. People in opposition to the new recommendations argued that mammograms for women aged 40 to 49 save lives and should continue to be routine.

The authors conceded that their study was poorly written and should have been more clear. Specifically, they believe that women aged 40 to 49 should not automatically be given mammograms, but should be informed that there are a lot of risks involved. The choice to get a mammogram should be made by each woman after a discussion with her doctor.

Of course, many health professionals, policy makers, and patients prefer to ignore these recommendations, saying that it is worth the risks of mammography to save just one life. They worry that women who would benefit from mammograms may opt out of them, putting them at greater risk for undetected breast cancer.

I think what this comes down to is an individual opinion of whether it's better to keep the total number of breast cancer mortalities as close to zero as possible, or to balance that number out with a reduction in the harm known to be caused by mammograms. I'm really not sure where I stand on this issue; it's a tough one.

Risks of Mammograms

Risks conferred by mammography include false-positives, which "cause anxiety and lead to additional imaging studies and invasive procedures." Another risk is overdiagnosis, when breast cancer is detected in a woman, usually older, who is likely to die of other causes before the breast cancer would have been clinically detected.

Overdiagnosis is the focus of a Jan. 19 article discussing the findings of a recent paper in the American Journal of Public Health. The study found that many elderly women with dementia, who have a 3.3 year average life expectancy, are getting mammograms. The American Cancer Society and other experts recommend against breast cancer screening for any woman with a life expectancy of less than five years, since any cancer detected is unlikely to progress far enough to be clinically significant before death.

In addition to mammograms, the USPSTF also gave recommendations for other types of breast cancer screening. Another surprising one was that breast self exams (BSEs) should not be performed. This is based on evidence that BSEs do not have any effect on the breast cancer mortality rate. The authors later clarified that this does not mean a patient shouldn't tell her doctor about an unusual lump.

Study Demographics

The USPSTF article was also criticized by NPR, bloggers, and other sources because of the demographics of the women involved in the studies upon which the recommendations are based. These sources argue that the higher rates of breast cancer in African American women combined with their low representation in clinical studies means that African American women should still get routine mammograms beginning at the age of 40. Skeptics point out that data on Hispanics and Asian-Americans is also limited. However, as this blogger points out, a common form of breast cancer in African American women grows so quickly that yearly mammograms would be too rare to detect it at an early stage.

Better Communication

The recent mammogram controversy and other similar ones, such as the statin controversy, have made me wonder if peer-reviewed medical journals should start paying more attention to how the language of a technical article might affect a layperson's interpretation of it. This is difficult, of course, because scientific accuracy often requires language that may take years to fully comprehend, and we don't want to have to sacrifice accuracy for readability. Another strategy may be to publish side-by-side guides to articles for non-experts. This could not only help avoid controversies, but could improve patient trust in medical science.

Top image source. Bottom image source.

Music and Art and Physics, Oh My!

2010-01-25T14:50:00.000-08:00

To kick off the new direction of Curious, here's an announcement about my musical project Focusbird. Just found out we're playing a show Feb 12 w/ Stephen Steinbrink, Foot Ox, and James Fella at the MIKE BARN, which is a house at 6738 Trigo Rd, Isla Vista. Hope to see you there!

Also, stumbled across the work of Morgan O'Hara:
Movement of the hands of
Conductor Riccardo Chailly
while conducting the Concertgebouw Orchestra in Mahler's Symphony No 4.
first movement
Carnegie Hall, New York City
10 February 2000

I love the curlicues off to the right in the above drawing, and I think it's interesting how it compares to this one:
Movement of the hands of
Composer Pierre Boulez
while conducting the London Symphony Orchestra
in Stravinsky's Petrouchka /
Carnegie Hall, New York City
13 March 2000

From the artist's description, it seems as though there are no actual instruments involved in the drawing process besides the artist's observations and artistic skill. I think it would be fun to put some sort of sensor on the end of a conductor's baton to even more accurately trace the path of the conducting.

This reminds me of a project done by a classmate in a class about symmetry and aesthetics in physics I took freshman year. He was looking at the way various parts of the body move, and made some very beautiful patterns by digitally tracking limb movements.

Time for some changes around here

2010-01-25T14:48:00.000-08:00

Hi readers! I’ve made a decision to combine this blog with a blog I started for my musical project Focusbird. As you may have noticed from my recent posts, I really like writing about music, and I hope to transform Curious! into a blog about all my intellectual interests, not just strict science. (Don’t worry, I’ll still make it very clear when I am giving an opinion or interpretation and when I am stating factual information from a reputable science source.) I hope this will be as much fun to read as I’m sure it will be to write!

Aesthetics: Sound Sleuths

2010-01-22T00:14:00.000-08:00

How do you solve a musical controversy? With science, of course! This colorful triangle may look like a piece of abstract art, but it's actually a visual representation of the similarities between different recordings of the same piece of music. It's called a "timescape" by its creators.

The horizontal axis represents time, and the colors show how similar the recording being analyzed is to other specific recordings. What is being measured is the relative duration of each note, or the artist's unique rubato. The image above is a timescape for Arthur Rubinstein's 1939 recording of the Mazurka Op. 68 No. 3. One can see that much of the recording is very similar to a recording represented by the color orange. It turns out that the "orange" recording is actually the artist's own 1966 recording of the same piece. The black coloring represents the average rubato of all the recordings used, and the colors toward the bottom represent fleeting similarities to various other recordings.

Developed by the Centre for the History and Analysis of Recorded Music (CHARM), these timescapes were used to explore a controversy surrounding the late pianist Joyce Hatto. Toward the end of her life, numerous critically acclaimed recordings were released under Hatto's name. Shortly before her death in 2006, several individuals claimed to hear unmistakable similarities between her recordings and the recordings of other artists. In 2007, various sources, including CHARM, used digital technology to confirm the fraud.

The triangle below is a timescape for the recording of Op. 68 No. 3 by Jerzy Śmidowicz on the compilation Fryderyk Chopin, Complete Works: The Golden Age of Polish Pianists (Muza PNCD 300). The mint color represents the artist's recording of the same piece on The Great Polish Chopin Tradition V: Śmidowicz (Selene CD-s 9905.50). The mint color permeates the triangle because both recordings are a re-issue of the same original 1948 recording. The colors at the bottom reflect limitations in precise data capture:
The following triangle is a recording of the same piece, released by Joyce Hatto in April 2006. It indicates the recording is virtually indistinguishable from a 1988 commercial recording credited to Eugen Indjic, represented by the yellow color:
This last triangle shows Joyce Hatto's recording of the Mazurka Op. 17 No. 4 compared with Indjic's own recording, again demonstrating similarity too close to be coincidental:
It tuns out that many of Hatto's releases were digitally altered versions of previous recordings. Despite the manipulations, however, the original rubato was preserved. It is unknown whether Hatto knew the fraud was being committed.

To me, this project highlights the impact of infographics in displaying data. CHARM also provides percent similarities between recordings of the same piece, which give the same information. But there is definitely a more fine-tuned sense of the extent of the similarity when we can visualize it in terms of size and shape and color.

All information and images from the CHARM website's project description and the Wikipedia page on Joyce Hatto.

Pleasant Surprises

2010-01-21T18:03:00.001-08:00

There's an interesting new post on The Frontal Cortex by Jonah Lehrer about a paper exploring the role of neural predictions in listening to music. According to the scientists:

The ability to anticipate forthcoming events has clear evolutionary advantages, and predictive successes or failures often entail significant psychological and physiological consequences. In music perception, the confirmation and violation of expectations are critical to the communication of emotion and aesthetic effects of a composition.

As Lehrer explains, the study's points are twofold. First, the scientists found that models based on statistics are better at simulating the mind than models based on hard and fast rules. Then, an experiment was performed in which it was found that unexpected notes in a piece of music trigger unusual neural events and an increase in brain activity. Lehrer points out that part of music's effectiveness comes from the fact that it "toys with" our natural habit of anticipation, and that consonance is merely used as a "frame" to set up the surprise of dissonance.

To those who have studied music, the importance of the unexpected is well known. And if one listens to enough contemporary composed music, the unexpected can become expected, so that consonance is the surprise.

But this study does raise some questions for me. A lot of currently popular music is actually very predictable, with frequent uses of the tonic (the note a listener most often expects in a piece). At first this simplicity seems to contradict the findings of the study because it suggests that the effectiveness of music that is most popular is based on its predictability, not on its ability to surprise. But perhaps the predictability of pop music is only apparent to those who have had some formal musical training. Maybe the majority of listeners find a pleasing amount of melodic surprises in most pop music.

But I think another important thing to consider is that a lot of the surprises in pop music aren't melodic, but rhythmic and timbral (timbre refers to the qualities of a sound that distinguish it from another sound of the same note). Syncopation is certainly a very important part of pop music, and electronics provide a seemingly infinite amount of different possible timbres. Also, especially in rap, clever lyrics may pack the surprising punch listeners love. It might be interesting to do another experiment where the "unexpected" variable was rhythm, timbre, or lyrics, rather than pitch.

Image source.

My Classroom: Navigating Epidemiology

2010-01-11T12:15:00.000-08:00

I just reread this article for a class I'm taking on media portrayals of scientific research. It's a great New York Times article outlining the problems associated with epidemiological studies, and, I think, a great article for any budding biologist to come back to every so often.

Gary Taubes uses the hormone replacement therapy (H.R.T.) debate as his main example of a therapy whose safety is still in question, despite large-scale epidemiological studies. In the 1990s, many women began to take estrogen to reduce the symptoms of menopause. In 2002, millions of women were taking H.R.T. when the results of an epidemiological study cast doubt on its safety. Taubes uses the rest of the article to explore several of the hidden factors that can cause such observational studies to be difficult to interpret (and sometimes misleading), including:

The healthy user bias, in which patients who appear to benefit from a particular treatment are also found to be wealthier and more health-conscious in many areas of their lives. On the surface, their positive response seems to support the use of the treatment in question. But, in reality, it is difficult and usually impossible to say whether one patient is healtheir than another due to the treatment or due to other lifestyle factors.

A related factor called the bias of compliance, in which patients who follow their doctors' orders are more likely to be healthy, whether they are treated with an actual drug or a placebo.

And, the prescriber effect, in which doctors (understandably) use highly subjective reasoning when deciding how to treat certain patients, plaguing observational studies with even more complex caveats. An example from the article: "A physician is not going to take somebody either dying of metastatic cancer or in a persistent vegetative state or with end-stage neurologic disease" and prescribe statins to get her cholesterol levels down. Thus, many people who end up on statins are already healthier than many people who aren't on statins, possibly making the drug seem more helpful than it really is.

Taubes covers several other issues with epidemiological studies in this extensive article, and I'd highly recommend it to anyone who looks to media reports on medical studies for health advice.

I wish Christmas wasn't over...

2010-01-04T20:42:00.000-08:00

...because I would have asked for this.
“Far Out: A Space-Time Chronicle,” by Michael Benson, looks like a beautiful book. (Images are from the slide show accompanying the article.)

For tinnitus patients, music is in the spaces between the notes

2010-01-04T19:54:00.000-08:00

Here are some fascinating findings on a potential therapy for treating the chronic ringing in the ears known as tinnitus. Researchers took each patient's favorite music and cut all notes corresponding to a range of frequencies centered on the patient's "ringing" frequency. The patients listened to their personalized music for 12 hours each week for a year, and experienced significant improvement in their tinnitus.

The idea behind the research is that tinnitus may be caused by reorganization of the auditory cortex of the brain as a result of noise exposure. (The auditory cortex perceives sound.) According to the researchers, the success of this therapy may be based on two mechanisms: The neurons responsible for the tinnitus are not being stimulated since their corresponding frequencies are absent from the music. Also, these neurons may be actively suppressed by neighboring auditory cortex neurons.

The research was published by PNAS, and the supporting information includes links to three movies with examples of "notched" music, or music in which a certain range of frequencies has been deleted. One movie is "target notched," meaning it is customized for the specific tinnitus frequency of the patient. A second is a placebo in that it has also been "notched," but in a range not centered on the patient's tinnitus frequency. The third movie plays the original audio for comparison (the Prelude to Bizet's Carmen, for my fellow music nerds).

(image source.)

Speaking of Methane...

2010-01-04T19:45:00.000-08:00

Check out this awesome photo of Kraken Mare, a liquid hydrocarbon lake on Titan, one of Saturn's moons:

The photo was taken last July on Cassini's 59th flyby of the moon. Image and info source.

SEEPS ’09: Alvin, Atlantis, Methane, and More!

2009-12-14T01:00:00.000-08:00

I want to share some long-overdue photos from a research trip taken in September by my lab at UCSB. I work for Dr. Dave Valentine, aiding in studies of methane-consuming microbes off the coast of Santa Barbara. Dave’s lab is primarily concerned with the biogeochemistry of marine hydrocarbon seeps.

Several times over the past few years, he’s taken his lab group on a ship for a half month-long research trip down the coast of California as part of the Study of the Ecology and Evolution of Petroleum Seeps (SEEPS) project.

The three-person submersible Alvin (of Titanic fame) was used to explore and collect samples from the sea floor, and this year we used an autonomous sub called Sentry to map and image the bottom of the ocean.

Here are some photos from the trip:

Our ship, R/V Atlantis, was huge! (This is only the middle portion.) Here, Atlantis is docked in San Francisco, one day before our departure. We headed down to Southern California, spending most of our time near Santa Barbara and LA.

We left San Francisco Bay under the care of a pilot who was soon retrieved by the red and white boat in the background.

Alvin and Sentry

Between dives, Alvin is kept in a sort of cave on the back of Atlantis.

Lowering Alvin into the water for a dive is a long and spectacular process.

It travels down this track and is lifted up by a giant rope.

After being decorated, a full-size foam head was sent down with Alvin in a mesh bag. The water pressure at the great depths of the seafloor shrank and distorted the head. Styrofoam cups and waterproof Sharpies were hot commodities on the ship!

I got to go on an Alvin dive! It was incredible. Deeper than sunlight could penetrate, we cruised along the featureless seafloor before arriving at some underwater hills teeming with life. We were trailed by inking squid for much of our trip. Toward the end, I got pretty sleepy due to the lower oxygen levels in the sub. (Oxygen levels are purposely kept low to minimize the risk of fire.)

Sentry being lowered into the water for some seafloor exploration.

One cloudy day, we found our ship surrounded by probably over 50 whales, surfacing to breathe.

The sunsets were beautiful. On this particular day, dolphins were swimming beside the ship as the sun set.

It was a great opportunity to have participated in this trip, thanks to the scientists, the Alvin crew, the Sentry crew, the SSSGs (who helped with the on-board equipment), the crew of the Atlantis, and Dave.

Meditating on Medicine

2009-10-30T01:24:00.000-07:00

(This is an article I wrote for a journalism class assignment.)

Self-awareness program for doctors may improve healthcare

A self-awareness education program to treat physician distress could improve patient care, according to a study published in the September 29/30 issue of the Journal of the American Medical Association.

Researchers at the University of Rochester Medical Center in New York designed and monitored the effects of a course emphasizing mindfulness, a self-awareness technique. The study is the first to suggest that mindfulness education to reduce primary care physician distress may also lead to improved patient care.

The year-long course was taught to 70 primary care physicians in the Greater Rochester, New York, community. It included mindfulness meditation and communication and self-awareness exercises.

Researchers surveyed the physicians before, during and after the course. Changes in factors such as emotional exhaustion and perceptions of personal accomplishment pointed to steady improvements in physician well-being. Factors correlated with better patient care, such as empathy, mood, and fatigue, also showed improvement.

High levels of stress lead to burnout in up to 60 percent of practicing physicians. Physician burnout is characterized by emotional exhaustion, low sense of accomplishment, and treatment of patients as objects.

Such distress leads to lower quality of patient care, including “patient dissatisfaction, increased medical errors, and lawsuits.” It also leads to “decreased ability to express empathy,” and major decreases in the number of practicing primary care physicians.

Physician burnout has been recognized as a significant problem for years, the study says, but few programs have been created to combat it. Of the programs that have been implemented, few studies have explored their effectiveness.

Programs for physician burnout based on mindfulness, “the practice of being fully present and attentive in the moment during everyday activities,” are increasingly frequent. Some studies have previously shown that mindfulness courses improve physician well-being.

This mindfulness program began with an eight-week intensive phase during which participants attended weekly 2.5-hour meetings and a seven-hour retreat between the sixth and seventh weeks. During a 10-month maintenance phase, the physicians attended monthly 2.5-hour meetings. Each 2.5-hour session consisted of presentation of a theme, writing exercises related to the theme, mindfulness meditation, and small and large group discussion.

The team measured outcomes with survey results taken at five points over the course of the study. The authors used widely accepted scales to measure burnout, physician empathy, mindfulness, mood, personality, and the belief that psychological and social issues are important in patient care.

Each scale consisted of several measures, and average scores were calculated for each measure. Most measures showed steady improvement throughout the study. Several measures showed only short-term improvements, and some only long-term.

The authors suggest their mindfulness program be offered as one of several options for doctors at risk of burnout. However, they stress the need for further studies of its effectiveness. These findings suggest improved patient care by physicians who participate in such a course based only on physician attitude. Data reflecting actual clinical outcomes or patient satisfaction is needed to accurately determine the clinical effectiveness of the course.

Top image source. Bottom image source.

Salty Martian Seas?

2009-05-20T23:21:00.000-07:00

An article posted on ScienceNOW yesterday describes research suggesting that water on Mars was able to resist freezing by containing salt concentrations as high as those of some lakes on Earth. Although the geography of Mars strongly suggests that water once flowed on the planet during a warmer past, climate models indicate that Mars' atmosphere has always been too thin to allow for temperatures greater than the freezing point of pure water. But, the article states, the most prevalent elements found in surface rocks on Mars can keep water from freezing until temperatures far below 0°C are reached.

While temperatures on Mars are much too cold to allow for liquid water today, past temperatures, while still below freezing, may have allowed for flowing water containing dissolved silicon, iron, sulfur, magnesium, calcium, chlorine, sodium, potassium, and aluminum. (An explanation of freezing-point depression can be found on Wikipedia.) While such salty conditions seem very harsh, some of the saltiest environments on Earth harbor thriving microbial communities. This article is a reminder of the usefulness of studying life in extreme environments on Earth in order to better understand the possibilities for life elsewhere in the universe.

The image above is from NASA's website. Caption: False-color image of gully channels in a crater in the southern highlands of Mars, taken by the High Resolution Imaging Science Experiment camera on the Mars Reconnaissance Orbiter.

Embryonic Bood: Pressure to Proliferate

2009-05-19T19:25:00.000-07:00

A short article in New Scientist today reports on two studies providing evidence that blood formation is activated by the change in pressure associated with the first few beats of the embryonic heart:

As the heart starts pumping a primitive blood-like fluid around the body of an embryo, the change in pressure from the flowing liquid is the cue for cells lining the aorta to change first into blood stem cells, then into all blood-cell types in the body. As they multiply and mature, these rapidly replace the initial embryonic "blood", which is composed of embryonic red blood cells in a nutrient-rich serum.

This discovery could have important implications beyond simply advancing our study of development:

The discovery could lead to a source of blood for people with leukaemia who need a transplant but don't have a matched donor, by exposing stem cells to flowing liquid...

Image source.

The Quiet Before the Quake

2009-05-18T17:31:00.000-07:00

Last night, a magnitude 4.7 earthquake hit Southern California. I didn't feel it, but judging by friends' Facebook profiles, many people did. One friend's Facebook status asked everyone to stop posting about the earthquake, saying that there were more important things, like recently released movies, to attend to. And it's true that in Southern California mild earthquakes are no big deal. Residents are well aware of the geological activity of the area and of the fact that one day we might get hit by the "big one." But not all deadly earthquakes, including last year's tragic earthquake in the Sichuan province of China, occur where you expect them to.

An article by Alexandra Witze published May 13 on Nature's News website explores the reasons why the Great Sichuan Earthquake was so unexpected, and what seismologists are learning from the event. The quake was caused by the geology of the Longmen Shan, a mountain range marking the conjunction of the Tibetan plateau and the Sichuan plain. This area apparently has the most extreme topological relief in the world, and mountains are uplifted by the opposing movement of the plain and the plateau. Geologists have measured this movement to be 1-2mm per year. This data is one reason the Great Sichuan Earthquake caught them off guard:

To a geologist, that rate seems relatively benign, because faults store up potential earthquake energy in proportion to the speed of the regional crustal motion. Take two spots on either side of a mountain range, for example. If one is moving quickly in relation to the other, the stress on rocks in between will build up quickly — stress that has to be released by rock movement along a fault. In most cases, that movement is not steady but happens only infrequently, when the stress grows great enough to overcome the friction between rocks on either side of the fault. That sudden release is the earthquake.

Given the slow movement of the plain and plateau, geologists calculate that an associated earthquake the size of the Great Sichuan Earthquake (magnitude 7.9) would only occur every 2,000 to 10,000 years. The rarity of such an event and the lack of evidence for similar events in the past caused scientists to overlook the area, focusing instead on other regions in China with more recent notable geological activity:

Large shocks in the past will have left their marks in local geology. But the record is hard to read in the Longmen Shan: heavy rains and high erosion rates have obscured much of the evidence, says Alexander Densmore, a geologist at Durham University, UK, who has mapped faults in the area. "There aren't that many places that you can really see the past history," he says. Most of the recent known quakes along the Beichuan fault have been much smaller than the 2008 quake, including one magnitude-6.2 quake in 1958 and another in 1970, says Chen Zhiliang, a geologist at the Chengdu Institute of Geology and Mineral Resources. There is no archaeological evidence that the town of Beichuan itself has ever been destroyed by a quake since it was founded some 1,500 years ago.

Scientists are digging trenches and sifting through data to learn as much as they can from The Great Sichuan Earthquake. For example, they have found that the fault system has other hidden secrets:

The Beichuan fault ruptured across several segments totalling 240 kilometres, while a secondary fault to its southeast, the Pengguan fault, broke for 72 kilometres. The segments apparently connect at depth, allowing the quake to grow larger than would have been expected. Chinese geologists are now beginning to map in detail the faults that connect with the Beichuan fault.

While tragic, the Great Sichuan Earthquake served as a wake up call to seismologists not to dismiss the possibility of a large earthquake occuring in an area with little movement. The knowledge gained from the study of this quake may save lives in the future, both in China and around the world.

Top image: The earthquake tore through a schoolyard in the town of Bailu. Bottom image: A trench dug in the same town will help seismologists understand the quake. Images are from article.

New Support for an RNA World

2009-05-14T09:30:00.000-07:00

Because of its greater stability and ability to catalyze certain reactions, many scientists agree that the first life on Earth may have been based on RNA as opposed to the more stable, but less flexible, DNA. However, there has yet to be a convincing explanation for the chemical development of a so-called RNA world. There's an article being published in Nature today in which researchers claim to have developed a plausible mechanism for the construction of a ribonucleotide (the subunit of RNA) from chemicals present in the primitive Earth environment. Instead of synthesizing a nucleotide from a sugar and a base, the scientists have found a way to make a molecule that is "half-base, half-sugar." When another is added and UV radiation is applied, the two fragments join to create a ribonucleotide. Once the nucleotides have been formed, they easily join together to form an RNA molecule. The next next goal is to see whether the scientists can find a plausible natural mechanism for the RNA molecules to be sequestered inside a membrane in a precursor to the cell.

source: New York Times article
image source.

13 billion years ago, in a galaxy far far away…

2009-04-28T17:51:00.000-07:00

…a giant star exploded. Nasa's Swift space observatory detected this huge blast on April 23 (see image). Called GRB 090423, it is the most distant object yet observed by any telescope. The long-deceased star was first discovered by detection of its emitted gamma-rays, and X-ray and ultraviolet/visible measurements were used to establish details of the find, such as its distance from Earth. According to an article from news.bbc.co.uk:

The Swift satellite was launched in 2004 to investigate the energetic flashes that characterise some of the Universe's most violent happenings. …the explosion is being viewed when the Universe was only 630 million years old, a mere one-20th of its current age (estimated to be 13.7 billion years old).

The star is thought to have exploded in a gamma-ray burst (hence the name GRB 090423), which occurs when a giant star burns out and collapses. The remnants of the exploded star usually form a black hole.

Image source.

Fighting the Flu

2009-04-28T16:52:00.000-07:00

As more cases of swine flu are confirmed in more countries, US scientists have begun development of a vaccine for the responsible virus in preparation for a pandemic that may necessitate a method for immunization of healthy civilians and/or volunteers.

Meanwhile, this outbreak is only the latest motivation for other scientists who have been working for years on creating a universal influenza vaccine. Ideally, such a vaccine would only be administered once in a person’s lifetime, and provide protection from all strains of the virus.

We get flu shots every winter because the surface proteins of the influenza virus recognized by antibodies produced in response to the vaccine mutate just enough each year for the previous year’s vaccine to be ineffective. This occurs either through genetic shift (upper image), in which genetic material from two strains is combined in a new strain, mixing the characteristics of the "parent" strains, or through genetic drift (lower image), in which random genetic mutations in a single strain result in a new strain with slightly different characteristics. Each year, scientists must make predictions about which influenza strains patients should be protected against, and manufacturers produce vaccines accordingly.

So, scientists must answer the question, what is a common component of all influenza strains that does not mutate over time, and could be easily targeted by the immune system? If such a component could be identified and targeted, a vaccine could potentially be developed that would allow patients’ immune systems to develop antibodies against the component, protecting them from all strains of the influenza virus.

Several groups have made very promising advances in identifying influenza virus components that could potentially be targeted in a universal vaccine. One group, led by Dr. Robert Belshe of the St. Louis University School of Medicine, presented recent findings at a national conference on Monday. Here’s a brief description of the findings from Scientific American’s 60 Second Science blog:

In a recent study of 377 healthy adults receiving three injections of a universal influenza vaccine, known as Bivalent Influenza Peptide Conjugate Vaccine (BIPCV), over a six month period, Saint Louis University Center for Vaccine Development researchers say they found that a low dose of the vaccine evoked an immune response—high antibody titers—similar to levels associated with protecting small animals infected with influenza from serious disease and death. Robert Belshe, the center's director and the lead researcher who studied the vaccine made with proteins from strains of influenza viruses A and B, said in a statement, however, that more research is needed to determine the effectiveness of this approach against a deadly influenza pandemic.

Hopefully, the day is not far off when the flu can join smallpox as one of the only diseases successfully eradicated through vaccination campaigns.

Upper image source. Lower image source.

On the Pathway to THC Cancer Treament

2009-04-27T11:48:00.000-07:00

Today in my cell death course, two students presented a paper published April 1, 2009, in the Journal of Clinical Investigation (JCI) that provides new information regarding the possibility of a THC-based cancer treatment. THC is the active component of marijuana, and owes its many interesting biological effects to its similarity with endocannabinoids, signaling molecules found naturally in the body. It has already been shown to inhibit glioma tumor growth, and several of the proteins involved in the pathway to THC-induced cancer cell death were already identified before this new paper was published.

A glioma is a cancer that arises from glial cells in the brain or spine. Glial cells are non-neuronal cells that aid neurons in many areas, including nutrition, pathogen destruction, development, and physical support. As one of the presenters pointed out, their name comes from the Greek word glia, meaning glue. So, glial cells can be thought of as glue that helps to support and maintain the entire nervous system.

Cannabinoid action induces autophagy-mediated cell death through stimulation of ER stress in human glioma cells, by Guillermo Velasco et al., presents research that illuminates the pathway by which THC induces cancer cell death in glioma cells. In this pathway, TCH induces autophagy through stimulation of a stress response in the ER (endoplasmic reticulum). (Autophagy is the intracellular degradation of cellular components; in different situations it can lead to either promotion or inhibition of cell death.) Autophagy then leads to apoptotic death of cancer cells.

In in vitro experiments, the scientists found that proteins necessary for autophagy were also necessary in THC-induced cell death, suggesting that autophagy is important in cancer cell death caused by THC. They also found that proteins involved in ER stress were expressed before autophagic proteins, and that ER stress induced autophagy. It was then shown that THC-induced autophagy leads to apoptotic cell death of cancer cells.

In vivo studies involving tumors grafted into mice showed that activation of autophagy is necessary for THC-induced inhibition of tumor growth. In addition, administration of THC to two patients enrolled in a clinical trial exploring the utility of THC in treating cancer indicated that THC might also induce cell death mediated by autophagy in human tumors.

My professor and other students in the class had a few interesting things to say about this article. My professor expressed her concern that the paper did not mention how THC affects normal cells; that is, how exactly do the responses of non-cancerous cells to THC differ from the responses of the cancer cells used in this study? What if the same proteins as those in the study are expressed, but cell death does not occur? What would that tell us about the actual THC pathway to cancer cell death?

One of the presenters pointed out that in the study, THC only significantly slowed cancer cell growth, and did not actually halt it. But another student replied that since there are no good treatments for serious gliomas, a drug that slowed growth would still be clinically valuable, even if it weren’t a cure.

We compared the article’s usage of assays and terms associated with cell death with the guidelines outlined by the Nomenclature Committee on Cell Death (see post from April 14, 2009). Most of us agreed that this article was satisfyingly thorough in terms of the assays employed. The article did, however, occasionally refer to their assays as measuring “cell death” as opposed to the actual cellular characteristics being measured, which the Committee discourages.

Because the paper ended with THC administration to two patients, the next step may be a wider clinical trial to determine the effectiveness of THC in inhibiting glioma tumor growth in a clinical setting. Previous studies have not shown any adverse effects of THC in healthy cells (unlike some radiation therapies or chemotherapies) so it could ultimately be a very desirable glioma treatment.

Image shows patient with glioblastoma multiforme, the most dangerous kind of glioma tumor. Image source.

Meditating on Science

2009-04-25T15:15:00.000-07:00

Yesterday I had the privilege of attending a talk by the Dalai Lama at UCSB. He actually gave two talks, one in the morning on the nature of the mind, and one in the afternoon on ethics. I was only able to attend the latter talk, but it was definitely a wonderful experience to hear this charismatic spiritual and political leader speak.

Having missed the first talk, I decided to explore the subject on my own. On His Holiness’ website, the Dalai Lama provides a link to a US organization he helped to establish, the Mind and Life Institute, based in Boulder, CO. According to the Mind and Life Institute’s website, the Dalai Lama has a particular fondness for science:

The Dalai Lama has always shown a strong mechanical aptitude and a keen personal interest in the sciences. He has said that if he were not a monk, he would have liked to have been an engineer. As a youth in Lhasa he taught himself to fix broken machinery, from clocks to movie projectors to cars. A highlight of his first trip to the west in 1973 was a visit to the University Observatory at the Institute of Astronomy in Cambridge England. Over the years he has enjoyed relationships with many scientists, including long friendships with the late renowned philosopher of science Sir Karl Popper, and physicists Carl von Weizsäcker and the late David Bohm. He has participated in many conferences on science and spirituality. It was at one such conference, the Alpbach Symposia on Consciousness in 1983, that His Holiness met Dr. Francisco Varela who, in partnership with Adam Engle, later created the unique form of in-depth dialogue between Buddhism and science that has grown into the Mind and Life Institute. Since the first Mind and Life meeting in 1987, His Holiness has regularly dedicated a full week of his busy schedule to these biennial meetings.

The Dalai Lama has even taken steps to bring science to his religion:

Along with his vigorous interest in learning about the newest developments in science, His Holiness brings to bear both a voice for the humanistic implications of the findings, and a high degree of intuitive methodological sophistication. As well as engaging personally in dialogue with Western scientists and promoting scientific research into Buddhist meditative practices, he has led a campaign to introduce basic science education in Tibetan Buddhist monastic colleges and academic centers, and has encouraged Tibetan scholars to engage with science as a way of revitalizing the Tibetan philosophical tradition. His Holiness believes that science and Buddhism share a common objective: to serve humanity and create a better understanding of the world. He feels that science offers powerful tools for understanding the interconnectedness of all life, and that such understanding provides an essential rationale for ethical behavior and the protection of the environment.

Much of the Western research the Dalai Lama is interested in concerns the science behind meditative states. And those skeptical of a religious leader's involvement in scientific research do not have to worry about any pseudo-science coming out of the partnership:

The Mind and Life Institute believes that in order for the dialogue between meditation and science to have a durable contribution to humanity, collaborative research programs must be conducted in first rate Western scientific laboratories and the results of those studies be published in prominent peer-review scientific journals. Thus far collaborative research has been focused on collecting data from highly trained meditative adepts using fMRI, EEG and MEG neuroimaging techniques and other psychological, neurological, and immunological measures. Most importantly, these meditative adepts are not only "subjects", in the classical sense. Instead, they are true collaborators, helping to design the scientific research protocols, and participating in analysis and publications.

Here's an article on the neurobiology of meditation in PNAS by one of the researchers involved in the Mind and Life Institute, Richard J. Davidson.

Images are from the Mind and Life Institute website.

Criminal Clusters

2009-04-25T14:57:00.000-07:00

Tiny nanoclusters of atoms appear to break the second law of thermodynamics. In a computer model simulating collisions between clusters of several hundred atoms, some head-on collisions resulted in the clusters departing with greater velocities than those with which they approached each other.

According to the second law of thermodynamics, when one body bounces off another (like two colliding billiard balls), some of the kinetic energy of the moving bodies is lost, and the bodies rebound with lower speeds. In this nanocluster model, developed by Hisao Hayakawa, of Kyoto University, and Hiroto Kuninaka, of Chuo University in Tokyo, most of the nanoclusters seemed to follow the law, either sticking together upon colliding or bouncing off at slower speeds. But 5% of the clusters gained speed from the collision.

The researchers say that this result can be explained by the tiny motions in the atoms making up the nanocluster. When these motions are just right, they can increase the rebound velocity of the nanoclusters. But in order for this to happen, the nanoclusters can only contain several hundred atoms, at most. Nanoclusters of 1000 atoms or more did not show the same rogue tendencies.

Indeed, the model still obeys the second law when the average speeds are compared. The average departing speed of the model’s nanoclusters is lower than the average approaching speed. Thus, the second law’s role as a rule explaining the statistically probable behaviors of large collections of atoms still holds.

The next step in this research is to see if this model accurately describes the real world. Researchers will attempt to recreate the model’s conditions with real nanoclusters of atoms. This will be challenging, but if the real world experiments confirm the model’s predictions, the researchers have hinted, we may be able to begin working on extracting the extra energy for our own purposes.

Here’s the primary article, and here’s where I found out about it. Image source: http://alfreesearch.org/almanach/2005/01.ttemp/billiards2.gif

Extraterrestrial Earths?

2009-04-23T17:37:00.000-07:00

Of course, no series of extremophile-inspired posts would be complete without the acknowledgment of the recent discovery of an Earth-like planet outside our solar system! As a group of scientists, led by Michel Mayor, announced Tuesday, the planet is ~20 light years (119 trillion miles) away from Earth and orbits the dim red star Gliese 581 in the constellation Libra (see image). It weighs ~2-3 times as much as the Earth, and is the smallest exoplanet yet discovered. Like the Earth, it is a rocky planet. Unfortunately, it lies too close to Gliese 581 to contain life as we know it.

However, in the same announcement, the scientists said that another planet, the outermost of four planets orbiting Gliese 581, has a smaller orbit than previously thought, placing it in the "habitable zone" of the star. In this zone, planets are thought to be able to harbor liquid water, and they are far enough away from the star to avoid deadly radiation levels. Although this outermost planet weighs ~7 times as much as Earth, it is thought to consist of both rock and ice, inviting visions of a habitable "water world."

The planets have been observed over a period of several years using the HARPS vacuum spectrograph, receiving input from the ESO 3.6-meter telescope at La Silla Observatory in Chile. The HARPS spectrograph was built in part specifically for the detection of very low mass expolanets.

The official announcement is a bit technical, so here's an article from the New York Times describing the discovery.

Bold Bacteria

2009-04-23T16:58:00.000-07:00

Monday's post reminded me of a fascinating paper, also from Science, that I read for a lab meeting a few months ago. This paper also concerns extremophiles, and outlines the discovery of a novel bacterium living 2.8 km (~1.74 miles) underground. The microbe (pictured, image is from paper's supplementary materials) was named Candidatus Desulforudis audaxviator. Audaxviator means "bold traveler" in Latin; the name was inspired by the following passage from Jules Verne's Journey to the Center of the Earth: "Descend, bold traveler ...and you will attain the center of the Earth." This paper invites the reader to think about the minimal conditions required for life and the limitations of existing life on Earth. And of course, research like this is really helpful in expanding our ideas of what kinds of life may exist on another planet (or moon!).

DNA extracted from filtered water pumped up from a 2.8 km-deep fracture in a South African gold mine revealed the presence of an ecosystem consisting entirely of a single species of bacterium. The genome of this bacterium, named Candidatus Desulforudis audaxviator, indicates that it is capable of performing all the metabolic processes necessary for life, including energy acquisition, carbon assimilation, and nitrogen fixation. This discovery is exciting for two main reasons. First, it is the least diverse, natural, independent microbial community ever discovered. Second, this ecosystem appears to be completely independent of the photosynthetically-driven biosphere. Instead, it relies on the energy provided by the radioactive decay of uranium. Here's a more detailed description of the research:

A metagenomics approach was used by Dylan Chivian et al. to analyze the ecosystem of a fracture 2.8 km deep in the Mponeng gold mine in South Africa. 5600 liters of water (pH 9.3, ~60°C) from the fracture were filtered to extract all microorganisms. Shotgun Sanger sequencing and 454 pyrosequencing revealed the presence of a single genome belonging to a chemoautotrophic thermophile the scientists named Candidatus Desulforudis audaxviator. Usually, metagenomics doesn’t lead to the sequencing of any complete genomes because the communities are so complex. However, 99.9% of the DNA obtained belongs to this bacterium. Most of the remaining 0.1% is due to laboratory contamination, and the rest of the DNA is so scarce that the scientists believe it does not belong to microbes with which Candidatus Desulforudis audaxviator has any ecological relationships. Of course, it is possible that some very small microbes and/or spores were not captured by the filter, or that the DNA extraction and sequencing methods were not suitable for the detection of DNA of certain microbes present in the water.

Nonetheless, the genome of Candidatus Desulforudis audaxviator encodes all the metabolic machinery necessary for independent survival in its environment. Geochemical analyses of the fracture indicate sulfate as the most energetically favorable electron acceptor, and the bacterium indeed has all the genes necessary for sulfate reduction. It appears that the microbe possesses machinery for heterotrophic as well as autotrophic carbon assimilation. Formate and CO may also be used when present. Ambient ammonia concentrations are high enough that the bacterium does not need to fix N2 (the genome encodes an ammonia transporter), but it also contains a nitrogenase gene, indicating that it can fix N2 if necessary. The genome encodes all the amino acid synthesis pathways, endospore-formation pathways, flagellar genes, and genes encoding mcp proteins for chemotaxis. Several genes, including ones in the sulfate reduction and nitrogen fixation pathways, are thought to have been horizontally transferred to the bacterium from archaeal species in the past. This deduction is based on g+c content of the genes in comparison to the rest of the genome, and sequence similarities with specific, known archaeal genes.

The bacterium has not been cultured, since it lacks a system for protection from O2, and O2-exposure would be difficult to avoid during sample collection. The lack of O2 resistance suggests long-term isolation from the atmosphere. In fact, Candidatus Desulforudis audaxviator appears to survive completely independently from all processes associated with Earth’s surface. Radioactive decay of uranium splits water molecules, allowing the oxygen to form the sulfate used by the bacterium. The doubling time of the microbe is estimated to be as high as 100s to 1000s of years because of severe nutrient deprivation. Based on SNP data and the presence of other possible niches for microbial life in the fracture, scientists suspect that a recent bottleneck event left Candidatus Desulforudis audaxviator on its own in this hostile environment.

Life in the Briny Depths

2009-04-20T06:37:00.000-07:00

A new paper in Science: A Contemporary Microbially Maintained Subglacial Ferrous "Ocean" describes the metabolism of a community of microbes living in ancient, anoxic marine brine beneath Taylor Glacier in Antarctica. The microbes were found in samples collected at the aptly named Blood Falls (pictured), where iron-rich discharge emerges from the glacier.

An active microbial assemblage cycles sulfur in a sulfate-rich,ancient marine brine beneath Taylor Glacier, an outlet glacierof the East Antarctic Ice Sheet, with Fe(III) serving as theterminal electron acceptor.

The paper is also reported in an article in the news section of Science's website.

Bioaesthetics

2009-04-15T21:14:00.000-07:00

I came across this picture today while studying for a class on oncology:

Heart of Steel (Hemoglobin) (2005) by Julian Voss-Andreae. The images show the 5' (1.60 m) tall sculpture right after installation, after 10 days, and after several months of exposure to the elements. -Wikipedia

It's a steel sculpture representing hemoglobin. Over time, the iron in the steel oxidizes, lending the sculpture an increasingly rusty hue. While it's not the prettiest of sculptures, there is a lot of beauty in its echoes of the biochemistry of human blood.

For more of the physicist-turned-sculptor Julian Voss-Andreae's science-inspired works, check out his website.

Death Defining

2009-04-14T05:19:00.000-07:00

This quarter I’m taking a journal club course on cell death. We started out with a paper by the Nomenclature Committee on Cell Death that outlines their latest recommendations for the vocabulary used by scientists to talk about cell death. At first, It seemed a little silly to me to prepare a committee to make rules about cell death vocabulary; surely, as in most fields, the vocabulary will straighten itself out as scientific understanding progresses. But the authors of the article point out that encouraging researchers and editors to follow certain guidelines could greatly enhance communication and allow for more efficient research. (Image: Section of mouse liver with stained apoptotic cell. Source: Wikipedia)

In the past decade, an explosion of research has revealed many pathways to cell death. Most of these pathways are not yet fully understood, making it difficult to cleanly differentiate between one pathway and another. Further complications arise from the different perceptions scientists have about when a cell is, indeed, dead. Some scientists define death in biochemical terms. Some define death in morphological terms. And some scientists describe a cell as being “dead” when that cell has been arrested in the cell cycle, even though it is still very much alive.

The authors of this paper outline some guidelines to help facilitate communication about the complex process of cell death. One major recommendation (with which I wholeheartedly agree) is to avoid vague terms like, “percent cell survival” or “percent apoptosis,” replacing them with phrases like, “percent cells with DNA fragmentation” or “percent cleaved caspase-3 positive,” which are more informative, giving a much better understanding of the nature of cell death being described.

Other recommendations include the adoption of specific criteria for the usage of terms describing different types of cell death, including apoptosis and necrosis. Many of these criteria are morphological, since the biochemical properties of the pathways are still being worked out. However, the authors hope that biochemical criteria will one day replace morphological criteria.

Keeping in mind that the recommendations of the committee could quickly become outdated (as occurred with their 2005 recommendations), I appreciate the spirit of this paper. It seems our knowledge about cell death is increasing at a faster rate than our development of a common vocabulary used to describe it. As in all disciplines, it is important that researchers think carefully about the language used to present their findings. This paper serves to remind researchers to make sure they are using precise terms that will give the most accurate view of their results.

article: Cell Death and Differentiation (2009) 16, 3-11; doi:10.1038/cdd.2008.150; published online 10 October 2008
image: http://en.wikipedia.org/wiki/File:Apoptosis_stained.jpg