Category Archives: Transhuman News

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(DALLAS) Karen Stipes always believed her missing mother was "Mountain Jane Doe," buried unidentified in a paupers' cemetery deep in the woods outside Harlan, Kentucky. But without proof, it took nearly half a century and the development of DNA technology for forensic scientists at the University of North Texas to confirm her intuition.

Police didn't know who Sonja Kaye Blair-Adams was when a man picking flowers on a trail found her body stabbed multiple times in 1969. It remained a mystery to the locals until advances in forensic science prompted renewed efforts to identify the body and resume the hunt for her killer. While police have yet to solve the killing, Stipes said the restoration of her mother's identity has provided at least some closure.

But now the same Texas lab that handled Blair-Adams' DNA has had to stop testing samples like hers that come from outside the state due to a lack of funding, meaning family members of missing and unidentified people are waiting longer for their cases to be solved.

"Everyone deserves to have their unidentified found," Stipes said. "I feel my mother was disrespected being unidentified for so long. There wasn't DNA testing in 1969 when my mother died, but it's 2017. I think it has gotten overlooked."

For years, law enforcement looking for a breakthrough in a cold case could count on sending samples of unknown bodies to the Center for Human Identification at the University of North Texas. The lab is a world leader in mitochondrial DNA testing from decomposing and partial remains and provided testing for missing and unidentified people at no cost to investigators.

But this year the National Institute of Justice decided not to offer millions of dollars in grants for DNA technology to identify missing people and instead reallocated that money to programs that help state and local governments audit and track backlogged rape kits. The U.S. agency also introduced new grants to help medical examiners and coroner's offices meet accreditation standards and recruit forensic pathologists.

Agency officials said the university will receive supplemental funding in the next fiscal year, which starts Oct. 1, but the drop in casework has brought new attention to the lab's value and the importance of DNA in solving missing persons cases.

"There was a lot of public tension," said Todd Matthews, a spokesman for the National Missing and Unidentified Persons System at the university. "These are precious resources, and we can't take for granted something we don't know will continue."

The lab's funding situation isn't unique. The National Institute of Justice is the only federal agency that provides grants for labs analyzing DNA to identify the missing. Without those resources, investigators are left with fewer options for critical testing. Detectives have had to bust their budgets on expensive testing at private labs or submit remains to lengthy queues at local FBI labs. Others have stored their samples and suspended investigations until testing can resume.

"I've been sending letters and making phone calls to the NIJ on UNT's behalf. This is an absolute priority," said Sgt. Jason Moran, a detective with the Cook County, Illinois, sheriff's office. "It's hard to work if you don't know the identity of the victim."

Investigators say the university has become a crucial resource in the work to identify the 100,000 missing persons and 40,000 sets of unidentified remains across the United States. Over the past two decades, the lab has identified victims of 9/11 and Hurricane Katrina. Last year, the lab received up to 4,000 out-of-state samples, which comprised half of all DNA testing in the country, lab director Bruce Budowle said.

But the U.S. also has a huge backlog of untested rape kits. The national nonprofit End the Backlog estimates that there are more than 185,000 in the 38 states for which data is available. Reducing that number has drawn approximately $131 million in federal funding for the Sexual Assault Kit Initiative.

"We had to make a tough decision to fund other programs," said Gerry LaPorte, director of the Office of Investigative and Forensic Sciences at the National Institute of Justice. "It was very difficult because there are so many needs in the community."

Even without the influx of funding, the University of North Texas has continued to work cases, including testing of the state's backlogged rape kits. The lab has also had success reducing its own backlog. Last month, it helped the Cook County sheriff's office solve a 40-year mystery by identifying a victim of Chicago serial killer John Wayne Gacy.

"If we keep doing quality work, people will want us to be around," Budowle said. "This is a national lab, and that's a good investment. We're optimistic at this point that everything will be addressed. Hopefully sooner rather than later."

More:
Federal Funding Cuts Put Missing Persons and John Doe Cases on the Back Burner - TIME

Humans have a penchant for organizing. We like order. This need for organization certainly drove Carl Linnaeus, a Swedish naturalist, to publish the first catalog of life, the Systema Naturae, in 1735. He devised the framework we still use in our taxonomy.

In the last column, we explored the challenges of recognizing species. New knowledge forces us to re-examine our understanding of species variation. We regularly gain or lose species on our life lists as former species are divided into two or more new species or others combined into a single species.

Taxonomists do have methods for defining a species. The problem is that there is more than one method, and the different approaches do not always get to the same conclusion.

Similar species are placed in a genus. Genera (the plural of genus) that are similar are placed in the same family. And on we go upward to order, then class, then phylum, then kingdom. Thus, the tree of life is organized.

Linnaeus based his taxonomy on similarity of form. In the next century, Charles Darwin saw that Linnaeus system could reflect relatedness. Species in the same genus had a more recent ancestor than two species in different genera or families. He said that our classification of life should be a genealogy.

But how does one decide how large a genus or order should be? Surprisingly, the answer is that it is arbitrary, depending on the preferences of the taxonomist. Some genera have a single species, like the genus Icteria, containing only the yellow-breasted chat. On the other hand, the snail genus Conus contains 750 species, and the sedge genus Carex has nearly 1,800 species.

Ultimately, the size of the genus or other taxonomic group is not important as long as it can be defended as a natural grouping. Any taxonomic group should be monophyletic (one branch), containing species more closely related to each other than to any species in other groups. Darwins desire to have our taxonomy be a genealogy is really a desire for our classifications to contain only monophyletic groups.

The job of erecting and revising a taxonomic system for any group of organisms had to rely on similarity of structure until the turn of the 21st century. Now, our ability to rapidly sequence and compare the DNA of organisms gives us a second powerful way to assess relatedness.

Some genes change through mutations quite rapidly, so DNA comparisons of these genes are useful for exploring closely related, recently separated species. Other genes mutate very slowly, so they can be used to assess the relationship between distant groups like phyla or classes. Some genes change at intermediate rates, so they can be used to assess the relatedness of orders and families.

DNA comparisons have shaken the foundation of our bird taxonomy. Such comparisons allow us to avoid the twin pitfalls of species from a common ancestor diverging strongly and species in different groups converging to similar shapes.

The grebe order was formerly placed close to the loon order. DNA comparisons now tell us that the closest relatives of grebes are flamingoes! Here we have a case where species have strongly diverged from their common ancestor. Another cool example is that the flightless penguins are most closely related to the albatrosses and shearwaters, masters of long-distant flight.

On the other hand, the hawks and falcons were formerly lumped into the same order. DNA tells us that convergence to high-speed, sharp-taloned predators has occurred. The two types of raptors are placed in different orders now. The closest relatives of the falcons are the parrots and perching birds. New World vultures share a common ancestor with hawks.

Look for these changes and more to be reflected in new editions of field guides.

Herb Wilson teaches ornithology and other biology courses at Colby College. He welcomes reader comments and questions at

[emailprotected]

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Birding: DNA technology gives us new insights into taxonomy - Press Herald

This sequence of images shows the development of embryos formed after eggs were injected with both CRISPR, a gene-editing tool, and sperm from a donor with a genetic mutation known to cause cardiomyopathy. OHSU hide caption

This sequence of images shows the development of embryos formed after eggs were injected with both CRISPR, a gene-editing tool, and sperm from a donor with a genetic mutation known to cause cardiomyopathy.

From the thirteenth floor of a glass tower at the Oregon Health & Science University, you get a panoramic view of downtown Portland and the majestic mountains in the distance. But it's what's happening inside the building that's brought me here.

"Should we go do this thing?" lab manager Amy Koski asks.

She's just gotten a call from the fertility clinic three floors down. A woman undergoing in vitro fertilization has had her eggs extracted. One of the eggs is too immature to be used to try to create a baby, so she's donating it to research.

Koski grabs a small metal box and rushes to the elevator. It's her portable incubator.

"You want to keep the eggs very happy and warm," she says. "When you're jostling them and moving them, they get a little unhappy."

Human eggs are the key starting point for the groundbreaking experiments underway in this lab. It's run by Shoukhrat Mitalipov, a biologist who's been on the cutting edge of embryonic genetic research for decades.

Mitalipov and his international team electrified the world this summer when the group announced it had successfully and seemingly safely figured out how to efficiently edit the DNA in human embryos.

For the first time, they said, they had corrected a mutation that causes a potentially fatal heart condition. The hope is this landmark step could someday help prevent thousands of genetic diseases that have plagued families for generations.

Critics, however, pounced on the news. They fear editing DNA in human embryos is unsafe, unnecessary and could open the door to "designer babies" and possibly someday to genetically enhanced people who are considered superior by society.

As the debate raged last week, I asked Mitalipov if I could visit his lab to see the next round of his experiments. He wants to confirm his initial results and determine whether the method can be used to repair other mutations.

He agreed to a visit, and on Monday, I became the first journalist to see these scientists cross a line that, until recently, had been taboo.

A small room for big science

I've followed Mitalipov's research for years and have visited the labs of other scientists doing related work in Stockholm, London and elsewhere.

Still, I stepped into Mitalipov's embryology lab unsure of exactly what I was about to see and eager to better understand what allowed these scientists to succeed where others had failed.

"This is our small room, but that's where usually lots of big science happened," says Mitalipov, who was born in the former Soviet Union. "We believe this room is really magic in terms of science."

Shoukhrat Mitalipov points to an image of an edited embryo inside an incubator at the Center for Embryonic Cell and Gene Therapy in Portland, Ore. Rob Stein/NPR hide caption

Shoukhrat Mitalipov points to an image of an edited embryo inside an incubator at the Center for Embryonic Cell and Gene Therapy in Portland, Ore.

He points to a microscope where his colleague, Nuria Marti-Gutierrez, has just positioned a Petri dish. I'm able to watch everything she's doing on a computer screen.

Mitalipov points to a round silvery blob. It's the egg. "You can see it moving," he says.

Suddenly, a bunch of tiny ovals flit across the screen. They are sperm from a donor who has a genetic mutation that causes cardiomyopathy, a potentially fatal heart condition.

Marti-Gutierrez draws the sperm into a thin glass rod called a pipette. She then adds a microscopic gene-editing tool a combination of chemical sequences known as CRISPR that can make very precise changes in DNA.

In this case, CRISPR will zero in on the cardiomyopathy mutation to literally slice the defect in the DNA.

Finally, she pierces the shell of the egg with the pipette and injects the sperm and CRISPR. Almost before I know it's happening, it's done. A human embryo has been created and edited before my eyes.

"That's it?" I ask.

"Yep," Mitalipov says, chuckling to himself.

It was amazingly fast and seemingly easy you could imagine a future where this sort of thing might become routine.

"This is how we do it," Mitalipov says matter-of-factly. He refers to the process as "DNA surgery."

Mitalipov and his team immediately do a second edit and then transfer the embryos to a larger incubator. The scientists will then spend the next few days monitoring live video of the two embryos, along with 17 others they had edited the weekend before, to see how they develop.

What's at work

Mitalipov thinks his team accomplished this feat by injecting the mutant sperm and the DNA editor into the egg at the same time. Previous attempts to edit DNA in human embryos were far less accurate and produced dangerous mutations elsewhere in the embryos' DNA.

Mitalipov and his colleagues are not sure exactly how it works. But they think that when CRISPR cuts the defective gene, the slice triggers the embryo to repair itself.

If future experiments confirm the results and show that the technique also works for other mutations, Mitalipov thinks the process could wipe out many diseases that have plagued families for generations, though he cautions that any practical application is still easily a decade or more away.

"[There are] about 10,000 different mutations causing so many different conditions and diseases," he says, pointing to Huntington's disease, cystic fibrosis and even possibly inherited forms of Alzheimer's and breast cancer.

"We're talking about millions of people affected. So I think the implications are huge," he says.

"I think this is a significant advance," says George Church, a Harvard geneticist. "This is important not only for parents who want to have healthy children, but more generally, it opens the door to preventative medicine where we can avoid a lot of painful genetic problems."

Skepticism, criticism and an ethical debate

While the results seem promising so far, there are still many questions. Some scientists remain skeptical that Mitalipov has really done what he says he's done.

"Unfortunately, the data do not allow the conclusion of correction for the embryos," says Dieter Egli, a biologist at Columbia University. "There are a number of other outcomes that are much more likely."

Mitalipov acknowledges that his work still needs to be reproduced by others, but he is confident his method is working.

Others are worried that less careful scientists might rush ahead too quickly and attempt to make babies before the technique has been proven to work and be safe.

"This is a strong statement that we can do genome editing," says George Daley, dean of the Harvard Medical School. "The question that remains is, 'Should we?' "

"I think it would be professionally irresponsible for any clinician to use this technology to make a baby," Daley adds. "It's just simply too early. It would be premature."

The idea of changing human DNA in ways that could be passed down for generations has long been considered off-limits. The fear is scientists could make mistakes and create new diseases that would persist for generations.

Some critics go so far as to say that scientists are essentially playing God by taking this step. They fear it will lead to parents picking and choosing the traits of their children. While that is not yet technically possible, critics say scientists are moving quickly toward that possibility.

"I think it's extraordinarily disturbing," says Marcy Darnovsky, who heads the Center for Genetics and Society, a watchdog group. "We'll see fertility clinics advertising gene editing for enhancement purposes. We'll see children being born who are said to biologically superior."

Mitalipov and his colleagues acknowledge the fears and agree the technique should be carefully regulated and only used for medical purposes. But, they argue, the fears should not stop the research.

"I don't think I'm playing God," Mitalipov says. "We have intelligence to understand diseases, eliminate suffering. And that's what I think is the right thing to do."

More:
Scientists Try Gene Editing In Human Embryos : Shots - Health ... - NPR

Photo Credit Joon Mo Kang

It is incredible enough that anyone ever discovered the structure of DNA. (James D. Watson, Francis Crick and Maurice Wilkins were awarded the Nobel Prize in 1962 for their research on the subject.) But the progress that has since been made in sequencing and editing our genetic building blocks is perhaps even more dizzying.

An updated edition of Watsons book DNA: The Story of the Genetic Revolution, first published in 2003, includes a new chapter on the progress in cancer research and another on the latest science in (and implications of) personal genomics. In 2007, Watson was one of the first people to have his own genome completely sequenced. He estimates that about 400,000 others have now been done.

Watson, 89, retired as chancellor of the Cold Spring Harbor Laboratory on Long Island in 2007 after an uproar that followed offensive remarks he made generalizing about the intelligence of people of African descent. Not often in the public eye since then, he uses the opportunity of the new version of DNA to opine on developments in the field.

Watson writes in one new part of the book: I for one wholeheartedly endorse consumers right to know their personal genetic information and to take what measures seem appropriate. But when he had his own DNA mapped, there was one thing even he didnt want to know: whether he had the gene associated with a heightened risk of Alzheimers disease. I had absolutely no desire, he writes, to waste time worrying about having some genetic predisposition to such a hideous disease.

Quotable

I do not think novels are necessarily more worthwhile than games. A novel can be a trivial waste of time, and a game can teach. . . . At their best, novels and games serve as vehicles for discovery. Allegra Goodman, in an interview with Commonweal

Tall Waves and Deep Thoughts

James Ryerson reviews Aaron Jamess Surfing With Sartre this week. Something about chasing a good wave does seem to lend itself to deep thoughts. Jaimal Yogiss new memoir, All Our Waves Are Water, seeks profound spiritual lessons in the ocean. In addition to earnestly New Age-y moments, like ruminating on the scientific similarity between amniotic fluid and saltwater, Yogiss approach makes room for self-deprecation. Its also not just about him; Yogiss previous memoir, Saltwater Buddha, detailed his running away from home to surf and join a monastery as a teenager. Much of this new book revolves around his friendship with a displaced Tibetan named Sonam, and so, Yogis writes, surfing and Zen are just big characters among many.

A version of this article appears in print on August 20, 2017, on Page BR4 of the Sunday Book Review.

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Updating DNA's Life Story - The New York Times - New York Times

By Sophie Egan By Sophie Egan August 18

Today is National Ice Cream Pie Day. (Its also the third week of National Crayon Collection Month, but whos counting?) You know whose arteries ice cream pie is good for? No one. Plain and simple. But Habit, one of the latest disrupters in the food tech sector, suggests we rethink the very notion of foods that are good for everyone or bad for everyone. Its part of a movement toward what is called personalized nutrition.

Habit, based in the San Francisco Bay area, tests for biomarkers and genetic variants using samples you provide, then generates a personalized report about how your body responds to food. Its your unique nutrition blueprint. Then the company pairs you with a nutrition coach and offers you custom-made meals, containing your ideal ratio of carbs, fats and protein, delivered to your home. All in the name of sending you on the path to a new you.

[Breakfast was the most important meal of the day until America ruined it]

I had to see for myself. So I endured the home test and shipped off my blood and DNA samples. (Gulp.) Then the companys chief executive walked me through the results of my newfound eater identity, and I observed how the diagnosis began to affect my relationship with food. Heres what happened and what it could mean for the future of eating in America.

Digesting the news

The Habit home kit is not for the faint of heart. After fasting for 10 hours, you answer lots of deeply personal questions, scrub DNA samples from your cheeks and puncture your fingertips with a self-pricking button (technical term: lancet). This sounds rough, but my lowest moment is actually chugging their special Habit Challenge Shake. It clocks in at 950 calories, 75 grams of sugar and 130 percent of daily saturated fat intake. It has a taste and smell I can only liken to Kahla. It makes me feel god-awful while drinking it nose pinched, pinkie out, face scrunched and even worse afterward. It was bad enough I had sacrificed my Saturday morning frittata ritual.

By the third blood sample, my dining table looks like a crime scene. Ive got bandages on two fingers, mini disinfectant pads strewn around, and cherry red blood dripping down my forearm. Im angling my elbow like a helicopter hovering over the little blood collection card, just trying to fill the darn box one last time so I can move on with my day. Finally, I pack it up and mail it all off in a rather alarming biohazard bag. The whole ordeal takes about three hours and costs $309.

[No food is healthy. Not even kale.]

Im told Ill receive my results in a few weeks. While I wait, I wander back to the Habit website and take a closer look at those pages and pages of fine print. I start to have second thoughts at sentences like, You may experience stress, anxiety, or emotional or physical discomfort when you learn about health problems or potential health problems.

Then theres this: Recommendations regarding diet provided to you may or may not be beneficial to you and may cause or exacerbate certain medical problems.

Say what?

Thankfully, when the results come in, I get labeled a Range Seeker. In official Habit-speak, it means you can be flexible with your macronutrient intake and thrive on a range of foods. Well, thats a relief.

[Heres how much giving up beef helps or doesnt help the planet]

There are seven Habit types, each with dozens of more specific sub-variations, varying from Slow Seeker (best suited for foods rich in fiber and carbs that are absorbed slowly) to Fat Seeker (fat is a valuable fuel source for you). Along with receiving your tribal designation, youre assigned a personalized eating plan, depicting your ideal plate, suggested nutrient goals and daily calorie target.

Id be lying if I said the results havent been affecting my food choices, or at least the way I feel about my food choices. For instance, since being told I have a genetic risk variant associated with slow production of omega-3s, I have been seeking salmon like a grizzly bear. Apparently, Im also genetically predisposed to caffeine sensitivity. Many a morning, this news has me sitting at my desk thinking I must be tripping out on my cup of joe despite the fact that I have consumed the exact same amount of coffee every day of my adult life.

Conviviality, an endangered species

On the face of it, personalized nutrition makes sense. Why wouldnt I want to understand the unique dietary yearnings and land mines of my own DNA? Many people seem to feel that the existing national dietary guidance of one-size-fits-all has failed them. Theyre sick, and theyre confused about what to buy and what to order.

But in reducing food to individualized nutrient optimization equating food with fuel, really what are we sacrificing? What are the implications for our food culture and the future of dining? Oh, gosh, Id love to go out for sushi with you, but I have to scurry home to my prearranged Range Seeker box in the fridge.

[Why your humble bowl of oatmeal could help feed a growing planet]

Neil Grimmer, Habits founder and chief executive, recognizes that food is social. He tells me that it knots us together culturally, so Habit is in the process of facilitating online communities for people with the same Habit type. Through a private Facebook page, they could share tips and the like. Its better than going it alone, I guess, but a far cry from actually sharing a meal.

Remember the $300 you put down for the home test? It includes a coaching session, so a nutritionist helps you put all your information into practice. During my session, Jae Berman, a registered dietitian, nutritionist and head coach of Habit, is a great help. But things dont look so rosy when I ask her how Im supposed to integrate Habit into regular life.

The family conversation has been one of the most common questions we have gotten, she says. It doesnt occur to me as a problem because I just want people to take ownership of their story ... have the empowerment to say, This is what my plate looks like; thats what your plate needs to look like, and move on. Even, she says, if that means everyone at the table eating something different. Have you ever tried being the short-order cook in that scenario? It all but requires outsourcing the meal making.

Imagine, Berman says, a mom whos stressed out, with kids running around, a husband who is a rail, all the while she has no time for herself, is struggling with her weight, and trying to figure out what on earth to cook for dinner. Most people dont want to talk about uncomfortable things, Berman says. But let your kids eat mac and cheese, let your husband do what he needs, and let you have this plate for your dinner. You dont need to do anything its going to show up at your door.

This desire to customize our food experiences stems from the uniquely American trait of individualism. Often subconscious, its a desire to be exceptional, distinct from those around us, as opposed to being part of a larger collective. By contrast, many other cultures around the world are characterized by interdependence. It turns out, individualism shapes our eating habits in stunning ways, from the rise of solo dining to customization as a firmly expected attribute of eating out.

Habit is the latest example of a new technology enabling that innate premium on personalization, and over time, these tools are pulling us further and further from the table. Think smartphones making us feel less alone while eating alone, and mobile ordering apps allowing us to tailor our meal delivery times and our restaurant orders with greater precision. With roughly half of all eating occasions now taking place when were by ourselves, were getting less and less practiced at eating with others.

This reality has major implications for our food culture, and for the rising rates of social isolation in the United States. You know what the single greatest predictor of happiness is? Social connectedness. And guess what: Its one of the greatest predictors of longevity, too.

Of course I want people to eat food thats right for them. But we also have to ask ourselves: Which is really going to make us live longer, and live better? The ability to pay more granular attention to our triglyceride levels, or the more holistic benefits of eating with family and friends?

My grandmother turned 100 this year. Between the birthday parties and the bridge club, her standing dinner dates and the three times a day she picks up her neighbors in their retirement home hallway to take their walkers down to the dining hall, a thriving social life is Almas secret to a long life. Whether Im chomping on my salad, face glued to my iPhone, or waving off her breakfast offer by citing the low-glycemic Kind bar I just finished off, she tells me time after time: Shed take the cake and the friendships any day.

Egan is author of Devoured: How What We Eat Defines Who We Are (William Morrow/HarperCollins), recently released in paperback.

Originally posted here:
I sent in my DNA for a personalized nutritional blueprint. Here's what ... - Washington Post