"Science, Chance, and Emotion with Real Cosima": A Longreads profile of Cosima Herter, the show's science consultant and the inspiration for Orphan Black's character Cosima. Mostly not directly about the show, but probably contains some spoilers if you're not fully caught up through season three.
This is my vision of life. A conversation with evolutionary biologist and author Richard Dawkins. (Video and transcript)
The CRISPR Revolution [ungated: 1,2,3] - "Biologists continue to hone their tools for deleting, replacing or otherwise editing DNA and a strategy called CRISPR has quickly become one of the most popular ways to do genome engineering. Utilizing a modified bacterial protein and a RNA that guides it to a specific DNA sequence, the CRISPR system provides unprecedented control over genes in many species, including perhaps humans. This control has allowed many new types of experiments, but also raised questions about what CRISPR can enable." [more inside]
Scientists are developing ways to edit the DNA of tomorrow’s children. Should they stop before it’s too late?
Unfortunately, what textbooks, lab manuals and web pages say about these human traits is mostly wrong. Most of the common, visible human traits that are used in classrooms do NOT have a simple one-locus, two-allele, dominant vs. recessive method of inheritance. Rolling your tongue is not dominant to non-rolling, unattached earlobes are not dominant to attached, straight thumbs are not dominant to hitchhiker's thumb, etc.
"A remarkable international effort to map out the avian tree of life has revealed how birds evolved after the mass extinction that wiped out the dinosaurs into more than 10,000 species alive today. More than 200 scientists in 20 countries joined forces to create the evolutionary tree, which reveals how birds gained their colourful feathers, lost their teeth, and learned to sing songs." Via iO9.
New GM technique injects mosquitoes with a gene that results in mostly male offspring, eventually leading to a population crash. Previous efforts to tackle the disease, that kills more than 1 million people each year – most of whom are African children – have included bed nets to protect people and insecticides to kill the mosquito species most responsible for the transmission of malaria (Anopheles gambiae). The new technique by a team at Imperial College London involves injecting mosquitoes with a gene that causes the vast majority of their offspring to be male, leading to an eventual dramatic decline in population within six generations as females disappear. “You have a short-term benefit because males don’t bite humans [and transmit malaria],” Andrea Crisanti, one of the authors of the new research, which was published in the journal Nature Communications on Tuesday, told the Guardian. “But in the long term you will eventually eradicate or substantially reduce mosquitoes. This could make a substantial contribution to eradicating malaria, combined with other tools such as insecticides.”
These new mosquitoes are now set to be used in Brazil, having been approved for use by the Brazilian government with a factory for their production now opened.[more inside]
Harvard University and XVIVO have come together again (Previouslyw/ a commercial focus, Previouslierw/an Academic focus) to add to the growing series of scientific animations for BioVisions -- Harvard's multimedia lab in the department of Molecular and Cellular Biology. 'Protein Packing' strives to more accurately depict the molecular chaos in each and every cell, with proteins jittering around in what may seem like random motion. Proteins occupy roughly 40% of the cytoplasm, creating an environment that risks unintentional interaction and aggregation. Via diffusion and motor protein transport, these molecules are directed to sites where they are needed.
Much of this is no doubt inspired by the beautiful art and explained illustrations of David Goodsell, a biologist at Scripps who has been accurately portraying the crowdedness of the cellular landscape for a long time now.[more inside]
Monsanto Is Going Organic in a Quest for the Perfect Veggie - "The lettuce, peppers, and broccoli—plus a melon and an onion, with a watermelon soon to follow—aren't genetically modified at all. Monsanto created all these veggies using good old-fashioned crossbreeding, the same technology that farmers have been using to optimize crops for millennia. That doesn't mean they are low tech, exactly. Stark's division is drawing on Monsanto's accumulated scientific know-how to create vegetables that have all the advantages of genetically modified organisms without any of the Frankenfoods ick factor." [more inside]
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]
Spider webs are incredibly strong and flexible. It’s no surprise, then, that spider silk proteins may someday form durable artificial ligaments for people who have injured their knees or shoulders. Six different kinds of silk are produced by orb-web weaving spiders. These silk fibers have very different mechanical properties that are so effective they have changed very little over millions of years. How to synthetically develop these silks is one focus of Lewis’ research. The secret to producing large quantities of spider silk is to use “factories” designed to manufacture spider silk proteins that are easily scale-able and efficient. Lewis uses transgenic goats, E.coli bacteria, transgenic alfalfa and transgenic silk worms to produce the spider silk proteins used to create spider silk. Spider silk is 100 times stronger than natural ligaments and 10 times stronger than natural tendons; it is stronger than Kevlar and more elastic than nylon.
A 6min brief on the work being done in Laramie, WY whereby spider silk is being spun from goat milk. SPIDERGOATS[more inside]
"During the most recent ice age, milk was essentially a toxin to adults because — unlike children — they could not produce the lactase enzyme required to break down lactose, the main sugar in milk. But as farming started to replace hunting and gathering in the Middle East around 11,000 years ago, cattle herders learned how to reduce lactose in dairy products to tolerable levels by fermenting milk to make cheese or yogurt. Several thousand years later, a genetic mutation spread through Europe that gave people the ability to produce lactase — and drink milk — throughout their lives. That adaptation opened up a rich new source of nutrition that could have sustained communities when harvests failed." - The Milk Revolution - how a single mutation expanded (some) of humanity's diet. (Nature.com)
The disease that sours oranges and leaves them half green, already ravaging citrus crops across the world, had reached the state’s storied groves. To slow the spread of the bacterium that causes the scourge, they chopped down hundreds of thousands of infected trees and sprayed an expanding array of pesticides on the winged insect that carries it. But the contagion could not be contained.They would have to alter the orange’s DNA — with a gene from a different species. (SLNYT)
With a precipitous decline in Florida’s harvest predicted within the decade, the only chance left to save it, Mr. Kress believed, was one that his industry and others had long avoided for fear of consumer rejection.
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]
Extinction got you down? Try de-extinction! Our species has played a role in the extinction of ... many other species. But now some scientists are proposing a radical turn of the tables: Bringing lost species back from the dead. How to Resurrect Lost Species. [more inside]
"Older parenthood will upend American society." "Is waiting to have kids a big mistake?" "Why do women believe they can delay children for so long?" "Older men are more likely than young ones to father a child who develops autism or schizophrenia, because of random mutations that become more numerous with advancing paternal age."
What we currently call breast cancer should be thought of as 10 completely separate diseases, according to an international study which has been described as a "landmark". The categories could improve treatment by tailoring drugs for a patient's exact type of breast cancer and help predict survival more accurately. The study in Nature analysed breast cancers from 2,000 women [Abstract] . It will take at least three years for the findings to be used in hospitals. [more inside]
Hacking the President’s DNA. "The U.S. government is surreptitiously collecting the DNA of world leaders, and is reportedly protecting that of Barack Obama. Decoded, these genetic blueprints could provide compromising information. In the not-too-distant future, they may provide something more as well—the basis for the creation of personalized bioweapons that could take down a president and leave no trace."
When looking for inspiration, most songwriters to go well-used emotional wells – triumph or loss, love or heartbreak. But Peter Larsen, a biologist at Argonne National Laboratory, looked to the microbes of the English Channel. He used seven years’ worth of genetic and environmental data, converting geochemical and microbial abundance measurements into notes, beats, and chords.
The Fat Trap (NYT pop review): Overweight individuals in Western nations (and, increasingly, beyond) face interpersonal and institutional stigma for their bodies*. Oftentimes, these stigmas are predicated on the belief that being overweight is a moral failure, that being overweight is usually a result of laziness, decadence, and/or characterlogical poor impulse control. However, an emerging consensus among obesity researchers points toward strong, common physiological and individual genetic factors as causative for heightened BMIs in the modern world and the general failure of dieting to produce BMI outcomes. A recent study in the New England Journal of Medicine (paywalled) adds to this body of evidence, suggesting that chemical messengers held to contribute to altered "efficient" metabolism and increased hunger in the wake of low-calorie dieting are (on average) significantly elevated up to a full year (if not longer) following a substantial drop in weight from dieting.> [more inside]
How can we better understand the interplay of nature and nurture in determining our personalities, behavior, and vulnerability to disease? Perhaps we should be looking at identical twins. (National Geographic January 2012 cover story) [more inside]
After decades of breeding, the complexity of cat color genetics is quite well understood. Genes which control pigmentation, hair length, color dilution, banding (agouti), white fur (dominant, spotting, or albino, sometimes linked with deafness), tabby patterns, and more combine to create a wide spectrum of possibilities. Specific traits such as white gloving among Birman cats and the amber color found only in Norwegian Forest Cats (which comes from a single female born in 1981!) have also been isolated and studied, and can be affordably tested for. On top of all that, fur color is epigenetic as well as genetic, and sometimes responds to the cat's environment. If you clone a calico cat, you get a kitten which doesn't have a similar coat due to X-inactivation, and pointed cats (such as Burmese, Siamese, and Tonkinese) have temperature-sensitive coloration. [more inside]
NASA Proves Building Blocks Of DNA Come From Space. "NASA researchers studying meteorites have found that they contain several of the components needed to make DNA on Earth. The discovery provides support for the idea that the building blocks for DNA were likely created in space, and carried to Earth on objects, like meteorites, that crashed into the planet’s surface. According to the theory, the ready-made DNA parts could have then assembled under Earth’s early conditions to create the first DNA."
Larry Gonick is a veteran American cartoonist best known for his delightful comic-book guides to science and history, many of which have previews online. Chief among them is his long-running Cartoon History of the Universe (later The Cartoon History of the Modern World), a sprawling multi-volume opus documenting everything from the Big Bang to the Bush administration. Published over the course of three decades, it takes a truly global view -- its time-traveling Professor thoroughly explores not only familiar topics like Rome and World War II but the oft-neglected stories of Asia and Africa, blending caricature and myth with careful scholarship (cited by fun illustrated bibliographies) and tackling even the most obscure events with intelligence and wit. This savvy satire carried over to Gonick's Zinn-by-way-of-Pogo chronicle The Cartoon History of the United States, along with a bevy of Cartoon Guides to other topics, including Genetics, Computer Science, Chemistry, Physics, Statistics, The Environment, and (yes!) Sex. Gonick has also maintained a few sideprojects, such as a webcomic look at Chinese invention, assorted math comics (previously), the Muse magazine mainstay Kokopelli & Co. (featuring the shenanigans of his "New Muses"), and more. See also these lengthy interview snippets, linked previously. Want more? Amazon links to the complete oeuvre inside! [more inside]
Allen Human Brain Atlas - Brain Explorer 2 is a desktop software application for viewing the human brain anatomy and gene expression data in 3D. "Until now, a definitive map of the human brain at this level of detail simply hasn't existed," said Allan Jones, the nonprofit institute's chief executive. "For the first time, we have generated a comprehensive map of the brain that includes the underlying biochemistry." | Functional Neuroanatomy | 10 Great Sites for Reviewing Brain Anatomy | Harvard Brain Atlas. Bonus link: Brain massage with cosmic energy application in Pushkar, India. [more inside]
Could the three established domains of life - eukaryotes, bacteria and archaea - be joined by a fourth?
Epidemiology: Study of a lifetime. "In 1946, scientists started tracking thousands of British children born during one cold March week. On their 65th birthday, the study members find themselves more scientifically valuable than ever before." [more inside]
In the 1940s Barbara McClintock discovered the remarkable phenomenon of mobile genetic elements, or transposons: parasitic DNA that makes up a significant fraction of the human genome. (Here is a video segment about McClintock: Part 1 & 2.) The discovery remains highly important: we now know that transposons play a role in driving genome evolution. Where do they come from? A compelling hypothesis is that some evolved from viruses.
Now a marine biology group at UBC has found a virus whose closest genetic relative is a type of transposon. (The paywalled paper's abstract is here.) But that is not even the interesting part. [more inside]
Now a marine biology group at UBC has found a virus whose closest genetic relative is a type of transposon. (The paywalled paper's abstract is here.) But that is not even the interesting part. [more inside]
The Price of Altruism - George Price, a (troubled) father of group selection thru his discovery of the eponymous Price Equation, has a rather interesting biography... [more inside]
Invasive amniocentesis and chorionic villi sampling (CVS) tests are commonly used to determine the chromosomal, structural and genetic abnormalities in fetuses. But could they eventually become obsolete? A Chinese study has found that a complete copy of the fetal genome exists in the mother's blood, suggesting many prenatal diagnoses could potentially be performed noninvasively. [more inside]
An Icelandic company called deCODE genetics (previously) has found evidence, though not conclusive, that an unknown American woman traveled to Iceland, possibly against her will, as early the year 1000 but not later than 1700. She had offspring in Iceland with natives. 80 of her descendants are still extant in that country. This finding has been announced in a pre-print online publication of the American Journal of Physical Anthropology. The work involved explorations of mitochondrial DNA, which are frequently employed to examine humans' centuries-old lineages. One surprising result is that this lineage does not seem to line up with previously known Native American genetic markers, but the authors believe that the explanation above is "[more] likely" than this common ancestor being European or Asian. (Via Daily Mail.) [more inside]
Our minds boggle at how the wolf could become the chihuahua, the Saint Bernard, the poodle and the Komondor. Artificial selection was likewise responsible for transforming the humble wild mustard plant Brassica oleracea into cabbage, broccoli, Brussels sprouts and the breathtaking fractal Romanesco, all in the span of a few centuries. [more inside]
New Adventures in Recent Evolution - In the last few years, biologists peering into the human genome have found evidence of recent natural selection. cf. Social Darwinism: 21st century edition [previously] (via ip) [more inside]
Tibetans May Be Fastest Evolutionary Adapters Ever. "A group of scientists in China, Denmark and the U.S. recently documented the fastest genetic change observed in humans. According to their findings, Tibetan adaption to high altitude might have taken just 3,000 years. That's a flash, in terms of evolutionary time, but it's one that's in dispute."
Followup to this post: A US District Court has ruled that Myriad Genetic's patents on breast cancer genes BRCA1 and BRCA2, which allow them to hold exclusive rights to a widely used genetic test for inherited breast and ovarian cancer susceptibility, are invalid. Genomics Law Report analyzes the ruling in two posts. The decision is likely to be challenged in a legal appeal — but if upheld, it could have huge implications for the biotechnology industry. [more inside]
"People who use sows to hunt for truffles often find it hard to prevent a sex-crazed animal from eating the truffle she has found and may lose fingers in the attempt." (via) The NYT on decoding the genome of the Périgord Black Truffle . Attempts to make truffles cheaper and more accessible in the past have been met with some resistance.
A new study suggests that humanity's sense of fair play and kindness towards strangers is determined by culture, not genetics. Speculation: the finding may be directly related to the rise of religion in human history, as well as more complex economies. (Via). [more inside]
We may soon be able to clone Neanderthals. But should we? An essay from Archaeology Magazine examines the ethical, scientific and legal ramifications. (Via Heather Pringle's Time Machine blog, where essay author Zach Zorich posted a reply and elicited a response.) [more inside]
The orchid hypothesis “profoundly recasts the way we think about human [genetic] frailty.”
grumblebee's post about cell size and scale the other day was quite fascinating. Pulling back to the home for that site, the Genetic Science Learning Center at the University of Utah delivers educational materials on genetics, bio-science and health topics ranging from stem cells to gene therapy, and from epigenetics to heredity. Explore the neurobiology of normal and addicted brains and the genetic contribution to this chronic disease.
The Home Office, the UK government department responsible for immigration control, has initiated a program to test the DNA from of potential asylum seekers in an attempt to confirm their true nationalities. The initial program is a six-month pilot limited to claimants arriving from the Horn of Africa. The program, currently using forensic samples provided on a voluntary basis, could potentially expand to other nationalities if successful. The Home Office spokeswoman said ancestral DNA testing would not be used alone but would be combined with language analysis, investigative interviewing techniques and other recognized forensic disciplines, but many are decrying the "deeply flawed" program, from refugee support groups to scientists in the genetic forensics fields (via). [more inside]
"In Massachusetts, a young woman makes genetically modified E. coli in a closet she converted into a home lab. A part-time DJ in Berkeley, Calif., works in his attic to cultivate viruses extracted from sewage. In Seattle, a grad-school dropout wants to breed algae in a personal biology lab. These hobbyists represent a growing strain of geekdom known as biohacking, in which do-it-yourselfers tinker with the building blocks of life in the comfort of their own homes." They might be discovering cures for diseases or developing new biofuels, but are their experiments too risky? Via. [more inside]
On behalf of medical organizations, universities, & individual patients, pathologists and genetics researchers, the ACLU has filed a lawsuit against Utah-based Myriad Genetics and the US Patent and Trademark Office. Myriad holds the US patents to the BRCA1 and BRCA2 genes, associated with hereditary causes of breast and ovarian cancers. Their patents guarantee the company the right to prevent anyone else from testing or studying those genes, which the ACLU says is unconstitutional and inhibits researchers from finding treatments and cures. [more inside]
My Genome, My Self: Steven Pinker considers what we can expect from personal genomics. Searching for Intelligence in Our Genes: Carl Zimmer looks at the hunt to learn about the role of genes in intelligence.
Now: The Rest of the Genome. "Only 1 percent of the genome is made up of classic genes. Scientists are exploring the other 99 percent and uncovering new secrets and new questions."