Posts Tagged ‘DNA’
By now you’ve probably read about the paper which reports that there seem to have been three waves of humans migrating into the New World prior to the arrival of Europeans. A major aspect of this result is that it does not emerge out of a vacuum, but rather comes close to settling an old question in linguistics…
The late Joseph Greenberg generated a series of audacious phylogenies of languages of the world. Greenberg’s attempts received mixed reviews. It seems that there is little controversy about some of his classifications of African languages, but linguists of American native dialects rejected his division of the languages of the New World into three broad families, Eskimo-Aleut, Na-Dene, and Amerind…The linguistic trichotomy also lent itself to a narrative of three migrations…
Despite all this drama, the scientific isn’t too hard to understand. Aside from the nifty statistics one problem is that many of these native groups have European and African admixture, but there are workarounds to that (e.g., just pull out genomic segments which are indigenous, and use those)…
On a big picture note this puts the lie to the idea that before agriculture hunter-gatherer societies were subject purely to differentiation in situ. The Eskimo-Aleut and Na-Dene erupted into a settled landscape, and dispossessed the indigenous groups of their lands…The First Americans “struck back” in this case, shoving aside the pioneers of northern living who had likely originated more recently from the margins of eastern Asia. Of course, the Eskimo-Aleut and related peoples were not First Americans only, rather, it was the old (First American) and new (Asian) ganging up upon the not so old or new (Asian).
The real deal – in a computer simulation
Step aside, DNA—new synthetic compounds called XNAs can also store and copy genetic information, a new study says. And, in a “big advancement,” these artificial compounds can also be made to evolve in the lab, according to study co-author John Chaput of the Biodesign Institute at Arizona State University.
Nucleotides, the building blocks of DNA are composed of four bases—A, G, C, and T. Attached to the bases are sugars and phosphates.
First, researchers made XNA building blocks to six different genetic systems by replacing the natural sugar component of DNA with one of six different polymers, synthetic chemical compounds…The team—led by Vitor Pinheiro…then evolved enzymes, called polymerases, that can make XNA from DNA, and others that can change XNA back into DNA.
This copying and translating ability allowed for genetic sequences to be copied and passed down again and again—artificial heredity.
Last, the team determined that HNA, one of the six XNA polymers, could respond to selective pressure in a test tube…As would be expected for DNA, the stressed HNA evolved into different forms.
This shows that “beyond heredity, specific XNAs have the capacity for Darwinian evolution,” according to the study…
All of XNA’S actions are “completely controlled by experimentalists—it’s 100 percent unnatural,” study co-author Chaput noted…But such control means that scientists can “use [XNA] to ask very basic questions in biology,” such as about the origins of life, Chaput said.
For instance, “it’s possible that life didn’t begin with DNA and proteins like we see today—it may have begun with something much, much simpler,” he said.
A scientist could potentially evolve XNA to discover various functions that would have been important for early life.
I love it. Opening biochemistry to the inventiveness of humankind. Practical and experimental modeling beyond computer models.
A paedophile who abducted four young girls from the street in the 1980s and 1990s and sexually abused them has appeared in court after cold-case detectives linked his DNA to the crimes.
David Bryant, a 65-year-old grandfather from Ulverston, Cumbria, was due to be sentenced at Newcastle crown court on Friday but the case was adjourned until next week.
The court heard that Bryant carried out separate attacks on young girls in Hampshire and Tyneside. He has admitted four counts of kidnap and four of sexual assault.
Mark Giuliani, for the prosecution, told the court: “A familiar feature of this offending is how the defendant targeted young girls out playing near their homes…
The prosecution told the court that Bryant was convicted of three sex offences against women between 1975 and 1984.
How many more cases could be solved if politicians felt like spending the money on computational analysis to link evidence already on file — instead of the crap that governments assign higher priority. Like wars, standing armies sufficient to “show the flag”, the war on drugs, subsidies to keep the prices of commodities higher than need be.
Day of Discovery
The first complete genome-sequencing of “Otzi,” Italy’s prehistoric iceman, is revealing a wealth of details about the man who roamed the Alps 5,300 years ago and could unleash a frenzy of activity among scientists thanks to open data.
Over the last 20 years, scientists have painstakingly collected data from the stomach, bowels and teeth of the 45-year old man, who was found sticking out of a glacier by German climbers in 1991 in the Tyrolean Alps on the Austro-Italian border.
But for the first time since the Copper-age individual was unearthed, his complete genetic profile has been reconstituted, revealing a very modern predisposition for cardiovascular diseases, lactose intolerance, and brown eyes that betray near-Eastern origins.
“He is more closely related to modern Sardinian or Corsican populations than, for instance, mainland Italy further to the south,” Angela Graefen, a human genetics researcher at the Eurac Institute for the Mummies and the Iceman in Bolzano, Italy, told Reuters…
“His ancestors were more plausibly from the first wave of migrants from the Near East. The genome group stuck in the isolated regions which were less affected by human migrations, Mediterranean islands but also remote Alpine valleys.”
Otzi, a hunter who was felled by an arrow while climbing the high mountains, was also predisposed to arteriosclerosis and heart diseases, conditions thought to be more linked to modern risk factors such as being overweight, smoking or drinking…
The research helps flesh out a picture of the iceman, who had brown hair, type-O blood, the lactose intolerance that was common among Neolithic agrarian societies. He also was the first-known carrier of Lyme disease, a bacterial infection spread by ticks.
But the full-genome sequencing also opens far more possibilities for researchers around the globe than the 2008 sequencing of his mitochondrial DNA — which is passed down through the mother’s line.
“This is more information than we could probably study in a lifetime,” Eurac’s Graefen said. “That’s why we have made the data public on a special browser so that a specialist in any field can look this up.”
“There are millions of genes out there which have yet to be identified. In the future, when we know what a particular gene is for, we can check what it was like 5,000 years ago,” she said.
I never miss a story about Otzi. I’ve hiked the region where he was found – and I wish I had found him.
Archaic DNA sequencing is such an interesting study. Yet another aspect of computational analysis I’d love to focus on – if I was starting out as a geek, nowadays.
The medical world is holding its breath, waiting for the revolution. It will be here any minute. Definitely by the end of the decade. Or perhaps it will take a little longer than that, but seriously, it’s right around the corner. More or less.
That’s the genomics revolution, with its promise of treatment focused on the individual rather than the group. At last, patients will be more than the product of their age, sex, ethnicity, illnesses and bad habits; treatments will be aimed like a laser at their personal genetic particulars, and if those genes are not quite what they should be, then those genes will be fixed.
…A particularly readable and comprehensive vision can be found in Dr. Eric J. Topol’s new book, “The Creative Destruction of Medicine.”
Dr. Topol, a cardiologist and researcher at the Scripps Research Institute with the energy of 10 (if his prose style and his honor-laden biography are any indication), dispenses in short order with our current population-based medical strategies. They are wasteful and inexact, he points out, often marginally beneficial to the group and downright harmful to the individual.
He presents an array of far better ideas, a few now actually being practiced in rudimentary form. These include pharmacogenomics, in which specific genes that govern responses to medications are routinely assayed, and cancer treatments that probe tumors for specific genetic targets rather than relying on standard chemotherapy…
In “Am I My Genes?,” the psychiatrist and ethicist Dr. Robert L. Klitzman plunges readers into the world of genomic medicine as it exists today: a barely mapped terrain of immense overlapping uncertainties. Many thousands of patients are bravely stumbling along in there…
Although written for an academic audience, this book should make compelling reading for anyone considering genetic testing for…many conditions: It provides an instant community of fellow travelers along with a sophisticated moderator. Dr. Klitzman moves through all the basic landmarks, including the big ones: “Do I want to know?,” “Whom should I tell?” and “Why me..?”
And that is exactly the phenomenon that fascinates H. Sebastian Seung, a professor of computational neuroscience at M.I.T. whose “Connectome” lays out the newest research into why we think the way we do. For Dr. Seung, it is self-evident that you are more than your genes. The real you sits firmly within your skull, and while your brain’s 100 billion nerve cells may carry your genes, the “you” they form is shaped by the ways they connect to one another…
As a newborn, Dr. Seung writes, you are pretty much just a product of your genes and some initial random connections, but every second of your first few years adds to the cumulative web of connections that form you. By the time you are a toddler you have more synapses, or connections among your neurons, than you ever will again: In some ways the adult you is just an edited 2-year old, one of many eminently pleasing thoughts he sets forth.
This is complicated stuff, and it is a testament to Dr. Seung’s remarkable clarity of exposition that the reader is swept along with his enthusiasm, as he moves from the basics of neuroscience out to the farthest regions of the hypothetical, sketching out a spectacularly illustrated giant map of the universe of man.
All added to the list. I may have to resume my practice back when I only edited and wrote for one blog. Take a chunk of Friday off to catch up with my reading.
Problem is – this site of mine is especially satisfying because readership and followers are within the margin of error for 50/50 women and men – and depending on the time of day here in the Rockies and time zones around the world, the audience varies from 18% to 68% US-based. The rest of the world is onboard just about all the time.
Michael Morton in the middle
State District Judge Louis Sturns of Tarrant County will lead a court of inquiry into complaints of prosecutorial misconduct against former Williamson County prosecutor Ken Anderson, who won a murder conviction in 1987 against a defendant who spent 25 years in prison before he was exonerated by DNA evidence.
Michael Morton was convicted of fatally beating his wife in their Austin home in 1986. Attorneys say the wrongful conviction would not have happened if Anderson, who is now a Williamson County state district judge, had not deliberately withheld evidence that indicated Morton’s innocence.
“This is a historic moment for Texas justice,” said John Raley, the Houston lawyer who has worked pro bono on Morton’s case for seven years. “We are confident that Judge Sturns will handle this important case with the seriousness and probity demonstrated by Judge [Sid] Harle and [Texas Supreme Court Chief] Justice [Wallace] Jefferson…”
Last week, Harle recommended that Jefferson appoint such a court after he decided that there was probable cause to believe that Anderson should face charges of contempt of court, tampering with evidence and tampering with government records…
Morton contended during his 1987 trial that his wife’s killer must have entered their home after he left for work about 5:30 a.m. Anderson told the jury that Morton, who had no criminal history, beat his wife to death in a perverted rage because she denied him sex. Meanwhile, Morton’s lawyers say, Anderson was concealing evidence that pointed to the very scenario Morton described.
Morton was sentenced to life in prison but continued to maintain his innocence. Starting in 2005, he pleaded with the court to test DNA on a collection of evidence, including a bandanna found near his home shortly after the murder.
Williamson County District Attorney John Bradley fought the request for DNA testing, based on advice from Anderson. In 2010, though, a Texas court ordered the testing. The results showed Christine Morton’s blood on the bandanna mixed with the DNA of Mark A. Norwood, a felon who lived near the Mortons at the time.
A Williamson County grand jury indicted Norwood this month. Norwood’s DNA has also been identified on a pubic hair found at the scene of the similar murder in 1988 in Austin…
The Innocence Project probably could spend all their time in Texas and Illinois – and that would cover 99% of those convicted illegally of violent crimes. Do we have any states left where the justice system considers protecting the innocent as important as getting a high conviction rate?
A prickly new arrival made its first public appearance at Perth Zoo yesterday. The Echidna Puggle, the latest breeding success at the zoo, was given a quick weigh and inspection by keepers, before being placed back in its nursery burrow where it will spend the next two to three months. The youngster weighed in at 526 grams and will continue to grow over the next three to four years before reaching the normal adult weight of around 4 kg.
The Puggle, named Kai (Nyoongar for surprise), weighed less than one gram when it hatched in September and spent the first two months of its life in its mother’s pouch. “Once the puggle’s spines started to emerge the mother deposited it in the nursery burrow,” Perth Zoo’s Australian Fauna Supervisor Arthur Ferguson said…
…“Once Kai leaves the nursery burrow, we will take a couple of small hairs for DNA sexing,” Mr Ferguson said “The previous five echidnas born at Perth Zoo were all females, so we are hoping that Kai is a male.” Echidnas are very difficult to breed in captivity. Perth Zoo began studying their secretive breeding habits and reproductive biology a few years ago…
The work undertaken with Short-beaked Echidnas may also help in conserving its endangered cousins, the Long-beaked Echidnas, which are facing extinction in the wild. Perth Zoo’s research provides a solid foundation for a captive breeding program to be established for Long-beaked Echidnas if required.
Delightful. And cuter than some humans.
A metal thief was caught after leaving a can of Polish lager covered with his DNA on the roof of a church he was raiding.
Saulius Ciuzas, 39, stripped £10,000 worth of lead from the 12th century church but left a near full can of Lech beer on the roof of the church.
He made off with 13 strips of lead from St Peter and St Paul Church in Algarkirk, Boston, Lincs., but church warden Peter Wilson found the can the morning after the theft on April 24 this year, Lincoln Crown Court heard on Friday.
Phil Howes, prosecuting, said: “Next to where the lead had been removed was a Lech beer can. It was upright and still had liquid in it. The can was linked to Ciuzas because his DNA was found on it.”
Lithuanian migrant Ciuzas lived 40 miles away in Lincoln but was tracked down and arrested…
He was jailed for 12 months after he was found guilty of the lead theft.
Tidying up after stealing includes a lot more than fingerprints on the chimney nowadays.