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  • May 1, 2012
  • 08:24 AM

Cybernetics – Left Ventricular Assist Device

by Jason Carr in Wired Cosmos

Left ventricular assist device technology isn’t necessarily new, but it is one of the biggest harbingers of cybernetic technology. People with weak hearts that are waiting for a donor can use these sorts of heart pumps to bridge patients over until they can receive a full transplant. However, such LVAD machines are usually located in [...]... Read more »

Rizzieri, A., Verheijde, J., Rady, M., & McGregor, J. (2008) Ethical challenges with the left ventricular assist device as a destination therapy. Philosophy, Ethics, and Humanities in Medicine, 3(1), 20. DOI: 10.1186/1747-5341-3-20  

  • April 30, 2012
  • 03:03 PM

Math Shows Today's Writers Are Less Influenced by the Past

by Elizabeth Preston in Inkfish

When Charles Dickens wrote It was the of, it was the of, the immortal first words in A Tale of Two Cities, he can't have imagined that 21st-century computer scientists would parse his prepositions and pronouns as part of vast literary data sets. But today's researchers are studying the unimportant words in books to find important literary trends. With the meaty words taken out, language becomes a numbers game.

To see how literary styles evolve over time--a science dubbed "stylometry"--researchers led by James Hughes at Dartmouth College turned to Project Gutenberg. The site contains the full text of more than 38,000 out-of-copyright books. Researchers began their mining expedition by digging out every author who wrote after 1550, had a known date of birth and (when relevant) death, and had at least 5 English-language books digitized.

These criteria gave the researchers a set of 537 authors with 7,733 published works. But they weren't interested in every word of those books. Nouns and adjectives were out: No Kareninas or Lolitas, nothing nice or bad or beautiful, no roads or homes or people. Most verbs were out, except for forms of the utilitarian to be. No one could speak or walk or Fly, good Fleance!

It may seem that the researchers were stripping all the information-containing words out of the sentences, and in fact that was their goal: "Content-free" words were all they wanted. The 307-word vocabulary that remained from the books was mostly prepositions, conjunctions, and articles.

This linguistic filler, the little stitches that hold together the good stuff, is known to contain a kind of authorial fingerprint. We may not think much about these words when we're writing or speaking, but scientists can use them to define our style.

Hughes and his team used computer analysis to score each author's similarity to every other author. They found that before the late 18th century, authors's stylistic similarity didn't depend on how close to each other they lived. (Each author was represented by a single year, the midpoint between his or her birth and death.) During this time period, authors who lived in the same generation didn't influence each other's styles much more than authors who lived hundreds of years away.

But from the late 18th century to today, it was a different story. Stylistically, authors were more similar to their contemporaries than to other writers. By the late 19th century, writers closely matched the style of other writers who lived at the same time (at least according to the computers tallying up their non-content words). This influence dropped off outside of 30 years. In other words, authors who lived more than three decades away each other may as well have lived centuries away, for all the similarity between their writing.

Looking at more recent books, that window of influence seems to become even tighter. Among authors from the first half of the 20th century, the similarity of style drops off beyond just 23 years.

Over time, authors have become more and more influenced by the other authors writing at the same time. The researchers say this may simply be due to the number of books published. In the early part of their dataset, there were few enough books around that a studious person could read, well, most of them. But as more and more books were published, contemporary books made up a larger share of what was available to read. Authors have filled more and more shelves in their libraries with books by their peers--and this has made them more likely to echo each other's styles.

Because Project Gutenberg relies on public-domain material, there weren't very many authors after the mid-20th century included in this study. Looking forward, "You would expect a continued diminishing of influence," says Daniel Rockmore, the paper's senior author. Contemporary books take up an ever greater portion of what's available to read. In addition to the huge number of books published each year (more than 288,000 in the United States in 2009), there are now e-books and e-readers and Japanese Twitter novels.

A century from now, we may be able to look back and see that today's authors had an ever-condensing frame of influence. Of course, by then literary styles might only last a week. Most books will be forgotten, but every author will be a revolutionary.

James M. Hughes, Nicholas J. Foti, David C. Krakauer, & Daniel N. Rockmore (2012). Quantitative patterns of stylistic influence in the evolution of literature PNAS : 10.1073/pnas.1115407109

Image: Library of Congress from ep_jhu/Flickr

... Read more »

James M. Hughes, Nicholas J. Foti, David C. Krakauer, & Daniel N. Rockmore. (2012) Quantitative patterns of stylistic influence in the evolution of literature. PNAS. info:/10.1073/pnas.1115407109

  • April 26, 2012
  • 10:43 PM

Phthalates–why you should care about these plastic additives

by Cath in Basal Science (BS) Clarified

Aside from cost, aesthetics, and functionality, materials selection is now a topic priority for many consumers when they make a purchase. Consumers are becoming more aware of their choices for sustainable and reusable materials—even the potential health risks/toxicity associated with materials. This is especially true for products containing plastics, particularly the additives used to make [...]... Read more »

  • April 25, 2012
  • 11:54 AM

Can a Horde of Idiots be a Genius?

by Miss Behavior in The Scorpion and the Frog

Let’s face it: The typical individual is not that bright. Just check out these human specimens: Yet somehow, if you get enough numbskulls together, the group can make some pretty intelligent decisions. We’ve seen this in a wide variety of organisms facing a number of different challenges.In a brilliant series of studies, Jean-Louis Deneubourg, a professor at the Free University of Brussels, and his colleagues tested the abilities of Argentine ants (a common dark-brown ant species) to collectively solve foraging problems. In one of these studies, the ants were provided with a bridge that connected the nest to a food source. This bridge split and fused in two places (like eyeglass frames), but at each split one branch was shorter than the other, resulting in a single shortest-path and multiple longer paths. After a few minutes, explorers crossed the bridge (by a meandering path) and discovered the food. This recruited foragers, each of which chose randomly between the short and the long branch at each split. Then suddenly, the foragers all started to prefer the shortest route. How did they do that?This figure from the Goss et al 1989 paper in Naturwissemschaften shows (a) the design of a single module, (b) ants scattered on the bridge after 4 minutes (I promise they’re there), and (c) ants mostly on the shortest path after 8 minutesYou can think of it this way: a single individual often tries to make decisions based on the uncertain information available to it. But if you have a group of individuals, they will likely each have information that differs somewhat from the information of others in the group. If they each make a decision based on their own information alone, they will likely result in a number of poor decisions and a few good ones. But if they can each base their decisions on the accumulation of all of the information of the group, they stand a much better chance of making a good decision. The more information accumulated, the more likely they are to make the best possible decision. In the case of the Argentine ant, the accumulated information takes the form of pheromone trails. Argentine ants lay pheromone trails both when leaving the nest and when returning to the nest. Ants that are lucky enough to take a shorter foraging route return to the nest sooner, increasing the pheromone concentration of the route each way. In this way, shorter routes develop more concentrated pheromone trails faster, which attract more ants, which further increase pheromone concentration of the shortest routes. In this way, an ant colony can make an intelligent decision (take the shortest foraging route) without any individual doing anything more intelligent than following a simple rule (follow the strongest pheromone signal). Home is where the heart is. Photo of a bee swarm by Tom SeeleyHoneybee colonies also solve complicated tasks with the use of communication. Tom Seeley at Cornell University and his colleagues have investigated the honeybee group decision-making process of finding a new home. When a colony outgrows their hive, hundreds of scouts will go in search of a suitable new home, preferably one that is high off the ground with a south-facing entrance and room to grow. If a scout finds such a place, she returns to the colony and performs a waggle dance, a dance in which her body position and movements encode the directions to her site and her dancing vigor relates to how awesome she thinks the site is.  Some scouts that see her dance may be persuaded to follow her directions and check out the site for themselves, and if impressed, may return to the hive and perform waggle dances too. Or they may follow another scout’s directions to a different site or even strike out on their own. Eventually, the majority of the scouts are all dancing the same vigorous dance. But interestingly, few scouts ever visit more than one site. Better sites simply receive more vigorous “dance-votes” and then attract more scouts to do the same. Like ants in search of a foraging path, the intensity of the collective signal drives the group towards the best decision. Once a quorum is reached, the honeybees fly off together to their new home.But groups can develop better solutions than individuals even without communication. Gaia Dell’Ariccia at the University of Zurich in Switzerland and her colleagues explored homing pigeon navigation by placing GPS trackers on the backs of pigeons and releasing them from a familiar location either alone or in a group of six. Because they were all trained to fly home from this site, they all found their way home regardless of whether they were alone or in a group. But as a flock, the pigeons left sooner, rested less, flew faster, and took a more direct route than did the same birds when making the trip alone. By averaging the directional tendencies of everyone in the group, they were able to mutually correct the errors of each individual and follow the straightest path. In each of these examples, each individual has limited and uncertain information, but each individual has information that may be slightly different than their neighbors’. By combining this diverse information and making a collective decision, hordes of idiots can make genius decisions.Want to know more? Check these out:1. Couzin, I. (2009). Collective cognition in animal groups Trends in Cognitive Sciences, 13 (1), 36-43 DOI: 10.1016/j.tics.2008.10.002 2. ... Read more »

Couzin, I. (2009) Collective cognition in animal groups. Trends in Cognitive Sciences, 13(1), 36-43. DOI: 10.1016/j.tics.2008.10.002  

Goss, S., Aron, S., Deneubourg, J., & Pasteels, J. (1989) Self-organized shortcuts in the Argentine ant. Naturwissenschaften, 76(12), 579-581. DOI: 10.1007/BF00462870  

Dussutour, A., Nicolis, S., Deneubourg, J., & Fourcassié, V. (2006) Collective decisions in ants when foraging under crowded conditions. Behavioral Ecology and Sociobiology, 61(1), 17-30. DOI: 10.1007/s00265-006-0233-x  

  • April 24, 2012
  • 09:46 AM

A hybrid social blogging platform

by David Bradley in Sciencetext

A while back I mentioned FriendLens as a tool for getting a different view of your friends’ Facebook photos. But, there is another Friend Lens being developed by John Gibbons and Arvin Agah of The University of Kansas, in Lawrence, using open source resources. (I suspect they will have to find a different name for [...]Post from: David Bradley's Sciencetext Tech TalkA hybrid social blogging platform
... Read more »

John W. Gibbons, & Arvin Agah. (2012) Friend Lens: novel web content sharing through strategic manipulation of cached html. Int. J. Web Based Communities, 8(2), 242-265. info:/

  • April 24, 2012
  • 05:38 AM

Let’s Explore Surface Electromyography

by Jason Carr in Wired Cosmos

Surface electromyography is apparently now able to recognize and even synthesize speech based on a certain pattern. An acoustic signal is corrupted by high environmental noise. Astronauts that perform operations in spacesuits fall victim to this phenomenon. Earthbound firefighters are … Continue reading →... Read more »

  • April 23, 2012
  • 12:15 PM

When Cellular Automata Come to Life

by Jason Carr in Wired Cosmos

Cellular automata are probably the closest things to machine life that most people have gotten an opportunity to experiment with in recent years. John Conway invented a piece of software titled the Game of Life in 1970. He carefully set up the rules to create a balanced world. While this might sound like old news, [...]... Read more »

Arima V, Iurlo M, Zoli L, Kumar S, Piacenza M, Della Sala F, Matino F, Maruccio G, Rinaldi R, Paolucci F.... (2012) Toward Quantum-dot Cellular Automata units: thiolated-carbazole linked bisferrocenes. Nanoscale, 4(3), 813-23. PMID: 22159165  

  • April 23, 2012
  • 07:27 AM

Robotic Telesurgery in Space

by Jason Carr in Wired Cosmos

Telemedicine is a field that uses telecommunications technology to provide healthcare at a distance. Certain computer systems can be linked to a physician’s office for diagnostic purposes. Different clinics and hospitals can be linked together. In the future, telemedicine could be used to perform robotic surgeries in space. Some forms of telemedicine have been in [...]... Read more »

  • April 19, 2012
  • 11:02 PM

Nanoparticle-treated wood minimizes biocide leaching

by Cath in Basal Science (BS) Clarified

Sitting on the deck to drink your morning cup of coffee is a great way to start the day—but not when your deck is rotting. Fortunately wood products are protected with wood preservatives, often with chromate copper arsenate (CCA) [3]. But growing concerns over the safety and health effects [...]... Read more »

  • April 19, 2012
  • 03:00 PM

Diagnosing Similar Diseases in Low Resource Settings

by Hector Munoz in Microfluidic Future

A lot of excitement surrounding microfluidics has been about its promising use in diagnosis in low-resource settings. Many infectious diseases present in developing countries are manageable or treatable with available medications, but still account for 1/3 of deaths. In these areas, multiple diseases present similar symptoms, leading to misdiagnosis and thus incorrect treatment. Hundreds of blood-based microfluidic immunoassays are available for diagnostic purposes, but they’re not all created equally. They require varying levels of sample processing or analysis that prohibit their deployment in low-resource settings. Further, while some diseases may have similar symptoms, they might require different detection techniques, with varying sample volumes, reagents and processing time, making it difficult to detect multiple diseases within the same system. This is the focus of recent work from Paul Yager of University of Washington. In his Lab on a Chip paper, “Progress toward multiplexed sample-to-result detection in low resource settings using microfluidic immunoassay cards,” he and his colleagues develop a system to detect both Typhoid fever and malaria.... Read more »

Lafleur, L., Stevens, D., McKenzie, K., Ramachandran, S., Spicar-Mihalic, P., Singhal, M., Arjyal, A., Osborn, J., Kauffman, P., Yager, P.... (2012) Progress toward multiplexed sample-to-result detection in low resource settings using microfluidic immunoassay cards. Lab on a Chip, 12(6), 1119. DOI: 10.1039/C2LC20751F  

  • April 19, 2012
  • 12:10 PM

The Merging of Biology and Electronics [Research]

by Jason Carr in Wired Cosmos

The boundary between electronics and biology is blurring with the first detection by researchers at Department of Energy’s Oak Ridge National Laboratory of ferroelectric properties in an amino acid called glycine. A multi-institutional research team led by Andrei Kholkin of the University of Aveiro, Portugal, used a combination of experiments and modeling to identify and [...]... Read more »

Heredia, A., Meunier, V., Bdikin, I., Gracio, J., Balke, N., Jesse, S., Tselev, A., Agarwal, P., Sumpter, B., Kalinin, S.... (2012) Nanoscale Ferroelectricity in Crystalline γ-Glycine. Advanced Functional Materials. DOI: 10.1002/adfm.201103011  

  • April 12, 2012
  • 12:24 PM

Why the RMS Titanic fractured: clues from the ship’s hull

by Cath in Basal Science (BS) Clarified

This Sunday will be 100th anniversary of the sinking of the Royal Mail Ship (RMS) Titanic. Over the years this tragic accident has been the topic of numerous books, films, exhibits—even a memorial cruise. Not only has this shipwreck captured the attention of the public, but the scientific community as well. Ever since the wreckage [...]... Read more »

  • April 12, 2012
  • 11:33 AM

Fast, Efficient Short Read Alignment with Gaps: Bowtie 2

by Daniel Koboldt in Massgenomics

I’ve always been a fan of Bowtie, one of the first algorithms to leverage Burrows-Wheeler Transform for short read alignment. When I first encountered it in 2008, it was incredibly fast. Faster than Maq and Novoalign, two of the early popular algorithms for read mapping. Perhaps more importantly, it was ultra memory-efficient, enabling one to [...]... Read more »

Langmead B, & Salzberg SL. (2012) Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-9. PMID: 22388286  

  • April 10, 2012
  • 02:01 PM

Narrowing the Gap to Characterize Sickle Cell Disease

by Hector Munoz in Microfluidic Future

Microfluidic Future is by no means an accurate representation of all the current, ongoing research in microfluidics. Nevertheless, the fact that you won’t be able to find any articles about assays relying on a biophysical marker isn’t too far off the reality in microfluidics. I suppose this is partly due to the incredible amount of previous work on molecular markers when high resolution control hadn’t been realized yet. Regardless, I was happy to come across an article about a microfluidic device that indicates sickle cell disease risk using the disease’s biophysical characteristics. The work “A Biophysical Indicator of Vaso-occusive Risk in Sickle Cell Disease” appeared in Science Translational Medicine this past February and is a result of ongoing sickle research by MIT and Harvard Medical School. My friend originally forwarded me an article about it on Medgadget, which you should also check out, along with the podcast it mentions.... Read more »

Wood DK, Soriano A, Mahadevan L, Higgins JM, & Bhatia SN. (2012) A Biophysical Indicator of Vaso-occlusive Risk in Sickle Cell Disease. Science Translational Medicine, 4(123), 1-8. PMID: 22378926  

  • April 10, 2012
  • 11:02 AM

Google Searches Give Away a Country's GDP

by Elizabeth Preston in Inkfish

Anytime we travel through the Internet we leave piles of data behind us, like Pigpen shedding his cloud of filth. It's too bad if you're concerned about privacy. But if you're a mathematician, that heap of dirt is more like a goldmine, and digging into it can turn up unexpected nuggets. A study of worldwide Google searches, for one thing, reveals that people in wealthier nations think less about the past.

Google collects data on what search terms people around the world are using. Researchers who want to use this data to compare search terms across different countries are usually restricted to places that share a language. But the authors of a new paper in Scientific Reports got around that problem by looking only at numerical search terms.

"We realized...that years represented in Arabic numerals are an almost universal written representation," author Helen Susannah Moat wrote in an email. By looking only at search terms such as 2011 or 2010, she and her coauthors could compare search data from nearly the whole globe.

"It seemed a logical first step to consider to what extent Internet users were searching for dates in the future compared to dates in the past," Moat says. For example, looking at data from 2010, the researchers compared searches including 2011 to those including 2009. The ratio of forward-looking to backward-looking searches in each country became its "future orientation" score.

The authors culled data from 45 countries with substantial Internet-using populations. Then they sorted those 45 countries by GDP ("also the most obvious variable," Moat says). A clear pattern popped out of the numbers: Countries with lower GDPs had lower future orientation scores, and vice versa. People in poorer countries did more searches concerning the previous year; those in wealthier nations searched more for the next year. The trend was strong, and it held up in data from 2009 and 2008 as well.

Countries with the lowest future orientation scores included Pakistan and Vietnam, where previous-year searches outnumbered next-year searches by a factor of three or four to one. In the United States and Canada, countries toward the higher end in future orientation, searches for the last year and the next year were roughly equal. Switzerland, Australia, and the United Kingdom were among the most forward-looking countries of all.

"One of the possible interpretations of our results," Moat writes, "is that a focus on the future supports economic success." In other words, populations that are more forward-thinking become wealthier. This up-by-the-bootstraps explanation doesn't seem like the simplest one, though.

Another possibility is that populations with more money and leisure time can afford to spend it thinking about the future. A person in a wealthier nation might search online for next year's concert tickets, dates of work holidays, or when the new iPad is coming out. Someone without disposable income, though, might not have many such events to look forward to.

Here's some good news for people in all nations: Google Trends is available online for aspiring data analysts to play with. Panning for gold in its graphs won't cost anything except your free time.

Preis, T., Moat, H., Stanley, H., & Bishop, S. (2012). Quantifying the Advantage of Looking Forward Scientific Reports, 2 DOI: 10.1038/srep00350

... Read more »

Preis, T., Moat, H., Stanley, H., & Bishop, S. (2012) Quantifying the Advantage of Looking Forward. Scientific Reports. DOI: 10.1038/srep00350  

  • April 10, 2012
  • 07:40 AM

Recent Advances in Genetic Research

by Jason Carr in Wired Cosmos

Those of you that read my posts regularly know that I believe the next (substantial) evolution of our species will involve either genetic modification, robotics, or a combination of both. So whenever I come across an interesting development happening in genetics research, AI, etc., I like to pass it along on here – even if [...]... Read more »

Zhiyu Peng, Yanbing Cheng, Bertrand Chin-Ming Tan, Lin Kang, Zhijian Tian, Yuankun Zhu, Wenwei Zhang, Yu Liang, Xueda Hu, Xuemei Tan.... (2012) Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome. Nature Biotechnology. DOI: 10.1038/nbt.2122  

  • April 8, 2012
  • 08:50 PM

Simulations of Sand-Solid Impacts

by DJ Busby in Astronasty

Math and computer simulation wizzes at the University of North Carolina at Chapel Hill have just taken a nice step forward in granular simulation by approaching the problem with math heretofore not applied to dynamic granular modeling. It's really quite impressive.
Narain and Gola's work may be favorable over previous methods both due to its 1) accuracy, as well as 2) the ability to trade off quality-over-precision / precision-over-quality as an easily implemented option. Whenever computation is involved, that flexibility is very valuable.... Read more »

Narain, R., Golas, A., & Lin, M. (2010) Free-flowing granular materials with two-way solid coupling. ACM Transactions on Graphics, 29(6), 1. DOI: 10.1145/1882261.1866195  

  • April 6, 2012
  • 08:00 AM

Brainbrawl round-up

by Zen Faulkes in NeuroDojo

Columbia University hosted a debate between Tony Movshon and Sebastian Seung last Monday, “Does the brain’s wiring make us who we are?” This became known informally as “brainbrawl.” I watched it livestreamed through the Radiolab site, and someone had the wherewithal to grab the video below (which Radiolab said they weren’t planning on archiving). Radiolab did archive the live chat here.

Where’s the fight?

As I predicted, it was a much more sedate affair than the “brainbrawl” moniker suggested. Seung set the tone in his first comments by pulling back from the big claims that he has made previously. Instead of discussing the nature of human identity (his TED talk) or immortality (his book), he was much more circumspect in outlining what a connectome could do for us. Near the end, he said, “All I want to do is map some connections!”

I liked this, actually. It is a far more sensible view of the promise of connectomes than we’ve sometimes seen. But yes, it would have been more fun if Seung had swung for the fences anf salked about uploading consciousness. At the end, co-moderator Robert Krulwich was apologizing for the lack of blood on the floor and the modesty of the speakers.

The fight (to the extent that there is a fight), then, is not about whether connectome research is feasible or useful, but about grand challenges and resources. Movshon nailed it when he said people are looking for “gigascience” projects, and that neuroscience has been a “cottage industry.” While nobody said it directly, “gigascience” is often about making a sales pitch. People want to be at the forefront of establishing big projects, because the prospect of money is there. Someone made a comment about keeping score, and Movshon said, “The NIH is.” Krulwich asked Movshon, “What’s your recruiting pitch? What do you tell the young mavericks to bring them into the field?” (Krulwich occasionally seems to confuse science with the Wild West; also here.)

It seems to me like Seung talks about connectomes as a way to pitch his research, which involves developing techniques to do high-throughput neuroanatomy (e.g., Jain et al. 2010). Faster, more automated electron microscopy would be a godsend. But I doubt Columbia UNiversity would have hosted a debate on, “Should we develop better EM?” One commenter on Twitter said:

I haven't heard alternatives to connectome that generate comparable ideas/excitement
I’m not sure we need it. It’s not as though neuroscience is suffering for people; remember, we hold the biggest scientific meeting in the world. personally am unconvinced that we need grand challenges in science. The history of science shows that the way you answer the big questions is by answering the small questions.

The invertebrate in the vertebrate brain

Invertebrates came up in the discussion a couple of times. Good circuit descriptions of the mammalian retina are actually fairly far along, and may be the first part of the brain for which we have a connectome. Seung commented, however, that the retina was like an invertebrate brain contained within a vertebrate brain. I think he was referring to several of the retinal cells being non-spiking, which is also true of the worm Caenorhabditis elegans.

On Twitter, Noah Gray said he didn’t think C. elegans informed the connectome debate at all, because it has non-spiking neurons. I disagree, but at the very least, it does point out the importance of the intrinsic properties of neurons. Movshon suggested that the reason that C. elegans had non-spiking neurons was that it was small. This is too simple an explanation. In crustaceans, you can find both spiking and non-spiking proprioceptive sensory neurons (e.g., Paul and Wilson, 1994), and there seems to be no readily apparent functional reason to favour one or the other.

As I’ve mentioned before, we have a connectome of C. elegans, and there was discussion about how useful it actually it. In his book, Seung admitted that the connectome hadn’t solved all the neurobiological research problems for that animal, but that it might be a special case. Seung tried to argue that C. elegans posed technical problems in recording from the neurons, but Carl Zimmer pointed out that if his hypothesis was true, that wouldn’t matter. I do think the moderators, and possibly Movshon, were too dismissive of what we have learned from the connectome of C. elegans. Seung is correct that the connectome is very important to guiding research in the nervous system of the animal.

What occurred to me, though, was that there might be another invertebrate example that shows the usefulness of determining neuronal circuits: the eye of the horseshoe crab.

Haldan K. Hartline won the Nobel prize for his work on horseshoe crab vision. Hartline was able to map connections between the photoreceptors in the crab’s eye. He had the advantages that the photoreceptors were spiking neurons (unlike in mammals), and that there was only one type of photoreceptor. That is, each was an interchangeable widget, and the properties of the neuron were largely determined by connections with other neurons. By figuring out the simple circuit in the eye, he showed how lateral inhibition was able to enhance contrast of edges. This is important because the horseshoe crab eye has very low resolution.

Many years later, Robert Barlow and colleagues used a connectome-like model to build a biologically realistic model of the horseshoe crab retina and the signal it sends to the brain (Passaglia et al. 1997; Barlow et al 2001). When it was published, it was the largest biologically realistic model that had been built. They showed that some previously puzzling features of the synapses, like neurons inhibiting themselves, did things like filter out flicker in the environment.

If the mammalian retina is an invertebrate nervous system trapped in a vertebrate brain, the horseshoe crab retina may be a vertebrate nervous system in an invertebrate brain.

Other tidbits

I liked Movshon’s comment that the brain is not a multi-purpose computer, but a specific purpose computer. That is, brains are the products of natural selection and need to do specific things very well. This contrasted with his earlier argument against studying connectomes by using a well-worm software analogy, used my many cognitive pyschologists: "Studying the hardware doesn’t tell you anything about the software.” True for your desktop computer, but the brain is not an electronic computer, as Seung noted.

The audience asked some very smart questions. I wished they’d had a chance to ask more.


Barlow R, Hitt J, Dodge F. 2001. Limulus vision in the marine environment. The Biological Bulletin 200(2): 169-176. DOI: 10.2307/1543311

Jain V, Seung HS, Turaga S. 2010. Machines that learn to segment images: a crucial technology for connectomics. Current Opinion in Neurobiology 20(5): 653-666. DOI: 10.1016/j.conb.2010.07.004

... Read more »

Barlow R, Hitt J, & Dodge F. (2001) Limulus vision in the marine environment. Biological Bulletin, 200(2), 169. DOI: 10.2307/1543311  

Passaglia C, Dodge F, Herzog E, Jackson S, & Barlow R. (1997) Deciphering a neural code for vision. Proceedings of the National Academy of Sciences of the United States of America, 94(23), 12649-54. PMID: 9356504  

  • April 4, 2012
  • 05:05 PM

how to make random machines do your bidding

by Greg Fish in weird things

Long time readers probably noticed that the last month was a little off. Posts weren't coming as per the blog's natural rhythm and the annual April Fools gag was also absent. But there was a good reason for this, one I'd be happy to share with you if it wasn't for the fact that you [...]... Read more »

  • April 4, 2012
  • 02:32 PM

Lubricating with silver nanoparticles for a better performance

by Cath in Basal Science (BS) Clarified

Oil changes are part of the routine maintenance for most drivers to keep their cars in good running condition. Engine oil reduces the friction between moving parts of the engine and minimize its wear and tear. Like cars, a variety of machinery—whether a printing press or an excavator—also relies on lubricants to prevent breakdowns and [...]... Read more »

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