Sunday, September 27, 2015

Hello! I am a science writer. I don't update this blog anymore, but you can find out more about me at Thanks!

Monday, August 15, 2011

Focusbird EP

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:
Lovely art by Julia Kostreva

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

Wednesday, July 27, 2011

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

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:

Thursday, November 11, 2010

Seeing the Beat

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

Sunday, August 29, 2010

Problems with Pitch: Congenital Amusia and Tone Languages

This post was chosen as an Editor's Selection for ResearchBlogging.orgWhat, 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:


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

Thursday, August 19, 2010

Unraveling the Ocean Methane Paradox 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:


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

Friday, August 6, 2010

An Arterial Scaffold for the Lymphatic System
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:

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

Sunday, July 25, 2010

Super Treehouse

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!

Friday, July 16, 2010

Puppet Science

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.

Wednesday, June 30, 2010

Worst Opening Line for a Novel

This isn't necessarily science or music related, but I always find the results of this contest entertaining:

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

Saturday, June 26, 2010

A Leap Across A Chasm

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.

Tuesday, June 22, 2010

Graduation Gift...To Myself

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...

Thursday, June 17, 2010

I am employed!

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.

Wednesday, June 2, 2010

Dancing Parrot

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.

Thursday, May 27, 2010

Measure Methane, Measure Oil Spill Extent

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

Friday, May 21, 2010

Mammalian Digit Regeneration

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