homeaboutarchives + tagsshopmembership!
aboutarchivesshopmembership!
aboutarchivesmembers!

kottke.org posts about genetics

The embryonic stem cell mess

posted by Jason Kottke   Aug 31, 2010

The New Yorker has a long profile of Francis Collins, the ardent Christian whom Obama picked to head up the NIH, and the NIH’s role in embryonic stem cell research.

A year later, Obama’s appointment of Collins seemed an inspired choice. The President had found not only a man who reflected his own view of the harmony between science and faith but an evangelical Christian who hoped that the government’s expansion of embryonic-stem-cell research might bring the culture war over science to a quiet end. On August 23rd, however, Judge Royce C. Lamberth, of the Federal District Court for the District of Columbia, halted federal spending for embryonic-stem-cell research, putting hundreds of research projects in limbo and plunging the N.I.H. back into a newly contentious national debate.

King Tut’s family tree

posted by Jason Kottke   Aug 25, 2010

According to DNA analysis described in the latest issue of National Geographic, Tutankhamun’s parents were most likely brother and sister, which may have contributed to his early death.

In my view, however, Tutankhamun’s health was compromised from the moment he was conceived. His mother and father were full brother and sister. Pharaonic Egypt was not the only society in history to institutionalize royal incest, which can have political advantages. But there can be a dangerous consequence. Married siblings are more likely to pass on twin copies of harmful genes, leaving their children vulnerable to a variety of genetic defects. Tut ankhamun’s malformed foot may have been one such flaw. We suspect he also had a partially cleft palate, another congenital defect. Perhaps he struggled against others until a severe bout of malaria or a leg broken in an accident added one strain too many to a body that could no longer carry the load.

It’s likely that Tut’s wife was his half-sister as well.

DNA and quantum entanglement

posted by Jason Kottke   Jul 16, 2010

Does quantum entanglement hold DNA together? Some physicists say it’s possible.

Rieper and co ask what happens to these oscillations, or phonons as physicists call them, when the base pairs are stacked in a double helix.

Phonons are quantum objects, meaning they can exist in a superposition of states and become entangled, just like other quantum objects.

To start with, Rieper and co imagine the helix without any effect from outside heat. “Clearly the chain of coupled harmonic oscillators is entangled at zero temperature,” they say. They then go on to show that the entanglement can also exist at room temperature.

That’s possible because phonons have a wavelength which is similar in size to a DNA helix and this allows standing waves to form, a phenomenon known as phonon trapping. When this happens, the phonons cannot easily escape. A similar kind of phonon trapping is known to cause problems in silicon structures of the same size.

DNA copying for everyone

posted by Jason Kottke   Jun 14, 2010

The OpenPCR project is trying to raise $6,000 on Kickstarter to design and build a DNA Xerox machine that costs less than $400, thereby enabling DNA hacking in one’s garage.

In 1983, Kary Mullis first developed PCR, for which he later received a Nobel Prize. But the tool is still expensive, even though the technology is almost 30 years old. If computing grew at the same pace, we would all still be paying $2,000+ for a 1 MHz Apple II computer. Innovation in biotech needs a kick start!

PCR machines currently cost $4-10,000. (via modcult)

Today only: $99 DNA test

posted by Jason Kottke   Apr 23, 2010

Today only, the usually $499 DNA test from 23andMe is only $99. Ship your spit off and in a few weeks, you’ll receive information about your ancestry, health risks, and so on.

DNA testing for $100! Stick that in your flying car’s tailpipe and smoke it!

DNA poetry

posted by Jason Kottke   Mar 25, 2010

Poet Christian Bök wants to compose a poem and encode it into the DNA of the Deinococcus radiodurans bacteria — “the most radiation-resistant organism known”.

He wants to inject the DNA with a string of nucleotides that form a comprehensible poem, and he also wants the protein that the cell produces in response to form a second comprehensible poem.

AGGCGT GCCACC AAT
TCT TACC GATTT CT
CA CTCTAG ACC CTG
AGCCCA CGC GGTTCA

(via mr)

How genetics works

posted by Jason Kottke   Feb 24, 2010

Genetic Shirts

As information visualizations go, you can’t get much better than this.

Not your father’s evolution

posted by Jason Kottke   Feb 04, 2010

Recent evidence of horizontal gene transfer — in which genes are exchanged from other organisms, not from ancestors — has some scientists thinking that the dominant form of evolution for most of the Earth’s history was between non-related organisms and not among ancestors.

In the past few years, a host of genome studies have demonstrated that DNA flows readily between the chromosomes of microbes and the external world. Typically around 10 per cent of the genes in many bacterial genomes seem to have been acquired from other organisms in this way, though the proportion can be several times that. So an individual microbe may have access to the genes found in the entire microbial population around it, including those of other microbe species. “It’s natural to wonder if the very concept of an organism in isolation is still valid at this level,” says Goldenfeld.

Read on for their hypothesis about how horizontal evolution drove innovation — development of a universal genetic code and genetic innovation-sharing protocols — in life forms early on in the Earth’s history. Fascinating.

The orchid hypothesis

posted by Jason Kottke   Jan 05, 2010

David Dobbs tells us about a new theory in genetics called the orchid hypothesis that suggests that the genes that underlie some of the most troubling human behaviors — violence, depression, anxiety — can, in combination with the right environment, also be responsible for our best behaviors.

Most of us have genes that make us as hardy as dandelions: able to take root and survive almost anywhere. A few of us, however, are more like the orchid: fragile and fickle, but capable of blooming spectacularly if given greenhouse care. So holds a provocative new theory of genetics, which asserts that the very genes that give us the most trouble as a species, causing behaviors that are self-destructive and antisocial, also underlie humankind’s phenomenal adaptability and evolutionary success. With a bad environment and poor parenting, orchid children can end up depressed, drug-addicted, or in jail — but with the right environment and good parenting, they can grow up to be society’s most creative, successful, and happy people.

From start to finish, this is one of the most interesting things I’ve read in weeks.

Slow beef

posted by Jason Kottke   Apr 24, 2009

The cow genome has been published and the results show changes due to millions of years of natural selection but also to the thousands of years of selective breeding by humans.

Both types of cattle show evidence of natural selection in genes that appear to be involved in making the animals — large, horned and potentially dangerous — docile. In some breeds, specific variants of behavior-related genes are “fixed,” or seen in essentially every animal. Curiously, some of those genes are in regions that in the human genome seem to be involved in autism, brain development and mental retardation.

So…by “docile”, you really mean “mentally retarded”. (via long now)

Some answers to the disappearing honeybee problem

posted by Jason Kottke   Mar 23, 2009

In an article for Scientific American, two scientists who are working on the causes of colony collapse disorder (CCD) say that they and other researchers have made some progress in determining what’s killing all of those bees.

The growing consensus among researchers is that multiple factors such as poor nutrition and exposure to pesticides can interact to weaken colonies and make them susceptible to a virus-mediated collapse. In the case of our experiments in greenhouses, the stress of being confined to a relatively small space could have been enough to make colonies succumb to IAPV and die with CCD-like symptoms.

It’s like AIDS for bees…the lowered immunity doesn’t kill directly but makes the bees more susceptible to other illness. One the techniques researchers used in investigating CDD is metagenomics. Instead of singling out an organism for analysis, they essentially mixed together a bunch of genetic material found in the bees (including any bacteria, virii, parasites, etc.) and sliced it up into small pieces that were individually deciphered. They went through those pieces one by one and assigned them to known organisms until they ran across something unusual.

The CSI-style investigation greatly expanded our general knowledge of honeybees. First, it showed that all samples (CCD and healthy) had eight different bacteria that had been described in two previous studies from other parts of the world. These findings strongly suggest that those bacteria may be symbionts, perhaps serving an essential role in bee biology such as aiding in digestion. We also found two nosema species, two other fungi and several bee viruses. But one bee virus stood out, as it had never been identified in the U.S.: the Israeli acute paralysis virus, or IAPV.

Twins commit perfect crime

posted by Jason Kottke   Mar 20, 2009

Twin brothers are suspected of stealing millions in jewelry and watches from KaDeWe in Berlin. DNA from the crime scene matches the brothers’ DNA. But their DNA is too similar to match either brother individually so the police have to let them go.

German law stipulates that each criminal must be individually proven guilty. The problem in the case of the O. brothers is that their twin DNA is so similar that neither can be exclusively linked to the evidence using current methods of DNA analysis. So even though both have criminal records and may have committed the heist together, Hassan and Abbas O. have been set free.

How long before this shows up on CSI?

Super cows!

posted by Jason Kottke   Feb 11, 2009

Myostatin is a protein that, along with its associated gene, limits the growth of muscle tissue in some mammals. The Belgian Blue cattle breed has a natural mutation of the gene associated with myostatin that supresses the protein, resulting in lean and heavily muscled cattle.

Belgian Blue

A myostatin inhibiting drug called Stamulumab is currently undergoing testing for treating those with muscular dystrophy. If approved, use and abuse by human athletes will surely follow. (via siege)

Update: Stamulumab is no longer undergoing testing. But a pharmaceutical company called Acceleron is developing a similar drug called ACE-031. (thx, stephen)

Jurassic Park not so far fetched

posted by Jason Kottke   Nov 21, 2008

Scientists are saying that we can make ourselves a whoolly mammoth for as little as $10 million. All it takes is a mammoth genome, a lot of painstaking work, and much computing power.

If the genome of an extinct species can be reconstructed, biologists can work out the exact DNA differences with the genome of its nearest living relative. There are talks on how to modify the DNA in an elephant’s egg so that after each round of changes it would progressively resemble the DNA in a mammoth egg. The final-stage egg could then be brought to term in an elephant mother, and mammoths might once again roam the Siberian steppes.

The article also notes that if this works for the mammoth, it might also be possible to do the same for a Neanderthal. What an age we live in.

The Genetic Information Nondiscrimination Act of 2008

posted by Jason Kottke   May 08, 2008

The purpose of the Genetic Information Nondiscrimination Act of 2008:

To prohibit discrimination on the basis of genetic information with respect to health insurance and employment.

It passed the Senate earlier this year is expected to be signed into law by the President soon. No Gattaca! (via nyer conference)

Nurture is really kicking ass these days….

posted by Jason Kottke   Dec 20, 2007

Nurture is really kicking ass these days….first the IQ thing and now this.

The offspring of expensive stallions owe their success more to how they are reared, trained and ridden than good genes, a study has found. Only 10% of a horse’s lifetime winnings can be attributed to their bloodline, research in Biology Letters shows.

That suggests, a la Moneyball, that buying horses with so-so lineages and training them really well could make for a better return on investment.

The pace of human evolution has accelerated

posted by Jason Kottke   Dec 13, 2007

The pace of human evolution has accelerated greatly over the last 40,000 years, partially due to our population growth.

The brisk rate of human selection occurred for two reasons, Dr. Moyzis’ team says. One was that the population started to grow, first in Africa and then in the rest of the world after the first modern humans left Africa. The larger size of the population meant that there were more mutations for natural selection to work on. The second reason for the accelerated evolution was that the expanding human populations in Africa and Eurasia were encountering climates and diseases to which they had to adapt genetically. The extra mutations in their growing populations allowed them to do so.

Dr. Moyzis said it was widely assumed that once people developed culture, they protected themselves from the environment and from the forces of natural selection. But people also had to adapt to the environments that their culture created, and the new analysis shows that evolution continued even faster than before.

Looks like this study answers the “Is Evolution Over?” question.

The facinating story of Aicuña,

posted by Jason Kottke   Oct 05, 2007

The facinating story of Aicuña, a small Argentinean town that’s been closed off from the outside world, has an unusually high percentage of albino residents, and where 8 out of 10 people share the same last name. (via 3qd)

Rare semi-identical twins born. “They are the

posted by Jason Kottke   Mar 27, 2007

Rare semi-identical twins born. “They are the result of two sperm cells fertilising a single egg, which then divided to form two embryos - and each sperm contributed genes to each child.”

Richard Dawkins answers some questions from readers

posted by Jason Kottke   Dec 06, 2006

Richard Dawkins answers some questions from readers of the Independent. “Terrible things have been done in the name of Christ, but all he ever taught was peace and love. What’s wrong with that?”

Researchers in Israel and Illinois say they’ve

posted by Jason Kottke   Jul 25, 2006

Researchers in Israel and Illinois say they’ve found a second code in DNA, one that deals with the positioning of proteins. Palimpsest anyone?

The Blue People of Troublesome Creek. Due

posted by Jason Kottke   Jul 10, 2006

The Blue People of Troublesome Creek. Due to a rare blood disorder, “four of the seven Fugate children were born with bright blue skin that lasted their entire lives.” “Over the years, the Fugates interbred repeatedly. Blue people proliferated.” (More here….scroll for the Science article.)

DNA evidence suggests that chimps and humans

posted by Jason Kottke   May 22, 2006

DNA evidence suggests that chimps and humans interbreed after splitting into separate species before splitting again for good.

Evolution on the molecular level appears to

posted by Jason Kottke   May 02, 2006

Evolution on the molecular level appears to happen significantly faster for tropical species than for those that live in more temperate climates.

The Edge has a transcript and an

posted by Jason Kottke   Mar 23, 2006

The Edge has a transcript and an mp3 recording of an event called The Selfish Gene: Thirty Years On. The speakers include Daniel Dennett and Richard Dawkins.

America’s Stone Age Explorers

posted by Jason Kottke   Mar 21, 2006

Watched America’s Stone Age Explorers on PBS this evening, a summary of recent findings about who the first Americans were, where they came from, and when they arrived. Recent genetic and archeological evidence suggests they arrived earlier than generally accepted and may have originated from Europe rather than Asia.

To Dr. David Hague, human pregnancy is

posted by Jason Kottke   Mar 15, 2006

To Dr. David Hague, human pregnancy is a struggle between the fetus and mother. Evolutionarily speaking, the fetus “wants” as many resources as possible for itself while the mother “wants” to do what she can to spread her resources across as many children as possible. In theory, this is a cause of the many serious health problems surrounding pregnancy.

Update: Carl Zimmer has more about this on his blog.

This is fascinating…”sex might have evolved

posted by Jason Kottke   Mar 07, 2006

This is fascinating…”sex might have evolved as a way to concentrate lots of harmful mutations into individual organisms so they could be easily weeded out by natural selection”.

Kian and Remee are twin daughters born

posted by Jason Kottke   Feb 27, 2006

Kian and Remee are twin daughters born to a UK couple…one is black and one is white. “If a sperm containing all-white genes fuses with a similar egg and a sperm coding for purely black skin fuses with a similar egg, two babies of dramatically different colours will be born. The odds of this happening are… a million to one.”

Justin reports on his family’s results of

posted by Jason Kottke   Feb 21, 2006

Justin reports on his family’s results of a neat project called the Geneographic Project, co-produced by National Geographic and IBM. If you purchase a testing kit, they’ll trace the specific genetic markers of your ancestors back to (possibly) our common African root.