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DNA evidence: humans are still evolving

posted by Jason Kottke   Oct 19, 2016

Jerry Coyne, University of Chicago professor and author of Why Evolution is True, shares the results of a recent paper called Detection of human adaptation during the past 2000 years. In the study, DNA sequencing was used to find human genes that have changed so quickly in the past 2000 years that the authors conclude natural selection must be responsible.

Now, however, we can, by DNA sequencing, look at DNA directly, and with some fancy statistical footwork, get an idea of which genes have changed in frequency so fast that they must have been due to positive natural selection. That’s the subject of a new paper in Science by Yair Field et al. (reference and free download below). The authors conclude that several traits, including lactose tolerance, hair and eye color, and parts of the immune system, as well as height, have evolved within the last 2,000 years.

Other genes that might have changed during that period include those for infant head circumference, insulin levels, birth weight, and female hip size.

We Work Remotely

Should we use CRISPR to engineer mosquitoes incapable of transmitting malaria?

posted by Jason Kottke   Sep 21, 2016

Thousands of people die every day from malaria, a disease that is transmitted to humans solely through mosquitoes. With CRISPR, scientists can easily genetically engineer mosquitoes incapable of transmitting malaria and using a technique called gene drive, they can force that genetic change into the native mosquito population. So, should we do it?

Scientists discover giraffes are actually four separate species

posted by Jason Kottke   Sep 09, 2016

Giraffe Species

Suddenly, there are four species of giraffe now. Previously there was only one. Scientists have analyzed the genetic code of hundreds of giraffes in Africa and found much variation in their DNA, enough to split one species into four.

Some of the differences were as large or larger than the differences between brown bears and polar bears.

Despite their similar appearances, members of the different species don’t appear to mate with each other. It’s amazing that scientists didn’t know this until now.

The coming CRISPR revolution

posted by Jason Kottke   Aug 11, 2016

Perfect eyesight. Curing cancer. Designer babies. Super-soldiers. Because of CRISPR, genetic engineering might make tinkering with life as easy as playing with Lego.

Imagine you were alive back in the 1980’s, and were told that computers would soon take over everything — from shopping, to dating, and the stock market, that billions of people would be connected via a kind of web, that you would own a handheld device orders of magnitudes more powerful than supercomputers.

It would seem absurd, but then all of it happened. Science fiction became our reality and we don’t even think about it. We’re at a similar point today with genetic engineering. So let’s talk about it.

Relatedly, I’m finishing up Neal Stephenson’s Seveneves right now and while it starts out as space science fiction, much of the book is concerned with the sort of genetic engineering issues discussed in the video.

The Gene: An Intimate History

posted by Jason Kottke   Jun 02, 2016

Siddhartha Mukherjee, who wrote The Emperor of All Maladies, a biography of cancer and one of my favorite recent reads, is out with a new book called The Gene: An Intimate History.

Siddhartha Mukherjee has a written a biography of the gene as deft, brilliant, and illuminating as his extraordinarily successful biography of cancer. Weaving science, social history, and personal narrative to tell us the story of one of the most important conceptual breakthroughs of modern times, Mukherjee animates the quest to understand human heredity and its surprising influence on our lives, personalities, identities, fates, and choices.

The book comes recommended by Tyler Cowen, who IIRC also recommended Emperor of All Maladies to me.

This book filled in a number of gaps in my knowledge, plus it is engaging to read. Overall it confirmed my impression of major advances in the science, but not matched by many medical products for general use.

This is on the must-read list this summer. Somehow. When I get a second.

CRISPR, a cheap and accurate copy/paste for DNA

posted by Jason Kottke   Nov 13, 2015

Michael Specter has a truly fascinating piece in the New Yorker about CRISPR, a relatively new genetic tool for editing genes that geneticists are very excited about.

With CRISPR, scientists can change, delete, and replace genes in any animal, including us. Working mostly with mice, researchers have already deployed the tool to correct the genetic errors responsible for sickle-cell anemia, muscular dystrophy, and the fundamental defect associated with cystic fibrosis. One group has replaced a mutation that causes cataracts; another has destroyed receptors that H.I.V. uses to infiltrate our immune system.

The story has everything: the cheap copy/paste of DNA, easily editable mice, pig Hitler, “destroyer of worlds” overtones, and an incredible tale of science that could actually revolutionize (or ruin, depending on who you talk to) the world. I was shocked at how easy it is to do genetic research nowadays.

Ordering the genetic parts required to tailor DNA isn’t as easy as buying a pair of shoes from Zappos, but it seems to be headed in that direction. Yan turned on the computer at his lab station and navigated to an order form for a company called Integrated DNA Technologies, which synthesizes biological parts. “It takes orders online, so if I want a particular sequence I can have it here in a day or two,” he said. That is not unusual. Researchers can now order online almost any biological component, including DNA, RNA, and the chemicals necessary to use them. One can buy the parts required to assemble a working version of the polio virus (it’s been done) or genes that, when put together properly, can make feces smell like wintergreen. In Cambridge, I.D.T. often makes same-day deliveries. Another organization, Addgene, was established, more than a decade ago, as a nonprofit repository that houses tens of thousands of ready-made sequences, including nearly every guide used to edit genes with CRISPR. When researchers at the Broad, and at many other institutions, create a new guide, they typically donate a copy to Addgene.

And CRISPR in particular has quickened the pace. A scientist studying lung cancer mutations said of her research:

“In the past, this would have taken the field a decade, and would have required a consortium,” Platt said. “With CRISPR, it took me four months to do it by myself.”

Also recommended: Radiolab’s podcast on CRISPR from back in June.

Copy and paste, but for DNA

posted by Jason Kottke   Jul 22, 2015

No hunger. No pollution. No disease. Wired’s Amy Maxmen welcomes you to the age of copy and paste DNA editing and the end of life as we know it.

Genome editing started with just a few big labs putting in lots of effort, trying something 1,000 times for one or two successes. Now it’s something that someone with a BS and a couple thousand dollars’ worth of equipment can do. What was impractical is now almost everyday. That’s a big deal.

[I recently listened to Radiolab’s show on Crispr. Recommended. -jkottke]

Self-destructing mosquitos

posted by Jason Kottke   Jul 16, 2015

A company called Oxitec has genetically modified mosquito eggs so that the mosquitos born from them pass along a gene to their offspring that prohibits the mosquitos from reaching sexual maturity and mating. They release the mosquitos into the wild, they mate with the local population of mosquitos, and those born from those matings will die before mating themselves. Voila! Pest control.

Oxitec has conducted trials with its modified mosquito in dengue-ridden regions of Panama, Brazil, Malaysia, and the Cayman Islands. The results show population suppression rates above 90 percent-far greater than the typical 30 percent achieved with insecticides.

The company is currently planning a trial in Florida using this technique to curb an influx of mosquito-borne illness.

Genetic algorithm walkers

posted by Jason Kottke   Jan 15, 2015

Genetic Walker

This simulator evolves increasingly effective walking creatures through genetic algorithms. After each round, the winners are sent through to the next round and copied by the rest of the competitors, with mutations introduced. At first, the pace of improvement is swift — two orders of magnitude within 100 generations — but slows pretty dramatically after that. (via @nickrichter)

The human family grows

posted by Jason Kottke   Dec 02, 2014

A new analysis of the genomes of two extinct human species (Neanderthals and Denisovans) shows more clearly that they interbred with our species of human, contributing 2-4% of our modern genomes in some cases.

“What it begins to suggest is that we’re looking at a Lord of the Rings-type world — that there were many hominid populations,” says Mark Thomas, an evolutionary geneticist at University College London who was at the meeting but was not involved in the work.

But, more interestingly, the analysis also detected the Denisovans also bred with an as-yet-unknown species of humans.

The Denisovan genome indicates that the population got around: Reich said at the meeting that as well as interbreeding with the ancestors of Oceanians, they also bred with Neanderthals and the ancestors of modern humans in China and other parts of East Asia. Most surprisingly, Reich said, the genomes indicate that Denisovans interbred with yet another extinct population of archaic humans that lived in Asia more than 30,000 years ago — one that is neither human nor Neanderthal.

Is this the first time a new human species has been discovered through DNA evidence alone?

The potential landmines of genetic testing services

posted by Jason Kottke   Sep 10, 2014

As part of a course he was teaching, a biologist sent away for a genetic testing kit from 23andMe for himself and his parents. When he went looking for other relatives on the service (which is now an automatic opt-out feature), he discovered he had a half-brother his dad had not told his family about.

At first, I was thinking this is the coolest genetics story, my own personal genetics story. I wasn’t particularly upset about it initially, until the rest of the family found out. Their reaction was different. Years of repressed memories and emotions uncorked and resulted in tumultuous times that have torn my nuclear family apart. My parents divorced. No one is talking to my dad. We’re not anywhere close to being healed yet and I don’t know how long it will take to put the pieces back together.

After this discovery was made, I went back to 23andMe and talked to them. I said, “I’m not sure all your customers realize that when they participate in your family finder program, what they’re participating in what are essentially really advanced paternity tests.” People find out that their parents aren’t who they think they are. They have nearly a million people in the database. If there happens to be anyone in there you’re related to, they’ll find your match. This is a solid science.

I know a family in which one of the children is adopted and they haven’t told her. Which is crazy…she’s gonna find out eventually (through something like 23andMe or because of some medical emergency or test) and go totally berzerk.

Alien DNA

posted by Jason Kottke   May 09, 2014

For the first time, scientists have created a living cell with DNA containing more than just the familiar A, T, C, and G units.

Hailed as a breakthrough by other scientists, the work is a step towards the synthesis of cells able to churn out drugs and other useful molecules. It also raises the possibility that cells could one day be engineered without any of the four DNA bases used by all organisms on Earth.

“What we have now is a living cell that literally stores increased genetic information,” says Floyd Romesberg, a chemical biologist at the Scripps Research Institute in La Jolla, California, who led the 15-year effort.

So instead of just using the GATTACA alphabet, scientists may eventually gain the use of an alphabet containing dozens or even hundreds or thousands of different letters. Potentially powerful stuff.

Test tube time machine

posted by Jason Kottke   Feb 27, 2014

Richard Lenski and his team of researchers utilize a clever technique to observe and study evolution of bacteria in realtime. Periodically freezing a sample of the bacteria every few generations allows them to go back in time to study particular traits and to pinpoint when differences occur.

After 30,000 generations, researchers noticed something strange. One population had evolved the ability to use a different carbon-based molecule in the solution, called citrate, as a power source.

Researchers wondered whether it was the result of a rare, single mutation, or a more complex change involving a series of mutations over generations. To find out, one of Lenski’s postdocs, Zachary Blount, took some of the frozen cells and grew them in a culture lacking glucose, with citrate as the only potential food source.

After testing 10 trillion ancestral cells from early generations, he got no growth. But when he tested cells from the 20,000th generation on, he began to get results, eventually finding 19 mutants that could use citrate as a power source. The results showed that the citrate-eating mutation was most likely not the result of a single mutation, but one enabled by multiple changes over 20,000 generations.

Supreme Court: human genes not patentable

posted by Jason Kottke   Jun 13, 2013

In a unanimous decision, the US Supreme Court ruled today that human genes cannot be patented.

The case involved Myriad Genetics Inc., which holds patents related to two genes, known as BRCA1 and BRCA2, that can indicate whether a woman has a heightened risk of developing breast cancer or ovarian cancer.

Justice Clarence Thomas, writing for the court, said the genes Myriad isolated are products of nature, which aren’t eligible for patents.

The high court’s ruling was a win for a coalition of cancer patients, medical groups and geneticists who filed a lawsuit in 2009 challenging Myriad’s patents. Thanks to those patents, the Salt Lake City company has been the exclusive U.S. commercial provider of genetic tests for breast cancer and ovarian cancer.

The challengers argued the patents have allowed Myriad to dictate the type and terms of genetic screening available for the diseases, while also dissuading research by other laboratories.

Fuck yes. A defect in her BRCA1 gene is what caused Angelina Jolie to recently have a preventive double mastectomy. (via @tylercowen)

Charlemagne for everyone!

posted by Jason Kottke   Jun 03, 2013

We are all mostly related to each other. But weirder still, you’re just about as related to the stranger next to you as to your great×12 grandparents.

Now, there’s another important implication of genomic ancestry studies: Most of the people you are descended from are no more genetically related to you than strangers are. Or to put it another way, your genealogical family tree, which includes all the history of your family going back thousands of years, is much larger than your genetic family tree-the people whom genome sequencing would pinpoint as related to you. 99.9 percent of your genome is the same as that of every other human being (apart from the x and y chromosomes), and that .1 percent of variation in each person gets thinned out pretty quickly across the generations, as each child gets half of each of her parents’ genomes, passes on half to each of her children, and so on. Geneticist Luke Jostins did a nice mathematical analysis and estimated that you have only about a 12 percent chance of being genetically related to an ancestor 10 generations ago; by the time you get to a 14-generation ancestor, the probability is nearly zero.

Human embryos successfully cloned (sort of)

posted by Jason Kottke   May 16, 2013

A group of researchers in Oregon have successfully cloned human embryos. No, really:

The researchers, at Oregon Health and Science University, took skin cells from a baby with a genetic disease and fused them with donated human eggs to create human embryos that were genetically identical to the 8-month-old. They then extracted stem cells from those embryos.

The embryo-creation technique is essentially the same as that used to create Dolly the sheep and the many cloned animals that have followed. In those cases, the embryos were implanted in the wombs of surrogate mothers.

These embryos won’t work for producing clones humans…they are being used to harvest stem cells.

The Oregon researchers, who published a paper on their work in the journal Cell, say their goal is what has been called therapeutic cloning: making embryonic stem cells that are genetically identical to a particular patient.

Embryonic stem cells can turn into any type of cell in the body, like heart cells, muscles or neurons. That raises the hope that one day the cells will be turned into replacement tissue or even replacement organs to treat a host of diseases.

Angelina Jolie had a preventive double mastectomy

posted by Jason Kottke   May 14, 2013

In this morning’s NY Times, Angelina Jolie writes about her decision to have a preventive double mastectomy to hopefully ward off cancer.

My mother fought cancer for almost a decade and died at 56. She held out long enough to meet the first of her grandchildren and to hold them in her arms. But my other children will never have the chance to know her and experience how loving and gracious she was.

We often speak of “Mommy’s mommy,” and I find myself trying to explain the illness that took her away from us. They have asked if the same could happen to me. I have always told them not to worry, but the truth is I carry a “faulty” gene, BRCA1, which sharply increases my risk of developing breast cancer and ovarian cancer.

It happens that just last night I read about the BRCA-1 gene in Siddhartha Mukhergee’s excellent biography of cancer, The Emperor of All Maladies. This part is right near the end of the book:

Like cancer prevention, cancer screening will also be reinvigorated by the molecular understanding of cancer. Indeed, it has already been. The discovery of the BRCA genes for breast cancer epitomizes the integration of cancer screening and cancer genetics. In the mid-1990s, building on the prior decade’s advances, researchers isolated two related genes, BRCA-1 and BRCA-2, that vastly increase the risk of developing breast cancer. A woman with an inherited mutation in BRCA-1 has a 50 to 80 percent chance of developing breast cancer in her lifetime (the gene also increases the risk for ovarian cancer), about three to five times the normal risk. Today, testing for this gene mutation has been integrated into prevention efforts. Women found positive for a mutation in the two genes are screened more intensively using more sensitive imaging techniques such as breast MRI. Women with BRCA mutations might choose to take the drug tamoxifen to prevent breast cancer, a strategy shown effective in clinical trials. Or, perhaps most radically, women with BRCA mutations might choose a prophylactic mastectomy of both breasts and ovaries before cancer develops, another strategy that dramatically decreases the chances of developing breast cancer.

Radical is an understatement…what a tough and brave decision to make. Again from the book, I liked this woman’s take on it:

An Israeli woman with a BRCA-1 mutation who chose this strategy after developing cancer in one breast told me that at least part of her choice was symbolic. “I am rejecting cancer from my body,” she said. “My breasts had become no more to me than a site for my cancer. They were of no more use to me. They harmed my body, my survival. I went to the surgeon and asked him to remove them.”

The genetic testing company 23andme screens for three common types of mutation in the BRCA1 or BRCA2 genes:

Five to 10 percent of breast cancers occur in women with a genetic predisposition for the disease, usually due to mutations in either the BRCA1 or BRCA2 genes. These mutations greatly increase not only the risk for breast cancer in women, but also the risk for ovarian cancer in women as well as prostate and breast cancer among men. Hundreds of cancer-associated BRCA1 and BRCA2 mutations have been documented, but three specific BRCA mutations are worthy of note because they are responsible for a substantial fraction of hereditary breast cancers and ovarian cancers among women with Ashkenazi Jewish ancestry. The three mutations have also been found in individuals not known to have Ashkenazi Jewish ancestry, but such cases are rare.

23andme testing kits are only $99.

Update: Two things. First, and I hope this isn’t actually necessary because you are all intelligent people who can read things and make up your own minds, but let me just state for the official record that you should never never never never NEVER take medical advice, inferred or otherwise, from celebrities or bloggers. Come on, seriously. If you’re concerned, go see a doctor.

Two: I have no idea what the $99 23andme test covers with regard to BRCA1 and BRCA2 gene mutations beyond what the company states. The most comprehensive test for BRCA1 and BRCA2 mutations was developed by a company called Myriad Genetics and costs about $3000. Myriad has patented the genes, a decision that has been sharply criticized and is currently being decided by the Supreme Court.

But many doctors, patients and scientists aren’t happy with the situation.

Some are offended by the very notion that a private company can own a patent based on a gene that was invented not by researchers in a lab but by Mother Nature. Every single cell in every single person has copies of the BRCA1 and BRCA2 genes.

Myriad officials say they deserves the patent because they invested a great deal of money to figure out the sequence and develop “synthetic molecules” based on that sequence that can be used to test the variants in a patient.

“We think it is right for a company to be able to own its discoveries, earn back its investment, and make a reasonable profit,” the company wrote on its blog.

I do know the 23andme test covers something related to the BRCA1 and BRCA2 mutations…a friend of a friend did the 23andme test, tested positive for the BRCA1 mutation, and decided to have a preventive double mastectomy after consulting her doctor and further tests. (thx, mark, allison, and ★spavis)

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!