Cognitive Labs

Dr. Leroy Hood, former Bill Gates professor of Biomedical Sciences at Washington, and who runs the Institute for Systems Biology, is calling for a Genome-based approach to healthcare.

Rather than treating symptoms after they begin occurring, why not get an alert about possible issues and be proactive?

More knowledge about genes makes this possible.

Hood is also on the advisory board of Taiwan Genome Sciences, a company which has proposed an extensive partnership with us (Cognitive Labs) before.

Wired reports on the several components of Hood's vision...

Predictive

The vision
Using genome sequencing and blood tests, a doctor will be able to determine a patient's probability of developing certain diseases. The price of these tests is dropping and will soon be less than $1,000 — the same as a CT scan today.

The challenge
Physicians will have to be trained to use the technology ethically. Patients will have to make sense of new kinds of choices.

Preventive

The vision
Based on an individualized risk profile, you could start therapies in advance to cut the likelihood of illness. Drugs could be designed to blunt the desire to overeat, drink, or smoke. Average lifespan could be extended by 10 to 30 years.

The challenge
What qualifies as a disease? Will we have fewer football players if we quiet the genes that drive aggression?

Personalized

The vision
With billions of data points for every patient, drug therapies can be created to suit each genome. This would eliminate the trial-and-error approach doctors use today.

The challenge
Having your genome on Google could be a huge privacy risk. With so much information around, data security will become an important field in the health care industry.

Participatory

The vision
People will maintain their own health, not just by treating existing illnesses but by learning about their own predispositions.

The challenge
How to explain biomarkers to someone with little grasp of science? Hood proposes games that teach health concepts, and his Institute for Systems Biology is working with school districts to develop top-notch science curricula.

Labels: caltech, genome, hood, taiwan, wired

 

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

The Origins Genome Resources Blog is one of the newest widget users. This is a publication of the Mt. Sinai School of Medicine, near Central Park in NY, Genome Behavior Project.

In their words...

"We are using neuroimaging and genetic methods to try to understand how genetic variation relates to individual differences in cognitive development, particularly in the area of attention and inhibitory control. Our research is one example of basic research that seeks to generate genomic- and biomarker-based tools to guide medical treatment and early intervention."

They have links to the best browser-based genomic expression databases including Allen and UC Santa Cruz. The lab is run by Dr. John Fossella.


The widget is spreading across the web...conceived, developed, and programmed by Dr. Michael Addicott.

We'll be posting our latest presentation shortly, so stay tuned.

Labels: blogger widgets, Central Park, Dr. John Fossella, genome, iBrain, John Fossella, Mt Sinai, Mt. Sinai School of Medicine

Good things do come in threes - we're now entering our third phase of working on the 'Rosetta Stone.' At Berkeley we got to translate some of this stone -it's often used to teach Demotic - the later derivative of hieroglyphics and hieratic - the cursive priestly language often written on tablets and papyri.


Ptolemy V - Silver Tetradrachm, Alexandria mint

Here's an excerpt of what is essentially an announcement of a tax cut by Greek ruler Ptolemeos V Epiphaneos, descendant of Alexander the Great's general Ptolemy, and founder of the Macedonian line of Kings - to be posted in the relevant temples. A few other copies of Ptolemy's decree have been found in Egypt:


In the reign of the new king, who was Lord of the diadems, great in glory, the stabilizer of Egypt, and also pious in matters relating to the gods, Superior to his adversaries, rectifier of the life of men, Lord of the thirty-year periods like Hephaestus the Great, King like the Sun, the Great King of the Upper and Lower Lands, offspring of the Parent-loving Gods, whom Hephaestus has approved, to whom the Sun has given victory, living image of Zeus, Son of the Sun, Ptolemy the ever-living, beloved by Ptah;

In the ninth year, when Aëtus, son of Aëtus, was priest of Alexander and of the Savior Gods and the Brother Gods and the Benefactor Gods and the Parent-loving Gods and the God Manifest and Gracious; Pyrrha, the daughter of Philinius, being athlophorus for Bernice Euergetis; Areia, the daughter of Diogenes, being canephorus for Arsinoë Philadelphus; Irene, the daughter of Ptolemy, being priestess of Arsinoë Philopator: on the fourth of the month Xanicus, or according to the Egyptians the eighteenth of Mecheir.

THE DECREE: The high priests and prophets, and those who enter the inner shrine in order to robe the gods, and those who wear the hawks wing, and the sacred scribes, and all the other priests who have assembled at Memphis before the king, from the various temples throughout the country, for the feast of his receiving the kingdom, even that of Ptolemy the ever-living, beloved by Ptah, the God Manifest and Gracious, which he received from his Father, being assembled in the temple in Memphis this day, declared:

Since King Ptolemy, the ever-living, beloved by Ptah, the God Manifest and Gracious, the son of King Ptolemy and Queen Arsinoë, the Parent-loving Gods, has done many benefactions to the temples and to those who dwell in them and also to all those subjects to his rule, being from the beginning a god born of a god and a goddess—like Horus, the son of Isis and Osirus, who came to the help of his Father Osirus—being benevolently disposed toward the gods, has concentrated to the temples revenues both of silver and of grain, and has generously undergone many expenses in order to lead Egypt to prosperity and to establish the temples... the gods have rewarded him with health, victory, power, and all other good things, his sovereignty to continue to him and his children forever

Demotic comes from the Greek word "demos" which means what? Just think 'democracy.'
Demotic originated in the Delta area after the 25th Dynasty, long after the invasion of the Peoples of the Sea and probably the diaspora of the Hebrews referred to in the Book of Exodus (if indeed this was a historical event and not an allegorical 'beginning' to the saga that was told by word of mouth.)

Rubbings of the stone can be had, and sometimes duplicates - the greatest contribution towards the understanding of the stone was perhaps made by 3 University of Pennsylvania undergraduates, whose concordance was duly hailed by the British Antiquities Society in London.

Following our experience with that text, we contibuted to RosettaNet and supply chain related EDI, whose main sponsor was the company Marshall Industries. One of our contributions was the ANSI EDI 204 transaction set, which governed information flows in the small package industry. This EDI specification was invented by UPS.

Having contributed to cross-platform supply chain rationalization and the real Rosetta Stone via the much less marketable Egyptian language, the third incidence of the Rosetta experience is the human genome, the grok of which is often compared to the transliteration of the Rosetta Stone. Our contribution here is a simple tool for evaluation of genetic risks as they relate to the brain and cognition, via Internet-enabled technologies - and this is the essence of the Revolution...

Labels: demotic, genome, ptolemy, rosetta

Global Cognitive Map is here: you can see (courtesy of Asynchronous data) where the people are located who are taking tests. This is a a tiny fraction of test-takers...we are creating a tiny version for the home page and a fuller version inside the site (bigger, as well) for people who want to explore without slowing down the home page excessively. (read more about genes and the brain)

other same day links: google map update - now you will be able to recreate history
and here's another on the National Geographic's effort...

Labels: brain, cognitive_labs, genome, map, national_geographic