The last ABI3730xl goes offline

Field Notes from the FutureJanuary 12, 20160

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.


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. (more…)

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

Field Notes from the FutureJanuary 11, 20160

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.


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. (more…)

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

Field Notes from the Future0

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 locked out of the server and content management system. Incidentally, the back-end of whatever future version of WordPress this is looks pretty swish, which only further highlights the fact that we haven’t updated the layout in a quarter century. Has the Southern Fried Science Team become curmudgeonly old academics with aging homepages from a different era?

I kind of hope so.

I have been able to backdoor my way into the server and at least get a look at the source code to see what’s going on. The code is just a complete disaster. Even the basic HTML looks like nothing I’ve ever seen. None of it makes an ounce of sense. There is nothing that ever begins to resemble natural language. This code was not designed to be written or edited by humans. I mean, most code looks like gibberish to me, but this is super gibberish. I don’t even know how to start.

We tried dialing all the way down into the machine code, just hoping to find something familiar. It has to get normal somewhere, right? At some point, it has to tell a contemporary computer how to deliver a website. I mean, the Javascript still (sort of) works and Javascript barely works in 2016!

It’s even worse than I imagined. It’s not just the blog that’s borked. It’s the whole damn server! And not just software, either. The old operating system is gone. Whatever this is has even gotten as far as corrupting the rootkit and BIOS. The BIOS! And not just “oh, here’s a new boot order” but a total rewrite. It doesn’t even look like binary anymore.

At first, I thought this was some kind of glitch. Maybe even a very clever virus. But this goes far beyond a simple infection.

This is a full blown invasion.

2040 was a record year for Northwest and Northeast Passage shipping

Field Notes from the FutureJanuary 10, 2016

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.

brokenThe 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. (more…)

The Legacy of the Invasivore Movement

Field Notes from the FutureJanuary 9, 2016

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.


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. (more…)

First viruses detected in DNA-based computers

Field Notes from the FutureJanuary 8, 2016

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.


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. (more…)

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

Field Notes from the FutureJanuary 7, 2016

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.


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. (more…)

Ocean Conservation Priorities for 2041

Field Notes from the Future

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.


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. (more…)

How cyborgs are like old wooden ships

Field Notes from the FutureJanuary 6, 2016

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.


It is not an easy task to repair a historic ship, especially one that still sails. Centuries of saltwater have crept into her planks, rotting wood and rusting iron. Eventually, everything needs to be replaced, the ship that sailed 400 years ago shares no original parts with the ship that sails today under the same name, under the same flag.

Stop. Go back. Let’s talk about cannons.

In the 17th century, we decided that we could own the sea, or rather, nations decided that they could lay claim to their coastal waters. In De dominio maris (1702), Cornelius Bynkershoek proposed a 3 mile limit for territorial seas. Coastal countries began laying claims, annexing oceans as they still annex new land. Eventually, the 3 mile limit expanded outward, first to 5, than 12, then finally 200 miles, staking claims against not just a coastline, but an entire continental shelf, a nation’s Exclusive Economic Zone. Even today, some nations continue to exert and maintain extreme control over their 3 mile limit.

Why three miles? The best cannons of the era could shell a ship from 3 miles away. This provided a strategic advantage for coastal cities, who could maintain heavier artillery than a warship could carry. Three miles meant that a state could fire upon an enemy entering its territory before the vessel brought its own guns within range.

That limit is now meaningless, and indeed, was rendered obsolete within a few decades of its adoption. Technology moves faster than law. Today, we can fire upon an enemy from anywhere in the world, at any time, without warning. And yet, the 3 mile limit remains, informing shipping, fishing, diplomacy, and resource management, long after the long guns it was created to thwart have rusted away. (more…)

Twenty Years Later, the Identity of Johnny Milkweedseed Finally Revealed

Field Notes from the FutureJanuary 5, 2016

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.


A team of journalists from WIRED have finally cracked the case on a twenty year mystery that, by now, has become almost the creation myth of the modern, radical techno-environmentalist movement. The identity of Johnny Milkweedseed, the name given to the anonymous person or persons responsible for the great milkweed explosion of 2021, was revealed to be Leslie Johnson of DuBuque, Iowa, now deceased.

The journalists re-opened the search for the mysterious actor after last year’s discovery of the original lab that was used to create the hybrid milkweed disseminated by Johnson in the summer of 2020. After tests confirmed the archive of plasmids indeed contained the roundup resistant gene found in milkweed 247a, a number of journalists followed them back to their source – an overgrown farm in Dubuque. The lead turned out to be Johnson’s nephew, Mark Lee, who had kept the garage biolab located in the back barn of the property in nearly perfect condition since his aunt’s passing in 2036. By then, she had moved onto more modern equipment that she was using to create apple and strawberry varieties for her farm, but the lab still housed a number of the classic devices Johnson used for that initial prototyping of milkweed 247a: petri dishes to grow bacteria, micropipettes for implantation, a huge archive of plasmids, as well as the DNA synthesizer that she used, which, as far as Lee knew, was “probably a second-hand machine she found on eBay.”   (more…)

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