The Genetic Rescue Foundation Blog

Darwin: a genomics co-processor provides up to 15,000x acceleration on long read assembly

Genomics is transforming medicine and our understanding of life in fundamental ways. Genomics data, however, is far outpacing Moore’s Law. Third-generation sequencing technologies produce 100× longer reads than second generation technologies and reveal a much broader mutation spectrum of disease and evolution. However, these technologies incur prohibitively high computational costs. Over 1,300 CPU hours are required for reference-guided assembly of the human genome, and over 15,600 CPU hours are required for de novo assembly. This paper describes “Darwin” — a co-processor for genomic sequence alignment that, without sacrificing sensitivity, provides up to 15,000× speedup over the state-of-the-art software for reference-guided assembly of third-generation reads. Darwin achieves this speedup through hardware/algorithm co-design, trading more easily accelerated alignment for less memory-intensive filtering, and by optimizing the memory system for filtering. Darwin combines a hardware-accelerated version of D-SOFT, a novel filtering algorithm, with a hardware-accelerated version of GACT, a novel alignment algorithm. GACT generates near-optimal alignments of arbitrarily long genomic sequences using constant memory for the compute-intensive step. Darwin is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.

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Science is being surrendered to cultural sensitivity

In 2010 New Zealand’s venerable science body, the Royal Society of New Zealand, amalgamated with the Humanities Council. Science doesn’t have all life’s answers. Where would we be without literature, art, music, diverse cultures and the work of humanities scholars? But warm, fuzzy talk of inclusion and connection papered over a fundamental and long-standing philosophical clash.

Most scientists believe their scientific method is a superior way of building factual knowledge and, through technology, contributing to humankind’s material well-being.

What other human endeavours have delivered the internet, space exploration, organ-transplantation or knowledge of natural selection and continental drift?

This is self-evident to the public, but many in the humanities dismiss the scientific stance as “Western arrogance” and consider science is merely one of many world-views, all equally valid.

The “Western arrogance” idea, and a revisionist interpretation of the Treaty of Waitangi, are presumably behind the policy at the University of Otago that all research proposals by its scientists must be vetted by a Maori committee. In similar vein, the draft of the Royal Society’s new code of conduct now places the Treaty central to the society’s work.

There follows a proposal that New Zealand zoologists should “partner with Maori” whenever they study native animals. This goes too far.

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Inside The High-tech Plot To Save The Northern White Rhino From Extinction

Immediately after the world’s last male northern white rhino died on March 19th, a team of vets got to work. Within 30 minutes, they had collected tissue from the ears, gums, spleen, windpipes, and testicles of the 45-year-old rhino, named Sudan. The precious genetic material was put in a solution and then frozen at the Ol Pejeta Conservancy in Kenya, where Sudan spent the last nine years of his life. Those cells could one day bring the northern white rhino back from the brink of extinction.

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The increasingly realistic prospect of ‘extinct animal’ zoos

Animal cloning is becoming more common – and cloning extinct species could be on the horizon. Could parks and zoos for these creatures be round the corner?

A traveller marvelling at snow leopards in a conservation park. A foodie who wants to taste pangolins without breaking the law. A game hunter tracking a black rhino which will be replenished after the kill.

To some people, these scenarios seem like dystopian nightmares. To others, they’re exciting prospects. And as the science advances, they may be more feasible than they might first appear. Some researchers are even exploring how animal cloning could change the tourism industry by 2070.

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Biological annihilation via the ongoing sixth mass extinction signaled by vertebrate population losses and declines

The population extinction pulse we describe here shows, from a quantitative viewpoint, that Earth’s sixth mass extinction is more severe than perceived when looking exclusively at species extinctions. Therefore, humanity needs to address anthropogenic population extirpation and decimation immediately. That conclusion is based on analyses of the numbers and degrees of range contraction (indicative of population shrinkage and/or population extinctions according to the International Union for Conservation of Nature) using a sample of 27,600 vertebrate species, and on a more detailed analysis documenting the population extinctions between 1900 and 2015 in 177 mammal species. We find that the rate of population loss in terrestrial vertebrates is extremely high—even in “species of low concern.”

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Scientists at Harvard University have assembled the first nearly complete genome of the little bush moa, a flightless bird that went extinct soon after Polynesians settled New Zealand in the late 13th century. The achievement moves the field of extinct genomes closer to the goal of “de-extinction” — bringing vanished species back to life by slipping the genome into the egg of a living species, “Jurassic Park”-like.

“De-extinction probability increases with every improvement in ancient DNA analysis,” said Stewart Brand, co-founder of the nonprofit conservation group Revive and Restore, which aims to resurrect vanished species including the passenger pigeon and the woolly mammoth, whose genomes have already been mostly pieced together.

For the moa, whose DNA was reconstructed from the toe bone of a museum specimen, that might require a little more genetic tinkering and a lot of egg: The 6-inch long, 1-pounder that emus lay might be just the ticket.

The work on the little bush moa has yet to be published in a journal (the researchers posted a non-peer-reviewed paper on a public site), but colleagues in the small world of extinct genomes sang its praises. Morten Erik Allentoft of the Natural History Museum of Denmark, an expert on moa DNA and other extinct genomes, called it “a significant step forward.” Beth Shapiro of the University of California, Santa Cruz, who led a 2017 study reconstructing the genome of the passenger pigeon, called it “super cool” because it “gives us an extinct genome on an evolutionary branch where we hadn’t had any before.”

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New Zealand’s two new (but long-lost) flightless birds

A goldmine of New Zealand’s prehistoric natural history has just yielded two more long-lost native species – tiny flightless rails.

Scientists discovered fossil bones of what have just been described as two new species of rail near St Bathans in Central Otago, where many other ancient specimens have been unearthed previously.

Canterbury Museum’s curator of natural history and study co-author, Dr Paul Scofield, said the new St Bathans rails join a host of other fossil birds recovered from these deposits that show New Zealand has long been a land of birds.

“The discovery of these two minuscule flightless rails raises the question, ‘Where did they come from?'” Schofield said.

“The new species are unlike any rail known elsewhere so their exact origin or closest relatives remain a mystery.”

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Researchers use CRISPR to detect HPV and Zika

Science published three studies today that all demonstrate new uses for CRISPR. The gene editing technology is typically thought of for its potential use in treating diseases like HIVALS and Huntington’s disease, but researchers are showing that applications of CRISPR don’t stop there.

The first study comes from the lab of CRISPR pioneer Jennifer Doudna. Her team discovered that a CRISPR system different from the CRISPR-Cas9 one we’re used to hearing about can not only snip away specific bits of double-stranded DNA, but can then also cut single-stranded DNA that’s near it. After they uncovered this ability of CRISPR-Cas12a, they used it to detect two common types of HPV. Once their CRISPR-Cas12a system detected HPV DNA in infected cells, it cleaved a another piece of DNA that then released a fluorescent signal, providing a visual sign of the presence of HPV. The researchers dubbed the system DETECTR and The Verge reports that it takes around an hour to work and costs less than a dollar.

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Fossil poop reveals critical role of giant birds in New Zealand’s ecosystem

When the first humans landed on what is now known as New Zealand 700 years ago, they didn’t find mammals. Instead, they discovered giant birds called moas, as well as a host of other indigenous bird species. Soon, they had eaten many of them into extinction.

Now, by deciphering ancient DNA found in fossilized bird droppings, researchers have a better idea of the toll those extinctions took on New Zealand’s forests and shrublands. The study shows that mushrooms and other fungi were important to the extinct birds’ diets, and suggests moas had a strong hand in shaping New Zealand’s native landscape by helping fungi spread, says co-author Alan Cooper, an ancient DNA specialist at The University of Adelaide in Australia. Now that the moas are gone, “The forest has potentially lost a potentially major way to spread.”

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The Tech Donors Backing the De-Extinction Movement

Even just five years ago, you’d have been forgiven for thinking an effort to resurrect woolly mammoths was a lark, perhaps a high-concept art project.

Increasingly, however, lumbering megafauna and revived flocks of passenger pigeons have become topics of serious discussion in research and conservation, along with a fierce debate over the ethics of using genetic engineering to bring back extinct species. As ecologist Douglas McCauley told Science last year, we’re progressing toward the “Holy crap, we can—so should we?” stage of the de-extinction conversation.

The work is still quite marginal, with a relatively small amount of funding coming from private donors—a varied bunch of individuals and foundations making mostly modest donations, but nonetheless helping to advance what once seemed like pure science fiction into mainstream dialogue.

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Can We Revive Extinct Species Like the Dodo?

Reviving extinct species is a trope of science fiction, but real-life scientists are working on every stage of the problem today. Meeting scientists focused on uncovering ancient animal genomes, or reviving individual cells to conserve species still around, Marnie Chesterton seeks out whether new technologies might, just possibly, bring back the iconic dodo.

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Overseas researchers interested in pest control or eradication are all looking at New Zealand

“Overseas researchers interested in pest control or eradication are all looking at New Zealand,” says Forest and Bird chief executive Kevin Hague.

There are several reasons for that. We are distant from other land masses, and we are surrounded by islands filled with pests that allow confined testing to eradicate whole populations.

We also have a natural ecology that once flourished in the absence of predators. Now infested with rats, we can target those pest populations without fear of killing protected mammals.

And there’s our national focus on killing pests. “This is a country in the world that has done the most in this area,” says Hague.

Not only that, but the government’s adoption of a grassroots ambition to become “predator free” by 2050 signalled to the world New Zealand was a country that took killing pests incredibly seriously.

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