I hate it when people go on and on about why they didn't blog today. I'd rather hear what someone had for breakfast ....

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I was recently fortunate enough to get a review copy of Cory Doctorow's new book, <a href="Little Brother">"Little Brother". I've never read Doctorow before, but the book was edited by Patrick Neilsen Hayden, who I think is the best editor in the business, and Patrick says that this book is one of the best things he's ever worked on. In his words, it's "one of the books that, should I happen to be run down by a beer truck next tuesday, I'd most like to be remembered for having helped into print". So when Patrick posted on his blog that he had review copies available, I jumped at the chance.

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Hoisted from the comments, Rod says

You guys are much more blunt than I usually am (except with students :-). You're also a lot more succinct.

This particular paper may be wrong, and the authors should be told that, but: as the field grows, and more engineers join, there are going to be more people who start with naive positions. The goal is not to run them off, but to teach them, so they can help us build these things :-).

To which, of course, I can only plead guilty, guilty, guilty. I mean no harm to engineers, that is for sure, especially considering the fact that I am surrounded by them ;) And damn straight I know how important engineers will be in building a quantum computer, and that physicists all by themselves are more likely to be doomed in this endeavor (but I might add that D-wave or Transmeta might demonstrate that just having the engineering bravado isn't necessarily enough. Damn straight sometimes those physics and theory people know what the hell they are talking about.)

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There are 49 new articles in PLoS ONE this week. Here are some titles I found interesting:

Echolocating Bats Cry Out Loud to Detect Their Prey:

Echolocating bats have successfully exploited a broad range of habitats and prey. Much research has demonstrated how time-frequency structure of echolocation calls of different species is adapted to acoustic constraints of habitats and foraging behaviors. However, the intensity of bat calls has been largely neglected although intensity is a key factor determining echolocation range and interactions with other bats and prey. Differences in detection range, in turn, are thought to constitute a mechanism promoting resource partitioning among bats, which might be particularly important for the species-rich bat assemblages in the tropics. Here we present data on emitted intensities for 11 species from 5 families of insectivorous bats from Panamá hunting in open or background cluttered space or over water. We recorded all bats in their natural habitat in the field using a multi-microphone array coupled with photographic methods to assess the bats' position in space to estimate emitted call intensities. All species emitted intense search signals. Output intensity was reduced when closing in on background by 4-7 dB per halving of distance. Source levels of open space and edge space foragers (Emballonuridae, Mormoopidae, Molossidae, and Vespertilionidae) ranged between 122-134 dB SPL. The two Noctilionidae species hunting over water emitted the loudest signals recorded so far for any bat with average source levels of ca. 137 dB SPL and maximum levels above 140 dB SPL. In spite of this ten-fold variation in emitted intensity, estimates indicated, surprisingly, that detection distances for prey varied far less; bats emitting the highest intensities also emitted the highest frequencies, which are severely attenuated in air. Thus, our results suggest that bats within a local assemblage compensate for frequency dependent attenuation by adjusting the emitted intensity to achieve comparable detection distances for prey across species. We conclude that for bats with similar hunting habits, prey detection range represents a unifying constraint on the emitted intensity largely independent of call shape, body size, and close phylogenetic relationships.

A New Concept for Medical Imaging Centered on Cellular Phone Technology:

According to World Health Organization reports, some three quarters of the world population does not have access to medical imaging. In addition, in developing countries over 50% of medical equipment that is available is not being used because it is too sophisticated or in disrepair or because the health personnel are not trained to use it. The goal of this study is to introduce and demonstrate the feasibility of a new concept in medical imaging that is centered on cellular phone technology and which may provide a solution to medical imaging in underserved areas. The new system replaces the conventional stand-alone medical imaging device with a new medical imaging system made of two independent components connected through cellular phone technology. The independent units are: a) a data acquisition device (DAD) at a remote patient site that is simple, with limited controls and no image display capability and b) an advanced image reconstruction and hardware control multiserver unit at a central site. The cellular phone technology transmits unprocessed raw data from the patient site DAD and receives and displays the processed image from the central site. (This is different from conventional telemedicine where the image reconstruction and control is at the patient site and telecommunication is used to transmit processed images from the patient site). The primary goal of this study is to demonstrate that the cellular phone technology can function in the proposed mode. The feasibility of the concept is demonstrated using a new frequency division multiplexing electrical impedance tomography system, which we have developed for dynamic medical imaging, as the medical imaging modality. The system is used to image through a cellular phone a simulation of breast cancer tumors in a medical imaging diagnostic mode and to image minimally invasive tissue ablation with irreversible electroporation in a medical imaging interventional mode.

Counting the Founders: The Matrilineal Genetic Ancestry of the Jewish Diaspora:

The history of the Jewish Diaspora dates back to the Assyrian and Babylonian conquests in the Levant, followed by complex demographic and migratory trajectories over the ensuing millennia which pose a serious challenge to unraveling population genetic patterns. Here we ask whether phylogenetic analysis, based on highly resolved mitochondrial DNA (mtDNA) phylogenies can discern among maternal ancestries of the Diaspora. Accordingly, 1,142 samples from 14 different non-Ashkenazi Jewish communities were analyzed. A list of complete mtDNA sequences was established for all variants present at high frequency in the communities studied, along with high-resolution genotyping of all samples. Unlike the previously reported pattern observed among Ashkenazi Jews, the numerically major portion of the non-Ashkenazi Jews, currently estimated at 5 million people and comprised of the Moroccan, Iraqi, Iranian and Iberian Exile Jewish communities showed no evidence for a narrow founder effect, which did however characterize the smaller and more remote Belmonte, Indian and the two Caucasus communities. The Indian and Ethiopian Jewish sample sets suggested local female introgression, while mtDNAs in all other communities studied belong to a well-characterized West Eurasian pool of maternal lineages. Absence of sub-Saharan African mtDNA lineages among the North African Jewish communities suggests negligible or low level of admixture with females of the host populations among whom the African haplogroup (Hg) L0-L3 sub-clades variants are common. In contrast, the North African and Iberian Exile Jewish communities show influence of putative Iberian admixture as documented by mtDNA Hg HV0 variants. These findings highlight striking differences in the demographic history of the widespread Jewish Diaspora.

A Pre-Hispanic Head:

This report on a male head revealed biologic rhythms, as gleaned from hydrogen isotope ratios in hair, consistent with a South-American origin and Atomic Mass Spectrometry radiocarbon dating (AMS) compatible with the last pre-Hispanic period (1418-1491 AD, 95.4% probability). Biopsies showed exceptionally well-preserved tissues. The hair contained high levels of toxic elements (lead, arsenic and mercury) incompatible with life. There was no evidence for lead deposition in bone consistent with post-mortem accumulation of this toxic element in the hair. We propose that the high content of metals in hair was the result of metabolic activity of bacteria leading to metal complexation in extra cellular polymeric substances (EPS). This is a recognized protective mechanism for bacteria that thrive in toxic environments. This mechanism may account for the tissues preservation and gives a hint at soil composition where the head was presumably buried. Our results have implications for forensic toxicology which has, hitherto, relied on hair analyses as one means to reconstruct pre-mortem metabolism and for detecting toxic elements accumulated during life. Our finding also has implications for other archaeological specimens where similar circumstances may distort the results of toxicological studies.

An Analysis of the Abstracts Presented at the Annual Meetings of the Society for Neuroscience from 2001 to 2006:

Annual meeting abstracts published by scientific societies often contain rich arrays of information that can be computationally mined and distilled to elucidate the state and dynamics of the subject field. We extracted and processed abstract data from the Society for Neuroscience (SFN) annual meeting abstracts during the period 2001-2006 in order to gain an objective view of contemporary neuroscience. An important first step in the process was the application of data cleaning and disambiguation methods to construct a unified database, since the data were too noisy to be of full utility in the raw form initially available. Using natural language processing, text mining, and other data analysis techniques, we then examined the demographics and structure of the scientific collaboration network, the dynamics of the field over time, major research trends, and the structure of the sources of research funding. Some interesting findings include a high geographical concentration of neuroscience research in the north eastern United States, a surprisingly large transient population (66% of the authors appear in only one out of the six studied years), the central role played by the study of neurodegenerative disorders in the neuroscience community, and an apparent growth of behavioral/systems neuroscience with a corresponding shrinkage of cellular/molecular neuroscience over the six year period. The results from this work will prove useful for scientists, policy makers, and funding agencies seeking to gain a complete and unbiased picture of the community structure and body of knowledge encapsulated by a specific scientific domain.

Network 'Small-World-Ness': A Quantitative Method for Determining Canonical Network Equivalence:

Many technological, biological, social, and information networks fall into the broad class of 'small-world' networks: they have tightly interconnected clusters of nodes, and a shortest mean path length that is similar to a matched random graph (same number of nodes and edges). This semi-quantitative definition leads to a categorical distinction ('small/not-small') rather than a quantitative, continuous grading of networks, and can lead to uncertainty about a network's small-world status. Moreover, systems described by small-world networks are often studied using an equivalent canonical network model - the Watts-Strogatz (WS) model. However, the process of establishing an equivalent WS model is imprecise and there is a pressing need to discover ways in which this equivalence may be quantified. We defined a precise measure of 'small-world-ness' S based on the trade off between high local clustering and short path length. A network is now deemed a 'small-world' if S>1 - an assertion which may be tested statistically. We then examined the behavior of S on a large data-set of real-world systems. We found that all these systems were linked by a linear relationship between their S values and the network size n. Moreover, we show a method for assigning a unique Watts-Strogatz (WS) model to any real-world network, and show analytically that the WS models associated with our sample of networks also show linearity between S and n. Linearity between S and n is not, however, inevitable, and neither is S maximal for an arbitrary network of given size. Linearity may, however, be explained by a common limiting growth process. We have shown how the notion of a small-world network may be quantified. Several key properties of the metric are described and the use of WS canonical models is placed on a more secure footing.

Of Mice and Men -- Universality and Breakdown of Behavioral Organization:

Mental or cognitive brain functions, and the effect on them of abnormal psychiatric diseases, are difficult to approach through molecular biological techniques due to the lack of appropriate assay systems with objective measures. We therefore study laws of behavioral organization, specifically how resting and active periods are interwoven throughout daily life, using objective criteria, and first discover that identical laws hold both for healthy humans subject to the full complexity of daily life, and wild-type mice subject to maximum environmental constraints. We find that active period durations with physical activity counts successively above a predefined threshold, when rescaled with individual means, follow a universal stretched exponential (gamma-type) cumulative distribution, while resting period durations below the threshold obey a universal power-law cumulative distribution with identical parameter values for both of the mammalian species. Further, by analyzing the behavioral organization of mice with a circadian clock gene (Period2) eliminated, and humans suffering from major depressive disorders, we find significantly lower parameter values (power-law scaling exponents) for the resting period durations in both these cases. Such a universality and breakdown of the behavioral organization of mice and humans, revealed through objective measures, is expected to facilitate the understanding of the molecular basis of the pathophysiology of neurobehavioral diseases, including depression, and lay the foundations for formulating a range of neuropsychiatric behavioral disorder models.

Dental Microwear and Diet of the Plio-Pleistocene Hominin Paranthropus boisei:

The Plio-Pleistocene hominin Paranthropus boisei had enormous, flat, thickly enameled cheek teeth, a robust cranium and mandible, and inferred massive, powerful chewing muscles. This specialized morphology, which earned P. boisei the nickname "Nutcracker Man", suggests that this hominin could have consumed very mechanically challenging foods. It has been recently argued, however, that specialized hominin morphology may indicate adaptations for the consumption of occasional fallback foods rather than preferred resources. Dental microwear offers a potential means by which to test this hypothesis in that it reflects actual use rather than genetic adaptation. High microwear surface texture complexity and anisotropy in extant primates can be associated with the consumption of exceptionally hard and tough foods respectively. Here we present the first quantitative analysis of dental microwear for P. boisei. Seven specimens examined preserved unobscured antemortem molar microwear. These all show relatively low complexity and anisotropy values. This suggests that none of the individuals consumed especially hard or tough foods in the days before they died. The apparent discrepancy between microwear and functional anatomy is consistent with the idea that P. boisei presents a hominin example of Liem's Paradox, wherein a highly derived morphology need not reflect a specialized diet.

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tags: chambers street subway art, subway art, NYC through my eye, photography, NYC

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Single-celled Bacterium Works 24/7:

Researchers at Washington University in St. Louis have gained the first detailed insight into the way circadian rhythms govern global gene expression in Cyanothece, a type of cyanobacterium (blue-green algae) known to cycle between photosynthesis during the day and nitrogen fixation at night.

How Birds Navigate: Research Team Is First To Model Photochemical Compass:

It has long been known that birds and many other animals including turtles, salamanders and lobsters, use the Earth's magnetic field to navigate, but the nature of their global positioning systems (GPS) has not been completely understood. One school of thought hypothesizes that birds use magnetically-sensitive chemical reactions initiated by light (called chemical magnetoreception) to orient themselves, but no chemical reaction in the laboratory, until now, has been shown to respond to magnetic fields as weak as the Earth's.

New Findings Challenge Conventional Ideas On Evolution Of Human Diet, Natural Selection:

New findings suggest that the ancient human "cousin" known as the "Nutcracker Man" wasn't regularly eating anything like nuts after all.

Legless Lizard And Tiny Woodpecker Among New Species Discovered In Brazil:

Researchers discovered a legless lizard and a tiny woodpecker along with 12 other suspected new species in Brazil's Cerrado, one of the world's 34 biodiversity conservation hotspots.

Ancient Ecosystems Organized Much Like Our Own:

Similarities between half-billion-year-old and recent food webs point to deep principles underpinning the structure of ecological relationships, as shown by researchers from the Santa Fe Institute, Microsoft Research Cambridge and elsewhere. Analyses of Chengjiang and Burgess Shale food-web data suggest that most, but not all, aspects of the trophic structure of modern ecosystems were in place over a half-billion years ago. It was an Anomalocaris-eat-trilobite world, filled with species like nothing on today's Earth. But the ecology of Cambrian communities was remarkably modern, say researchers behind the first study to reconstruct detailed food webs for ancient ecosystems. Their paper suggests that networks of feeding relationships among marine species that lived hundreds of millions of years ago are remarkably similar to those of today.

Bison Can Thrive Again, Study Says:

Bison can repopulate large areas from Alaska to Mexico over the next 100 years provided a series of conservation and restoration measures are taken, according to continental assessment of this iconic species by the Wildlife Conservation Society and other groups.

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tags: red fan parrot, hawk-headed parrot, Deroptyus accipitrinus accipitrinus, parrots, birds, photograph

I took this picture yesterday morning to share with you;

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Albert Hofmann, the chemist who synthesized lysergic acid diethylamide (LSD) in 1938 died of a heart attack on April 29, 2008 at the age of 102. Hofmann (Wikipedia entry) also discovered the hallucinogenic properties of LSD because of an accidental ingestion about five years after he first synthesized the compound. The impact of this train of events on our understanding of the neurochemical function of the brain stretches across many disciplines from basic neuroscience to studies of consciousness and theology.

Obituaries: NYT, LA Times, Reuters.

[and thanks to reader Neuro-conservative who already noted this for the DM readers]

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You may want to advocate for gender equity in science and engineering. But you are just wasting your energy. Pat O'Hurley tells us so.

I'm simply saying that it is [foolish] to expect female engineering enrollment to be equal to men's enrollment, if engineering is a field which is, statistically speaking, more attractive to men than to women.

This would be an insight gained from the following sort of deeply objective and scientific analysis:

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As former Kansas congressman Jim Slattery kicks off his campaign to replace Senator Pat "Memory Pills" Roberts, Roberts is already having trouble keeping his facts straight. Sean Tevis explains:

I heard that Senator Pat Roberts, who is seeking his third Senate term, issued an ad criticizing Slattery for his work as a lobbyist in Washington. “He stopped working for Kansas 14 years ago and made millions for himself,” the ad says.

But I can tell you first-hand that’s not true.

The company I work for, based in Overland Park, contacted Jim Slattery three years ago to help us. We designed a radical new technology called Air2Air that makes power plants work more efficiently. But the technology we designed is really big and no customer wants to spend a few million dollars on something that’s never been built before no matter how promising the science is.

We asked Jim Slattery to help us because we’d heard that he helps out Kansas companies.

Jim’s work in Washington helped raise the issue of water conservation and the importance of sustainable water supplies, resulting in stronger incentives for water conservation in the Energy Act of 2005. Subsequently, we successfully received a grant from the DOE to perform a test of this technology in a full-sized power plant.

It was a fantastic success and now we have orders from all over the world for these things. So, as a lobbyist, he helped a Kansas company thrive and helped the U.S. energy infrastructure, which is what our politicians should be doing. Maybe Senator Roberts needs to take a lesson from Jim Slattery.

If Pat Roberts had a better memory, he'd remember that these are exactly the sort of things a Senator should be doing, and his constituents shouldn't have to be going to lobbyists to get their voices heard in Congress. Unfortunately for Kansans, Roberts has shown more concern with covering up Bush and Cheney's political abuse of the intelligence process, and with rubber-stamping Bush's illegal and unconstitutional scheme to allow bureaucrats to wiretap innocent American citizens.

Slattery faces an uphill battle, since he'll have to raise and spend millions of dollars to unseat the addlepated incumbent. Help however you can; Slattery has put together a great team and has a great shot at unseating the unpopular and unsuccessful Sen. Roberts.

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