What happened was, I was looking for a Creatively Commons licensed picture of Pedro Mendes to upload to commons.wikimedia.org. That’s not the footballing Pedro Mendes who played for Rangers, Spurs, Pompey and Porto but the systems biologist Pedro Mendes who plays for Virginia Tech and Manchester. Thankfully, another systems biologist, Michael Hucka kindly pointed to his impressive collection of pictures, taken at various events over the years which include some shots of Pedro. Looking at these pictures made me idly wonder: What is the collective noun for a group of systems biologists?
Systems biology is the study networks of various kinds [2,3] so it’s ripe for a collective noun, and there were several suggested on twitter. Since twitter has recently developed a nasty habit of disappearing tweets, here is a collection gathered and preserved for posterity from the twitterome...... Read more »
On Microfluidic Future I like reviewing advancements in therapeutic or diagnostic devices because I’m really drawn to those areas of research. Every once in a while, however, I take interest in research for the sake for knowledge, like the Root Chip. I recently came across an article from Dino Di Carlo of UCLA that describes a microfluidic device used to study cancer cells. The article, “Increased Asymmetric and Multi-Daughter Cell Division in Mechanically Confined Microenvironments” appeared in PLoS ONE, which is an open access journal (very cool!).... Read more »
Henry Tat Kwong Tse, Westbrook McConnell Weaver, & Dino Di Carlo. (2012) Increased Asymmetric and Multi-Daughter Cell Division in Mechanically Confined Microenvironments. PLoS ONE, 7(6). info:/
Let Me Answer Your Questions: part 2, in which I answer your very important questions via google search terms. Part 1 and all subsequent LMAYQ posts will be archived in the LMAYQ index.by LikariousSo let's get to it, what fascinating questions are you asking google? 1. "Can odor be recorded?" This likely brought someone to my post "You can't trust your receptors:smell" in which I discuss the EOG (electrolfactogram) where you can record the electrical activity of a smell receptor while certain smells are presented. But it does not answer the question of whether a smell itself can be recorded.So I looked into it a little bit and surprisingly, the answer is yes! Nakamoto and others have created an "odor recorder" Nakamoto 2005 figure 1Unlike visual recording, which only need red, green, and blue to make essentially all the colors, odor recording requires a few more components. For example, the authors created an apple smell using 8 components. I would love to say that this odor recorder is going to appear in every living room and plug into the TV so that restaurant and perfume marketing can be truly effective, I just don't see the demand being strong enough to make it worth mass producing. Though, I think it would be pretty amazing. I also had doubts as to whether the odor recorder could accurately transmit the scent of a really nice perfume which is not static, but develops over time. But The 2005 Nakamoto paper shows that they can actually record the changes of an odor over time! While there is always the fact that a perfume reacts differently with every one's skin, the odor recorder actually seems like a promising device and might find a market in die hard perfume fans. or..."odor recorder prevents murder"The quest to permanently record the scent of a woman drives a man to murder in the mediocre movie "Perfume: the Story of a Murderer." If only he was in possession of an odor recorder.© TheCellularScaleNakamoto T (2005). Study of odor recorder for dynamical change of odor. Chemical senses, 30 Suppl 1 PMID: 15738143... Read more »
Nakamoto T. (2005) Study of odor recorder for dynamical change of odor. Chemical senses. PMID: 15738143
Concerns about the likely consequences of continuing climate change have greatly increased interest in geoengineering – whether the Earth’s climate could be deliberately modified to counteract global warming due to anthropogenic greenhouse gas emissions. In November 2010, the Royal Society hosted a Discussion Meeting: ‘Geoengineering: taking control of our planet’s climate’ that critically assessed many of the schemes currently being considered. The meeting also took stock of the relationship of geoengineering to conventional greenhouse gas mitigation as well as how geoengineering is perceived by the public. Papers in this issue directly reflect the outcome of that Discussion Meeting.... Read more »
Andy Ridgwell, Chris Freeman, & Richard Lampitt. (2012) Geoengineering: taking control of our planet's climate?. Phil. Trans. R. Soc. A 13 , 370 (1974), 4163-4165. DOI: 10.1098
From Dilbert’s PHB to The Office, the incompetent manager is such a popular trope that it’s in danger of becoming …Continue reading »... Read more »
Alessandro Pluchino, Andrea Rapisarda, & Cesare Garofalo. (2009) The Peter Principle Revisited: A Computational Study. Physica A 389 (2010) 467-472. arXiv: 0907.0455v3
The Canadian National Exhibition (CNE) opens in Toronto next Friday (can’t wait!) and they hold an international sand sculpting competition every year. I’m always impressed by the size and detail [...]... Read more »
An L-system or Lindenmayer system is a parallel rewriting system, namely a variant of a formal grammar.I have implemented a simple L-system class with HTML5 Canvas or WebGL output. Feel free to explore the predefined models or create your own.... Read more »
Insects are experts when it comes to adhesion on dry surfaces. However, in nature, plants may be covered by water for quite a long period of time, especially after rain. The bionic expert Professor Stanislav Gorb of Kiel University, Germany, and the material scientist Professor Naoe Hosoda of the National Institute for Material Science in Japan, discovered the remarkable ability of the terrestrial leaf beetle to walk underwater. Picking up the beetle’s locomotion mechanism, they designed an artificial material, which sticks to surfaces underwater. Their scientific results are published today (8th August) in the online journal “Proceedings of the Royal Society B”.... Read more »
Kiel University Press, Text: Claudia Eulitz, & Translation: Ann-Christin Wimber. (2012) “The beetle shows us how”. Proceedings of the Royal Society B . info:/
I've been itching to announce this for months, but I've been biting my tongue. Now I can finally let the neuron out of the bag.Ladies and gentlemen I'm proud to introduce to you a joint project between my wife Jessica Voytek and our friend Erica Warp: The Adventures of Ned the Neuron! To get the important pitch out of the way first, please go contribute some money to their Kickstarter campaign to help them get started if you want to help. Also, please consider following their company on Facebook. I promise they're not spammy.For several months now Jessica and Erica have been working on their company, Kizoom, to develop the first of what I hope to be many science education eBooks for kids. The fact that this is being built using open or semi-open tools and platforms is also pretty amazing.Note that I'm in no way connected to this company, though the obvious disclosure is that my wife and I are financially entwined and, as unbiased as I try to be, I of course cannot be completely so. I mean, I'm writing this post, aren't I? But... as a new father I'm coming to appreciate more and more the joys of well-written, scientifically accurate educational materials.So who are Erica and Jessica and why should you trust what they write?Erica earned her PhD in neuroscience from Berkeley working on spinal cord development. She published three super cool papers during that time, one each in Nature, PNAS, and Current Biology. I promise you she knows her brains.Jessica is the primary author on our brainSCANr paper which we published in The Journal of Neuroscience Methods earlier this year. She earned her Masters degree in Information Management and Systems at Berkeley, which she completed while very pregnant with our son. Not only does she know her brains, she's also technically and artistically very savvy.The two of them have been working hard on this baby of theirs (that's them celebrating after submitting their NIH grant). They have managed to put together a book that is fun and interactive for kids (their target audience) while being educational and totally neuroscientifically accurate.No neuro nonsense. Just good science and good fun.So many of us neuroscientists complain about the poor public understanding of our field that it's time for us to stop being critics and start trying to make the changes we want to see. And that's what I love about Kizoom and The Adventures of Ned the Neuron: two very smart neuroscientists and techies are putting themselves forward and trying to make science more approachable to the most scientifically vulnerable group.Kids.Erica wrote the story and drew the early artwork while Jessica has been working on getting the whole thing coded up, animated, etc. Basically the techy nerd work.What's impressed me the most is that, throughout all of this had work, they've also been doing a lot of science outreach and communication for kids. Jessica worked for the Girl Scouts for years, including developing a cookie booth finder to help people locate the nearest Girl Scout troop selling cookies in their area!In May Jessica and Erica volunteered at a Girl Scout event to teach young women about neuroscience and the brain with the help of Ned the Neuron!We also recently learned that, out of the thousands of abstracts and poster submissions to the Society for Neuroscience Conference this October, their poster "User experience design for children's neuroscience education" has been selected as one of nine in the new "Dynamic Posters" session.What's that? Well, according to the email they received,A dynamic poster is an electronic version of the current paper-based format, displayed on an LCD screen rather than a poster board. However, it’s more than just an e-poster, which is typically an electronic - but still static - PDF version of a paper poster. Embedding multimedia content is encouraged such as videos, slides, animated charts or graphs, scrolling text, or a 3D rotation of a model. A dynamic poster presentation is designed for face-to-face interaction: like a regular poster presentation, the dynamic presentation will be driven by the primary author while attendees visit the poster. Some text elements of the poster will always be viewable for browsing by people walking by or waiting for their turn to speak with the presenter. Other parts of the poster will be operated by the presenter, who can click on and play a video or enlarge a graph to better illustrate a method or result.I definitely applaud the Society for Neuroscience for finally taking this kind of tech-based approach.I wish I could convey to you in words the emotional love the both of them have for this project. I'm really proud to have seen it grow from nothing into a nearly completed project. Please check it out and consider helping if you can.Thanks everyone.Voytek JB, & Voytek B (2012). Automated cognome construction and semi-automated hypothesis generation. Journal of neuroscience methods, 208 (1), 92-100 PMID: 22584238Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, & Isacoff EY (2012). Emergence of patterned activity in the developing zebrafish spinal cord. Current biology : CB, 22 (2), 93-102 PMID: 22197243... Read more »
Voytek JB, & Voytek B. (2012) Automated cognome construction and semi-automated hypothesis generation. Journal of neuroscience methods, 208(1), 92-100. PMID: 22584238
Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, & Isacoff EY. (2012) Emergence of patterned activity in the developing zebrafish spinal cord. Current biology : CB, 22(2), 93-102. PMID: 22197243
Marriott G, Mao S, Sakata T, Ran J, Jackson DK, Petchprayoon C, Gomez TJ, Warp E, Tulyathan O, Aaron HL.... (2008) Optical lock-in detection imaging microscopy for contrast-enhanced imaging in living cells. Proceedings of the National Academy of Sciences of the United States of America, 105(46), 17789-94. PMID: 19004775
Wyart C, Del Bene F, Warp E, Scott EK, Trauner D, Baier H, & Isacoff EY. (2009) Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature, 461(7262), 407-10. PMID: 19759620
Over at @BBCSport and @BBC2012 there are some Olympian feats of big data wrestling going on behind the scenes for London 2012 . While we all enjoy the Olympics on a range of platforms and devices, a team of twenty engineers is busy making it all happen. It’s great that the BBC, unlike other large organisations, can talk openly about their technology and share hard-won knowledge widely.... Read more »
Loasby Karen. (2006) Changing approaches to metadata at bbc.co.uk: From chaos to control and then letting go again. Bulletin of the American Society for Information Science and Technology, 33(1), 26. DOI: 10.1002/bult.2006.1720330109
Butkus Andrius, & Petersen Michael. (2007) Semantic Modelling Using TV-Anytime Genre Metadata. Lecture Notes in Computer Science, 234. DOI: 10.1007/978-3-540-72559-6_24
Assuming that we never achieve FTL travel, generational colony ships may become a necessary method used to traverse great distances. Inherent in the term generational, individuals will live their entire lives on these massive spaceships as will their descendants. In other words, these space ships will be the only home many generations of inhabitants will [...]... Read more »
Apostolos Papanikolaou. (2010) Holistic ship design optimization . Computer-Aided Design, 42(11), 1028-1044. info:/10.1016/j.cad.2009.07.002
Cooper RA. (2008) Quality-of-life technology. A human-centered and holistic design. IEEE engineering in medicine and biology magazine : the quarterly magazine of the Engineering in Medicine , 27(2), 10-1. PMID: 18472458
When it comes to online dating, who should make the first move? You or them? ... Read more »
Rosen, L. D., Cheever, N. A., Cummings, C., & Felt, J. (2008) The impact of emotionality and self-disclosure on online dating versus traditional dating. Computers in Human Behavior, 24(5), 2124-2157. DOI: 10.1016/j.chb.2007.10.003
You may already be familiar with various technologies that minimize the generation of carbon dioxide (CO2) emissions like hybrid-electric vehicles, biodegradable plastics, or even solar panels. But what happens when [...]... Read more »
Yasutaka Kuwahara, Dun-Yen Kang, John R. Copeland, Nicholas A. Brunelli, Stephanie A. Didas, Praveen Bollini, Carsten Sievers, Takashi Kamegawa, Hiromi Yamashita, & Christopher W. Jone. (2012) Dramatic Enhancement of CO2 Uptake by Poly(ethyleneimine) Using Zirconosilicate Supports. J. Am. Chem. Soc. DOI: 10.1021/ja303136e
Yesterday I posted some research about cell phone anxiety. You may have noticed that while I referenced a science journal article I didn't talk much about the results. Indeed, the only results I listed were descriptive (basic counting that describes a behavior) and qualitative (as opposed to quantitative). This is because of some fundamental flaws with the data as described in the article. So for those of you interested in such things here is the extended review enumerating three big problems I had with the data:Sampling Error. The author state that they began with 47 participants but 24 had dropped out or otherwise been disqualified before the start of the experiment. The problem is we can't be sure if there was some other extraneous variable contributing to the high attrition rate. For example, if those 24 dropped out because the idea of being without their cell phone for 3 or 5 days was too threatening then the study missed the opportunity to measure their anxiety. Or maybe not. The thing is that we don't, and can't, know the possible confound of the sample selection. Median Split. The authors used a median split (M=92) to determine high- vs low- texting participants. The problem here is that someone with 91 texts per day is in one group while someone with 93 is in another. Sure the line has to be drawn somewhere, but when you have a small sample size, it is hard to distinguish the difference between groups with a median split, especially if data is clustered near the median (although we don't know if that was the case here). A better solution might be to use thirds so you have a high-, moderate, and low-texting groups, which might lead to more meaningful comparisons between high- and low-.Low Sample Size. Of course this is the big one. With only 23 participants stretched across four groups there simply is not enough data for meaningful statistical analysis, not with humans anyway. When doing animal research your samples are so homogeneous (there is little individual difference between rats) that you can get away with small sample sizes. In fact to do regression the rule of thumb I'd always heard was that you'd need at least 60 per group. That might be hard to get for some researchers and there are statistical tricks that get used (like bootstrapping) to work around that number. But for this study, the sample is just way to small and, to be fair, the authors acknowledge this in the discussion.That said the lit review and theory in the paper were good. Some of the descriptive and qualitative results were interesting. So while statistically almost meaningless, I feel as though the paper is still a valuable contribution to the relatively barren landscape of research into cell phone restriction anxiety. Dorothy Skierkowski & Rebecca M. Wood (2012). To text or not to text? The importance of text messaging among college-aged youth Computers in Human Behavior, 28 (2), 744-756 DOI: 10.1016/j.chb.2011.11.023... Read more »
Earlier I wrote about cell phone rudeness in the classroom. In that post I mentioned that asking students to go without cell phones is like asking them to go without friends. That statement generated a lot of interest from faculty and students int he comments, on facebook, and in person so I thought I would share a little bit of research that backs up my statement.In a recently published article (see below for reference) Dorothy Skierkowski and Rebecca Wood tracked college-aged youth's anxiety over a 3- or 5-day texting restriction. That is to say, for three or five days participants in the study were not allowed to use text messaging. In spite of the studies extremely small sample size (n=23), they had some interesting results. They found that participants that were identified has high-volume texters (greater than 92 texts per day on average) thought about texting an average of 47 times per day during the restricted period. Even the low-volume texters thought about it 23 times on average. In psychology we might consider those repetitive worrisome thoughts as rumination, a hallmark of anxiety.Another important finding from this study involved the open-ended survey responses from students collected during the restriction. The authors sum those responses with the following sentence: "Clearly, asking students to restrict their texting behavior made a powerful impact on most study participants, to the extent that some were not able to refrain from doing so, a large number believed their relationships had worsened over the duration of the study, and most endured the effects of texting restriction with a moderate to high degree of annoyance, anxiety, and/or stress. "So it is because of this and similar studies that I think we need to review the idea of the cell-phone ban in the classroom setting. While this study involved restricted use over a matter of days, it was still observed that students frequently thought about texting and failed to comply with text-messaging restrictions. So my fear is that banning cell phones might be just as detrimental to learning as allowing them in class. I decided to do my own experiment to gather data on how cell phones impact learning in MY classroom. I let you know how that turned out in a future post.Dorothy Skierkowski & Rebecca M. Wood (2012). To text or not to text? The importance of text messaging among college-aged youth Computers in Human Behavior, 28 (2), 744-756 DOI: 10.1016/j.chb.2011.11.023... Read more »
A photo of a red-eyed treefrog taken by Carey James Balboa at Wikimedia.At night, male red-eyed treefrogs gather on saplings over Central American forest ponds to show off their stuff for the ladies, producing self-advertising “chack” calls. Despite the fact that they gather in groups, they defend their calling territories from flirtatious male competition. Females assess the available males and usually mate with a single male, who mounts her and clings on for dear life in a behavior called amplexus until she lays eggs that he then fertilizes. Occasionally, multiple males will try to mate with the same female at the same time, which usually results in two ticked-off male frogs. What does an angry red-eyed treefrog do, you may ask? A mildly irritated treefrog will likely produce territorial “chuckle” calls, to let rivals know this is his favorite calling-plant and they’d better step-off. But a really ticked-off red-eyed treefrog rapidly lifts and lowers his hind end in a behavior called tremulation. "Step off, I'm doing the hump!" Video by Michael Caldwell. Not much is known about this tremulation behavior. Is it something they do just to release anxiety or is it a communication signal? If it is a communication signal, is it a visual signal or a vibrational signal or both? And what exactly might it communicate?Michael Caldwell, Karen Warkentin and Gregory McDaniel from Boston University, and Gregory Johnston from Flinders University in Australia, set out to ask the red-eyed treefrog if the tremulations were a communication signal and what they may mean. But without Dr. Doolittle’s powers of talking to the animals, how can scientists determine what and how animals are communicating?First, the researchers observed natural interactions between males at choruses in the wild and recorded everything they did. They found that male red-eyed treefrogs will often approach another male while making “chuckles” and “chacks”. These males also tremulated in every aggressive interaction observed. Some of these males kicked with their back legs and some encounters even escalated to wrestling. Eventually (usually anywhere from a minute to an hour later, but occasionally several hours later), one of the males would submit by fleeing the plant or remaining silent and motionless. The dominant male would then resume his self-advertising “chack” calls. So males use tremulation in aggressive contexts with other males, but does that mean that it is a signal?Males that won encounters tremulated more and used more "chack" and "chuckle" calls than did males that lost encounters. Figure from Caldwell et al. 2010 Current Biology paper.The researchers then conducted staged contests by placing pairs of calling males on the same sapling. In these staged contests, males showed all the same aggressive behaviors the researchers had observed in natural conditions, and most ended in a wrestling match. The males that won their encounter produced more calls and more tremulations than did males that lost their encounter (Check out the graph above). So tremulations are used in the context of aggression with other males and winners tremulate more than losers. It looks like these tremulations are an aggressive communication signal, but to know for sure, we need to know if other males respond to them. And are tremulations a visual signal, a vibrational signal, or both?So the researchers had to get creative and take it one step further: They put a robotic frog on a vibrating shaker that could mimic the visual display of a tremulation. They attached a separate vibrating shaker to the plant to mimic the vibrations of a tremulation. Now, they could look at the effects of the visual and vibrational components of the tremulation behavior separately! Robofrog! Notice the jointed limbs and the metal rod sticking out of the robot's belly. That rod is connected to a shaker that moves the robot so it looks like he is performing a tremulation display. A separate shaker is connected to the sapling to send the vibrational component of the display. This way, the researchers can expose frogs to the visual component and the vibrational component of the tremulation display separately. Photo by Michael Caldwell.The researchers compared male red-eyed treefrogs that were exposed to (1) nothing, (2) a frog robot that does nothing, (3) a frog robot that “tremulates” with both plant vibrations and visible movement, (4) “tremulation” vibrations in the plant, without the frog robot, (5) a frog robot that moves it’s butt up and down but doesn’t produce vibrations, and (6) white noise vibrations in the plant (this is just a generic vibration). Males responded aggressively to the imitated tremulation vibrations, visual or combined but not to any of the other treatments. This suggests that tremulations are a communication signal that rival males respond to. Interestingly, males only tremulated in response to tremulation vibrations. This suggests that the vibrational component is important to sending the full aggressive signal.... Read more »
Caldwell MS, Johnston GR, McDaniel JG, & Warkentin KM. (2010) Vibrational signaling in the agonistic interactions of red-eyed treefrogs. Current biology : CB, 20(11), 1012-7. PMID: 20493702
Inside our cells, the battle with viruses has a lot in common with 1980s action-comedy Lethal Weapon. Both feature an unlikely pair of heroes. Each partnership - proteins and LA cops alike - has a reliable, straight-laced, by-the-book one and a loose canon, maverick one.
New research suggests that whether they're crime fighting or fighting an infection, the odd couple always gets the job done.... Read more »
Ratushny AV, Saleem RA, Sitko K, Ramsey SA, & Aitchison JD. (2012) Asymmetric positive feedback loops reliably control biological responses. Molecular systems biology, 577. PMID: 22531117
by Artem Kaznatcheev in Evolutionary Games Group
Three days ago, Jonathan R. Karr, Jayodita C. Sanghvi and coauthors in Markus W. Covert’s lab published a whole-cell computational model of the life cycle of the human pathogen Mycoplasma genitalium. This is the first model of its kind: they track all biological processes such as DNA replication, RNA transcription and regulation, protein synthesis, metabolism [...]... Read more »
Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012) A whole-cell computational model predicts phenotype from genotype. Cell, 389-401. DOI: 10.1016/j.cell.2012.05.044
A pixel by pixel method has been proved useful to detect unhealthy regions using leaf images. For this reason I have implemented a pixel by pixel algorithm in order to detect damaged leaf sections and to calculate leaf area in pixels.... Read more »
Pérez Rodríguez F., Camino Saco A., Mendes Lopes D.M., Rojo Alboreca A., Gómez García E. (2012) SCANNING LEAVES ALGORITHM BASED IN “RGB PIXEL BY PIXEL” METHOD. Proceedings of V European Congress of Methodology. info:/
The way that people look at mathematical statistics is changing. Statistics show up in the news media left and right. People probably view graphs on a daily basis. They’re becoming desensitized to data. However, statistics will be one of the most important aspects of communication in the future. Statistics can actually allow us to predict [...]... Read more »
John W. Tukey. (1967) The Future of Data Analysis. The Annals of Mathematical Statistics, 33(1), 1-67. info:/10.1214/aoms/1177704711
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