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 13, 2013

The imaginary trade-off between ecology and economics

Filed under: Economics, Environment, Food, Media, Technology — Tags: , , — Nicholas @ 09:37

Matt Ridley on the improvements in the environment in the western world:

Extrapolate global average GDP per capita into the future and it shows a rapid rise to the end of this century, when the average person on the planet would have an income at least twice as high as the typical American has today. If this were to happen, an economist would likely say that it’s a good thing, while an ecologist would likely say that it’s a bad thing because growth means using more resources. Therein lies a gap to be bridged between the two disciplines.

The environmental movement has always based its message on pessimism. Population growth was unstoppable; oil was running out; pesticides were causing a cancer epidemic; deserts were expanding; rainforests were shrinking; acid rain was killing trees; sperm counts were falling; and species extinction was rampant. For the green movement, generally, good news is no news. Many environmentalists are embarrassed even to admit that some trends are going in the right direction.

[. . .]

Why are environmental trends mainly positive? In short, the gains are due to “land sparing,” in which technological innovation allows humans to produce more from less land, leaving more land for forests and wildlife. The list of land sparing technologies is long: Tractors, unlike mules and horses, do not need to feed on hay. Advances in fertilizers and irrigation, as well as better storage, transport, and pest control, help boost yields. New genetic varieties of crops and livestock allow people to get more from less. Chickens now grow three times as fast in they did in the 1950s. The yield boosts from genetically modified crops is now saving from the plow an area equivalent to 24 percent of Brazil’s arable land.

What is really making a positive dent in the environmental arena is the unintended effects of technology rather than nature reserves or exhortations to love nature. Policy analyst Indur Goklany calculated that if we tried to support today’s population using the methods of the 1950s, we would need to farm 82 percent of all land, instead of the 38 percent we do now. The economist Julian Simon once pointed out that with cheap light, an urban, multi-story hydroponic warehouse the size of Delaware could feed the world, leaving the rest for wilderness.

It is not just food. In fiber and fuel too, we replace natural sources with synthetic, reducing the ecological footprint. Construction uses less and lighter materials. Even CO2 emissions enrich crop yields.

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 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.”

October 28, 2012

Got Milk (mutation)?

Filed under: Environment, Food, Health, History, Science — Tags: , — Nicholas @ 12:33

Lactose intolerance is part of humankind’s genetic inheritance, which is why the mutation that allowed (some) adult humans to digest milk is of great interest to geneticists:

A genetic mutation appeared, somewhere near modern-day Turkey, that jammed the lactase-production gene permanently in the “on” position. The original mutant was probably a male who passed the gene on to his children. People carrying the mutation could drink milk their entire lives. Genomic analyses have shown that within a few thousand years, at a rate that evolutionary biologists had thought impossibly rapid, this mutation spread throughout Eurasia, to Great Britain, Scandinavia, the Mediterranean, India and all points in between, stopping only at the Himalayas. Independently, other mutations for lactose tolerance arose in Africa and the Middle East, though not in the Americas, Australia, or the Far East.

In an evolutionary eye-blink, 80 percent of Europeans became milk-drinkers; in some populations, the proportion is close to 100 percent. (Though globally, lactose intolerance is the norm; around two-thirds of humans cannot drink milk in adulthood.) The speed of this transformation is one of the weirder mysteries in the story of human evolution, more so because it’s not clear why anybody needed the mutation to begin with. Through their cleverness, our lactose-intolerant forebears had already found a way to consume dairy without getting sick, irrespective of genetics.

[. . .]

A “high selection differential” is something of a Darwinian euphemism. It means that those who couldn’t drink milk were apt to die before they could reproduce. At best they were having fewer, sicklier children. That kind of life-or-death selection differential seems necessary to explain the speed with which the mutation swept across Eurasia and spread even faster in Africa. The unfit must have been taking their lactose-intolerant genomes to the grave.

Milk, by itself, somehow saved lives. This is odd, because milk is just food, just one source of nutrients and calories among many others. It’s not medicine. But there was a time in human history when our diet and environment conspired to create conditions that mimicked those of a disease epidemic. Milk, in such circumstances, may well have performed the function of a life-saving drug.

H/T to Marginal Revolution for the link.

September 25, 2012

A bit more progress in autism research

Filed under: Health, Science — Tags: , , , — Nicholas @ 10:19

An article at the Wall Street Journal discusses some recent advances in uncovering the causes of autism:

Scientists say that roughly 20% of autism cases can be linked to known genetic abnormalities, and many more may be discovered.

Pinpointing a genetic explanation can help predict whether siblings are likely to have the disorder — and even point to new, targeted treatments. Last week, for example, researchers reported that an experimental drug, arbaclofen, reduced social withdrawal and challenging behaviors in children and adults with Fragile X syndrome, the single most common genetic cause of autism.

[. . .]

Autism spectrum disorder (ASD) is a collection of conditions that can range in severity from the social awkwardness and narrow interests seen in Asperger’s to severe communication and intellectual disabilities. ASD now affects 1 in every 88 U.S. children — nearly double the rate in 2002 — according to the Center for Disease Control and Prevention.

No single blood test or brain scan can diagnose autism spectrum disorders — in part because environmental factors also play a major role. But once a child is diagnosed, on the basis of symptoms and behavioral tests, researchers can work backward looking for genetic causes.

Both the American Academy of Pediatrics and the American College of Medical Genetics recommend that all children diagnosed with ASD be tested for Fragile X Syndrome and other chromosome abnormalities. The newest tests, called chromosomal microanalysis, can identify submicroscopic deletions or duplications in DNA sequences known to be associated with autism. Together, these tests find genetic explanations for more than 10% of autism cases.

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).

June 27, 2012

California primed to make bad decision for “good” reasons

Filed under: Environment, Food, Government, Health, Science, USA — Tags: , , , , — Nicholas @ 00:05

California’s already bad economic situation could be made even worse by mandating that genetically modified foods be labelled to call attention to themselves:

The American Medical Association resolved this week that “there is no scientific justification for special labeling of bioengineered foods.”

The association has long-held that nothing about the process of recombinant DNA makes genetically engineered (GE) crop plants inherently more dangerous to the environment or to human health than the traditional crop plants that have been deliberately but slowly bred for human purposes for millennia. It is a view shared by the National Academy of Sciences, the World Health Organization, the Food and Agriculture Organization of the U.N., the European Commission, and countless other national science academies and non-governmental organizations.

And yet Californians will consider on their November ballots a law that mandates cigarette-like labeling of food derived from GE plants. Proponents claim to promote opportunities for consumers to make informed choices about the foods they eat. But to build support for the measure, they have played on consumer fears about a promising technology that is nevertheless prone to “Frankenfoods” demagoguery. If successful, they may well imperil the ability of Californians, and consumers around the world, to choose a technology that scientists contend could end hunger and malnutrition, lift hundreds of millions from poverty, and reduce the environmental impact of feeding an evermore populous world.

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.

July 22, 2011

Mark Lynas goes from green activist to “denier”

Filed under: Books, Environment, Media, Politics — Tags: , , , — Nicholas @ 09:28

Ben Pile reviews Mark Lynas’s new book:

Since becoming an advocate of genetic modification (GM) and nuclear power, Mark Lynas has drawn increasingly hostile criticism from his erstwhile comrades in the green movement. In turn, he has sharpened his criticism of environmentalists for their hostility to technological and economic development. In his new book, The God Species: How the Planet Can Survive the Age of Humans, he attempts to reformulate environmentalism to overcome the excesses that have so far prevented it from saving the planet. This book will no doubt provoke debate, but what is this transformation really about, and is it really based on new ideas or merely the revision of old ones?

[. . .]

As a result, there is much to agree with in The God Species. Most importantly, Lynas makes a clean break from deep ecology — the idea that ‘nature’ has intrinsic moral value and a ‘right’ to be protected from our ambitions. He rebukes the environmentalism that imagines a return to a pristine nature, and that shows contempt for development as an attempt to ‘play god’ over nature. We should ‘play god’, he says, for the planet’s sake as well as our own comfort. There is a convincing criticism of green demands for austerity and environmentalists’ unrealistic expectations that people should make do with ‘happiness’ rather than material progress. These are the conceits of well-off, middle-class and self-indulgent whingers, Lynas explains. Some of us have been making similar arguments for a very long time.

In spite of some of his accurate criticisms, Lynas fails to get to the substance of environmentalism. We do not find out what takes environmentalists to their bleak view of the world and their low view of humanity. This is a shame, because Lynas is in a unique position to reflect on it, having once thrust a custard pie into Bjorn Lomborg’s face, with the words: ‘That’s for everything you say about the environment which is complete bullshit. That’s for lying about climate change. That’s what you deserve for being smug about everything to do with the environment.’

A decade on, Lynas now emphasises science and pragmatism rather than… erm… pies. It’s worth remembering that Lomborg started out on mission similar to Lynas’s: as an environmentalist, keen to establish the sensible limits of our interaction with the natural world. Before writing The Skeptical Environmentalist, Lomborg aimed to debunk the works of the economist, Julian Simon, but ended up sympathetic to many of his arguments. Lynas, too, now finds himself sympathetic to many of the ideas from the economic right (he calls for the privatisation of all publicly owned water companies, for instance). And like Lynas, Lomborg never ended up ‘denying’ climate change, but instead sought to bring a sense of proportion to the problem, and to put it into context with other problems in the world. That is all it takes to find oneself called a ‘denier’: merely seeking a sense of proportion about environmental problems will put you in the lowest moral category, as Lynas, the ‘Chernobyl death denier’, has now discovered.

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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