Showing posts sorted by relevance for query genomics. Sort by date Show all posts
Showing posts sorted by relevance for query genomics. Sort by date Show all posts

Saturday, July 11, 2015

synthetic genomics and genome engineering rewriting the blueprint of life


genomebiology |  Biology is now undergoing a rapid transition from the age of deciphering DNA sequence information of the genomes of biological species to the age of synthetic genomes. Scientists hope to gain a thorough mastery of and deeper insights into biological systems by rewriting the genome, the blueprint of life. This transition demands a whole new level of biological understanding, which we currently lack. This knowledge, however, could be obtained through synthetic genomics and genome engineering, albeit on a trial and error basis, by redesigning and building naturally occurring bacterial and eukaryotic genomes whose sequences are known. 

Synthetic genomics arguably began with the report from Khorana’s laboratory in 1970 of the total synthesis of the first gene, encoding an artificial yeast alanine tRNA, from deoxyribonucleotides. Since then, rapid advances in DNA synthesis techniques, especially over the past decade, have made it possible to engineer biochemical pathways, assemble bacterial genomes and even to construct a synthetic organism [1]–[11]. Genome editing approaches for genome-wide scale alteration that are not based on total synthesis of the genome are also being pursued and have proved powerful; for example, in the production of a reduced-size genome version of Escherichia coli[4] and engineering of bacterial genomes to include many different changes simultaneously [8]. 

Progress has also been made in synthetic genomics for eukaryotes. Our group has embarked on the design and total synthesis of a novel eukaryotic genome structure - using the well-known model eukaryote Saccharomyces cerevisiae as the basis for a designer genome, known as ‘Sc2.0’. The availability of a fully synthetic genome will allow direct testing of evolutionary questions that are not otherwise approachable. Sc2.0 could also play an important practical role, since yeasts are the pre-eminent organisms for industrial fermentations, with a wide variety of practical uses, including production of therapeutic proteins, vaccines and small molecules through classical and well-developed industrial fermentation technologies. 

This article reviews the current status of synthetic genomics, starting with a historical perspective that highlights the key milestones in the field (Fig. 1) and then continuing with a particular emphasis on the total synthesis of the first functional designer eukaryotic (yeast) chromosome, synIII, and the Sc2.0 Project. Genome engineering using nuclease-based genome editing tools such as zinc finger nucleases, transcription activator-like effector nucleases and RNA-guided CRISPR-Cas9 is not within the scope of this minireview (Box 1). Recent advances in gene synthesis and assembly methods that have accelerated the genome synthesis efforts are discussed elsewhere [12].

Thursday, October 29, 2009

genomics richard stallman?

The Scientist | In the future, Hubbard says that gene-prediction programs need to get good enough that they can find genes without the aid of experimental data or comparative genome analyses to guide them. “Because that’s cheating,” he says. “For example, an RNA polymerase does not go and look at the mouse genome when it’s working out whether to transcribe a particular stretch of human sequence. But that’s what many of our algorithms do now.” Instead, he says that annotation programs should take an RNA polymerase–eye-view of the sequence, modeling the biology closely enough to accurately locate and assess the activity of genes. As we move into an era of personal genomics, such an approach will be necessary for predicting the effect that a certain SNP variant might have on gene function. He and his team have had some early success, producing a transcription start-site predictor that nails about half the genes in a genome sequence with very few false positives.

Hubbard also spends quite a bit of time working on issues of open access and the economics of innovation. “Governments are spending all this money for research and then not maximizing its value because they’re not investing enough in making sure people can access and reuse that data,” says Hubbard, who has discussed these issues at meetings of the Organisation for Economic Cooperation and Development (OECD) and the World Health Organization. Much of this work he does in his spare time. “Other people go fishing,” laughs Birney. “Tim likes to reform international patent law and go to UN conferences to discuss how open-access agreements should be arranged to maximize the way science gets translated into meaningful outcomes.”

Those outcomes, of course, include potential improvements in the diagnosis and treatment of disease, which makes the issue more urgent and more fraught. “If you look at the health implications of all the work being done in genomics, the opportunities are tremendous and the obstacles are staggering—and a lot of those are political,” says Haussler. “I just have the ultimate respect for Tim, as he’s willing to move through those political hurdles and try to get things to happen.”

“In a way, Tim’s contribution to the scientific endeavor is a very interesting one and rather different from most scientists,” says EBI director Janet Thornton. “Although he’s had a hand in producing many of the big genome publications, his unique input lies in his broad perspective, his sense of fairness, and his openness to new ideas. His diplomatic efforts have really been fundamental in making these large-scale, collaborative genomics projects work—and in making the data available so that the science can be put to good use for biology and medicine around the world.”

“A lot of things can be done by one person with a computer,” adds Flicek. “If the Internet age taught us anything, it’s taught us that.”

Thursday, December 05, 2013

if it doesn't predict disease or illuminate neurodiversity, who cares?

This Dillweed Here

discover | It’s been a busy few days in the world of personal genomics. By coincidence I have a coauthored comment in Genome Biology out, Rumors of the death of consumer genomics are greatly exaggerated (it was written and submitted a while back). If you haven’t, please read the FDA’s letter, and 23andMe’s response, as much as there is one right now. Since Slate ran my piece on Monday a lot of people have offered smart, and more well informed, takes. On the one hand you have someone like Alex Tabarrok, with “Our DNA, Our Selves”, which is close to a libertarian cri de coeur. Then you have cases like Christine Gorman, “FDA Was Right to Block 23andMe”. It will be no surprise that I am much closer to Tabarrok than I am to Gorman (she doesn’t even seem to be aware that 23andMe offers a genotyping, not sequencing, service, though fuzziness on the details doesn’t discourage strong opinions from her). An interesting aspect is that many who are not deeply in the technical weeds of the issue are exhibiting politicized responses. I’ve noticed this on Facebook, where some seem to think that 23andMe and the Tea Party have something to do with each other, and the Obama administration and the FDA are basically stand-ins. In other words, some liberals are seeing this dispute as one of those attempts to evade government regulation, something they support on prior grounds. Though Tabarrok is more well informed than the average person (his wife is a biologist), there are others from the right-wing who are taking 23andMe’s side on normative grounds as well. Ultimately I’m not interested in this this argument, because it’s not going to have any significant lasting power. No one will remember in 20 years. As I implied in my Slate piece 23andMe the company now is less interesting than personal genomics the industry sector in the future. Over the long term I’m optimistic that it will evolve into a field which impacts our lives broadly. Nothing the United States government can do will change that.

Yet tunneling down to the level of 23andMe’s specific issues with the regulatory process, there is the reality that it has to deal with the US government and the FDA, no matter what the details of its science are. It’s a profit-making firm. Matt Herper has a judicious take on this, 23andStupid: Is 23andMe Self-Destructing? I don’t have any “inside” information, so I’m not going to offer the hypothesis that this is part of some grand master plan by Anne Wojcicki. I hope it is, but that’s because I want 23andMe to continue to subsidize genotyping services (I’ve heard that though 23andMe owns the machines, the typing is done by LabCorp. And last I checked the $99 upfront cost is a major loss leader; they’re paying you to get typed). I’m afraid that they goofed here, and miscalculated. As I said above, it won’t make a major difference in the long run, but I have many friends who were waiting until this Christmas to purchase kits from 23andMe.

Then there are “the scientists,” or perhaps more precisely the genoscenti. Matt Herper stated to the effect that the genoscenti have libertarian tendencies, and I objected. In part because I am someone who has conservative and/or libertarian tendencies, and I’m pretty well aware that I’m politically out of step with most individuals deeply involved in genetics, who are at most libertarian-leaning moderate liberals, and more often conventional liberal Democrats. Michael Eisen has a well thought out post, FDA vs. 23andMe: How do we want genetic testing to be regulated? Eisen doesn’t have a political ax to grind, and is probably representative of most working geneticists in the academy (he is on 23andMe’s board, but you should probably know that these things don’t mean that much). I may not know much about the FDA regulatory process, but like many immersed in genomics I’m well aware that many people talking about these issues don’t know much about the cutting edge of the modern science. Talk to any geneticist about conversations with medical doctors and genetic counselors, and they will usually express concern that these “professionals” and “gatekeepers” are often wrong, unclear, or confused, on many of the details. A concrete example, when a friend explained to a veteran genetic counselor how my wife used pedigree information combined with genomic data to infer that my daughter did not have an autosomally dominant condition, the counselor asserted that you can’t know if there were two recombination events within the gene, which might invalidate these inferences. Though my friend was suspicious, they did not say anything, because they were not a professional. As a matter of fact there just aren’t enough recombinations across the genome for an intra-genic event to be a likely occurrence (also, recombination likelihood is not uniformly distributed, and not necessarily independent, insofar as there may be suppression of very close events). And this was a very well informed genetic counselor.

Monday, October 22, 2007

Synthetic Genomics

The popular view in the British press; Imagine if the engineers of 18th-century Britain could have foreseen the consequences of industrialisation. If they had been warned that it would bring untold wealth and comfort to millions, but would also disrupt human communities, lead to a terrible escalation of war and huge environmental degradation, how then would they have weighed the massive and momentous consequences? And how are we going to? In a couple of decades we could have a nature to organise entirely as we like - the scientist Freeman Dyson suggested black-leaved forests for more efficient use of sunlight in an article on synbio in a recent New York Review of Books. We could be busy creating our own biodiversity to replace the one we will have lost. We might have a "new, improved nature" which is more efficient in meeting our needs and ensuring the survival of future generations: is that a threat or a promise of salvation? And who are we going to trust to make that judgment call?

The governance blueprint at the JCVI; Synthetic genomics combines methods for the chemical synthesis of DNA with computational techniques to design it. These methods allow scientists and engineers to construct genetic material that would be impossible or impractical to produce using more conventional biotechnological approaches. For example, using synthetic genomics it is possible to design and assemble chromosomes, genes and gene pathways, and even whole genomes.

Scientists foresee many potential positive applications including new pharmaceuticals, biologically produced (“green”) fuels, and the possibility of rapidly generating vaccines against emerging microbial diseases. However, as with many technologies, there is the potential for misuse and accidents.

Designing ways to impede malicious uses of the technology while at the same time not impeding, or even promoting beneficial ones, poses a number of policy challenges for all who wish to use or benefit from synthetic genomics. The report presents governance options that attempt to reduce security- and safety risks without imposing undue burdens on researchers, industry, or government.

Saturday, March 20, 2021

The SMART Healthcards Framework

unlimitedhangout |  The SMART Health Cards framework was developed by a team led by the chief architect of Microsoft Healthcare, Josh Mandel, who was previously the Health IT Ecosystem lead for Verily, formerly Google Life Sciences. Verily is currently heavily involved in COVID-19 testing throughout the United States, particularly in California, and links test recipients’ results to their Google accounts. Their other COVID-19 initiatives have been criticized due to still-unresolved privacy concerns, something that has also plagued several of Verily’s other efforts pre-COVID-19, including those involving Mandel.

Of particular concern is that Verily, and by extension Google, created Project Baseline, which has been collecting “actionable genetic information” with a focus on “population health” from participants since 2017. Yet, during the COVID-19 process, Project Baseline has become an important component of Verily’s COVID-19 testing efforts, raising the unsettling possibility that Verily has been obtaining Americans’ DNA data through its COVID-19 testing activities. While Verily has not addressed this possibility directly, it is worth noting that Google has been heavily involved in amassing genomic data for several years. For instance, in 2013, Google Genomics was founded with the goal of storing and analyzing DNA data on Google Cloud servers. Now known as Cloud Life Sciences, the Google subsidiary has since developed AI algorithms that can “build your genome sequence” and “identify all the mutations that an individual inherits from their parents.”

Google also has close ties with the best-known DNA testing companies in the United States, such as Ancestry.com. Ancestry, recently purchased by private-equity behemoth Blackstone, shares data with a secretive Google subsidiary that uses genomic data to develop lifespan-extending therapies. In addition, the wife of Google cofounder Sergey Brin, Anne Wojcicki, is the cofounder and CEO of DNA testing company 23andMe. Wojcicki is also the sister of the CEO of Google-owned YouTube, Susan Wojcicki.

Google and the majority of VCI’s backers—Microsoft, Salesforce, Cerner, Epic, the Mayo Clinic, and MITRE Corporation, Change Healthcare—are also prominent members of the MITRE-run COVID-19 Healthcare Coalition. Other members of that coalition include the CIA’s In-Q-Tel and the CIA-linked data-mining firm Palantir, as well as a myriad of health-care and health-record companies. The coalition fits well with the ambitions of Google and like-minded companies that have sought to gain access to troves of American health data under the guise of combatting COVID-19.

The COVID-19 Healthcare Coalition describes itself as a public-private partnership that has enabled “the critical infrastructure to enable collaboration and shared analytics” on COVID-19 through the sharing of health-care and COVID-19 data among members. That this coalition and VCI are intimately involved with MITRE Corporation is significant, given that MITRE is a well-known, yet secretive, contractor for the US government, specifically the CIA and other intelligence agencies, which has developed Orwellian surveillance and biometric technologies, including several now focused on COVID-19.

Just three days before the public announcement of VCI’s establishment, Microsoft Healthcare and Google’s Verily announced a partnership along with MIT and Harvard’s Broad Institute to share the companies’ cloud data and AI technologies with a “global network of more than 168,000 health and life sciences partners” to accelerate the Terra platform. Terra, originally developed by the Broad Institute and Verily, is an “open data ecosystem” focused on biomedical research, specifically the fields of cancer genomics, population genetics, and viral genomics. The biomedical data Terra amasses includes not only genetic data but also medical-imaging, biometric signals, and electronic health records. Google, through its partnership with the Pentagon, which was announced last September, has moved to utilize the analysis of such data in order to “predictively diagnose” diseases such as cancer and COVID-19. US military contractors, such as Advanced Technology International, have been developing wearables that would apply that AI-driven predictive diagnosis technology to COVID-19 diagnoses.

Sunday, October 27, 2013

back to stuff that matters - 4-D printing...,


foreignaffairs | In May 2010, the richest, most powerful man in biotechnology made a new creature. J. Craig Venter and his private-company team started with DNA and constructed a novel genetic sequence of more than one million coded bits of information known as nucleotides. Seven years earlier, Venter had been the first person in history to make a functioning creature from information. Looking at the strings of letters representing the DNA sequence for a virus called phi X174, which infects bacteria, he thought to himself, “I can assemble real DNA based on that computer information.” And so he did, creating a virus based on the phi X174 genomic code. He followed the same recipe later on to generate the DNA for his larger and more sophisticated creature. Venter and his team figured out how to make an artificial bacterial cell, inserted their man-made DNA genome inside, and watched as the organic life form they had synthesized moved, ate, breathed, and replicated itself.

As he was doing this, Venter tried to warn a largely oblivious humanity about what was coming. He cautioned in a 2009 interview, for example, that “we think once we do activate a genome that yes, it probably will impact people’s thinking about life.” Venter defined his new technology as “synthetic genomics,” which would “start in the computer in the digital world from digitized biology and make new DNA constructs for very specific purposes. . . . It can mean that as we learn the rules of life we will be able to develop robotics and computational systems that are self-learning systems.” “It’s the beginning of the new era of very rapid learning,” he continued. “There’s not a single aspect of human life that doesn’t have the potential to be totally transformed by these technologies in the future.”

Today, some call work such as Venter’s novel bacterial creation an example of “4-D printing.” 2-D printing is what we do everyday by hitting “print” on our keyboards, causing a hard copy of an article or the like to spew from our old-fashioned ink-printing devices. Manufacturers, architects, artists, and others are now doing 3-D printing, using computer-generated designs to command devices loaded with plastics, carbon, graphite, and even food materials to construct three-dimensional products. With 4-D printing, manufacturers take the next crucial step: self-assembly or self-replication. What begins as a human idea, hammered out intellectually on a computer, is then sent to a 3-D printer, resulting in a creation capable of making copies of and transforming itself. In solid materials, Skylar Tibbits of the Massachusetts Institute of Technology creates complex physical substances that he calls “programmable materials that build themselves.” Venter and hundreds of synthetic biologists argue that 4-D printing is best accomplished by making life using life’s own building blocks, DNA.

When Venter’s team first created the phi X174 viral genome, Venter commissioned a large analysis of the implications of synthetic genomics for national security and public health. The resulting report warned that two issues were impeding appropriate governance of the new science. The first problem was that work on synthetic biology, or synbio, had become so cheap and easy that its practitioners were no longer classically trained biologists. This meant that there were no shared assumptions regarding the new field’s ethics, professional standards, or safety. The second problem was that existing standards, in some cases regulated by government agencies in the United States and other developed countries, were a generation old, therefore outdated, and also largely unknown to many younger practitioners.

Venter’s team predicted that as the cost of synthetic biology continued to drop, interest in the field would increase, and the ethical and practical concerns it raised would come increasingly to the fore. They were even more prescient than they guessed. Combined with breakthroughs in another area of biology, “gain-of-function” (GOF) research, the synthetic genomics field has spawned a dizzying array of new possibilities, challenges, and national security threats. As the scientific community has started debating “human-directed evolution” and the merits of experiments that give relatively benign germs dangerous capacities for disease, the global bioterrorism and biosecurity establishment remains well behind the curve, mired in antiquated notions about what threats are important and how best to counter them. 

In the United States, Congress and the executive branch have tried to prepare by creating finite lists of known pathogens and toxins and developing measures to surveil, police, and counter them; foreign governments and multilateral institutions, such as the UN and the Biological Weapons Convention, have been even less ambitious. Governance, in short, is focused on the old world of biology, in which scientists observed life from the outside, puzzling over its details and behavior by tinkering with its environment and then watching what happened. But in the new biology world, scientists can now create life themselves and learn about it from the inside. As Venter put it back in 2009, “What we have done so far is going to blow your freakin’ mind.”

Sunday, September 05, 2010

everything else is merely conversation....,

NYTimes | Dr. Venter, now 63, made his name as a gene hunter. He was co-founder of a company, Celera Genomics, that nearly left the federally funded Human Genome Project in the dust in the race to determine the complete sequence of DNA in human chromosomes. He garnered admiration for some path-breaking ideas but also the enmity of some scientific rivals who viewed him as a publicity seeker who was polluting a scientific endeavor with commercialism.

Now Dr. Venter is turning from reading the genetic code to an even more audacious goal: writing it. At Synthetic Genomics, he wants to create living creatures — bacteria, algae or even plants — that are designed from the DNA up to carry out industrial tasks and displace the fuels and chemicals that are now made from fossil fuels.

“Designing and building synthetic cells will be the basis of a new industrial revolution,” Dr. Venter says. “The goal is to replace the entire petrochemical industry.”

Wednesday, May 18, 2016

Dystopian Now: the future is here - just not evenly distributed



CSMonitor | Dr. Church told The Washington Post that the meeting wasn’t open to the public or to media because its theme overlapped with a paper written by many scientists that’s pending publication in a major scientific journal. The organizers didn’t want to be accused of "science by press release," reported the Post, so decided not to share their project publicly until they had a peer-reviewed article validating their research.

"It wasn't secret. There was nothing secret or private about it," said Church, who told the Post that the video of the event will be released when the scientific paper is published, likely soon.

Church also said that the project is not aimed at creating people, only cells, and not just for human genomes, despite that an invitation to the meeting at Harvard said that the primary goal “would be to synthesize a complete human genome in a cell line within a period of 10 years,” as the Times reports.

There has been tremendous progress in genomics since scientists finished sequencing the entire human genome in 2003. As the Times reports:
Scientists and companies can now change the DNA in cells, for example, by adding foreign genes or changing the letters in the existing genes. This technique is routinely used to make drugs, such as insulin for diabetes, inside genetically modified cells, as well as to make genetically modified crops. And scientists are now debating the ethics of new technology that might allow genetic changes to be made in embryos. But synthesizing a gene, or an entire genome, would provide the opportunity to make even more extensive changes in DNA.
A team headed by genomics pioneer J. Craig Venter first synthesized the chromosome of one bacterium in 2010 and inserted it into another species, thereby replacing the host species's DNA. The result, named Syn 1.0, was a microbial cell that was able to replicate and make a new set of proteins, powered by its synthetic genome, as the Monitor has reported.

Tuesday, February 02, 2021

(B x C x D = AHH) Biological Knowledge X Computing Power X Data = Ability To Hack Humans

Reuters |  BGI Group, the world’s largest genomics company, has worked with China’s military on research that ranges from mass testing for respiratory pathogens to brain science, a Reuters review of research, patent filings and other documents has found.

The review, of more than 40 publicly available documents and research papers in Chinese and English, shows BGI’s links to the People’s Liberation Army (PLA) include research with China’s top military supercomputing experts. The extent of those links has not previously been reported.

BGI has sold millions of COVID-19 test kits outside China since the outbreak of the new coronavirus pandemic, including to Europe, Australia and the United States. Shares of BGI Genomics Co, the company’s subsidiary listed on the Shenzhen stock exchange, have doubled in price over the past 12 months, giving it a market value of about $9 billion.

But top U.S. security officials have warned American labs against using Chinese tests because of concern China was seeking to gather foreign genetic data for its own research. BGI has denied that.

The documents reviewed by Reuters neither contradict nor support that U.S. suspicion. Still, the material shows that the links between the Chinese military and BGI run deeper than previously understood, illustrating how China has moved to integrate private technology companies into military-related research under President Xi Jinping.

The U.S. government has recently been warned by an expert panel that adversary countries and non-state actors might find and target genetic weaknesses in the U.S. population and a competitor such as China could use genetics to augment the strength of its own military personnel.

BGI has worked on PLA projects seeking to make members of the ethnic Han Chinese majority less susceptible to altitude sickness, Reuters found, genetic research that would benefit soldiers in some border areas.

Elsa Kania, an adjunct senior fellow at the Center for a New American Security think tank, who has provided testimony to U.S. Congressional committees, told Reuters that China’s military has pushed research on brain science, gene editing and the creation of artificial genomes that could have an application in future bioweapons. She added that such weapons are not currently technically feasible.

BGI’s pattern of collaboration with the Chinese military was a “reasonable concern to raise” for U.S. officials, said Kania.

 

Friday, March 06, 2015

left behind...,


guardian |  As science progresses the upgrades that become available will increasingly widen the gap between rich and poor. Research on implantable devices called brain-computer interfaces (BCIs) are in trials to help disabled people move their defunct limbs or robotic prosthetics.

More advanced devices could link people's brains directly to the internet, giving them vast and faithful memory storage, and seamless access to information, even if that does include endless footage of cats in hats.

Work is ongoing into BCIs that connect many brains at once, allowing animals to cooperate by accessesing each others' brain power - work which raises deep questions about the future meaning of identity.

Genetic engineering will be more disruptive still. A new genome editing procedure called Crispr has given scientists their first real hope of making safe, precise changes to the human genome. They have already used it to correct cells with genetic faults that cause cataracts and cystic fibrosis. Similar therapies might allow improvements to human performance.

Western history has made many of today's researchers flinch at studies into the genetic basis of intelligence. But the Beijing Genomics Institute, the world's largest genomics research centre, has taken on the job . If the project bears fruit, it might drive attempts to boost human intelligence by genetically modifying embryos.

George Church, a geneticist at Harvard University, suggests another radical possibility. He has developed tools that can scramble the genetic code leaving it functional but unrecognisable to invading viruses. His first goal is to engineer a bacterium that is resistant to viral infection. But he does not dimiss the possibility of changing human DNA too – leading to a biologically new kind of human.

"In the 21st century, there is a real possibility of creating biological castes, with real biological differences between rich and poor," said Harari. "The end result could be speciation. We're used to being the only human species around, but there is no law of nature that says there can only be one species of human. With this kind of upgrading treatment we could have, in the not too distant future, more than one human species on Earth again."

Sunday, March 08, 2020

I'm NOT The Only Cat Seriously Fixated On The Low-Hanging Cornucopia Of SARS-CoV2 Fruit


harvardtothebighouse |  Some of the dystopian carnage creeping across China may be due to the fact that much of China’s population may have already been exposed to coronavirus infection via SARS or other less notorious strains, which would allow the Wuhan Stain COVID-19 to use antibody-dependent enhancement to much more efficiently enter into cells, and then become much more virulent since this enhancement hijacks the body’s preexisting immune response to coronavirus infections and allows easier entry. However whether or not people have been exposed to a coronavirus infection before, once it’s been circulating in a population for long enough the Wuhan Strain may be able to reinfect its own past hosts and use this molecular hijacking on antibodies left from its own previous infection to become far more virulent, regardless of whether or not someone has been exposed to other coronaviruses before COVID-19. And early reporting from Chinese doctors indicates that re-infections of the Wuhan Strain are far more lethal than the first.

– Additionally, although another since-retracted pre-print noted several very short genomic sequences in COVID-19’s spike-protein gene that look far more similar to sequences found in HIV than to other coronaviruses – critics quickly pointed out that the shared homology didn’t reach statistical significance. However a closer look at the data reveals that there were a few small shared genomic segments that, despite being physically separated from each other along each strand of DNA, all worked together to code for the Wuhan Strain’s protein-spike’s crucial receptor binding site. Something that is highly unlikely to have happened by chance. And despite most of its protein-spike being shared with SARS, these substituted segments weren’t shared at all – nor were they found in any other coronavirus. One possible but likely reason for these HIV-like segments is that they were meant to be epitopes, or molecular flags meant to mark intruders for a vaccine to target. It is mathematically possible for this to happen in nature – but only in a ten-thousand bats chained to ten-thousand Petri dishes and given until infinity sense. Alternatively, it could also be produced by infecting a room full of ferrets with a bespoke coronavirus vaccine and sifting through the wreckage for your genomic needle.

– Critics have brushed off the Wuhan Strain’s shared homology with HIV as statistically insignificant, however clinical reporting indicates that the Wuhan Strain may be using this shared HIV homology to attack CD4 immune cells just like HIV does, as an unusually high percentage of patients are showing low white blood cell counts, especially the sickest ones. This pathogenicity may well be due to the unique HIV-live genomics of the Wuhan Strain, as one white-paper by LSU’s professor emeritus of Microbiology, Immunology, and Parasitology who’s also a Harvard-educated virologist with a PhD in Microbiology and Molecular Genetics notes: “This is the first description of a possible immunosuppressive domain in coronaviruses… The three key [mutations] common to the known immunosuppressive domains are also in common with the sequence from [the spike-protein]. While coronaviruses are not known for general immunosuppression of the style shown by HIV-1, this does not rule out immunosuppression at the site of active infection in the lung, which would prolong and potentially worsen infection at that site.” And early research has indicated that this unique region may make COVID-19 up to 1,000 times more likely to bind to human cells than SARS.

– Even more troubling, a peer-reviewed study noted that one particular part of the Wuhan Strain’s spike-protein genome also wasn’t found in any of its relatives, “and may provide a gain-of-function to [COVID-19] for efficient spreading in the human population.”  And according to that paper, this particular type of furin cleavage site makes similar viruses both more pathogenic and more neurotoxic.

– Evidence for the Wuhan Strain’s neurotoxicity arrived in late February, in a published paper which notes that “the most characteristic symptom of COVID‐19 patients is respiratory distress, and most of the patients admitted to the intensive care could not breathe spontaneously.” Combined with the observation that “some COVID‐19 patients also showed neurologic signs such as headache, nausea and vomiting,” this paper asserts that since SARS was found heavily concentrated in the brainstems of its autopsied victims, COVID-19 is also probably crossing the blood-brain barrier and killing its victims not just via pneumonia, but also by causing neurological respiratory failure.

– And it should be noted that SARS – much ballyhooed as a close relative to the Wuhan Strain – didn’t notable effect white blood cell counts.  Additionally, clinical treatment guides published online in late January by established Chinese medical sources note the progressive reduction of white blood cells, as well as the importance of monitoring this decline. And reporting from Thailand indicates that adding a cocktail of two different anti-HIV drugs to the typical flu treatment regime seemed to effectively knock back the Wuhan Strain. Additionally, one of the only autopsies performed outside of China to date found that the deceased had a severely depleted white blood cell count. These lowered counts may come from this shared similarity with HIV, or it could also be the result of antibody-dependent enhancement as well, since this phenomenon primarily targets white blood cells for its hijackings and may help explain why consecutive infections are so lethal.

– In a highly concerning turn, scientists have noted that the Wuhan Strain can have a “striking” short term rate of mutation which doesn’t indicate an artificial origin but captures the unique threat posed by this coronavirus regardless of its providence, since a faster mutation rates makes it more likely this virus can dodge testing and neutralize vaccines. Something there is already early evidence for. Further concerning are reports out of China that even patients who appear cured still harbor COVID-19 in their system, and although the full implications of this are not yet known – none of them are good.

– One of the worst possible scenarios for COVID-19’s mutation rate would be if it falls into the Goldilocks range that would allow it to form mutant viral swarms: too many mutations will cause a virus to eventually implode, not enough allows host immune systems to catch-up, but if things are just right mutant swarms can form and spread across host populations, burrowing into host nervous systems and causing permanent neurological damage. Mutant swarms form when a virus produces mutationally-damaged copies of itself inside a host, some of which aren’t infectious but find their way into the nervous system where they burrow in causing damage, and others that combine with complimentary broken copies inside host cells to produce working infectious copies of the virus. So a host can not only become crippled with neurological issues, but also still be producing infectious copies of the virus. And it seems as if COVID-19 has many characteristics that indicate the potential to form mutant swarms: the “striking” mutation rate mentioned above and the fact a second widespread mutated strain seems to have already emerged in Washington State with many other isolated strains reported elsewhere, crossing between species is another factor and a dog in Hong Kong appears to have tested positive, the fact that the Wuhan Strain can infect not only the respiratory tract but feces as well – multi-organ involvement is an important contributor to viral swarms, and finally the markedly viral load rate of COVID-19 compared to SARS – SARS produced a viral load several times lower which decreased over time, while COVID-19 produces a “very high” viral load that appears to increase over time and can peak several orders of magnitude higher than SARS was measured to reach. And alarming evidence that this phenomenon is occurring emerged from a Chinese pre-print which noted that over one-third of the roughly 200 patients studied has some neurological symptoms, with nearly half of the most severe patients exhibiting neurological issues.

– Another exceptional trait of the Wuhan Strain COVID-19 is that not only does it form its own clade, it’s calculated to have diverged from SARS and its other sister coronaviruses some 260 years ago. And yet in all that time, while it every other branch of the coronavirus tree was busy branching-off into countless variants, if it emerged naturally, COVID-19 somehow spent a quarter of a millennium as the lone known example of its clade, somehow not mutating into related lineages in all that time. Another simpler explanation is that this apparent hereditary distance and genetic uniqueness is the just the result of being altered in a lab. And although two distinct strains of COVID-19 have been identified, there’s no reason to believe this mutational differentiation happened before contact with humans in December of 2019. Additionally, when neutral sites, the specific points in the genome which most reliably show evolutionary change, were examined: COVID-19 looks even more evolutionarily distant from any of its possible relatives.

– Also giving credence to the idea that the Wuhan Strain was bio-engineered is the existence of a patent application registered to a scientist from Wuhan that looks to modulate a coronavirus’ spike-protein genes – the precise region altered by Zhengli Shi at UNC to make a hyper-virulent strain of coronavirus, and whose alteration and adaptation would explain the Wuhan Strain’s unusual behavior as discussed above.

Wednesday, July 25, 2018

Father Of Synthetic Genomics Better Be Careful Tampering With Whydte Folks Money....,


Genomeweb |  Human Longevity (HLI) is suing the J. Craig Venter Institute (JCVI) and a number of unknown defendants over the misappropriation and use of trade secrets passed along by Craig Venter, the founder of both the company and the institute that bears his name.

In a complaint filed last Friday with the US District Court for the Southern District of California, Human Longevity alleges that upon his termination from HLI on May 24, Venter took a company-owned laptop with trade secrets and passed on protected information to the Venter Institute, of which he is chairman and CEO. HLI also claims that the institute is working on a product that will compete with its own business.

According to the complaint, Venter was CEO of Human Longevity from 2014 until January 2017, when he became the firm's executive chairman and signed a "proprietary information and inventions" agreement. He assumed the role of interim CEO in November of 2017 until his employment was terminated in May of this year. During his time at HLI, Venter used a company-owned laptop computer, the contents of which were backed up in the cloud, and consistently used his JCVI email address rather than his HLI email to conduct company business, the complaint states.

In the spring of this year, Venter "withheld critical information from the board and the HLI investors regarding the conduct of an HLI key executive which would likely result in termination," the complaint says. Further, in May, Venter had an HLI-paid counsel "draft a Venter-favorable employment contract" and appointed a new interim president without conferring with the HLI board first.

On May 24, the HLI board "considered a rushed investor deal which Venter presented to them only less than two weeks earlier," the terms of which the board considered one-sided. The deal would have provided financial incentives to Venter and offered the new investor rights that had already been granted to another party, according to the complaint. "At that point, the HLI board voted to terminate Venter from HLI," it states.

Following his termination, Venter left the HLI offices with the company-owned laptop and "immediately began using the HLI computer and server to communicate to the public, solicit HLI investors and employees," the complaint says. In a Twitter message on May 24, Venter said that he was retiring from HLI and returning to JCVI.

His access to the HLI server and HLI emails was disabled the next day, but the company alleges that "even after his HLI termination, Venter used the HLI computer, accessed and sent HLI proprietary information and trade secrets," including communications involving Series C and Asia JV Series A documents.

Friday, March 25, 2016

geneticists/molecular biologists are indispensible knowledge-workers...,


harvarddesignmagazine |  GC  The synthetic biology revolution is not just about going from reading to writing. Genomics already went from reading single genes to reading multiple genes; now synthetic biology is going from writing single genes to writing whole genomes. Both reading and writing are tangled up in the design process. In many fields, there is a design-build-analyze loop: you build something, and then you look for its failure modes. After living in a building for a while, you notice that it leaks. Then you do another round of design; you radicalize your structures and hold them to stronger standards until they fail. Then you slowly eek your way back to something that works, but works better than before. The same thing is true in synthetic biology. We have design software, like BIOCAD, cadnano, Millstone, and others.

But I see two fundamental differences between synthetic biology and architecture. In architecture, you might start with walls and windows as your standard parts. In biology, our standard parts have been refined by three billion years of evolution, on 1021 liters of soil and water. That’s a lot of debugging. Also, in synthetic biology we have the ability to recreate that refinement process ourselves, on a smaller scale and in a more directed way. We can run our own evolutions. When you do the design-build-analyze loop for buildings, you might make one small prototype, build it, and, if it starts to go wrong, you debug it in real time. Like the John Hancock Tower, in downtown Boston—you know its history, right?





MA

Glass panels mysteriously falling off …



GC

It was being debugged as it was being used. With synthetic biology, we can make a billion or a trillion designs, build them all, test them all, take the winner from that testing, and then do it all again.



MA

What is the timescale for this type of experiment?



GC

It depends on your goal. If your goal is to make a chemical, say, or to build a little factory that makes chemicals, you can design, build, and test a billion things in one day. If your goal is to make a pig, you’re talking more in the order of years. And if you are creating a human pharmaceutical, you’re talking about 10 years just to get it through all the regulatory phases. You might find a clever way of doing billions of prototypes by working with human cells in the lab, but when you want to introduce it into the marketplace, you’re going to be testing one drug at a time, just like you test one building at a time.




MA

You’ve worked on some things that are pretty far removed from our daily concerns—like how to bring the wooly mammoth back to life—but a lot of your work stands to affect our everyday bodily experience. What are you working on that you might want to use to change your own genome?



GC

There is an APP (amyloid precursor protein) allele that I wouldn’t mind having—it gives an extra 10 years of resistance to Alzheimer’s. That’s something that’s preventative, and it’s something we more or less know how to do. But there are some things we don’t know how to do yet, such as having better memory or making more effective use of the brain. Those would be great. Reversing aging would be nice, too.



MA

Aren’t our inadequacies part of what makes us human? How would it affect the human experience if we could live much longer, for example?



GC

I think what makes us human is mainly our ability to plan and to care for others. Chimpanzees form little cliques, and they certainly care for their families, but I think our ability to imagine scenarios that have never happened—to think of ways to avoid having an asteroid eliminate all life on the planet—is uniquely human. We have an ability to be thoughtful about ourselves and oth- ers over long periods of time. I think that would remain true if we lived longer.

Tuesday, April 08, 2008

The Race

Craig Venter on the great race;
"We've been digitizing biology, and now we're trying to go from that code to designing biology. We've tried various approaches, paring it down to basic components, digitizing it, now we're trying to ask: can we regenerate life or create new life out of this digital universe? The pace of digitizing life has been increasing exponentially. Our ability to write genetic code has been growing more slowly. Turns out synthesizing DNA is difficult. In a biological system the software builds its own hardware, but design is critical, and if you start with digital information, it has to be really accurate. How do we boot-up a synthetic chromosome? We can do a transplant of a chromosome from one cell to another and activate it. We may be about to create a new version of the Cambrian explosion, where there is massive new speciation (the formation of new and distinct species) based on this digital design. We have now a database with about 20 million genes, and we like to think of them as the design component of the life of the future. We now have techniques to do combinatorial genomics, to build a robot that can make a million chromosomes a day.

We're now focusing on fourth-generation designer fuels. Curent biofuels aren't the solution. The only way that biology can have an impact on fuel without increasing the price of food, it's to start with CO2 as the feed stock -- create new energy out of CO2, and we think we will have something within the next 18 months. Future uses of this technology: increase the basic understanding of life; replace the petro-chemical industry; become a major source of energy; enhance bioremediation. We're changing the evolutionary tree with new bacteria and species."
I suspect that this memetically recursive path is the ONLY viable path out of the evolutionary bottleneck. Because of the choices made on large institutional and cultural scales, I begin to doubt whether or not this path will be explored hard enough and fast enough to make the difference that it could make. This is where the world should invest its space race fervor.

Saturday, August 22, 2009

building better bacteria

The Scientist | Researchers from the J. Craig Venter Institute have developed a technique for generating modified strains of bacteria with novel, genetically engineered properties, they report online today (August 20) in Science. The advance could help scientists tweak microorganisms to more efficiently produce biofuels, the researchers say.

"I think it's an important and interesting advance," said James Collins, a bioengineer at Boston University who was not involved in the study. "I suspect this will turn out to be quite important for bioengineering and bioenergy systems."

Last year, Venter, an author on the paper (and a member of The Scientist's editorial board), reported that he and his collaborators had created a synthetic bacterial genome and cloned it into a yeast cell. However, they were unable to transfer the genome into a cell that would use the genetic code to produce a functioning version of the organism. In the current paper, the researchers present a technique for doing just that.

The Venter team first cloned the genome of the bacterium Mycoplasma mycoides into a yeast cell. They then altered the genome, using the myriad tools available for yeast gene manipulation. In the procedure's trickiest step, they transplanted the yeast-bound bacterial genome into a closely related bacterium, Mycoplasma capricolum, coaxing it to "take this bacterial genome and boot it up" and generate their mutant strain, said Sanjay Vashee, a synthetic biologist at the institute and the corresponding author on the paper.

The hurdle Vashee and his team had to overcome to achieve this feat involved bypassing the bacterial equivalent of an immune system -- essentially a collection of restriction enzymes. These enzymes, thought to have evolved to chew up the genomes of viruses infecting bacterial cells, were preventing the successful transplantation of the modified M. mycoides genome into wild-type M. capricolum. So the group developed two fixes, which together solved the problem: First, they inactivated M. capricolum's restriction enzymes. Then, they chemically modified their mutant M. mycoides genome where these enzymes typically cleave the genomes of intruders.

Decades of research on yeast genetics have yielded the know-how to do extensive genomic manipulations in yeast, but that capability doesn't exist for other microorganisms. "There are so many organisms in nature that we cannot manipulate," said Vashee. "If we can extend this -- and put those genomes into yeast, to manipulate them there -- we've got a new technology that can bring genomics to a wide host of organisms." (Vashee noted that the current study was conducted in a natural Mycoplasma genome -- not the synthetic genome the group assembled last year.)

Saturday, February 17, 2018

Future Genomics: Don't Edit A Rough Copy When You Can Print A Fresh New One


technologyreview  |  It took Boeke and his team eight years before they were able to publish their first fully artificial yeast chromosome. The project has since accelerated. Last March, the next five synthetic yeast chromosomes were described in a suite of papers in Science, and Boeke says that all 16 chromosomes are now at least 80 percent done. These efforts represent the largest amount of genetic material ever synthesized and then joined together.

It helps that the yeast genome has proved remarkably resilient to the team’s visions and revisions. “Probably the biggest headline here is that you can torture the genome in a multitude of different ways, and the yeast just laughs,” says Boeke.

Boeke and his colleagues aren’t simply replacing the natural yeast genome with a synthetic one (“Just making a copy of it would be a stunt,” says Church). Throughout the organism’s DNA they have also placed molecular openings, like the invisible breaks in a magician’s steel rings. These let them reshuffle the yeast chromosomes “like a deck of cards,” as Cai puts it. The system is known as SCRaMbLE, for “synthetic chromosome recombination and modification by LoxP-mediated evolution.”

The result is high-speed, human-driven evolution: millions of new yeast strains with different properties can be tested in the lab for fitness and function in applications like, eventually, medicine and industry. Mitchell predicts that in time, Sc2.0 will displace all the ordinary yeast in scientific labs.

The ultimate legacy of Boeke’s project could be decided by what genome gets synthesized next. The GP-write group originally imagined that making a synthetic human genome would have the appeal of a “grand challenge.” Some bioethicists disagreed and sharply criticized the plan. Boeke emphasizes that the group will “not do a project aimed at making a human with a synthetic genome.” That means no designer people.

Ethical considerations aside, synthesizing a full human genome—which is over 250 times larger than the yeast genome—is impractical with current methods. The effort to advance the technology also lacks funding. Boeke’s yeast work has been funded by the National Science Foundation and by academic institutions, including partners in China, but the larger GP-write initiative has not attracted major support, other than a $250,000 initial donation from the computer design company Autodesk. Compare that with the Human Genome Project, which enjoyed more than $3 billion in US funding.

Saturday, September 18, 2021

"Behavioral Genetics" "Social Science Genomics" - By Any Name - Race "Science" Still Turd-Frosting

newyorker |  Last summer, an anonymous intermediary proposed to Harris and Harden that they address their unresolved issues. Harden appeared on Harris’s podcast, and patiently explained why Murray’s speculation was dangerously out in front of the science. At the moment, technical and methodological challenges, as well as the persistent effects of an unequal environment, would make it impossible to conduct an experiment to test Murray’s idly incendiary hypotheses. She refused to grant that his provocations were innocent: “I don’t disagree with you about insisting on intellectual honesty, but I think of it as ‘both/and’—I think that that value is very important, but I also find it very important to listen to people when they say, ‘I’m worried about how this idea might be used to harm me or my family or my neighborhood or my group.’ ” (Harris declined to comment on the record for this piece.) As she once put it in an essay, “There is a middle ground between ‘let’s never talk about genes and pretend cognitive ability doesn’t exist’ and ‘let’s just ask some questions that pander to a virulent on-line community populated by racists with swastikas in their Twitter bios.’ ”

Harden is not alone in her drive to fulfill Turkheimer’s dream of a “psychometric left.” Dalton Conley and Jason Fletcher’s book, “The Genome Factor,” from 2017, outlines similar arguments, as does the sociologist Jeremy Freese. Last year, Fredrik deBoer published “The Cult of Smart,” which argues that the education-reform movement has been trammelled by its willful ignorance of genetic variation. Views associated with the “hereditarian left” have also been articulated by the psychiatrist and essayist Scott Alexander and the philosopher Peter Singer. Singer told me, of Harden, “Her ethical arguments are ones that I have held for quite a long time. If you ignore these things that contribute to inequality, or pretend they don’t exist, you make it more difficult to achieve the kind of society that you value.” He added, “There’s a politically correct left that’s still not open to these things.” Stuart Ritchie, an intelligence researcher, told me he thinks that Harden’s book might create its own audience: “There’s so much toxicity in this debate that it’ll take a long time to change people’s minds on it, if at all, but I think Paige’s book is just so clear in its explanation of the science.”

The nomenclature has given Harden pause, depending on the definition of “hereditarian,” which can connote more biodeterminist views, and the definition of “left”—deBoer is a communist, Alexander leans libertarian, and Harden described herself to me as a “Matthew 25:40 empiricist” (“The King will reply, ‘Truly I tell you, whatever you did for one of the least of these brothers and sisters of mine, you did for me’ ”). The political sensitivity of the subject has convinced many sympathetic economists, psychologists, and geneticists to keep their heads below the parapets of academia. As the population geneticist I spoke to put it to me, “Geneticists know how to talk about this stuff to each other, in part because we understand terms like ‘heritability,’ which we use in technical ways that don’t always fully overlap with their colloquial meanings, and in part because we’re charitable with each other, assume each other’s good faith—we know that our colleagues aren’t eugenicists. But we have no idea how to talk about it in public, and, while I don’t agree with everything she said, sometimes it feels like we’ve all been sitting around waiting for a book like Paige’s.”

Harden’s outspokenness has generated significant blowback from the left. On Twitter, she has been caricatured as a kind of ditzy bourgeois dilettante who gives succor to the viciousness of the alt-right. This March, after she expressed support for standardized testing—which she argues predicts student success above and beyond G.P.A. and can help increase low-income and minority representation—a parody account appeared under the handle @EugenicInc, with the name “Dr. Harden, Social Justice Through Eugenics!” and the bio “Not a determinist, but yes, genes cause everything. I just want to breed more Hilary Clinton’s for higher quality future people.” One tweet read, “In This House We Believe, Science is Real, Womens Rights are Human Rights, Black Lives Matter, News Isnt Fake, Some Kids Have Dumb-Dumb Genes!!!”

In 2018, she wrote an Op-Ed in the Times, arguing that progressives should embrace the potential of genetics to inform education policy. Dorothy Roberts, a professor of law, sociology, and Africana studies at the University of Pennsylvania, strongly disagreed: “There’s just no way that genetic testing is going to lead to a restructuring of society in a just way in the future—we have a hundred years of evidence for what happens when social outcomes are attributed to genetic differences, and it is always to stigmatize, control, and punish the people predicted to have socially devalued traits.” Darity, the economist, told me that he doesn’t see how Harden can insist that differences within groups are genetic but that differences between them are not: “It’s a feint and a dodge for her to say, ‘Well, I’m only looking at variations across individuals.’ ”

There is a good precedent for this kind of concern. In “Blueprint,” Robert Plomin wrote that polygenic scores should be understood as “fortune tellers” that can “foretell our futures from birth.” Jared Taylor, a white-supremacist leader, argued that Plomin’s book should “destroy the basis for the entire egalitarian enterprise of the last 60 or so years.” He seized on Plomin’s claim that, for many outcomes, “environmental levers for change are not within our grasp.” Taylor wrote, “This is a devastating finding for the armies of academics and uplift artists who think every difference in outcome is society’s fault.” He continued, “And, although Blueprint includes nothing about race, the implications for ‘racial justice’ are just as colossal.” Harden has been merciless in her response to behavior geneticists whose disciplinary salesmanship—and perhaps worse—inadvertently indulges the extreme right. In her own review of Plomin’s book, she wrote, “Insisting that DNA matters is scientifically accurate; insisting that it is the only thing that matters is scientifically outlandish.” ​(Plomin told me that Harden misrepresented his intent. He added, “Good luck to Paige in convincing people who are engaged in the culture wars about this middle path she’s suggesting. . . . My view is it isn’t worth confronting people and arguing with them.”)

With the first review of Harden’s book, these dynamics played out on cue. Razib Khan, a conservative science blogger identified with the “human biodiversity” movement, wrote that he admired her presentation of the science but was put off by the book’s politics; though he notes that a colleague of his once heard Harden described as “Charles Murray in a skirt,” he clearly thinks the honorific was misplaced. “Alas, if you do not come to this work with Harden’s commitment to social justice, much of the non-scientific content will strike you as misguided, gratuitous and at times even unfair.” This did not prevent some on the Twitter left from expressing immediate disgust. Kevin Bird, who describes himself in his Twitter bio as a “radical scientist,” tweeted, “Personally, I wouldn’t be very happy if a race science guy thought my book was good.” Harden sighed when she recounted the exchange: “It’s always from both flanks. It felt like another miniature version of Harris on one side and Darity on the other.”

Thursday, November 15, 2007

I - Is the Establishment Reviving Eugenics?

On Sunday, the New York Times published one of the most deeply embarrassing articles I have ever read. This article was so bad that it should have never even had a chance of seeing the editorial light of day. Let me get this point out front and let's be perfectly clear about the focus of my concerns. My liminal awareness suggests to me that this was an intentional move by a very important element of the U.S. media Establishment that has demonstrated a long-standing pattern and praxis of promulgating "scientific" racism to support another and geographically local element of the U.S. Establishment which was recently humiliated by its trusted employee James Watson's clumsy ideological disclosure of some of its institutional and Establishmentarian ass.
THE NY TIMES has a science reporter, Nicholas Wade, who makes very similar claims, using rhetoric that is much less provocative. In Wade’s recent book, BEFORE THE DAWN, he writes: “Over the course of many generations the peoples of each continent emerged as different races” (181). And he later suggests that Jews “may be genetically more intelligent” than other races (that is, other groups, he regards as “races”; see pp. 252-56). Let me say that I believe that Watson and Wade have every right to express their views; I believe in free speech, almost with no limits. But when Watson and Wade say such things, there ought to be ample opportunity for others to lay out the factual and logical errors in their arguments and conclusions. This paper calls attention to Watson’s provocative claims about human races, but when will THE NY TIMES provide space to those who disagree with the more soberly expressed, but in many ways convergent, views of its reporter, Nicholas Wade?
Tell me till you're blue in the face that Watson's views were unknown to the board of trustees at Cold Spring Harbor (and don't be fooled because they host this "Never Forget" archive) and that Wade's pseudo-scientific essentialism is unknown to the NY Times. Cause if you truly believe that, I've got some stories to tell you about Santa Clause and his elves and some swampland to sell you at a firesale discount....,

Such categorical violations of editorial standards for journalistic integrity, scientific validity, and source accountability have to have had a subtextual motivation. That the "grey lady" which has a track record for supporting "scientific" racism would carry it is bad enough. However, this piece of propagandistic garbage was put on the wire and uncritically repeated far-and-wide by such media chains as McClatchy - which themselves never paused to exercise editorial standards for integrity, accountability, and validity.

It took up half of page 8 in the front section of the Kansas City Star as a Sunday Health and Science feature with the even more ridiculous title Geneticists worry data could fuel racial prejudices. That something like this was promulgated far and wide suggests to me that elements in the U.S. Establishment have taken the decision to resuscitate and legitimize eugenics in the U.S.. First and foremost let me be clear that I believe that big money is the prime mover behind this effort. Highly credentialed negrodemics are staging protests in support of genetic racial pseudo-science because there's a buck to be made off of it.

Pharmaceutical and genomics companies have $trong in$entives to grease this pseudo-science on the skids of public awareness and acceptance. However, it never hurts to kill multiple birds with one stone - and to the extent that race remains a vital lever in the U.S. Establishment's system of governance - why not cast fundamental and scientific doubt on the human worth of Black folks - while you set the stage for raking in the big bucks? Isn't this exactly what happened in the entertainment industry in 1988 when organic and politically conscious HipHop was sacked in favor of the race pornography of gangsta RaP. (Rhyming and Posing)

Sunday, April 22, 2018

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:










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.