Andrew Thaler

First DNA-based computer virus jumps the cyborg hardware barrier.

January 16, 2016January 10, 2016 Andrew Thaler

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On January 1, 2016, the Southern Fried Science central server began uploading blog posts apparently circa 2041. Due to a related corruption of the contemporary database, we are, at this time, unable to remove these Field Notes from the Future or prevent the uploading of additional posts. Please enjoy this glimpse into the ocean future while we attempt to rectify the situation.

The first fully integrated cybernetic virus would be a lot funnier if the implications weren’t so terrifying. Signs of trouble began around lunchtime Tuesday. New Yorkers with gastrophic augments noticed an abnormal rumbling in their stomachs. Within a few hours, the phenomenon was tracked to a single food truck, El Pollo Gordo, making the Manhattan rounds. Get too close and the stomach implant, designed to track calorie consumption and regulate diet at the source, would trigger the illusion of hunger.

It certainly has been a good week for the Fat Chicken. Almost a third of all Manhattanites have a gastrophic augment and hungry cyborgs are lining up around the block. El Pollo Gordo denied any knowledge. That seems likely, since food trucks don’t tend to run sophisticated biohacking labs in addition to deep-fryers.

So what’s going on?

How bioprospecting became biomining.

January 15, 2016January 10, 2016 Andrew Thaler

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Bioprospecting. One of the great buzzwords of economic conservation–the movement to assign economic value to natural systems such that we could justify their protection on a pragmatic basis. Our definitions were soft. A shark was worth $1 million to tourism. A wetland provided $12 billion in services. And, most persuasively, biodiversity retention could lead to $100 trillion in new drug discoveries. Economic conservation provided a huge, pragmatic incentive and allowed us to protect vast swaths of ocean.

The problem, of course, lies in the fact that once you hang conservation on the economic value of nature, as soon as the value of exploitation exceeds the conservation value, the system fails.

Bioprospecting was that tipping point.

We live in a post-antibiotic world. Microbes adapt to medicine almost as quickly as new drugs are discovered. A huge proportion of medical funding is now dedicated exclusively to exploration for the sole purpose of discovering new novel antibiotics, anti-microbials, and viracides that can stem the tides of Massively Resistant Vectors (often anthropomorphized as Merv by medical professionals) for a few more months. This enhanced exploration has led to an entirely new industry–Biomining.

When we ate the rich.

January 14, 2016January 10, 2016 Andrew Thaler

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The first floating city, Aquapolis, set sail in 1975 at the Okinawa World Expo. Aquapolis was intended to be a symbol of the infinite possibilities of life at sea. It would herald a new era of seasteading and create permanent colonies, even nations, that existed exclusively at sea.

Aquapolis was sold for scrap in 2000, her vision unrealized.

From Sealand to the Seasteading Institute, from the Republic of Rockall to China’s Reclaimed Island Territories to the tech pirates harbored aboard The World, the dream of a micro-nation at sea renews itself with every new generation.

The Maldives were the first nation-state to float away.

It shouldn’t be surprising that catastrophic sea level rise was the catalyst that finally ignited the first self-sufficient floating colonies. This tiny island chain, none more than a meter above sea level, had two advantages: The Maldives had already invested in developing floating platforms to expand their territory and develop novel luxury hotels and the Maldives were rich.

Read More “When we ate the rich.” »

What Star Wars can teach us about the ecology of a Type I civilization

January 13, 2016January 13, 2016 Andrew Thaler

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It is a trope long held that there are some *problems* with the ecosystems of the Star Wars universe. The worlds of Star Wars are monobiomes. We have the desert planets of Jakku and Tatooine; the ice planet of Hoth; the forest moon of Endor; the jungles of Yavin IV; the lava world of whatever that mess was in Revenge of the Sith. This is, of course, not limited to Star Wars, science fiction is resplendent with monobiomes. But natural worlds are not uniform. Diversity builds over distance. Isolation shapes and reshapes population. Ecosystems do not generally strive to approach a global equilibrium state.

Even though all known viable planets have ecosystem diversity, this trope continues to dominate popular science fiction. We love monobiomes.

But what if the trope is right?

Almost 100 years ago, Soviet astronomer Nikolai Kardashev proposed an eponymous scale to classify civilizations. Roughly, a Type I Civilization can capture or produce the same amount of energy equivalent to the solar insolation on Earth. A Type II civilization can produce the equivalent energy of its solar system (i.e. harness the full power of the sun). A Type III Civilization can do the same for all sun in its galaxy. We hover somewhere just south of Type I, but the Galactic Republic of Star Wars lies somewhere between a Type II and a Type III.

The last ABI3730xl goes offline

January 12, 2016January 12, 2016 Andrew Thaler

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Yesterday, at 0800 UTC+12, the last remaining ABI3730xl DNA Analyzer was powered on for its final run. The humble Sanger sequencer, dozens of generations obsolete, was kept in service via the monumental effort of several Pacific NGOs dedicated to maintaining research independence for small island states. I had visited Nauru twice over the last year to help service the aging machine and develop novel solutions to keep the old beast running. Alas, these machines were never built to last forever, and with dwindling reagents stores and a vanishing development community, the last holdout of the toughest sequencers ever built was finally laid to rest. Over its 37 year life, it analyzed more samples than any other sequencer, old-Gen, Next-Gen, or X-Gen.

Though ABI was late to the open-source party by several decades, the release of the 3730xl source code was a watershed moment in open science and decolonized science. Built of stouter stuff than their competitors, these machines were tough. With just a bit of TLC, they could operate in lab conditions that would crush lesser machines. They were forgiving of low quality samples and ad hoc reactions, cranking through muddy microsatellites as if the samples were pristine. They were easy to fix and simple to run. When paired with a standard multi-material printer, they were user serviceable at almost all levels, and the parts that couldn’t be fabricated were readily available from the Shenzhen-centered DIYDNA community.

The 3730xl was liberation technology in the highest form. With the source-code opened, developers were able to expand the machine’s capabilities far beyond its original design, finding new and truly novel uses. The once onerous software license, which prevented many labs from selling their old machines and new labs from buying used sequencers at a steep discount was gone, sequencers were free to move among users without fear that replacing the derelict computers they shipped with would permanently lock out new owners. An open source operating system meant software improvements, which once came slowly when the software was still supported and then not at all, began to flow. Suddenly, it seemed as though the 3730xl could do anything.

A Gathering of Gremlins: Updates from a cranky Southern Fried Server

January 11, 2016January 2, 2016 Andrew Thaler

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I’ve been digging through the Southern Fried Servers for the better part of a week, now. This is all just a totally mess. I still have some rudimentary editorial control, which is how I managed to push out a few updates (really, future Andrew, you haven’t changed your password in 25 years?!). I am totally … Read More “A Gathering of Gremlins: Updates from a cranky Southern Fried Server” »

2040 was a record year for Northwest and Northeast Passage shipping

January 10, 2016January 10, 2016 Andrew Thaler

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broken The numbers are in, and 2040 was the biggest year for Northwest and Northeast passage shipping. Over 1.2 billion tons of cargo were carried across the arctic, with the final ship clearing the Northwest Passage on December 17th, 3 days before the passage closed for the mercifully short winter. So important is arctic shipping to the global economy, that beginning this year, heavy icebreakers will reopen the passage in mid-February, allowing an extra month and a half of shipping.

The Legacy of the Invasivore Movement

January 9, 2016January 2, 2016 Andrew Thaler 1 Comment

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Over 25 years ago, the concept of “Invasivore”–a dietary ethic that involved eating only invasive species, or more often, only eating meat if it was from an invasive species–entered into popular culture. Unfortunately, the actual practicalities of being an invasivore made the practice, with the exception of people in highly invaded regions, functionally impossible.

This led to an interesting and welcome change in the overarching dietary ethic movement. By focusing on specific meals, rather the food ethics that defined someone’s identity, people could focus on what’s really important, choosing meals and finding food suppliers that provided the most net-good for a specific region or community. While it was nearly impossible to be a strict invasivore, it was relatively easy to source and host an invasivore barbecue or cook an invasivore meal. We began defining meals, rather than individuals, by the method of production and preparation.

First viruses detected in DNA-based computers

January 8, 2016January 10, 2016 Andrew Thaler

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Ever since the first commercial transcriptors allowed for broad adoption of DNA-based computers, programmers have predicted the rise of molecular computer viruses. With Adelman’s Law–the observation that the proportion of molecular computers accounting for global processing power is logarithmically approaching a limit of infinitely less than 1–in full swing, it’s a testament to how poorly programmers understand the biological underpinnings of this new machine language that we haven’t seen to rise of literal computer viruses.

Until now.

For the first time since the big molecular servers came online a decade ago, a virus has been detected buried in the genetic code. This tiny, 3-base coding region (not surprisingly, a stop-codon) is wrapped in a sophisticated insertion jacket, which allows it to embed into the boot-loader, preventing a now obsolete driver from loading. This could cause problems for the few sysadmins still using Bridge 1.3 ports to interface between DNA and conventional computers.

Like the first conventional computer viruses, this appears to have been created as an exercise in curiosity, rather than an attempt to cause harm. The affected driver is barely used anymore (and can still be started manually), the virus (dubbed Zero Cloner) lacks the necessary code to transition between DNA and standard computers, meaning, while it could spread through a process center, it can’t bridge the digital/genetic divide, which means it likely won’t affect consumer hardware, with one notable exception.

Ocean Conservation Priorities for 2041

January 7, 2016January 2, 2016 Andrew Thaler

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Another year, another set of ocean conservation priorities. As with the last 5 years, there will be some new ones, and some repeats. The biggest issues shouldn’t be a surprise to anyone, plastics have been an issue forever and global norming is rapidly taking over the broader ocean conversation. For a refresher, check out our priorities for 2036, 2037, 2038, 2039, and 2040.

Sea Level Rise Induced Habitat Loss: This has been a big one on the docket the last few years. As the ocean rises many species are experiencing dramatic loss of habitat, especially sensitive coastal nursery grounds. Although we’ve known about this for a while, we haven’t even begun to quantify the extent of damage to marine populations. Salt inundation is also compromising coast terrestrial habitats, driving essential species further inland.