kottke.org posts about genetics
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.
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.
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]
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.
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)
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?
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.
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.
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.
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)
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.
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.
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)
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.
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.
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.
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.
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.
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.
Not just a Cold War-era relic...
...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.
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.
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 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.
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.
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.
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, 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!
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
As information visualizations go, you can't get much better than this.
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.
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.
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)
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.
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?
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.
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)
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 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....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 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, 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 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 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?"
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.)
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 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.
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 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.
Why do people believe in God? Evidence suggests that it's partially inherited. "The degree of religiosity was not strongly related to the environment in which the twin was brought up. Even if one identical twin had been brought up in an atheist family and the other in a religious Catholic household, they would still tend to show the same kind of religious feelings, or lack of them."
For some real controversy over evolution, check out evo devo, or "evolutionary developmental biology". Its proponents claim that evolution works primarily by changing when certain genes are expressed, not via changing genes themselves. Scientific American has more.
In the five years since the sequencing of the human genome, "much of the data have little immediately useful meaning, and the research has produced only a trickle of medicine". And where medical science has failed, hucksters have filled the gap.
Twenty percent of the human genome is patented. I expect that someday in the future, my morning will be interrupted by a lawyer telling me that the company he represents holds a patent on the biochemical conversion of foodstuffs to energy suitable for powering a biological organism and that I should cease and desist eating my Cheerios.
Two of the biggest pessimists in the business, Bill Joy and Ray Kurzweil, outline their case for not releasing the genome for the 1918 influenza virus. "The genome is essentially the design of a weapon of mass destruction. No responsible scientist would advocate publishing precise designs for an atomic bomb, and in two ways revealing the sequence for the flu virus is even more dangerous."
Flowers don't smell as good as they used to and part of the reason is breeding...they're breeding flowers for looks and longevity, not for scent. I believe Michael Pollan discusses this in his excellent The Botany of Desire (tulip chapter).
Scientists are having a bit of fun wondering about the genetics of wizardry in Harry Potter. "This suggests that wizarding ability is inherited in a mendelian fashion, with the wizard allele (W) being recessive to the muggle allele (M). According to this hypothesis, all wizards and witches therefore have two copies of the wizard allele (WW)."
Here's a sampling of the rest of the AIGA Design Conference, stuff that I haven't covered yet and didn't belong in a post of it's own:
Juan Enriquez gave what was probably my favorite talk about what's going on in the world of genetics right now. I've heard him give a variation of this talk before (at PopTech, I think). He started off talking about coding systems and how when they get more efficient (in the way that the Romance languages are more efficient than Chinese languages), the more powerful they become in human hands. Binary is very powerful because you can encode text, images, video, etc. using just two symbols, 1 and 0. Segue to DNA, a four symbol language to make living organisms...obviously quite powerful in human hands.
- Enriquez: All life is imperfectly transmitted code. That's what evolution is, and without the imperfections, there would be no life. The little differences over long periods of time are what's important.
- Enriquez again: The mosquito is a flying hypodermic needle. That's how it delivers malaria to humans. We could use that same capability for vaccinating cows against disease.
- Along with his list of 20 courses he didn't take in design school, Michael Bierut offered some advice to young designers:
1. Design is the easy part.
2. Learn from your clients, bosses, collaborators, and colleagues.
3. Content is king.
4. Read. Read. Read.
5. Think first, then design.
6. Never forget how lucky you are. Enjoy yourself.
Nicholas Negroponte: If programmers got paid to remove code from sofware instead of writing new code, software would be a whole lot better.
- Negroponte also shared a story about outfitting the kids in a school in Cambodia with laptops; the kids' first English word was "Google", and from what Negroponte said, that was followed closely by "Skype". He also said the children's parents loved the laptops because at night, it was the brightest light in the house.
- Christi recorded Milton Glaser's mother's spaghetti recipe. "Cook until basically all of the water is evaporated. Mix in bottle of ketchup; HEINZ ketchup."
- Ben Karlin and Paula Scher on the challenges of making America, The Book: Books are more daunting than doing TV because print allows for a much greater density of jokes. In trying to shoot the cover image, they found that bald eagles cannot be used live for marketing or advertising purposes. The solution? A golden eagle and Photoshop. And for a spread depicting all the Supreme Court Justices in the buff, they struggled -- even with the Web -- to find nude photos of older people until they found a Vermont nudist colony willing to send them photos because they were big fans of The Daily Show.
Bill Strickland blew the doors off the conference with his account of the work he's doing in "curing cancer" -- his term for revitalizing violent and crime-ridden neighborhoods -- in Pittsburgh. I can't do justice to his talk, so two short anecdotes. Strickland said he realized that "poor people never have a nice day" so when he built his buildings in these poor black neighbohoods, he put nice fountains out front so that people coming into the building know that they're entering a space where it's possible to have a good day. Another time, a bigwig of some sort was visiting the center and asked Strickland about the flowers he saw everywhere. Flowers in the hood? How'd these get here? Strickland told him "you don't need a task force or study group to buy flowers" and that he'd just got in his car, bought some flowers, brought them back, and set them around the place. His point in all this was creating a place where people feel less dissimilar to each other...black, white, rich, poor, everybody has a right to flowers and an education and to be treated with respect and to have a nice day. You start treating people like that, and surprise!, they thrive. Strickland's inner city programs have produced Fulbright Scholars, Pulitzer Prize winners, and tons of college graduates.
- I caught 30 minutes of David Peters' presentation of Typecast: The Art of the Typographic Film Title and realized I should have gotten there in time to see the whole thing. I could sit and watch cool movie titles all day long. Among the titles he showed were Bullit, Panic Room, Dr. Strangelove, Barbarella, The Island of Dr. Moreau, and Superman. The title sequence for Napoleon Dynamite (which was discussed on Design Observer last year) was shown later in the main hall.
- At the closing party at the Museum of Science, we checked out the cool Mathematica exhibit that was designed by Charles and Ray Eames, two designers who were also pretty big science/math nerds.
- And some final thoughts from others at the conference. Peter Merholz says that "form-makers", which make up the vast majority of the AIGA audience, "are being passed by those who are attempting to use design to serve more strategic ends". (That's an interesting thought...) A pair of reviews from Speak Up: Bryony was a bit disappointed with the opening Design Gala but left, like everyone else, in love with emcee John Hockenberry while Armin noted that the preservation of digital files is a big concern for museums in building a collection of graphic design pieces...in 35 years, how are you going load that Quark file or run that Flash movie?
For more of what people are saying about the conference, check out IceRocket. There's a bunch of photos on Flickr as well.
Lengthy examination of what makes people gay by the Boston Globe. "What makes the case of [identical twins] Patrick and Thomas so fascinating is that it calls into question both of the dominant theories in the long-running debate over what makes people gay: nature or nurture, genes or learned behavior."
A small ocean microbe called Pelagibacter has the smallest genome of any self-sufficient organism with 1,354 genes. It also doesn't appear to have any extra DNA...no junk or redundant copies of genes.
The Red Delicious apple has fallen out of favor. It's been dumbed down too much for the market. For more on apples, see Michael Pollan's excellent The Botany of Desire.
Male and female fire ants maintain their own independent gene pools. "The sperm of the male ant appears to be able to destroy the female DNA within a fertilized egg, giving birth to a male that is a clone of its father. Meanwhile the female queens make clones of themselves to carry on the royal female line."
Advancing scientific research means that chimeric animals are on the way. "In the case of human cells' invading the germ line, the chimeric animals might then carry human eggs and sperm, and in mating could therefore generate a fertilized human egg. Hardly anyone would desire to be conceived by a pair of mice."