Tagged: DNA

Dogs have been man’s best friend longer than we thought

The bond between humans and dogs can feel very strong, deep and profound. It may also be much older than we once thought.

A group of researchers discovered an ancient wolf bone and say its DNA suggests dogs diverged from wolves 27,000 to 40,000 years ago — not 11,000 to 16,000 years ago, as previous research has suggested. The researchers published their findings Thursday in the journal Current Biology.

In this latest study, researchers radiocarbon-dated a Taimyr wolf bone they found in Siberia and concluded it to be about 35,000 years old. Researchers point to the ancient wolf as possibly the most recent common relative of modern wolves and dogs.

That means two things could have happened about 40,000 years ago, with the simplest scenario being that dogs became domesticated.

“The only other explanation is that there was a major divergence between two wolf populations at that time, and one of these populations subsequently gave rise to all modern wolves,” study co-author Love Dalén of the Swedish Museum of Natural History said in a release.

Under that theory, the second wolf population would had to have gone extinct…

“The difference between the earlier genetic studies and ours is that we can calibrate the rate of evolutionary change in dog and wolf genomes directly, and we find that the first separation of dog ancestors must have been in the older range,” Skoglund told Reuters.

Another implication of this study: re-imagining how dogs became an important part of human society. As the BBC notes, a prevalent theory is that dogs became domestic creatures once humans settled into agricultural-based communities.

Humans could have also “caught wolf cubs and kept them as pets and this gradually led to these wild wolves being domesticated,” Dalen told BBC. “If this model is correct, then dogs were domesticated by hunter gatherers that led a fairly nomadic lifestyle.”

Being a longterm dog family, we’ve always felt that some extra smart dogs figured out we were a soft touch and moved in.

Ancestry.com sharing DNA data with coppers — without a warrant

Would you find it frightening— perhaps even downright Orwellian — to know that a DNA swab that you sent to a company for recreational purposes would surface years later in the hands of police? What if it caused your child to end up in a police interrogation room as the primary suspect in a murder investigation?

In an extremely troubling case out of Idaho Falls, that’s exactly what happened.

Police investigating the 1996 murder of Angie Dodge targeted the wrong man as the suspect, after looking to Ancestry.com owned Sorensen Database labs for help. The labs look for familial matches between the murderers DNA and DNA submitted for genealogical testing after failing to find a match using traditional methods.

The cops chose to use a lab linked to a private collection of genetic genealogical data called the Sorenson Database (now owned by Ancestry.com), which claims it’s “the foremost collection of genetic genealogy data in the world.” The reason the Sorenson Database can make such an audacious claim is because it has obtained its more than 100,000 DNA samples and documented multi-generational family histories from “volunteers in more than 100 countries around the world.” Some of these volunteers were encouraged by the Mormon Church—well-known for its interest in genealogy—to provide their genetic material to the database. Sorenson promised volunteers their genetic data would only be used for “genealogical services, including the determination of family migration patterns and geographic origins” and would not be shared outside Sorenson….

Despite this promise, Sorenson shared its vast collection of data with the Idaho police. Without a warrant or court order, investigators asked the lab to run the crime scene DNA against Sorenson’s private genealogical DNA database. Sorenson found 41 potential familial matches, one of which matched on 34 out of 35 alleles—a very close match that would generally indicate a close familial relationship. The cops then asked, not only for the “protected” name associated with that profile, but also for all “all information including full names, date of births, date and other information pertaining to the original donor to the Sorenson Molecular Genealogy project.”

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40 years after fall of Saigon, the children of our soldiers are still there

Vo Huu Nhan was in his vegetable boat in the floating markets of the Mekong Delta when his phone rang. The caller from the United States had stunning news — a DNA database had linked him with a Vietnam vet thought to be his father.

Nhan, 46, had known his father was an American soldier named Bob, but little else.

“I was crying,” Nhan recalled. “I had lost my father for 40 years, and now I finally had gotten together with him.”

The journey toward their reconciliation has not been easy. News of the DNA match set in motion a chain of events involving two families 8,700 miles apart that is still unfolding and has been complicated by the illness of the veteran, Robert Thedford Jr., a retired deputy sheriff in Texas.

When the last American military personnel fled Saigon on April 29 and 30, 1975, they left behind a country scarred by war, a people uncertain about their future and thousands of their own children.

These children — some half-black, some half-white — came from liaisons with bar girls, “hooch” maids, laundry workers and the laborers who filled sandbags to protect American bases.

They are approaching middle age with stories as complicated as the two countries that gave them life. Growing up with the face of the enemy, they were spat on, ridiculed, beaten…They were called “bui doi,” which means “the dust of life.”

Forty years later, hundreds remain in Vietnam, too poor or without proof to qualify for the program created by the Amerasian Homecoming Act of 1987 that resettles the children of American soldiers in the United States.

Now, an Amerasian group has launched a last-chance effort to reunite fathers and children with a new DNA database on a family heritage website. Those left behind have scant information about their GI dads. DNA matches are their only hope.

RTFA for detail, anecdotes – even some good news. I’m not surprised the grunt side of the war is doing something to sort out what our nation “accomplished” in Southeast Asia.

I don’t expect today’s crew in Congress to do a damned thing?

NYC subway cultures drug resistant bacteria, DNA from Anthrax, Plague


Click to enlargeHeatmap of the Pseudomonas genus

The study, published in Cell Systems, demonstrates that it is possible and useful to develop a “pathogen map” — dubbed a “PathoMap” — of a city, with the heavily traveled subway a proxy for New York’s population. It is a baseline assessment, and repeated sampling could be used for long-term, accurate disease surveillance, bioterrorism threat mitigation, and large scale health management for New York, says the study’s senior investigator, Dr. Christopher E. Mason…

The PathoMap findings are generally reassuring, indicating no need to avoid the subway system or use protective gloves, Dr. Mason says. The majority of the 637 known bacterial, viral, fungal and animal species he and his co-authors detected were non-pathogenic and represent normal bacteria present on human skin and human body. Culture experiments revealed that all subway sites tested possess live bacteria.

Strikingly, about half of the sequences of DNA they collected could not be identified — they did not match any organism known to the National Center for Biotechnology Information or the Centers for Disease Control and Prevention. These represent organisms that New Yorkers touch every day, but were uncharacterized and undiscovered until this study. The findings underscore the vast potential for scientific exploration that is still largely untapped and yet right under scientists’ fingertips.

WTF? They’re under everyone’s fingertips.

“Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract,” Dr. Mason says. “These bacteria may even be helpful, since they can out-compete any dangerous bacteria.”

But the researchers also say that 12 percent of the bacteria species they sampled showed some association with disease. For example, live, antibiotic-resistant bacteria were present in 27 percent of the samples they collected. And they detected two samples with DNA fragments of Bacillus anthracis (anthrax), and three samples with a plasmid associated with Yersinia pestis (Bubonic plague) — both at very low levels. Notably, the presence of these DNA fragments do not indicate that they are alive, and culture experiments showed no evidence of them being alive.

RTFA to see why the researcher say we shouldn’t worry. Certainly, the diversity of microorganisms is a positive activator for our immune systems.

Interesting how they went about the research – and what this presents as a baseline for future evaluations. And an added plus is the unique – and still closed – station shuttered since Superstorm Sandy. Marine species still alive and stable in what should be an abnormal environment for them.

Thanks, Helen

How far back do you want your “Heritage” fruits and veggies to go?

Fruits and vegetables have changed a lot since the onset of agriculture 10,000 years ago, as generation after generation of farmers artificially bred crops to select for more desirable traits like size and taste.

But that change can be hard to visualize. So James Kennedy, a chemistry teacher in Australia, created some terrific infographics to show just how drastic the evolution has been. This one, for instance, shows how corn has changed in the last 9,000 years — from a wild grass in the early Americas known as teosinte to the plump ears of corn we know today…

Mind you, not all attempts at selective breeding turn out so well. As Sarah Yager recently wrote at The Atlantic, apple-growers in the United States during the 20th century tried to breed Red Delicious apples to be as bright and shiny as possible and stay on shelves for as long as possible without noticeable bruising. The result? “As genes for beauty were favored over those for taste, the skins grew tough and bitter around mushy, sugar-soaked flesh.” Nowadays, as storage and transport have become more advanced, tastier apple varieties like the Honeycrisp or Gala are surpassing the Red Delicious.

The article gives watermelon and peaches the same treatment and ends with links to FDA definitions that range from selective breeding to the difference between cisgenesis and transgenesis. I’ll launch into that some other time – once again – trying to explain to the Vegan Left that science doesn’t define DNA as good or evil.

Thanks, Mike

Sugary soft drinks linked to accelerated aging

Consumption of sugary soda drinks such as cola and lemonade may be linked to accelerated DNA ageing, say researchers who have studied the impact of the drinks in more than 5,000 people.

High-sugar fizzy drinks have been under fire from campaigners for contributing to obesity and type-2 diabetes, but this is the first study to suggest a link with ageing. The researchers found that people who reported drinking a 350ml bottle of fizzy drink per day had DNA changes typical of cells 4.6 years older.

Yes, this sort of sugar consumption shortens your life much as smoking.

The study, published in the American Journal of Public Health, asked 5,309 healthy adults aged between 20 and 65 about their consumption of fizzy drinks and examined the DNA from each participant’s white blood cells.

The team found that telomeres – protective DNA caps on the end of chromosomes – were shorter in people who reported habitually drinking more fizzy drinks.

Telomeres are repetitive sections at the end of chromosomes that get shorter each time cells divide. They act as a kind of genetic ticking clock and in the past have been associated with human lifespan as well as the development of some forms of cancer, heart disease and diabetes. Other studies have suggested a link between telomere length and lifestyle factors such as smoking and psychological stress.

Prof Elissa Epel, of UCSF, stressed that the study only showed an association and did not prove that sugary drink consumption caused cell ageing. If high soda consumption was to blame, it may be due to the huge rush of sugars into the blood after a drink, leading to oxidative stress and inflammation – “the perfect storm for degrading telomeres,” said Epel.

Next in line for study – a tighter focus on sugar. Overdue as far as I’m concerned.

Thanks, Mike

TV CSI’s – and a few thugs – lose their plot because of new DNA test

A Boston-area man long suspected of two 2004 rapes was formally charged after a new DNA test linked him to the crimes and excluded his twin brother.

Dwayne McNair, 33, of Dedham pleaded not guilty Monday. His bail was set at $500,000.

McNair had been charged earlier and spent almost two years in jail. A judge ordered him released, and prosecutors dropped the charges while the new test, which can distinguish between identical twins, was conducted.

Prosecutors in Suffolk County said the test, used for the first time in Massachusetts, found there was only a 1 in 2 billion chance the DNA in the samples being tested could have come from McNair’s brother, Dwight. McNair was indicted on eight counts of rape and two of armed robbery.

Another man, Anwar Thomas, 32, pleaded guilty in the case in 2011. But the prosecution of McNair was stymied by the possibility the DNA could have been his brother’s.

Silly me. I wrote the headline up top because CSI Cop Shows will lose part of a favorite plot-line. Now, they have acquired a new twist to the same old plot.

And, yes, “same old plot” isn’t especially appropriate since police-level DNA analysis has only been around 1986.

Black convicts free after 30 years: five questions racist cops must answer

brown and mccollum
Leon Brown and Henry McCollum

Henry McCollum, North Carolina’s longest-serving death row inmate, and his half-brother Leon Brown were released after more than 30 years in prison on Tuesday after DNA tests proved their innocence of rape and murder. The exoneration followed dogged investigations by the two men’s lawyers and by the North Carolina Innocence Inquiry Commission, an independent body that operates with the full statutory powers of the state.

The exoneration and release of the two men now puts the spotlight on the police department in Red Springs, North Carolina, that carried out the initial investigation leading to the 1984 convictions of the then teenagers and their subsequent languishing behind bars.

Here are five questions the police authorities in Red Springs now have to answer:

1. Why did the Red Springs police department consistently deny that it had any evidence in its possession relevant to the murder convictions of McCollum and Brown? Only last month the commission found a box full of physical evidence being held by the police that had been in the department’s possession since the early 1990s.

2. Why did the Red Springs police department consistently fail to disclose to lawyers for the two men or to the local district attorney’s office that detectives had requested a potentially critical fingerprint test just days before the 1984 McCollum-Brown trial? The test would have compared the print found on a beer can at the crime scene with the fingerprints of Roscoe Artis, a convicted sex offender and murderer who lived just feet away from the field in which the body of the victim, Sabrina Buie, was found. Neither the request for the test, nor the fact that it was cancelled a year later before being completed, was ever disclosed.

3. Why was the crime scene investigator, who knew all the details of the crime scene as well as key findings from the autopsy of the victim, involved in the interrogation of McCollum, thus risking that his “confession” would be contaminated?

4. Why did detectives write out confessions for both Brown, then 15, and McCollum, then 19, and ask them to sign the statements? Why did they do so knowing that the confessions were incriminating, that the boys were both intellectually disabled and that they were being interrogated in the absence of any legal representation?

5. Why did the police continue to pursue McCollum and Brown knowing that key elements of their confessions were inconsistent with each other? In their “confessions” the two boys incriminated three other youths as accomplices, and yet when the police investigated those three individuals they found they had watertight alibis and were never prosecuted?

Incompetent racist creeps! And you can extend that subtle description all the way up to the Supreme Court and scumbags like Anthony Scalia.

Take a wander through this companion article at slate.com – the second half of the article focuses in on Scalia’s Old Testament ideology. He actually advocates that if someone [by his low-life standards] receives a fair trial, they should be executed even if innocent!

Thanks, Mike

Row over cow settled by DNA tests


The cow in question

A woman in the southern Indian state of Kerala is set to win a court battle to keep a cow after DNA tests proved it belongs to her, her lawyer says…The woman, TS Sashilekha, had been accused by her neighbour Geetha of stealing the animal.

The acrimonious dispute even saw the cow in question appear in court.

It is thought to be the first time an ownership battle over an animal has been decided by DNA tests in India, where Hindus consider cows to be holy.

The legal battle between the two women began last year when Geetha claimed that a cow in her herd was the mother of the disputed animal…But DNA tests ordered by the court did not match, meaning that Sashilekha will get to keep the cow.

…N Chandra Babu, lawyer for Sashilekha, told the BBC, “It is a rare case and possibly the first of its kind in history. Perhaps this is the first time a DNA test was held on a cow to find out its real owner.”

After the disputed cow was produced in court, Sashilekha was allowed to keep it in her possession – but only after paying 45,000 rupees in securities.

I understand why the court would ask the eventual victor to provide security presumably covering the value of the cow. Hopefully, returned without charges. Another good reason why she is suing the accuser for costs and compensation.

Human-Chicken Interactions project gets off the ground


Modern chickens are descended primarily from the red junglefowl

The meat and eggs of domestic chickens are a source of protein for billions. Yet how and when the birds were domesticated remains a mystery. The answers to these questions could reveal a wealth of information about the genetics of domestication, as well as human behaviour, and how we can improve our husbandry of the birds.

In a bid to learn more about the chicken and its lineage, the UK government is funding a £1.94-million (US$3.3-million) effort to determine how the chicken went from being a wild fowl roaming the jungles of southeast Asia several thousand years ago to one of the world’s most abundant domesticated animals. The Cultural and Scientific Perceptions of Human–Chicken Interactions project — ‘Chicken Coop’ for short — will examine human history from the perspective of the fowl…

But no domestic animal has been moulded and remoulded by humans as extensively as chickens, says Greger Larson, an evolutionary geneticist. The animals have been bred for eating, egg-laying and fighting. And in the case of one particularly vocal breed, the creatures have even been strapped to the masts of Polynesian boats to act as foghorns. “Chickens are polymaths,” he says…

Because…mutations are so common in contemporary chickens, Larson’s team and others assumed that humans influenced these traits through selective breeding early in the course of domestication. But DNA from chickens recovered at archaeological sites across Europe, spanning the period from around 280 bc to ad 1800, has turned that idea on its head. In an analysis published last month, Larson’s team reported that none of 25 ancient chickens would have had yellow legs, and that just 8 out of 44 birds carried two copies of the TSHR variant…universal in modern breeds. So even 200 years ago, chickens may have been very different from those we know today.

With the help of other Chicken Coop members, Larson is also trying to get to grips with the wider evolutionary forces that shaped modern chickens. He hopes to determine why, for instance, chickens have not been wiped out by disease. This might have been expected because their very rapid selection — much of which has taken place since 1900 — should have led to inbreeding and, by whittling down immune genes, a reduced ability to respond to infections.

I love chicken almost as much as I love pork. I wasn’t raised with any religious or philosophical beliefs that inhibit the consumption of animal protein. So, no problem there. :)

Until modern science comes up with a sound reason to avoid healthfully-raised specimens of foods my progenitors used to catch in the wild – and eat – I will continue to do the same. Though restricting my hunt to the aisles of markets of all types, from chain stores to local farmers.