Southern Fried Science

When we ate the rich.

January 14, 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 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.

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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.

Skeptical David is skeptical of new efforts to de-extinct the smalltooth sawfish

January 11, 2016January 11, 2016 David Shiffman

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Over Christmas, I finally got to tour the Ram Myers Center for Ocean Biodiversity Restoration captive breeding facility. The millions of gallons of saltwater tanks and the state of the art husbandry and genetics labs look like something out of Jurassic Park. The building itself is almost as impressive as the list of heavy-hitters who work for or consult with the Center, and they’ve had undeniable success with temperature-resistant reef-building corals and pH resistant shellfish and phytoplankton that can survive in our increasingly warm and acidified seas.

I was there to investigate their recently-announced efforts to de-extinct smalltooth sawfish by releasing captive-bred animals into the Everglades and the Bahamas. Once found as north as New York and as west as Texas, habitat destruction and bycatch caused these amazing animals’ range to shrink to one small part of South Florida by the late 1990’s. In the early 2000’s they became the first elasmobranch to be listed on the U.S. Endangered Species Act, and in 2027, they were sadly declared extinct in the wild. In the interest of transparency, I should say that I started my tour skeptical of the Center’s plans to de-extinct smalltooth sawfish, and my opinion remains the same after further investigation.

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.

Remote Protests are visually impressive, but not as effective as public comments

January 7, 2016January 2, 2016 David Shiffman

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Yesterday, tens of thousands of people’s avatars teleported into the lobby of the National Marine Fisheries Service headquarters in Plaza. Most avatars wore a temporary skin that made them appear to be fish, marine mammals, sea turtles, or sharks. Almost all of them of them carried signs protesting the newly-announced shark fishing quota , which greatly increases total allowable catch for scalloped hammerhead sharks. This was the latest remote protest effort organized by the new, but undeniably augemented reality- and media-savvy, Ocean Conservation Solutions , which also designed all of the custom avatar skins.

Last summer, I predicted that this change to the quota would come. There’s no doubt that scalloped hammerhead sharks have greatly increased in population in the decades since they became the first shark species listed on the U.S. Endangered Species Act (as regular readers now, there are now 18 shark species and 43 batoid species on listed under the ESA). Despite concerns raised by conservationists (including myself), it seems that NMFS’ plan to allow a low-level of fisheries exploitation for hammerheads did indeed allow for overfished populations to rebuild. The newly reauthorized Magnuson-Stevens Fisheries Conservation Act, just like every previous iteration, requires that NMFS allow fisheries for any species whose populations can support them.

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.