Cognitive Labs

A signal tower

Stanford scientists have concluded that the predominant theory of aging may be incorrect, or at best, incomplete.

Aging presently is understood as comprehensive and cumulative tissue damage due to oxidation, toxin absorption, disease and stress. We degrade like the rusting hull of an old ship.

However, a new study involving the roundworm c elegans  conducted by biologist Stuart Kim has found that changes in genetic transcription herald the stages of aging. Since the nematode has a life span of only 2-3 weeks, it is easy to observe the entire life cycle.

Using microarrays - silicon chips that detect changes in gene expression - the scientists hunted for genes that were turned on differently in young and old worms. They found hundreds of age-regulated genes switched on and off by a single transcription factor called elt-3, which becomes more abundant with age. Two other transcription factors that regulate elt-3 also changed with age.

To determine whether these signal molecules were part of a wear-and-tear aging mechanism, the researchers exposed worms to stresses thought to cause aging, such as heat (a known stressor for nematode worms), free-radical oxidation, radiation and disease. But none of the stresses affected the genes that make the worms get old.

It appears that worm aging wasn't due to chemical damage. Instead, Kim said, key regulatory pathways optimized for youth have drifted off track in older animals. Natural selection can't fix problems that arise late in the animals' life spans, so the genetic pathways for aging become entrenched by mistake. Kim's team refers to this slide as "developmental drift."

"We found a normal developmental program that works in young animals, but becomes unbalanced as the worm gets older," he said. "It accounts for the bulk of the molecular differences between young and old worms."

While the complexity of the human organism may point to additional longevity factors outside of possible genetic drift, scientists can begin searching for this new aging mechanism in humans now that it has been discovered in a model organism.

"Everyone has assumed we age by rust," Kim said. "But then how do you explain animals that don't age?"

Some tortoises lay eggs at the age of 100, he points out. There are whales that live to be 200, and clams that make it past 400. Those species use the same building blocks for their DNA, proteins and fats as humans, mice and nematode worms. The chemistry of the wear-and-tear process, including damage from oxygen free-radicals, should be the same in all cells, which makes it hard to explain why species have dramatically different life spans.

"A free radical doesn't care if it's in a human cell or a worm cell," Kim said.

If aging is not a cost of unavoidable chemistry but is instead driven by changes in regulatory genes, the aging process may not be inevitable. It is at least theoretically possible to slow down or stop developmental drift.

"The take-home message is that aging can be slowed and managed by manipulating signaling circuits within cells," said Marc Tatar, PhD, a professor of biology and medicine at Brown University who was not involved in the research. "This is a new and potentially powerful circuit that has just been discovered for doing that."

Kim added, "It's a new way to think about how to slow the aging process."

Humans evolved so that energies are focused on certainty of growth to reproduction age rather than longevity. Once the initial mission of the organism in its environment is carried out, breakdowns in communication between genetic signal towers introduce gaps into the replicating code of life - and hence more errors as cells die and are replaced by new cells that draw information from the increasingly flawed codebase that is scattershot with lacunae. Up until now, natural selection would have been weighted heavily towards effective reproductive ability rather than lifespan. However, the environment no longer demands this tradeoff. It's straightforward to see how, with continuing research, we'll be living much longer by maintaining signal transcription integrity across the generations of replacement (or replicant) cells that are created every second in virtually every area of our bodies.


Source: Stanford University

Labels: aging, dna, elt3, kim, longevity, transcription

This is a question that is germane in California. It doesn't impact us because we're not in the test-tube DNA assessment business. But one is reminded of the practices of a high priesthood, such as the devotees of Amun in Egypt who chanted up the essential unknowability of Amun who was nicknamed "he-who-is-hidden" or ironically, the "double-concealed"

From the Hymn to Amun in the Leiden papyrus:

"One who is Amun,
who keeps Himself concealed from them,
who hides Himself from the gods,
no one knowing His nature.
He is more remote than the sky,
He is deeper than the netherworld.

None of the gods knows His true form.
His image is not unfolded in the papyrus rolls.
Nothing certain is testified about Him.

He is too secretive
for His Majesty to be revealed,
He is too great to be enquired after,
too powerful to be known."

The essential mystery of Amun was a strong incentive to support the priests as intermediaries in this cosmic dialog between man and the unknown. Thomas Goetz, in Wired, inquires about the deeper meaning in this modern era where knowledge is being unbundled at an exponential pace. In fact, incredible breakthroughs are happening every day in our ability to access and share what's important and are still under the radar. But, as a question of public policy, shouldn't we be in charge of our own information?

Over the weekend, one of the top stories was "ADHD may have a genetic link." Scientists have discovered (in fact have known for awhile) that certain hunter-gatherers have a higher preponderance of short attention spans related to their genetic configuration...and that this was a positive for the last 99.9% of the human experience because it made these individuals more creative and successful at accessing resources, rather than being satisfied and sedentary, with health and aging implications as well.

Taking it a step further, a creative, but impulsive student might say to the teacher..."Sorry I didn't work on the journal project every day, it was just too long. My genes say I'm a hunter gatherer, and I'm programmed to zip from topic to topic like a sprinter. Here's my genetic report, sorry." Here's a case of genes impacting our environment.

Labels: 23andme, adhd, california, dna, goetz, kenya, navigenics, wired

Scientists have announced that two chemicals isolated on an extraplanetary meteorite fragment from Australia, xanthine and uracil, also are present in human RNA and DNA.

Following the logical thread, one could deduce that the theory of panspermia has found more supporting evidence.

Francis Crick, discoverer of the double-helix structure of DNA, advocated a concept known as "directed panspermia," that is a view that an intelligent process or organizing algorithm resembling independent intelligence or sentience was behind the distribution of DNAs factors. What scientists announced today implies that panspermia could be a reagent to the life-forming process itself.

Labels: crick, dna, panspermia, reagent, rna, uracil, xanthine

But don't tell that to Yves Rossy, a Swiss inventor who strapped on a pair of wings coupled with a jetpack of his invention and soared above the Alps.



During the flight, Rossy reached a speed of 186 MPH and executed loops, figure-eights, and barrel rolls.

This brings up an important point. The point is that we evolve (and so do all organisms) through stress. Stress reveals weaknesses in body systems, change is driven by the need to adapt and in the very short-term, by the development of work-arounds and quick fixes in one system which ultimately influence other systems and then finally, DNA is amended, like a Bill entering the House, getting support, getting vetoed by the president, being sent back for legislative review, and then finally passing.

A skeptical view would be that flight is impossible. Once man flew too close to the sun and suffered molten waxen wings and an interminable spiral back to earth, why try again? "Everyone knows that xyz is impossible," the conventional wisdom says, and even if it is possible, and you prove it with something akin to executing the tough yo-yo trick 'walking the dog', then there are a legion of reasons why they'll tell you it should not be done now. Many officials take this posture, not necessarily intentionally - they want to believe, but because of the downside of risk. This stance is not even unique to industries, you could say it is axiomatic behavior for all incumbents...you just have to keep chiseling away

Labels: alps, bill, chiseling, dna, flight, president, rossy, stress, swiss

A "Barcode of Life" will transliterate the DNA of trees, according to Deepthi Hajela of the AP who writes...

The New York Botanical Garden may be best known for its orchid shows and colorful blossoms, but its researchers are about to lead a global effort to capture DNA from thousands of tree species from around the world.


The Bronx garden is hosting a meeting this week where participants from various countries will lay the groundwork for how the two-year undertaking to catalog some of the Earth's vast biodiversity will proceed.

The project is known as TreeBOL, or tree barcode of life. As in a similar project under way focusing on the world's fish species, participants would gather genetic material from trees around the world.

A section of the DNA would be used as a barcode, similar to way a product at the grocery store is scanned to bring up its price. But with plants and animals, the scanners look at the specific order of the four basic building blocks of DNA to identify the species.

The resulting database will help identify many of the world's existing plant species, where they are located and whether they are endangered. The results are crucial for conservation and protecting the environment as population and development increases, said Damon Little, assistant curator of bioinformatics at the Botanical Garden and coordinator of the project. (more)

--------------

I think that I shall never see
A poem lovely as a tree.

A tree whose hungry mouth is prest
Against the earth's sweet flowing breast;

A tree that looks at God all day,
And lifts her leafy arms to pray;

A tree that may in summer wear
A nest of robins in her hair;

Upon whose bosom snow has lain;
Who intimately lives with rain.

Poems are made by fools like me,
But only God can make a tree.


by Sgt. Alfred Joyce Kilmer, poet, U.S. 165th Infantry
(deceased 1918, Battle of the Marne)

Labels: dna, joyce, kilmer, NYBG, trres

Researchers in Denmark tracked a genetic mutation showing that people with blue eyes have a single, common ancestor.

Hans Eiberg of the University of Copenhagen and his team examined mitochondrial DNA and compared the eye color of blue-eyed individuals in countries as diverse as Jordan, Denmark and Turkey.

"Originally, we all had brown eyes," Eiberg said in a statement. "But a genetic mutation affecting the OCA2 gene in our chromosomes resulted in the creation of a 'switch,' which literally 'turned off' the ability to produce brown eyes."

The switch, which is located in the gene adjacent to OCA2 does not, however, turn off the gene entirely, but rather limits its action to reducing the production of melanin in the iris -- effectively "diluting" brown eyes to blue.

Variation in eye color from brown to green can be explained by the amount of melanin in the iris, but blue-eyed individuals only have a small degree of variation in the amount of melanin in their eyes, Eiberg explained.

"From this we can conclude that all blue-eyed individuals are linked to the same ancestor," Eiberg said. "They have all inherited the same switch at exactly the same spot in their DNA."

The mutations responsible for blue eye colour most likely originate from the north-west part of the Black Sea region, where the great agricultural migration of the northern part of Europe took place in the Neolithic periods about 6,000 to 10,000 years ago," the researchers report in Human Genetics.

What's the bluest-eyed nation? Estonia - with 92.9% of the population blue-eyed. Norway, Sweden, Denmark, and Germany follow - with 75% of Germans blue-eyed.

Most significantly, this illustrates how fast genetic change can propagate from a single mutation-in practically a millisecond of the human experience. Change is constant. Imagine tomorrow a baby is born with plaid eyes-in a few thousand years this could become the norm! The Blink of an Eye Test:


type="text/javascript"src="http://cognitivelabs.com/cognitive.js">

Labels: blue, blueeyes, dna, estonia

// posted by neurofuture10:35 PM permanent link

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  tags: take a quick memory test | games for your brain | moving pix for your brain | gamer IQ

A Russian scientist, Alexander Zaitsev, advocates not only listening for intelligent life through efforts such as Arecibo or the Allen array of radio telescopes, but actively sending messages to nearby stars.

Only 163 years ago the telegraph was introduced and the first message was "What hath God wrought?" Now, we've moved on to IM and Facebook.

It could be that sending interesting messages (SPAM) out there is just the trick to get a response. "Hello, we're Earth. We're great. We're #1. We're great because we're sending this. And by the way this is really old technology."

Then again, an ant might consider that its pheromone-based communications intended to reach other ant colonies would comprise the best option to reveal all that is unknown in the ant's conception. "I'm a worker ant from the nest under the leaf pile. If you can understand my message well then you're a friend. If you cannot, you're not an Argentinian ant and woe to you."

In fact, the ant's message is invisible and incomprehensible to other insects in a backyard, to say nothing of amphibians, birds, squirrels, cats, dogs, plants and people, or undersea life, for example. It's difficult for one kind of consciousness to know or conjecture anything meaningful about another, and therein lies the problem.

Complexity = Privileged Position?

"We're No. 1." In Astronomy, people settled early on a geocentric view of the universe which encompassed the land from horizon to horizon. With the awakening, heliocentrism came into vogue. Now, we know the sun is just a star among 100 billion stars in our galaxy. However, the rest of science and virtually all human endeavor is based on a variant of the original geocentrism in the way that a baby focuses only on objects in its immediate vicinity.

  

Looking at DNA, simple white rice has far more genes than humans - almost 40,000, while humans have under 25,000.

Therefore, on an ordinal scale, rice is more intelligent or advanced due to its more complex architecture, right? If our fundamental assumption derived intrinsic merit from genetic complexity, rice would be loftier in the pyramid of living things than people.

There's Bugs in Your Code

Before Champollion, Europeans could not read hieroglyphs. It appeared to be a jumble of unknown objects along with images derived from nature-junk, if you will, or even more accurately: absurd. In fact, this 'primitive' language and the activities necessary to decode it obscures that it was entirely forgotten. In human genetic code, a similar terra incognita appears, that we call 'junk' DNA.

However, the pufferfish, well known to divers and snorkelers, lacks 'junk DNA' altogether and has a clean genetic blueprint. Human code, on the other hand, is filled with ellipses, parenthetical marks, lacunae, and the diacritical red marks of life's editor. In fact, the majority of human genes fall into this category.

Why?

That's what geneticists are trying to find out.

Labels: allen-array, arecibo, copernicus, dna, et, galaxy, junk, junkdna, pufferfish, rice, spam, zaitsev

Cognitive Labs traffic reaches 3 million visitors, and the 18th straight month of increases. We've passed 1 million visits this quarter. Thanks.

Compared with some of the large casual game networks, we're around 5-10% of their traffic-but just focused on the brain-including scientific games-the DNA of a revolution in how you train your mind.

Labels: 3million, arcade, casual, cognitive, dna, fish, real

 

30 Years ago George Lucas released Star Wars with the expectation that it might be more successful than his first science-fiction film, THX-1138. Certainly, critics at the studio didn't expect much, threatening the project's funding due to its apparent lack of progress, sheer weirdness, and reliance on undeveloped special effects that had to be improvised as the crew went along. But oftentimes genius emerges from the frenetic but focused efforts of desperation.

The story also borrowed liberally from heroic archetypes in many cultures, out of style in the post-modern, realist 1970's, but a long absent piece of a rich puzzle of cultural memories in both oral tradition and literature that extended back for thousands of years. The hunger for heroic meaning, which had faded at the end of the 1950's, or even in the aftermath of WW2 with its descent into darkness, automated brutality, and the unleashing of the energy of a new star in a four-ton, portable package, was sated by likeable characters who represented nothing less than a reflection of the audience itself - forming a strong neurotransmitter-approved connection with humanity.

Also in 1977, and thirty years ago this week, the Voyager spacecraft was launched by NASA. At the time, Voyager was a much bigger story than a mere movie, for Voyager included a First in human history: a recorded archive of what it meant to be human in 1977, designed by scientific experts (including Carl Sagan) and politicians to be a testament - a communication, if you will, for other civilizations that might come across Voyager in the decades ahead. Currently, Voyager is 9.6 Billion miles from earth headed in the direction of the constellation Camelopardalis.

Thirty years later, the testament of humanity which was intended to communicate clearly and forcefully with the great unknown and any inhabitants of a galactic terra incognita is a relic to people who were children at the time and unrecognizable to anyone younger, even though the science mission - and examination of interstellar plasma - continues.

Some observations:

(1) The format is a golden disk in the shape of a record (LP)
There is no readily available technology on earth that can play this testament.
How could we expect anyone else to play it if we can't on our own planet.

(2) A message is included, composed by Jimmy Carter
"We human beings are still divided into nation-states, but these states are
rapidly becoming a single global civilization..."

Mr. Carter was only briefly in power as spokesman for Earth. The communication,
while well-intentioned - was more hopeful than accurate. Within two years,
Carter's presidency was tarnished in the fiasco of Desert One and the hostage
crisis. Wars and upheavals continue...

(3) There is no mention of the Internet; it existed at the time. The Internet, if
you will, is not even restricted to earth's surface - already Java and software
from Wind River systems (and others) power rovers on Mars and interplanetary
probes

(4) There is no reference to the human genome or DNA, instruction sets for life

In the popular memory, Luke Skywalker, Darth Vader and Obi Wan have far outdistanced Voyager and Humanity's testament. Imagine if it was as difficult to playback Star Wars today as the unique 'golden disk.' How many times has the visual and auditory stimuli of Star Wars and its successors lit up the frontal lobe and amygdala of viewers? How many times has the 70's Golden disk done the same? The multifaceted nature of humanity, a Trinity of youthful idealism, darkness and evil, and benevolent Wisdom, is more accurately exemplified in those characters...than in the crafted message of officialdom.

The testament is the equivalent of an old newspaper, printed by a media company long out of business, with an editor in chief who retired long ago; in the interim, the old headquarters building was torn down. What would happen if the message was received? Where would a response be sent?

Labels: darth, dna, genome, java, lucas, sagan, skywalker, star wars, voyager, windriver

People are less alike than scientists had thought when it comes to the billions of building blocks that make up each individual's DNA, according to a new analysis.

"Instead of 99.9 percent identical, maybe we're only 99 percent (alike)," said J. Craig Venter, an author of the study — and the person whose DNA was analyzed for it.

Several previous studies have argued for lowering the 99.9 percent estimate. Venter says this new analysis "proves the point."

The new work, in the latest issue of PLoS Biology, marks the first time a scientific journal has presented the entire DNA makeup, or human genome, of an individual. However, James D. Watson — co-discoverer of DNA's molecular structure — received his own personal DNA map from scientists a few months ago. And the genomes for both him and Venter are already posted on scientific Web sites.

Venter is president of the J. Craig Venter Institute in Rockville, Md., which does genetics research. He and scientists at his institute and elsewhere collaborated on the work that produced his genetic map.

The order of building blocks along a strand of DNA encodes genetic information, somewhat like the way a sequence of letters creates a sentence. Particular sequences form genes. Landmark studies published in 2001 indicated that the DNA of any two people is about 99.9 percent alike. The new paper suggests estimates of 99.5 percent to just 99 percent, Venter said.

The Venter paper joins several others published over the past three to four years that indicate an estimate of around 99 percent, said Richard Gibbs, a DNA expert at the Baylor College of Medicine in Houston who didn't participate in Venter's study.

The studies produce the lower figure because they uncovered chunks of DNA that differ among people, whereas previous studies focused on differences in individual building blocks.

The 99 percent figure is close to what scientists have often estimated for the similarity between humans and chimps. But the human-chimp similarity drops to more like 95 percent when the more recently discovered kinds of DNA variation are considered, Venter said.

Gibbs called the Venter paper significant, along with a similar but not-yet-published analysis of Watson's DNA that he has worked on. That's because the analyses show more differences than expected from the standard human DNA sequence published by the federal government, he said. (The federal sequence was based on a mix of DNA from different people.)

That finding in turn is shedding light on how DNA varies among people, with implications for understanding the genetic underpinnings of disease, Gibbs said.

Although the new paper analyzes just Venter's genetic material, it can make estimates about how individuals differ in their DNA. Everybody inherits two sets of DNA, one from each parent. Venter's paper compared the DNA he inherited from his mother with the DNA from his father

Labels: craig venter, dna, genome, plosbiology

Real time DNA replication is featured in the following visualization video...Fascinating. Then test your brain

Labels: apoee4, coglabs, dna, DNA replication, myDNA, youtube

Call it an archaeological faux pas.

Where's Indiana Jones when you need him?

The Egyptian Supreme Head of Antiquities Zahi Hawass has the field in turmoil today with his announcement (via CNN) that at least one, and possibly all, Egyptian mummies have an inaccurate provenance. The controversy stems from the fact that the body of pharaoh Tuthmosis, rather than being as expected, in his mid 60's at the time of death - was revealed by technology to be around 20 and killed by an arrow.

The CT and MRI scanning being carried out by the Antiquities department - combined with DNA analysis, might have the result of proverbially toppling the pyramids.

How much, indeed, of the science of Egyptology is established on Victorian era theorizing - from the former circus strongman turned archaeologist Giovanni Belzoni, who excavated with gusto (and little documentation), to the neat, compartmentalized reductionism of Sir William Matthew Flinders Petrie?

How can this be answered?

One possibility is to find an intermediate source...writing between the time of the New Kingdom, when Egypt was perhaps its height - and the present. The one source that most classicists recall is Herodotus; others, the mostly lost work of the geographer Strabo; a third source is a "digression" from the work of the historian Ammianus - who touches on the links between technology, law and medicine of Classical times and links them all back to Egypt, including philosophy. Therefore I am attaching this recent translation and arangement c. 2007 (in the public domain)which is quite instructive. (Ammianus, Book 22, section 15. Note: Ammianus History started with the emperor Nerva and continued through Valens, who lost the Battle of Adrianople, along with his life, to the Goths. All books up to the reign of Constantius in 337 are lost, so the history is an eyewitness account of the author, who served as an officer in the Imperial guard, ending in about 378 A.D.)

1. Let us then, since the occasion seems to require it, touch briefly on the affairs of Egypt, of which we have already made some mention in our account of the emperors Hadrian and Severus, where we related several things which we had seen.

2. The Egyptian is the most ancient of all nations, except indeed that its superior antiquity is contested by the Scythians: their country is bounded on the south by the greater Syrtes, Cape Eas, and Cape Borion, the Garamantes, and other nations; on the east, by Elephantine, and Meroe, cities of the Ethiopians, the Catadupi, the Red Sea, and the Scenite Arabs, whom we now call Saracens. On the north it joins a vast track of land, where Asia and the Syrian provinces begin; on the west it is bounded by the Sea of Issus, which some call the Parthenian Sea.

3. We will also say a few words concerning that most useful of all rivers, the Nile, which Homer calls the Aegyptus; and after that we will enumerate other things worthy of admiration in these regions.

4. The sources of the Nile, in my opinion, will be as unknown to posterity as they are now. But since poets, who relate fully, and geographers who differ from one another, give various accounts of this hidden matter, I will in a few words set forth such of their opinions as seem to me to border on the truth.

5. Some natural philosophers affirm that in the districts beneath the North Pole, when the severe winters bind up everything, the vast masses of snow congeal; and afterwards, melted by the warmth of the summer, they make the clouds heavy with liquid moisture, which, being driven to the south by the Etesian winds, and dissolved into rain |308 by the heat of the sun, furnish abundant increase to the Nile.

6. Some, again, assert that the inundations of the river at fixed times are caused by the rains in Ethiopia, which fall in great abundance in that country during the hot season; but both these theories seem inconsistent with the truth - for rain never falls in Ethiopia, or at least only at rare intervals. (In fact this is correct, but the source of the Nile, like the mythological Northwest passage, was unknown by Europeans until midway through the Victorian period)

7. A more common opinion is, that during the continuance of the wind from the north, called the Precursor, and of the Etesian gales, which last forty-five days without interruption, they drive back the stream and check its speed, so that it becomes swollen with its waves thus dammed back; then, when the wind changes, the force of the breeze drives the waters to and fro, and the river growing rapidly greater, its perennial sources driving it forward, it, rises as it advances, and covers everything, spreading over the level plains till it resembles the sea.

8. But King Juba, relying on the text of the Carthaginian books, affirms that the river rises in a mountain situated in Mauritania, which looks on the Atlantic Ocean, and he says, too, that this is proved by the fact that fishes, and herbs, and animals resembling those of the Nile are found in the marshes where the river rises.

9. But the Nile, passing through the districts of Ethiopia, and many different countries which give it their own names, swells its fertilizing stream till it comes to the cataracts. These are abrupt rocks, from which in its precipitous course it falls with such a crash, that the Ati, who used to live in that district, having lost their hearing from the incessant roar, were compelled to migrate to a more quiet region.

10. Then proceeding more gently, and receiving no accession of waters in Egypt, it falls into the sea through seven mouths, each of which is as serviceable as, and resembles, a separate river. And besides the several streams which are derived from its channel, and which fall with others like themselves, there are seven navigable with large waves; named by the ancients the Heracleotic, the Sebennitic, the Bolbitic, the Phatnitic, the Mendesian, the Tanitic, and the Pelusian mouths.

11. This river, rising as I have said, is driven on from |309 the marshes to the cataracts, and forms several islands; some of which are said to be of such extent that the stream is three days in passing them.

12. Among these are two of especial celebrity, Meroe and Delta. The latter derives its name from its triangular form like the Greek letter; but when the sun begins to pass through the sign of Cancer, the river keeps increasing till it passes into Libra; and then, after flowing at a great height for one hundred days, it falls again, and its waters being diminished it exhibits, in a state fit for riding on, fields which just before could only be passed over in boats.

13. If the inundation be too abundant it is mischievous, just as it is unproductive if it be too sparing; for if the flood be excessive, it keeps the ground wet too long, and so delays cultivation; while if it be deficient, it threatens the land with barrenness. No landowner wishes it to rise more than sixteen cubits. If the flood be moderate, then the seed sown in favourable ground sometimes returns seventy fold. The Nile, too, is the only river which does not cause a breeze.

14. Egypt also produces many animals both terrestrial and aquatic, and some which live both on the earth and in the water, and are therefore called amphibious. In the dry districts antelopes and buffaloes are found, and sphinxes, animals of an absurd-looking deformity, and other monsters which it is not worth while to enumerate.

15. Of the terrestrial animals, the crocodile is abundant in every part of the country. This is a most destructive quadruped, accustomed to both elements, having no tongue, and moving only the upper jaw, with teeth like a comb, which obstinately fasten into everything he can reach. He propagates his species by eggs like those of a goose.

16. And as he is armed with claws, if he had only thumbs his enormous strength would suffice to upset large vessels, for he is sometimes ten cubits long. At night he sleeps under water; in the day he feeds in the fields, trusting to the stoutness of his skin, which is so thick that missiles from military engines will scarcely pierce the mail of his back.

17. Savage as these monsters are at all other times, yet as if they had concluded an armistice, they are always quiet laying aside all their ferocity, during the seven days |310 of festival on which the priests at Memphis celebrate the birthday of Apis.

18. Besides those which die accidentally, some are killed by wounds which they receive in thoir bellies from the dorsal fins of some fish resembling dolphins, which this river also produces.

19. Some also are killed by means of a little bird called the trochilus, which, while seeking for some picking of small food, and flying gently about the beast while asleep, tickles its cheeks till it comes to the neighbourhood of its throat. And when the hydrus, which is a kind of ichneumon, perceives this, it penetrates into its mouth, which the bird has caused to open, and descends into its stomach, where it devours its entrails, and then comes forth again.

20. But the crocodile, though a bold beast towards those who flee, is very timid when it finds a brave enemy. It has a most acute sight, and for the four months of winter is said to do without food.

21. The hippopotamus, also, is produced in this country; the most sagacious of all animals destitute of reason. He is like a horse, with cloven hoofs, and a short tail. Of his sagacity it will be sufficient to produce two instances.

22. The animal makes his lair among dense beds of reeds of great height, and while keeping quiet watches vigilantly for every opportunity of sallying out to feed on the crops. And when he has gorged himself, and is ready to return, he walks backwards, and makes many tracks, to prevent any enemies from following the straight road and so finding and easily killing him.

23. Again, when he feels lazy from having his stomach swollen by excessive eating, it rolls its thighs and legs on freshly-cut reeds, in order that the blood, which is discharged through the wounds thus made may relieve his fat. And then he smears his wounded flesh with clay till the wounds get scarred over.

24. This monster was very rare till it was first exhibited to the Roman people in the aedileship of Scaurus, the father of that Scaurus whom Cicero defended, when he charged the Sardinians to cherish the same opinion as the rest of the world of the authority of that noble family. Since that time, at different periods, many specimens have |311 been brought to Rome, and now they are not to be found in Egypt, having been driven, according to the conjecture of the inhabitants, up to the Blemmyae by being incessantly pursued by the people.

25. Among the birds of Egypt, the variety of which is countless, is the ibis, a sacred and amiable bird, also valuable, because by heaping up the eggs of serpents in its nest for food it causes these fatal pests to diminish.

26. They also sometimes encounter flocks of winged snakes, which come laden with poison from the marshes of Arabia. These, before they can quit their own region, they overcome in the air, and then devour them. This bird, we are told, produces its young through its mouth.

27. Egypt also produces innumerable quantities of serpents, destructive beyond all other creatures. Basilisks, amphisbaenas, scytalae, acontiae, dipsades, vipers, and many others. The asp is the largest and most beautiful of all; but that never, of its own accord, quits the Nile.

28. There are also in this country many things exceedingly worthy of observation, of which it is a good time now to mention a few. Everywhere there are temples of great size. There are seven marvellous pyramids, the difficulty of building which, and the length of time consumed in the work, are recorded by Herodotus. They exceed in height anything ever constructed by human labour, being towers of vast width at the bottom and ending in sharp points.

29. And their shape received this name from the geometricians because they rise in a cone like fire (πῦρ). And huge as they are, as they taper off gradually, they throw no shadow, in accordance with a principle of mechanics.

30. There are also subterranean passages, and winding retreats, which, it is said, men skilful, in the ancient mysteries, by means of which they divined the coming of a flood, constructed in different places lest the memory of all their sacred ceremonies should be lost. On the walls, as they cut them out, they have sculptured several kinds |312 of birds and beasts, and countless other figures of animals, which they call hieroglyphics.

31. There is also Syene, where at the time of the summer solstice the rays surrounding upright objects do not allow the shadows to extend beyond the bodies. And if any one fixes a post upright in the ground, or sees a man or a tree standing erect, he will perceive that their shadow is consumed at the extremities of their outlines. This also happens at Meroe, which is the spot in Ethiopia nearest to the equinoctial circle, and where for ninety days the shadows fall in a way just opposite to ours, on account of which the natives of that district are called Antiscii.

32. But as there are many other wonders which would go beyond the plan of our little work, we must leave these to men of lofty genius, and content ourselves with relating a few things about the provinces.

1. In former times Egypt is said to have been divided into three provinces: Egypt proper, the Thebais, and Libya, to which in later times two more have been added, Augustamnica, which has been cut off from Egypt proper, and Pentapolis, which has been detached from Libya.

2. Thebais, among many other cities, can boast especially of Hermopolis, Coptos, and Antinous, which Hadrian built in honour of his friend Antinous. As to Thebes, with its hundred gates, there is no one ignorant of its renown.

3. In Augustamnica, among others, there is the noble city of Pelusium, which is said to have been founded by Peleus, the father of Achilles, who by command of the gods was ordered to purify himself in the lake adjacent to the walls of the city, when, after having slain his brother Phocus, he was driven about by horrid images of the Furies; and Cassium, where the tomb of the great Pompey is, and Ostracine, and Rhinocolura.

4. In Libya Pentapolis is Cyrene, a city of great antiquity, but now deserted, founded by Battus the Spartan, and Ptolemais, and Arsinoe, known also as Teuchira, and Darnis, and Berenice, called also Hesperides. |313

5. And in the dry Libya, besides a few other insignificant towns, there are Paraetonium, Chaerecla, and Neapolis.

6. Egypt proper, which ever since it has been united to the Roman empire has been under the government of a prefect, besides some other towns of smaller importance, is distinguished by Athribis, and Oxyrynchus, and Thmuis, and Memphis.

7. But the greatest of all the cities is Alexandria, ennobled by many circumstances, and especially by the grandeur of its great founder, and the skill of its architect Dinocrates, who, when he was laying the foundation of its extensive and beautiful walls, for want of mortar, which could not be procured at the moment, is said to have marked out its outline with flour; an incident which foreshowed that the city should hereafter abound in supplies of provisions.

8. At Inibis the air is wholesome, the sky pure and undisturbed; and, as the experience of a long series of ages proves, there is scarcely ever a day on which the inhabitants of this city do not see the sun.

9. The shore is shifty and dangerous; and as in former times it exposed sailors to many dangers, Cleopatra erected a lofty tower in the harbour, which was named Pharos, from the spot on which it was built, and which afforded light to vessels by night when coming from the Levant or the Libyan sea along the plain and level coast, without any signs of mountains or towns or eminences to direct them, they were previously often wrecked by striking into the soft and adhesive sand.

10. The same queen, for a well-known and necessary reason, made a causeway seven furlongs in extent, admirable for its size and for the almost incredible rapidity with which it was made. The island of Pharos, where Homer in sublime language relates that Proteus used to amuse himself with his herds of seals, is almost a thousand yards from the shore on which the city stands, and was liable to pay tribute to the Rhodians.

11. And when on one occasion the farmers of this revenue came to make exorbitant demands, she, being a wily woman, on a pretext of it being the season of solemn holidays, led them into the suburbs, and ordered the work to be carried on without ceasing. And so seven furlongs were |314 completed in seven days, being raised with the soil of the adjacent shore. Then the queen, driving over it in her chariot, said that the Rhodians were making a blunder in demanding port dues for what was not an island but part of the mainland.

12. Besides this there are many lofty temples, and especially one to Serapis, which, although no words can adequately describe it, we may yet say, from its splendid halls supported by pillars, and its beautiful statues and other embellishments, is so superbly decorated, that next to the Capitol, of which the ever-venerable Rome boasts, the whole world has nothing worthier of admiration.

13. In it were libraries of inestimable value; and the concurrent testimony of ancient records affirm that 70,000 volumes, which had been collected by the anxious care of the Ptolemies, were burnt in the Alexandrian war when the city was sacked in the time of Caesar the Dictator.

14. Twelve miles from this city is Canopus, which, according to ancient tradition, received its name from the prophet of Menelaus, who was buried there. It is a place exceedingly well supplied with good inns, of a most wholesome climate, with refreshing breezes; so that any one who resides in that district might think himself out of our world while he hears the breezes murmuring through the sunny atmosphere.

15. Alexandria itself was not, like other cities, gradually embellished, but at its very outset it was adorned with spacious roads. But after having been long torn by violent seditions, at last, when Aurelian was emperor, and when the intestine quarrels of its citizens had proceeded to deadly strife, its walls were destroyed, and it lost the largest half of its territory, which was called Bruchion, and had long been the abode of eminent men.

16. There had lived Aristarchus, that illustrious grammarian; and Herodianus, that accurate inquirer into the fine arts; and Saccas Ammonius, the master of Plotinus, and many other writers in various useful branches of literature, among whom Didymus, surnamed Chalcenterus, a man celebrated for his writings on many subjects of science, deserves especial mention; who, in the six books in which he, sometimes incorrectly, attacks Cicero, imitating those malignant farce writers, is justly blamed by |315 the learned as a puppy barking from a distance with puny voice against the mighty roar of the lion.

17. And although, besides those I have mentioned, there were many other men of eminence in ancient times, yet even now there is much learning in the same city; for teachers of various sects flourish, and many kinds of secret knowledge are explained by geometrical science. Nor is music dead among them, nor harmony. And by a few, observations of the motion of the world and of the stars are still cultivated; while of learned arithmeticians the number is considerable; and besides them there are many skilled in divination.

18. Again, of medicine, the aid of which in our present extravagant and luxurious way of life is incessantly required, the study is carried on with daily increasing eagerness; so that while the employment be of itself creditable, it is sufficient as a recommendation for any medical man to be able to say that he was educated at Alexandria. And this is enough to say on this subject.

19. But if any one in the earnestness of his intellect wishes to apply himself to the various branches of divine knowledge, or to the examination of metaphysics, he will find that the whole world owes this kind of learning to Egypt.

20. Here first, far earlier than in any other country, men arrived at the various cradles (if I may so say) of different religions. Here they still carefully preserve the elements of sacred rites as handed down in their secret volumes.

21. It was in learning derived from Egypt that Pythagoras was educated, which taught him to worship the gods in secret, to establish the principle that in whatever he said or ordered his authority was final, to exhibit his golden thigh at Olympia, and to be continually seen in conversation with an eagle.

22. Here it was that Anaxagoras derived the knowledge which enabled him to predict that stones would fall from heaven, and from the feeling of the mud in a well to foretell impending earthquakes. Solon too derived aid from the apophthegms of the priests of Egypt in the enactment of his just and moderate laws, by which he gave great confirmation to the Roman jurisprudence. From this source too Plato, soaring amid sublime ideas, rivalling Jupiter |316 himself in the magnificence of his voice, acquired his glorious wisdom by a visit to Egypt.

23. The inhabitants of Egypt are generally swarthy and dark complexioned, and of a rather melancholy cast of countenance, thin and dry looking, quick in every motion, fond of controversy, and bitter exactors of their rights. Among them a man is ashamed who has not resisted the payment of tribute, and who does not carry about him wheals which he has received before he could be compelled to pay it. Nor have any tortures been found sufficiently powerful to make the hardened robbers of this country disclose their names unless they do so voluntarily.

24. It is well known, as the ancient annals prove, that all Egypt was formerly under kings who were friendly to us. But after Antony and Cleopatra were defeated in the naval battle at Actium, it became a province under the dominion of Octavianus Augustus. We became masters of the dry Libya by the last will of king Apion. Cyrene and the other cities of Libya Pentapolis we owe to the liberality of Ptolemy. After this long digression, I will now return to my original subject.

Labels: ammianus, archaeology, cnn, dna, eagle, egypt, mri, PT scan, tuthmosis, Zahi Hawass

Science moves closer to Artificial life, not just Cloning

J. Craig Venter, he-of-the-Phosphorescent-blue-eyes, works on Artificial life of a sort (research to be published in Science)


Scientists have taken a first step toward making synthetic life by transferring genetic material from one bacterium into another, transforming the second microbe into a copy of the first.

They intend to use their technique to custom-design bacteria to perform functions such as producing artificial fuel or cleaning up toxic waste, the researchers report in Friday's issue of the journal Science.

"This is equivalent to changing a Macintosh computer to a PC by inserting a new piece of software," Craig Venter, a genome pioneer who now heads his own institute in Rockville, Maryland, told reporters in a telephone briefing.

"I think eventually we could make artificial cells," Venter added. "This is a first step."

Venter has been trying for years to create a microbe from scratch. This is not quite it, but his team re-programmed one species of bacteria by adding in the genetic material from a closely related species.

They gene-engineered the replacement chromosome to resist an antibiotic and then flooded their experiment with the drug. The bacteria that survived all carried only the genes that had been spliced in.

They believe all the others simply died, but they are in fact not sure how the new DNA re-programmed some of the bacteria or what happened to the original DNA.

"I think that we don't know for certain how the donor genome takes over," Venter Institute researcher Ham Smith told reporters.

Nonetheless, Venter's team has applied for a patent on the process and they hope to exploit it industrially. Venter believes it will be relatively straightforward to build a new chromosome from scratch, one that performs the desired functions, to create a custom-made bacterium.

"What we are reporting in this Science paper is not anything about a synthetic organism," Venter said.

BOOTING UP LIFE

"It's a key enabling step so that once we have a synthetic chromosome we know it is now possible to boot that up. So synthetic biology itself and synthetic genomics is much closer to being proven," Venter added.

"We look forward to having fuels from genetically modified organisms within the next decade and perhaps in half that time."

The key to the experiment was using a very simple bacterium called Mycoplasma capricolum, which often infects goats. Bacteria do not have a nucleus as do cells from more complex organisms.

The research team injected a chromosome from a related species called Mycoplasma mycoides.

They do not know how well it worked but at least some of the M. capricolum were transformed into what looked and acted like M. mycoides.

The scientists concede it will be much more difficult to do this with more complex organisms, even bacteria, that have cell walls and all sorts of defensive mechanisms to keep out foreign

DNA.

A non-profit Canadian organization called the ETC Group expressed concern about the experiment and Venter's patent application. "We are extremely concerned about the breadth and implications of this patent and of its monopoly claims," the group's Jim Thomas said in an e-mail.

"We will be requesting that patent offices worldwide refuse this patent."

But Venter defended the patent. "At every stage of what the team has done here over the past several years, we have had to develop novel technologies and approaches that have not existed before because the field has not existed before," he said.

Labels: artificial life, craig venter, dna, genetics, ham smith, microbes, mycoplasma

6.03.07 - DNA has been deciphered, thanks to Nobel prize winning Dr. James Watson, along the lines of the work of Jean Francois Champollion, who translated Egyptian heiroglyphs. Here is a piece in slashdot. The next step is personal DNA mapping.

This should usher in the era of personalized 'alert' services as a preliminary step. If you have spent time here and taken a few tests, you have already entered into this new world, where the web itself and your computer becomes your lab assistant and your key to self-discovery. Several of our tests have correlated with possible genetic predisposition for Alzheimer's, so your score, in coming months and years will likely be a gateway into this exciting new world of Knowing. Dr Watson himself was unsure if he wanted to know about predisposition for Alzheimer's, but many people do want find out so they can take action. Another benefit of speed-based brain exercise, more so than other forms, is the development of additional cognitive reserve.

Labels: alerts, champollion, dna

Dr. James Watson, usually credited with unraveling of DNA along with Francis Crick, became one of the first people to have his own personal genome mapped - maybe the first.

This entails a thorough assessment which can lead to a better understanding of risk factors for certain diseases and conditions which append their outcomes to genetic antecedents.

Think of it, perhaps, as a structural engineer conducting a risk assessment or failure analysis on a highway overpass or skyscraper - a personal genome map accomplishes this task for the superstucture of your physical body.

With this information in hand, 'bugs' in the program can be identified and corrected, sometimes due to junk code in our DNA left over from an evolutionary branch that was not followed.

With the Brain - APOEe4 positive is one of the genetic conditions to watch for since it greatly impacts Alzheimer's Disease and early onset cases across the human family.
So, exercising your brain and building cognitive reserve is good for everyone - APOEe4 assessment is key for those who are APOEe4 positive. Normally people are diagnosed without any genetic assessment when symptoms are already apparent. APOEe4 begins to impact individuals at a young age before there are any symptoms - knowing about it helps you take charge of your life.

Labels: apoee4, crick, dna, genome mapping, watson

Larry Page talked to the AAAS in San Francisco about DNA and its small footprint. (an OS smaller than Windows or Linux)

The programming language of humans, if you will, would include the workings of your brain, said Page, who offered his hypothesis Friday night during a plenary lecture here at the annual American Association for the Advancement of Science conference. His guess, he said, was that the brain's algorithms weren't all that complicated and could be approximated, eventually, with a lot of computational power.

"We have some people at Google (who) are really trying to build artificial intelligence and to do it on a large scale," Page said to a packed Hilton ballroom of scientists. "It's not as far off as people think."

Page, the director of products at the 8-year-old search giant, described several of his areas of interest in science and technology during the hour-long talk, which was a rare engagement for the nerdy billionaire. But the common thread in the lecture seemed to be enthusiasm for what Page (and co-founder Sergey Brin) managed to do well with Google: good old-fashioned entrepreneurialism while solving a single problem.

Here's a response.

Labels: apoe, cnet, cognitivelabs.com, dna, page

Scientists have unveiled results of the largest study of the genetics of autism, involving DNA from almost 1,200 affected families worldwide. Two key clues have already been isolated.

Discoveries in two areas of the genome -- a region on chromosome 11 suspected of having links to autism, and aberrations in a brain-development gene called neurexin 1 -- could spur more targeted research, the experts noted.

"That's the real promise here," said Autism Genome Project co-researcher Dr. Stephen Scherer, director of the Center for Applied Genomics at The Hospital for Sick Children in Toronto. "When you identify certain genes, you can then develop genetic tests -- in some cases prenatal and in some cases postnatal -- because early diagnosis is crucial here."

Genetic discoveries can also further research toward a cure for autism, Scherer said.

"When we have this type of knowledge, we can actually think about designing better therapies based on what we know is not happening properly in the [brain] cell. We can try and design things to make it work better," he explained.

The Autism Genome Project was funded by the U.S.
National Institutes of Health and the nonprofit advocacy group Autism Speaks. Its findings were published in the Feb. 18 online edition of Nature Genetics.

Autism remains a real health crisis, with the U.S. Centers for Disease Control and Prevention announcing recently that one in every 150 American 8-year-olds now have some form of autistic spectrum disorder. That number is higher than prior estimates, and the debate rages as to just why the disease might be becoming more prevalent.

Experts agree that autism's causes remain cloaked in mystery, although prior research has pointed to a strong genetic component. For example, "there's about 90 percent concordance [of autism] between identical twins -- that's a significant genetic contribution," Scherer said.

So, the Autism Genome Project, which took five years to complete, sought to probe much deeper into the DNA driving the disorder. The project involved more than 120 scientists working at 50 institutions in 19 countries. They painstakingly sought out almost 1,200 families worldwide in which at least two members were affected by autism. The scientists then collected DNA samples from family members and analyzed these samples in the most advanced and standardized manner, looking for genomic "commonalities."

Those efforts have met with real success.

"First, we found several regions of the genome, particularly one region on chromosome 11, that seem to be very highly associated with the development of autism," said Scherer, who is also professor of medicine at the University of Toronto. While prior research had suggested chromosome 11 as a potential hotspot for autism-linked DNA, this study greatly strengthens that view, he said.

The researchers also used cutting-edge technologies to seek out what are known as "copy number variations" -- genes that appear not in pairs (as most genes passed down from mom and dad are), but as just a single copy, or as three or more copies.

"We found several regions of the genome -- sometimes the same region popping up in unrelated individuals -- with 3 or more copies," Scherer said. "We didn't see these in the individuals' parents, so that implies that these regions are harboring susceptibility genes for autism."

One gene in particular, called neurexin 1, appeared in some cases in just one copy. "In one family, both of the children who were autistic actually had that piece missing," Scherer said. "That's kind of a smoking gun that the gene is implicated."

It makes intuitive sense that dysfunctional neurexin 1 might play some role in autistic disorders, another expert said.

The neurexin 1 protein and its kin, "are very important in determining how properly the brain is wired up from one nerve cell to another, and in the chemical transmission of information from one nerve cell to another," said Dr. Bradley Peterson, a professor of child psychiatry at Columbia University Medical Center and the New York State Psychiatric Institute, in New York City.

Peterson, who was not involved in the project, said genes that effect early neural growth could be key to autistic disorders, since "the genetic and the non-genetic contributions to autism, by definition, have to exert their effect very early in brain development, either in utero or in the first months or couple of years of life."

Still, he and Scherer both stressed that the new study only points to potential leads for future research. Because of the study's particular methodology, no one finding reached statistical significance, Peterson said. "This is all very strong evidence, and a very good set of leads, but we can't yet say that we have proved the involvement of these regions in autism," he said.

Scherer said that, except in very rare instances, there isn't likely to be a single gene responsible for autism. Instead, a variety of genetic abnormalities may work on each other during development to create some level of autism. And experts don't discount the potential role of environmental stresses on that mix, either.

"Remember, autism is actually a grab bag of different developmental disorders. And what we show here is that many genes can be involved, and also these copy number variants," Scherer said. "And could it be that environment is contributing? Absolutely."

One thing is for sure, however: Autism research holds more promise now than ever before, the experts said.

"Anybody that's working out here can use this information now, and it really provides a great path forward as to how we need to do our experiments over the next five years or so," Scherer said. "We've now got all these new candidate genes --- the neurexins, the various copy number variants -- and we can tackle the problem in a much more focused and organ ized way."

Labels: autism, dna, genetics

Scientists in the SF Bay Area have succeeded in analyzing DNA of the homo Neandertalis (Neanderthal). The remains of bones from Europe were airlifted to a lab in Walnut Creek, run by the U.S. Dept of Energy. The scientists conducting the investigation susp