Science leads the way: cloning is used to create embryonic stem cells!
Ants: when should ants just wait out bad weather and when should they forage? Evolution works out an answer.
Brinicles: yes, super cold “icicles of brine” can reach below the surface of water and become a finger of death for the things that it touches:
I can see how an ancient person might see this as a “finger of god”.
Workout notes 51:04 for my hilly 5.1 mile Cornstalk course; perfect weather; this is the best time of the year to be outside. But I was heavy legged from the start.
Monday Morning Quaterbacking
Some events are all but impossible to foresee, no matter how much data you gather: (via Bruce Schneier)
The FBI and the CIA are being criticized for not keeping better track of Tamerlan Tsarnaev in the months before the Boston Marathon bombings. How could they have ignored such a dangerous person? How do we reform the intelligence community to ensure this kind of failure doesn’t happen again?
It’s an old song by now, one we heard after the 9/11 attacks in 2001 and after the Underwear Bomber’s failed attack in 2009. The problem is that connecting the dots is a bad metaphor, and focusing on it makes us more likely to implement useless reforms.
Connecting the dots in a coloring book is easy and fun. They’re right there on the page, and they’re all numbered. All you have to do is move your pencil from one dot to the next, and when you’re done, you’ve drawn a sailboat. Or a tiger. It’s so simple that 5-year-olds can do it.
But in real life, the dots can only be numbered after the fact. With the benefit of hindsight, it’s easy to draw lines from a Russian request for information to a foreign visit to some other piece of information that might have been collected.
In hindsight, we know who the bad guys are. Before the fact, there are an enormous number of potential bad guys. [...]
Piling more data onto the mix makes it harder, not easier. The best way to think of it is a needle-in-a-haystack problem; the last thing you want to do is increase the amount of hay you have to search through. The television show Person of Interest is fiction, not fact.
There’s a name for this sort of logical fallacy: hindsight bias. First explained by psychologists Daniel Kahneman and Amos Tversky, it’s surprisingly common. Since what actually happened is so obvious once it happens, we overestimate how obvious it was before it happened.
We actually misremember what we once thought, believing that we knew all along that what happened would happen. It’s a surprisingly strong tendency, one that has been observed in countless laboratory experiments and real-world examples of behavior. And it’s what all the post-Boston-Marathon bombing dot-connectors are doing.
Before we start blaming agencies for failing to stop the Boston bombers, and before we push “intelligence reforms” that will shred civil liberties without making us any safer, we need to stop seeing the past as a bunch of obvious dots that need connecting.
Schneier concludes: there will always be incidents; it is impossible to stop them all.
In statistics, one can often back fit key factors AFTER the fact and come up with a model that…well…might “make sense” but utterly fail the next time.
Politics and Economics
Paul Krugman reminds the Very Serious People that, yes, there was political bickering over the last stimulus fight, but the politics was mostly from the right wing. All too often Republicans turn economic policy debates into a morality play of sorts.
So, why hasn’t President Obama been as effective as, say, President Franklin Roosevelt? Hint: look at how Congress was made up during President Roosevelt’s time. Look at it during President Johnson’s time. The caveat is that during those eras, the president did have to compromise with southern Democrats (who are now Republicans)
Yes, some scientists behave badly and fake data.
But most don’t. Here are two good articles:
1. This is one about human brain cells which were grown in the laboratory and then put into mice...where they functioned…AS MOUSE brain cells.
A key type of human brain cell developed in the laboratory grows seamlessly when transplanted into the brains of mice, UC San Francisco researchers have discovered, raising hope that these cells might one day be used to treat people with Parkinson’s disease, epilepsy, and possibly even Alzheimer’s disease, as well as and complications of spinal cord injury such as chronic pain and spasticity.
“We think this one type of cell may be useful in treating several types of neurodevelopmental and neurodegenerative disorders in a targeted way,” said Arnold Kriegstein, MD, PhD, director of the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research at UCSF and co-lead author on the paper.
The researchers generated and transplanted a type of human nerve-cell progenitor called the medial ganglionic eminence (MGE) cell, in experiments described in the May 2 edition of Cell Stem Cell. Development of these human MGE cells within the mouse brain mimics what occurs in human development, they said.
Kriegstein sees MGE cells as a potential treatment to better control nerve circuits that become overactive in certain neurological disorders. Unlike other neural stem cells that can form many cell types — and that may potentially be less controllable as a consequence — most MGE cells are restricted to producing a type of cell called an interneuron. Interneurons integrate into the brain and provide controlled inhibition to balance the activity of nerve circuits.
Honey Bees and Pesticides
Yes, there is a bee die off and some have wondered if pesticides are to blame. Well, lots of things are to blame:
This week’s federally sponsored report about the mysterious disappearance of honeybees, known as colony collapse disorder, pointed to a complex combination of factors, ranging from parasitic mites to pesticides. But what are experts going to do about it? And what about the pesticides known as neonicotinoids, which are facing a ban in European countries?
In an email to NBC News, the Environmental Protection Agency says it’s speeding up its schedule for reviewing research on neonicotinoids and their potential effects on honeybees. It’s also fine-tuning existing regulatory practices and setting up new educational efforts to deal with colony collapse disorder. Here’s how the EPA responded to NBC News’ questions about the next steps to counter the honeybee die-off:
Are there any specific policy questions under consideration? Anything relating to the next steps in the wake of the report?
“EPA is working collaboratively with beekeepers, growers, pesticide manufacturers, seed manufacturers, equipment manufacturers, USDA and states to apply technologies to reduce pesticide dust drift, to advance best management practices, to improve enforcement guidance and to explore enhancing pesticide labeling in order to protect bees.
Specifically, EPA is:
Moving to change pesticide labels which will limit applications to protect bees and be more clear and precise.
Moving to add warning statements to each bag of pesticide-treated seed.
Issuing new enforcement guidance to federal, state and tribal enforcement officials to help them investigate bee kills.
Working with the equipment manufacturer and pesticide and seed industry and USDA to develop and apply technologies to reduce pesticide dust drift during planting seasons.
Working with USDA and other partners to promote Best Management Practices for growers and beekeeping via a new website, education and training modules for professional applicators, video, and other mechanisms
Finally, EPA is working on a range of national and international efforts to develop appropriate tests for evaluating both exposure to and effects of pesticides on insect pollinators. EPA is also requiring new lab and field studies to inform the risk assessment process to better understand pollinator risks.”
I had heavy legs this morning; this worried me a bit. It turns out that my legs were heavy from doing three sets of 5 squats with…45 pounds. OMG, my legs are weak.
So I ran outside in perfect weather; 1:01:10 for 6.4 hilly miles; 9:45 out, 8:49 back: 35:40, 12:33, 4:07, 8:49. (9:33 mpm pace) and then did some light leg exercises afterward. I’ll probably start this program and do these after my runs. My legs are too weak.
Note: last night, I did 2 miles of walking with the group and another 2 (harder) with Vickie.
Yes, the hotness is being bred out of the jalapeno pepper; it isn’t just your imagination. This is what happens when you aim for the mean.
Genes and cancer:
Via the New York Times:
Scientists have discovered that the most dangerous cancer of the uterine lining closely resembles the worst ovarian and breast cancers, providing the most telling evidence yet that cancer will increasingly be seen as a disease defined primarily by its genetic fingerprint rather than just by the organ where it originated. [...]
Over the past year, as part of this project, researchers have reported striking genetic changes in breast, colon and lung cancers that link them to other cancers. One kind of breast cancer was closely related to ovarian cancer. Colon cancers often had a genetic change found in breast cancer. And about half of squamous cell lung cancers might be attacked by drugs being developed for other cancers.
The endometrial cancer and leukemia efforts alone involved more than 100 researchers who studied close to 400 endometrial tumors and 200 leukemias. Endometrial cancer is the most common gynecological cancer in American women and strikes nearly 50,000 of them a year, killing about 8,000. Acute myeloid leukemia, the most prevalent acute adult leukemia, is diagnosed in about 14,000 Americans a year and kills about 10,000.
“This is exploring the landscape of cancer genomics,” said Dr. David P. Steensma, a leukemia researcher at the Dana-Farber Cancer Institute who was not involved with the studies. “Many developments in medicine are about treatments or tests that are only useful for a certain period of time until something better comes by. But this is something that will be useful 200 years from now. This is a landmark that will stand the test of time.”
Dr. Douglas Levine of Memorial Sloan Kettering Cancer Center, the principal investigator on the endometrial cancer study, said the group scoured the country for samples of this cancer.
The cancer has long been evaluated by pathologists who examine thin slices of endometrial tumors under a microscope and put them in one of two broad categories. But the method is not ideal. In general, one category predicts a good prognosis and tumors that could be treated with surgery and radiation, while the other holds a poorer prognosis and requires chemotherapy after surgery. But pathologists often disagree about how to classify the tumors and can find it difficult to distinguish between the two types, Dr. Levine said.
The new genetic analysis of hundreds of tumors found patterns of genetic aberrations that more precisely classify the tumors, dividing them into four distinct groups. About 10 percent of tumors that had seemed easily treated with the old type of exam now appear to be more deadly according to the genetic analysis and would require chemotherapy.
Another finding was that many endometrial cancers had a mutation in a gene that had been seen before only in colon cancers. The mutation disables a system for repairing DNA damage, resulting in 100 times more mutations than typically occur in cancer cells.
“That was a complete surprise,” Dr. Levine said.
It turned out to be good news. Endometrial cancers with the mutation had better outcomes, perhaps because the accumulating DNA damage is devastating to cancer cells.
Another surprise was that the worst endometrial tumors were so similar to the most lethal ovarian and breast cancers, raising the tantalizing possibility that the three deadly cancers might respond to the same drugs.
The bottom line: cancers shouldn’t really be classified by what organ they attack but rather by their genomes; it is this classification which should determine which treatment to use.
Why are some drugs so effective at treating cancer cells? It might depend on how the drug causes proteins to be polarized in the cell: (via University of Manchester):
Professor Daniel Davis and his team used high quality video imaging to investigate why the drug rituximab is so effective at killing cancerous B cells. It is widely used in the treatment of B cell malignancies, such as lymphoma and leukaemia – as well as in autoimmune diseases like rheumatoid arthritis.
Using high-powered laser-based microscopes, researchers made videos of the process by which rituximab binds to a diseased cell and then attracts white blood cells known as natural killer (NK) cells to attack. They discovered that rituximab tended to stick to one side of the cancer cell, forming a cap and drawing a number of proteins over to that side. It effectively created a front and back to the cell – with a cluster of protein molecules massed on one side.
But what surprised the scientists most was how this changed the effectiveness of natural killer cells in destroying these diseased cells. When the NK cell latched onto the rituximab cap on the B cell, it had an 80% success rate at killing the cell. In contrast, when the B cell lacked this cluster of proteins on one side, it was killed only 40% of the time.
Professor Davis says: “These results were really unexpected. It was only possible for us to unravel the mystery of why this drug was so effective, through the use of video microscopy. By watching what happened within the cells we could clearly identify just why rituximab is such an effective drug – because it tended to reorganise the cancerous cell and make it especially prone to being killed.”
He continues: “What our findings demonstrate is that this ability to polarise a cell by moving proteins within it should be taken into consideration when new antibodies are being tested as potential treatments for cancer cells. It appears that they can be up to twice as effective if they bind to a cell and reorganise it.”
Hurray for Science!
Woo and yoga
Someone asked me how I could like yoga and be down on “alternative (quack) medicine”. Well, there have been some rigorous studies done on yoga and it CAN be recommended for physical therapy purposes (e. g. back aches). Via our National Institute of Health.
This Tiger Frog from Ghana is a cutie:
Movies: I want to see this one:
Note: my beef with religion, at least as practiced in the west, is that too many of them require people to accept “miracles” (resurrections, parting seas, virgin births, etc.) on “faith” (sans evidence). So once you “accept” that the laws of science (naturalism) can be suspended at set times, then, well, why trust science with anything? Seriously: if there is, say, water on your basement floor and a pipe joint above that with green on the joint…well…if you didn’t SEE it drip, then maybe the water and the green just appeared because of the work of some devil or pixie? Why not…if suspensions of naturalism are allowed?
My beef is NOT with religions that don’t require acceptance of miracles.
It is my opinion that a deity/spirit/whatever that is interested in humans and human affairs makes no sense, but that is the realm of opinion.
The eye of a super-hurricane at Saturn’s north pole looks like a peaceful red rose in a fresh bouquet of pictures from NASA’s Cassini orbiter. But don’t be fooled: That rosy appearance is merely due to the false colors ascribed to infrared wavelengths.
This storm’s eye measures 1,250 miles (2,000 kilometers) in diameter, about 20 times wider than the average hurricane’s eye on Earth. The outer clouds at the hurricane’s edge are traveling at 330 mph (530 kilometers per hour), which would be off the scale on our planet. The vortex whirls inside Saturn’s mysterious hexagonal cloud pattern, and it’s not going anywhere.
How do you like this image of the moon taking from space near the earth?
Here is a picture of a solar eclipse via Scientific American:
Miloslav Druckmüller, a mathematician at the Brno University of Technology in the Czech Republic, and his colleagues were on Enewetak as the eclipse’s shadow raced toward them from the northwest at more than twice the speed of sound. This composite of 31 images from the eclipse shows the solar corona, the wispy “atmosphere” of the sun peeking out from behind the moon as well as the cratered, rayed surface of the moon itself.
Back on Earth Again
This species of fish, commonly found in China, Russia and Korea, has been found in New York. It is an invasive species.
Even more interestingly, it can actually breathe outside of water for a short period of time (days) and even hunt.
Baby octopi hatching.
Evolution About that fish to land animal transition:
In the hope of reconstructing a pivotal step in evolution — the colonization of land by fish that learned to walk and breathe air — researchers have decoded the genome of the coelacanth, a prehistoric-looking fish whose form closely resembles those seen in the fossils of 400 million years ago.
Often called a living fossil, the coelacanth (pronounced SEE-luh-canth) was long believed to have fallen extinct 70 million years ago, until a specimen was recognized in a fish market in South Africa in 1938. The coelacanth has fleshy, lobed fins that look somewhat like limbs, as does the lungfish, an air-breathing freshwater fish. The coelacanth and the lungfish have long been battling for the honor of which is closer to the ancestral fish that first used fins to walk on land and give rise to the tetrapods, meaning all the original vertebrates and their descendants, from reptiles and birds to mammals.
The decoding of the coelacanth genome, reported online Wednesday in the journal Nature, is a victory for the lungfish as the closer relative to the first tetrapod. But the coelacanth may have the last laugh because its genome — which, at 2.8 billion units of DNA, is about the same size as a human genome — is decodable, whereas the lungfish genome, a remarkable 100 billion DNA units in length, cannot be cracked with present methods. The coelacanth genome is therefore more likely to shed light on the central evolutionary question of what genetic alterations were needed to change a lobe-finned fish into the first land-dwelling tetrapod.
Another helpful preadaptation is a snippet of DNA that enhances the activity of the genes that drive the formation of limbs in the embryo. The Amemiya team focused on the enhancer DNA sequence because it occurred in the coelacanth and animals but not in ordinary fish. They then inserted the coelacanth enhancer DNA into mice.
“It lit up right away and made an almost normal limb,” said Neil Shubin, meaning that the coelacanth gene enhancer successfully encouraged the mouse genes to make a limb. Dr. Shubin, a member of the team, is a paleontologist at the University of Chicago.
Surf to the New York Times article to read more. Note: Neil Shubin wrote a couple of good books on evolution: Your Inner Fish and The Universe Within. I highly recommend both.
The not so good
See a GIF that shows, in graphic form, how each individual state’s obesity rates went up with the passing years. Read the accompanying article at Slate.
Pesticides: it is no secret that bees are dying. Part of the reason is the weather. It sure appears that part of the reason is new pesticides:
In the last half century, the domesticated honeybee population has declined by about 50 percent. In the United States, this year marks the highest losses of honeybee populations, with some of the biggest beekeepers losing more than 60 percent of their insects. But identifying the culprit has proved daunting. Pathogens, parasites, pesticides, and habitat loss are likely involved. Recently, the potential role of neonicotinoid pesticides has taken center stage, as a flurry of studies has yielded conflicting findings—and the controversy is getting political.[...]
Neonicotinoids—“neonics”—are systemic pesticides broadly used in Europe and the United States. Absorbed by plants from the soil, they eventually reach the pollen and nectar, which is ingested by bees and other insects. Last year, research demonstrated that even low levels of neonics can strongly affect bee behavior. In one study, bumblebees that were exposed to the neonic imidacloprid in the lab, then allowed to forage in the field, had sharply reduced colony growth rates and produced 85 percent fewer queens to found new colonies in the spring. In another study, more than 30 percent of free-ranging honeybees exposed to the neonic thiamethoxam got lost, failing to return to the hive.
The papers were “the straw that broke the camel’s back,” said David Goulson of the University of Stirling in the U.K., a coauthor of the bumblebee study. Previous research implicating neonics in bee decline had been done entirely in the lab. “We wanted to see what happens when the bees have to navigate over realistic distances, find patches of flowers, and bring the food back to the hive,” he said. “We found really striking results.”
So striking that the U.K.’s Department for Environment, Food and Rural Affairs (DEFRA) decided to reevaluate existing publications. But the agency concluded last month that “the risk to bee populations from neonics, as they are currently used, is low.” Moreover, DEFRA’s own research, also released last month, stated that “laboratory-based studies demonstrating sub-lethal effects on bees from neonics did not replicate realistic conditions, but extreme scenarios.”
But many researchers disagree. “We used exactly the levels found in a treated crop in the field,” said Goulson. Suggesting that the experiments linking neonics to bee decline use doses that are unrealistically high is “part of the smoke screen of lies and confusion that have been thrown up by the agrochemical industry” to defend the use of neonics, he added.
Independently, the European Commission asked the European Food Safety Authority (EFSA) to also review the existing literature on neonics, specifically Syngenta’s thiamethoxam and Bayer’s clothianidin and imidacloprid. EFSA’s report, released this January, concluded that neonics pose an unacceptable risk to bees and that they should not be used on flowering crops. This prompted the E.U.’s ban proposal and fevered campaigning from both sides of the debate.
Now I know some GMO “activists” are concerned about this. The problem here is that the GMO crop isn’t the culprit but rather the pesticides used on those crops. There really is a distinction.
Of course, this area of science is beyond my professional expertise (way beyond it) so I’ll be following this dust up closely.
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