Thursday, December 11, 2008

differentiation

ok it's been awhile since i've actually blogged about something. so here it goes. 

heh, don't let the title scare you. its not about math, its about us.
what separates man from animal? i mean, ultimately everyone with the slightest bit of trust in our biological field knows that the current theory is that ah meng's our long long long long long distance cousin. but so many of us are so certain that there's something different and special about us that separates us from animals. so what's our trait that differentiates us from animals? 

is it intelligence? i don't think so. so far, we've trained dolphins to learn our language. we've taught gorillas sign language. we've taught dogs to specifically pick out drugs (how many of us can stand outside a random kitchen and tell us exactly what are the spices being used and what's being cooked now?). we've trained pigeons to pilot missiles (trust me on this, its true). we've even taught chimpanzees to send electronic signals to a mechanical arm to bring bananas to them. heck, we've taught WASPS to pick out bombs. so far, we've shown how we can use animals, but really, all it has successfully done is to show to every alien in the universe that all the animals here have a significant ability to learn. heck, put food in a bottle and screw the cap on. leave it with an octopus, and it will figure out that the cover opens by unscrewing it. can we do that? i mean we've SEEN people open bottle caps. octopuses haven't. do we possess such abilities? how bout learning what dolphins are saying? or knowing which bark means i'm hungry and which means "dammit, i have to sit again?" all we have done so far is to show that we know how to make other things more knowledgeable. but does that equate intelligence?

is it love? HA don't even get me started. which other freaking species have waged a 106 year war with its own because one thinks that their jesus is better than their enemy's jesus? which other species have created weapons SPECIFICALLY DESIGNED to kill their own kind? i mean honestly speaking, i don't think you can use a gattling gun for ANY other reason. and neither do i think F-16 falcons were designed to kill pigeons. wanna know what other animals exhibit monogamy? lovebirds are monogamous. heck, lets move into the reptile category. shingleback lizards are one such examples. they have only one partner and will always remain faithful to that partner, even after that partner has died. we're talking about reptiles here. 

self awareness. right. some studies have shown that bees possess self awareness. yes there are specific tests to show that one possesses such traits, and yes, it is possible to test it on a bee. so, example of insect. Q.E.D, don't need to go further.

logical mind. heh. if logical mind= beyond animal, then a VAST majourity of humans on earth are no different from savage donkeys. i mean really, honestly, how many of you dare to even sit in a room with an aids patient? even at lower secondary level, where you already know that HIV is only transmittable via intimate body contact. how many would dare share a meal with one of them? logically, they are perfectly harmless, as long as you don't start acting out your fantasies with them. the number of people who smoke, who take drugs, who endulge in alcohol, all with full knowledge that they're just heavily investing in a suicide. "addiction" you say, then why even start? 

it took years to let people realise that they do not have divine right to rule over other people. how much longer do we need to take before we can finally accept the fact that we have no rights over any thing on this earth? if we can never understand such a truth, we don't even possess any of the above mentioned traits, and are really no better than self centred, egoistic, weak monkeys. 

Wednesday, December 10, 2008

ooh airheaded reptiles

hmm.. so herbivorous dinosaurs might have been warm blooded...

ScienceDaily (Dec. 9, 2008) — Paleontologists have long known that dinosaurs had tiny brains, but they had no idea the beasts were such airheads.

A new study by Ohio University researchers Lawrence Witmer and Ryan Ridgely found that dinosaurs had more air cavities in their heads than expected. By using CT scans, the scientists were able to develop 3-D images of the dinosaur skulls that show a clearer picture of the physiology of the airways.

“I’ve been looking at sinuses for a long time, and indeed people would kid me about studying nothing—looking at the empty spaces in the skull. But what’s emerged is that these air spaces have certain properties and functions,” said Witmer, Chang Professor of Paleontology in Ohio University’s College of Osteopathic Medicine.

Witmer and Ridgely examined skulls from two predators, Tyrannosaurus rex and Majungasaurus, and two ankylosaurian dinosaurs, Panoplosaurus and Euoplocephalus, both plant eaters with armored bodies and short snouts. For comparison, the scientists also studied scans of crocodiles and ostriches, which are modern day relatives of dinosaurs, as well as humans.

The analysis of the predatory dinosaurs revealed large olfactory areas, an arching airway that went from the nostrils to the throat, and many sinuses—the same cavities that give us sinus headaches. Overall, the amount of air space was much greater than the brain cavity.

The CT scans also allowed Witmer and Ridgely to calculate the volume of the bone, air space, muscle and other soft tissues to make an accurate estimate of how much these heads weighed when the animals were alive. A fully fleshed-out T. rex head, for example, weighed more than 1,100 pounds.

“That’s more than the combined weight of the whole starting lineup of the Cleveland Cavaliers,” Witmer said.

Witmer suggests that the air spaces helped lighten the load of the head, making it about 18 percent lighter than it would have been without all the air. That savings in weight could have allowed the predators to put on more bone-crushing muscle or even to take larger prey.

These sinus cavities also may have played a biomechanical role by making the bones hollow, similar to the hollow beams used in construction — both are incredibly strong but don’t weigh as much their solid counterparts. A light but strong skull enabled these predators to move their heads more quickly and helped them hold their large heads up on cantilevered necks, explained Witmer, who published the findings in a recent issue of The Anatomical Record.

Though most researchers have assumed that the nasal passages in armored dinosaurs would mimic the simple airways of the predators, Witmer and Ridgely found that these spaces actually were convoluted and complex. The passages were twisted and corkscrewed in the beasts’ snouts and didn’t funnel directly to the lungs or air pockets.

“Not only do these guys have nasal cavities like crazy straws, they also have highly vascular snouts. The nasal passages run right next to large blood vessels, and so there’s the potential for heat transfer. As the animal breathes in, the air passed over the moist surfaces and cooled the blood, and the blood simultaneously warmed the inspired air,” said Witmer, whose research is funded by the National Science Foundation. “These are the same kinds of physiological mechanisms we find all the time in warm-blooded animals today.”

These twisty nasal passages also acted as resonating chambers that affected how the ankylosaurs vocalized. The complex airways would have been somewhat different in each animal and might have given the dinosaurs subtle differences in their voices.

“It’s possible that these armored dinosaurs could recognize individuals based on the voice,” said Witmer, who noted that his research team’s studies of the inner ear revealed a hearing organ that probably had the capability to discriminate these subtle vocal nuances.

Though Witmer found few similarities between the dinosaur and human sinuses—our brain cavities take up much more space relative to our sinuses— the scientist did find a resemblance between the air spaces of the crocodiles and ostriches and the ancient beasts under study.

“Extra air space turns out to be a family characteristic,” he said, “but the sinuses may be performing different roles in different species. Scientists have tended to focus on things such as bones and muscle, and ignored these air spaces. If we’re going to decipher the mysteries of these extinct animals, maybe we need to figure out just why it is that these guys were such airheads.”

http://www.sciencedaily.com/releases/2008/12/081209052145.htm

Wednesday, December 3, 2008

hypocrisy, another fact that we need to think about..

i've been outdone.. but really, a nice article to ponder over. sometimes, the emotional us can lead us to our undoing. 

The Truth about Hypocrisy

Charges of hypocrisy can be surprisingly irrelevant and often distract us from more important concerns

By Scott F. Aikin and Robert B. Talisse

Former U.S. vice president Al Gore urges us all to reduce our carbon footprint, yet he regularly flies in a private jet. Former drug czar William Bennett extols the importance of temperance but is reported to be a habitual gambler. Pastor Ted Haggard preached the virtues of “the clean life” until allegations of methamphetamine use and a taste for male prostitutes arose. Eliot Spitzer prosecuted prostitution rings as attorney general in New York State, but he was later found to be a regular client of one such ring.

These notorious accusations against public figures all involve hypocrisy, in which an individual fails to live according to the precepts he or she seeks to impose on others. Charges of hypocrisy are common in debates because they are highly effective: we feel compelled to reject the views of hypocrites. But although we see hypocrisy as a vice and a symptom of incompetence or insincerity, we should be exceedingly careful about letting our emotions color our judgments of substantive issues.

Allegations of hypocrisy are treacherous because they can function as argumentative diversions, drawing our attention away from the task of assessing the strength of a position and toward the character of the position’s advocate. Such accusations trigger emotional reflexes that dominate more rational thought patterns. And it is precisely in the difficult and important cases such as climate change that our reflexes are most often inadequate.

Thus, listeners should temper such knee-jerk reactions toward the messenger and instead independently consider the validity of the message itself. It also pays to examine closely what the duplicitous deeds really mean: from some vantage points, such behavior may actually support a hypocrite’s point of view, significantly softening the hypocrisy charge in those cases.

Undermining Authority
One surprising truth about hypocrisy is its irrelevance: the fact that someone is a hypocrite does not mean that his or her position on an issue is false. Environmentalists who litter do not by doing so disprove the claims of environmentalism. Politicians who publicly oppose illegal immigration but privately employ illegal immigrants do not thereby prove that contesting illegal immigration is wrong. Even if every animal-rights activist is exposed as a covert meat eater, it still might be wrong to eat meat.

More generally, just because a person does not have the fortitude to live up to his or her own standards does not mean that such standards are not laudable and worth trying to meet. It therefore seems that charges of hypocrisy prove nothing about a topic. Why, then, are they so potent?

The answer is that such allegations summon emotional, and often unconscious, reactions to the argument that undermine it. Such indictments usually serve as attacks on the authority of their targets. Once the clout of an advocate is weakened, the stage is set for dismissal of the proponent’s position. Consider the following two examples:

Dad: You shouldn’t smoke, son. It’s bad for your health, and it’s addictive.
Son: But, Dad! You smoke a pack a day!

Amy: Have you seen Al Gore’s An Inconvenient Truth? We need to reduce our carbon footprint right away.
Jim: Al Gore? You know he leaves a huge footprint with all his private jet flights!

In the first example, the son feels that his father is not an appropriate source of information on smoking because Dad is a hypocrite. The accusation of hypocrisy does not so much defeat Dad’s position as nullify it, almost as if Dad had never spoken. The same holds in the case of Gore’s airplane, although the speaker, Amy, is not the alleged hypocrite but rather Gore, the authority to which she appeals. In both cases, hypocrisy is proffered as evidence of the insincerity or incompetence of a source, providing ammunition for ignoring his or her advice or instruction.

Such ammunition is particularly potent because of the power of such personal portrayals. Once people have characterized someone in a negative light, they tend to ignore evidence to the contrary. In a 2007 study psychologists David N. Rapp of Northwestern University and Panayiota Kendeou of McGill University asked student volunteers to read 24 different stories involving a character who behaves in a way that suggests he is sloppy or lazy. Later in each story, however, the individual acts in a manner that contradicts this judgment. Nevertheless, less than half of the respondents revised their view of the character.

These results suggest that a first impression of someone as lazy or hypocritical actively inhibits the consideration of other information that might be important to understanding that person or the issue at hand. In the smoking and airplane examples, the son and Jim foolishly focus on the father’s and Gore’s hypocrisy rather than on the perils of smoking or the human contribution to global warming.

Duplicity Understood
In fact, if the son and Jim had focused on the issues, they might have viewed the father’s and Gore’s behavior radically differently. Consider what Dad’s smoking suggests: Dad believes smoking is bad for him, yet he continues to smoke because, of course, he is addicted. So Dad’s behavior—his hypocrisy—actually supports his point that smoking is addictive. Gore’s behavior also bolsters one of his arguments for change in national energy policy: that certain ingrained aspects of the American lifestyle, such as our penchant for driving SUVs and distaste for riding city buses, lead to environmental irresponsibility—even Gore cannot escape it. (To his credit, Gore compensates for his plane trips by buying carbon offsets, which pay for projects that reduce greenhouse gas emissions.)

Of course, hypocrisy does not always support the hypocrite’s view. Spitzer’s visits to prostitutes do nothing to reinforce his official opposition on prostitution. And in some cases, hypocrisy has precisely the significance that the son and Jim assign to it: it is reason enough to dismiss a source because the person has lost his credibility. For example, when the preacher who presents himself as a moral authority gets caught having an adulterous affair, his followers may rightly call his teachings into question.

Thus, hypocrisy is sometimes sufficient to undermine a person’s authority. It can warrant the thought, “Why pay attention to what he says?” But hypocrisy does not always have this effect, as the Dad and Gore cases show.

Whether hypocrisy is relevant to a person’s credibility usually depends on the content of the hypocrite’s statements. And yet hypocrisy charges, as they are popularly deployed, tend to short-circuit rational examination of that content. To skirt this danger, people should suppress their instinctual responses to accusations of duplicity so that they can focus on the real issues at hand. Such concentration is essential to our ability to rationally judge our leaders, colleagues and friends as well as to make decisions about important social issues that affect our lives.

Monday, December 1, 2008

ants-fungus-bacterium: 3 way mutualism. nature still surprises us.

ScienceDaily (Nov. 30, 2008) — One of the most important developments in human civilisation was the practice of sustainable agriculture. But we were not the first - ants have been doing it for over 50 million years. Just as farming helped humans become a dominant species, it has also helped leaf-cutter ants become dominant herbivores, and one of the most successful social insects in nature.

According to an article in the November issue of Microbiology Today, leaf-cutter ants have developed a system to try and keep their gardens pest-free; an impressive feat which has evaded even human agriculturalists.

Leaf-cutter ants put their freshly-cut leaves in gardens where they grow a special fungus that they eat. New material is continuously incorporated into the gardens to grow the fungus and old material is removed by the ants and placed in special refuse dumps away from the colony. The ants have also adopted the practice of weeding. When a microbial pest is detected by worker ants, there is an immediate flurry of activity as ants begin to comb through the garden. When they find the pathogenic 'weeds', the ants pull them out and discard them into their refuse dumps.

"Since the ant gardens are maintained in soil chambers, they are routinely exposed to a number of potential pathogens that could infect and overtake a garden. In fact, many of the ant colonies do become overgrown by fungal pathogens, often killing the colony," said Professor Cameron Currie from the University of Wisconsin-Madison, USA. "Scientists have shown that a specialized microfungal pathogen attacks the gardens of the fungus-growing ants. These fungi directly attack and kill the crop fungus, and can overrun the garden in a similar fashion to the way weeds and pests can ruin human gardens."

A curious observation was that some worker ants had a white wax-like substance across their bodies. When they looked at it under a microscope scientists discovered that this covering was not a wax, but a bacterium! These bacteria are part of the group actinobacteria, which produce over 80% of the antibiotics used by humans. The bacteria produce antifungal compounds that stop the microfungal pathogen from attacking the garden. This discovery was the first clearly demonstrated example of an animal, other than humans, that uses bacteria to produce antibiotics to deal with pathogens.

"Research in our laboratory has revealed a number of interesting properties between the bacteria and the pathogenic fungus. The bacteria appear to be specially suited to inhibiting the pathogenic fungi that infect the ants' fungus garden," said Professor Currie.

The interaction between the ants and their fungus crop, and the ants and the bacteria is known as a mutualistic relationship. In general a mutualism is established when both members of the interaction benefit from the relationship. In the ant–fungus mutualism, the ants get food from the fungus. This mutualism is so tight that if the fungus is lost, the entire colony may die. In return, the fungus receives a continuous supply of growing material, protection from the environment, and protection from disease-causing pests.

So what do the bacteria get out of producing pesticides for the ants? "For starters, they get food. Many species of fungus-growing ants have evolved special crypts on their bodies where the bacteria live and grow. Scientists believe that the ants feed the bacteria through glands connected to these crypts," said Dr Garret Suen, a post-doctoral fellow in Professor Currie's lab. "Also, the bacteria get a protected environment in which to grow, away from the intense competition they would face if they lived in other environments such as the soil."

"Interestingly, the tight association between ant, bacteria and pathogen will sometimes result in the pathogen winning. This interplay has been described as a chemical 'arms race' between the bacteria and fungus, with one side beating the other as new compounds are evolved," said Professor Currie. "At the moment, we are beginning to understand the chemical warfare at the genetic level, and it is likely that these types of interactions are more prevalent in nature than previously thought."

So how exactly does an ant go about forming partnerships with a fungus and a bacterium? No one really knows. With new advances in molecular and genetic technologies, such as whole-genome sequencing, Professor Currie and Dr Suen hope to discover how these associations were established, and to understand how these interactions resulted in the remarkable fungus-growing ability of the ants.

Sunday, November 30, 2008

if i had fingers that fast, i could pinch off flesh

Panamanian Termite Goes Ballistic: Fastest Mandible Strike In The World

ScienceDaily (Nov. 29, 2008) — A single hit on the head by the termite Termes panamensis (Snyder), which possesses the fastest mandible strike ever recorded, is sufficient to kill a would-be nest invader, report Marc Seid and Jeremy Niven, post-doctoral fellows at the Smithsonian Tropical Research Institute and Rudolf Scheffrahn from the University of Florida.

Niven and Seid conducted the study at the Smithsonian's new neurobiology laboratory in Panama, established by a donation from the Frank Levinson Family Foundation. The laboratory was built to use Panama's abundant insect biodiversity to understand the evolution of brain miniaturization.

"Ultimately, we're interested in the evolution of termite soldiers' brains and how they employ different types of defensive weaponry," says Seid. Footage of the soldier termite's jaws as they strike an invader at almost 70 meters per second was captured on a high speed video camera in the laboratory at 40,000 frames per second. "Many insects move much faster than a human eye can see so we knew that we needed high speed cameras to capture their behavior, but we weren't expecting anything this fast. If you don't know about the behavior, you can't hope to understand the brain," Seid adds.

Why are the termites so fast? When insects become small they have difficulty generating forces that inflict damage. "To create a large impact force with a light object you need to reach very high velocities before impact," Niven explains.

The Panamanian termite's strike is the fastest mandible strike recorded, albeit over a very short distance. Because a termite soldier faces down its foe inside a narrow tunnel and has little room to parry and little time to waste, this death blow proves to be incredibly efficient.

The force for the blow is stored by deforming the jaws, which are held pressed against one another until the strike is triggered. This strategy of storing up energy from the muscles to produce fast movements is employed by locusts, trap-jaw ants and froghoppers. "The termites need to store energy to generate enough destructive force. They appear to store the energy in their mandibles but we still don't know how they do this—that's the next question," says Niven.

A full report of the study appears in the Nov. 25, 2008 issue of the journal Current Biology.

beetles with antibiotics

yay, enough emoing, back to awesome articles

Some Beetles Can Quickly Neutralize Bacteria And Reduce Emergence Of Resistant Bacteria At Same Time

ScienceDaily (Nov. 29, 2008) — In less than an hour, the immune system of the beetle Tenebrio molitor neutralizes most of the bacteria infecting its hemolymph (the equivalent to blood in vertebrates); this is rendered possible by a cascade of ready-to-use cells and enzymes.

Bacteria that resist these "front-line" defenses are then dealt with by antimicrobial peptides – a sort of natural antibiotic – which halt their proliferation. A clearer understanding of these actors in insect immunity may make it possible to design treatments that prevent the development of drug resistance.

This has been shown in the results of a study carried out by the Equipe Ecologie Evolutive in the Laboratoire Biogéosciences (CNRS/Université de Bourgogne in Dijon), in collaboration with a British research group, and published in the journal Science.

Microorganisms have a considerable capacity for adaptation to the many strategies implemented to destroy them. Over the past 400 million or so years, the immune system of animals, and notably the relatively simpler system in insects, appears to have succeeded in preventing the evolution of microbial resistance. The secret to this achievement lies in a small toolbox of targeted natural antibiotics, the antimicrobial peptides.

In the present case, the researchers showed that the so-called "constitutive" front-line of cellular and enzymatic defenses in the insect immune system spares a small number of bacteria and thereby favors the development of microbial resistance.  However, a second line of defenses involving antimicrobial peptides synthesized following the elimination of most bacteria by the front line, is able to restrict the growth of these surviving microorganisms, which may lead to their removal.

Thus the principal function of the antimicrobial peptides produced by the insect immune system is to prevent the resurgence of bacteria resistant to the host's constitutive defenses, which will consequently reduce the emergence of resistant bacteria.


Saturday, November 29, 2008

is it worth it?

Alright, it's time for some reflection I guess. For the past 4 years, I gave up opportunities, just so that I could help set up a culture for the school. I changed not only my decisions, but also my way of life and personality, to tell the school that I would be there to help them build up what they need to build up, and set down what is needed. In the first year, I accepted 3 leadership positions, sleeping less in 3 days than I usually sleep in a day, just to get things going. 

Scouts: we started with nothing. Absolutely nothing. In a year, we changed 3 different teacher mentors. Only i was left to make sure that everything flowed smoothly. I personally trained my juniors, forcing myself to relearn things that I probably would never need in my life. This set the foundations of the present scout troop. 

House: how many people knew I was the house captain of 2005? Most, even within Nobel itself, thought I was the vice captain. The shit I put in, staying up till 1am to call everyone down, not an easy job. At least i had the help of my co captain to do the showy stuff, which of course led everyone to think that I was a nobody. We got first in 2005, whatever the school said. 

Council: pretty much my pride and joy. Joined in 2005 because i befriended the right people. But at least I was in. Met 3 friends, who with me, organised one of the best youth days in the history of our school. I will never forget them. watched council rise, fall, rise again, always with it. sat till 9pm to stock take council supplies. stayed till 10 to ensure that programmes went well. stressed over limited resources. never once complained about the lack of recognition. just because i was the least public centred of the lot.

now i look back, how much have i put in? how much could i have done to bring up my name? should i be as glory hunting as the others? i could do less, and still get more in return. anyway, this is how life works no? 
my first team in council: yingzhen, yunzhi, nat. All three have been awesome in many ways. just take a closer look at the awards given out on the 1st of december. outstanding contribution. turns out ultimately, i still haven't done enough to stand out from the remaining 80% of the level. to the school, i'm still just a face in the crowd. just another one of the could be's. 80% of the level, at least a fifth of them never done a single thing for the school. i can't differentiate myself from them. pathetic. i could have rejected the responsibilites. i could have taken a backseat in council, scouts, house. would that make any difference in what the school is now? let someone else take the lead. i would have more time, more sleep, less pain, but no less recognition. because in terms of recognition, i have already hit rock bottom. perhaps, my grades might even have been better, i might even be able to break into the distinction category. oh look, MORE recognition for doing less. 

School: please don't give me false hopes. "because of your contribution to the school, we have decided to put you as vice president for alumni" was that to pacify me? because i think it's failed. 5 students given the award of outstanding contribution. 60% of them NOT in the alumni. ms valedictarian: NOT in alumni. they contributed so much already. why not let THEM lead the alumni? honestly speaking. you just had to pick 4 people from the list of volunteers, and give reasons for why you chose them. please give honest answers. "we needed to find people. we rolled some dice. you came up" will do. i can take it. telling me something you don't believe in. that, i won't. 

4 years of my time in NUS High School. 3 years, attention was directed only at the school's wellbeing. last year to try and save my own sorry ass from the depths of "just another face". looks like it wasn't enough. was it worth it?

Saturday, November 22, 2008

a plastic brain. interesting.

Forgotten But Not Gone: How The Brain Re-learns

ScienceDaily (Nov. 22, 2008) — Thanks to our ability to learn and to remember, we can perform tasks that other living things can not even dream of. However, we are only just beginning to get the gist of what really goes on in the brain when it learns or forgets something. What we do know is that changes in the contacts between nerve cells play an important role. But can these structural changes account for that well-known phenomenon that it is much easier to re-learn something that was forgotten than to learn something completely new?

Scientists at the Max Planck Institute of Neurobiology have been able to show that new cell contacts established during a learning process stay put, even when they are no longer required. The reactivation of this temporarily inactivated "stock of contacts" enables a faster learning of things forgotten.

While an insect still flings itself against the window-pane after dozens of unsuccessful attempts to gain its freedom, our brain is able to learn very complex associations and sequences of movement. This not only helps us to avoid accidents like walking into glass doors, but also enables us to acquire such diverse skills as riding a bicycle, skiing, speaking different languages or playing an instrument. Although a young brain learns more easily, we retain our ability to learn up to an advanced age. For a long time, scientists have been trying to ascertain exactly what happens in the brain while we learn or forget.

Flexible connections

To learn something, in other words, to successfully process new information, nerve cells make new connections with each other. When faced with an unprecedented piece of information, for which no processing pathway yet exists, filigree appendages begin to grow from the activated nerve cell towards its neighbours. Whenever a special point of contact, called synapse, forms at the end of the appendage, information can be transferred from one cell to the next - and new information is learned. Once the contact breaks down, we forget what we have learned.

The subtle difference between learning and relearning

Although learning and memory were recently shown to be linked to the changes in brain structure mentioned above, many questions still remain unanswered. What happens, for example, when the brain learns something, forgets it after a while and then has to learn it again later? By way of example, we know from experience that, once we have learned to ride a bicycle, we can easily pick it up again, even if we haven’t practiced for years. In other cases too, "relearning" tends to be easier than starting "from scratch". Does this subtle difference also have its origins in the structure of the nerve cells?

Cell appendages abide the saying "a bird in the hand …"

Scientists at the Max Planck Institute of Neurobiology have now managed to show that there are indeed considerable differences in the number of new cell contacts made - depending on whether a piece of information is new or is being learned second time around. Nerve cells that process visual information, for instance, produced a considerably higher number of new cell contacts if the flow of information from their "own" eye was temporarily blocked. After approximately five days, the nerve cells had rearranged themselves so as to receive and process information from the other eye - the brain had resigned itself to having only one eye at its disposal. Once information flowed freely again from the eye that had been temporarily closed, the nerve cells resumed their original function and now more or less ignored signals from the alternative eye.

"What surprised us most, however, was that the majority of the appendages which developed in response to the information blockade, continued to exist, despite the fact that the blockade was abolished ", project leader Mark Hübener explains. Everything seems to point to the fact that synapses are only disabled, but not physically removed. "Since an experience that has been made may occur again at a later point in time, the brain apparently opts to save a few appendages for a rainy day", Hübener continues. And true enough, when the same eye was later inactivated again, the nerve cells reorganized themselves much more quickly - because they could make use of the appendages that had stayed in place.

Useful reactivation

Many of the appendages that develop between nerve cells are thus maintained and facilitate later relearning. This insight is crucial to our understanding of the fundamental processes of learning and memory. And so, even after many years of abstinence, it should be no great problem if we want to have a go at skiing again this winter.

should probably stop getting surprised at what earth can offer.

New Life Beneath Sea And Ice

ScienceDaily (Nov. 21, 2008) — Scientists have long known that life can exist in some very extreme environments. But Earth continues to surprise us.

At a European Science Foundation and COST (European Cooperation in the field of Scientific and Technical Research) 'Frontiers of Science' meeting in Sicily in October, scientists described apparently productive ecosystems in two places where life was not known before, under the Antarctic ice sheet, and above concentrated salt lakes beneath the Mediterranean. In both cases, innumerable tiny microbes are fixing or holding onto quantities of organic carbon large enough to be significant in the global carbon cycle.

Lakes under the ice

Brent Christner of Louisiana State University, in the US, told the conference about the microbes living within and beneath the ice on Antarctica. In the last decade, scientists have discovered lakes of liquid water underneath the Antarctic ice sheet. So far we know of about 150 lakes, but this number will probably increase when the entire continent has been surveyed. These lakes occur as a result of geothermal heat trapped by the thick ice, melting it from underneath, and the great pressure from the ice above, which lowers the melting point of water.

The largest subglacial lake, Lake Vostok, lies beneath the coldest place on the planet, where the temperature at the surface often falls below minus 60 degrees Celsius. "It's the sixth largest freshwater lake on the planet by volume, and about the size of Lake Ontario," says Christner. "If you were on a boat in the middle of the lake, you would not see shores."

Christner has examined microbial life in ice cores from Vostok and many other global locations. While direct samples of water from subglacial Antarctic lakes have yet to be obtained, the lower 80m or so of the Vostok ice core represents lake water that progressively freezes onto the base as the ice sheet slowly traverses the lake. "Microbial cell and organic carbon concentrations in this accreted ice are significantly higher than those in the overlying ice, which implies that the subglacial environment is the source," says Christner.

Based on accumulating measurements of microbes in the subglacial environment, he calculates that the concentration of cell and organic carbon in the Earth's ice sheets, or 'cryosphere', may be hundreds of times higher than what is found in all the planet's freshwater systems. "Glacial ice is not currently considered as a reservoir for organic carbon and biology," says Christner, "but that view has to change."

Salt below the sea

Beneath the Mediterranean lurks a similar surprise. Michail Yakimov of the Institute of the Coastal Marine Environment, Messina, Italy is a project leader for the European Science Foundation's EuroDEEP programme on ecosystem functions and biodiversity in the deep sea. His team studies lakes of concentrated salt solution, known as anoxic hypersaline basins, on the floor of the Mediterranean. They have discovered extremely diverse microbial communities on the surfaces of such lakes.

The anoxic basins, so called because they are devoid of oxygen, occur below 3,000 m beneath the surface and are five to ten times more saline than seawater. One theory says they exist uniquely in the Mediterranean, because this sea entirely evaporated after it was cut off from the Atlantic around 250 million years ago. Its salt became a layer of rock salt, called evaporite, which was then buried by windblown sediment. Now the sea is filled again, the salt layer has been exposed in some places, perhaps by small seaquakes, and the salts from the ancient Mediterranean have dissolved again, making the water very salty.

Despite the harsh conditions, hypersaline brines have been shown to possess a wide range of active microbial communities. Together with other international partners, Yakimov's team has already identified more than ten new lineages of bacteria and archaea (these are ancient bacteria-like organisms), which they have named the Mediterranean Sea Brine Lake Divisions.

There is ample life at the boundary between the concentrated basin and the ordinary seawater. "Because of the very high density of the brine, it does not mix with seawater," he explains, "and there is a sharp interface, about 1m thick."

In that layer, microbial diversity is incredibly rich. The research shows that these microbes largely live by sulphide oxidation. Like the communities at hydrothermal vents in the deep ocean, they can survive independently of sunlight and oxygen. But they are an important store for organic carbon. "The deep-sea microbial communities in the Mediterranean fix as much or even more carbon dioxide each year as those in the surface layers," says Yakimov. "This carbon sink should be taken into account at the global scale."

This research was presented at the "Complex Systems: Water and Life" Frontiers of Science conference, organized by European Science Foundation and COST, 29-31 October, Taormina, Sicily.

Friday, November 21, 2008

fatal to dawin theory? creationists, take that!

Darwin Was Right About How Evolution Can Affect Whole Group

ScienceDaily (Nov. 20, 2008) — Worker ants of the world, unite! You have nothing to lose but your fertility. The highly specialized worker castes in ants represent the pinnacle of social organization in the insect world. As in any society, however, ant colonies are filled with internal strife and conflict. So what binds them together? More than 150 years ago, Charles Darwin had an idea and now he's been proven right.

Evolutionary biologists at McGill University have discovered molecular signals that can maintain social harmony in ants by putting constraints on their fertility. Dr. Ehab Abouheif, of McGill's Department of Biology, and post-doctoral researcher, Dr. Abderrahman Khila, have discovered how evolution has tinkered with the genes of colonizing insects like ants to keep them from fighting amongst themselves over who gets to reproduce.

"We've discovered a really elegant developmental mechanism, which we call 'reproductive constraint,' that challenges the classic paradigm that behaviour, such as policing, is the only way to enforce harmony and squash selfish behaviour in ant societies," said Abouheif, McGill's Canada Research Chair in Evolutionary Developmental Biology.

Reproductive constraint comes into play in these ant societies when evolutionary forces begin to work in a group context rather than on individuals, the researchers said. The process can be seen in the differences between advanced ant species and their more primitive cousins. The study was published in the Nov. 18 edition of the Proceedings of the National Academy of Sciences.

Ants – organized in colonies around one or many queens surrounded by their specialized female workers – are classic examples of what are called eusocial organisms.

"More primitive, or ancestral, ants tend to have smaller colony sizes and have much higher levels of conflict over reproduction than the more advanced species," Abouheif explained. "That's because the workers have a much higher reproductive capacity and there is conflict with the queen to produce offspring."

To their surprise, Khila and Abouheif discovered that "evolution has tinkered with the molecular signals that are used by the egg to determine what's going to be the head and what's going to be the tail, to stop the worker ants from producing viable offspring," Abouheif explained. "Different species of ants have different levels of this "reproductive constraint," and we believe those levels provide a measure of how eusocial the colony is. The less the workers reproduce, the more coherent the group becomes."

The existence of sterile castes of ants tormented Charles Darwin as he was formulating his Theory of Natural Selection, and he described them as the "one special difficulty, which at first appeared to me insuperable, and actually fatal to my theory." If adaptive evolution unfolds by differential survival of individuals, how can individuals incapable of passing on their genes possibly evolve and persist?

Darwin proposed that in the case of ant societies natural selection applies not only to the individual, because the individual would never benefit by cutting its own reproduction, but also to the family or group. This study supports Darwin's prescient ideas, and provides a molecular measure of how an entire colony can be viewed as a single or "superorganism."

Tuesday, November 18, 2008

philosophy can eat shit today. i'm blogging about this. 

i'm starting to get pissed. i mean, what's wrong with courts? they tell me the comp is nice, i pay 1.6k for it, they send me the wrong comp, take another 2 weeks to get it right, decide to come over to add the ram later, effectively destroying the acer warrantee, while looking like freaking beginners while adding it.

NOW, with no acer warrantee, but only with courts warrantee, my comp starts screwing up with the stupid flickering screen, which doesn't happen when i put it on my 4 year old comp, and then my comp starts blue screening for starting up windows, i send it over to courts, and they tell me my comp is fine? after handling it myself (means the goodness knows how much paid for the 3 year courts warrantee is pointless), i get it to normal. and now it's still crashing on me. for? using google chrome. for? using msn. software problem? no. i reformatted it, deleting all my beautiful saved games and anime cos it crashes when i try to back THAT up. 

what's the freaking problem with courts man? give me lousy shit, then tell me the shit's strawberries? you think i'm a 2 year old pooper? i know shit when i get smacked in the face with it. should have realised it was shit when i saw it from 2 miles off.

Tuesday, November 11, 2008

catalytic power of emzymes

Without Enzyme, Biological Reaction Essential To Life Takes 2.3 Billion Years

ScienceDaily (Nov. 11, 2008) — All biological reactions within human cells depend on enzymes. Their power as catalysts enables biological reactions to occur usually in milliseconds. But how slowly would these reactions proceed spontaneously, in the absence of enzymes – minutes, hours, days? And why even pose the question?

One scientist who studies these issues is Richard Wolfenden, Ph.D., Alumni Distinguished Professor Biochemistry and Biophysics and Chemistry at the University of North Carolina at Chapel Hill. Wolfenden holds posts in both the School of Medicine and in the College of Arts and Sciences and is a member of the National Academy of Sciences.

In 1995, Wolfenden reported that without a particular enzyme, a biological transformation he deemed "absolutely essential" in creating the building blocks of DNA and RNA would take 78 million years.

"Now we've found a reaction that – again, in the absence of an enzyme – is almost 30 times slower than that," Wolfenden said. "Its half-life – the time it takes for half the substance to be consumed – is 2.3 billion years, about half the age of the Earth. Enzymes can make that reaction happen in milliseconds."

With co-author Charles A. Lewis, Ph.D., a postdoctoral scientist in his lab, Wolfenden published a report of their new findings recently in the online early edition of the Proceedings of the National Academy of Science. The study is also due to appear in the Nov. 11 print edition.

The reaction in question is essential for the biosynthesis of hemoglobin and chlorophyll, Wolfenden noted. But when catalyzed by the enzyme uroporphyrinogen decarboxylase, the rate of chlorophyll and hemoglobin production in cells "is increased by a staggering factor, one that's equivalent to the difference between the diameter of a bacterial cell and the distance from the Earth to the sun."

"This enzyme is essential for both plant and animal life on the planet," Wolfenden said. "What we're defining here is what evolution had to overcome, that the enzyme is surmounting a tremendous obstacle, a reaction half-life of 2.3 billion years."

Knowing how long reactions would take without enzymes allows biologists to appreciate their evolution as prolific catalysts, Wolfenden said. It also enables scientists to compare enzymes with artificial catalysts produced in the laboratory.

"Without catalysts, there would be no life at all, from microbes to humans," he said. "It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction."

Experimental methods for observing very slow reactions can also generate important information for rational drug design based on cellular molecular studies.

"Enzymes that do a prodigious job of catalysis are, hands-down, the most sensitive targets for drug development," Wolfenden said. "The enzymes we study are fascinating because they exceed all other known enzymes in their power as catalysts."

Wolfenden has carried out extensive research on enzyme mechanisms and water affinities of biological compound. His work has also influenced rational drug design, and findings from his laboratory helped spur development of ACE inhibitor drugs, now widely used to treat hypertension and stroke. Research on enzymes as proficient catalysts also led to the design of protease inhibitors that are used to treat HIV infection.

"We've only begun to understand how to speed up reactions with chemical catalysts, and no one has even come within shouting distance of producing, or predicting the magnitude of, their catalytic power," Wolfenden said.

Support for this research came from the National Institute of General Medicine, a component of the National Institutes of Health.

another you

this is a nice song... ^^

Saturday, November 8, 2008

Female models and male self consciousness

Surprisingly, Female Models Have Negative Effect On Men

ScienceDaily (Nov. 7, 2008) — Many studies have shown that media images of female models have had a negative impact on how woman view their own bodies, but does this same effect hold true when men view male models? A leading researcher of media effects on body image at the University of Missouri looked at the effect of male magazines on college-age men.

Completing three different studies, Jennifer Aubrey, assistant professor of communication in the College of Arts and Science, found that unlike their female classmates, it was not the same-sex models that affected the males negatively, but quite the opposite.

In her research, which will be published in Human Communication Research, Aubrey found that the cultural expectation for men is not that they have to be as attractive as their peers, but that they need to be attractive enough to be sexually appealing to women.

In her first study, Aubrey measured male exposure to 'lad' magazines, such as Maxim, FHM and Stuff, which she observes contains two main messages: the visual, which mostly contain sexually suggestive images of women; and textual, which contain articles that speak in a bawdy, male voice about topics including fashion, sex, technology and pop culture. Aubrey also measured male body self-consciousness (a participant's awareness and tendency to monitor one's appearance) and appearance anxiety (the anticipation of threatening stimuli). Participants were asked questions such as "During the day, I think about how I look," and then asked the same questions a year later.

"We found that reading lad magazines was related to having body self-consciousness a year later," said Aubrey. "This was surprising because if you look at the cover of these magazines, they are mainly images of women. We wondered why magazines that were dominated by sexual images of women were having an effect of men's feelings about their own bodies."

To help answer this question, Aubrey collaborated with University of California-Davis Assistant Professor Laramie Taylor. The researchers divided male study participants into three groups. Group one examined layouts from lad magazines that featured objectified women along with a brief description of their appearances. The second group viewed layouts about male fashion, featuring fit and well-dressed male models. The final group inspected appearance-neutral layouts that featured topics including technology and film trivia.

"Men who viewed the layouts of objectified females reported more body self-consciousness than the other two groups," Aubrey said. "Even more surprising was that the male fashion group reported the least amount of body self-consciousness among the three groups."

Aubrey speculated that the exposure to objectified females increased self-consciousness because men are reminded that in order to be sexually or romantically involved with a woman of similar attractiveness, they need to conform to strict appearance standards.

To test her theory, Aubrey and Taylor completed a third study that involved breaking men into two groups. Group one received lad magazine layouts of sexually idealized females and group two received the same layouts with average-looking 'boyfriends' added to the photos, with captions about how the female models are attracted to the average-looking men.

"We found that the men who view the ads with the average-looking boyfriend in the picture reported less body self-consciousness than the men who saw the ads with just the model," Aubrey said.  "When the men felt that the model in the ad liked average-looking guys, it took the pressure off of them and made them less self-conscious about their own bodies."

Wednesday, October 29, 2008

Sexy red one, male brain zero

Now I have even less to say when someone tells me men think only with the trouser titan.

Red Enhances Men's Attraction To Women, Psychological Study Reveals


 

Psychologist Daniel Niesta holding one of the images used in the study. Participants were asked questions including: "Imagine that you are going on a date with this person and have $100 in your wallet. How much money would you be willing to spend on your date?"' (Credit: Image courtesy of University of Rochester)

ScienceDaily (Oct. 28, 2008) — A groundbreaking study by two University of Rochester psychologists to be published online Oct. 28 by the Journal of Personality and Social Psychology adds color—literally and figuratively—to the age-old question of what attracts men to women.

Through five psychological experiments, Andrew Elliot, professor of psychology, and Daniela Niesta, post-doctoral researcher, demonstrate that the color red makes men feel more amorous toward women. And men are unaware of the role the color plays in their attraction.

The research provides the first empirical support for society's enduring love affair with red. From the red ochre used in ancient rituals to today's red-light districts and red hearts on Valentine's Day, the rosy hue has been tied to carnal passions and romantic love across cultures and millennia. But this study, said Elliot, is the only work to scientifically document the effects of color on behavior in the context of relationships.

"It's only recently that psychologists and researchers in other disciplines have been looking closely and systematically at the relationship between color and behavior. Much is known about color physics and color physiology, but very little about color psychology," said Elliot. "It's fascinating to find that something as ubiquitous as color can be having an effect on our behavior without our awareness."

Although this aphrodisiacal effect of red may be a product of societal conditioning alone, the authors argue that men's response to red more likely stems from deeper biological roots. Research has shown that nonhuman male primates are particularly attracted to females displaying red. Female baboons and chimpanzees, for example, redden conspicuously when nearing ovulation, sending a clear sexual signal designed to attract males.

"Our research demonstrates a parallel in the way that human and nonhuman male primates respond to red," concluded the authors. "In doing so, our findings confirm what many women have long suspected and claimed – that men act like animals in the sexual realm. As much as men might like to think that they respond to women in a thoughtful, sophisticated manner, it appears that at least to some degree, their preferences and predilections are, in a word, primitive."

To quantify the red effect, the study looked at men's responses to photographs of women under a variety of color presentations. In one experiment, test subjects looked at a woman's photo framed by a border of either red or white and answered a series of questions, such as: "How pretty do you think this person is?" Other experiments contrasted red with gray, green, or blue.

When using chromatic colors like green and blue, the colors were precisely equated in saturation and brightness levels, explained Niesta. "That way the test results could not be attributed to differences other than hue."

In the final study, the shirt of the woman in the photograph, instead of the background, was digitally colored red or blue. In this experiment, men were queried not only about their attraction to the woman, but their intentions regarding dating. One question asked: "Imagine that you are going on a date with this person and have $100 in your wallet. How much money would you be willing to spend on your date?"

Under all of the conditions, the women shown framed by or wearing red were rated significantly more attractive and sexually desirable by men than the exact same women shown with other colors. When wearing red, the woman was also more likely to score an invitation to the prom and to be treated to a more expensive outing.

The red effect extends only to males and only to perceptions of attractiveness. Red did not increase attractiveness ratings for females rating other females and red did not change how men rated the women in the photographs in terms of likability, intelligence or kindness.

Although red enhances positive feelings in this study, earlier research suggests the meaning of a color depends on its context. For example, Elliot and others have shown that seeing red in competition situations, such as written examinations or sporting events, leads to worse performance.

The current findings have clear implications for the dating game, the fashion industry, product design and marketing.

http://www.sciencedaily.com/releases/2008/10/081028074323.htm

Friday, October 24, 2008

more ironies: skin moisturizing cream makes skins dryer

hmm, expected i guess? just like taking medicine, or painkillers, the more you take, the less your body is adapted to it.

Skin Creams Can Make Skin Drier

ScienceDaily (Oct. 23, 2008) — Many people have noticed that as soon as you start using a skin cream, you have to continue with it; if you stop lubricating, your skin becomes drier than when you started. And now there is research to confirm for the first time that normal skin can become drier from creams.

Izabela Buraczewska presents these findings in the dissertation she is publicly defending at Uppsala University in Sweden on October 24.

The findings in Izabela Buraczewska’s dissertation confirm what many have suspected: creams can make the skin drier. She has studied what happens in the skin at the molecular level and also what positive and negative effects creams have on the skin. Her research shows that differences in the pH of creams do not seem to play any role.

Different oils were also studied in a seven-week treatment period, but no difference was established between mineral oil and a vegetable oil. Both oils resulted in the skin being less able to cope with external stresses. Treatment with a more complex cream compound, however, resulted in more resistant skin with no signs of dryness.

Tissues samples taken from the treated skin areas also show that the weakening of the skin’s protective barrier can be tied to changes in the activity of certain genes involved in producing skin fats, among other functions. The conclusion is that the contents of creams impact these effects on the skin. This knowledge enhances our potential to develop creams that reinforce the skin’s protective barrier in a positive way, without making the skin drier. Such creams would mean that various groups of patients with dry skin, for example eczema and ichthyosis, could enjoy a better quality of life.

“My findings show that creams differ and that knowledge of the effect of various ingredients is important for us to be able to tailor the treatment to various skin types,” says Izabela Buraczewska.

Vetenskapsrådet (The Swedish Research Council) (2008, October 23). Skin Creams Can Make Skin Drier. ScienceDaily. Retrieved October 24, 2008, from http://www.sciencedaily.com­ /releases/2008/10/081022101500.htm

Tuesday, October 21, 2008

twitter?

right, was in a state of "I'M BLOODY PISSED WITH THE SCHOOL EMAIL FOR MAKING ME CLICK 700 TIMES JUST TO DELETE MY INBOX" when i decided these kinds of rants shouldn't go on my blog since its so "high and mighty and so educational" and stuff. technically this shouldn't even be here -.-

alright.. stuff like this shall go on my twitter instead. XD

ok. since this IS supposed to be educational, i'll just throw in a couple of food for thought.

these giant magnets are smaller than i thought... =/

Ancient microbes made giant magnets

Magnetic fossils show how climate change creates new extremes.

Scientists have unearthed giant magnetic fossils, the remnants of microbes buried in 55-million-year-old sediment. The growth of these unusual structures during a period of massive global warming provides clues about how climate change might alter the behaviour of organisms.

Some bacteria, both living and fossilized, contain magnetite — magnetic iron oxide crystals — that the organisms are thought to use to navigate, orienting themselves along the magnetic field lines of the Earth. But the new fossils are "unlike any magnetite crystal ever described", says Dirk Schumann of McGill University in Montreal, Canada.

Schumann and his colleagues found the fossils in sediment taken from a borehole in Ancora, New Jersey. The team dissolved the sediment in water and used a magnet to extract magnetite, which they then studied under the electron microscope. They found that the magnetite crystals contained oxygen isotopes that showed they were of aquatic origin.

Here be giants

Most of the fossils were "giants" in the world of magnetite producing microorganisms, says Schumann, up to eight times as large as those previously seen. Some were up to 4 micrometres in length. Even the shapes, like spear heads and elongated diamonds, were forms that have never been seen before in the magnetite structures of fossils or living organisms. The team reports its findings in the Proceedings of the National Academy of Sciences.1

Scientists know of no microorganisms that create such large or oddly shaped magnetite crystals. Schumann says that the newly discovered crystals must have come from eukaryotes — a more complex form of life than the bacteria from which most previous magnetite crystals are thought to have come. "That's a convincing argument, and these new fossils are very intriguing," says Richard Frankel, a retired California Polytechnic State University physicist in San Luis Obispo, who studied magnetite-loving bacteria.

The giant microbes may have been using their crystals for orientation. It is also possible that some used the spear-like crystals as coats of armour, says co-author Robert Kopp of Princeton University in New Jersey. A type of living snail, discovered near deep-sea vents in the Indian Ocean, uses a similar material for protection. The snail grows iron-sulphide scales over its foot, from which it can excrete toxic sulphides.

Perfect climate

The sediments in which the crystals were found dated back 55 million years, to the Paleocene-Eocene Thermal Maximum. This was a time period stretching tens of thousands of years, during which Earth's global temperature spiked abruptly by around 5–9° Celsius.

This suggests that major changes in climate made the conditions perfect for bigger microbes to start "loving" iron oxide, says earth scientist James Zachos at University of California, Santa Cruz. The finding backs predictions that the ecology of the coastal oceans will change in unexpected ways as temperatures rise with current global warming, he says.

To pin down the function of the crystals, the team will search for modern microorganisms that make magnetite structures of the same sizes and shapes. They might find them in tropical oceanic shelves fed by energetic river systems, such as the Amazon, where the amount of reactive iron is twice that of delta environments such as New Jersey's coast. This will tell scientists "a lot about the conditions that allowed these structures to grow in the first place", says Kopp.

  • References

    1. Schumann, D. et al. Proc. Natl Acad. Sci doi: 10.1073/pnas.0803634105 (2008).

Thursday, October 9, 2008

Again, women takes the backseat in research front..

Who cares about eggs and ovaries when you can get the same from sperm and balls?

We have more too! XD

Human Testicles Yield Stem Cells

Brian Handwerk 
for National Geographic News

October 8, 2008

  

Scientists have derived potentially therapeutic stem cells from adult, human testicles—a development that may eventually make new medical treatments possible while avoiding moral dilemmas.

Stem cell generation for individual therapies could address a wide range of ailments, including Parkinson's disease, leukemia, and spinal cord injuries.

So far, the most versatile human stem cells have come from embryos—fertilized eggs—that critics say should not be used in scientific research because they are potential humans. 

(Read about the stem cell divide in National Geographic Magazine.) 

Study co-author Thomas Skutella, of the University of Tübingen in Baden-Württemberg, Germany, and his team isolated stem cells from adult, human testicles and cultivated them to become pluripotent cells, which can develop into many other types of cells.

"In the sense that they become pluripotent, they are like embryonic stem cells," Skutella wrote in an email. 

Easing Concerns

A major breakthrough was made in 2006, when several research teams harvested stem cells from the testicles of adult mice

Duplicating the feat in humans had proved elusive prior to research published online this week in Nature

Japanese researchers announced in August that they had isolated stem cells in adult, human teeth, but the team's work was not peer reviewed. 

"As you might imagine, this is a pretty significant step forward," said Chad Cowan of Harvard University's Department of Stem Cell and Regenerative Biology. 

Cowan is unaffiliated with the research. 

"It looks like [the cells] have a broader development potential to become a lot of the different cell types we'd be interested in," he added. 

"It's very exciting that we may now have a non-ethically troubling source of pluripotent cells for humans—or at least males." 

One's Own Cells

The cells, which can be harvested from living men, may also remove some immunological obstacles.

"The exciting thing about this source of stem cells is that they are the patient's own and can be used to develop individual cell-based therapies that will not provoke any kind of immune reaction," Skutella said.

"That is one of the big drawbacks of embryonic stem cells: Quite aside from the grave ethical considerations, they remain a foreign body and will always create immunological problems." 

Scientists hope that a similar cell source can be found in women. 

Cellular Toolbox

But Skutella cautioned that the research is just a valuable step forward, and scientists must learn how to harness the cells to benefit patients. 

Though pluripotent stem cells can be differentiated into any other kind of cell, they can't be implanted in their pluripotent state. They must be differentiated so that they self-renew as only one specific type of cell. 

"Stem cell therapy is extremely promising, but it is still in its infancy," Skutella explained. 

"You could think of it like this: What we have successfully done right now is identify a mother lode. That ore now needs to be forged into tools, i.e. the various differentiated cell lines," he wrote. 

"Then someone needs to figure out how to use those tools to fix what's broken, [that is] to develop concrete therapies."

Tuesday, October 7, 2008

Enzymes that do TWO things! Whoa!

Cool, more general than it's supposed to be. Also, the bio teacher's nightmare: proteins are extremely specific, and can only do one thing. "but sir, there's this virus with a protein that can do TWO things! HA!!"

'Two In One' Enzyme: Unusually Flexible

ScienceDaily (Oct. 6, 2008) — Scientists from the Ruhr-University Bochum (RUB) have solved the structure of an unusually flexible enzyme in a virus that infects marine bacteria.

The virus, which infects the marine cyanobacterium Prochlorococcus, can produce specific pigments more effectively than its host can. It requires only one enzyme, in contrast to the host Prochlorococcus, which needs two enzymes. The virus makes use of phycoerythrobilin synthase, a "two in one" enzyme.

As part of his dissertation, Thorben Dammeyer, a member of the research team under the supervision of Prof. Nicole Frankenberg-Dinkel (Physiology of Microorganisms) and Assistant Professor Dr. Eckhard Hofmann (X-ray diffraction analysis of proteins), solved the 3D structure of the enzyme. An unexpected flexibility was discovered, allowing sections of the protein to assume different positions – an unusual property for proteins in combination with their substrate.

The scientists have documented their results, honored as "Paper of the Week," in the current issue of the Journal of Biological Chemistry.

Pigments are produced in two steps

The so-called P-SSM2 virus with the "two in one" enzyme infects the cyanobacterium Prochlorococcus, a cyanobacterium found in extremely large numbers in the worlds oceans. The virus does however differ in that - in contrast to its cyanobacterial relatives - it does not harvest light for photosynthesis via red and blue pigments, but with chlorophyll, as is the case with higher plants. Nevertheless Prochlorococcus contains all the genetic information for the entire machinery required to produce these pigments. This takes place in two steps with two different enzymes as catalysts.

Green turns red in one step

Nicole Frankenberg-Dinkel stated that "we have discovered the genetic blueprint for an enzyme within the virus. This enzyme is capable of producing the red pigment more effectively than its host, which has convinced us that the pigment cannot be unimportant for Prochlorococcus, even if it is not required for light trapping. On the other hand, we obviously wanted to know how this enzyme can combine two functions."

The scientists used X-ray diffraction analysis to determine the 3D structure of the enzyme at atomic resolution both alone and in complex with its natural substrate, the green biliverdin IXa. This molecule was found in the binding pocket of the protein, where the conversion into a red pigment takes place.

Prof. Frankenberg-Dinkel explained that the scientists were able to observe how different parts of the enzyme around the binding pocket are capable of assuming different positions. "This property might not be unusual for proteins in solution, but is extremely rarely found in protein crystals." The structural variations observed supplied the scientists with the first indications of the movements of the enzyme during catalysis.

Next step: tracking the evolution

The next stage of research will consist of studies of targeted and randomly genetically altered forms of the unusually flexible protein. Using this system, the scientists want to observe the in vitro evolution of this specific enzyme. Nicole Frankenberg-Dinkel's and Eckhard Hofmann's research teams are funded by the Collaborative Research Centre 480 "Molecular Biology of Complex Functions in Botanical Systems."

Monday, October 6, 2008

Not kidding. This article is not for the faint of heart.

Big Bang or Big Bounce?: New Theory on the Universe's Birth

Our universe may have started not with a big bang but with a big bounce—an implosion that triggered an explosion, all driven by exotic quantum-gravitational effects

By Martin Bojowald

Atoms are now such a commonplace idea that it is hard to remember how radical they used to seem. When scientists first hypothesized atoms centuries ago, they despaired of ever observing anything so small, and many questioned whether the concept of atoms could even be called scientific. Gradually, however, evidence for atoms accumulated and reached a tipping point with Albert Einstein's 1905 analysis of Brownian motion, the random jittering of dust grains in a fluid. Even then, it took another 20 years for physicists to develop a theory explaining atoms—namely, quantum mechanics—and another 30 for physicist Erwin Müller to make the first microscope images of them. Today entire industries are based on the characteristic properties of atomic matter.

Physicists' understanding of the composition of space and time is following a similar path, but several steps behind. Just as the behavior of materials indicates that they consist of atoms, the behavior of space and time suggests that they, too, have some fine-scale structure—either a mosaic of spacetime "atoms" or some other filigree work. Material atoms are the smallest indivisible units of chemical compounds; similarly, the putative space atoms are the smallest indivisible units of distance. They are generally thought to be about 10–35 meter in size, far too tiny to be seen by today's most powerful instruments, which probe distances as short as 10–18 meter. Consequently, many scientists question whether the concept of atomic spacetime can even be called scientific. Undeterred, other researchers are coming up with possible ways to detect such atoms indirectly.

The most promising involve observations of the cosmos. If we imagine rewinding the expansion of the universe back in time, the galaxies we see all seem to converge on a single infinitesimal point: the big bang singularity. At this point, our current theory of gravity—Einstein's general theory of relativity—predicts that the universe had an infinite density and temperature. This moment is sometimes sold as the beginning of the universe, the birth of matter, space and time. Such an interpretation, however, goes too far, because the infinite values indicate that general relativity itself breaks down. To explain what really happened at the big bang, physicists must transcend relativity. We must develop a theory of quantum gravity, which would capture the fine structure of spacetime to which relativity is blind.

The details of that structure came into play under the dense conditions of the primordial universe, and traces of it may survive in the present-day arrangement of matter and radiation. In short, if spacetime atoms exist, it will not take centuries to find the evidence, as it did for material atoms. With some luck, we may know within the coming decade.

Pieces of Space
Physicists have devised several candidate theories of quantum gravity, each applying quantum principles to general relativity in a distinct way. My work focuses on the theory of loop quantum gravity ("loop gravity," for short), which was developed in the 1990s using a two-step procedure. First, theorists mathematically reformulated general relativity to resemble the classical theory of electromagnetism; the eponymous "loops" of the theory are analogues of electric and magnetic field lines. Second, following innovative procedures, some that are akin to the mathematics of knots, they applied quantum principles to the loops. The resulting quantum gravity theory predicts the existence of spacetime atoms [see "
Atoms of Space and Time," by Lee Smolin; Scientific American, January 2004].

Other approaches, such as string theory and so-called causal dynamical triangulations, do not predict spacetime atoms per se but suggest other ways that sufficiently short distances might be indivisible [see "The Great Cosmic Roller-Coaster Ride," by Cliff Burgess and Fernando Quevedo; Scientific American, November 2007, and "The Self-Organizing Quantum Universe," by Jan Ambjørn, Jerzy Jurkiewicz and Renate Loll; Scientific American, July]. The differences among these theories have given rise to controversy, but to my mind the theories are not contradictory so much as complementary. String theory, for example, is very useful for a unified view of particle interactions, including gravity when it is weak. For the purpose of disentangling what happens at the singularity, where gravity is strong, the atomic constructions of loop gravity are more useful.

The theory's power is its ability to capture the fluidity of spacetime. Einstein's great insight was that spacetime is no mere stage on which the drama of the universe unfolds. It is an actor in its own right. It not only determines the motion of bodies within the universe, but it evolves. A complicated interplay between matter and spacetime ensues. Space can grow and shrink.

Loop gravity extends this insight into the quantum realm. It takes our familiar understanding of particles of matter and applies it to the atoms of space and time, providing a unified view of our most basic concepts. For instance, the quantum theory of electromagnetism describes a vacuum devoid of particles such as photons, and each increment of energy added to this vacuum generates a new particle. In the quantum theory of gravity, a vacuum is the absence of spacetime—an emptiness so thorough we can scarcely imagine it. Loop gravity describes how each increment of energy added to this vacuum generates a new atom of spacetime.

The spacetime atoms form a dense, ever shifting mesh. Over large distances, their dynamism gives rise to the evolving universe of classical general relativity. Under ordinary conditions, we never notice the existence of these spacetime atoms; the mesh spacing is so tight that it looks like a continuum. But when spacetime is packed with energy, as it was at the big bang, the fine structure of spacetime becomes a factor, and the predictions of loop gravity diverge from those of general relativity.

Attracted to Repulsion
Applying the theory is an extremely complex task, so my colleagues and I use simplified versions that capture the truly essential features of the universe, such as its size, and ignore details of lesser interest. We have also had to adapt many of the standard mathematical tools of physics and cosmology. For instance, theoretical physicists commonly describe the world using differential equations, which specify the rate of change of physical variables, such as density, at each point in the spacetime continuum. But when spacetime is grainy, we instead use so-called difference equations, which break up the continuum into discrete intervals. These equations describe how a universe climbs up the ladder of sizes that it is allowed to take as it grows. When I set out to analyze the cosmological implications of loop gravity in 1999, most researchers expected that these difference equations would simply reproduce old results in disguise. But unexpected features soon emerged.

Gravity is typically an attractive force. A ball of matter tends to collapse under its own weight, and if its mass is sufficiently large, gravity overpowers all other forces and compresses the ball into a singularity, such as the one at the center of a black hole. But loop gravity suggests that the atomic structure of spacetime changes the nature of gravity at very high energy densities, making it repulsive. Imagine space as a sponge and mass and energy as water. The porous sponge can store water but only up to a certain amount. Fully soaked, it can absorb no more and instead repels water. Similarly, an atomic quantum space is porous and has a finite amount of storage space for energy. When energy densities become too large, repulsive forces come into play. The continuous space of general relativity, in contrast, can store a limitless amount of energy.

Because of the quantum-gravitational change in the balance of forces, no singularity—no state of infinite density—can ever arise. According to this model, matter in the early universe had a very high but finite density, the equivalent of a trillion suns in every proton-size region. At such extremes, gravity acted as a repulsive force, causing space to expand; as densities moderated, gravity switched to being the attractive force we all know. Inertia has kept the expansion going to the present day.

In fact, the repulsive gravity caused space to expand at an accelerating rate. Cosmological observations appear to require such an early period of acceleration, known as cosmic inflation. As the universe expands, the force driving inflation slowly subsides. Once the acceleration ends, surplus energy is transferred to ordinary matter, which begins to fill the universe in a process called reheating. In current models, inflation is somewhat ad hoc—added in to conform to observations—but in loop quantum cosmology, it is a natural consequence of the atomic nature of spacetime. Acceleration automatically occurs when the universe is small and its porous nature still quite significant.

Time before Time
Without a singularity to demarcate the beginning of time, the history of the universe may extend further back than cosmologists once thought possible. Other physicists have reached a similar conclusion [see "The Myth of the Beginning of Time," by Gabriele Veneziano; Scientific American, May 2004], but only rarely do their models fully resolve the singularity; most models, including those from string theory, require assumptions as to what might have happened at this uneasy spot. Loop gravity, in contrast, is able to trace what took place at the singularity. Loop-based scenarios, though admittedly simplified, are founded on general principles and avoid introducing new ad hoc assumptions.

Using the difference equations, we can try to reconstruct the deep past. One possible scenario is that the initial high-density state arose when a preexisting universe collapsed under the attractive force of gravity. The density grew so high that gravity switched to being repulsive, and the universe started expanding again. Cosmologists refer to this process as a bounce.

The first bounce model investigated thoroughly was an idealized case in which the universe was highly symmetrical and contained just one type of matter. Particles had no mass and did not interact with one another. Simplified though this model was, understanding it initially required a set of numerical simulations that were completed only in 2006 by Abhay Ashtekar, Tomasz Pawlowski and Parampreet Singh, all at Pennsylvania State University. They considered the propagation of waves representing the universe both before and after the big bang. The model clearly showed that a wave would not blindly follow the classical trajectory into the abyss of a singularity but would stop and turn back once the repulsion of quantum gravity set in.

An exciting result of these simulations was that the notorious uncertainty of quantum mechanics seemed to remain fairly muted during the bounce. A wave remained localized throughout the bounce rather than spreading out, as quantum waves usually do. Taken at face value, this result suggested that the universe before the bounce was remarkably similar to our own: governed by general relativity and perhaps filled with stars and galaxies. If so, we should be able to extrapolate from our universe back in time, through the bounce, and deduce what came before, much as we can reconstruct the paths of two billiard balls before a collision based on their paths after the collision. We do not need to know each and every atomic-scale detail of the collision.


Unfortunately, my subsequent analysis dashed this hope. The model as well as the quantum waves used in the numerical simulations turned out to be a special case. In general, I found that waves spread out and that quantum effects were strong enough to be reckoned with. So the bounce was not a brief push by a repulsive force, like the collision of billiard balls. Instead it may have represented the emergence of our universe from an almost unfathomable quantum state—a world in highly fluctuating turmoil. Even if the preexisting universe was once very similar to ours, it passed through an extended period during which the density of matter and energy fluctuated strongly and randomly, scrambling everything.

The fluctuations before and after the big bang were not strongly related to each other. The universe before the big bang could have been fluctuating very differently than it did afterward, and those details did not survive the bounce. The universe, in short, has a tragic case of forgetfulness. It may have existed before the big bang, but quantum effects during the bounce wiped out almost all traces of this prehistory.

Some Scraps of Memory
This picture of the big bang is subtler than the classical view of the singularity. Whereas general relativity simply fails at the singularity, loop quantum gravity is able to handle the extreme conditions there. The big bang is no longer a physical beginning or a mathematical singularity, but it does put a practical limitation on our knowledge. Whatever survives cannot provide a complete view of what came before.

Frustrating as this may be, it might be a conceptual blessing. In physical systems as in daily life, disorder tends to increase. This principle, known as the second law of thermodynamics, is an argument against an eternal universe. If order has been decreasing for an infinite span of time, the universe should by now be so disorganized that structures we see in galaxies as well as on Earth would be all but impossible. The right amount of cosmic forgetfulness may come to the rescue by presenting the young, growing universe with a clean slate irrespective of all the mess that may have built up before.

According to traditional thermodynamics, there is no such thing as a truly clean slate; every system always retains a memory of its past in the configuration of its atoms [see "The Cosmic Origins of Time's Arrow," by Sean M. Carroll; Scientific American, June]. But by allowing the number of spacetime atoms to change, loop quantum gravity allows the universe more freedom to tidy up than classical physics would suggest.

All that is not to say that cosmologists have no hope of probing the quantum-gravitational period. Gravitational waves and neutrinos are especially promising tools, because they barely interact with matter and therefore penetrated the primordial plasma with minimal loss. These messengers might well bring us news from a time near to, or even before, the big bang.

One way to look for gravitational waves is by studying their imprint on the cosmic microwave background radiation [see "Echoes from the Big Bang," by Robert R. Caldwell and Marc Kamionkowski; Scientific American, January 2001]. If quantum-gravitational repulsive gravity drove cosmic inflation, these observations might find some hint of it. Theorists must also determine whether this novel source of inflation could reproduce other cosmological measurements, especially of the early density distribution of matter seen in the cosmic microwave background.

At the same time, astronomers can look for the spacetime analogues of random Brownian motion. For instance, quantum fluctuations of spacetime could affect the propagation of light over long distances. According to loop gravity, a light wave cannot be continuous; it must fit on the lattice of space. The smaller the wavelength, the more the lattice distorts it. In a sense, the spacetime atoms buffet the wave. As a consequence, light of different wavelengths travels at different speeds. Although these differences are tiny, they may add up during a long trip. Distant sources such as gamma-ray bursts offer the best hope of seeing this effect [see "Window on the Extreme Universe," by William B. Atwood, Peter F. Michelson and Steven Ritz; Scientific American, December 2007].

In the case of material atoms, more than 25 centuries elapsed between the first speculative suggestions of atoms by ancient philosophers and Einstein's analysis of Brownian motion, which firmly established atoms as the subject of experimental science. The delay should not be as long for spacetime atoms.