Quotulatiousness

March 2, 2013

Ethical debates of the very near future: species de-extinction

Filed under: Science — Tags: , , , — Nicholas @ 12:12

Matt Ridley on the soon-to-be-possible reversal of species extinction:

The founders of Revive and Restore aren’t mainstream scientists, but they’re not people to be taken lightly, either. Stewart Brand and Ryan Phelan are a husband-and-wife team with a track record of starting unusual but successful organizations — in his case, the Whole Earth Catalog and the Global Business Network; in hers, the consumer-focused startups Direct Medical Knowledge and DNA Direct. They’ve attracted the interest of the pioneering Harvard University DNA sequencing and synthesis expert George Church.

Their argument is that it’s time to start tentatively trying de-extinction and thinking through its ethical and ecological implications. There are already projects under way to revive extinct subspecies like the European aurochs (a type of wild cattle) and the Pyrenean ibex, or bucardo. In the latter case, when the last female (Celia) was killed by a falling tree in 2000, her tissue was cloned. At least one fetus survived to term in a surrogate mother goat, but it died soon after birth.

A full species that’s been extinct for decades like the thylacine (Tasmanian tiger) or the passenger pigeon — the last one of which, Martha, died in the Cincinnati Zoo 99 years ago — will be a taller order, since the DNA from long dead specimens is fragmented. Yet Ben Novak, a young researcher working with the ancient-DNA expert Beth Shapiro at the University of California, Santa Cruz, has extracted passenger pigeon DNA from the toe pad of a museum specimen and sequenced it. Dr. Church hopes to use one of the newly invented letter-by-letter gene-replacement techniques, such as Talens or Crispr, to transform the genome of a related species called the band-tailed pigeon into that of a passenger pigeon.

February 18, 2013

Opening the food testing can of worms: “We don’t test for hedgehog either”

Filed under: Britain, Europe, Food, Health, India, Science — Tags: , , , — Nicholas @ 10:20

Tim Worstall on some of the issues with demands that all British beef for human consumption be tested for horsemeat:

Now let’s turn to that meat problem. We’re going to test something to make sure that it is indeed what it says. Most of the time, usually, we’d go looking for beef DNA and on finding it say, yup, that’s beef.

But now we’re talking about trace amounts of other species. Some of this horse contamination is someone deliberately substituting, yes. But a lot of it, those trace amounts, is someone not cleaning the pipes between species being processed. Or the knives even. Which leads us to something of a problem.

How many species do we test for? Some minced beef… or pink slime perhaps. Do we test for beef and horse? For beef, horse, mutton, pork, chicken, duck, goose? What about rat and mouse? For I’ll guarantee you that however much people try there will often be the odd molecule of either one of those in there. Sparrow? That’s more of a problem with grain processing but still.

For example, one lovely story about vegetarianism. Those (umm, OK, some) who have moved from the sub-continent to the UK. They carry on eating the (possibly Hindu caste based) vegetarian diet they are used to. And they start falling prey to all sorts of dietary deficiencies. Anaemia, there have even been reports of kwashikor (a protein deficiency). The grains and the pulses of the sub-continent have rather more insect and other residue in them than our more modern processing and storage systems provide.

People don’t test for hedgehog DNA in meat supplies, no. But how many species should they test for?

February 5, 2013

What did King Richard III look like?

Filed under: Britain, History, Science — Tags: , , — Nicholas @ 09:33

A facial reconstruction based on the skull of Richard III:

A facial reconstruction based on the skull of Richard III has revealed how the English king may have looked.

The king’s skeleton was found under a car park in Leicester during an archaeological dig.

The reconstructed face has a slightly arched nose and prominent chin, similar to features shown in portraits of Richard III painted after his death.

Historian and author John Ashdown-Hill said seeing it was “almost like being face to face with a real person”.

The development comes after archaeologists from the University of Leicester confirmed the skeleton found last year was the 15th Century king’s, with DNA from the bones having matched that of descendants of the monarch’s family.

I was unable to find an image of the reconstruction that is okay to use, but you can see various pictures on Google Image Search.

February 4, 2013

University of Leicester confirms that the remains are those of King Richard III

Filed under: Britain, History, Science — Tags: , , , — Nicholas @ 09:16

BBC News rounds up the details:

A skeleton found beneath a Leicester car park has been confirmed as that of English king Richard III.

Experts from the University of Leicester said DNA from the bones matched that of descendants of the monarch’s family.

Lead archaeologist Richard Buckley, from the University of Leicester, told a press conference to applause: “Beyond reasonable doubt it’s Richard.”

Richard, killed in battle in 1485, will be reinterred in Leicester Cathedral.

Mr Buckley said the bones had been subjected to “rigorous academic study” and had been carbon dated to a period from 1455-1540.

Dr Jo Appleby, an osteo-archaeologist from the university’s School of Archaeology and Ancient History, revealed the bones were of a man in his late 20s or early 30s. Richard was 32 when he died.

Battle wounds

His skeleton had suffered 10 injuries, including eight to the skull, at around the time of death. Two of the skull wounds were potentially fatal.

One was a “slice” removing a flap of bone, the other caused by bladed weapon which went through and hit the opposite side of the skull, a depth of more than 10cms (4ins).

Dr Appleby said: “Both of these injuries would have caused an almost instant loss of consciousness and death would have followed quickly afterwards.

“In the case of the larger wound, if the blade had penetrated 7cm into the brain, which we cannot determine from the bones, death would have been instantaneous.”

Other wounds included slashes or stabs to the face and the side of the head.

Update: New Scientist still has concerns that the trail of evidence is not strong enough to constitute proof of identity:

Mitochondrial DNA is passed down the maternal line and has 16,000 base pairs in total. Typically, you might expect to get 50 to 150 fragments from a 500-year-old skeleton, says Ian Barnes at Royal Holloway, University of London, who was not involved in the research. “You’d want to get sequences from lots of those fragments,” he says. “There’s a possibility of mitochondrial mutations arising in the line from Richard III.”

“It’s intriguing to be sure,” says Mark Thomas at University College London. It is right that they used mitochondrial DNA based on the maternal line, he says, since genealogical evidence for the paternal lineage cannot be trusted.

But mitochondrial DNA is not especially good for pinpointing identity. “I could have the same mitochondrial DNA as Richard III and not be related to him,” says Thomas.

The researchers used the two living descendents to “triangulate” the DNA results. The evidence will rest on whether Ibsen and his cousin have sufficiently rare mtDNA to make it unlikely that they both match the dead king by chance.

January 23, 2013

Tyler Cowen explains why recreating Neanderthals won’t be happening soon

Filed under: Science, Technology — Tags: , , , — Nicholas @ 10:14

Even if we have the technology to do it, there are lots of ways for the experiment to go very wrong (without going the Jurassic Park route):

…could they be taught in our schools? Who would rear the first generation? Would human parents find this at all rewarding? Do they have enough impulse control to move freely in human society? How happy would they be with such a limited number of peers? What public health issues would be involved and how would we learn about those issues in advance? What would happen the first time a Neanderthal kills a human child? Carries and transmits a contagious disease? By the way, how much resistance would the Neanderthals have to modern diseases?

What kinds of “human rights” would we issue to them? Would we end up treating them better than lab chimpanzees? Would they be covered by ACA and have emergency room rights?

Unlike the debate over recreating extinct animal species like the dodo or the passenger pigeon, Neanderthals were close relations to modern humans: under most of our ethical and moral systems, they would be people, not animals. Unless we’re so debased that we can countenance restarting the Nazi experiment that we forcefully terminated in 1945, we could not treat neoNeanderthals as anything other than intelligent, self-directing, self-owning beings. By bringing them back from the dead, we’d be taking on the moral requirement to maintain them and sustain them.

We have no way of knowing if a group of neoNeanderthals could peacefully co-exist with humanity, and no way of finding that out without running the experiment. That’s not a decision that can or should be taken by a single person or a group of scientists at a university. This wanders too close to “playing god” of old science fiction stories: those stories rarely turned out well for the non-gods.

January 14, 2013

The increasing precision of DNA editing

Filed under: Food, Science, Technology — Tags: , , — Nicholas @ 09:56

Matt Ridley looks at the vastly improved editing tools becoming available for DNA manipulation:

Little wonder that precision genetic engineering has taken a while to arrive. In truth, it has been moving steadily toward greater precision for 10,000 years. Early farmers in what’s now Turkey introduced a mutation to wheat plants in the “Q gene” on chromosome 5A, which made the seed-head less brittle and the seed husks easier to harvest efficiently.

They did so unknowingly, of course, by selecting from among random mutations.

Fifty years ago, scientists used a nuclear reactor to fire gamma rays at barley seeds, scrambling some of their genes. The result was “Golden Promise,” a high-yielding, low-sodium barley variety popular with (ironically) organic farmers and brewers. Again, the gene editing was random, the selection afterward nonrandom.

Twenty years ago, scientists inserted specific sequences for four enzymes into rice plants so that they would synthesize vitamin A and relieve a deadly vitamin deficiency-the result being “golden rice.” This time the researchers knew exactly what letters they were putting in but had no idea where they would end up.

December 23, 2012

More copper to fight superbugs

Filed under: Health, Science — Tags: , , , , — Nicholas @ 11:01

Brass and other copper-alloyed metals may have a bright future in doorknobs, handles, and other frequently handled surfaces due to a recent discovery about the metal’s ability to fight bacteria:

Researchers have discovered that copper and alloys made from the metal, including brass, can prevent antibiotic resistance in bacteria from spreading.

Plastic and stainless steel surfaces, which are now widely used in hospitals and public settings, allow bacteria to survive and spread when people touch them.

Even if the bacteria die, DNA that gives them resistance to antibiotics can survive and be passed on to other bacteria on these surfaces. Copper and brass, however, can kill the bacteria and also destroy this DNA.

Professor Bill Keevil, head of the microbiology group at Southampton University, said using copper on surfaces in public places and on public transport could dramatically cut the threat posed by superbugs.

[. . .]

In research published in the journal Molecular Genetics of Bacteria, Professor Keevil and his colleagues found that compared to stainless steel bacteria on copper surfaces bacterial DNA rapidly degraded at room temperature.

Professor Keevil added: “We live in this new world of stainless steel and plastic, but perhaps we should go back to using brass more instead.”

Tim Worstall points out that much of the stainless steel came in through health and safety regulation:

But isn’t this just great? All that modernity, all that ripping out of the old and replacement with futuristic design actually kills people?

It’s almost as fun as the discovery that the wooden chopping boards, which they made illegal, contain natural antibiotics which the plastic chopping boards, which they made compulsory, do not.

The Man from Whitehall really does not know best. And given that, can we hang them all from the Christmas tree please? It would usher in such a jolly New Year.

December 14, 2012

The revolution will not be revolutionary … soon

Filed under: Health, Media, Science — Tags: , , , — Nicholas @ 11:09

In the Globe and Mail, Timothy Caulfield explains that we need to be careful not to drink the “healthcare revolution” Kool-Aid:

It has been suggested that this technological advance will usher in a new health-care “revolution.” It will allow us, or so it’s promised, to individualize health-care treatments and preventive strategies — an approach often called “personalized medicine.” It will allow us to become fully aware of our genetic shortcomings and the diseases for which we’re at increased genetic risk, thus providing the impetuous to adopt healthier lifestyles.

But will having your personal genome available really revolutionize your health-care world? Will you be able to use this information to significantly improve your chances of avoiding the most common chronic diseases? Not likely.

Tangible benefits will be (and have been) achieved. But, for the most part, these advances are likely to be incremental in nature – which, history tells us, is the way scientific progress usually unfolds.

Why this “we are not in a revolution” message? Overselling the benefits of personal genomics can hurt the science, by creating unrealistic expectations, and distract us from other, more effective areas of health promotion.

The relationship between our genome and disease is far more complicated than originally anticipated. Indeed, the more we learn about the human genome, the less we seem to know. For example, results from a major international initiative to explore all the elements of our genome (the ENCODE project) found that, despite decades-old conventional wisdom that much of our genome was nothing but “junk DNA,” as much as 80 per cent of our genome likely has some biological function. This work hints that things are much more convoluted than expected. So much so that one of ENCODE’s lead researchers, Yale’s Mark Gerstein, was quoted as saying that it’s “like opening a wire closet and seeing a hairball of wires.”

September 20, 2012

Over-hyping the importance of the Richard III archaeological dig

Filed under: Britain, History — Tags: , , , , — Nicholas @ 08:50

At the History Today blog, Linda Porter points out that some of the breathless claims about the historical significance of the Leicester archaeological dig are rather overblown:

Major finds don’t come along very often and this would certainly be one of the most significant in the last hundred years. But the huge claims being made for it are not the sort that sit well with most historians. Assertions that, if DNA tests prove positive, this discovery ‘has the potential to rewrite history’ and is of ‘global importance’ make me sigh.

Historians have long known that the Tudor narratives on Richard III are propaganda. Shakespeare’s compelling villain may still resonate with the man on the street but has nothing to do with a measured analysis of the past and anyone with even a general interest in the late fifteenth century will be aware of this. And ‘global significance’? Cross the Channel and I’d be surprised if you found anyone outside the academic world who knew about Richard III and the saga of the Princes in the Tower. Those involved in the project, which appears to have been rigorously conducted from the archaeological perspective, clearly want headlines. As someone who has worked in public relations herself I congratulate them on a successful communications campaign — it has to be acknowledged that the Richard III Society is very good at this kind of thing — but wearing my historian’s hat extravagant claims make me uncomfortable.

September 15, 2012

The Richard III debate moves to “where should we bury him this time”

Filed under: Britain, History — Tags: , , , — Nicholas @ 10:33

In the Telegraph, Dan Hodges calls for giving Richard III “a last, glorious summer”:

It’s a brilliant idea. Seriously. Think of where Richard stands. At the centre of our history, our art, our education, our national identity. What a staggering opportunity this represents.

Let’s give him a full, no-holds-barred state funeral. Everyone’s been banging on about preserving the Olympic spirit; well here — DNA tests permitting — is our chance. This is a once in a generation opportunity. In fact, it’s a once in about 20 generations opportunity. Let’s bring our history alive.

Just imagine the crowds that would gather for the chance of watching a 21st century ceremonial to a Plantagenet king. And not just an English king, but thanks to Shakespeare, a global monarch.

Picture the moment. A silent Mall. A slow drum beat. An honor guard, heads bowed in tribute to their leader who fell 500 years before. Richard, making his last journey, laid upon a ceremonial gun carriage, draped in the flag of the kingdom he died fighting for. And ahead of him walks a riderless horse. The horse that in his last moments, he would have swapped that kingdom for.

Bloody hell, I’d miss an episode of Strictly for that. And I bet a few million others would as well.

Okay, there’s the slightly unfortunate business of the Princes and the Tower. But we’ve all made the odd mistake. Plus, if you read Josephine Tay’s the Daughter of Time, it was a fit up anyway.

If there’s one thing we’ve learnt over the past couple of months it’s that — to borrow a phrase from another high profile if much maligned senior statesman — we are at our best when at our boldest. Or more accurately, when we say “damn it, let’s do it”.

Now is one of those moments. Damn it. Let’s give Richard III one last, glorious summer.

September 12, 2012

Richard III’s remains may have been found in Leicester

Filed under: Britain, History — Tags: , , , , — Nicholas @ 09:17

Fascinating announcement today from the dig site:

11.12: He says one skeleton and other human remains have been found and a barbed metal arrowhead was found between vertebrae of the skeleton’s upper back. The arrow was near the spine, but not embedded in the bones.

11.15: Mr Taylor says that an articulated skeleton has been found that is of significant interest to us. Scientists have also found a set of “disarticulated human remains” but because they are female and therefore not Richard III.

The skeleton shows signs of “near death trauma” that “appears to be consistent with injury from battle”. Scientists now hope to extract DNA from the bones.

He added:

“It also has spinal abnormalities and an individual form of spinal curvature, which makes his right shoulder visibly higher than his left shoulder. We believe the individual would have had severe scoliosis. The skeleton was not a hunchback.”

It is consistent with other accounts of Richard III.”

It is now at an undisclosed laboratory where it is going through “rigorous” testing.

September 6, 2012

It’s time to retire the pop-sci term “Junk DNA”

Filed under: Health, Science — Tags: , , — Nicholas @ 08:42

In the Wall Street Journal, Gautam Naik and Robert Lee Hotz report on the most recent discoveries about the human genome:

The new insight is the product of Encode, or Encyclopedia of DNA Elements, a vast, multiyear project that aims to pin down the workings of the human genome in unprecedented detail.

Encode succeeded the Human Genome Project, which identified the 20,000 genes that underpin the blueprint of human biology. But scientists discovered that those 20,000 genes constituted less than 2% of the human genome. The task of Encode was to explore the remaining 98% — the so-called junk DNA — that lies between those genes and was thought to be a biological desert.

That desert, it turns out, is teeming with action. Almost 80% of the genome is biochemically active, a finding that surprised scientists.

In addition, large stretches of DNA that appeared to serve no functional purpose in fact contain about 400,000 regulators, known as enhancers, that help activate or silence genes, even though they sit far from the genes themselves.

The discovery “is like a huge set of floodlights being switched on” to illuminate the darkest reaches of the genetic code, said Ewan Birney of the European Bioinformatics Institute in the U.K., lead analysis coordinator for the Encode results.

August 31, 2012

The search for the burial place of Richard III

Filed under: Britain, Cancon, History — Tags: , , , , , — Nicholas @ 07:40

Elizabeth sent me another link on the ongoing archaeological search for the burial place of King Richard III:

A high-profile search for the gravesite of the 15th-century monarch King Richard III — begun Saturday beneath a parking lot in the English city of Leicester — has a remarkable connection to a Canadian family whose members hold the genetic key to solving one of British history’s most enduring mysteries: Where is Richard III’s body?

The London, Ont.-based Ibsen family, recently proven to be descended from King Richard’s maternal line, has provided DNA samples aimed at confirming the regal identity of any human remains found during the unprecedented dig, which continues this week at the former site of a medieval church where — 527 years ago — the violently overthrown monarch was buried.

The University of Leicester-led archeological project was launched after the discovery that the maternal bloodline of the last Plantagenet king — killed in 1485 in the climactic battle of the War of the Roses — survived into the 21st century through Joy Ibsen, a British-born woman who immigrated to Canada after the Second World War and raised a family in southwestern Ontario.

If nothing else, the media coverage of this dig may generate lots of new members for the Richard III Society (Canadian branch, American branch).

March 10, 2012

Some diseases may be caused by “endogenous” retrovirii

Filed under: Health, Science — Tags: , , , , — Nicholas @ 12:17

Matt Ridley on some recent discoveries in genetics and medicine that may help to explain certain diseases like multiple sclerosis:

The virus implicated in multiple sclerosis is called HERV-Fc1, a bizarre beast called an “endogenous” retrovirus. What this means is that its genes are part of the human genome. For millions of years, they have been integrated into our own DNA and passed on by normal heredity. It was one of the shocks of genomic science to find that the human genome contains more retroviral than “human” genes: some 5% to 8% of the entire genome.

Normally, the genes of endogenous retroviruses remain dormant, but — a bit like a computer virus that springs into action on a trigger — something wakes them up sometimes, and actual viruses are made from them, which then infect other cells in the body. The Danish scientists suggest that this is what happens in multiple sclerosis. Bjørn Nexø of Aarhus University writes that “retroviral infections often develop into running battles between the immune system and virus, with the virus mutating repeatedly to avoid the immune system, and the immune system repeatedly catching up. One can see the episodic nature of multiple sclerosis as such a running battle.”

The possibility that you can inherit the genes of a virus blurs the distinction between a genetic and an infectious disease. The HERV-Fc1 genes lie on the X chromosome. Since women have twice as many X chromosomes as men, this might explain why some forms of MS are more common in women. Dr. Nexø concludes hopefully: “The finding that a disease is caused by an infectious agent is an encouraging one. These are the diseases which we know best how to treat.

The research also appears to show a link between cat ownership and schizophrenia:

Human beings can also catch toxoplasma from cats, and it’s known to affect behavior: altering personalities, slowing reaction times and increasing the risk of car accidents. More than 20 studies have now found an association between schizophrenia and toxoplasma. Schizophrenia is more common among those who had pet cats in their childhood homes (but not in those who had pet dogs).

Indeed, some scientists think that schizophrenia only became common, around 1870, when keeping cats as indoor pets became fashionable. The parasite has genes for dopamine, a neurochemical found in excess in schizophrenics.

January 25, 2011

The genomic treasure trove of Quebec

Filed under: Cancon, History, Science — Tags: , , , — Nicholas @ 07:36

Thanks to relatively thorough genealogical records, the people of Quebec are of great and growing interest to genetic researchers:

One of the great things about the mass personal genomic revolution is that it allows people to have direct access to their own information. This is important for the more than 90% of the human population which has sketchy genealogical records. But even with genealogical records there are often omissions and biases in transmission of information. This is one reason that HAP, Dodecad, and Eurogenes BGA are so interesting: they combine what people already know with scientific genealogy. This intersection can often be very inferentially fruitful.

But what about if you had a whole population with rich robust conventional genealogical records? Combined with the power of the new genomics you could really crank up the level of insight. Where to find these records? A reason that Jewish genetics is so useful and interesting is that there is often a relative dearth of records when it comes to the lineages of American Ashkenazi Jews. Many American Jews even today are often sketchy about the region of the “Old Country” from which their forebears arrived. Jews have been interesting from a genetic perspective because of the relative excess of ethnically distinctive Mendelian disorders within their population. There happens to be another group in North America with the same characteristic: the French Canadians. And importantly, in the French Canadian population you do have copious genealogical records. The origins of this group lay in the 17th and 18th century, and the Roman Catholic Church has often been a punctilious institution when it comes to preserving events under its purview such as baptisms and marriages. The genealogical archives are so robust that last fall a research group input centuries of ancestry for ~2,000 French Canadians, and used it to infer patterns of genetic relationships as a function of geography, as well as long term contribution by provenance.

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