The Use of Clustered, Regularly Inter-spaced, Short, Palindromic Repeats

fortunascorner | “CRISPRs are elements of an ancient system that protects bacteria, and other, single-celled organisms from viruses, acquiring immunity to them by incorporating genetic elements from the virus invaders,” Mr. Wadhwa wrote.  “And, this bacterial, antiviral defense serves as an astonishingly cheap, simple, elegant way to quickly edit the DNA of any organism in the lab.  To set up a CRISPR editing capability, a lab only needs to order an RNA fragment (costing about $10) and purchase off-the-shelf chemicals and enzymes for $30 or less.”  

 

“Because CRISPR is cheap, and easy to use, it has both revolutionized, and democratized genetic research,” Mr. Wadhwa observes.  “Hundreds, if not thousands of labs are now experimenting with CRISPR-based editing projects.” And, access to the WorldWide Web, provides instantaneous know-how, for a would-be terrorist — bent on killing hundreds of millions of people.  As Mr. Wadhwa warns, “though a nuclear weapon can cause tremendous, long-lasting damage, the ultimate biological doomsday machine — is bacteria, because they can spread so quickly, and quietly.”

 

“No one is prepared for an era, when editing DNA is as easy as editing a Microsoft Word document.”

 

This observation, and warning, is why the current scientific efforts aimed at developing a vaccine for the plague; and, hopefully courses of action for any number of doomsday biological weapons.  With the proliferation of drones as a potential method of delivery, the threat seems overwhelming.  Even if we are successful in eradicating the world of the cancer known as militant Islam, there would still be the demented soul, bent on killing as many people as possible, in the shortest amount of time, no matter if their doomsday bug kills them as well.  That’s why the research currently being done on the plague is so important.  

 

As the science fiction/horror writer Stephen King once wrote  “God punishes us for what we cannot imagine.”

The Ghettoization of Genetic Disease

gizmodo |  Today in America, if you are poor, you are also more likely to suffer from poor health. Low socioeconomic status—and the lack of access to healthcare that often accompanies it—has been tied to mental illness, obesity, heart disease and diabetes, to name just a few. 

Imagine now, that in the future, being poor also meant you were more likely than others to suffer from major genetic disorders like cystic fibrosis, Tay–Sachs disease, and muscular dystrophy. That is a future, some experts fear, that may not be all that far off.

Most genetic diseases are non-discriminating, blind to either race or class. But for some parents, prenatal genetic testing has turned what was once fate into choice. There are tests that can screen for hundreds of disorders, including rare ones like Huntington’s disease and 1p36 deletion syndrome. Should a prenatal diagnosis bring news of a genetic disease, parents can either arm themselves with information on how best to prepare, or make the difficult decision to terminate the pregnancy. That is, if they can pay for it. Without insurance, the costs of a single prenatal test can range from a few hundred dollars up to $2,000. 

And genome editing, should laws ever be changed to allow for legally editing a human embryo in the United States, could also be a far-out future factor. It’s difficult to imagine how much genetically engineering an embryo might cost, but it’s a safe bet that it won’t be cheap.

“Reproductive technology is technology that belongs to certain classes,” Laura Hercher, a genetic counselor and professor at Sarah Lawrence College, told Gizmodo. “Restricting access to prenatal testing threatens to turn existing inequalities in our society into something biological and permanent.”

Hercher raised this point earlier this month in pages of Genome magazine, in a piece provocatively titled, “The Ghettoization of Genetic Disease.” Within the genetics community, it caused quite a stir. It wasn’t that no one had ever considered the idea. But for a community of geneticists and genetic counsellors focused on how to help curb the impact of devastating diseases, it was a difficult thing to see articulated in writing.

Prenatal testing is a miraculous technology that has drastically altered the course of a woman’s pregnancy since it was first developed in the 1960s. The more recent advent of noninvasive prenatal tests made the procedure even less risky and more widely available. Today, most women are offered screenings for diseases like Down syndrome that result from an abnormal presence of chromosomes, and targeted testing of the parents can hunt for inherited disease traits like Huntington’s at risk of being passed on to a child, as well. 

But there is a dark side to this miracle of modern medicine, which is that choice is exclusive to those who can afford and access it.

Genetics in the Madhouse: The Unknown History of Human Heredity

nature  |  Who founded genetics? The line-up usually numbers four. William Bateson and Wilhelm Johannsen coined the terms genetics and gene, respectively, at the turn of the twentieth century. In 1910, Thomas Hunt Morgan began showing genetics at work in fruit flies (see E. Callaway Nature 516, 169; 2014). The runaway favourite is generally Gregor Mendel, who, in the mid-nineteenth century, crossbred pea plants to discover the basic rules of heredity.

Bosh, says historian Theodore Porter. These works are not the fount of genetics, but a rill distracting us from a much darker source: the statistical study of heredity in asylums for people with mental illnesses in late-eighteenth- and early-nineteenth-century Britain, wider Europe and the United States. There, “amid the moans, stench, and unruly despair of mostly hidden places where data were recorded, combined, and grouped into tables and graphs”, the first systematic theory of mental illness as hereditary emerged.

For more than 200 years, Porter argues in Genetics in the Madhouse, we have failed to recognize this wellspring of genetics — and thus to fully understand this discipline, which still dominates many individual and societal responses to mental illness and diversity.

The study of heredity emerged, Porter argues, not as a science drawn to statistics, but as an international endeavour to mine data for associations to explain mental illness. Few recall most of the discipline’s early leaders, such as French psychiatrist, or ‘alienist’, Étienne Esquirol; and physician John Thurnam, who made the York Retreat in England a “model of statistical recording”. Better-known figures, such as statistician Karl Pearson and zoologist Charles Davenport — both ardent eugenicists — come later.

Inevitably, study methods changed over time. The early handwritten correlation tables and pedigrees of patients gave way to more elaborate statistical tools, genetic theory and today’s massive gene-association studies. Yet the imperatives and assumptions of that scattered early network of alienists remain intact in the big-data genomics of precision medicine, asserts Porter. And whether applied in 1820 or 2018, this approach too readily elevates biology over culture and statistics over context — and opens the door to eugenics.

In Bourne Legacy A 1.5% Gain Of Mitochondrial Function Yielded Super Soldiers

thescientist |  Since the 1970s, when researchers turned up similarities between DNA in eukaryotes’ mitochondria and bacterial genomes, scientists have suspected that the organelles descended from symbionts that took up residence within larger cells. A diverse class of bacteria called Alphaproteobacteria soon emerged as a likely candidate for the evolutionary origins of mitochondria. 

But a new analysis, published today (April 25) in Nature, suggests that mitochondria are at best distant cousins to known alphaproteobacteria lineages, and not descendents as previously thought.

“We are still left hungry for the ancestor of mitochondria,” says Puri Lopez-Garcia, a biologist at the University of Paris-South who was not involved in the study.

While it’s generally agreed that Alphaproteobacteria includes the closest bacterial relatives of mitochondria, that relationship doesn’t reveal much about how mitochondrial ancestors made a living or how they made the jump to acting as organelles. That’s because “Alphaproteobacteria is a particularly diverse group of organisms in terms of kinds of metabolism,” Lopez-Garcia explains. 

“You find more or less everything in there.” Some studies have found genetic similarities between mitochondria and an order of alphaproteobacterial symbionts known as Rickettsiales, but other, free-living candidates have also emerged.

The question of where on the alphaproteobacteria family tree the mitochondrial ancestor fell has pestered study coauthor Thijs Ettema throughout his scientific career. “Now, with all the available data from all these new lineages in all sorts of environments, we thought we should just do one bold approach and see where this ends up,” says Ettema, an evolutionary biologist at Uppsala University in Sweden.

Much of the genomic data he and colleagues used in their analysis came from the Tara Oceans dataset, which includes metagenomic sequences from microbes in ocean waters sampled from various depths. “For reasons that are not extremely clear . . . it seems that oceanic waters are extremely enriched for Alphaproteobacteria, and not just one species—it seems to be a whole array,” Ettema explains. The datasets were “good and deep enough to make an effort to reconstruct near-complete genomes.”

DIY DNA Tinkering...,

NYTimes  |  If nefarious biohackers were to create a biological weapon from scratch — a killer that would bounce from host to host to host, capable of reaching millions of people, unrestrained by time or distance — they would probably begin with some online shopping.

A site called Science Exchange, for example, serves as a Craigslist for DNA, a commercial ecosystem connecting almost anyone with online access and a valid credit card to companies that sell cloned DNA fragments.

Mr. Gandall, the Stanford fellow, often buys such fragments — benign ones. But the workarounds for someone with ill intent, he said, might not be hard to figure out.

Biohackers will soon be able to forgo these companies altogether with an all-in-one desktop genome printer: a device much like an inkjet printer that employs the letters AGTC — genetic base pairs — instead of the color model CMYK.

A similar device already exists for institutional labs, called BioXp 3200, which sells for about $65,000. But at-home biohackers can start with DNA Playground from Amino Labs, an Easy Bake genetic oven that costs less than an iPad, or The Odin’s Crispr gene-editing kit for $159.

Tools like these may be threatening in the wrong hands, but they also helped Mr. Gandall start a promising career.

At age 11, he picked up a virology textbook at a church book fair. Before he was old enough for a driver’s permit, he was urging his mother to shuttle him to a research job at the University of California, Irvine.

He began dressing exclusively in red polo shirts to avoid the distraction of choosing outfits. He doodled through high school — correcting biology teachers — and was kicked out of a local science fair for what was deemed reckless home-brew genetic engineering.

Mr. Gandall barely earned a high-school diploma, he said, and was rebuffed by almost every college he applied to — but later gained a bioengineering position at Stanford University.

“Pretty ironic, after they rejected me as a student,” he said.

He moved to East Palo Alto — with 14 red polo shirts — into a house with three nonbiologists, who don’t much notice that DNA is cloned in the corner of his bedroom.

His mission at Stanford is to build a body of genetic material for public use. To his fellow biohackers, it’s a noble endeavor.

To biosecurity experts, it’s tossing ammunition into trigger-happy hands.

“There are really only two things that could wipe 30 million people off of the planet: a nuclear weapon, or a biological one,” said Lawrence O. Gostin, an adviser on pandemic influenza preparedness to the World Health Organization.

“Somehow, the U.S. government fears and prepares for the former, but not remotely for the latter. It baffles me.”

Why BeeDeeist Racetardism Maintains Its Hold On AltRightwing Imagination

Guardian  |  The recent revival of ideas about race and IQ began with a seemingly benign scientific observation. In 2005, Steven Pinker, one of the world’s most prominent evolutionary psychologists, began promoting the view that Ashkenazi Jews are innately particularly intelligent – first in a lecture to a Jewish studies institute, then in a lengthy article in the liberal American magazine The New Republic the following year. This claim has long been the smiling face of race science; if it is true that Jews are naturally more intelligent, then it’s only logical to say that others are naturally less so.

The background to Pinker’s essay was a 2005 paper entitled “Natural history of Ashkenazi intelligence”, written by a trio of anthropologists at the University of Utah. In their 2005 paper, the anthropologists argued that high IQ scores among Ashkenazi Jews indicated that they evolved to be smarter than anyone else (including other groups of Jews).

This evolutionary development supposedly took root between 800 and 1650 AD, when Ashkenazis, who primarily lived in Europe, were pushed by antisemitism into money-lending, which was stigmatised among Christians. This rapid evolution was possible, the paper argued, in part because the practice of not marrying outside the Jewish community meant a “very low inward gene flow”. This was also a factor behind the disproportionate prevalence in Ashkenazi Jews of genetic diseases such as Tay-Sachs and Gaucher’s, which the researchers claimed were a byproduct of natural selection for higher intelligence; those carrying the gene variants, or alleles, for these diseases were said to be smarter than the rest.

Pinker followed this logic in his New Republic article, and elsewhere described the Ashkenazi paper as “thorough and well-argued”. He went on to castigate those who doubted the scientific value of talking about genetic differences between races, and claimed that “personality traits are measurable, heritable within a group and slightly different, on average, between groups”.

In subsequent years, Nicholas Wade, Charles Murray, Richard Lynn, the increasingly popular Canadian psychologist Jordan Peterson and others have all piled in on the Jewish intelligence thesis, using it as ballast for their views that different population groups inherit different mental capacities. Another member of this chorus is the journalist Andrew Sullivan, who was one of the loudest cheerleaders for The Bell Curve in 1994, featuring it prominently in The New Republic, which he edited at the time. He returned to the fray in 2011, using his popular blog, The Dish, to promote the view that population groups had different innate potentials when it came to intelligence.

Sullivan noted that the differences between Ashkenazi and Sephardic Jews were “striking in the data”. It was a prime example of the rhetoric of race science, whose proponents love to claim that they are honouring the data, not political commitments. The far right has even rebranded race science with an alternative name that sounds like it was taken straight from the pages of a university course catalogue: “human biodiversity”.

A common theme in the rhetoric of race science is that its opponents are guilty of wishful thinking about the nature of human equality. “The IQ literature reveals that which no one would want to be the case,” Peterson told Molyneux on his YouTube show recently. Even the prominent social scientist Jonathan Haidt has criticised liberals as “IQ deniers”, who reject the truth of inherited IQ difference between groups because of a misguided commitment to the idea that social outcomes depend entirely on nurture, and are therefore mutable.

Defenders of race science claim they are simply describing the facts as they are – and the truth isn’t always comfortable. “We remain the same species, just as a poodle and a beagle are of the same species,” Sullivan wrote in 2013. “But poodles, in general, are smarter than beagles, and beagles have a much better sense of smell.”

---

The race “science” that has re-emerged into public discourse today – whether in the form of outright racism against black people, or supposedly friendlier claims of Ashkenazis’ superior intelligence – usually involves at least one of three claims, each of which has no grounding in scientific fact.

Silly Peasants, Open Facebook Got NOTHING On Open "Consumer" DNA...,

NYTimes |  The California police had the Golden State Killer’s DNA and recently found an unusually well-preserved sample from one of the crime scenes. The problem was finding a match.

But these days DNA is stored in many places, and a near-match ultimately was found in a genealogy website beloved by hobbyists called GEDmatch, created by two volunteers in 2011.

Anyone can set up a free profile on GEDmatch. Many customers upload to the site DNA profiles they have already generated on larger commercial sites like 23andMe.

The detectives in the Golden State Killer case uploaded the suspect’s DNA sample. But they would have had to check a box online certifying that the DNA was their own or belonged to someone for whom they were legal guardians, or that they had “obtained authorization” to upload the sample.

“The purpose was to make these connections and to find these relatives,” said Blaine Bettinger, a lawyer affiliated with GEDmatch. “It was not intended to be used by law enforcement to identify suspects of crimes.”

But joining for that purpose does not technically violate site policy, he added.

Erin Murphy, a law professor at New York University and expert on DNA searches, said that using a fake identity might raise questions about the legality of the evidence.

The matches found in GEDmatch were to relatives of the suspect, not the suspect himself.

Since the site provides family trees, detectives also were able to look for relatives who might not have uploaded genetic data to the site themselves. 

What Does Responsibility Have To Do With Reproduction?

nursingclio |  Genetic counseling, as the previous two posts in this series suggested, has a lot to offer for navigating the tricky decisions things like prenatal testing and preimplantation genetic diagnosis raise. Well, in this post I’d like to make things a little more complicated. Enter the sheer messiness of history. I still believe genetic counseling is the best approach we have right now for helping prospective parents with hard choices, but it has a complicated — and not so distant — past that continues to shape counselors’ ways of interacting with clients and their decisions.

A LITTLE REVIEW

In the first post I shared a little bit of the history of genetic counseling in the United States and gave some examples of how, today, it can help prospective parents understand why they’re being tested and what those tests might mean. The second post discussed the history of blame and disability more broadly and introduced the fact that ideas about what disability means have changed over time — often significantly.

I’ve argued that genetic counseling has the potential to address feelings of blame, guilt, and confusion in the face of genetic testing results. Further, it can help answer questions like: What will life actually be like for parents and their children? What do genetic tests say and what don’t they say? What are the options after having a test?

My optimism about genetic counseling, evident in these two posts, is tempered by the fact that it has a complex and challenging past with origins in eugenics ideology that have influenced the way counseling is provided today. In a sense what I’m suggesting is that genetic counseling still has a lot of issues that need to be talked about and worked on, but that it’s way better than nothing.

Lets take a look at what I mean about how eugenic ideas shaped genetic counseling.

EUGENIC BEGINNINGS

Most of the first genetic counselors in the 1940s, 1950s, and 1960s were human geneticists, but the origins of human genetics lay in eugenics. Early genetic counselors identified self-proclaimed eugenicists like Charles Davenport, founder of the Eugenics Record Office at Cold Spring Harbor — one of the nation’s leading eugenics institutions between 1910 and the 1930s — as some of the first human geneticists in the United States. And four of the first five presidents of the American Society of Human Genetics, founded in 1948, were also board members of the American Eugenics Society.[1] Human geneticists tried to distance themselves from aspects of the traditional eugenics movement, particularly its racial prejudices and some of its scientific methods, but were still concerned about the eugenic effects of their work. They worried about what effect their counseling might have on the population as a whole.

Try? Been Doing It For A Minute, Consequences Be Damned...,

gizmodo |  Imagine a scenario, perhaps a few years from now, in which Canada decides to release thousands of mosquitoes genetically modified to fight the spread of a devastating mosquito-borne illness. While Canada has deemed these lab-made mosquitoes ethical, legal and safe for both humans and the environment, the US has not. Months later, by accident and circumstance, the engineered skeeters show up across the border. The laws of one land, suddenly, have become the rule of another.

If modern science can can defy the boundaries of borders, who exactly should be charged with deciding what science to unleash upon the world?

A version of this hypothetical scenario is already unfolding in the UK. Last year, the British government gave scientists the green light to genetically engineer human embryos. But in the US and most other nations, this possibility is still both illegal and morally fraught. Opponents to the practice argue that it risks opening up a Pandora’s Box of designer babies and genetically engineered super-humans. Even many more neutral voices argue that the technology demands further scrutiny.

And yet, the UK, at the vanguard of genetic engineering human beings, has already opened that box. In 2015, the British government approved the use of a controversial gene-editing technology to stop devastating mitochondrial diseases from being passed on from mothers to their future children. And last February, the UK granted the first license in the world to edit healthy human embryos for research. Recently, a Newsweek headline asked whether the scientists of this small island nation are in fact deciding the fate of all of humanity. It is a pretty good question.

This alarming ethical conundrum has not escaped the notice of global governments. A National Intelligence Council report released this month concluded that “genome editing and human enhancement” are “likely to pose some of the most contentious values questions in the coming decades.” Advancements in these arenas, the report said, “will affect relations between states.”

American Nations As Revealed In Identity By Descent (IBD) Networks

medium  |  Earlier this summer, I presented the American Nations: the eleven regional cultures that comprise the United States and North America. Their existence explains much about our history, our constitutional arrangements, and, indeed, our political fissures — past and present. If you have any ancestors who were living in North America prior to the Civil War, the existence of these rival nations is likely reflected in parts of your family tree and, according to a recent study published in Nature Communications, may very well have left a mark on your DNA.

I couldn’t miss this study, because shortly after it came out, readers of my 2011 book, American Nations: A History of the Eleven Rival Regional Cultures of North America, were stuffing my inbox and flooding my social media feeds with it. A glance at the thumbnail illustration that accompanied the study made it clear why: Unbeknownst to the scientists who’d written the paper, the map depicting the key results of their research on the patterns of genetic variation in North America over time and space mirrored the American Nations map to an uncanny degree.

Here they are for comparison:

Clustering of 770,000 genomes reveals post-colonial population structure of North america. Nature Communications 8 (2017)

This is remarkable because the American Nations paradigm is resolutely not about genetics or genealogy. Rather, it’s built on the late cultural geographer Wilbur ZeFrolinsky’s Doctrine of First Effective Settlement, which argues that when a “new” society is settled, the cultural characteristics of the initial settlement group will have a lasting and outsized effect on the future trajectory of that society — even if their numbers were very small and those of later immigrants of different origins were very large. These lasting characteristics, which inform the dominant culture of entire regions of North America, are passed down culturally, not genetically, which explains why the Dutch-settled area around New York City still has obvious and distinct characteristics inherited from Golden Age Amsterdam, even though the portion of people there reporting Dutch ancestry to census takers is a vanishingly small 0.2 percent. Culture is learned, not inherited.

And yet the Nature study — powered by the enormous cross-referenced genomics and genealogy databases of Ancestry.com — reveals that the regional cultures have left a significant genetic imprint as well. That’s because members of a regional culture tended to mate with one another, rather than with people from rival areas, even when those rivals lived nearby, in the very same colony or state.

“Who we are today — the genetics of Americans all over the place — is the result of all kinds of cycles of reproductive isolation and the release of that isolation,” says Catherine A. Ball, a geneticist and the chief scientific officer at Ancestry who oversees the company’s DNA work. “Who your mates would be was linked to geography, politics, religion, war, and all of that is showing today in people walking on the streets and who they are related to.”

Ball wasn’t familiar with American Nations before I spoke with her, but the results show that the boundaries of the regional cultures were very real when it came to human reproduction, creating reproductive clusters centuries ago that geneticists have been able to recreate through the examination of nearly a million living Americans’ DNA.

Ban Baby-Making Unless Parents Are Licensed

ieet  |  For the sake of the children, let’s control human breeding. No one should be permitted to reproduce until they pass a battery of tests.

Does that proposal enrage you? Go ahead, hate me. Call me vile names like “Neo-Nazi-Elitist-Baby-Killing-Totalitarian-Sicko.” Or simply “Eugenicist.” I don’t care. I know I’m right. 

It’s blatantly clear that 15-year-old intoxicated half-wits can easily spawn, but should they? Hell no. Let’s control human breeding, please. Let’s keep babies away from buffoons, and let’s test fetuses meticulously to guarantee healthy infants. No one should be permitted to reproduce unless and until they pass a battery of tests. 

Philosophers, psychologists, and social workers have advanced this idea for 30+ years, notably Hugh LaFollette in his seminal essay, “Licensing Parents” (1980), and Peg Tittle, editor of Should Parents Be Licensed? (2004). Their suggested reform—based on humanitarian concerns for the rights of children—is always booed down hysterically with the shrill vocabulary that I listed above. 

But the reformers are right. Completely. Ethically. I agree with Joseph Fletcher, who notes, “It is depressing…to realize that most people are accidents,” and with George Schedler, who states, “Society has a duty to ensure that infants are born free of avoidable defects.”

Traditionalists regard pregnancy and parenting as a natural right that should never be curtailed. But what’s the result of this laissez-faire attitude? Catastrophic suffering. Millions of children born disadvantaged, crippled in childhood, destroyed in adolescence. Procreation cannot be classified as a self-indulgent privilege—it needs to be viewed as a life-and-death responsibility. 

Look at it this way: adoption centers don’t allow knuckleheads to walk out with a child; they maintain standards that we should apply to every wannabe parent.

Below I’ve compiled a list of deplorable situations caused by flawed individuals who should not be allowed to impregnate, gestate, reproduce, and parent because they’re mentally, physically, emotionally, or genetically unsuitable for the ambitious task.

Viruses Modulate the Function and Evolution of All Living Things

NYTimes |  High in the Sierra Nevada mountains of Spain, an international team of researchers set out four buckets to gather a shower of viruses falling from the sky.

Scientists have surmised there is a stream of viruses circling the planet, above the planet’s weather systems but below the level of airline travel. Very little is known about this realm, and that’s why the number of deposited viruses stunned the team in Spain. Each day, they calculated, some 800 million viruses cascade onto every square meter of the planet.

Most of the globe-trotting viruses are swept into the air by sea spray, and lesser numbers arrive in dust storms.

“Unimpeded by friction with the surface of the Earth, you can travel great distances, and so intercontinental travel is quite easy” for viruses, said Curtis Suttle, a marine virologist at the University of British Columbia. “It wouldn’t be unusual to find things swept up in Africa being deposited in North America.”

The study by Dr. Suttle and his colleagues, published earlier this year in the International Society of Microbial Ecology Journal, was the first to count the number of viruses falling onto the planet. The research, though, is not designed to study influenza or other illnesses, but to get a better sense of the “virosphere,” the world of viruses on the planet.

Generally it’s assumed these viruses originate on the planet and are swept upward, but some researchers theorize that viruses actually may originate in the atmosphere. (There is a small group of researchers who believe viruses may even have come here from outer space, an idea known as panspermia.)

Whatever the case, viruses are the most abundant entities on the planet by far. While Dr. Suttle’s team found hundreds of millions of viruses in a square meter, they counted tens of millions of bacteria in the same space.

Mostly thought of as infectious agents, viruses are much more than that. It’s hard to overstate the central role that viruses play in the world: They’re essential to everything from our immune system to our gut microbiome, to the ecosystems on land and sea, to climate regulation and the evolution of all species. Viruses contain a vast diverse array of unknown genes — and spread them to other species.

Last year, three experts called for a new initiative to better understand viral ecology, especially as the planet changes. “Viruses modulate the function and evolution of all living things,” wrote Matthew B. Sullivan of Ohio State, Joshua Weitz of Georgia Tech, and Steven W. Wilhelm of the University of Tennessee. “But to what extent remains a mystery.”

Nature Bats Last: Bacterium "Figures Out" How to Eat Plastic

theguardian |  Scientists have created a mutant enzyme that breaks down plastic drinks bottles – by accident. The breakthrough could help solve the global plastic pollution crisis by enabling for the first time the full recycling of bottles.

The new research was spurred by the discovery in 2016 of the first bacterium that had naturally evolved to eat plastic, at a waste dump in Japan. Scientists have now revealed the detailed structure of the crucial enzyme produced by the bug.

The international team then tweaked the enzyme to see how it had evolved, but tests showed they had inadvertently made the molecule even better at breaking down the PET (polyethylene terephthalate) plastic used for soft drink bottles. “What actually turned out was we improved the enzyme, which was a bit of a shock,” said Prof John McGeehan, at the University of Portsmouth, UK, who led the research. “It’s great and a real finding.”

The mutant enzyme takes a few days to start breaking down the plastic – far faster than the centuries it takes in the oceans. But the researchers are optimistic this can be speeded up even further and become a viable large-scale process.

“What we are hoping to do is use this enzyme to turn this plastic back into its original components, so we can literally recycle it back to plastic,” said McGeehan. “It means we won’t need to dig up any more oil and, fundamentally, it should reduce the amount of plastic in the environment.”

About 1m plastic bottles are sold each minute around the globe and, with just 14% recycled, many end up in the oceans where they have polluted even the remotest parts, harming marine life and potentially people who eat seafood. “It is incredibly resistant to degradation. Some of those images are horrific,” said McGeehan. “It is one of these wonder materials that has been made a little bit too well.”

However, currently even those bottles that are recycled can only be turned into opaque fibres for clothing or carpets. The new enzyme indicates a way to recycle clear plastic bottles back into clear plastic bottles, which could slash the need to produce new plastic.

“You are always up against the fact that oil is cheap, so virgin PET is cheap,” said McGeehan. “It is so easy for manufacturers to generate more of that stuff, rather than even try to recycle. But I believe there is a public driver here: perception is changing so much that companies are starting to look at how they can properly recycle these.”

Hush Now Bout Digital Tricknology..., Bill Gates Talkin Bout Gene-Editing For the 3rd World!!

foreignaffairs |  Today, more people are living healthy, productive lives than ever before. This good news may come as a surprise, but there is plenty of evidence for it. Since the early 1990s, global child mortality has been cut in half. There have been massive reductions in cases of tuberculosis, malaria, and HIV/AIDS. The incidence of polio has decreased by 99 percent, bringing the world to the verge of eradicating a major infectious disease, a feat humanity has accomplished only once before, with smallpox. The proportion of the world’s population in extreme poverty, defined by the World Bank as living on less than $1.90 per day, has fallen from 35 percent to about 11 percent.

Continued progress is not inevitable, however, and a great deal of unnecessary suffering and inequity remains. By the end of this year, five million children under the age of five will have died—mostly in poor countries and mostly from preventable causes. Hundreds of millions of other children will continue to suffer needlessly from diseases and malnutrition that can cause lifelong cognitive and physical disabilities. And more than 750 million people—mostly rural farm families in sub-Saharan Africa and South Asia—still live in extreme poverty, according to World Bank estimates. The women and girls among them, in particular, are denied economic opportunity.

Some of the remaining suffering can be eased by continuing to fund the development assistance programs and multilateral partnerships that are known to work. These efforts can help sustain progress, especially as the world gets better at using data to help guide the allocation of resources. But ultimately, eliminating the most persistent diseases and causes of poverty will require scientific discovery and technological innovations.

That includes CRISPR and other technologies for targeted gene editing. Over the next decade, gene editing could help humanity overcome some of the biggest and most persistent challenges in global health and development. The technology is making it much easier for scientists to discover better diagnostics, treatments, and other tools to fight diseases that still kill and disable millions of people every year, primarily the poor. It is also accelerating research that could help end extreme poverty by enabling millions of farmers in the developing world to grow crops and raise livestock that are more productive, more nutritious, and hardier. New technologies are often met with skepticism. But if the world is to continue the remarkable progress of the past few decades, it is vital that scientists, subject to safety and ethics guidelines, be encouraged to continue taking advantage of such promising tools as CRISPR.

We Won't Engineer Superhumans Any Time Soon...,

aeon |  A paper published in Nature Genetics in 2017 reported that, after analysing tens of thousands of genomes, scientists had tied 52 genes to human intelligence, though no single variant contributed more than a tiny fraction of a single percentage point to intelligence. As the senior author of the study Danielle Posthuma, a statistical geneticist at the Vrije Universiteit (VU) Amsterdam and VU University Medical Center Amsterdam, told The New York Times, ‘there’s a long way to go’ before scientists can actually predict intelligence using genetics. Even so, it is easy to imagine social impacts that are unsettling: students stapling their genome sequencing results to their college applications; potential employers mining genetic data for candidates; in-vitro fertilisation clinics promising IQ boosts using powerful new tools such as the genome-editing system CRISPR-Cas9.

Some people are already signing on for this new world. Philosophers such as John Harris of the University of Manchester and Julian Savulescu of the University of Oxford have argued that we will have a duty to manipulate the genetic code of our future children, a concept Savulescu termed ‘procreative beneficence’. The field has extended the term ‘parental neglect’ to ‘genetic neglect’, suggesting that if we don’t use genetic engineering or cognitive enhancement to improve our children when we can, it’s a form of abuse. Others, like David Correia, who teaches American Studies at the University of New Mexico, envisions dystopian outcomes, where the wealthy use genetic engineering to translate power from the social sphere into the enduring code of the genome itself.

Such concerns are longstanding; the public has been on guard about altering the genetics of intelligence at least since scientists invented recombinant DNA. As long ago as the 1970s, David Baltimore, who won a Nobel Prize, questioned whether his pioneering work might show that ‘the differences between people are genetic differences, not environmental differences’.

I say, dream on. As it turns out, genes contribute to intelligence, but only broadly, and with subtle effect. Genes interact in complex relationships to create neural systems that might be impossible to reverse-engineer. In fact, computational scientists who want to understand how genes interact to create optimal networks have come up against the kind of hard limits suggested by the so-called travelling salesperson problem. In the words of the theoretical biologist Stuart Kauffman in The Origins of Order (1993): ‘The task is to begin at one of N cities, travel in turn to each city, and return to the initial city by the shortest total route. This problem, so remarkably simple to state, is extremely difficult.’ Evolution locks in, early on, some models of what works, and hammers out refining solutions over millennia, but the best computer junkies can do to draw up an optimal biological network, given some input, is to use heuristics, which are shorthand solutions. The complexity rises to a new level, especially since proteins and cells interact at higher dimensions. Importantly, genetics research is not about to diagnose, treat or eradicate mental disorders, or be used to explain the complex interactions that give rise to intelligence. We won’t engineer superhumans any time soon.

Social Inequality Leaves An Outsized Genetic Mark

nautil.us |  In humans, the profound biological differences that exist between the sexes mean that a single male is physically capable of having far more children than is a single female. Women carry unborn children for nine months and often nurse them for several years prior to having additional children.¹ Men, meanwhile, are able to procreate while investing far less time in the bearing and early rearing of each child. So it is that, as measured by the contribution to the next generation, powerful men have the potential to have a far greater impact than powerful women, and we can see this in genetic data.

The great variability among males in the number of offspring produced means that by searching for genomic signatures of past variability in the number of children men have had, we can obtain genetic insights into the degree of social inequality in society as a whole, and not just between males and females. An extraordinary example of this is provided by the inequality in the number of male offspring that seems to have characterized the empire established by Genghis Khan, who ruled lands stretching from China to the Caspian Sea. After his death in 1227, his successors, including several of his sons and grandsons, extended the Mongol Empire even farther—to Korea in the east, to central Europe in the west, and to Tibet in the south. The Mongols maintained rested horses at strategically spaced posts, allowing rapid communication across their more than 8,000-kilometer span of territory. The united Mongol Empire was short-lived—for example, the Yüan dynasty they established in China fell in 1368—but their rise to power nevertheless allowed them to leave an extraordinary genetic impact on Eurasia.²

A 2003 study led by Chris Tyler-Smith showed how a relatively small number of powerful males living during the Mongol period succeeded in having an outsize impact on the billions of people living in East Eurasia today.³ His study of Y chromosomes suggested that one single male who lived around the time of the Mongols left many tens of millions of direct male-line descendants across the territory that Mongols occupied. The evidence is that about 8 percent of the male population in the lands the Mongol Empire once occupied share a characteristic Y-chromosome sequence and a cluster of similar sequences differing by just a few mutations. Tyler-Smith and his colleagues called this a “Star Cluster” to reflect the idea of a single ancestor with many descendants, and estimated the date of the founder of this lineage to be 1,300 to 700 years ago based on the estimated rate of accumulation of mutations on the Y chromosome. The date coincides with that of Genghis Khan, suggesting that this single successful Y chromosome may have been his.

Star Clusters are not limited to Asia. Geneticist Daniel Bradley and his colleagues identified a Y-chromosome type that is present in 2 to 3 million people today and derives from an ancestor who lived around 1,500 years ago.⁴ It is especially common in people with the last name O’Donnell, who descend from one of the most powerful royal families of medieval Ireland, the “Descendants of Niall”—referring to Niall of the Nine Hostages, a legendary warlord from the earliest period of medieval Irish history. If Niall was real, he would have lived at about the right time to match the Y-chromosome ancestor.

Star Clusters capture the imagination because they can be tied, albeit speculatively, to historical figures. But the more important point is that Star Cluster analysis provides insights about shifts in social structure that occurred in the deep past that are difficult to get information about in other ways. This is therefore one area in which Y-chromosome and mitochondrial DNA analysis can be instructive, even without whole-genome data. For example, a perennial debate among historians is the extent to which the human past is shaped by single individuals whose actions leave a disproportionate impact on subsequent generations. Star Cluster analysis provides objective information about the importance of extreme inequalities in power at different points in the past.

Race Is A Social Construct, But I'm Desperate To Make It A Genetic One...,

NYTimes |  In 1942, the anthropologist Ashley Montagu published “Man’s Most Dangerous Myth: The Fallacy of Race,” an influential book that argued that race is a social concept with no genetic basis. A classic example often cited is the inconsistent definition of “black.” In the United States, historically, a person is “black” if he has any sub-Saharan African ancestry; in Brazil, a person is not “black” if he is known to have any European ancestry. If “black” refers to different people in different contexts, how can there be any genetic basis to it?

Beginning in 1972, genetic findings began to be incorporated into this argument. That year, the geneticist Richard Lewontin published an important study of variation in protein types in blood. He grouped the human populations he analyzed into seven “races” — West Eurasians, Africans, East Asians, South Asians, Native Americans, Oceanians and Australians — and found that around 85 percent of variation in the protein types could be accounted for by variation within populations and “races,” and only 15 percent by variation across them. To the extent that there was variation among humans, he concluded, most of it was because of “differences between individuals.”

In this way, a consensus was established that among human populations there are no differences large enough to support the concept of “biological race.” Instead, it was argued, race is a “social construct,” a way of categorizing people that changes over time and across countries.

It is true that race is a social construct. It is also true, as Dr. Lewontin wrote, that human populations “are remarkably similar to each other” from a genetic point of view.

But over the years this consensus has morphed, seemingly without questioning, into an orthodoxy. The orthodoxy maintains that the average genetic differences among people grouped according to today’s racial terms are so trivial when it comes to any meaningful biological traits that those differences can be ignored.

The orthodoxy goes further, holding that we should be anxious about any research into genetic differences among populations. The concern is that such research, no matter how well-intentioned, is located on a slippery slope that leads to the kinds of pseudoscientific arguments about biological difference that were used in the past to try to justify the slave trade, the eugenics movement and the Nazis’ murder of six million Jews.

I have deep sympathy for the concern that genetic discoveries could be misused to justify racism. But as a geneticist I also know that it is simply no longer possible to ignore average genetic differences among “races.”

Groundbreaking advances in DNA sequencing technology have been made over the last two decades. These advances enable us to measure with exquisite accuracy what fraction of an individual’s genetic ancestry traces back to, say, West Africa 500 years ago — before the mixing in the Americas of the West African and European gene pools that were almost completely isolated for the last 70,000 years. With the help of these tools, we are learning that while race may be a social construct, differences in genetic ancestry that happen to correlate to many of today’s racial constructs are real.

Luxturna Is An Apt Name For An $850,000 Drug...,

technologyreview |  The $850,000 price of a newly approved gene therapy for blindness stunned patient advocates, but the sticker shock could quickly wear off.

Many costly drugs need to be purchased year after year. But gene therapies are given only once, with potentially permanent effects.

Mark Trusheim, who directs MIT’s New Drug Development Paradigms program, says gene therapies are moving medicine from a model of “renting” treatments to one of “buying” long-term health improvements.

“The challenge is like going from being an apartment renter to a condo buyer and being shocked at [the] purchase price,” he says.

Philadelphia-based Spark Therapeutics said yesterday that it planned to charge $425,000 per eye for Luxturna, the first gene therapy for an inherited disease to reach the U.S. market.

David Mitchell, founder and president of the advocacy group Patients for Affordable Drugs, is concerned that the treatment will be out of reach for people with high-deductible health plans and would bankrupt those without insurance.

SMDH@Creepy Old Harelips Tryna Bust...,

CNN | What did Franks do, you ask? Let's let Franks tell you himself. Here's an excerpt from his statement announcing his resignation:

"Due to my familiarity and experience with the process of surrogacy, I clearly became insensitive as to how the discussion of such an intensely personal topic might affect others.

 

"I have recently learned that the Ethics Committee is reviewing an inquiry regarding my discussion of surrogacy with two previous female subordinates, making each feel uncomfortable. I deeply regret that my discussion of this option and process in the workplace caused distress."

 

Um, what?

 

So, here's how the Franks statement -- in meticulous detail -- casts how this whole thing came about:

1. He and his wife had problems conceiving and carrying a baby to term. (Franks notes in the statement his wife had three miscarriages.)

2. Eventually they found a woman to be a surrogate. That woman gave birth to twins.

3. He and his wife wanted more children. So did their kids. ("We continued to have a desire to have at least one additional sibling, for which our children had made repeated requests," writes Franks.)

4. He discussed the possibility of surrogacy with two women who worked for him.

 

Simple enough!

 

Peasants Will Be Matched and Bred Via eHarmony and 23andMe...,

DailyMail |   Location-based apps like Tinder have transformed the dating world.

But how will technology help us find Mr or Mrs Right 25 years from now?

According to a new report, the future of romance could lie in virtual reality, wearable technology and DNA matching.

These technologies are set to take the pain out of dating by saving single people time and effort, while giving them better matches, according to the research.

Students from Imperial College London were commissioned by relationship website eHarmony.co.uk to produce a report on what online dating and relationships could look like by 2040.

They put together a report based on analysis of how people's lifestyle habits have evolved over the past 100 years.