Bio · Science · Technology · Vital-Edible-Health

How A Virus Hid In Our Genome For Six Million Years

In the mid-2000s, David Markovitz, a scientist at the University of Michigan, and his colleagues took a look at the blood of people infected with HIV. Human immunodeficiency viruses kill their hosts by exhausting the immune system, allowing all sorts of pathogens to sweep into their host’s body. So it wasn’t a huge surprise for Markovitz and his colleagues to find other viruses in the blood of the HIV patients. What was surprising was where those other viruses had come from: from within the patients’ own DNA.

HIV belongs to a class of viruses called retroviruses. They all share three genes in common. One, called gag, gives rise to the inner shell where the virus’s genes are stored. Another, called env, makes knobs on the outer surface of the virus, that allow it to latch onto cells and invade them. And a third, called pol, makes an enzyme that inserts the virus’s genes into its host cell’s DNA.

It turns out that the human genome contains segments of DNA that match pol, env, and gag. Lots of them. Scientists have identified 100,000 pieces of retrovirus DNA in our genes, making up eight percent of the human genome. That’s a huge portion of our DNA when you consider that protein coding genes make up just over one percent of the genome.

Excerpt form an article written by Carl Zimmer. Continue HERE

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ENCODE: the rough guide to the human genome

Back in 2001, the Human Genome Project gave us a nigh-complete readout of our DNA. Somehow, those As, Gs, Cs, and Ts contained the full instructions for making one of us, but they were hardly a simple blueprint or recipe book. The genome was there, but we had little idea about how it was used, controlled or organized, much less how it led to a living, breathing human.

That gap has just got a little smaller. A massive international project called ENCODE – the Encyclopedia Of DNA Elements – has moved us from “Here’s the genome” towards “Here’s what the genome does”. Over the last 10 years, an international team of 442 scientists have assailed 147 different types of cells with 24 types of experiments. Their goal: catalog every letter (nucleotide) within the genome that does something. The results are published today in 30 papers across three different journals, and more.

For years, we’ve known that only 1.5 percent of the genome actually contains instructions for making proteins, the molecular workhorses of our cells. But ENCODE has shown that the rest of the genome – the non-coding majority – is still rife with “functional elements”. That is, it’s doing something.

Excerpt from an article by Discover. Continue HERE

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Why Google Isn’t Making Us Stupid…or Smart

Last year The Economist published a special report not on the global financial crisis or the polarization of the American electorate, but on the era of big data. Article after article cited one big number after another to bolster the claim that we live in an age of information superabundance. The data are impressive: 300 billion emails, 200 million tweets, and 2.5 billion text messages course through our digital networks every day, and, if these numbers were not staggering enough, scientists are reportedly awash in even more information. This past January astronomers surveying the sky with the Sloan telescope in New Mexico released over 49.5 terabytes of information—a mass of images and measurements—in one data drop. The Large Hadron Collider at CERN (the European Organization for Nuclear Research), however, produces almost that much information per second. Last year alone, the world’s information base is estimated to have doubled every eleven hours. Just a decade ago, computer professionals spoke of kilobytes and megabytes. Today they talk of the terabyte, the petabyte, the exabyte, the zettabyte, and now the yottabyte, each a thousand times bigger than the last.

Some see this as information abundance, others as information overload. The advent of digital information and with it the era of big data allows geneticists to decode the human genome, humanists to search entire bodies of literature, and businesses to spot economic trends. But it is also creating for many the sense that we are being overwhelmed by information. How are we to manage it all? What are we to make, as Ann Blair asks, of a zettabyte of information—a one with 21 zeros after it?1 From a more embodied, human perspective, these tremendous scales of information are rather meaningless. We do not experience information as pure data, be it a byte or a yottabyte, but as filtered and framed through the keyboards, screens, and touchpads of our digital technologies. However impressive these astronomical scales of information may be, our contemporary awe and increasing worry about all this data obscures the ways in which we actually engage it and the world of which it and we are a part. All of the chatter about information superabundance and overload tends not only to marginalize human persons, but also to render technology just as abstract as a yottabyte. An email is reduced to yet another data point, the Web to an infinite complex of protocols and machinery, Google to a neutral machine for producing information. Our compulsive talk about information overload can isolate and abstract digital technology from society, human persons, and our broader culture. We have become distracted by all the data and inarticulate about our digital technologies.

Excerpt of a paper written by Chad Wellmon, at The Hedgehog Review. Continue HERE

Bio · Science · Technology · Vital-Edible-Health

Will knowing your DNA for $1,000 improve you life?

The claim by Ion Torrent on Tuesday that a reasonably affordable machine capable of mapping an individual’s complete genetic makeup for $1,000 will be ready by the end of the year has technology geeks in a tizzy.

The $1,000 genome has been hotly sought ever since a crude map of the human genome was first published in 2001. The Carlsbad, Calif. biotech company, part of Life Technologies, will sell its device to research labs and medical clinics for $99,000 to $149,000, compared to the current price of about $750,000 for existing sequencers, Reuters reported on its website Tuesday. According to Reuters, a doctor will be able to sequence a patient’s entire genome for $1,000, compared to the current rate of $3,000 just to test for breast cancer gene mutations, for example. And the company says its new machine can complete the genome analysis within a day, rather than the two months previously needed.

It’s widely believed this type of genetic analysis will revolutionize medicine, that patients will learn their risk profile for potential diseases by having their DNA read right in the doctor’s office. Drugs and vaccines will be designed to fit our genes, in order to maximize efficacy and minimize any side-effects. Newborn babies would have someone peek at their genes so parents could take steps to prevent genetic risks from becoming realities.

Text by Art Caplan, Ph.D. Continue HERE