Network Theory Overview - "The idea: nature and the world of human technology are full of networks! People like to draw diagrams of networks. Mathematical physicists know that in principle these diagrams can be understood using category theory. But why should physicists have all the fun? This is the century of understanding living systems and adapting to life on a finite planet. Math isn't the main thing we need, but it's got to be part of the solution... so one thing we should do is develop a unified and powerful theory of networks." (via ;)
The Mammoth Cometh. "Bringing extinct animals back to life is really happening — and it’s going to be very, very cool. Unless it ends up being very, very bad." [Previously, Via]
Open warfare erupts in the world of mathematical biology, as Lior Pachter of UC-Berkeley writes three blog posts attacking two papers in Nature Bioscience, accusing one of them of being "dishonest and fraudulent": The Network Nonsense of Albert-Laszlo Barabasi, The Network Nonsense of Manolo Kellis, and Why I Read the Network Nonsense Papers. Kellis (MIT) and his co-authors respond (.pdf.)
Pictures have been going around of a small jelly like creature a fisherman pulled into his boat off New Zealand. The creature has been identified as a salp most likely Thetys vagina Salps may look like jellyfish but they are more closely related to vertebrates. [more inside]
Take a stroll through French artist Vincent Fournier‘s [previously] gallery of animal photographs, and you’re likely to come across some creatures you’ve never seen before. Like, for instance, a jellyfish that is capable of electronically transmitting data across the Abyssal depths of the ocean. Or, perhaps, a scorpion that can perform semi-automated surgery on humans. “These creatures come from the future—an imagined future, based loosely on current research on synthetic biology and genetic engineering,” says Fournier, of his project Post-Natural History, a series of digitally-altered photos of animals that do not yet exist. “The idea is that these are living species, reprogrammed by mankind to better fit our environment as well as to adapt to new human desires.”
Bacteria have a Hobo Code. Next month's Science News carries a pretty interesting overview about the cutting edge of microbial science, including recent studies showing "in many mammals a microbial community ferments various sweats, oozes and excretions into distinctive scents that reveal age, health and much more to knowing noses in a select social circle". That's right, microbes are posting status updates to each other through smells, sharing with other microbes what they've learned about host animals.
After a species goes extinct, in some cases its "ghost" may linger in the ecosystem it leaves behind in the form of evolutionary anachronisms. [more inside]
"After two to three hours, the body is transformed into a sterile coffee-colored liquid the consistency of motor oil that can be safely poured down the drain, alongside a dry bone residue similar in appearance to cremated remains." GOOD magazine: The emergence of the sustainable death industry.
"My subject is a barren one – the world of nature, or in other words life; and that subject in its least elevated department, and employing either rustic terms or foreign, nay barbarian words that actually have to be introduced with an apology. Moreover, the path is not a beaten highway of authorship, nor one in which the mind is eager to range: there is not one of us who has made the same venture, nor yet one Roman who has tackled single-handed all departments of the subject."Naturalis Historia was written by Pliny the Elder between 77 and 79 CE and was meant to serve as a kind of proto-encyclopedia discussing all of the ancient knowledge available to him, covered in enough depth and breadth to make it by a reasonable margin the largest work to survive to the modern day from the Roman era. The work includes discussions on astronomy, meteorology, geography, mineralogy, zoology and botany organized along Aristotelian divisions of nature but also includes essays on human inventions and institutions. It is dedicated to the Emperor Titus in its epistle to the Emperor Vespasian, a close friend of Pliny who relied on his extensive knowledge, and its unusually careful citations of sources as well as its index makes it a precursor to modern scholarly works. It was Pliny's last work, as well as sadly his sole surviving one, and was published not long before his death attempting to save a friend from the eruption of Mt. Vesuvius that destroyed Pompeii and Herculaneum, famously recounted by Pliny's eponymous nephew Pliny the Younger.
Here is a reasonable translation that is freely available to download from archive.org for your edification.[more inside]
Recently Emily Graslie, of the fantastic natural history tumblr and youtube series TheBrainScoop, was asked a question about whether she had personally experienced sexism in her field. Her response is fucking amazing.
Inside is her goldmine of awesome female science educators online with channels that focus on Science Technology Engineering and Math. My work day is fucked.[more inside]
The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong.
Growing Out My Bush is a fascinating Tumblr where one woman explores the perception of the female body by first shaving and then photographing the re-growth of her pubic hair. Especially interesting are "The Reality of Nude Photos" and "How Breasts Can Look."
Bacteria from personalities has been used to make human cheese as part of an exhibition on synthetic biology in Dublin. This included cheeses grown from bacteria from various belly buttons, noses, armpits, tears, mouths and toes. If that's a bit too strong for you, then other exhibits in the show include humans reproducing dolphins for food, and mice cloned from Elvis Presley's DNA.
The Nazi Anatomists. "How the corpses of Hitler's victims are still haunting modern science—and American abortion politics."
Say It With Sea Otters is a blog where adorable cartoon animals deliver difficult messages. Here are some examples: 1, 2, 3, 4 and 5. While the sea otter has a well deserved reputation for extreme cuteness, these aquatic weasels engage in behavior that to humans seems truly reprehensible. Of course, we humans haven't exactly treated them well throughout history. Indeed, the first scientist to describe them, George Wilhelm Steller, emphasized their valuable fur in his description of them.
CreatureCast - Rhizocephala - a charmingly animated look at the lifecycle of rhizocephalan barnacles, one of the more horrifying (non-charming) parasitic crustaceans (likewise). NOT a practitioner of parasitic castration but still disturbing: The bobbit worm. Happy swimming!
For a long time, there have been newspaper stories and covers of magazines that talked about “The end of antibiotics, question mark?” Well, now I would say you can change the title to “The end of antibiotics, period.”
The Course of Their Lives. While much in medicine has changed over the last century, the defining course of a first year medical student's education is still 'Gross Anatomy.' This is their hands-on tour of a donated cadaver -- an actual human body -- and is an experience which cannot be replicated by computer models. When Milwaukee Journal Sentinel reporter Mark Johnson came up with the idea of following a med school gross anatomy class for a feature story, his editor challenged him to make it different. So he chose to intertwine the students' stories with that of Geraldine 'Nana' Fotsch, a living future donor, as sort of a stand-in for the cadaver. (Via. This four-part series contains descriptions of a human dissection. Some may find it disturbing.) [more inside]
In a nutshell, this new study provides evidence that we need a certain amount of sleep every night, because the brain takes this time to rid itself of toxic metabolic byproducts, which would otherwise accumulate in the brain and impair brain function, destroy neurons — and potentially cause neurodegenerative disorders.
A study [PDF] by CUNY Professor Diana Reiss and Rachel Morrison (Biopsychology and Behavioral Neuroscience Subprogram in Psychology The Graduate Center of CUNY) was published last week in Zoo Biology detailing for the first time a whisper‐like behavior in a non‐human primate, the cotton top tamarin at the Central Park Zoo. [more inside]
"Read this carefully so that you understand it. When you come home we will show you the model. Lots of love, Daddy." In 1953 Francis Crick, sat down to write his twelve-year-old son Michael a letter explaining his brand-new discovery: the double-helix structure of DNA. Now you can read the original, seven-page hand-written letter, complete with an interactive feature that lets you click for details, context and explanations. Courtesy of the Smithsonian. [more inside]
Intermeshing, rotating mechanical gears have been found in an insect. The gears act to ensure that the legs of the hopping insect move at the same rate when jumping, and are lost during molting to an adult stage. Via reddit, where the journalist is participating. Science magazine report (paywalled).
Teaching Cliteracy 101: "It is a curious dilemma to observe the paradox that on the one hand the female body is the primary metaphor for sexuality, its use saturates advertising, art and the mainstream erotic imaginary. Yet, the clitoris, the true female sexual organ, is virtually invisible." ~ Artist Sophia Wallace is using street art and an art exhibition that incorporates pithy slogans, 'scientific data, historical information as well as references to architecture, porn, pop culture and human rights' to make "the case for the clit". (Links throughout this post may be NSFW.) [more inside]
The Thoreau Poison - Caleb Crain of The New Yorker takes a closer look at the ideas explored in Upstream Color (spoilers)
"I sent this paper to JK Rowling explaining how the wizarding gene could be singular, autosomal, and dominant despite the protests of a bunch of fans who stopped learning genetics after Punnett squares." See also: Wizarding Genetics: More Complicated Than Mendel! and Purple Orchids and Muggleborn Wizards: A Theory of Wizard Genetics
British comedian Josie Long explores All the Planet's Wonders in a very short series on BBC radio: Collecting. Animals. Astronomy. Plants.
Men to Blame for Menopause: Younger Women Preferred in Human Evolutionary History. Humans are actually the only species where females cannot reproduce throughout their lives, and previous studies have suggested that there may be a "grandmother effect." This suggests that women lose their fertility at an age where they may not live to care for another child. Instead, they're available to care for younger women's children. Yet some scientists weren't satisfied with this theory. "How do you evolve infertility? It is contrary to the whole notion of natural selection" ... Original paper published in PLOS Computational Biology - Mate Choice and the Origin of Menopause [more inside]
Oliver the green moray eel loves to be petted. With small children, a fish popsicle, and commentary about barracudas. (SLYT) [more inside]
"OpenWorm is an attempt to build a complete cellular-level simulation of the nematode worm Caenorhabditis elegans. Of the 959 cells in the hermaphrodite, 302 are neurons and 95 are muscle cells. The simulation will model electrical activity in all the muscles and neurons. An integrated soft-body physics simulation will also model body movement and physical forces within the worm and from its environment." -- Bonus: explore the worm's cellular anatomy in 3D (WebGL required.)
After more than 25 years of studying the calls of prairie dog in the field, one researcher managed to decode just what these animals are saying. And the results show that prairie dogs aren't only extremely effective communicators, they also pay close attention to detail.
The Olympus Microscopy Resource Center digital video gallery, with: live cells, pond life and more, crystals and more.
Mosses Make Two Different Plants From the Same Genome, and a Single Gene Can Make the Difference
One of the most astonishing secrets in biology is this: every plant you see makes two different plants from the same genome. And, scientists recently reported, a single gene from an ancient, powerful lineage can make the difference.
Peter Nonacs, a professor at UCLA, let his students cheat on an exam he called "impossibly difficult", saying, "Let’s see what you can accomplish when you have no restrictions."
Celebrate the 60th anniversary of the discovery of DNA's structure with a pictorial story behind DNA's double helix and the Rosalind Franklin papers, including correspondences and lab notes that detail some of her crystallography research, findings that laid the groundwork for Watson and Crick's later publication.
"Is organic produce better for you?" is a simple question asked by a middle schooler in a science fair. Using fruit flies fed organic vs. conventional produce, Ria Chhabra tracked the flies and saw improvements based on their diet. Now barely a sophomore in high school, the project lead to university research labs, science fair awards, publication in top-tier peer-reviewed journals, and quite likely, scholarships at her pick of top-flight universities.
After a decade or so of legal back-and-forth between Utah-based Myriad Genetics and medical researchers, the ACLU, and the Public Patent Forum, the US Supreme Court will hear a case next week which attempts to address whether genes — isolated (derivative) or original — can be patented. The stakes are high on both sides: opponents use Myriad's actions to argue that giving short-term monopoly control over humanity's genetic constituency is not in the public interest, while proponents defend the use of patents to spur private research in biotech, alternative energy and other nascent industries.
Is Psychometric g a Myth? - "As an online discussion about IQ or general intelligence grows longer, the probability of someone linking to statistician Cosma Shalizi's essay g, a Statistical Myth approaches 1. Usually the link is accompanied by an assertion to the effect that Shalizi offers a definitive refutation of the concept of general mental ability, or psychometric g." [more inside]
A selection of glass viruses by artist Luke Jerram (a full gallery and photographs of other sculptural work are also available directly from his site)
Researchers have found that size does matter as it relates to overall proportions of the male body (PNAS link, PDF)
Pictures of some brains from the Texas State Mental Hospital. (Not for the squemish.) "I walked into a storage closet filled with approximately one-hundred human brains, none of them normal, taken from patients at the Texas State Mental Hospital. The brains sat in large jars of fluid, each labeled with a date of death or autopsy, a brief description in Latin, and a case number."
In temperate climates, "fairy rings" appear in grassy meadows and lawns, and these are caused by fungi, with some rings expanding for hundreds of years. But in the western part of Southern Africa, there are a different sort of "fairy circles," barren circles that are surrounded by long-lived perennial grasses. The Himba people, an ethnic group in northern Namibia, attribute them to original ancestor, Mukuru, or consider them "footprints of the gods," and scientists have been stumped for decades. Professor Norbert Jürgens, from the University of Hamburg, might have finally solved the riddle: a species of termites that are most active at night and don't build big, noticeable nests, have engineered the ecosystem by eating the roots of grasses that grow within the circle, keeping the soil moist for long periods of time. The discussion continues, as some scientists who have studied the phenomena aren't so sure about the theory.
Is it time to put natural selection in its place? Jello Biafra once famously wrote that "If evolution is outlawed, only outlaws will evolve." But while it likely comes as no surprise to specialists working in the field or to those who've been following developments in evolutionary biology closely, there's an emerging view among experts that Darwin's view of natural selection as the primary driver of speciation and evolutionary change may be incorrect or at least drastically overstated. It's long been understood that non-adaptive evolutionary mechanisms like "genetic drift" and random mutation also play non-trivial roles in evolutionary processes, but a recent study (link to abstract with full-text PDF available) casts new doubts on the primary role of natural selection, finding that "Neutral models, in which genetic change arises through random variation without fitness differences have proven remarkably successful in describing observed patterns of biodiversity." [more inside]