Category Archives: Transhuman News

NEW YORK CITYSince the Human Genome Project (HGP) was completed in 2003, scientists have sequenced the full genomes of hundreds, perhaps thousands, of species. Octopuses. Barley. Mosquitoes. Birch trees. Reading genomes is now commonplace, but thats not enough for the group of scientists who gathered at the New York Genome Center on Tuesday. They want to write entire genomes with the same ease, synthesizing them from scratch and implanting them into hollow cells.

One team already did this for a tiny bacterium in 2010, creating a synthetic cell called Synthia. But the New York group has set its sights on building the considerably larger genomes of plants, animals, and yesafter a lot of future discussionhumans.

For now, thats technically implausible. Youd have to make millions of short stretches of DNA, assemble them into larger structures, get them into an empty cell, and wrap and fold them correctly. In the process, youd go bankrupt. Although we can sequence a human genome for less than $1,000, writing all 3 billion letters would still cost around $30 million. Still, even that exorbitant price has fallen from $12 billion in 2003, and should reach $100,000 within the next 20 years. And the group assembled in New York wants to double that pace.

Theyre pushing for an international project called Genome Project-writeGP-writethat aims to reduce the costs of building large genomes by 1,000 times within 10 years. Its an aggressive goal, but based on what we saw with the HGPthe reading project, if you willwe think we can do this, said Jef Boeke from New York University School of Medicine. And just as the HGP helped to drive down the cost of DNA-sequencing, the GP-write team hopes that the demand created by their initiative will push down the cost of DNA-writing tech. I want to see a time in the not-too-distant future when, in elementary schools, itll be routine to think: I want to do some DNA synthesis as a project, said Pamela Silver from Harvard Medical School.

But GP-Write is still more of an idea than an actual thing. The group hopes to raise $100 million, but in the year since the project was first proposed, little of that sum has materialized. That cast a strange air upon the first day of the New York meeting, as if speakers were pitching ideas to a collaboration that has yet to successfully pitch itself.

Better news arrived on Wednesday, when the team announced that Boeke and Harris Wang from Columbia University have secured $500,000 for a GP-write pilot project, from the Defense Advanced Research Projects Agency (DARPA). Theyll use that money to engineer human cells into self-sufficient nutrient factories. Early on in our evolution, animals lost the ability to manufacture certain vitamins and amino acids, forcing us to get these essential nutrients from our diet. But plants, fungi, and bacteria can still produce these nutrients, and by exploiting their genes, we could restore that lost manufacturing ability to our own cells. That would make it much easier and cheaper to grow such cells in laboratory cultures.

DARPAs involvement inevitably invites visions of self-sustaining soldiers who dont need to eat, but the GP-Write team has explicitly said that theyre not trying to make synthetic people. Theyre only ever planning to create synthetic cells, or blobs of tissue (organoids) made from those cellsnot eggs or embryos.

For example, another possible pilot project involves creating lineages of ultrasafe human cells. Such cells could have their cancer genes deactivated so they could be more safely injected during stem cell treatments. They could be tweaked to avoid triggering an immune reaction, and so be used to grow organs for transplants. They could be made resistant to viruses, so that biotechnology companies could use them to pump out medicines and vaccines without fear of costly contamination. (In 2008, Genzyme lost millions of dollars after a virus hit its cell lines and forced it to close a manufacturing plant for months.)

Scientists can already do some of that with gene-editing techniques like CRISPR, which allow them to make precise changes to an organisms DNA. But powerful though CRISPR is, it has limits. And as Nili Ostrov from Harvard University reminded me, editing requires synthesisto use CRISPR, you need to make genetic material to guide editing enzymes to the right spot. And if you want to make a lot of edits, it might be more efficient to just build everything from scratch.

For example, the human genome is full of repetitive chunks called retroelements. These are the result of ancient viruses that wheedled their way into our DNA, stayed there, and copied themselves again and again. Yasunori Aizawa from the Tokyo Institute of Technology wants to know whether these sequences are important, but because theyre all very similar, he cant use CRISPR to target any particular one of them. But with better DNA-writing tech, he could create cells with any number of retroelements, and test if theyre affected.

Meanwhile, June Medford from Colorado State University wants to eventually engineer the genomes of plants so they could filter water or detect chemicalsshe showed a slide of an airport gate encircled by explosive-detecting shrubbery. These are complicated traits involving large networks of genes, and many plant genomes are already disproportionately big. I dont think you could do it just by modification, she told me.

Building genomes also allows you to effectively test genomes. You could make cells with every possible mutation in critical genes to see which ones are likely to cause disease. You could reconstruct genomes from earlier points of a species evolutionary history. Its an engineers mentality: repeated cycles of designing, building, and testing. I want to know the rules that make a genome tick, says Boeke. [Physicist Richard] Feynman said, What I cannot create, I cannot understand. That has become a manifesto for our field.

The first genomes to be completely synthesized were that of tiny viruses, like poliovirus back in 2002. It took another 8 years to do the same for a bacterium, with a million DNA letters in its genome. Boekes team of international colleagues is on the verge of repeating that feat for bakers yeasta simple fungus with a 12-million-letter genome. The pace of their progress is impressive, but the human genome is almost 300 times bigger still.

It is also far more controversial. When GP-write was first announced last year, it had an H (for human) at its head and bad publicity already at its heels. Boeke, Church, and their colleagues had invited 135 scientists and other interested parties to discuss the project at a meeting at Cambridge, Massachussetts. But because they had submitted a paper about HGP-write to the journal Science, whose embargo process forbids any prior announcements or interactions with the press, the meeting took place behind closed doors.

The lack of transparency drew sharp rebuke from Drew Endy, a synthetic biologist at Stanford University who had been invited (and who founded a DNA synthesis company), and Laurie Zoloth, a professor of bioethics and medical humanities at Northwestern University. They published an opinion piece lambasting the group for holding a closed meeting and failing to engage with the ethical consequences of their goals. After all, the HGP-write project may not be looking to make designer humans but as journalist Antonio Regalado has pointed out, one of its leadersGeorge Churchclearly discussed that option as the climax of such research, in his 2012 book Regenesis.

To which Endy and Zoloth wrote: To create a human genome from scratch would be an enormous moral gesture whose consequences should not be framed initially on the advice of lawyers and regulators alone, the duo wrote. Critical voices representing civil society, who have long been skeptical of synthetic biologys claims, should also be included. The creation of new human life is one of the last human-associated processes that has not yet been industrialized or fully commodified. It remains an act of faith, joy, and hope.

The GP-write group have listened. The New York meeting was more open than the Cambridge one. And they dropped the H to emphasize that theyre working toward techniques that will be broadly applicable all kinds of organisms. HGP-write will still exist within that umbrella, but as a slower-moving project that will leave time for public discussion. These are all good steps, says Zoloth. What matters now is how the community wrestles with important questions. In whose interest is the work being done? she asks. For what purpose? Over whose oversight? In a world where we cannot assure that everyone can get a clean glass of water, how is just to imagine a powerful technology being fairly developed and fairly distributed?

The answers were not yet forthcoming at the New York meeting. Speakers included several ethicists who rightly noted the need for transparency, responsible communication, and open dialogue. But the discussions felt thin and all-too-familiar. When I asked if GP-write had unique ethical dimensions that differed from those that have already been endlessly discussed for CRISPR, stem cells, cloning, and other biotech, no one offered a clear answer. One attendee noted that the discussion largely echoed that from the Asilomar conference in 1975, when delegates debated the ethics of nascent genetic-engineering technology. Another noted that if GP-write finally takes off next year, it would coincide with the 200th anniversary of Mary Shelleys Frankenstein.

Still, the GP-write group has committed to detailed ethical discussions over the next several years, and will dedicate a certain portion of any future funds towards that. The notion that we could write a human genome is simultaneously thrilling to some and not so thrilling to others, says Boeke. We recognize that this will take a lot of discussion.

Indeed, thats partly why the project needs to exist, says Virginia Cornish from Columbia University. Any new field needs to be out front, thinking about ethical and safety implicationsand thats not something I as a single scientist can do, she says. We need to be well-organized to have a real presence with government, industry, and the public.

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Now That We Can Read Genomes, Can We Write Them? - The Atlantic

N

EW YORK As scientists aiming to create genomes from scratch see it, nature had her chance 3.8 billion years, to be precise, the length of time that life on Earth has been evolving and, supposedly, getting more finelyadapted and more complex. Now its the turn of scientists, who think they can do better.

Halfway through a two-day meeting of Genome Project-write at the New York Genome Center in New York City, more than 250 attendees from 10 countries had unveiled dozens of ways that designing and building genomes might make possible a dazzling litany of futuristic advances.

Scientists outlined ways to change the genomes of the microbes that live in the human gut so as to protect people from obesity and chronic stress; to change plant genomes so they detect the explosive TNT (cue the photograph of airport security surrounded by bomb-detecting philodendrons); to make bacteria that produce pharmaceuticals resistant to viruses that have shut down expensive production lines, and more.

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These new ideas will not become realityas quickly as GP-write organizers hoped, however. Last year, its leaders said they wantedto raise $100 million by now, from corporations, perhaps the National Institutes of Health, and donors. But only an initial $250,000, from software company Autodesk, is in the kitty.

Audacious project plans to create human genomes from scratch

As a result, project co-leader Nancy Kelley said, GP-write has been able to fund only one pilot project. The pitches from (mostly) junior scientists on Tuesday were therefore more to get the projects stamp of approval Kelley said its leaders would write letters of support so the researchers could seek funding elsewhere than an actual check.

The overall goal of GP-write (the GP stands for genome project) is to advance the cause of human health, said Kelley, who is founding executive director of the New York Genome Center. But it is also to change how we as scientists learn about the world, said biochemist and project co-leader Jef Boeke of New York University. Physicist Richard Feynmans observation that what I cannot create I cannot understand, he added, has become a kind of manifesto for our field.

The meeting was part pitch-fest, as scientists proposed projects that could be part of GP-write, and part progress report on research that was underway long before GP-write, most notably the constructionof five out of the 16 chromosomes that make up the yeast genome, a project Boeke co-leads. The line to register in the morning was out the door onto Sixth Avenue, the room was standing room only with spillover into the adjacent cafeteria, and hundreds more watched the livestream of the first session.

GP-write sparked controversy last year when its first organizing meeting, at Harvard Medical School, was closed to the mediaand public, triggering suspicion that something nefarious was being done in secret. Ethicists and others also grew alarmed at what the project, then named HGP-write (the H is for human), might do. Visions of designer humans danced in some critics heads. (The write in the name is meant to distinguish this from the Human Genome Project, which read the 3 billion chemical letters that constitute human DNA.)

In fact, as far as I know, there is no plan to make embryos or humans, said Barbara Evans, a law professor at the University of Houston, looking around the room at the projects leaders, who nodded vigorously.

Top scientists hold closed meeting to discuss building a human genome from scratch

Initially, GP-write will support the development of technology todesign and synthesize (from chemical building blocks) genomes, the full complement of an organisms DNA. The chief aim is to reduce the cost of doing that by 1,000-fold over the next 10 years; it now costs about 10 cents to synthesize one base pair, or a single duo of the 3 billion in the human genome.

Unlike reading genomes, Boeke said, writing has a sort of element of creativity, an artistic side if you will. The possibility of writing a human genome, therefore, is simultaneously thrilling to some and frightening to others. A human genome, he said, might be produced from scratch by 2027.

Such a synthetic genome would not get slipped into, say, a human egg and allowed to develop into the first genetically bespoke person, he and others said. Instead, the hope is to learn the rules that make a genome tick, Boeke said. We want to do only good things and not bad things.

Allthe studies presented at the meeting are independent of GP-write but might eventually contribute to it. Using funding from the Pentagons Defense Advanced Research Projects Agency, for instance, biologist Harris Wang of Columbia University is figuring out how to change the genomes in the microbes that live in and on people, called the human microbiome. These bugs seem to influence metabolism and, therefore, obesity and diabetes; affect whether someone develops irritable bowel syndrome; and might influence the nervous system.

Were asking, how do we manipulate microbiomes associated with the human body, and possibly introduce new functions, Wang said. One possibility is to modify the genomes ofhumans hitchhikers so they can synthesize every essential amino acid, freeing people from having to get these protein building blocks from food. Another is to give these microbes genomes that secrete compounds that improve the motility of the gastrointestinal tract, to treat irritable bowel syndrome; genomes that sense and respond to infection; or even genomes that produce neurotransmitters that might affect memory and other brain functions.

How would engineered gut microbes get into patients? As it happens, fecal transplants are already used to treat infections with C. difficile.

Writing genomes isnt limited to animals. Although existing genetic techniques have led to plants that can sense TNT at levels ten-to-hundredfold lower than bomb-sniffing dogs, said biologist June Medford of Colorado State University, techniques developed by GP-write might do even better.

We want to engineer plants to filter water and secrete pure water, she said. Imagine if we could filter seawater and provide unlimited water for life on earth.

One unansweredquestion is when it will be necessary to construct a genome from scratch rather than tweakingwhat nature provided, such as with the genome-editing tool CRISPR. Nili Ostrov of Harvard Medical School, for instance, is editing the genomes of bacteria to make them resistant to viral infection. Thats a big problem for the biotech industry, which uses bacteria and other cells to produce a whole drugstores worth of pharmaceuticals.

Ostrov and her colleagues are therefore changing bacterial DNA so that the DNA that a virus injects into a cell which is how a virus forces an infected cell to produce zillions more viruses doesnt work. That would make the host cell virus resistant, she said.

Legal scholars and bioethicists had prominent roles at the meeting, mostly discussing how to keep the public informed about the project.

It should have a plan for doing that in the next year, said bioethicist Jonathan Moreno of the University of Pennsylvania: 2018 brings the 200th anniversary of the publication of Mary Shelleys Frankenstein, which might if GP-write is well underway lead someone to ask, Isnt that a coincidence?

Sharon Begley can be reached at sharon.begley@statnews.com Follow Sharon on Twitter @sxbegle

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'Genome writers' gather to pitch bomb-sniffing plants and more ... - STAT

In a study that offers clues why tea is so popular worldwide, Chinese researchers announced Monday they have successfully sequenced the genome of the evergreen shrub Camelliasinensis, known as tea tree, for the first time.

The genus Camellia contains over 100 species, but the most popular varieties of tea, including black tea, green tea, Oolong tea, white tea, and chai, all come from the leaves of the evergreen shrub Camelliasinensis.

"There are many diverse flavors, but the mystery is what determines or what is the genetic basis of tea flavors?" GAOLizhi, plant geneticist of Kunming Institute of Botany in China and senior author of the study published in the journalMolecular Plant, told Xinhua. "We believe that sequencing tea tree genome would help to solve these problems."

GAO, who got training in genomics and bioinformatics in the UnitedStates,becamethe first scientist to do such a job in 2010, and even with modern sequencing, assembling the genome took his team over five years.

It turned out that the tea tree genome is much larger than initially expected. At 3.02 billion base pairs in length, it is more than four times the size of the coffee plant genome and much larger than most sequenced plant species.

GAO estimated that more than half of the tea tree genome are made of "jumping genes", which have copied-and-pasted themselves into different spots in the genome numerous times.

This resulted in a dramatic expansion in genome size of tea tree, which could have helped the plant adapt to different climates and environmental stresses in Asia, Europe, Africa, the Americas and Oceania, he said.

Previous studies have suggested that tea owes much of its flavor to caffeine, an amino acid called theanine, and a group of antioxidants called flavonoids, including a bitter-tasting one called catechin.

GAO's team found that tea tree leaves not only contain high levels of catechins, caffeine and other flavonoids, but also have multiple copies of the genes that produce caffeine and flavonoids.

But they observed no significantdifferentsin theanine content between tea tree and other species in the Camellia family that are unsuitable for making teas.

"This answers why leaves from some well-known camellias with their attractive flowers and the traditional oil tree Camelliaoleiferacan notbe used to make tea, (that's) because of significantly low production of catechins and caffeine but not theanine," Gao said.

"In other words, expression levels of most flavonoid and caffeine but not theanine-related genes determines the tea processing suitability."

Tea is among the world's most oldest and important nonalcoholic caffeine-containing beverage, and tea tree was originally domesticated in Southwest China. It's estimated that some three billion people worldwide drink tea.

"So, our achievement of tea tree genome sequencing is bringing tea tree biology out of the dark that will greatly help worldwide tea breeders to breed new varieties with more diverse tea taste without pesticide residues and also help to potentiate medicinal uses," said GAO, who called himself "a good tea drinker" for a long time.

"It is our hope that more new tea tree cultivars would finally satisfy and attract more tea drinkers worldwide." (Xinhua)

Link:
Chinese Researchers: Tea Tree Genome Sequencing Offers Clues To Tea's Popularity - VendingMarketWatch

More helpful is Thesis 4 (p. 183) which involves the proposition that we do not have original sin understood as original guilt and damnation for the whole race on the basis of Adams sin in Paul. Perhaps that is deducing too much from Paul. But it is not a helpful either/or to say the issue however is not whether the historical Adam is important to soteriology but what kind of Adam Paul has in mind in Romans 5.12-21. Does Paul reveal an Adam who is a real person, who is biologically connected to all humans, a genetic or DNA Adam? Or does Paul have in mind the standard Jewish Adamthat is the literary, genealogical Adam who becomes an adjustable figure [he uses the term wax in some places] who can be used in theology for a variety of presentations and ideas? This is a false dichotomy.

A discussion of genealogy of begats is necessarily a discussion of biology. And whether or not one says there is a transmission of a sin nature from Adam to all us, or that Adams sin led to a curse on all us which distorts our relationships and leads to sin and spiritual death, either way the outcome is the same, and it is not just because we have all sinned and lack the glory of God at this point. There is a history to our sinning, and Paul says the rot started at the outset as do various other early Jewish interpreters. Death spread to all, not just because of Adams sin, but also because of our own sin, but Paul mentions both in the same breath, in the same argument, as causes. Im fine with the cited quote from Wright on p. 187: Pauls meaning must in any case be both that an entail of sinfulness has spread throughout the human race from its first beginnings and that each individual has contributed their own share to it. Paul offers no further clue as to how the first of these actually works or how the two interrelate. Fair enough, but it is clear Paul wants to say BOTH from the beginning of the race, and yes we contributed to the problem.

Finally, it is not adequate to follow J. Fitzmyers suggestion that in Genesis, Adam is a mere cipher for or symbolic figure for the whole of humanity. Clearly not since we have human mates showing up from somewhere else for Cain and Abel! It is not true that Paul should be charged with historicizing Adam. This is demeaning to Paul, and indeed to the whole Jewish tradition before him that assumes Adam was real person in space and time. So the conclusion on p. 191 is incorrect the historical Adam doesnt show up first after Paul was dead.

This involves an overloaded concept of what the term historical must mean. In fact, he shows up in the very beginning chapters of the Bible. We should not be beguiled by the poetic form and the saga like qualities of the Genesis account. This is no myth of origins, it is rather a historical narrative that deconstructs the myths of origins of other ANE accounts.

Original post:
Adam and the Genome Part Twenty Five - Patheos (blog)

Genome Analytics Driving a Healthcare Revolution

By Bill Mannel, Vice President & General Manager HPC Segment Solutions and Apollo Servers, Data Center Infrastructure Group, Hewlett Packard Enterprise

In comparison to other medicinal practices, next-generation sequencing is in its relative infancy. Manual DNA sequencing methods only first appeared in the 1970s, and the shift to more automated methods finally allowed the first whole genome to be sequenced in 2003.

However, the practice has progressed rapidly in a very short period of time.

Today, genomic analytics is becoming more common and is transforming the landscape of the biotech, pharmaceutical, and life sciences fields. Next-generation sequencing (NGS) is making it possible for human genomes to be profiled in record time and with great granularity, helping researchers pinpoint and analyze more types of genetic abnormalities than they would be able to with conventional DNA sequencing technologies.

Its an exciting time for the healthcare industry as the field of genomics undergoes a period of hyper-innovation. Raju Kucherlapati, a genetics professor at Harvard Medical Schools Department of Genetics, summed it up by saying, All of us in genetics think were going through a golden age. He went on to explain that the accumulation of knowledge is mounting at an ever increasing pace.

With this increase in knowledge comes a tidal wave of data. Genomic data is growing so quickly that scientists are predicting that this data will soon take the lead as the largest data category in the world, eventually creating more digital information than astronomy, particle physics and even popular Internet sites like YouTube.

Here are a few real-life examples of how NGS is helping medical professionals drive a healthcare revolution:

Next-generation sequencing methods are empowering doctors and researchers to improve their ability to treat diseases, predict and prevent diseases before they occur, and personalize treatments to specific patient profiles. However, the continued ramp-up of NGS utilization and the explosive growth of genomic data is driving a need for a commensurate increase in computational capacity. High performance computing (HPC) solutions that are specifically designed for the needs of NGS are now necessary in order to keep pace with the expected number of genomes per day to be sequenced and analyzed.

As genomic data continues to mount, the field will need to adopt new computational tools and approaches in order to extract insight from these increasingly large and complex datasets. Luckily, there are HPC life sciences systems available now that are addressing the requirements of research institutions performing sequencing and assembly on a daily basis, and delivering unmatched levels of performance, scalability, and affordability.

To learn more about how next-gen sequencing is revolutionizing the healthcare industry, please follow me on Twitter at @Bill_Mannel.

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Genome Analytics Driving a Healthcare Revolution - HPCwire (blog)

San Diegos Edico Genome, which makes a fast processing platform for next generation gene sequencing, said Tuesday that it has raised $22 million in a second round of venture capital funding led by Dell Technologies Capital.

Though it has been quietly investing in startups for a couple of years, Dell Technologies Capital revealed its $100 million start-up fund on Monday after previously operating in stealth mode.

Along with Dell Technologies, existing Edico Genome investors, including Qualcomm Ventures, Axon Ventures and Greg Lucier, former head of Life Technologies, also participated.

Edico launched its fast data processor, called Dragen, three years ago. The company says customers include some of the top clinical and academic research institutions and high-throughput sequencing centers in the world. To date, these customers have processed more than 12 petabytes of data using Dragen. A petabyte equals 1 million gigabytes.

"Edico's Dragen Bio-IT Processor is truly the pioneer in the use of a processor -- specifically a field-programmable gate array -- to tackle big data in genomics," said Gregg Adkin, managing director of Dell Technologies Capital, in a statement. And with precision medicine still only in its infancy, the applications and opportunities are increasing exponentially."

Edico, a graduate of the EvoNexus start-up incubator program in San Diego, and Dells EMC division have worked together to combine rapid analysis with data storage of next-generation gene sequencing information.

"Dell's backing will help enable the Dragen platform to radically change healthcare by unlocking data to reveal new insight into diseases, speed critical diagnoses and guide precision medicine," said Pieter van Rooyen, chief executive officer of Edico Genome, in a statement.

mike.freeman@sduniontribune.com;

Twitter:@TechDiego

760-529-4973

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San Diego start-up Edico Genome raises $22M from Dell tech fund - The San Diego Union-Tribune