Monday, May 13, 2013

What Is Wrong with Dissections?

Hint? It is not what you think.

Here is a story you might find a bit laughable. At the end of the dark ages in what is now Italy, when knowledge was being reborn, anatomists would read from an ancient Greek text while their assistants dissected a human body and pointed out its parts. If the body looked different from what was written in the thousand year old text it was seen to be mutant, deviant, wrong. No matter that the ancient Greek knowledge was flawed and many of the rather ordinary observations that were being made would have improved dramatically upon what was known. Man, those early anatomists were dopes. It would take a major scientific revolution for anatomists to begin to actually observe and learn from dissections. The idea that more knowledge could be gained was a breakthrough. Isn?t it crazy how hard it was for early scientists to figure out obvious things? Boy oh boy.

Image 1. An early anatomy theater at the University of Leiden.

I was thinking about this the other day when I walked past a classroom in which undergraduates were dissecting cats.? Around the world, millions of cats, dogs, pigs and other mammals, including thousands and thousands of humans are dissected in anatomy classes. They are dissected in order to teach students?including all of those who will eventually operate on your body?about how an average mammal, amphibian or other body works.

One can discuss the merits of having students perform dissections. ?One can also discuss the morality of such dissections. I won?t do either. I want to get at something else, the issue of whether these students are doing exactly the same sort of science that was being done at the end of the dark ages.

In an average anatomy class dead animals are handed out to students. A tired/sometimes grumpy/overworked/underpaid teaching assistant discusses how the dissection should be done. Students perform various forms of butchery. Students label/point to/remove parts of the body on which the teaching assistant has told them to focus. In focusing on these parts of the body, the students are told about how it works, or at least how it works in general. More body parts are dissected. More knowledge is provided. The bodies are then thrown away in special trashcans. The teaching assistant goes home to work on their thesis and to wonder if he/she will ever get the job. The students go home to think about other students/beer/ or other students. The whole process repeats with a new group the next morning.

I don?t mean to make fun of the hard work of students or teaching assistants. What I do mean to make fun of is that we seem to now teach anatomy in exactly the same way that it was being taught at the end of the dark ages. Specifically, students look at bodies of animals, but are not encouraged in any way to make real observations. Instead, they are encouraged to look for what is already known and then if it does not look quite right, do depict it the way it ?should,? look. Even where the differences among bodies are noted, they are seldom measured. Even when measurements are taken, they are seldom recorded.

Now, you might say, Rob, you are confusing things. At the end of the dark ages we were ignorant about the body. Simple measurements could produce new knowledge. Now we understand the body. Of course, there is that difference. You are right, or you would be except that we still don?t understand the bodies of animals all that well. The function of the appendix is under new scrutiny. The stomach too. In fact, when it comes to basic morphology, the sorts of things that can be measured by preoccupied students in large classes, we haven?t made that much progress in the last hundred years (This is where you, as the reader, cue in on your favorite exception to my sweeping generalization and then go on to mention it in the comments section). How and why do intestines vary among individuals? How frequent are different deformations of particular organs. Are there tradeoffs between investment in one organ and in another? How frequent are rare mutations in the bodies of cats, pigs or even humans, mutations that we still don?t understand very well at all. Such mutations are hard to study because of their very rarity, but we dissect so many pigs, cats and other animals that even something that turns up in just one in a million animals turns up somewhere in some class each year. What else could be studied? I?m sure you can think of obvious features I am missing. The point is there are discoveries right beneath students as they look up at their teaching assistants or teachers, but we are training them to ignore them, to see the general story at the expense of the truth.

What now? I have one idea, probably an overly simple one, inspired by work in citizen science. ?I would have students take real measurements along with high-resolution digital images of the animals, including humans, that they dissect. They would also take a sample of some tissue of each animal (This might need to occur before the animals were preserved which would be harder, but still possible). The images and measurements would be sent to a database where they could be compared with others of the same. The tissue would be shipped to a tissue bank. With the database, anyone could compare the features of animals to understand how much they vary. With the tissue bank, the genes associated with unusual features could be narrowed down upon. With every moment in class, the students, however sleepy, however focused on the girl or boy in front of them, would be reminded that the body they are looking at is, like their own body, still imperfectly, understood. That was the revelation that would come after the dark ages, in the late renascence. It is a revelation we would do well to build upon as we consider how our own science and education might, together, be reborn, or, if not reborn, just done in such a way as to allow students to pay a little more attention to the dead pig in the hand, which, as they say, is worth ten in the book. Maybe they don?t really say that, but you get the idea.

Image 2. Evidence of Michelangelo?s hard work paying attention during the dissections he performed.

I was going to end there but then I remembered the one place, the only place in which students are actually taught to pay attention to the bodies they see before them, art classes. In figure drawings classes a naked man or woman stands in front of a room of students and is observed, drawn, piece by piece. We could learn something from these art students and their teachers. Ironically, the same was also true at the end of the dark ages, when, long before the scientists began to pay attention to bodies, the artists did. The artists had to, they were charged by their instructors with portraying truths in contrast to the science students who were (and are) charged only with portraying what is already known.

Note: I use the term ?dark ages? here. As one commenter notes, Early Middle Ages is the term historians now tend to use. However, from the point of view of biology in general and anatomy in particular, the times were dark. For many fields of biology more was known in 100 BC than was known in 1400 AD. Whatever you call the intervening years, scientifically they were illuminated by precious little light.

Source: http://rss.sciam.com/click.phdo?i=64bacbc23bb267d009ac02d6e349a8d3

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Gates worries about escalation of Korean tension

(AP) ? A former Pentagon chief says he worries that North Korea's young leader and his generals don't realize there's been a "dramatic change" in public opinion in South Korea in how to respond to belligerent actions by the North.

Robert Gates says that after many years of "swallowing provocation," the South Koreas "are not prepared to take that anyone."

Gates says that creates a situation where the next act of provocation "could result in an escalation and the situation getting out of control."

Gates tells CBS' "Face the Nation" that he worries that the North's young leader, Kim Jong Un (kim jawng oon), "does not have an understanding of that."

He says that while Chinese do have influence with Kim, "they don't have control and that worries me."

Associated Press

Source: http://hosted2.ap.org/APDEFAULT/89ae8247abe8493fae24405546e9a1aa/Article_2013-05-12-US-US-North-Korea/id-5fff2c9c36654814854f6ce6bb93096d

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Egypt says thwarts suicide attack on foreign embassy

By Tom Perry and Yasmine Saleh

CAIRO (Reuters) - Egyptian have security forces thwarted a plan by an al Qaeda-linked cell to carry out a suicide attack on a foreign embassy, capturing three militants, the interior minister said on Saturday.

Mohamed Ibrahim said the men, who he accused of having links to militants in the Middle East and Pakistan, were found in possession of 10 kg (22 lb) of aluminium nitrate, which is used to make bombs.

He declined to say which embassy had been targeted.

"The Interior Ministry was able to direct a qualitative blow to a terrorist cell that was planning suicide operations against vital, important and foreign facilities in the country," he said in a televised news conference.

Egypt has long been an incubator for Islamist militancy. Al Qaeda's leader, Ayman al-Zawahiri, is Egyptian.

Security has deteriorated since a 2011 uprising that ousted President Hosni Mubarak, whose 30 years in power were marked by militant violence including an armed Islamist insurrection.

Armed Islamist groups expanded in the Sinai Peninsula after revolt, but militancy has been less apparent in the Nile Delta, where the majority of the population is concentrated.

Two of the suspects were from Alexandria on Egypt's Mediterranean coast, the state news agency reported. It did not say where the third was from.

It was the second time since President Mohamed Mursi, a Muslim Brotherhood politician, came to power that the authorities have said they had uncovered a militant Islamist group in the Nile Valley.

Twenty-six alleged Islamist militants including two former military officers went on trial last month for planning attacks against the state. Ibrahim said that group - known as the Nasr City cell - was connected to the militants whose arrest was announced on Saturday.

He said the militants had been in contact with a militant leader identified as Kurdi Dawud al-Assadi, whom he described as the head of al Qaeda in some countries in west Asia.

Assadi had instructed them to get in touch with members of the Nasr City cell and another militant group based in Sinai - where militants killed 16 Egyptian border guards in an attack last August, he said.

The state security prosecutor's office ordered two of the men detained for 15 days pending investigations. The third was ordered not to leave his house, state news agency MENA reported.

Ibrahim said one of the suspects had traveled to Pakistan and Iran to receive training, and was a member of al Qaeda in Algeria, where 37 foreign hostages were killed January when Islamist militants laid siege to a gas plant.

MENA said two of them had been to countries in northwest Africa and Mali to get "acquainted" with militants abroad.

Ibrahim said they were also in contact with al Qaeda in Pakistan and "elements responsible for receiving terrorist elements on the Turkish borders".

They had been found in possession of statements issued by al Qaeda in the Islamic Maghreb, he added.

(Additional reporting by Alexander Dziadosz; Editing by Alison Williams)

Source: http://news.yahoo.com/egypt-says-thwarts-suicide-attack-foreign-embassy-132228781.html

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Sunday, May 12, 2013

Carnivorous plant throws out 'junk' DNA

May 12, 2013 ? Genes make up about 2 percent of the human genome. The rest consists of a genetic material known as noncoding DNA, and scientists have spent years puzzling over why this material exists in such voluminous quantities.

Now, a new study offers an unexpected insight: The large majority of noncoding DNA, which is abundant in many living things, may not actually be needed for complex life, according to research set to appear in the journal Nature.

The clues lie in the genome of the carnivorous bladderwort plant, Utricularia gibba.

The U. gibba genome is the smallest ever to be sequenced from a complex, multicellular plant. The researchers who sequenced it say that 97 percent of the genome consists of genes -- bits of DNA that code for proteins -- and small pieces of DNA that control those genes.

It appears that the plant has been busy deleting noncoding "junk" DNA from its genetic material over many generations, the scientists say. This may explain the difference between bladderworts and junk-heavy species like corn and tobacco -- and humans.

The international research team, led by the Laboratorio Nacional de Gen?mica para la Biodiversidad (LANGEBIO) in Mexico and the University at Buffalo, will report its findings on May 12 in Nature.

The study was directed by LANGEBIO Director and Professor Luis Herrera-Estrella and UB Professor of Biological Sciences Victor Albert, with contributions from scientists in the United States, Mexico, China, Singapore, Spain and Germany.

"The big story is that only 3 percent of the bladderwort's genetic material is so-called 'junk' DNA," Albert said. "Somehow, this plant has purged most of what makes up plant genomes. What that says is that you can have a perfectly good multicellular plant with lots of different cells, organs, tissue types and flowers, and you can do it without the junk. Junk is not needed."

Noncoding DNA is DNA that doesn't code for any proteins. This includes mobile elements called jumping genes that have the ability to copy (or cut) and paste themselves into new locations of the genome.

Scientists have spent countless hours puzzling over why noncoding DNA exists -- and in such copious amounts. A recent series of papers from ENCODE, a highly publicized international research project, began to offer an explanation, saying that the majority of noncoding DNA (about 80 percent) appeared to play a role in biochemical functions such as regulation and promotion of DNA conversion into its relative, RNA, which for genes, feeds into the machinery that makes proteins.

But Herrera-Estrella, Albert and their colleagues argue that organisms may not bulk up on genetic junk for reasons of benefit.

Instead, they say, some species may simply have an inherent, mechanistic bias toward deleting a great deal of noncoding DNA while others have a built-in bias in the opposite direction -- toward DNA insertion and duplication. These biases are not due to the fact that one way of behaving is more helpful than the other, but because there are two innate ways to behave and all organisms adhere to them to one degree or the other. The place that organisms occupy on this sliding scale of forces depends in part on the extent to which Darwin's natural selection pressure is able to counter or enhance these intrinsic biases.

The new U. gibba genome shows that having a bunch of noncoding DNA is not crucial for complex life. The bladderwort is an eccentric and complicated plant. It lives in aquatic habitats like freshwater wetlands, and has developed corresponding, highly specialized hunting methods. To capture prey, the plant pumps water from tiny chambers called bladders, turning each into a vacuum that can suck in and trap unsuspecting critters.

The U. gibba genome has about 80 million DNA base pairs -- a miniscule number compared to other complex plants -- and the deletion of noncoding DNA appears to account for most of that size discrepancy, the researchers say. U. gibba has about 28,500 genes, comparable to relatives like grape and tomato, which have much larger genomes of about 490 and 780 million base pairs, respectively.

The small size of the U. gibba genome is even more surprising given the fact that the species has undergone three complete genome doublings since its evolutionary lineage split from that of tomato.

That is, at three distinct times in the course of its evolution, the bladderwort's genome doubled in size, with offspring receiving two full copies of the species' entire genome. "This surprisingly rich history of duplication, paired with the current small size of the bladderwort genome, is further evidence that the plant has been prolific at deleting nonessential DNA, but at the same time maintaining a functional set of genes similar to those of other plant species" says Herrera-Estrella.

Besides LANGEBIO and UB, institutions with researchers contributing to the study included: University of Arizona, Tucson; Universidad de Guanajuato, Irapuato; Chongqing University of Science and Technology; Departamento de Gen?tica, Unidad Irapuato, Centro de Investigaci?n y de Estudios Avanzados del Instituto Polit?cnico Nacional; Universidad Veracruzana; Michigan State University; Universidad de Guadalajara, Ocotl?n; Pennsylvania State University; Nanyang Technological University; Centre for Genomic Regulation in Barcelona; Universitat Pompeu Fabra; Max Planck Institute for Molecular Genetics; Indiana University; Rutgers University; and the Donald Danforth Plant Science Center.

The study was supported by CONACyT (Mexico), Howard Hughes Medical Institute, the University at Buffalo College of Arts and Sciences and the National Science Foundation.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/most_popular/~3/EGMZRcm1uB8/130512140559.htm

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Notion Ink Adam II teased at India's National Technology Awards, reportedly priced at $218

Notion Ink Adam II teased at India's National Technology Awards, reportedly priced at $218

Remember the Notion Ink Adam? We'll forgive you if you don't -- the device fell a bit short of expectations, and news of its successor has been scarce. Save for a few teasing tweets, Notion Ink has kept the project pretty close to its chest. That changed this weekend, however, when the tablet's price and specifications were announced at India's National Technology Awards. According to a press release (after the break) and a pamphlet reportedly given to attendees, the Adam II will sell for 12,000 Indian Rupees (about $217) later this year, packing in a 1.5 Ghz Dual-Core ARM Cortex CPU, twin 2MP cameras, 1GB RAM and up to 10 hours of battery life.

The tablet also boasts a secondary screen, albeit a small one: a monochrome ticker that displays Android notifications on the Adam's book-like spine. HDMI, headphone and a micro USB ports crowd the device's adjacent edges, which wrap around a 10.1-inch 1280 x 800 IPS display -- a concession that was apparently made to increase longevity. Specific and international availability was sadly left out of the announcements, but its nice to finally see this project gain some steam.


[Thanks, Anonymous]

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Source: http://www.engadget.com/2013/05/12/notion-ink-adam-ii-teased-at-indias-national-technology-awards/?utm_medium=feed&utm_source=Feed_Classic&utm_campaign=Engadget

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See the pic: Rick has a follower on 'Walking Dead'

TV

12 hours ago

"The Walking Dead" won't be back until October, but AMC on Friday whetted fans' appetites with a first look photo of season four.

Image: Andrew Lincoln

AMC

Andrew Lincoln as Rick Grimes on "The Walking Dead."

No, it's nothing super exciting ... just Rick (Andrew Lincoln) being stalked by a lady zombie that's wearing a men's suit jacket! And notice, they're in the woods, not the safety of the prison.

Season three ended with Rick bringing a group of weaker-looking survivors from Woodbury to the prison after the town's governor -- and Rick's nemesis -- murdered many of his own band of fighters.

The cast and crew kicked off work on season four Monday on location in Georgia.

Source: http://www.today.com/entertainment/rick-has-follower-walking-dead-1C9875176

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Ice Cores Reveal Green Arctic

60-Second Science

Analyses of sediment cores show that Arctic summers 3.6 million years ago were a good 8 degrees C warmer than they are today, and supported Douglas Fir and hemlock. Sophie Bushwick reports.

More 60-Second Science

The Arctic wasn't always covered in ice. Samples of sediment layers beneath a frozen lake show this region used to be a lot warmer?and may thaw out again in the future. The work is in the journal Science. [Julie Brigham-Grette et al, Pliocene Warmth, Polar Amplification, and Stepped Pleistocene Cooling Recorded in NE Arctic Russia]

El'gygytgyn, a Russian lake 100 kilometers north of the Arctic Circle, contains layers of sediment that date back to the lake's formation 3.6 million years ago. Analyses of sediment cores have revealed that back then summers reached about 15 to 16 degrees Celsius, a good 8 degrees warmer than modern Arctic summers. These warm temperatures, which supported plants like Douglas fir and hemlock, lasted until about 2.2 million years ago.

Using a sediment core as a detailed history of climate change, scientists can see how the forested Arctic gradually became covered in ice and snow. These changes help us understand details about the development of Ice Ages. In addition, the sediment comes from a window of time during the Pliocene Epoch, when greenhouse gas levels were only slightly higher than they are today. Such sensitivity to small carbon dioxide changes hint at a warm Arctic future.

?Sophie Bushwick

[The above text is a transcript of this podcast]


Source: http://rss.sciam.com/click.phdo?i=431f4eb8f8979ad78bfd16f26665468b

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