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NOAA OKEANOS EXPLORER Program, Gulf of Mexico 2014 Expedition via Flickr Creative Commons // CC BY 2.0

Cephalopods Evolve Differently From the Rest of Us, Study Finds

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NOAA OKEANOS EXPLORER Program, Gulf of Mexico 2014 Expedition via Flickr Creative Commons // CC BY 2.0

The octopus is an animal with a seemingly endless amount of weird and wonderful traits, all the way down to its DNA. A new report published in the journal Cell has revealed yet another bizarre facet of cephalopod biology: the way they update their genes.

Coeloid cephalopods (that’s octopuses, squid, and cuttlefish) have evolved some truly mind-boggling abilities, from Houdini-like escape to crafting makeshift hunting blinds. They lack the standard optical equipment for color vision, yet scientists believe they can see in color anyway. And where warming waters have weakened other species, cephalopods populations appear to be booming.

The original cephalopod ancestor did not have all these traits. Their unique gifts, like ours, are the result of millions of years of evolution.

Animal evolution works like this: the genetic code of every member of a species is almost identical, but not quite. Each individual has a few DNA mutations that make it unique. When those mutations are advantageous in the environment, their owners will survive, reproduce, and pass the mutated DNA down to the next generation.

We also make changes to our RNA, but these are so scarce—in humans, just a few dozen sites amid roughly 20,000 genes—that their influence is relatively small.

But our rubbery-armed friends have apparently turned this system on its head. Researchers reviewing coeloid genomes say the cephalopods have evolved mostly through small, fluid changes to their RNA, and that their DNA doesn’t look like it’s been updated much at all.

The scientists found that around 11,000 of a squid’s 20,000 genes code for mutable RNA. Octopuses and cuttlefish genetics showed similar ratios, especially in the genes associated with their super-amazing, super-complex nervous systems. Nautiluses, those simpletons of the cephalopod family, looked more like us.

Liscovitch-Brauer et al. 2017. Cell.

Neurobiologist Clifton Ragdale of the University of Chicago was unaffiliated with the research but has worked on cephalopod genetics in the past. Speaking with Scientific American, he said the animals’ bizarro evolution scheme essentially represents “an alternative engine for cephalopod evolution.”

Ragsdale noted that scientists use DNA changes, not RNA, when determining evolutionary history. “This may mean that our molecular clock estimates of when different cephalopod lineages arose and diverged might be too recent. The Nobel Prize–winning biologist Sydney Brenner once said that octopi were the first intelligent beings on Earth. This could prove he was right.”

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iStock // Ekaterina Minaeva
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technology
Man Buys Two Metric Tons of LEGO Bricks; Sorts Them Via Machine Learning
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iStock // Ekaterina Minaeva

Jacques Mattheij made a small, but awesome, mistake. He went on eBay one evening and bid on a bunch of bulk LEGO brick auctions, then went to sleep. Upon waking, he discovered that he was the high bidder on many, and was now the proud owner of two tons of LEGO bricks. (This is about 4400 pounds.) He wrote, "[L]esson 1: if you win almost all bids you are bidding too high."

Mattheij had noticed that bulk, unsorted bricks sell for something like €10/kilogram, whereas sets are roughly €40/kg and rare parts go for up to €100/kg. Much of the value of the bricks is in their sorting. If he could reduce the entropy of these bins of unsorted bricks, he could make a tidy profit. While many people do this work by hand, the problem is enormous—just the kind of challenge for a computer. Mattheij writes:

There are 38000+ shapes and there are 100+ possible shades of color (you can roughly tell how old someone is by asking them what lego colors they remember from their youth).

In the following months, Mattheij built a proof-of-concept sorting system using, of course, LEGO. He broke the problem down into a series of sub-problems (including "feeding LEGO reliably from a hopper is surprisingly hard," one of those facts of nature that will stymie even the best system design). After tinkering with the prototype at length, he expanded the system to a surprisingly complex system of conveyer belts (powered by a home treadmill), various pieces of cabinetry, and "copious quantities of crazy glue."

Here's a video showing the current system running at low speed:

The key part of the system was running the bricks past a camera paired with a computer running a neural net-based image classifier. That allows the computer (when sufficiently trained on brick images) to recognize bricks and thus categorize them by color, shape, or other parameters. Remember that as bricks pass by, they can be in any orientation, can be dirty, can even be stuck to other pieces. So having a flexible software system is key to recognizing—in a fraction of a second—what a given brick is, in order to sort it out. When a match is found, a jet of compressed air pops the piece off the conveyer belt and into a waiting bin.

After much experimentation, Mattheij rewrote the software (several times in fact) to accomplish a variety of basic tasks. At its core, the system takes images from a webcam and feeds them to a neural network to do the classification. Of course, the neural net needs to be "trained" by showing it lots of images, and telling it what those images represent. Mattheij's breakthrough was allowing the machine to effectively train itself, with guidance: Running pieces through allows the system to take its own photos, make a guess, and build on that guess. As long as Mattheij corrects the incorrect guesses, he ends up with a decent (and self-reinforcing) corpus of training data. As the machine continues running, it can rack up more training, allowing it to recognize a broad variety of pieces on the fly.

Here's another video, focusing on how the pieces move on conveyer belts (running at slow speed so puny humans can follow). You can also see the air jets in action:

In an email interview, Mattheij told Mental Floss that the system currently sorts LEGO bricks into more than 50 categories. It can also be run in a color-sorting mode to bin the parts across 12 color groups. (Thus at present you'd likely do a two-pass sort on the bricks: once for shape, then a separate pass for color.) He continues to refine the system, with a focus on making its recognition abilities faster. At some point down the line, he plans to make the software portion open source. You're on your own as far as building conveyer belts, bins, and so forth.

Check out Mattheij's writeup in two parts for more information. It starts with an overview of the story, followed up with a deep dive on the software. He's also tweeting about the project (among other things). And if you look around a bit, you'll find bulk LEGO brick auctions online—it's definitely a thing!

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iStock
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Health
One Bite From This Tick Can Make You Allergic to Meat
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iStock

We like to believe that there’s no such thing as a bad organism, that every creature must have its place in the world. But ticks are really making that difficult. As if Lyme disease wasn't bad enough, scientists say some ticks carry a pathogen that causes a sudden and dangerous allergy to meat. Yes, meat.

The Lone Star tick (Amblyomma americanum) mostly looks like your average tick, with a tiny head and a big fat behind, except the adult female has a Texas-shaped spot on its back—thus the name.

Unlike other American ticks, the Lone Star feeds on humans at every stage of its life cycle. Even the larvae want our blood. You can’t get Lyme disease from the Lone Star tick, but you can get something even more mysterious: the inability to safely consume a bacon cheeseburger.

"The weird thing about [this reaction] is it can occur within three to 10 or 12 hours, so patients have no idea what prompted their allergic reactions," allergist Ronald Saff, of the Florida State University College of Medicine, told Business Insider.

What prompted them was STARI, or southern tick-associated rash illness. People with STARI may develop a circular rash like the one commonly seen in Lyme disease. They may feel achy, fatigued, and fevered. And their next meal could make them very, very sick.

Saff now sees at least one patient per week with STARI and a sensitivity to galactose-alpha-1, 3-galactose—more commonly known as alpha-gal—a sugar molecule found in mammal tissue like pork, beef, and lamb. Several hours after eating, patients’ immune systems overreact to alpha-gal, with symptoms ranging from an itchy rash to throat swelling.

Even worse, the more times a person is bitten, the more likely it becomes that they will develop this dangerous allergy.

The tick’s range currently covers the southern, eastern, and south-central U.S., but even that is changing. "We expect with warming temperatures, the tick is going to slowly make its way northward and westward and cause more problems than they're already causing," Saff said. We've already seen that occur with the deer ticks that cause Lyme disease, and 2017 is projected to be an especially bad year.

There’s so much we don’t understand about alpha-gal sensitivity. Scientists don’t know why it happens, how to treat it, or if it's permanent. All they can do is advise us to be vigilant and follow basic tick-avoidance practices.

[h/t Business Insider]

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