Stars' rants: Should they matter to us? Monroe Evening News You can do interviews to tell us how you're at peace now and maybe even give us regular people with nonpiercing eyes advice on spiritual enlightenment. ... |
SPIRITUAL HUNGER Our Quest for Psycho-Spiritual Freedom, Authentic Sacredness … – OpEdNews
SPIRITUAL HUNGER Our Quest for Psycho-Spiritual Freedom, Authentic Sacredness ... OpEdNews The second passkey is self-examination and self-examination is the main ingredient of enlightenment. Regardless of the many definitions of enlightenment ... |
Moon Over Oregon
Moon over Oregon. Credit: Greg Lyons
Here is an image taken by one of our readers, Greg Lyons, of the moon as seen presumably in his back yard.
This is obviously a very good image, guess what? He took this with a little Kodak C875 camera! This proves you can take some pretty remarkable images of the night sky with affordable equipment you may already own. He used the manual mode in the camera and a tripod.
Greg has sent me a few photos, in this one he caught the planetary lineup of Venus, Mars, Saturn and of course the moon.
I need to find my little tripod! He gave me some of the settings he used and I want to try them out with my little Cannon 520.
I really-really like this image and made it into various sized wallpapers and it looks great on my screen. I did not modify the image at all, other than changing the size to reduce the file size.
Thank you very much Greg for all the great pictures. Hopefully this will inspire more to get out there and give it a try, I’m gonna – right after I get done dodging the thunderstorms I’m getting this afternoon.
Here’s some wallpaper sized versions:
NCBI ROFL: Ever wonder how much electricity your penis can take? | Discoblog
Determination of Human Penile Electrical Resistance and Implication on Safety for Electrosurgery of Penis.
“Electrosurgery has been a surgical application since the late 19th century. Although many urologists take this daily application for granted, the effects of electrical treatment on penile nerves and vessels have not been well documented. Aim. To investigate the electrical characteristics of the penis and erectile tissues and to discover the potential hazards of electrosurgery on the penis. Methods. Measurement of the electrical characteristics of three human penises in order to create models to analyze the effect of electricity on penile nerves and vessels. Main Outcome Measures. Electrical resistivity of the penile shaft, electrical current density, and electric field strength on penile nerves and vessels, proportion of generated heat on the penis and electrical current density of the electrosurgery return electrode. Results. Electrical resistivity (rho) of the penile shaft is 127.14 Omega . cm at 500 kHz. Electrical current density (J) of the penis shaft is 71.06 mA/cm(2), nerve (60.23 mA/cm(2)), vessel (67.93 mA/cm(2)), and return electrode (2.11 mA/cm(2)). Electrical field strength (E) of the whole penis shaft is 9.03 volt/cm. The proportion of generated heat on the penis is four times as much as on other body parts of the circuit. Conclusions. Potential and subclinical injury to erectile tissue caused by electrosurgery on the penis cannot be underestimated. The injury mechanism can be attributed to a thermal (electrical current) effect and a nonthermal (mainly electrical field) effect. Ways to avoid the electrosurgical injury are: using less power (W)/electrical field and less time, biopolar electrosurgery confining the injured area, ligation to achieve hemostasis, and new laser technologies.”
Related content:
Discoblog: NCBI ROFL: Civilian gunshot injuries of the penis: the Miami experience.
Discoblog: NCBI ROFL: Bonus double feature: Acute management of the zipper-entrapped penis.
Discoblog: NCBI ROFL: Fine-touch pressure thresholds in the adult penis.
WTF is NCBI ROFL? Read our FAQ!
Photos From the Gulf’s Great Sea Turtle Relocation | 80beats
In early July we brought you news of the Great Sea Turtle Relocation–an ambitious plan dreamed up by conservationists to scoop up some 70,000 sea turtle eggs from Gulf Coast beaches, to prevent the hatchlings from crawling straight into oil-fouled waters. The U.S. Fish and Wildlife Service noted that the plan carried considerable risks to the unborn turtles, but said it was the best chance of preventing the die-off an entire generation.
Now the update: Over the past week, the plan has gone into action, and baby turtles are now swimming free in the Atlantic Ocean. But some experts question whether the launched turtles have a chance.
On Alabama and Florida beaches workers are carefully digging up nests, marking the eggs with “this end up” symbols, and packing them in styrofoam coolers for the truck ride to a Kennedy Space Center warehouse. The eggs belong mostly to threatened loggerheads, along with some endangered green, leatherback, and Kemp’s ridley turtles.
Check out a photo gallery of the turtle rearing and release operations after the jump.
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The first batch of turtles gave the project managers cause for optimism, according to Jane A. Provancha, a contractor working in the warehouse:
On Saturday and Monday evenings, she released 56 baby turtles into the dark waters of the Atlantic and watched them swim away. Turtles from about 83% of the eggs in the first nest have emerged and swum out to sea, she said. “They looked really great. They were a little slow at first, but then they started moving around,” she said. [Los Angeles Times]
But some experts are worried that these newly released hatchlings will run into navigation trouble. Marine biologist Ken Lohmann notes that these baby turtles typically take their first swims in the Gulf of Mexico, but instead they’re being released into the Atlantic from Florida’s east coast. That may be enough to scramble their navigational systems and interfere with their normal migratory routes.
His view is backed up by evidence that suggests turtles are programmed from birth to follow a specific migratory path once in water. Indeed, turtles from different nesting sites seem to inherit different sets of navigational instructions. And that means a turtle born in the Gulf but displaced to the Atlantic coast may follow the wrong path out to the open ocean, Lohmann says. [New Scientist]
Recent posts on the BP oil spill:
80beats: BP’s Cap Has Stopped the Oil Leak–for Now
80beats: Gulf Coast Turtle News: No More Fiery Death; Relocating 70,000 Eggs
80beats: Next from X Prize: An Award for Cleaning up BP’s Oil Spill?
80beats: Obama’s Speech on the Oil Spill: What Do You Think of His “Battle Plan”?
80beats: BP to Kevin Costner: We’ll Take 32 of Your Oil Clean-up Machines
Images: NASA
Steve Jobs: There’s No iPhone “Antenna-Gate,” But Here’s a Free Case | 80beats
Earlier today on Apple’s Cupertino campus, Steve Jobs held a press conference regarding the iPhone 4 reception saga, which he said is not “antenna-gate.” The overall gist: Jobs says the iPhone 4’s reception isn’t perfect, but not any worse than other phone’s, and Apple will give out a free “bumper” case to iPhone 4 phone buyers.
The cases are meant to reduce the dropped reception problem that can occur if a person’s hand covers a crucial bit of the antenna. The bumpers will be free until September 30th, and buyers can return their phones for a refund if still unhappy.
We’ve rounded up opinions of Jobs’ conference, which you can catch a video of through Apple’s site, here.
Jobs started the meeting by showing other phones (BlackBerry Bold, Droid Eris…) also dropping signal strength depending on how they’re held. But some think that comparing the iPhone 4 to other devices isn’t a valid excuse when you have a brand built on exclusivity (and expense).
It didn’t matter whether Jobs thought complaints about the reception problem were overblown. Nor did it matter if other phones had similar problems–if you set yourself up as a premium brand generating fanatical loyalty, the last thing you want to do is say “but others have the same glitch.” [Computer World]
Others think Jobs kept his cool in a situation that might have had some executives pressing the recall button, a reflex that will at least make investors happy.
Journalists are howling. Customers are complaining. Late night comics are cracking wise. Drama, however is Apple Chief Steve Jobs’ thing. . . . The master showman didn’t flub any of his lines Friday as he sought to reframe the discussion about problems with the new iPhone’s antenna, which wraps along the outside edge of the phone to form an integral part of the smart phone’s shell. [Forbes]
If the phone is no worse than others, then why the apparent reception debacle? Jobs implies that it’s a matter of perception; in part, the phone has gotten too much bad press and not enough cases (which improve reception). But if the dropped call ratio is in fact worse than the previous 3G model (Job says less than 1 more dropped call per 100), some argue, you can’t blame the phone’s problems all on image.
Like Mark Twain’s death, reports of the iPhone 4’s reception problems have been greatly exaggerated, Jobs insisted. A mere 0.55 per cent of iPhone 4 users have called AppleCare about reception problems, he said. Only 1.7 per cent have returned their phones, under a third of the six per cent returns of its predecessor, the iPhone 3GS. That 1.7 per cent, by the way, apparently didn’t include the unfortunate phone of TV talk-show [the View] host Whoopi Goldberg, who instead “murdered” her malfunctioning iPhone 4, according to CNET. [The Register]
Though originally some customers called for nothing short of a recall, Andy Ihnatko at the Chicago Sun-Times empathizes with Apple, defending the device which he happily purchased after testing, despite knowing that it “sporadically” lost its reception.
It’s a demonstrable and repeatable problem, but mostly it’s being experienced by people who are actively trying to make it happen … folks like me, who write about technology and review new hardware. “There’s yet to be any video of a baby dolphin coated in spilled iPhone 4’s, adorably drowning,” I said in a morning blog post. So in the end, it was the trickiest kind of PR problem imaginable: the kind in which the company can do way more damage by responding poorly than they might by simply letting events take their course. A massive recall of the iPhone 4 would have heaved the phone on the scrapheap next to the G4 Cube, a desktop Mac design that was just as innovative as the new iPhone, but which was never heard from again. [Chicago Sun-Times]
Do you have an iPhone 4? Did you see Jobs’ speech? What are your thoughts on Apple’s response?
Related content:
80beats: The iPhone 4: Snappy Visuals and Shiny New Video Chats
Discoblog: Lefties Cry Discrimination Over iPhone’s Faulty Antenna
Discoblog: Shoot it, Blend it, Burn it: 3 Ways to Destroy Your iPhone 4
Bad Astronomy: Resolving the iPhone Resolution
Image: flickr / William Hook
Phil Plait on Point of Inquiry | The Intersection
The show just went up, and he's my latest guest. Here's the write-up:
Our guest this week needs no introduction for those in the skeptical and secular world. After all, he has a frakkin' asteroid named after him.
He’s Phil Plait—science blogger extraordinaire for Discover Blogs, where he authors “Bad Astronomy.” Recently, Plait joined Point of Inquiry for a wide ranging conversation about standing eggs on end, Apollo moon landing deniers, wacky yet endearing Hollywood bad science, something called “spaghettification," ... and the end of the world.
Phil Plait is a skeptic and an astronomer, and former president of the James Randi Educational Foundation. He lectures widely across the country and is the author of two books, most recently Death from the Skies: These Are the Ways the World Will End.
Check the show out here, and stream it here....
Humans, Fish, & Flies Share a 600-Million-Year-Old Sperm Gene | 80beats
Dear male reader: Just so you know, your sperm isn’t that different from a sea anemone’s.
Sperm is so vital, a new study in PLoS Genetics found, that one of the genes responsible for it hasn’t changed in 600 million years. Insects, humans, marine invertebrates, other mammals, even fish—the males of all these creatures share a common sperm gene that dates back to before all those animals diverged all those millions of years ago, according to the team led by Eugene Xu.
From an evolutionary point of view, that longevity is simply stunning.
“It’s really surprising because sperm production gets pounded by natural selection,” Xu said. “It tends to change due to strong selective pressures for sperm-specific genes to evolve. There is extra pressure to be a super male to improve reproductive success. This is the one sex-specific element that didn’t change across species. This must be so important that it can’t change” [MSNBC].
The gene in question in called BOULE. Xu and colleagues went hunting for versions of it in all those creatures listed above, trying to find out whether sperm evolved multiple times, or rather arose once in a long-ago ancestor. When they found some form of the gene in all of them, even sea anemones, they had their answer.
Next, the researchers tested mice to be sure the gene was in charge of just sperm production, not more general cell processes. Sure enough, the protein encoded by the gene was found only in mouse testes. And if the BOULE gene was disrupted, otherwise healthy mice didn’t produce sperm [Science News].
That part of the find could be crucial; beyond explaining how our “sex-specific elements” evolved, it could have practical applications, too.
BOULE is the only gene known to function only for the production of sperm, said Xu. This makes it an ideal target for designing a male contraceptive drug or agents that halt the reproduction of infectious parasites or the carriers of germs, he said, because knocking it out wouldn’t harm other bodily processes [Wired.com].
Related Content:
80beats: New Contraceptive Wins Gates Money: Blasting Testicles with Ultrasound
80beats: Revealed: The Secret of the Sperm’s Wild Dash to the Egg
Discoblog: Warning All Male Competitive Cyclists: Less Than 5% of Your Sperm May Be Normal
Image: iStockphoto
Insane Clown Posse Dissed Scientists; Lab-Coated Geeks Strike Back | Discoblog
In 2009, the hip hop duo Insane Clown Posse released the song “Miracles.” The song asks how certain things work: stars, rainbows, inherited genetic traits, magnets–and other stuff to “shock your eyelids.” The exact lyrics are a bit off-color for this blog, but the two singing clowns certainly ask some valid questions. Unfortunately, the song attributes these scientific happenings to “magic” noting, “I don’t wanna talk to a scientist.”
For members of the somewhat nontraditional science outreach group Nosebridge, that simply wouldn’t do. Surely, Insane Clown Posse fans–called juggalos–wanted to know the real answer to how a “[expletive] magnet” works! So earlier this summer, the Nosebridge crew brought their posters to a crowd of fans waiting to go into a concert. Surely those fans would be interested in understanding the science behind apparent miracles like magnetism.
The videos and other pictures, available on the blog Laughing Squid, show the real magic that unfolded that evening. The Nosebridge team reports that many juggalos were very receptive to learning, for example, why a solar eclipse happens, but eventually San Francisco police had to step in to make sure things didn’t get too physical.
Related content:
Discoblog: Evolution, With Dope Rhymes and a Funky Hip-Hop Beat
Discoblog: Sneak Preview of Darwin: The Musical
Discoblog: Worst (and Best) Science Rap of the Week
Discoblog: Buzz Aldrin, Rapper?
Image: flickr /michiexile
More Jews, fewer markers | Gene Expression
At around the same time that the two big Jewish genetics papers came out, there was another one in BMC Genetics which I had overlooked. It’s open access so you can read the whole thing, but seems like they used 32 STR’s as markers. Their primary finding about Jewish populations was that there was a north vs. south distinction, illustrated in this map:
Grant me some Bacon | Bad Astronomy
Speaking of Brea Grant…
Many years ago, I wasn’t a huge fan of Kevin Bacon until I saw "The Big Picture", and then "Tremors", and so I finally decided he cracks me up and is cool.
Then someone told me about the Oracle of Bacon, where you enter an actor’s name and get their Bacon Number; their degree of separation from Kevin Bacon (if you don’t know what this is then I won’t explain because you are hopelessly unhip).
I put my name into The Oracle and it came up with nothing. Drat. But wait a sec…
I’m in this video with Brea Grant (see below), who was in "Halloween II" with Octavia Spencer, who was in "Beauty Shop" with… Kevin Bacon.
I have a Bacon Number of 3!
OK, not officially, since my video with Brea probably doesn’t count. So I looked again at The Oracle, and realized it was only searching movies. As it happens I’ve done a few documentaries which are listed on IMDB, so I hit the "allow all" button on the Oracle which includes documentaries…
Aha! It still works! It doesn’t include Brea, sadly, but I suspect Aretha is pretty cool, too.
Hey, cool! I still have a Bacon number of 3.
Still, since both methods are a little dodgy, I think it’s fair to fudge it a bit. Let’s just say I have a Bacon Number of a tad more than three… say, 3.1415.
Mmmmm. Bacon Pi.
Related posts:
- Brea Grant rocks Bad Astronomy!
- Grant me a geek
How to Speak a Language That Your Robot Will Understand | Discoblog
Biwu English kokafo wapisi? That’s “Will English kick the bucket?” in a new language called ROILA (Robert Interaction Language). Perhaps it’s an apt question of my mother tongue. Under development by a group of researchers at Eindhoven University of Technology in the Netherlands, ROILA is a language made specifically for human-robot communication.
The language hopes to make up for speech-recognition software’s shortcomings by modifying human language to be more comprehensible for machines. Using an algorithm, it takes parts of natural and artificial languages and combines them to make sure that no two words sound too similar.
But a quick look at its grammar shows that ROILA goes a step further: when it comes to sentences, ROILA has cut out all the patap (English: the crazy). Irregular verbs? No. Most gendered words? No. Most punctuation? No. From the grammar website:
Every sentence will conclude with a full stop: “.” Question marks can be used in sentences where a question is asked. We do not support commas, apostrophes and quotation marks.
In a world where awkward computer-communication quirks easily turn into hip sentence stylings, as in @people #hashTagsAreUgly, one could see a language named with an acronym getting some real traction.
Perhaps I’m overreacting. As Popular Science duly notes, there have been similar computer-required human languages, like Palm Inc.’s Graffiti for hand-held devices to aid in stylus writing; most people I know aren’t making their Ts look like 7s. There is also safety in the fact that ROILA is not yet a spoken language.
Something should also be said for ROILA’s simplicity. “What color is the museum?” becoming “Biwu wekepo buse kulil bubas?” which back into English is “What color not new house?” has some real charm.
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Discoblog: Robot Model Struts the Catwalk in Japan
Discoblog: Tiny Jumping Robot Can Find Enemies, Scale Fences
Discoblog: Update: “Corpse-Eating Robot” Actually a Vegetarian
Image: flickr / a voir etc…
Inception: Rarely Is Getting Your Mind So Messed With So Fun | Science Not Fiction
You’ve been running for hours, chased by a crazed grizzly bear. Suddenly you lose your footing, and you’re balancing on the edge of a cliff. Your stomach lurches as gravity pulls you down. Instantly you’re jolted awake and find yourself teetering precariously over the edge of your bed in your New York apartment. You’ve been asleep for just 5 minutes.
Like me (or whoever I stole that bizarre-o dream about the crazed grizzly from), everyone has dreams that strangely intertwine with reality. That’s what makes Chris Nolan’s newest thriller, Inception, so fun to watch. It plays with ideas we’ve all experienced—how dreams can reveal our most guarded memories, feel like days when only hours have passed, or affect our emotions when we wake up.
Inception’s Leonardo DiCaprio plays Dom Cobb, a man trained in the art of stealing personal info using a process called dream sharing. He builds the world of a dream, brings his subject into that world, and guides events so he can extract needed information, or plant a life-altering idea. Cobb is charged with creating a dream to convince Robert Fischer, the son of a multi-billionaire businessman, to use his inheritance to build his own company. To do this, Cobb and his crew induce an incredibly deep sleep, and enter a dream, within a dream, within a dream, and at one point (I think) within another dream.
Sure, busting into dreams and planting very specific ideas in someone’s mind is pretty far removed from even the most leading-edge brain science, but Nolan got the basic idea right: Neuroscientists say sleep plays an important role in memory consolidation. While we’re sleeping (or perhaps dreaming), our long-term memories stabilize deep in our hippocampuses. If someone were to plant a memory in a dream, who knows how long it would persist.
As the plot develops, the dreams are so realistic that it becomes challenging for the characters—and audience—to distinguish the dream state from reality. But that’s all part of the game, drawing us in as we attempt to sift fact from fiction. The film’s cinematographer, Wally Pfister, told me that in his earliest conversations about the film with Nolan, the director said “Remember, this is a dream world. When you’re in a dream, it feels real and you want to believe it’s real.” This warped reality triggers some moments of confusion (as you try to keep track of which dreamscape you’re in, and how actions in one realm affect the others) but by the end my brain had adjusted to the scheme.
I emerged from the theater into a chatty crowd—some firing questions excitedly at their neighbors or calling friends to announce how confused they were, while others praised the film’s brilliance. Fans and critics alike, everyone was talking.
—DISCOVER reporter/researcher Amy Barth
Osiris: The Scorched Exoplanet With a Comet-Like Tail | 80beats
We know about exoplanet HD 209458b, nicknamed “Osiris.” We know it’s 153 light years away, that it has water in its atmosphere, and that it orbits its star in three and a half days at a distance 100 times closer than Jupiter is to the sun. But we didn’t know this for sure until now: This planet has a tail.
In a study in The Astrophysical Journal, a research team says Osiris, a gas giant, orbits so close that its star is blasting away its atmosphere. As the planet progresses on its blazing hot and hasty revolutions, a tail like that of a comet follows behind it. The Hubble Space Telescope’s Cosmic Origins Spectrograph caught the effect as Osiris made repeated transits in front of its star.
The instrument detected the heavy elements carbon and silicon in the planet’s super-hot 2,000 degrees F (1,100 C or so) atmosphere. This detection revealed the parent star is heating the entire atmosphere, dredging up the heavier elements and allowing them to escape the planet.
Jeffrey Linsky, of the University of Colorado, who led the study, said: “We have measured gas coming off the planet at specific speeds, some coming toward Earth. The most likely interpretation is that we have measured the velocity of material in a tail” [Christian Science Monitor].
The planet may be losing material to that tail at a rate of 10,000 tons per second. But fear not for brave Osiris. Even at that rate, hot Jupiters don’t disappear overnight.
“It will take about a trillion years for the planet to evaporate,” Linsky said [Space.com].
New exoplanets catch our attention all the time, especially with the Kepler mission now out in space and on the hunt. But Osiris is one of the best-studied alien worlds.
Scientists first spotted it in 1999. Since then, studies have shown it holds not only water vapor in its atmosphere, but also compounds connected to life, like methane and carbon dioxide (though Osiris is probably a little toasty for life as we know it). And just last month, astronomers found fierce storms raging on Osiris with wind speeds in excess of 3,000 miles per hour—making the strongest winds known in our own solar system look meek by comparison.
If you like these artist’s impressions of this exoplanet, check out an astronomer’s thoughts on such creative renderings.
Related Content:
80beats: Weather Report from an Exoplanet Shows Winds of 4,300 MPH
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Visual Science: Astronomer Mike Brown on Arty Exoplanets
Image: G. Bacon, NASA/ESA
From the Vault: What’s A Gene For? | The Loom
[An old post from 2005 I'm fond of]
There was a time not that long ago when sequencing a single gene would be hailed as a scientific milestone. But then came a series of breakthroughs that sped up the process: clever ideas for how to cut up genes and rapidly identify the fragments, the design of robots that could do this work twenty-four hours a day, and powerful computers programmed to make sense of the results. Instead of single genes, entire genomes began to be sequenced. This year marks the tenth anniversary of the publication of the first complete draft of the entire genome of a free-living species (a nasty little microbe called Haemophilus influenzae). Since then, hundreds of genomes have emerged, from flies, mice, humans, and many more, each made up of thousands of genes. More individual genes have been sequenced from the DNA of thousands of other species. In August, an international consortium of databases announced that they now had 100 billion “letters” from the genes of 165,000 different species.
But this data glut has created a new problem. Scientists don’t know what many of the genes are for.
The classic method for figuring out what a gene is for is good old benchwork. Scientists use the gene’s code to generate a protein and then figure out what sort of chemical tricks the protein can perform. Perhaps it’s good at slicing some other particular protein in half, or sticking two other proteins together. It’s not easy to tackle this question with brute force, since a mystery protein may interact with any one of the thousands of other proteins in an organism. One way scientists can narrow down their search is by seeing what happens to organisms if they take out the particular gene. The organisms may suddenly become unable to digest their favorite food or withstand heat, or show some other change that can serve as a clue.
Even today, though, these experiments still demand a lot of time, in large part because they’re still too complex for robots and computers. Even when it comes to E. coli, a bacterium that thousands of scientists have studied for decades, the functions of a thousand of its genes remain unknown.
This dilemma has helped give rise to a new kind of science called bioinformatics. It’s an exciting field, despite its woefully dull name. Its mission is to use computers to help make sense of molecular biology–in this case, by traveling through vast oceans of online information in search of clues to how genes work.
One of the most reliable ways to find out what a gene is for is to find another gene with a very similar sequence. The human genes for hemoglobin and the chimpanzee genes for hemoglobin are a case in point. Since our ancestors diverged about six million years ago, the genes in each lineage have mutated a little, but not much. The proteins they produce still have a similar structure, which allows them to do the same thing: ferry oxygen through the bloodstream. So if you happen to be trolling through the genome of a gorilla–another close ape relative–and discover a gene that’s very similar to chimpanzee and human hemoglobins, you’ve got good reason to think that you’ve found a gorilla hemoglobin gene.
Scientists sometimes use this same method to match different genes in the same genome. There isn’t just one hemoglobin gene in humans but seven. They carry out different slightly functions, some carrying oxygen in the fetus, for example, and others in the adult. This gene family, as it’s known, is the result of ancient mistakes. From time to time, the cellular machinery for copying genes accidentally creates a second copy of a gene. Scientists have several lines of evidence for this. Some people carry around extra copies of genes not found in other people. Scientists have also tracked gene duplication in laboratory experiments with bacteria and other organisms.
In many cases, these extra genes offer no benefit and disappear over the generations. But in some cases, extra genes appear to provide an evolutionary advantage. They may mutate until they take on new functions, and gradually spread through an entire species. Round after round of gene duplication can turn a single gene into an entire family of genes. Knowing that genes come in families means that if you find a human gene that looks like hemoglobin genes, it’s a fair guess that it does much the same thing as they do.
This method works pretty well, and bioinformaticists (please! find a better name!) have written a number of programs to search databases for good matches between genes. But these programs tend to pick the low-hanging fruit: they are good at recognizing relatively easy matches and not so good at identifying more distant cousins. Over time, related genes can undergo different mutations rates, which can make it difficult to recognize their relationship simply by eyeballing them side by side. Another hazard is the way a gene can be “borrowed” for a new function. For example, snake venom genes turn out to have evolved from families of genes that carry out very different functions in the heart, liver, and other organs. These sorts of evolutionary events can make it hard for simple gene-matching to yield clues to what a new gene is for.
To improve their hunt for the function of new genes, bioinformaticists are building new programs. One of the newest, called SIFTER, was designed by a team of computer scientists and biologists at UC Berkeley. They outline some of their early results in the October issue of PLOS Computational Biology (open access paper here). SIFTER is different than previous programs in that it relies on a detailed understanding of the evolutionary history of a gene. As a result, it offers significantly better results.
To demonstrate SIFTER’s powers of prediction, the researchers tested it on well-studied families of genes–ones that contained a number of genes for which there was very good experimental evidence for their functions. They used SIFTER to come up with hypotheses about the function of the genes, and then turned to the results of experiments on those genes to see if the hypotheses were right.
Here’s how a typical trial of SIFTER went. The researchers examined the family of (big breath) Adenosine-5′-Monophosphate/Adenosine Deaminase genes. Scientists have identified 128 genes in this family, in mammals, insects, fungi, protozoans, and bacteria. With careful experiments, scientists have figured out what 33 of these genes do. The genes produce proteins that generally hack off a particular part of various molecules. In some cases, they help produce nitrogen compounds we need for metabolism, while in other cases they help change the information encoded in genes as it is translated into proteins. In still other cases they have acquired an extra segment of DNA that allows them to help stimulate growth.
The SIFTER team first reconstructed the evolutionary tree of this gene family, calculating how all 128 genes are related to one other. The shows how an ancestral gene that existed in microbes billions of years ago was passed down to different lineages, duplicating and mutating along the way. The researchers then gave SIFTER the experimental results from just five of the 128 genes in the family. The program used this information to infer how the function of the genes evolved over time. That insight then allowed it to come up with hypotheses about what the other 123 genes in the family do.
Aside from the 5 genes whose function the researchers had given SIFTER, there are 28 with good experimental evidence. The scientists compared the real functions of these genes to SIFTER’s guesses. It got 27 out of 28 right.
SIFTER’s 96% accuracy rate is significantly better than other programs that don’t take evolution so carefully into consideration. Still, the Berkeley team cautions that they have more work to do. The statistics that the program uses (Bayesian probability) get harder to use as the range of possible functions gets bigger. What’s more, the model of evolution that it relies on is fairly simple compared to what biologists now understand about how evolution works. But these aren’t insurmountable problems. They’re the stuff to expect in SIFTER 2.0 or some other future upgrade.
Those who claim to have a legitimate alternative to evolution might want to try to match SIFTER. They could take the basic principles of whatever they advocate and use them to come up with a mathematical method for comparing genes. No stealing any SIFTER code allowed–this has to be original work that doesn’t borrow from evolutionary theory.
They could then use their method to compare the 128 genes of the Adenosine-5′-Monophosphate/Adenosine Deaminase family. Next, they could take the functions of five of the genes, and use that information to predict how the other 123 genes work. And then they could see how well their predictions were by looking at the other 28 genes for which there’s good experimental evidence about their function.
All the data to run this test is available for free online, so there’s no excuse for these antievolutionists not to take the test. Would they match SIFTER’s score of 96%? Would they do better than random? I doubt we’ll ever find out. Those who attack evolution these days aren’t much for specific predictions of the sort SIFTER makes, despite the mathematical jargon they like to use. Until they can meet the SIFTER challenge, don’t expect most scientists to take them very seriously.
Identifying the functions of genes is important work. Scientists need to know how genes work to figure out the causes of diseases and figure out how to engineer microbes to produce insulin and other important molecules. The future of medicine and biotech, it appears, lies in life’s distant past.
Update Monday 10:30 am: John Wilkins says that bioinformatician is the proper term, although no improvement. I then googled both terms and found tens of thousands of hits for both (although bioinformatician has twice as many as bioinformaticist). Is there an authority we can turn to? And can it try to come up with a better name? Gene voyagers? Matrix masters?
Proved By Science: Wearing High Heels Can Damage Leg Tendons | 80beats
High heel wearers likely guessed it: Walking around on your tiptoes isn’t great for your calf muscles. Researchers looking at leg sonograms of women who frequently wear 2-inch or higher heels found that these women had calf muscle fibers that were an average of 13 percent shorter than their flat-wearing counterparts.
The small study, published yesterday in the Journal of Experimental Biology, has given some credence to complaints of lasting pain even after the pumps come off.
Anecdotally it has long been said that regularly wearing high heels shortens the calf muscle. Study leader Professor Marco Narici, from Manchester Metropolitan University, said in the 1950s secretaries who wore high heels complained that they struggled to walk flat-footed when they took their shoes off. [BBC]
From a group of 80 women, the researchers chose 11 women who had frequently worn two-inch or higher heals over the past two years and complained of pain when they weren’t wearing the shoes. MRI scans showed no difference in the calf muscle length of these women, but sonograms did. Sonograms showed that the Achilles’ tendons were stiffer, making it difficult for the calf muscles to stretch when the women were not wearing their heels.
“This confirmed the hypothesis that when you place the muscle in a shorter position, the fibres become shorter,” said Prof Marco Narici, who led the study. “We found the Achilles’ tendon was the same length in the two groups, but in women who wore high heels it was much thicker and stiffer, making it harder for them to stretch their feet out when they were on the flat.” [The Telegraph]
The researchers say that this doesn’t mean that heel-wearers should give up their favorite shoes entirely. They suggest stretching exercises and switching now and again from stilettos to other shoes.
Fortunately, only die-hard fashionistas appear to be at risk. Discomfort “will primarily occur in women wearing almost exclusively high-heeled shoes,” says [coauthor Robert] Csapo. In the study, the women who experienced pain wore heels for an average of about 60 hours a week. [CNN]
Related content:
80beats: The Ur-Sneaker: 5500-Year-Old Shoe Found in Armenian Cave
80beats: No Shoes, No Problem? Barefoot Runners Put Far Less Stress on Their Feet
80beats: Scientist Smackdown: Are A Sprinter’s Prosthetic Legs An Unfair Advantage?
DISCOVER: Born To Run, on humanity’s long-distance running abilities
Image: flickr / Herr Bert
BP’s Cap Has Stopped the Oil Leak—for Now | 80beats
Do you hear that? That’s the sound of oil not gushing uncontrollably into the Gulf of Mexico from BP’s leak, for the first time in nearly three months. BP is still running tests on the new cap the company installed this week, but at least for now there’s some for slight optimism.
The flow stopped yesterday afternoon, and BP video feed of its leak site showed quiet containment.
The view on Thursday afternoon was eerily tranquil, just the slate blue of the deep interspersed with small white particles floating across the screen. Though the exact amount of the oil that has poured out of the well may never be known, it was suddenly and for the first time a fixed amount. The disaster was, for a little while at least, finite [The New York Times].
The task now is a pressure test, which will take place over two days. Lower pressure inside the well would mean the surrounding rocks are leaking a little; high pressure would indicate the well is sealed off.
Things won’t stay this way, though. The capping stack—as this newest in a long line of BP jargon is known—isn’t meant to be any kind of permanent stopper. It provides the option to seal the well temporarily for testing (or if a hurricane sweeps through), but it may not stay on after the tests are done. If the pressure test show the well is leaking still, BP will resume pumping oil to its tankers on the surface. Meanwhile, the company is still trying to reach the leak site with its (hopefully) end-all solution, the relief wells.
Regardless of whether BP and the government decide to keep the well closed at the top, the ultimate solution to the blowout is a mud and cement bottom-kill from a relief well that is four feet from Macondo laterally and has only about 150 feet vertically to drill. During the integrity test, drilling of the relief well has been suspended as a precaution against oil and gas surging into the new hole from Macondo [Washington Post].
Even if BP succeeds, its convoluted and strung-out attempts to cap the leak may look simple compared to the cleanup task ahead. But for now, just for a moment, it’s a sigh of relief to pull up the video feed and see no black clouds of crude bursting into the bottom of the sea.
“I was excited. I was happy about it,” New Orleans resident Michael Jackson, 50, said of reports that the gushing oil well had been capped. “But who’s to say that cap’s going to hold?” [CNN].
Check out the Facebook home of DISCOVER’S wild new Internet TV show, “Joe Genius.”
Recent posts on the BP spill:
80beats: One Cap Off, One Cap On: BP Tries Another Plan To Catch Leaking Oil
80beats: BP Oil Update: Tar Balls in Texas & Lake Pontchartrain
80beats: Gulf Coast Turtle News: No More Fiery Death; Relocating 70,000 Eggs
80beats: Next from X Prize: An Award for Cleaning up BP’s Oil Spill?
Image: BP
Today in Austin Texas! | The Intersection
It's always fun to give a talk in my own town, so I'm especially excited for this afternoon's event in Austin at UT's Cactus Cafe. I'll be speaking at 5pm with Lindsay Patterson of EarthSky at Science In The Pub and would love to meet some readers from the neighborhood! Here a copy of the flier for details:
It’s been too long since we walked on the Moon | Bad Astronomy
BABloggee Jason Marsh sent me an interesting picture he put together. He was thinking about what was current in our culture when Apollo 17 went to the Moon… the last time a human set foot on another world.
The date was 1972. Here’s what he put together:
[Click to embiggen.]
Hmmm. Gas lines. Viet Nam. Nixon. Elvis with Nixon. Disco.
It’s been too long. We need to go back. I certainly hope the President and Congress can figure out how; my biggest gripe about Obama’s space plan (scroll down to Point #4 in that link) is ignoring the Moon for other goals. I think we do need to go back to the Moon, create a base and then a colony there, and use that knowledge to go to asteroids and beyond (even concurrently, to tell the truth).
Posters like this one really drive the point home. It’s been too long.
The Quivering Brain [Science Tattoo] | The Loom
Kristin writes,
“This is a rendition of Andreas Vesalius’ ‘The Quivering Brain.’ I admired many of his anatomy studies in art school, as I spent fifteen years as a painter, but I was always a little more interested in science than art. I even considered a career as a medical illustrator at one point.
Using science as artistic reference and researching for a painting was my favorite part of painting. Actually, it was the only thing I really enjoyed. It took me many years to realize this. I got this tattoo right before going back to school to study neuroscience. It couldn’t be more perfect.”
Click here to go to the full Science Tattoo Emporium.
