Field Notes from the Future | Southern Fried Science

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

Posted on January 16, 2016 by Andrew Thaler

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? Read More

Ramblings of an old codger academic #146: What the graduating student has to look forward to.

Posted on January 15, 2016 by Chris Parsons

I have come back, rather the worse for wear (my elderly liver, despite regenerative medication, really can’t take the pace anymore!) from a celebration for my 200^th successful graduate student. The Head of my Department (actually a past grad student of one of my past grad students, or my grand-grad student I guess!) actually pushed the budgetary boat out and we had some very agreeable Canadian Cabernet and a chocolate cake that tasted like it was covered in chocolate from the days when there were still cacao plants. It really was quite a happy celebration, apart from the fact that this newly graduated PhD was heading out into an academic world that is sadly red in tooth and claw. There’s only a month until my 71^st birthday, and with luck I’ll be able to retire within the next ten years. I’d retire happy, and live out the rest of my years reading and drinking nice wine, if it wasn’t for my concerns about my old students.

Not having children myself, many of my graduate students have become part of my family – I have many whom I have nurtured through undergraduate, masters, doctorates and even the super doctoral degrees they introduced in response to the glut of unemployed PhDs. Back in the day, there used to be something called tenure, when professors essentially had job security and the academic freedom to study whatever they wanted. What we call a professor in present times was called an “adjunct’ back in the day. As a professor back then most of us only had to teach two classes a semester, not six or seven. And you could basically teach whatever you wanted, without multiple committees scrutinizing and editing your course content for subversive political statements or accounts of the past that did not match with the approved official historical timeline! Read More

How bioprospecting became biomining.

Posted on January 15, 2016 by Andrew Thaler

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. Read More

Sharks and Global Norming in North Carolina

Posted on January 14, 2016 by Chuck Bangley

I’ve been posting very sporadically due to spending the past month or so compiling all the data from the Marine Species Distribution Survey’s Cape Lookout leg. This was an exciting part of the survey for me because it brought me back to the waters I worked in while earning my PhD, so it a lot of ways it was like coming home. I happily took the lead on the apex predator portion of the survey so that’s mostly what I’ll be recapping first, but future posts will have more details on the trap, core, and genetic surveys.

Of course a lot has changed since then. For one thing, the ocean was two meters shallower, though parts of Beaufort and Morehead City used to flood at high tide even back in 2015. The biggest change may be the collapse and migration of many of North Carolina’s barrier islands, especially after Hurricane Monty rolled through ten years ago. In my mind I still picture Cape Lookout, now an island sitting by itself southeast of the Down East Banks, as part of a chain of barrier islands that once outlined all the North Carolina sounds. Core and Shackleford Banks are still on the map, but as shallow subsurface shoals that have a nasty habit of grounding whatever daring (or foolish) freighters still land cargo in Morehead City. They do draw in a lot of fish though, and still act as a sort of sill that allows Back and Core Sounds to function pretty much as shallow lagoons. If rumors of coral growth on some of the banks are true, it’s possible that the shoals could become fixed in place again.

When we ate the rich.

Posted on January 14, 2016 by Andrew Thaler

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

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

Posted on January 13, 2016 by Andrew Thaler

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. Read More

The last ABI3730xl goes offline

Posted on January 12, 2016 by Andrew Thaler

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. Read More

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

Posted on January 11, 2016 by David Shiffman

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. Read More

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

Posted on January 11, 2016 by Andrew Thaler

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

Posted on January 10, 2016 by Andrew Thaler

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. Read More