Fascinating

Largest Family Tree Constructed From Ancient DNA Reveals Neolithic Society Was Monogamous

Wow

I knew about human chimeras, but, wow.

'Human chimera': Man fails paternity test because genes in his saliva are different to those in sperm: It is thought cells from a miscarried sibling were absorbed by the man while he was in the womb

A US man has failed a paternity test after doctors revealed his dead twin, whose DNA the man absorbed in the womb, is the genetic father of the child.

The 34-year-old man is the first ever reported case of a paternity test being fooled by a human chimera, someone with extra genes absorbed from a twin lost in early pregnancy.

Approximately one in eight single childbirths are thought to start as multiple pregnancies and occasionally cells from the miscarried siblings are sometimes absorbed in the womb by a surviving twin.

According to my mother, when she was pregnant with me, they didn't do ultrasounds, but there were two distinct foetal heartbeats heard, and she was supposed to be carrying twins. About four months into the pregnancy, my mother started bleeding badly, and after that there was only one foetal heartbeat, and she had to be on bed rest for the rest of the pregnancy or possibly lose me, too. For reasons I won't go into, we never had confirmation that she had miscarried my twin, but it is common and it sounds very much like that is what happened. My friend says I 'ate my twin'. I've often wondered if there were any residual effects from that. Did I absorb cells from that twin? And if I did...and say, it was a boy, could that be why I've had odd hormonal issues most of my life? [High androgens, for one.]

Hmmm....

Study Reveals Genetic Path of Modern Britons

In A.D. 410, Roman authority in Britain collapsed and Romano-British society disappeared from history under the invading tides of Angles and Saxons from northern Europe. Historians have been debating ever since whether the Romano-British were wiped out or survived by adopting their conquerors’ language and culture.

A fine-scale genetic analysis of the British population has now provided the answer. The invaders and the existing population lived side by side and eventually intermarried extensively. The people of south and central England are now genetically well mixed, with Saxon genes accounting for only about 20 percent of the mix, says a genetics team led by Stephen Leslie of the Murdoch Childrens Research Institute in Victoria, Australia, and by Peter Donnelly and Walter Bodmer of Oxford University.

DNA study shows Celts are not a unique genetic group

A DNA study of Britons has shown that genetically there is not a unique Celtic group of people in the UK.

According to the data, those of Celtic ancestry in Scotland and Cornwall are more similar to the English than they are to other Celtic groups.

The study also describes distinct genetic differences across the UK, which reflect regional identities.

And it shows that the invading Anglo Saxons did not wipe out the Britons of 1,500 years ago, but mixed with them.

I found this very interesting

24,000-Year-Old Body Shows Kinship to Europeans and American Indians

The genome of a young boy buried at Mal’ta near Lake Baikal in eastern Siberia some 24,000 years ago has turned out to hold two surprises for anthropologists.

The first is that the boy’s DNA matches that of Western Europeans, showing that during the last Ice Age people from Europe had reached farther east across Eurasia than previously supposed. Though none of the Mal’ta boy’s skin or hair survives, his genes suggest he would have had brown hair, brown eyes and freckled skin.

The second surprise is that his DNA also matches a large proportion — about 25 percent — of the DNA of living Native Americans. The first people to arrive in the Americas have long been assumed to have descended from Siberian populations related to East Asians. It now seems that they may be a mixture between the Western Europeans who had reached Siberia and an East Asian population.

Granted, it's one skeleton's DNA, but it is definitely worth more research, I think.

Cool

Europeans All Related by Genetic Footprint Dating Back Only 1,000 Years Ago

After centuries of bloody wars and political disputes, new genetic research reveals that Europeans all share a common ancestor that dates back just a mere 1,000 years ago. Even Europeans geographically separated by thousands of miles, such as a Portuguese and a Turk are still related, according to a new study of genome data published today in the journal PLOS Biology.

"What's remarkable about this is how closely everyone is related to each other. On a genealogical level, everyone in Europe traces back to nearly the same set of ancestors only a thousand years ago," University of California researcher Graham Coop said.

Who controls the information about your genes?

The Immortal Life of Henrietta Lacks, the Sequel by Rebecca Skloot

Last week, scientists sequenced the genome of cells taken without consent from a woman named Henrietta Lacks. She was a black tobacco farmer and mother of five, and though she died in 1951, her cells, code-named HeLa, live on. They were used to help develop our most important vaccines and cancer medications, in vitro fertilization, gene mapping, cloning. Now they may finally help create laws to protect her family’s privacy — and yours.

The family has been through a lot with HeLa: they didn’t learn of the cells until 20 years after Lacks’s death, when scientists began using her children in research without their knowledge. Later their medical records were released to the press and published without consent. Because I wrote a book about Henrietta Lacks and her family, my in-box exploded when news of the genome broke. People wanted to know: did scientists get the family’s permission to publish her genetic information? The answer is no.

Skloot's book, The Immortal Life of Henrietta Lacks, details the various ways science, in its press to go forward, did so with certain degree of ignorance and disregard for the people who were genetically connected to the most successful cell line in history. The HeLa line saved millions (among so many other things, it was used to develop the polio vaccine), but science never seems to be able to get it right when dealing with the family Henrietta Lacks left behind. Now they've stumbled yet again. At least the team did apologise when they heard of the family's reaction, and took down the data they'd made public, but of course that's like shutting the barn door after the horses have escaped, as it was downloaded and most likely deseminated.

In the United States there are laws that protect seemingly every bit of medical privacy, laws that weren't extant when Lacks lived and died. But laws related to research are still a bit murky. Can someone take tissue or samples from you, remove direct connexion to your name and then publish your genome or use your cells in research without your consent, patenting the result, reaping billions? Science is moving fast, and our legal and ethics system isn't necessarily moving fast enough. Even with consent, most people don't realise what they're signing; they don't understand the legalese or the medicalese, not because of stupidity, but because it's complex and they're untrained in it. So ethics would suggest that we protect those who don't have the knowledge to truly make informed consent by at the very least requiring it be said in simple terms, and, respecting the wishes of those who would rather not participate. Personally I think it's rather wrong to profit from a person's material without compensation or knowledge, unless expressly donated. I recognise the cells are doing nothing sitting in a tube without the scientific manipulation and development, but at the same time, the person or heirs should at least share in the ownership of the cells, which came from his or her body. Would that cripple scientific research? Probably not.

Cool

Origin of the Romani People Pinned Down

Europe's largest minority group, the Romani, migrated from northwest India 1,500 years ago, new genetic study finds.

The Romani, also known as the Roma, were originally dubbed "gypsies" in the 16th century, because this widely dispersed group of people were first thought to have come from Egypt. Today, many consider "gypsy" to be a derogatory term.

The Indian theory has been around for awhile, but has now been backed up through genetic testing. The Romany people have suffered discrimination throughout Europe and, like the Jews, were targeted by the Nazis during World War II and sent to death camps. In some post-war Communist countries, there was forced sterilisation. Even outside Europe there is a lot of prejudice against the group. The phrase 'I was gypped', for example, comes from the term 'gypsy' and relates to the perception of thievery and trickery of the often nomadic people. This, to my mind, is as offensive as the phrase 'to jew a deal', which is used to a lesser extent by the ignorant around here and beyond. Most people know enough not to use the latter expression. They don't realise the origin of the former, though, and the Romany are sparse enough here that thoughtless words don't get corrected. While I never heard the latter phrase growing up, I did grow up with the former, and I try to make sure I do not use it.

I've been intrigued by the Roanoke colony from the time I first heard about it as a child

Now people are taking an interesting approach to disappearance of the 'Lost Colony' by trying to prove they were assimilated into the native peoples of the area through genotyping.

Lost Colony DNA

Genotyping could answer a centuries-old mystery about a vanished group of British settlers.

Archaeological digs, weather records, historical writings, genealogy—none have fully answered the question of what happened during White’s absence. But Roberta Estes, who owns DNAeXplain, a company that interprets the results of genetic heritage tests, is looking to DNA for help. Her hypothesis is that the Lost Colonists survived, and that evidence of their salvation is tucked away in the mitochondrial or Y chromosomal DNA of living descendents.

“They were stranded,” Estes says of the settlers. “They knew they couldn’t survive there on the island.” The colonists’ solution, in her estimation, was to go native.

I don't know if it will bear fruit, but it's an interesting angle.

Another mystery cracked with genetics

Cave Painters Were Realists, DNA Study Finds

Scientists have wondered for years how much imagination went into animal drawings etched in caves around Europe, for example with depictions of spotted horses experts didn't think actually existed. Now, after DNA analysis from the fossilized bones of prehistoric horses, they found a genetic mutation that gives rise to a spotted coat.

Spotted Horses in Cave Art Weren’t Just a Figment, DNA Shows

Roughly 25,000 years ago in what is now southwestern France, human beings walked deep into a cave and left their enduring marks. Using materials like sticks, charcoal and iron oxides, they painted images of animals on the cave walls and ceilings — lions and mammoths and spotted horses, walking and grazing and congregating in herds.

Fascinating

Black Death genetic code 'built'

The genetic code of the germ that caused the Black Death has been reconstructed by scientists for the first time.

The researchers extracted DNA fragments of the ancient bacterium from the teeth of medieval corpses found in London.

They say the pathogen is the ancestor of all modern plagues.

The research, published in the journal Nature, suggests the 14th Century outbreak was also the first plague pandemic in history.

It uses very little actual sample material, so I don't know if it's completely accurate, but the technique could be useful in studying other endemics as well. They found that the Black Death of the 14th century was, indeed caused by a strain of Yersinia pestis that is an ancestor of plague strains today. However, it was not the same pathogen from previous plagues such as the Justinian plague of the 6th century.

This is one reason I'm not an advocate for the death penalty

Oh, there are many people who need to be gaoled for life, without ever having the possibility of parole. They need to be removed from society, and never interact with it again. Punishment? My idea of punishment requires Star Trek-level technology, where you record the relevant parts of the victim's experience and then force the perpetrator to relive it every day for the rest of his or her life, in full experience as if he or she was the victim. But we're not there yet. I think putting people on Death Row is expensive and does nothing to really punish, nor does it really bring closure. And of course, Death Row inmates are by definition not going to be rehabilitated, which is the stated reason some people use concerning prisons, those who prefer to not focus on the punishment factor.

Then there are those who may be innocent. There are cases of men (usually) and women who have been incarcerated for years, sometimes on Death Row, for crimes they did not commit. This appears to be one of those cases.

Fresh DNA evidence boosts defense in 1993 Arkansas slayings

Newly tested DNA evidence in the 1993 killings of three 8-year-old Cub Scouts in Arkansas has failed to link the crimes to the men convicted in the murders, including one on Death Row, advocates for the men said on Wednesday.

The DNA, including materials from the crime scene, instead matched three unidentified people, furthering supporters' claims that the so-called West Memphis Three are innocent, the advocates told Reuters.

This is one of the reasons I will probably never serve on a jury where the death penalty is on the table. I realise (and have told the court in the past, when I have been selected for jury duty), that I do not think I could sentence someone to death. Give me a throw-them-in-gaol-and-throw-away-the-key option, and I'm fine. Some people have to be put away for the safety of everyone else, either because they're deranged, or because they're just plain evil, and are not likely to rehabilitate. But for others, I think the punishment should fit the crime, that it can be a turning point in their lives from which they can choose a different path when they get out, and that there should be ways to integrate them back into society.

If these men are innocent, it would have meant that they were teenagers when arrested for a crime 18 years ago--meaning they've lost a great deal of their lives. If true, they should be freed and compensated, although nothing can replace nearly two decades of lost freedom. Also, I hope the DNA evidence helps find those who were responsible for the murders of these children. For more on the West Memphis Three, and the mess the case was, see the Wikipedia article.

Well, that does make sense

Dogs and humans share DNA, thanks to viruses: Research suggests genetic material was exchanged over millennia

Humans and dogs may have exchanged genetic material over the millennia via viruses, scientists conjecture.

Retroviruses — the most infamous example of which is likely HIV, the virus that causes AIDS — have the ability to incorporate their genetic material into that of their hosts. In this manner, these hitchhikers can reproduce when their hosts do.

All mammals and most vertebrates, or creatures with backbones, apparently possess these "endogenous retroviruses" in their genomes. In fact, nearly 1 percent of the human genome consists of these unwelcome guests. Mice and opossums are even more greatly compromised, with these viruses making up about 2 percent of their genomes.

I really love this quote I came across today

From How to Build a Chickenosaurus: Extinction doesn't have to be forever, according to a renowned dinosaur expert visiting UK

"Kids really like dinosaurs, and the really neat thing is, kids can understand what I talk about," Horner explained. "They know more about dinosaurs than adults do. Sometimes, if I get too many adults in the lecture hall, I have to dumb it down."

Jack Horner is giving a talk at the University of Kentucky on genetic engineering of dinosaurs from their modern-day descendants--birds. The lecture is based on his book, How to Build a Dinosaur: Extinction Doesn’t Have to Be Forever. It's at 7:30 pm on Thursday, February 10th, at the Singletary Center for the Arts, and is free.

If I left work a little early, I could go to it. Hmmm....

Three men lost decades of their lives--and one died in prison an innocent man

Miss. judge frees 2 men wrongly jailed 30 years

A judge on Thursday freed two men who spent three decades in prison before DNA evidence showed they didn't rape a woman and cut her throat in a grisly 1979 attack.

A crowded courtroom erupted in applause after Forrest County Circuit Judge Robert Helfrich's ruled to set aside the men's guilty pleas, ending what some described as a 30-year ordeal for the imprisoned men.

One of the men had been released for medical reasons last month. He has lung cancer and a brain tumor. A third man jailed for the crime died in prison in 2002.

The only witness to the murder, the victim's then 4-year-old son, has always maintained that there was one attacker. DNA evidence not only absolved the man, it matched someone who is already imprisoned for a rape in 1981.

See, Star Trek was right....

Remember the one Next Generation episode with the planet of clones stealing genetic material from the crew of the Enterprise because after so many copies, the genetic integrity broke down, and they needed an influx? This is somewhat similar.

Trees can't live forever without sex, study shows

Certain trees are able to clone themselves, which raises the tantalising possibility that they could effectively "live forever".

But a study published in the journal PLoS Biology has dashed that hope.

Dr Dilara Ally and her team at the University of British Columbia, Canada, found that the fertility of clones declines with age.

This means that a tree cannot clone itself indefinitely; it must eventually sexually reproduce, or it will die.

The secret of eternal life has been sought by human alchemists for centuries, but certain trees were thought to have evolved the knack, through cloning.

I have to admit, I'm concerned

'Artificial life' breakthrough announced by scientists

Scientists in the US have succeeded in developing the first synthetic living cell.

The researchers constructed a bacterium's "genetic software" and transplanted it into a host cell.

The resulting microbe then looked and behaved like the species "dictated" by the synthetic DNA.

The advance, published in Science, has been hailed as a scientific landmark, but critics say there are dangers posed by synthetic organisms.

The researchers hope eventually to design bacterial cells that will produce medicines and fuels and even absorb greenhouse gases.

Synthesized DNA and the Presidential Commission for the Study of Bioethical Issues

Artificially created cell called a scientific feat

First 'synthetic life': Scientists 'boot up' a bacterial cell with a synthetic genome

Because current machines can only assemble relatively short strings of DNA letters at a time, the researchers inserted the shorter sequences into yeast, whose DNA-repair enzymes linked the strings together. They then transferred the medium-sized strings into E. coli and back into yeast. After three rounds of assembly, the researchers had produced a genome over a million base pairs long.

Wooly mammoth's DNA yields haemoglobin that released oxygen at low temperatures

Mammoths had 'anti-freeze blood', gene study finds

The mammoth DNA sequences were converted into RNA (a molecule similar to DNA which is central to the production of proteins) and inserted into E. coli bacteria.

The bacteria faithfully manufactured the mammoth protein.

"The resulting haemoglobin molecules are no different than 'going back in time' and taking a blood sample from a real mammoth," said co-author Kevin Campbell, from the University of Manitoba in Canada.

Scientists then tested the "revived" mammoth proteins and found three distinctive changes in the haemoglobin sequence allowed mammoth blood to deliver oxygen to cells even at very low temperatures.

This is something the haemoglobin in living elephants cannot do.

Interesting

New hominin found via mtDNA

--this time from a cave upon a mountainous steppe in Siberia.

Homo erectus, the first hominin to move from Africa to Eurasia, did so 1.9 million years ago. After that, two known migrations occurred: Neanderthals are thought to have left Africa between 300,000 and 500,000 years ago, while early modern humans -- immediate ancestors of Homo sapiens -- took a later wave, migrating some 50,000 to 60,000 years ago. However, because the lineage of the hominin whose finger was found in the cave split off before Neanderthals and early modern humans arrived, the researchers speculate that that this new human form must have moved to Eurasia after H erectus but before Neanderthals -- probably a couple of hundred thousand years after the divergence.

All this information came from extracting mitochondrial DNA from the pinky bone of a small child in a manner to keep from contaminating the results with researcher's own material. The new hominin's DNA was compared with a variety of other known species (modern humans, Neanderthals, and the bonabo, for example) and came up with unique features.

I find what they can tell through DNA these days to be fascinating. If I'd stayed a biology major, I might have gone into that instead of oecology, but it was all so new then.

A mixed blessing

Medicine's Future Could Lie in Each Patient's Genome: In two studies, scientists quickly scanned individuals' DNA to get at causes of disease

On the one hand, single-gene disorders such as Charcot-Marie-Tooth disease could be detectable earlier and help doctors hone in on correct treatments. It's not so helpful for more complex yet common diseases such as diabetes or Alzheimer's. But it holds possibilities of targeted prevention as our technology grows and the cost of DNA sequencing goes down.

The article doesn't, however, address privacy concerns and what happens in terms of a person's chances of getting insurance in a world where newborns' genes are sequenced and their potential disorders are catalogued in their medical record. Even now, for example, there are women whose families have a strong history of breast cancer who are afraid to test for the genes--even though the test has been around for awhile--because of what it might do if it fell into the hands of insurance companies. The idea is that you could be blacklisted for conditions you might develop. That's not so bad in a healthcare system where everyone is treated equally (such as with socialised medicine). But for one based on health management organisations and the like, where costs to the insurer are very important--it could be devastating.

Still, the two studies are remarkable. The future is now, as the saying goes.

It's not you, it's your germs

Could germs be making you fat?

Gut Bacteria Cause Overeating in Mice

That's not saying diet and exercise have no bearing on weight, but scientists have observed that transplanting gut bacteria from obese mice to those of normal weight results in the thinner mice gaining weight. So it may be one of the factors in obesity.

On the topic of diet and obesity, here's another scientific finding from today's news:

DNA test 'could predict most effective diet'

A simple DNA test may predict whether someone is more likely to lose weight on a low fat or a low carbohydrate diet, say US researchers.

The results from the small preliminary study of 101 women showed those on the best diet for their genes lost two to three times more weight than the rest.