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  • July 17, 2010
  • 11:35 PM
  • 933 views

Quasars in the very early universe

by Charles Daney in Science and Reason

Quasars are powered by the gravitational (potential) energy of their central supermassive black holes. However, their distinctive features – their extremely high luminosity in particular – are very dependent on characteristics of matter close to the black hole. Most supermassive black holes (SMBH), including those at the centers of the Milky Way and our close neighbor M31 (Andromeda), are responsible for fairly small amounts of radiation in any part of the electromagnetic spectrum. This is generally because the radiation of a quasar is produced mainly by the infall of matter during a relatively brief period of the object's life – a few percent of the total, i. e. a few hundred million years. Once the nearby matter is used up, the lights go out.(For earlier articles on quasars, see here.)In a quasar, where matter in significant quantities is still being accreted, most of the radiation originates in a central "accretion disk" close to the black hole. The radiation is thermal ("black body") produced by very hot gas consisting mostly of hydrogen and helium. This radiation covers the spectrum from infrared to X-rays. Since quasars are so bright, they can be seen individually at high redshifts – z≥6, which is not true of ordinary galaxies. That corresponds to times within a billion years of the big bang. At z≈6 photon wavelengths are stretched by a factor of 7, so what we actually see is not the rest-frame spectrum, but a considerably red-shifted version of it.If rs is the Schwarzschild radius, then the accretion disk extends from a radius of about 3 times rs outward to a few hundred times rs. To give a sense of the scale, a largish SMBH has a mass of a billion solar masses. So for such an object rs is about the radius of the orbit of Uranus, by a simple calculation given here.Quasars and active galaxies (i. e. just smaller versions of the same thing) have been intensively studied for several decades. In that time, a fairly clear picture has emerged of how matter is distributed further out from the accretion disk. The most prominent feature of this region is a thick (compared to the accretion disk) torus-shaped ring of cooler gas and dust. The "dust" consists of very small particles composed of various elements heavier than helium. Electromagnetic radiation from the torus is mostly in the infrared part of the spectrum (rest frame), and is produced by re-emission (at lower energies) of higher energy photons from the accretion disk.The shape of this region is not strictly a torus, since it's considerably flattened, especially at higher distances from the center, but it's referred to as a torus for simplicity. The outer limits of quasar tori are hard to determine, but probably extend hundreds of light years from the center. However, the inner parts are thick enough that unless we are seeing the quasar almost face-on (i. e., along the symmetry axis of the accretion disk and torus), we cannot clearly see the accretion disk itself, because it's obscured by the dust in the torus.One interesting thing about quasars is that as far as we can tell (until quite recently), their characteristics are very similar no matter how distant they are. Although the present-day universe is quite different in many respects from what it was a billion years after the big bang, quasars seem hardly different at all.Research published just this year is starting to change this story:Dust-free quasars in the early UniverseThe most distant quasars known, at redshifts z ≈ 6, generally have properties indistinguishable from those of lower-redshift quasars in the rest-frame ultraviolet/optical and X-ray bands. This puzzling result suggests that these distant quasars are evolved objects even though the Universe was only seven per cent of its current age at these redshifts. Recently one z ≈ 6 quasar was shown not to have any detectable emission from hot dust, but it was unclear whether that indicated different hot-dust properties at high redshift or if it is simply an outlier. Here we report the discovery of a second quasar without hot-dust emission in a sample of 21 z ≈ 6 quasars. Such apparently hot-dust-free quasars have no counterparts at low redshift. Moreover, we demonstrate that the hot-dust abundance in the 21 quasars builds up in tandem with the growth of the central black hole, whereas at low redshift it is almost independent of the black hole mass. Thus z ≈ 6 quasars are indeed at an early evolutionary stage, with rapid mass accretion and dust formation. The two hot-dust-free quasars are likely to be first-generation quasars born in dust-free environments and are too young to have formed a detectable amount of hot dust around them.Some things in these results are actually more interesting than that a few very early quasars are different from all other quasars. In the very early universe at z>6, less intergalactic dust is to be expected. This is because the dust – which is composed of elements heavier than helium – is (by conventional accounts) produced mostly in stars. It is expelled from stars only either gradually, as the star evolves, or suddenly in the rare case of supernova explosions. We still don't know very precisely when the very first stars formed (see here), but that probably happened only a few hundred million years after the big bang. Since the very first stars must have consisted almost entirely of hydrogen and helium, star-formation models indicate they should have been much more massive than typical later stars, and they should have expoded as supernovae after only a few tens of millions of years. As heavier elements gradually accumulated in the universe, stars of a more modern sort, initially containing small amounts of heavier elements, began to form. These later stars were small enough so that most never ended as supernovae, but they continued to manufacture and expel heavier elements – and hence dust.Observations of very early quasars therefore tell us a little about the pace of this process. We now know, for example, of at least two quasars that formed so early that they do not have any dust around them that we can observe. The evidence for this is that emissions of these two quasars at rest-frame wavelengths from ultraviolet to very near infrared appear normal. Dust, however, should also produce rest-frame emissions in farther infrared – and that's not seen in these two examples, although it is in all other of the sampled z≈6 quasars. One other feature of z≈6 quasars is particularly interesting. The mass of a quasar can be estimated from total luminosity and certain spectral features. In all z≈6 quasars that do have evidence of dust, the amount of dust is roughly proportional to the SMBH mass. However, in low-redshift quasars, dust abundance is almost uncorrelated with mass. The implication, then, is that in their youngest stages, but not later, quasars accumulate dust at about the same rate as SMBH mass. And indeed, the two quasars without apparent dust also have the smallest SMBH mass of any in the sample, about 2 to 3×108 M⊙.This raises another interesting, unanswered question. Just where does this dust come from? It's generally thought that in the present universe most of the existing dust originated from ordinary stars. However, at z≈6 most stars would be less than 500 million years old, and it's not at all clear this would have allowed enough time for the production of sufficient dust. Supernovae are another possibility, but even in the early universe we don't know whether they would have been common enough.Further, the existence of elements heavier than helium is necessary but not sufficient to produce dust. Most models assume also a proper combination of relatively low temperature (<2000 K) and high density is also required for dust to form. But a theoretical study (astro-ph/0202002) suggests that dust could actually form in the vicinity of a quasar itself. Some combination of all these possibilities may be the answer, but a lot more research will probably be needed to clear this up.Every time we learn something new, it seems, we also find new questions.... Read more »

Jiang, L., Fan, X., Brandt, W., Carilli, C., Egami, E., Hines, D., Kurk, J., Richards, G., Shen, Y., Strauss, M.... (2010) Dust-free quasars in the early Universe. Nature, 464(7287), 380-383. DOI: 10.1038/nature08877  

  • July 17, 2010
  • 10:30 PM
  • 770 views

Collaboration 2.0

by Aurametrix team in Health Technologies

Information technology is letting people around the world come together in unprecedented ways. Wikis, blogs and microblogs like twitter, crowdsourcing and crowd-task-solving sites continue to flatten the planet. Scientific innovation used to be a private endeavor, with very narrowly specialized scientists. The Internet changed some of this but there is plenty of room for improvement.... Read more »

Johnston SC, & Hauser SL. (2009) Crowdsourcing scientific innovation. Annals of neurology, 65(6). PMID: 19562693  

Wright MT, Roche B, von Unger H, Block M, & Gardner B. (2010) A call for an international collaboration on participatory research for health. Health promotion international, 25(1), 115-22. PMID: 19854843  

Marsh A, Carroll D, & Foggie R. (2010) Using collective intelligence to fine-tune public health policy. Studies in health technology and informatics, 13-8. PMID: 20543334  

Huss JW 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, & Su AI. (2010) The Gene Wiki: community intelligence applied to human gene annotation. Nucleic acids research, 38(Database issue). PMID: 19755503  

  • July 17, 2010
  • 05:41 PM
  • 971 views

How are British kids doing these days?

by Tom Rees in Epiphenom

British society, like that of most industrialized nations, has gone through enormous changes in recent decades. But it's hard to get objective data on what the impact has been on the people living there.

Which is why I was interested to see a recent study by Stephen Collishaw, of Cardiff University, and colleagues. They compared data from two studies, one in 1986 and one in 2006, that asked adolescents (aged 16-17) about their state of mind. Whether they felt anxious, depressed, worried, irritable, had disturbed sleep - things like that.

They found that kids in 2006 were more likely to report emotional problems than those in 1986. In particular, both boys and girls were more likely to say that they felt irritable, had disturbed sleep, and felt worn out or under strain. Their parents, too, were more likely to report similar problems.

Overall, the percentage saying they were frequently anxious or depressed has roughly doubled since 1986.

It's possible, of course, that kids today are simply more open about talking about admitting their feelings. That could be the case, although the authors point out that they did not see a general increase in all emotional problems. Instead, they found that some problems (irritable, disturbed sleep, worn out) increased, while others did not.

So, assuming that this is a real effect, what could be causing it? To investige, they looked at kids living with single parents compared with those living with step parents with step parents (see figure). They also looked at kids from disadvantaged homes compared with advantaged homes.

They found no consistent differences. The increase in emotional problems seems to be roughly the same across all social backgrounds. If anything, the greatest increase seems to be among girls with both natural parents and advantaged backgrounds.

Why could this be? It's very hard to say. Potentially, the higher levels of uncertainty of modern life, coupled with more fractured social networks. But this is just speculation.

What can be said is that while life has not got any harder for the children of divorced parents, it doesn't seem, on this evidence at least, to have got much easier - and that has got to be troubling, given the increasing numbers of children living in homes without both natural parents.

Collishaw, S., Maughan, B., Natarajan, L., & Pickles, A. (2010). Trends in adolescent emotional problems in England: a comparison of two national cohorts twenty years apart Journal of Child Psychology and Psychiatry, 51 (8), 885-894 DOI: 10.1111/j.1469-7610.2010.02252.x

This article by Tom Rees was first published on Epiphenom. It is licensed under Creative Commons.

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  • July 17, 2010
  • 02:53 PM
  • 1,123 views

How viruses hijack cellular transport systems

by Lab Rat in Lab Rat

Even in the world of the very small, there are significant differences in size. A eukaryote cell (i.e a human cell) for example is relatively big, in microscopic terms. Most other things that interact with the cell at the microscopic level, are far smaller than it, such as bateria, viruses and signalling molecules.A virus isn't much more than a small capsule of proteins with a little bit of DNA inside. Once it gets inside a eukaryote cell, it's very much in the position of a small child wandering into a big city. In front of it lies the vast interior of the cell, full of reactions, enzymes, proteins scurrying too and fro, mRNA being translated, proteins being folded and other busy bustling cellular processes. Surrounding it are large organelles (larger than the virus particle!) with strange and mysterious procedures going on inside them...That sort of view, stretching across to both horizonsFrom here, the virus has to make its way to the nucleus, pushing its way through the crowded and complex cellular interior without being spotted as an intruder. Fortunately it has some help here, because it's facing the same problem faced by every molecule and organelle already in the cell. Transport mechanisms are already in place so that things can move around the large intracellular space with relative ease. The viruses simply hijack these transport systems and get a free ride all the way too the nucleus.Work on the herpes simplex virus helped to produce a model of how the viral particles move around the cell. After entering the cell through the cell surface membrane, the virus is picked up by dynein which carries it along microtubes towards the nucleus. The microtubules form a network within the cell (like train rails) which the dynein motors along (using ATP energy). This is shown pictorally below:Dynein moves in one direction along the microtubule while kinesin moves in the other direction. Together they move molecules all around the cell.Once at the nucleus, the viral DNA enters through the nuclear membrane and is replicated inside the nucleus (entering the nucleus is a critical step for DNA-viruses; for those viruses that contain RNA this step is not so vital). The replicated DNA then comes back out of the nucleus and is transcribed into protein in the cytoplasm, which leads to the formation of new viral particles. These new viruses then have to travel back down the microtubule (carried by kinesin) to the outer membrane of the cell where they can be released into the surrounding environment and go on to infect more cells.One interesting question is what exactly the dynein (and kenesin) bind to on the virus cell surface. As well as being an interesting point, answering this comes with the usual funding bait that if you find how viruses move inside the cell you may be able to find ways of stopping them from moving which would leave them at a severe disadvantage. To examine this the virus was isolated and the parts of the surrounding protein coat that bound to cellular factors further separated. These separated capsid proteins were then tested for their ability to bind to mammalian intracellular proteins. They found that several of the capsid proteins could bind to important transporter molecules, and furthermore that several different transporter molecules could sometimes bind to the same capsid protein.Drawing showing the site of attachment of the motor transport proteins to the (green) virus capsule. The other end of the motor proteins is used to move along the microtubule.As I'm in a fairly syntheticly-biological mood, I couldn't help but notice the mention at the end of the paper that this could have implications beyond virus treatment or vaccinations. The ability to create a little molecule that the cell can carry to the nucleus could have implications for both future genetic treatments and nanotechnology. The ability to get a little capsule of treatment right to the nucleus of cells could even have the potential for treating cancer cells, as it utilizes the cells own transport mechanisms to deliver treatment to the intracellular place it is needed.---Kerstin Radtke, Daniela Kieneke, André Wolfstein, Kathrin Michael, Walter Steffen, Tim Scholz, Axel Karger, Beate Sodeik (2010). Plus- and Minus-End Directed Microtubule Motors Bind Simultaneously to Herpes Simplex Virus Capsids Using Different Inner Tegument Structures PLoS Patholgens, 6 (7) : e1000991---Follow me on Twitter!... Read more »

Kerstin Radtke, Daniela Kieneke, André Wolfstein, Kathrin Michael, Walter Steffen, Tim Scholz, Axel Karger, Beate Sodeik. (2010) Plus- and Minus-End Directed Microtubule Motors Bind Simultaneously to Herpes Simplex Virus Capsids Using Different Inner Tegument Structures. PLoS Patholgens, 6(7). info:/e1000991

  • July 17, 2010
  • 12:47 PM
  • 1,025 views

Across disciplines, what motivates or prevents faculty staff archiving?

by Christina Pikas in Christina's LIS Rant

This article is in early view at JASIST. It looks like it comes from the author's dissertation. It isn't terribly earth-shattering, but it's well done, it provides more evidence, and there are definitely some implications for library/IR manager practice. Here's the citation: Kim, J. (2010). Faculty self-archiving: Motivations and barriers Journal of the American Society for Information Science and Technology DOI: 10.1002/asi.21336 The author went through a complicated process to identify 1,500 faculty members at 17 research institutions with DSpace IRs (not immediately clear why only DSpace IRs). The faculty members were at all levels (associate, assistant, full) and from several areas of science (includes math), several areas of engineering (includes CS, hm), several areas of social science, and several areas of the humanities. Some had items in their IR and some didn’t. There was a web-based survey and with a 45% response rate (sounds good, but the author mailed the people and e-mailed them a bunch of times, so she worked for it).  The survey is included in the appendix. It has a bunch of likert scale questions, some yes/no, some multiple choice, and some open questions. Forty-one telephone interviews were done with survey respondents to get more in-depth information. So what did she find? Altruism – but this isn’t exactly what you think. It’s more like generalized reciprocity combined with quid pro quo combined with access for those in less developed countries. Coming from a self-archiving culture. Some actually mentioned peer pressure – if it weren’t expected of them, they wouldn’t do it. Copyright concerns. Some don’t self archive because they believe they don’t have the right. The nice part is that at least a few knew that they could amend the publication agreement. This sort of counteracts the idea that faculty don’t know about or get copyright. These folks were pretty clear on it. Technical skills and age. Younger and those who rated their technical skills more highly were more likely to self archive. Impact on tenure or promotion. They all seemed to think there would be a positive or no impact on promotion and tenure. Time and effort. It’s too much of a PITA for its priority. Applications/implications for librarians: If concern about copyright is preventing a lot of self-archiving, then there's real education that can be done. Also - the fact that it's a hassle. If they can populate their website by using a badge or widget from the IR, that would make things easier, eh? A couple of trivial things about the article: it seems really redundant - it repeats itself a lot. Some good editing would make it a bunch tighter. It has a great reference list - this might be a useful collection for anyone writing or presenting on the topic. Read the comments on this post...... Read more »

Kim, J. (2010) Faculty self-archiving: Motivations and barriers. Journal of the American Society for Information Science and Technology. DOI: 10.1002/asi.21336  

  • July 17, 2010
  • 12:41 PM
  • 865 views

Human health effects of oil spills and implications for the BP spill

by Ashartus in exposure/effect

A lot of the media (and scientific) attention to oil spills in the ocean focuses on the effects on marine ecosystems. The ecological effects, particularly in the short term, are undeniable – the pictures of oil-soaked birds are an obvious example. However, less attention is given to the potential effects on human health – both [...]... Read more »

Aguilera, F., Méndez, J., Pásaro, E., & Laffon, B. (2010) Review on the effects of exposure to spilled oils on human health. Journal of Applied Toxicology. DOI: 10.1002/jat.1521  

  • July 17, 2010
  • 09:00 AM
  • 758 views

Rodent Saturday!

by EcoPhysioMichelle in C6-H12-O6 (old)

Now, for my contribution to Saturday’s rodent blog, I will tell you about a new mouse species of the South American Akodon genus that was described earlier this year by Braun and colleagues in New species of Akodon (Rodentia: Cricetidae: Sigmodontinae) from central Argentina.... Read more »

  • July 17, 2010
  • 07:40 AM
  • 717 views

Running experiments on Twitter? Don’t forget the bug

by ---a in Bodyspacesociety.eu

There's nothing that error analysis wouldn't fix. But I prefer to sit here and ponder the epistemological ramifications of the way bugs are impacting the traditional way we make science...... Read more »

Scott A. Golder and Sarita Yardi. (2010) Structural Predictors of Tie Formation in Twitter: Transitivity and Mutuality. Proceedings of the Second IEEE International Conference on Social Computing. August 20-22, Minneapolis, MN. info:/

  • July 17, 2010
  • 04:46 AM
  • 666 views

Pleasure or Pain?

by The Neurocritic in The Neurocritic

Robert Mapplethorpe - Untitled (Self Portrait)The previous post (Erotic or Disgusting?) covered a functional MRI experiment on the neural responses to erotic films in heterosexual and homosexual males (Zhang et al., 2010). Specifically, the study examined sexual arousal and disgust while the participants viewed various types of porn. Neuroimaging results were reported only for the stimuli deemed distasteful by each group, wherein the left ventromedial prefrontal cortex was more active for gay men, and the left cuneus [visual cortex] was more active for straight men. It was unclear why this particular outcome was obtained. Other problems with the paper included the comparison condition (passive rest, rather than viewing neutral film clips) and the analysis strategy.An earlier study, however, took a more comprehensive look at arousal and disgust in a different sexual minority group: those with sadomasochistic preferences, who were compared to those without (Stark et al., 2005). Here, the stimuli were pictures from four categories: neutral, disgust-inducing, erotic, and sadomasochistic:The erotic pictures included either pictures of single naked subjects or pictures of couples in an intimate situation. The pictures with sadomasochistic content either had a submission/dominance theme (e.g. a naked man pulling a coach with a dressed woman), or showed sadomasochistic techniques (e.g. hurting someone with hot wax, pictures of bound subjects). The scenes depicted single subjects (male and female), couples, and groups of subjects.The disgust-inducing pictures showed a broad range of different disgust elicitors: unusual food (e.g. man eating a grasshopper, man biting into a monkey head), disgusting animals (e.g. snails, maggots), poor hygiene (e.g. dirty toilet, garbage piles, and body products (e.g. excrements, vomit). Neutral pictures showed household articles, geometric figures, and nature scenes.This allowed within-subject and between-subject approaches in the same experiment. Presumably, rotting garbage would be disgusting to everyone, while the groups would differ in their reactions to images with erotic or sadomasochistic content.Participants were 24 adults, 12 of whom identified as having sadomasochistic sexual preferences (SM)1 and 12 without sadomasochistic preferences (non-SM). Each group was comprised of 6 men and 6 women. Subjects were initially classified by asking, “Are you interested in sadomasochistic sexual activities?” This was followed by an 8 item questionnaire asking about sexual orientation, identity, and experiences, with each item rated on a 5-point scale (e.g., “I describe myself as a sadomasochist”, “I describe myself as sadistic/dominant”, etc.).All pictures were rated in advance by separate groups of SM and non-SM participants on the dimensions of disgust and sexual arousal using 9-point visual analog scales, and on valence, arousal, and dominance using the self-assessment manikin (also on a scale from 1 to 9). The scanned subjects also rated the pictures after the fMRI experiment was over. The emotional ratings for neutral and disgust-inducing stimuli did not differ between the two groups. As expected, however, ratings for the other two stimulus classes were divergent:The erotic pictures revealed more positive affect, more arousal, and more sexual arousal for the nonSM group in comparison to the SM group. SM subjects indicated to have felt more positive, more dominant, less disgusted, and more sexually aroused during the presentation of the pictures with sadomasochistic content than the nonSM subjects.Statistically speaking, emotion ratings for the disgust-inducing and sadomasochistic images did not differ in the non-SM group.2 On the other hand, ratings for the sadomasochistic pictures in the SM participants were similar to those for erotic pictures in the non-SM group. These findings were important for the between-subjects comparison of disgust and sexual arousal.During the fMRI experiment, each category of pictures was presented in separate blocks. Subjects were instructed to “let the pictures affect you”. For data analysis purposes, a number of different comparisons were performed:Several T-contrasts were calculated for each subject: the emotional conditions versus the neutral condition (Disgust Neutral, Erotic Neutral, Sm Neutral), and for the positive emotion versus negative emotion (Erotic Disgust, Sm Disgust, Sm Erotic). For a random effect analysis the individual contrast images (first level) were used in a second level analysis.As you can imagine, the amount of data reported in this paper is voluminous. Brain regions of interest (ROIs) were selected from the meta-analysis of Phan et al. (2002) on neuroimaging studies of emotion. Exploratory analyses were performed as well.The Erotic or Disgusting? Pleasure or Pain? series will conclude next time with the functional neuroanatomy associated with states of disgust and sexual arousal in those with vanilla and BDSM preferences.Footnotes1 Specific orientations were as follows:In the SM group three subjects reported a bisexual orientation (two male, one female). Furthermore, the SM group could be separated into eight masochists (four female), one sadist (female) and three switchers (one female).2 Numerically speaking, however, disgust ratings were higher for the former than for the latter (6.67 vs. 4.25).ReferencesPhan KL, Wager T, Taylor SF, Liberzon I. (2002). Functional neuroanatomy of emotion: a meta-analysis of emotion activation studies in PET and fMRI. Neuroimage 16:331-48.STARK, R., SCHIENLE, A., GIROD, C., WALTER, B., KIRSCH, P., BLECKER, C., OTT, U., SCHAFER, A., SAMMER, G., & ZIMMERMANN, M. (2005). Erotic and disgust-inducing pictures—Differences in the hemodynamic responses of the brain. Biological Psychology, 70 (1), 19-29 DOI: 10.1016/j.biopsycho.2004.11.014
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STARK, R., SCHIENLE, A., GIROD, C., WALTER, B., KIRSCH, P., BLECKER, C., OTT, U., SCHAFER, A., SAMMER, G., & ZIMMERMANN, M. (2005) Erotic and disgust-inducing pictures—Differences in the hemodynamic responses of the brain. Biological Psychology, 70(1), 19-29. DOI: 10.1016/j.biopsycho.2004.11.014  

  • July 17, 2010
  • 12:03 AM
  • 906 views

P. aeruginosa, Biofilms and Honey

by James Byrne in Disease Prone

A biofilm is generally described as a ‘synthesised environment housing a bacterial community on a surface’. This essentially means that organisms (not just bacteria) start to produce huge amount of ‘muck’ containing proteins, sugars and DNA and export it from the cell once bound to a ‘surface’. When it does this it generates its own little environmental niche and as that bacterial cell divides within the biofilm it can pool its resources allowing easier growth for the community as a whole. It also has other effects. Biofilms are largely resistant to disinfection and antibiotics as the bacteria can keep the actual environment at bay whilst happily existing in its own filth.... Read more »

PITTET, B., MONTANDON, D., & PITTET, D. (2005) Infection in breast implants. The Lancet Infectious Diseases, 5(2), 94-106. DOI: 10.1016/S1473-3099(05)01281-8  

  • July 16, 2010
  • 08:06 PM
  • 814 views

Which came first, the scientist or the sensationalist?

by Casey Rentz in The Lay Scientist

The best headline I read last week is from Metafilter blog: "Scientists prove that lunch came before breakfast." In fact, journalists at major news sites all around the web reported that scientists have solved the infamous chicken-and-egg problem.
Which came first? The chicken. Definitively.




--
read more... Read more »

Freeman CL, Harding JH, Quigley D, & Rodger PM. (2010) Structural Control of Crystal Nuclei by an Eggshell Protein. Angewandte Chemie (International ed. in English), 49(30), 5135-5137. PMID: 20540126  

  • July 16, 2010
  • 07:39 PM
  • 1,047 views

Acro-tastic! (with additional GADZOOKS!)

by Emma in we are all in the gutter

I’m in need of some cheering up today, as the fun observations I wanted to make with the Herschel Space Telescope have turned out to be impossible. Luckily, this observation planning also involved a lot of procrastination, which led me to this: the Dumb Or Overly Forced Astronomical Acronyms Site (DOOFAAS). On this site astronomer [...]... Read more »

John F. Beacom, & Mark R. Vagins. (2003) GADZOOKS! Antineutrino Spectroscopy with Large Water Cerenkov Detectors. Phys.Rev.Lett. 93 (2004) 171101. arXiv: hep-ph/0309300v1

  • July 16, 2010
  • 02:08 PM
  • 612 views

Boost your Guitar Hero skills 101 - SLEEP! Really?

by Psychothalamus in Psychothalamus

We have been told that feeling well-rested while studying and reviewing your work just before bedtime enhances your memory for what you have studied. But when it comes to the role of sleep in motor memory, the answer is less clear. A recent research abstract presented at the 24th annual meeting of the Associated Professional Sleep Societies LLC by Dr Kevin Peters from Trent University suggests that sleep enhances our performance in complex motor learning tasks, as measured by an larger increase in accuracy levels obtained in playing guitar hero in the sleep condition compared to the wake condition. However, an earlier paper by Cai & Rickard (2009) suggests that after controlling for circadian (time of day) and homeostatic (time since sleep) confounds, participants in the sleep conditions did not display any benefits in a motor sequence task. The participants in their research were categorized into 3 conditions - a wake group, a 1 night sleep post-training group and a 2 night sleep post-training group. Participants were tasked to tap a number sequence, 4-1-3-2-4 repeatedly and reaction times (RTs) were measured. All participants trained at about 9.30am and were tested on 5.30pm on the day itself or on Day 2 and Day 3 depending on which conditions they were in. Comparing difference scores of their RTs for the 3 different groups revealed no significant differences between them. If sleeping does indeed improve motor memory, we would expect a significant reduction in RTs for the sleep groups compared to the wake group. Therefore, it appears that after controlling for circadian and homeostatic factors, sleeping after training does not improve motor sequence performance. Unfortunately, I do not have access to the exact methodology and results of Peter's study to verify if the concerns about the relevant confounds raised by Cai & Rickard (2009) are adequately addressed. Therefore, as far as I'm concerned, the jury is still out on the specific benefits (if any) conferred to motor memory by sleep. But I must say that Peter's design holds much promise (he certainly won't have any trouble finding willing and good subjects). Well, regardless of whether sleeping helps you perfect that golf swing or ramp up your skill level on guitar hero, it’s still a good idea to get a good night of rest to ward of the negative effects associated with sleep deprivation in other domains of our life. Afterall, according to a study by Falleti, Maruff, Collie, Darby & McStephen (2003), driving after being awake for 24hrs is like driving with a blood alcohol concentration of 0.05%. Not quite enough to get you arrested but probably more than enough to make you think twice about pulling that all-nighter.Cai, D., & Rickard, T. (2009). Reconsidering the role of sleep for motor memory. Behavioral Neuroscience, 123 (6), 1153-1157 DOI: 10.1037/a0017672Falleti MG, Maruff P, Collie A, Darby DG, & McStephen M (2003). Qualitative similarities in cognitive impairment associated with 24 h of sustained wakefulness and a blood alcohol concentration of 0.05%. Journal of sleep research, 12 (4), 265-74 PMID: 14633237... Read more »

  • July 16, 2010
  • 02:02 PM
  • 1,116 views

Perception of Supply Risk

by Daniel Dumke in SCRM Blog - Supply Chain Risk Management


One of the most published supply risk researchers is George A. Zsidisin. In his 2003 article he describes the characteristics of inbound supply that affect the perception of risk.

Supply Risk
The author defines supply risk as the potential occurrence of an incident associated with inbound supply from individual supplier failures or the supply market, in which its outcomes result in the inability of the purchasing firm to meet customer demand or cause threats to customer life and safety.
He therefore includes the probability and significance of an adverse event.
Continue reading "Perception of Supply Risk"
... Read more »

Zsidisin, G. (2003) Managerial Perceptions of Supply Risk. The Journal of Supply Chain Management, 39(1), 14-26. DOI: 10.1111/j.1745-493X.2003.tb00146.x  

  • July 16, 2010
  • 11:53 AM
  • 802 views

Prehistoric mammal Prolibytherium had a “butterfly face”

by Laelaps in Laelaps

Exactly what Prolibytherium magnieri was, no one is quite sure. Since the time it was described in 1961, the 17-16.5 million year old mammal from Egypt and Libya has been closely allied with prehistoric relatives of deer (Palaeomerycidae), ancient giraffes (such as Sivatherium), and a motley group of giraffe cousins (Climacoceratidae). Many experts now agree [...]... Read more »

  • July 16, 2010
  • 11:53 AM
  • 609 views

Phase synchronization

by Brandon Goodell in Bored Lunatic



Consider two pendula (penduli? pendulums?) that are on a bit of a wobbly table, oscillating back and forth.

Eventually, they synchronize. Once a huge mystery to physics, the fact that placing two pendulums on the same surface causes minute vibrations to transmit through that surface, causing the devices to become weakly coupled. The result is that, after a sufficiently long period of time swinging back and forth, the two pendulums become fully synchronous.

The Scholarpedia article, "Phase Model" discusses this phenomenon, how it is modeled, and "what it all means." It lists the different methods of forming coupled oscillating systems, and describes a few coupled oscillating systems that we simply do not have the mathematics to analyze... yet.

The model I'm particularly interested in is the phase model. See, most of these models are described by considering two (or more) little beads on a circular wire hoop.  All of the beads are marching along clockwise at a constant speed, but when two beads are near each other, they are attracted to one another; the bead in the lead (ha!) slows down a little bit and the trailing bead speeds up a little bit so that they can catch up with each other.  The result is that, after a sufficiently long period of time has passed, the beads stay as close to each other as can be for the rest of eternity.  At least, this is the case with two beads.

If we have an arbitrary number of n beads, far more complex behavior occurs - we can even use the phase model to describe chaotic systems, which is pretty neat.  Keep in mind here we aren't talking about actual beads on an actual wire hoop, we are talking about points that can collide and pass each other as if they were not there - ghost beads marching on a hoop.

Okay, so the real-life analogy starts to break down.  Whatever.

The point is that emergent behavior pops up left and right - while two beads behave in an entirely predictable way (converging to one another), three beads behave in a less-than-predictable fashion.  The whole is greater than the sum of it's parts - take one bead, and it marches along boringly.  Take two beads, and they converge to one another.  Take three beads, and crazy shit happens, so the complexity of 3 does not equal the complexity of 2 plus the complexity of 1.

Get it?

So why the hell am I interested in this?  Well, I'm currently testing some software I have written that estimates the average phase angle between two signals that vary in time.  In the context of the phase model, I can interpret the two signals as the position of two separate beads on the same hoop.  Consequentially, I'm going to use the phase model to test my software to make sure it is working properly.  I am going to generate several simulations of these beads, then run those through my software to see if the output makes sense in the context of arbitrary phase oscillators.

In the meantime, I'm brushing up on my synchrony reading - to say that it can be a bit mind-bending is likely an understatement.  For example, the quick and dirty rundown I just gave you is for weakly coupled phase oscillators - but they are continuously coupled.  We could develop a pulse-coupled model, like neurons, which give each other little discontinuous nudges every time they get sufficiently close to one another, and that would be equally interesting, and there is a mathematical framework to analyze that as well.

I find it fascinating that there are no mainstream methods of analyzing non-continuous yet non-pulse coupled oscillators.  I imagine something like the stock market could be described by millions of coupled oscillators, but that system has sharp discontinuities in momentum oftentimes, because the stock market can change at the speed of our brains.  That is, I imagine the stock market is actually an amalgam of the continuously-coupled and pulse-coupled oscillator models.


Izhikevich, E., & Ermentrout, B. (2008). Phase model Scholarpedia, 3 (10) DOI: 10.4249/scholarpedia.1487

... Read more »

Izhikevich, E., & Ermentrout, B. (2008) Phase model. Scholarpedia, 3(10), 1487. DOI: 10.4249/scholarpedia.1487  

  • July 16, 2010
  • 11:27 AM
  • 2,671 views

‘Molecular relay race’ at the heart of new targeted cancer therapy

by Cancer Research UK in Cancer Research UK - Science Update

A big problem in cancer treatment is how to deliver enough of the drugs needed to treat the tumour without causing excessive side effects. To make matters worse, cancers can develop resistance to drugs over time, meaning that increasingly higher doses and more potent cocktails of drugs are often needed to tackle the disease. But [...]... Read more »

Middleton, M., Knox, R., Cattell, E., Oppermann, U., Midgley, R., Ali, R., Auton, T., Agarwal, R., Anderson, D., Sarker, D.... (2010) Quinone Oxidoreductase-2-Mediated Prodrug Cancer Therapy. Science Translational Medicine, 2(40), 40-40. DOI: 10.1126/scitranslmed.3000615  

  • July 16, 2010
  • 11:24 AM
  • 858 views

Evidence for role of microRNA in Melanoma

by Sally Church in Pharma Strategy Blog

Twitter is great for highlighting interesting journal articles, as I found when Edward Winstead from the NIH shared this paper from PLOSone on the importance of microRNA in melanoma in his Twitter stream (thanks, Ted!). There has been a lot...... Read more »

Haflidadóttir, B., Bergsteinsdóttir, K., Praetorius, C., & Steingrímsson, E. (2010) miR-148 Regulates Mitf in Melanoma Cells. PLoS ONE, 5(7). DOI: 10.1371/journal.pone.0011574  

  • July 16, 2010
  • 11:07 AM
  • 340 views

Childhood Adversities Predict Suicidal Behaviours

by Ultimo167 in Strong Silent Types

Bruffaerts et al. (2010) argue that by preventing childhood adversities to the fullest extent possible, we will witness a corresponding, marked decline in the suicide rate.... Read more »

Bruffaerts R, Demyttenaere K, Borges G, Haro JM, Chiu WT, Hwang I, Karam EG, Kessler RC, Sampson N, Alonso J.... (2010) Childhood adversities as risk factors for onset and persistence of suicidal behaviour. The British journal of psychiatry : the journal of mental science, 197(1), 20-7. PMID: 20592429  

  • July 16, 2010
  • 10:58 AM
  • 627 views

Does one size fit all when it comes to star formation?

by Kelly Oakes in Basic Space

It is widely known (among astrophysicists at least!) that disks of accumulated matter are an essential component in the formation of low mass stars. These disks form when a rotating cloud of dust and gas collapses, and they direct material from the cloud onto a protostar at the centre. This protostar keeps accreting more and [...]... Read more »

Kraus, S., Hofmann, K., Menten, K., Schertl, D., Weigelt, G., Wyrowski, F., Meilland, A., Perraut, K., Petrov, R., Robbe-Dubois, S.... (2010) A hot compact dust disk around a massive young stellar object. Nature, 466(7304), 339-342. DOI: 10.1038/nature09174  

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