Dictyostelium discoideum - dicty to its friends - has long been recognized as the world's most fascinating slime mold. A (previously) has a good introduction from a decade ago. You might be fascinated by their life cycle, which goes from individual cells, to animal-like slug, to plant-like fruiting body. You might be fascinated by their starvation-prompted altruism, in which most cells give up their lives so that a few can reproduce, and cheaters are punished. You might be fascinated by the way they farm and protect their crops. (Or maybe the farmed bacteria are farming them; it's hard to tell.) Or you might be fascinated by a brand new study about the DNA nets they use to trap and kill pathogens.
In the wake of the sequencing of the human genome in the early 2000s, genome pioneers and social scientists alike called for an end to the use of race as a variable in genetic research. Unfortunately, by some measures, the use of race as a biological category has increased in the postgenomic age. Although inconsistent definition and use has been a chief problem with the race concept, it has historically been used as a taxonomic categorization based on common hereditary traits (such as skin color) to elucidate the relationship between our ancestry and our genes. We believe the use of biological concepts of race in human genetic research—so disputed and so mired in confusion—is problematic at best and harmful at worst. It is time for biologists to find a better way. - An editorial in Science exploring the conundrum facing genomic researchers where race is both fundamentally flawed as a scientific model and violently dangerous but still the only consistent lens through which study participants understand the information they have about their own connection to human diversity [more inside]
Humans 2.0 - "With CRISPR, scientists can change, delete, and replace genes in any animal, including us. Working mostly with mice, researchers have already deployed the tool to correct the genetic errors responsible for sickle-cell anemia, muscular dystrophy, and the fundamental defect associated with cystic fibrosis. One group has replaced a mutation that causes cataracts; another has destroyed receptors that H.I.V. uses to infiltrate our immune system." [more inside]
Since it folds in three dimensions, we could store all of the world’s current data—everyone’s photos, every Facebook status update, all of Wikipedia, everything—using less than an ounce of DNA. And, with its propensity to replicate given the right conditions, millions of copies of DNA can be made in the lab in just a few hours. Such favorable traits make DNA an ideal candidate for storing lots of informations, for a long time, in a small space.But how stable is DNA? The Reed-Solomon method, long used to error-check data transmission and duplication, is now being explored as an adjunct to the long-term archiving of information encoded in DNA. A post by Alex Riley at the PBS Science blog NOVA/NEXT.
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]
"No one really wants to admit I exist," says co-discoverer of the DNA molecule, James Watson, who after years of shunning over controversial statements is auctioning his 1962 Nobel Prize medal this Thursday to help pay bills and buy some artwork. Online bidding is an option.
Clones Are People Too: The Science and Science Fiction of BBC America’s Orphan Black. BBC America's science fiction series Orphan Black has returned for a second season, with Tatiana Maslany reprising her extraordinary performance playing half a dozen different clone characters. Meanwhile, in the real world, scientists have created cloned embryonic stem cells from the DNA of two adult humans. [Previously]
"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]
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.
The Hidden Life Of the Cell (57:24) There is a battle playing out inside your body right now. It started billions of years ago and it is still being fought in every one of us every minute of every day. It is the story of a viral infection - the battle for the cell. This film reveals the exquisite machinery of the human cell system from within the inner world of the cell itself - from the frenetic membrane surface that acts as a security system for everything passing in and out of the cell, the dynamic highways that transport cargo across the cell and the remarkable turbines that power the whole cellular world to the amazing nucleus housing DNA and the construction of thousands of different proteins all with unique tasks. The virus intends to commandeer this system to one selfish end: to make more viruses. And they will stop at nothing to achieve their goal. Exploring the very latest ideas about the evolution of life on earth and the bio-chemical processes at the heart of every one of us, and revealing a world smaller than it is possible to comprehend, in a story large enough to fill the biggest imaginations.
You may be familiar with molecular movies from my two previous megaposts collecting them, but this extended documentary uses original animation that is collected into a coherent educational narrative and is just so fucking gorgeous. Enjoy.[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."
The Genome Compiler is an IDE for DNA projects for all you DIYbio enthusiasts. Previously. Previously.
With the possible exception of the Nobel awards, physicists seem to get all the press these days, whether they're doing quantum level work at the LHC, or cosmology via the latest satellite data. Biologists, not so much. It's too bad, because Richard Lenski is running one of the great evolutionary experiments of our time, and it's producing interesting results. [more inside]
In 2001, we learned the sequence of our genome; now, we have amassed a vast amount of knowledge about what those sequences actually do. Yesterday, the data from the ENCODE project went live. [more inside]
The quest for the $500 home molecular biology laboratory Molecular diagnostics and molecular biology in general are becoming more pervasive every day in a range of applications. For some time there have been attempts to build an affordable diy machine to explore this fascinating science. OpenPCR (polymerase chain reaction) received quite a bit of publicity with their $599 system. Each of these have had problems and were not quite suitable for students. Here is an attempt to get the price even lower and to simply the construction process. Previously on Metafilter
Could the three established domains of life - eukaryotes, bacteria and archaea - be joined by a fourth?
"The ability to design and create new forms of life marks a turning-point in the history of our species and our planet." - Freeman Dyson, on the J.C. Venter Institute's creation of a cell controlled by a synthetic genome. We are now in the business of engineering life.
Neandertals are the closest ancestral relatives to modern humans. Today, Nature published a special report on the Neandertal genome, for which a draft sequencing of three billion nucleotides has been completed. This high-throughput sequencing project shows how the genetic relationship between Neandertals and modern Europeans and Asians suggests localized interbreeding between the two species roughly 40-80,000 years ago, complicating the common "out-of-Africa" story of how modern humans originated. Additional research extends this low-coverage, first-pass sequencing with a microarray approach that uncovers specific differences between the human and Neandertal genomes.
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]
An Outsider's View "Over the past fifty years, factions of biologists have had a complex relationship. Some scientists have continued to carry out relatively traditional natural history work, with little need to delve into molecular (or computational) biology. Others have given little attention to natural history, focusing their efforts instead on deciphering the complexities of a membrane channel, or building new algorithms for identifying open reading frames. In some cases, biologists have bridged this divide, and the result has been a fruitful collaboration. But in other cases—such as the DNA studies on whales and hippos—one group moves into the other's traditional territory, sparking new conflict."[via]
DNA Not The Same In Every Cell Of Body. "...calls into question one of the most basic assumptions of human genetics: that when it comes to DNA, every cell in the body is essentially identical to every other cell... if it turns out that blood and tissue cells do not match genetically, these ambitious and expensive genome-wide association studies may prove to have been essentially flawed from the outset"
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."
U.S. military practices genetic discrimination in denying benefits. "Those medically discharged with genetic diseases are left without disability or retirement benefits. Some are fighting back."
View the Milky Way at 10 million light years from the Earth. Then move through space towards the Earth in successive orders of magnitude until you reach a tall oak tree just outside the buildings of the National High Magnetic Field Laboratory in Tallahassee, Florida. After that, begin to move from the actual size of a leaf into a microscopic world that reveals leaf cell walls, the cell nucleus, chromatin, DNA and finally, into the subatomic universe of electrons and protons.