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kottke.org posts about genetics

Portraits made using found DNA

posted by Jason Kottke   May 06, 2013

Heather Dewey-Hagborg collects hair, chewed gum, and smoked cigarettes, pulls the DNA out of them, and uses the genetic information to produce models of what the people who used those items might have looked like.

Heather Dewey Hagborg

From this sequence, Dewey-Hagborg gathers information about the person’s ancestry, gender, eye color, propensity to be overweight and other traits related to facial morphology, such as the space between one’s eyes. “I have a list of about 40 or 50 different traits that I have either successfully analyzed or I am in the process of working on right now,” she says.

Dewey-Hagborg then enters these parameters into a computer program to create a 3D model of the person’s face.” Ancestry gives you most of the generic picture of what someone is going to tend to look like. Then, the other traits point towards modifications on that kind of generic portrait,” she explains. The artist ultimately sends a file of the 3D model to a 3D printer on the campus of her alma mater, New York University, so that it can be transformed into sculpture.

DNA has a 521-year half-life

posted by Jason Kottke   Oct 10, 2012

Researchers in Copenhagan and Perth used DNA found in the leg bones of the extinct moa bird to determine the half-life of DNA: 521 years.

By comparing the specimens’ ages and degrees of DNA degradation, the researchers calculated that DNA has a half-life of 521 years. That means that after 521 years, half of the bonds between nucleotides in the backbone of a sample would have broken; after another 521 years half of the remaining bonds would have gone; and so on.

The team predicts that even in a bone at an ideal preservation temperature of -5 ºC, effectively every bond would be destroyed after a maximum of 6.8 million years. The DNA would cease to be readable much earlier — perhaps after roughly 1.5 million years, when the remaining strands would be too short to give meaningful information.

That means no real-life Jurassic Park, folks.

What percentage Neanderthal are you?

posted by Jason Kottke   Oct 10, 2012

In the last few years, scientists have discovered that before Neanderthals went extinct around 30,000 years ago, they interbred with modern humans. As a result, many humans alive today contain Neanderthal DNA in their genomes, typically between 1-4%.

Yesterday, a few of the editors at The Atlantic had their genes analyzed for Neanderthal DNA: Alexis Madrigal had 3.6%, Steve Clemons had 4.3%, and James Fallows had 5%. Personal genetic information company 23andMe added the ability to determine your Neanderthal DNA percentage a few months ago and it turns out 2.7% of my DNA is from Neanderthals, compared to 2.5% for the average 23andMe user.

If you have a 23andMe acct, you can check your percentage by logging in and going to “Ancestry Labs” in the sidebar.

Re-engineering human cells to attack cancer

posted by Jason Kottke   Sep 13, 2011

This crazy-experimental therapy uses a modified HIV virus to attack cancer cells in humans. Only three people have tried this therapy for chronic lymphocytic leukemia; two are in complete remission and one showed improvement.

Doctors removed a billion of his T-cells — a type of white blood cell that fights viruses and tumors — and gave them new genes that would program the cells to attack his cancer. Then the altered cells were dripped back into Mr. Ludwig’s veins.

At first, nothing happened. But after 10 days, hell broke loose in his hospital room. He began shaking with chills. His temperature shot up. His blood pressure shot down. He became so ill that doctors moved him into intensive care and warned that he might die. His family gathered at the hospital, fearing the worst.

A few weeks later, the fevers were gone. And so was the leukemia.

There was no trace of it anywhere — no leukemic cells in his blood or bone marrow, no more bulging lymph nodes on his CT scan. His doctors calculated that the treatment had killed off two pounds of cancer cells.

A year later, Mr. Ludwig is still in complete remission. Before, there were days when he could barely get out of bed; now, he plays golf and does yard work.

(via @marcprecipice)

Neanderthal sex made modern humans fitter

posted by Jason Kottke   Jun 17, 2011

There is evidence that modern humans mating with Neanderthals helped humans spread out of Africa to distant parts of the globe.

While only 6 per cent of the non-African modern human genome comes from other hominins, the share of HLAs acquired during interbreeding is much higher. Half of European HLA-A alleles come from other hominins, says Parham, and that figure rises to 72 per cent for people in China, and over 90 per cent for those in Papua New Guinea.

This suggests they were increasingly selected for as H. sapiens moved east. That could be because humans migrating north would have faced fewer diseases than those heading towards the tropics of south-east Asia, says Chris Stringer of the Natural History Museum in London.

The adventures of the Atomic Gardening Society

posted by Jason Kottke   Apr 22, 2011

Not just a Cold War-era relic…

Atomic tomatoes

the use of radiation to introduce genetic changes in food (aka “atomic gardening”) is alive and well today.

What’s more, the Times adds, nearly 2,000 gamma radiation-induced mutant crop varieties have been registered around the world, including Calrose 76, a dwarf varietal that accounts for about half the rice grown in California, and the popular Star Ruby and Rio Red grapefruits, whose deep colour is a mutation produced through radiation breeding in the 1970s. Similarly, Johnson tells Pruned that “most of the global production of mint oil,” with an annual market value estimated at $930 million, is extracted from the “wilt-resistant ‘Todd’s Mitcham’ cultivar, a product of thermal neutron irradiation.” She adds that “the exact nature of the genetic changes that cause it to be wilt-resistant remain unknown.”

The atomic gardening photos from Life magazine in 1961 are kind of great.

Perhaps the best Reddit question ever

posted by Jason Kottke   Apr 05, 2011

And that’s saying something. But look at this gem of a thread: I like big butts and I cannot lie, but is there some evolutionary reason as to why? Some of the answers:

My homeboys tried to warn me, but that butt you got makes me so confident of your current well-being and future child-rearing potential

So, ladies! (Yeah!) Ladies (Yeah!)

If you wanna roll in my Mercedes (Yeah!)

Then turn around! Stick it out! Even white boys have to make sure that their partner is of high genetic caliber so they can pass on their genes successfully.

My anaconda don’t want none unless you have a high likelihood of producing healthy offspring with a minimal chance of genetic disabilities, hun.

(via @stevenbjohnson)

Mutations in genes and text not dissimilar

posted by Jason Kottke   Nov 18, 2010

In a post called Mutated Manuscripts: The Evolution of Genes and Texts, Sam Arbesman compares genetic mutations with textual mutations caused by humans.

While fun to chronicle such similarities, these similarities can also be exploited in the same way. Mutational differences between DNA sequences can be used to understand the evolutionary history of a population, or even a group of species. And so too with variants of the same manuscript. A famous example of this is from a 1998 research article in the journal Nature that quantitatively studied the differences between the 80 surviving versions of Geoffrey Chaucer’s The Canterbury Tales. By subjecting the variants to a battery of genetic analyses, the researchers were able to better understand the contents of the ancestral version, Chaucer’s own copy!

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.)