Category Archives: Life Science

8 Percent of the Human Genome is Old Virus Genes

In Our Genes, Old Fossils Take On New Roles

It turns out that about 8 percent of the human genome is made up of viruses that once attacked our ancestors. The viruses lost. What remains are the molecular equivalents of mounted trophies, insects preserved in genomic amber, DNA fossils.

The thousands of human endogenous retroviruses, or HERVs, sketch a history of rough times during the 550 million years of vertebrate evolution. The best-preserved one, HERV-K113, probably arrived less than 200,000 years ago, long after human beings and chimpanzees diverged from a common ancestor.

But these retroviruses are more than just curiosities. They are some of the most important enemies we ever had. They helped mold the immune system that is one of the evolutionary marvels of life on Earth.

I must say there is tons of amazing stuff I learn about but I still find retroviruses amazing.

General Biology Berkeley Course Webcast

General Biology Course at University of California – Berkeley, Fall 2007. Instructors John Forte, R Fischer and R Malkin. “General introduction to cell structure and function, molecular and organism genetics, animal development, form and function. Intended for biological sciences majors, but open to all qualified students.” A great service from Berkeley with video and audio… Topics include: Macromolecules structure and function, How cells function-an introduction to cellular metabolism and biological catalysts, Microbes – Viruses, Bacteria, Plasmids, Transposons and Homeostasis: The body’s defenses.

Patent Gridlock is Blocking Developing Lifesaving Drugs

How patent gridlock is blocking the development of lifesaving drugs by Michael Heller, Forbes

Since a 1980 Supreme Court decision allowing patents on living organisms, 40,000 dna-related patents have been granted. Now picture a drug developer walking into an auditorium filled with dozens of owners of the biotech patents needed to create a potential lifesaving cure. Unless the drugmaker can strike a deal with every person in the room, the new drug won’t be developed.
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Nicholas Naclerio, who used to head the BioChip Division at Motorola , told Scientific American, “If we want to make a medical diagnostic with 40 genes on it, and 20 companies hold patents on those genes, we may have a big problem.”
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And it’s not just drugs we’re losing. Today anything high tech–banking, semiconductors, software, telecom–demands the assembly of innumerable patents. Innovation has moved on, but we’re stuck with old-style ownership that’s easy to fragment and hard to put together. This debacle’s only upside is that assembling fragmented property is one of the great entrepreneurial and political opportunities of our era.

This is a critical problem I have written about before. The broken patent system is a serious problem that needs to be fixed.

Backyard Wildlife: Great Spreadwing Damselfly

photo of Dragonfly

If you know the what type of dragonfly is in the photo, please add a comment (update: a comment indicates it is not a dragonfly but a Great Spreadwing Archilestes grandis damselfly – I really enjoy getting feedback like this. It appears the most common way to differentiate the two is how the wings are at rest but the Spreadwing is an exception). I had a small preying mantis drop on my head, and then the ground, a month ago in my backyard. But when I got my digital camera I couldn’t find it again. The variety of insects you can see can be amazing, especially if you don’t use poisons and chemicals in your yard.

Photo by John Hunter, creative commons attribution license.

Autism and the MMR vaccine

Science Tuesday: Back into the hornets nest is a thoughtful follow-up post on the decision of a scientist to vaccinate his child.

Autism isn’t like tuberculosis, there’s not a bacteria that causes the disease. In fact,most researchers believe that “autism” is not a discrete disorder, rather “autism is a clinically defined pervasive developmental disorder with phenotypically diverse neuropsychiatric symptoms and characteristics. These manifest as a spectrum of social and communicative deficits, stereotypical patterns and disturbances of behaviour.”Â¹
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If a particular trait’s heritability is 100% then the trait is due entirely to genetic variation, if the heritability is 0% then the trait is due entirely to environmental variation. By some estimates, heritability of autism spectrum disorders exceeds 90%
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repeated studies have found that autism diagnoses continue to rise even after the removal of thimerosal from the vaccine.
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Finally, when thinking about the environmental influences on autism, it’s important to explore the role of the environment on genetics. Many of the types of genetic changes that have been identified as causative in autism are indicative of some sort of DNA damage – DNA damage that may result from exposure to an environmental toxin. Many scientists, and I count myself in their number, feel that the recent autism ‘epidemic’ is due primarily to improved screening and diagnosis. In other words, prior to the 1980’s, many people suffering from autism were diagnosed as “slow” or misdiagnosed with another type of mental retardation. Unfortunately, there is no way to quantify this hypothesis.

This is one of the examples of what is so good about blogs. Great content that probably would not be available but through a blog.

Huge Ant Nest

[Google broke the original link when they trashed Google Video in poor way, which has become their habit. There history now shows they create very unreliable web services that are an embarrassment to any engineer. Still YouTube is difficult to avoid, Vimeo while not suffering from being a Google product and therefore unreliable based on Google’s history, Vimeo offers only a small fraction of the content found on YouTube.]

Very cool webcast. The ant nest goes 8 meters into the earth. The nest is engineered with vents to promote the flow of air, bringing in fresh air and expelling carbon dioxide created by the large fungus gardens. The scientists filled the ant next with concrete to excavate it: 10 tons of concrete were needed.

Superbugs – Deadly Bacteria Take Hold

Superbugs by Jerome Groopman, New Yorker:

“My basic premise,” Wetherbee said, “is that you take a capable microÃ¶rganism like Klebsiella and you put it through the gruelling test of being exposed to a broad spectrum of antibiotics and it will eventually defeat your efforts, as this one did.” Although Tisch Hospital has not had another outbreak, the bacteria appeared soon after at several hospitals in Brooklyn and one in Queens. When I spoke to infectious-disease experts this spring, I was told that the resistant Klebsiella had also appeared at Mt. Sinai Medical Center, in Manhattan, and in hospitals in New Jersey, Pennsylvania, Cleveland, and St. Louis.
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Unlike resistant forms of Klebsiella and other gram-negative bacteria, however, MRSA can be treated. “There are about a dozen new antibiotics coming on the market in the next couple of years,” Moellering noted. “But there are no good drugs coming along for these gram-negatives.” Klebsiella and similarly classified bacteria, including Acinetobacter, Enterobacter, and Pseudomonas, have an extra cellular envelope that MRSA lacks, and that hampers the entry of large molecules like antibiotic drugs. “The Klebsiella that caused particular trouble in New York are spreading out,” Moellering told me. “They have very high mortality rates. They are sort of the doomsday-scenario bugs.”

Great article. Related: Bacteria Survive On All Antibiotic Diet – Bacteria Can Transfer Genes to Other Bacteria – New Yorker on CERN’s Large Hadron Collider – posts on health related topics

Viruses and What is Life

Viruses are generally considered not to be alive (they must use a host cell of something else to reproduce). However, defining exactly what life is, is not as easy as you might think.

The debate about what counts as a living thing is fuelled today by the discovery of the first virus that is able to fall “ill” by being infected with another virus.
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the discovery of a giant virus that itself falls ill through infection by another virus seems to suggest they too are alive, highlighting how there is no watertight definition of what exactly scientists mean when they refer to something as “living”.

“There’s no doubt, this is a living organism,” the journal Nature is told by Prof Jean-Michel Claverie, director of the Mediterranean Institute of Microbiology in Marseilles, part of France’s basic-research agency CNRS. “The fact that it can get sick makes it more alive.”

Massive Gorilla Population Found

photo of western lowland gorillas

New Census Shows Massive Gorilla Population in Northern Republic of Congo

The new census tallied more than 125,000 western gorillas in two adjacent areas in the northern part of the country, covering an area of 18,000 square miles (47,000 square kilometers). Previous estimates from the 1980s placed the entire population of western lowland gorillas, which occur in seven Central African nations, at fewer than 100,000. Since then, however, scientists had believed that this number had dwindled by at least half, due to hunting and disease.
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The Wildlife Conservation Society (WCS) says a combination of factors account for such high numbers of gorillas, including successful long-term management of the Republic of Congo’s protected areas; remoteness and inaccessibility of some of the key locations where the gorillas were found; and a habitat where there is plenty to eat, particularly in some of the swamp forests and the “Marantaceae” forests, which are rich in herbs.

WCS has worked with the Government of Republic of Congo in the northern area of the country for nearly 20 years, helping to establish the NouabalÃ©-Ndoki National Park and manage the Lac TÃ©lÃ© Community Reserve, while working with logging companies outside of protected areas to reduce illegal hunting.

“These figures show that northern Republic of Congo contains the mother lode of gorillas,” said Dr. Steven E, Sanderson, President and CEO of the Wildlife Conservation Society. “It also shows that conservation in the Republic of Congo is working. This discovery should be a rallying cry for the world that we can protect other vulnerable and endangered species, whether they be gorillas in Africa, tigers in India, or lemurs in Madagascar.”

Malaysian Shrew Survives on Beer

photo of Malaysian tree shrew

Malaysian Shrew Survives on Beer

The shrew lives in the forest of Malaysia and feeds on the flowers of the bertam palm. Produced year-round and constantly fermenting, its nectar is about 3.8 percent alcohol — roughly equivalent to a Sam Adams light.

“Fine,” you say, “except that’s a light beer!” But cut the shrew some slack — it doesn’t eat anything else. Let’s see you subsist on nothing but beer, light or not, and stay sober.

That’s the shrews’ most amazing quality: they don’t get drunk. On any given night, said researchers in a study published today in the Proceedings of the National Academy of Sciences, one-third of the shrews have a blood-alcohol level that would leave us under the bar — but there’s no evidence of intoxication.