The Life Scientists

I think this generalizes to scholarly publishing, including research. There will come a weepin' and a wailin' and a gnashin' o' teeth. - Bill Hooker

"The vascular system of a leaf provides its structure and delivers its nutrients. When you light up that vascular structure with some fluorescent dye and view it using time-lapse photography, details begin to emerge that reveal nature's mathematical formula for survival. (...) "If you begin looking at them in any degree of detail, you will see all of those beautiful arrangements of impinging angles and where the big veins meet the little veins and how well they are arranged," (...) It's a pattern that can neutralize the effect of a wound to the leaf, such as a hole in its main vein. Nutrients bypass the hole and the leaf remains completely intact. "Something that looks pretty looks pretty for a really good reason. It has a well defined and elegant function. We can scan the leaves at extremely high resolution and reconstruct every single little piece of vein, who talks to who, who is connected to who and so forth," (...) - Amira from Bookmarklet

"This research is a unique interdisciplinary partnership in which physics is used to address biological problems, and it is our belief that the mathematical and physical sciences will play a major role in biomedical research in this century," (...) Magnasco says this research is a jumping off point for understanding other systems that branch and rejoin, including everything from river... more... - Amira

Revealing Nature's Mathematical Formula for Survival (video) http://www.youtube.com/watch... - Amira

"MUCH of the plastic swirling around the sea ends up in the North Pacific Gyre, where four great ocean currents meet to create a swirl of water moving clockwise that is twice the size of the United States. Its less polite name is the North Pacific Garbage Patch. A new study led by Miriam Goldstein of the Scripps Institute of Oceanography and published in Biology Letters has quantified the increase in scraps of plastic there between 1972-87 and 1999-2010. The number of small particles of less than 5mm in diameter floating in the areas sampled increased about 100 times (from virtually nothing). This is bad news for almost everything apart from Halobates sericeus, a small insect that now has lots of nice little floating platforms on which to lay its eggs." - sofarsoSean

"Zerbino et al. review the development of computational methods and algorithms for efficient analysis, from the initial genome reconstruction to their use in comparing individuals and organisms, reconstructing phylogenies, and tying genotype to phenotype. Munsky et al. note that phenotypic variation can occur even in genetically identical cells. They discuss stochastic gene expression as the likely source of this variability and describe how the analysis of variability can give insight into the mechanisms of gene regulation. At the level of morphogenesis that so fascinated Turing, Morelli et al. describe how a combination of theory and experiment is being used to investigate developmental processes. They describe how patterning can arise from molecular gradients, from coupled biological oscillations, or from mechanical deformations of cells and tissues. Underlying all of this analysis is computer code; Morin et al. call for this code to be made widely available and suggest how this might be implemented." - Adriano

Featuring thousands of full-text journals, this scholarly collection offers unmatched coverage of information spanning a broad range of important areas of academic study including: anthropology, astronomy, biology, chemistry, civil engineering, engineering, ethnic & multicultural studies, geology, law, materials science, mathematics, music, pharmaceutical sciences, physics, psychology, religion & theology, veterinary science, women's studies, zoology, and many other fields. Available via the powerful EBSCOhost research platform, Academic Search Complete offers critical information from many sources unique to this massive collection. - Ami Iida

ref. http://academic.research.microsoft.com/ - Ami Iida

"Wilson is challenging one of the central pillars of evolutionary biology—that natural selection acts far more strongly on individuals and genetic relatives than on broader social groups. The book is also a reversal of Wilson's own earlier view that the evolution of altruism was driven by kin selection. Now he promotes the highly contested idea that group selection—the competition of one group against others—is the driving force, favoring self-sacrificial behaviors in individuals that benefit all group members, even those that aren't related. Not only social insects but humans too—especially art, religion and other unique facets of the human condition—are better viewed, through the lens of group selection. Because of our special human eusociality—we are being driven to greater cooperation and together will conquer the ills of the world." - Adriano from Bookmarklet

NOOOOOOO! I hate group selection arguments and especially one from my hero. :((((((( - Kelli H., ain't shit from Android

Can I ask you why you feel that way, Kelli? - Friar Will

It has been around for a bit... search this paper for it.. http://www.ncbi.nlm.nih.gov/pmc... - Oliver Slay

Some topics covered: Commonality between Turing machines and biological cells \\ Assessing the divide between neuroscience and computing \\ Impact of Turing's influential work on morphogenesis \\ Incomputable reality: natural world's interconnectivity should inspire better models of the Universe \\ + Podcast by Turing's biographer, Andrew Hodges. - Adriano from Bookmarklet

Authors@Google presents George DYSON, re: his new book _Turing's Cathedral_ http://youtu.be/_FibuHyIHnU -- 7 March 2012. \\ Related: viral geneticist, Nils Aall BARRICELLI, shows up at Princeton in early 1953 and begins experiments to see if he could inoculate a two-dimensional matrix with random strings that can self-replicate and cross-breed. But von Neumann's papers on self-reproducing automata never mentioned Barricelli. http://edge.org/convers... - Adriano

Summary Why did our earliest hominin ancestors begin to walk bipedally as their main form of terrestrial travel? The lack of sufficient fossils and differing interpretations of existing ones leave unresolved the debate about what constitutes the earliest evidence of habitual bipedality. Compelling evidence shows that this shift coincided with climatic changes that reduced forested areas, probably forcing the earliest hominins to range in more open settings [1]. While environmental shifts may have prompted the origins of bipedality in the hominin clade, it remains unknown exactly which selective pressures led hominins to modify their postural repertoire to include a larger component of bipedality [2]. Here, we report new experimental results showing that wild chimpanzees walk bipedally more often and carry more items when transporting valuable, unpredictable resources to less–competitive places. - Ami Iida

We never shut-up about the E. coli crowd-sourcing last summer (see: http://blogs.openaccesscentral.com/blogs...), but there are still nice studies coming out that used the raw data, including this paper on a targeted therapy just out in PLoS One http://www.plosone.org/article... - GigaScience

Organisms are remarkably adapted to diverse environments by specialized metabolisms, morphology, or behaviors. To address the molecular mechanisms underlying environmental adaptation, we have utilized a Drosophila melanogaster line, termed “Dark-fly”, which has been maintained in constant dark conditions for 57 years (1400 generations). We found that Dark-fly exhibited higher fecundity in dark than in light conditions, indicating that Dark-fly possesses some traits advantageous in darkness. - Ami Iida

Self-organization is the spontaneous often seemingly purposeful formation of spatial, temporal, spatiotemporal structures or functions in systems composed of few or many components. In physics, chemistry and biology self-organization occurs in open systems driven away from thermal equilibrium. The process of self-organization can be found in many other fields also, such as economy, sociology, medicine, technology. Many objects in our surrounding and daily life such as furniture, houses, cars, tv-sets, computers are man made. On the other hand, especially in the animate world, objects grow, acquire their form, and function without being created by humans. The animal kingdom abounds of examples. It is increasingly recognized that even the human brain may be considered as a self-organizing system as well as quite a number of manifestations of human activity, such as in economy and sociology. But processes of self-organization can be found also in the inanimate world: formation of cloud... more... - Ami Iida

Yessir Evind I apologize and here's why (Scoble transition). Yesterday I was speaking with Dr. Kellogg , she knows Blackburn and gave myanswer which differs from his (she even said its better, which is reedick cuz it's Bburn *blush*) I combo'ed game theory and quantum mechanics. So I was all it's just so easy peasy Japanesey, forest for the trees, sorta thing. Nextly she replied, I'm paraprasing here, "No it's not easy you bitch; because you have a background in math yes, but that's goddamn weird. Don't be so ignorantly blithe with what YOU may know you stupid fucktard," Because this religious plague will only be cured with right knowledge ~ that last parts me - sofarsoSean

I love you Cristo. Just not in "that" way :) UPDATE!, I just say Eivind's comment, lol that was a joke on reading quantum mechanics for dummies, I dn't believe there is such a thing. But you misread I wrote stochaistic as part of game theory not quantum, and here's my error I mixed up superposed with superposition of initial states. Further game theory isn't everything these days... more... - sofarsoSean

Sometime late 2005 I think. I got an email from Nucleic Acids Research asking about the notion of them making content available, with authors paying a fee. I sent back a comment telling them they were barking mad, I couldn't afford to pay, and who would want to read my papers anyway. I grew up a bit later ;-) Also the paper that lead to me getting the survey is now freely available online from NAR... - Cameron Neylon

About 2001, from Michael Ashburner when I was in his department. I then got a job with BioMed Central in 2003. - Matt Hodgkinson

"Ulrich’s lists about 65,000 peer reviewed scholarly journals of any kind" is that correct? Everybody seems to be citing 25k... - Björn Brembs

@Björn & Heather - nice link. Had always wondered where the 25k figure comes from, and have never seen ulrichweb from inside. - Daniel Mietchen

"More than 500 million years ago, single-celled organisms on Earth’s surface began forming multi-cellular clusters that ultimately became plants and animals. (…) The yeast “evolved” into multi-cellular clusters that work together cooperatively, reproduce and adapt to their environment—in essence, they became precursors to life on Earth as it is today. (…) How one-celled organisms made the switch to living as a group, as multi-celled organisms.” (…) Analysis showed that the clusters were not just groups of random cells that adhered to each other, but related cells that remained attached following cell division." - Amira from Bookmarklet

See also: Emergence and Complexity - prof. Robert Sapolsky's lecture | Stanford University -- "How a small difference at one place in nature can have a huge effect on a system as time goes on. He calls this idea fractal magnification and applies it to many different systems that exist throughout nature." http://www.youtube.com/watch... - Amira

The ability of neurons to undergo regenerative growth after injury is governed by cell-intrinsic and cell-extrinsic regeneration pathways. These pathways represent potential targets for therapies to enhance regeneration. However, the signaling pathways that orchestrate axon regeneration are not well understood. In Caenorhabditis elegans, the Jun N-terminal kinase (JNK) and p38 MAP kinase (MAPK) pathways are important for axon regeneration. We found that the C. elegans SVH-1 growth factor and its receptor, SVH-2 tyrosine kinase, regulate axon regeneration. Loss of SVH-1–SVH-2 signaling resulted in a substantial defect in the ability of neurons to regenerate, whereas its activation improved regeneration. Furthermore, SVH-1–SVH-2 signaling was initiated extrinsically by a pair of sensory neurons and functioned upstream of the JNK-MAPK pathway. Thus, SVH-1–SVH-2 signaling via activation of the MAPK pathway acts to coordinate neuron regeneration response after axon injury. - Ami Iida

Bone homeostasis is maintained by the balance between osteoblastic bone formation and osteoclastic bone resorption1, 2, 3. Osteoclasts are multinucleated cells that are formed by mononuclear preosteoclast fusion1, 2, 4, 5. Fat-soluble vitamins such as vitamin D are pivotal in maintaining skeletal integrity. However, the role of vitamin E in bone remodeling is unknown. Here, we show that mice deficient in α-tocopherol transfer protein (Ttpa−/− mice), a mouse model of genetic vitamin E deficiency6, have high bone mass as a result of a decrease in bone resorption. Cell-based assays indicated that α-tocopherol stimulated osteoclast fusion, independent of its antioxidant capacity, by inducing the expression of dendritic-cell–specific transmembrane protein, an essential molecule for osteoclast fusion, through activation of mitogen-activated protein kinase 14 (p38) and microphthalmia-associated transcription factor, as well as its direct recruitment to the Tm7sf4 (a gene encoding DC-STAMP)... more... - Ami Iida

There are 18,000 married gay and lesbian couples in California and at least 131,000 nationwide according to the 2010 census, conducted before New York state legalized same-sex marriage in July. Rick Santorum says he'll try to unmarry all of them if he's elected president. Once the U.S. Constitution is amended to prohibit same-gender marriages, "their marriage would be invalid," the former Pennsylvania senator said Dec. 30 in an NBC News interview. "We can't have 50 different marriage laws in this country," he said. "You have to have one marriage law." The comments didn't attract nearly as much attention as Santorum's recent invocation of his Catholic faith to denounce government support for birth control, prenatal testing and resource conservation - which, in the last case, he attributed to President Obama's "phony theology." But his declared intention to nullify past as well as future same-sex marriages has reinforced his position to the right of the other Republican contenders, even... more... - sofarsoSean

Lol oh YES!! THEY'RE THIEVES WHAT ABOUT US JOB CREATING TAX PAYERS (0-15% MAX!! MAX!!) ~i thought you were talking about an African policy, and though, a lil out of jurisdiction, but we do have the bombs... - sofarsoSean

Sirolimus (INN/USAN), also known as rapamycin, is an immunosuppressant drug used to prevent rejection in organ transplantation; it is especially useful in kidney transplants. It prevents activation of T cells and B-cells by inhibiting their response to interleukin-2 (IL-2). - Ami Iida