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February 22 2011
Self-Doubting Monkeys Know What They Don’t Know
The number of traits chalked up as “distinctly human” seem to dwindle each year. And now, we can’t even say that we’re uniquely aware of the limits of our knowledge: It seems that some monkeys understand uncertainty too.
A team of researchers taught macaques how to maneuver a joystick to indicate whether the pixel density on a screen was sparse or dense. Given a pixel scenario, the monkeys would maneuver a joystick to a letter S (for sparse) or D (for dense). They were given a treat when they selected the correct answer, but when they were wrong, the game paused for a couple seconds. A third possible answer, though, allowed the monkeys to select a question mark, and thereby forgo the pause (and potentially get more treats).
And as John David Smith, a researcher at SUNY Buffalo, and Michael Beran, a researcher at Georgia State University, announced at the AAAS meeting this weekend, the macaques selected the question mark just as humans do when they encounter a mind-stumping question. As Smith told the BBC, “Monkeys apparently appreciate when they are likely to ...
December 22 2010
Mutant Mouse Chirps Like a Bird—So What Are They Saying?
It’s furry like a mouse but sings like a bird. What is it? It’s a mutant mouse developed by the genetic engineers at the University of Osaka that is able to tweet and chip like a bird, instead of a mouse’s normal squeak.
Like dog breeders, who actively select for certain traits (like size, hair color, or disposition) the researchers from the Evolved Mouse Project crossbred their mutant mice to select for various traits. When they find one they like, like this singing mouse or the one that looks like a miniature Dachshund, they breed them until they have a sizable breeding stock of animals to establish a new breed.
The research group currently has over a hundred singing mice (it must get noisy in those labs) and they are continuing to study how they use their chirps, researcher Arikuni Uchimura told the AFP:
“Mice are better than birds to study because they are mammals and much closer to humans in their brain structures and other biological aspects,” Uchimura said. “We are watching how a mouse that emits new sounds would affect ordinary mice in the same group… in other words if it has social connotations.”
The researchers hope to learn about language from the mice, since it seems that they use their chirp in different ways than normal mice use their squeaks. The more conventional squeaks are used when a mouse is stressed, while the singing mouse seems to use its chirp in different environments, including in the presence of mates, the researchers told the AFP:
Uchimura said their chirps “may be some sort of expressions of their emotions or bodily conditions.” The team has found that ordinary mice that grew up with singing mice emitted fewer ultrasounds than others, which could indicate that communication methods can spread in the same group like a dialect.
While the mouse sounds really interesting and could give researchers insight into what genes control sound and possibly language production, studies of the mouse haven’t yet been published in a peer-review journal; so far the news comes directly from the researchers themselves. I’m a little skeptical to jump to any conclusions about how useful they will be: the ability to make bird-like sounds doesn’t necessarily come with the social and psychological changes that would let mice can use those sounds to communicate in the ways that birds do.
Now, if only they could get to work on those mutant turtles we’ve been hearing about.
Related content:
Discoblog: Turning a Mouse Into a Bat(-Like Weirdo) in One Easy Step
Discoblog: Scientists Milking Mice for All the Human Milk Protein They’ve Got
80beats: Mice Two Dads: Scientists Create Mice With Two Genetic Fathers
80beats: Green-Glowing Monkeys Are Called a Genetic Engineering Milestone
80beats: Will Venter’s “Synthetic Cell” Patents Give Him a Research Monopoly?
80beats: Fast-Track Evolution Gave Rise to Deer Mouse’s Pale Coat
Science Not Fiction: Genetic Engineering Lets Designer Kids Be Kids
Image: Graduate School of Frontier Biosciences, University of Osaka
December 06 2010
NASA Found Aliens! Or Not. The Worst Coverage of Arsenic-Loving Bacteria
While watching the science news for you here at Discover blogs, we’ve seen our share of bad science coverage. Most of the time, we let it slide. Most of the time, we write the truth and hope to overshadow the erroneous and exaggerated stories. But this time… this time we’re calling it out.
Last week’s coverage of the bacteria that live in Mono Lake, CA was over hyped because of a cryptic message in a NASA press release (namely, that the discovery would “impact the search for evidence of extraterrestrial life”). And even after all the build up, the early embargo break, and a long press conference, many news outlets STILL got the story wrong.
First, a quick recap of the important findings from DISCOVER blogger Ed Yong at Not Exactly Rocket Science, for those who were off-planet last week:
In California’s Mono Lake, Felisa Wolfe-Simon has discovered bacteria that not only shrug off arsenic’s toxic effects, but positively thrive on it. They can even incorporate the poisonous element into their proteins and DNA, using it in place of phosphorus.
While the discovery is amazing and definitely sheds new light on the search for life in extreme (even extraterrestrial) environments, it is important to remember that this doesn’t mean that aliens exits and definitely doesn’t mean that this bacteria is alien. I’m talking to you, Telegraph:
‘Life as we don’t know it’ discovery could prove existence of aliens
NASA has sent the internet into a frenzy after it announced an “astrobiology finding” that could suggest alien life exists–even on earth.
While the bacteria live in a relatively high-arsenic environment, which made them able to tolerate the presence of the poison, the critters typically still used phosphorus to build the “backbone” of their DNA double helix. It wasn’t until the researchers weaned them off the phosphorus in the lab that the bacteria began to incorporate arsenic.
This doesn’t mean these little bacteria are the second (or third, or fourth) coming of life on earth–they are the same “strain of life” as everything else on the planet (including us). This point seems to escape The Huffington Post, who led their incredibly misleading article with the title:
NASA Announcement LIVE: New Life Form Discovered (VIDEO)
Though, if both the headline and the article are misleading, is it really misleading? It seems that they got their false information from an article published by Gizmodo (also posted to Wired Science). In its original form (Gizmodo edited the post once they realized how wrong they’d gotten it), the post says:
NASA has discovered a completely new life form that doesn’t share the biological building blocks of anything currently living on planet Earth. This changes everything…. Discovered in poisonous Mono Lake, California, this bacteria is made of arsenic, something that was thought to be completely impossible.
No, actually, it doesn’t change everything. While the exciting claims may change the way we think about life in extreme environments, there are still doubters in the scientific community. Many are saying that additional research is necessary to confirm Wolfe-Simon’s results, and some scientists are even suggesting that the study’s authors got it all wrong. We’ll keep you updated on the developments, but we can tell you one thing right now: it’s definitely not aliens.
Related Content:
The Loom: Of Arsenic and Aliens
Not Exactly Rocket Science: Mono Lake Bacteria Build Their DNA Using Arsenic (and No, This Isn’t About Aliens)
Bad Astronomy: NASA’s Real News: Bacterium on Earth That Lives Off Arsenic!
Gene Expression: The Alien Embargo and Other Follies
Image: adapted from Flickr/MJTR
November 30 2010
Guilt-Free Procrastination: This Online Game Could Cure Genetic Diseases
Have a brain for puzzles? What about ones that help advance science?
A new online game called Phylo is harnessing the power of idle brains on the Internet–asking any and all to help align genomic sequences. Human brain power is used instead of computer power because, as the researchers explain in the press release, humans are still better at some things than computers are:
“There are some calculations that the human brain does more efficiently than any computer can, such as recognizing a face,” explained lead researcher Dr. Jérôme Waldispuhl of the School of Computer Science. “Recognizing and sorting the patterns in the human genetic code falls in that category. Our new online game enables players to have fun while contributing to genetic research–players can even choose which genetic disease they want to help decode.”
When game players find the best arrangements of colorful little boxes, they’re really making the best matches they can between the genome sequences of different animals–like a human and a monkey, or a dog and a bat. The researchers, from the structural biology group at McGill University, loaded the sequences of genes related to diseases like breast cancer into the program, adding in the genetic data for many different species. You can then slide the colored boxes (stand-ins for the nucleotides in DNA) around to minimize the number of mismatches and gaps and maximize the number of matched nucleotides. The matches show which parts of the genes have been preserved across different species and are therefore important, according to the Phylo about page:
These similarities may be consequences of functional, structural, or evolutionary relationships between the sequences. From such an alignment, biologists may infer shared evolutionary origins, identify functionally important sites, and illustrate mutation events. More importantly, biologists can trace the source of certain genetic diseases.
What I noticed in playing the game is that the scoring doesn’t seem to fit the game’s objective–the highest points are sometimes awarded for just squishing all the code together, not necessarily for making the most nucleotide matches. I also think the penalty for opening a gap (a stand-in for a genetic mutation) is too weighty. But all in all it’s quite addictive, until you get stuck on a sequence–you can’t move on to the next level until you equal the computer’s score, which, at least in my experience, can be tricky at times, and you can run out of time if you get stuck. Play the tutorial for more information and detailed directions.
In the end, you compare the gene sequences for up to eight different species, trying to make the best matches and beat the computer. Everyone’s alignments are analyzed by the game, and will contribute to the global database as an “optimization” of the computer’s sequence alignments. The creators even plan to create a Facebook application to play the game (which they optimistically say could rival Farmville in popularity), but right now it’s hosted at the group’s website. Give it a try and let us know what you think in the comments.
Related Content:
Discoblog: The Computer Game That Could Cure HIV
Discoblog: Impact: Earth! Lets You Smash Your Home Planet to Bits
80beats: Crowdsourced Science: 5 Ways You Can Help the Hive-Mind
Not Exactly Rocket Science: Foldit – tapping the wisdom of computer gamers to solve tough scientific puzzles
Not Exactly Rocket Science: Tetris could prevent post-traumatic stress disorder flashbacks (but quiz games make them worse)
DISCOVER: This is Your Brain on Video Games
Image: Phylo
November 23 2010
Big Scientists Pick Big Science’s Biggest Mistakes
Earlier this week Richard H. Thaler posted a question to selected Edge contributors, asking them for their favorite examples of wrong scientific theories that were held for long periods of time. You know, little ideas like “the earth is flat.”
The contributor’s responses came from all different fields and thought processes, but there were a few recurring themes. One of the biggest hits was the theory that ulcers were caused by stress–this was discredited by Barry Marshall and Robin Warren, who proved that the bacteria H. pylori bring on the ulcers. Gregory Cochran explains:
One favorite is helicobacter pylori as the main cause of stomach ulcers. This was repeatedly discovered and then ignored and forgotten: doctors preferred ’stress’ as the the cause, not least because it was undefinable. Medicine is particularly prone to such shared mistakes. I would say this is the case because human biology is complex, experiments are not always permitted, and MDs are not trained to be puzzle-solvers–instead, to follow authority.
Another frequent topic of disbelief among Edge responders was theism and its anti-science offshoots–in particular the belief in intelligent design, and the belief that the Earth is only a few thousand years old. Going by current political discussions in America it may seem that these issues are still under contention and shouldn’t be included on the list, but I’m going to have to say differently, and agree with Milford Wolpoff:
Creationism’s step sister, intelligent design, and allied beliefs have been held true for some time, even as the mountain of evidence supporting an evolutionary explanation for the history and diversity of life continues to grow. Why has this belief persisted? There are political and religious reasons, of course, but history shows than neither politics nor religion require a creationist belief in intelligent design.
Along similar lines, many people still believe in the idea of souls and spirits, though the scientific search for a vital “life force” ended long ago, as Sue Blackmore pointed out:
Of course many people still believe in various versions of this, such as spirits, souls, subtle energy bodies and astral bodies, but scientists long ago gave up the search once they realized that being alive is a process that we can understand and that needs no special force to make it work.
Early scientists didn’t only seek “special forces” in our bodies, but also looked for them in the world around–and so fastened on the idea of “ether.” Clay Shirky liked the ether misconception the best, as it illustrates how hard it is to disprove some ideas:
It was believed to be true by analogy–waves propagate through water, and sound waves propagate through air, so light must propagate through X, and the name of this particular X was ether. It’s also my favorite because it illustrates how hard it is to accumulate evidence for deciding something doesn’t exist. Ether was both required by 19th century theories and undetectable by 19th century apparatus, so it accumulated a raft of negative characteristics: it was odorless, colorless, inert, and so on.
One funny distinction that many responders picked out was Thaler’s misconception that “the world is flat” idea would qualify as a long-held misconception. Confused yet? Geoffrey Carr will sort it out for you:
Believing that people believed the Earth was flat is a good example of a modern myth about ancient scientific belief. Educated people have known it was spherical (and also how big it was) since the time of Eratosthenes. That is pretty close to the beginning of any system of thought that could reasonably merit being called scientific…
So, why do we so often miss the right answer, when it’s often right there in front of us? Thaler asked his respondents to give us a hint. Haim Harari, a physicist, noted that what’s important isn’t the answer, but the question being asked:
Part of the problem is that, in order to find the truth, in all of these cases, you need to ask the right question. This is more important, and often more difficult, than to find the answer. The right questions in the above cases are of different levels of complexity.
Some, like Derek Lowe, think the lack of an alternate idea is the driving factor behind many long-held mistaken ideas:
Finally, there’s the factor that’s kept all sorts of erroneous beliefs alive — lack of a compelling alternative. The idea of strange-looking living creatures too small to see being the cause of infections wouldn’t have gotten much of a hearing, not in the face of more tangible explanations. That last point brings up another reason that error persists — the inability (or unwillingness) to realize that man is not the measure of all things.
Visit the article to view a complete list of the respondents’ answers, and leave a link to your favorite in the comments here.
Related Content:
DISCOVER: Science’s Most Spectacular Fails
DISCOVER: The Dr. Who Drank Infectious Broth, Gave Himself an Ulcer, and Solved a Medical Mystery
Discoblog: Crazy Pseudoscience Theory of the Day: Cell Phone Ringtone Can Cure Your Allergies!
Bad Astronomy: New Symphony of Science: Wave of Reason
Bad Astronomy: Uncritical thinking kills
The Intersection: Creationism Disguised as Science
Images: (1) Flickr/striatic (2) Flickr/PinkMoose
September 22 2010
The Fruit That Hit Newton’s Head Is Down With the Fruit of Darwin’s Head
Apple may not allow porn on its product line, but it has no problem with another source of controversy: evolution. A new, free iPad/iPhone application called Timetree, distributed by Arizona and Penn State Universities, allows users to map how long ago two living creatures separated on the tree of life, a subject that can get a bit sticky with creationists, says The Register:
Now, Apple has taken a stance which will upset a lot of Americans: it has allowed an app which specifies quite clearly that evolution is real and that humans and monkeys share a common ancestor some 30 million years in the past.
Querying the Timetree application accesses a vast database of data, the National Center for Biotechnology Information’s comprehensive taxonomy browser, which contains information on more than 160,000 organisms. Timetree even provides you with the publications relating to these connections, which can sometimes disagree with each other but, which The Register has discovered, all happily ignore creationism:
As far as our user tests have been able to determine, Timetree does not reveal one disagreement regarding evolution which is now becoming prominent in US politics: namely the issue of whether or not evolution actually happens or has happened. Religious hardliners on the American right are known for espousing the view that actually it doesn’t and didn’t, and that the various species were all created by God during one week just a few thousand years ago.
And while the information contained in the Timetree database may not provide credence to the creationists’ stance, the ability to see current clashes in the field is an important part of investigating the science of evolution, Sudhir Kumar, who helped develop the project, told the Penn State press office:
“One of the most important things about this knowledge base,” Kumar said, “is that it makes it possible for anyone to see the current agreements and disagreements in the field — immediately.”
The same functionality is available though the Timetree website, and more information can be found in the free e-book, The Time Tree of Life ,the downloadable poster (both available at the Timetree website) and in the paper documenting how Timetree works. But you don’t need all that documentation. If it’s in the app store, it must be right!
Related content:
Discoblog: An iPhone App, a Refractometer, an Objectively Perfect Cup of Coffee
Discoblog: Augmented Reality Phone App Can Identify Strangers on the Street
Discoblog: iPhone App Lets You Tell Drivers Exactly What You Think of Them
Discoblog: Can an iPhone App Clear up Your Acne?
Discoblog: NASA iPhone App Lets You Drive a Lunar Rover (Just Try Not to Get Stuck)
Bad Astronomy: Three iPhone science apps
The Loom: Google Earth for The Tree of Life
Image: Penn State Department of Public Information
September 15 2010
Mexican Religious Rite Has Created Super Poison-Tolerant Cave Fish
Any culture’s religious ceremonies can seem strange to outsiders: For example, take the indigenous Zoque people of southern Mexico. To ask their gods for bountiful rains during the growing season they head to a sulfur cave where molly fish swim in the subterranean lake. They then toss in leaf bundles that contain a paste made from the mashed-up root of the Barbasco plant, which has a powerful anesthetic effect.
When the stunned fish–which the Zoque people consider a gift from underworld gods–go belly-up, people scoop them from the water and bring them home for supper. This fishy protein helps them make it through until the harvest.
This ritual came to the attention of scientists studying the molly fish, who wondered how the toxic root might be affecting fish populations in the caves. So evolutionary ecologist Michael Tobler and his colleagues did a little field research.
From LiveScience:
“We learned about the ceremony, and actually attended it in 2007,” Tobler recalled. “The families each take a certain amount of the fish home. The way we had ours prepared was that they were just mixed with scrambled eggs, although I hear other families fry them. They had a funny salty taste to them, although I’m not sure if that’s because of their sulfuric environment, or something the cook messed up.”
The researchers got more than a taste of local culture, they also came up with evidence of evolution-in-action that they published in a study in Biology Letters. In lab experiments they compared molly fish from the ritual cave to others from an area upstream that had never swam in poisoned water, and found that the cave fish had a much higher tolerance for the Barbasco toxin.
Study coauthor Mark Tobler of Texas A&M University told New Scientist the results show that within the ritual cave, evolution has selected for fish that can survive the poison.
“The study indicates that the fish have adapted to the local Zoque traditions,” says Tobler, who describes the effect as “an intimate bond between nature and local culture.”
The relationship may be intimate, but the Mexican government is worried that it’s also detrimental–officials have banned the ceremony, saying it’s bad for the fish.
Related Content:
80beats: Unnatural Evolution: Fishing Eliminates Cod Adapted for Shallow Waters
80beats: Researchers Catch Lake Victoria Fish in the Act of Evolving
The Loom: When Love Shocks
Image: Biology Letters
July 26 2010
Scientists Find Giant, 15-Pound Rat. (Don’t Worry, It’s Extinct.)
The rats scuttling around the tracks of the New York City subway pale in comparison to a gargantuan species recently discovered in East Indonesia. In fact, the recently discovered rat tipped the scales at a somewhat frightening 13 pounds. That’s sizably heftier than today’s house rat (which averages 5 ounces) and burliest wild rats (which weigh about four-and-a-half pounds). This mega-rat lived in Timor until it went extinct between 1,000 and 2,000 years ago. It was one of 11 new species discovered at the excavation site–eight of which weighed more than two pounds, and only one of which survives today.
But the now-extinct rats didn’t die off until well after humans first arrived, according to LiveScience:
“People have lived on the island of Timor for over 40,000 years and hunted and ate rats throughout this period, yet extinctions did not occur until quite recently,” said study researcher Ken Aplin… adding that the arrival of humans to an area doesn’t necessarily have to equate with extinctions… “Large-scale clearing of forest for agriculture probably caused the extinctions, and this may have only been possible following the introduction of metal tools.”
East Indonesia is a hotspot for rat evolution, with unique species found on each island, and the possibility of finding more.
“Although less than 15 percent of Timor’s original forest cover remains, parts of the island are still heavily forested, so who knows what might be out there?” [researcher] Aplin said.
Which is fine with us–as long as they stay far, far away from our homes.
Related content:
Discoblog: Weird Science Roundup: Super-Rats, Heart-Attack Virus, and the Real Breakfast of Champions
Magazine: English Super-Rats
Magazine: A-maze-ing Mole Rats
Image: flickr / korobukkuru
June 16 2010
New Study: If a Dude Sounds Strong, He Probably Is
It’s pretty clear that–in a fight–Darth Vader would crush Jar Jar Binks, Optimus Prime would beat Starscream, and Batman could pummel the Joker. Though some of these fictional characters don’t even look like humans, when it comes to strength, their voices give it all away. New research seems to confirm this: humans, like other animals, can accurately predict physical strength from voice alone.
In a study appearing today in The Proceedings of the Royal Society, researchers asked subjects to evaluate the upper-body strength of speakers from four distinct populations and language groups just by listening to their voices. Even when unfamiliar with a speaker’s language, listeners could tell which men might be good in a fight. The men they judged as sounding brawny were in fact physically stronger as measured by tests of hand grip, chest strength, shoulder strength, and bicep circumference.
As lead author Aaron Sell told Discovery News:
“Information about male formidability would have been important for both sexes over evolutionary time,” said Sell. “Both men and women would have benefitted from knowing who would likely win fights in order to make prudential alliances and for other reasons. Men would need this information to regulate their own fighting behavior. Women would also need this information in order to make effective mate choices.”
They study failed to make a similar link between women’s voices and strength. The study’s authors speculate that this is because early men were more likely to spar. The researchers also couldn’t determine what it was about certain male voices that made them sound strong–it wasn’t just a deep timbre–and say listeners may respond to a complex mix of cues.
For men, the finding proves especially interesting given the non-menacing statement researchers asked English speakers to say: “When the sunlight strikes raindrops in the air, they act like a prism and form a rainbow.” Apparently this sentence contains all the sounds of the English language, but those certainly aren’t fighting words.
Related content:
Discoblog: Speaking French? Your Computer Can Tell
Discoblog: Penn State’s Football Stadium: Now 50% Louder!
Discoblog: NCBI ROFL: Did Gollum have schizophrenia or multiple personality disorder?
May 06 2010
Evolution, With Dope Rhymes and a Funky Hip-Hop Beat
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