Archive for the ‘Genetics and bio-babble’ Category

So you’ve watched Orphan Black for a while and one of the big end season 1 revelations turns out to be …

-Beware, spoilers ahead ..-

… evil corporation Dryad has actually encoded a copyright on the DNA of the clones. And one may think, so what’s the big deal? Yep, you knew you were all clones so why care if you find hard coded copyright in your genes? This is discussed further in the series, but we can move immediately to the real world on this.

Actually gene patenting is a very spiky issue. And we can discuss on law and consequences. Let’s start with law.

Human genes cannot be patented in US, according to a Supreme Court Ruling released on June 13, 2013. The argument is clear: a naturally occurring DNA segment is a product of nature and, hence, not patent-eligible. Think, for example, that someone wants to patent air, or water.

Of course, major companies working on the field claim that they are investing large amounts of money on research to isolate nucleotide sequences in specific genes that may help with preemptive diagnosis and/or treatment of severe conditions like cancer. Despite this claim, it’s been stated that any naturally occurring DNA segment is a product of nature and not patent-eligible merely because it has been isolated. However, companies can actually patent sequences that are synthetically created: in the case of Orphan Black, any DNA sequence not coming from the biological parents of the clones as such. If this law was applied to Orphan Black and assuming that clones DNA were mostly synthetic, Cosima would actually be under copyright infringement if she studied her own DNA to heal herself unless she worked directly for Dryad. And that brings us all the way into (real) consequences.

Major protests against gene patenting focus (with reason) on monopolies. If a company has a patent on a sequence of DNA that is related to, e.g. breast cancer, they’d be the only ones allowed for testing of that sequence and, hence, they could ask for as much money as they wanted for any test. Furthermore, scientists not belonging to the company would not be allowed to keep studying on that specific sequence, so progress would slow down. This is a proven fact: let’s evaluate the Myriad Genetics case, which actually led to  the United States Supreme Court decision.

Myriad Genetics Inc. was prevented from holding patents on two genes, BRCA1 and BRCA2, which are linked with a increase in the risk of breast and ovarian cancer. Using its patents, they have tested more than 1 million women since the late 1990s for mutations that often lead to breast and ovarian cancer. The price of the procedure was 3340 USD for breast cancer, plus an additional amount of 700 USD for final confirmation if the initial result was not clear enough. Shortly after the decision against gene patenting was released, DNATraits, a division of Gene by Gene, said they could offer the test for just $995.

Actually, Orphan Black even suggests at (hypothetical) consequences derived from patenting artificial sequences of DNA. If one can actually mutate a sequence inside a person to, let’s say, achieve resistance against cancer, any child of the person could actually carry the mutated sequence and, by definition, be a walking copyright infringement … or (partially) belong to the company.

In any case, thousands of genes have been patented thus far. It would be interesting to keep in mind why inventions like the polio vaccine were never patented. And there’s still people who wonder why we spend money on public research …

Source: Live Science

So, yup, Cameron’s Avatar and Nickolodeon Avatar, the Last Airbender (the movie never existed. Period), actually had a common point: veggie communication networks. Yay!

In the first case, Na’vi were already physiologically equipped to connect to the Hometrees. In ATLA, both the Avatar (Aang and Korra incarnations) and Toph use the roots of an ancient Banyan Grove Tree to gain information about what happens on a different part of the world. In both cases, the overall idea was that the world, just like the trees, was one living organism where everything was connected.

Actually, the idea is not as crazy as it might sound. For a time, scientists have been aware of a mutual beneficial relationship between plants and (mycorrhizal) fungi, that grow around their roots and are known to promote overall plant growth. At the moment, they are evaluating whether they allow plants to communicate with each other to warn about coming insects attacks and, hence, prepare their chemical defense systems.

Scientists actually proposed that communication occurs through the release and detection of information-carrying chemicals that traverse the soil matrix through mycorrhizal networks (any brain analogy here?). In this sense, fungi, which are highly interconnected underground via their mycelia, conform a sort of plant Internet.

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Image taken from Biology Pictures

This theory was tested by researchers from the University of Aberdeen, the James Hutton Institute and Rothamsted Research. They basically grew multiple sets of bean plants in groups. Some of these plants were connected viamycorrhizal networks, whereas others were kept purposefully isolated from the rest. Then, researchers infested single plants with aphids -a damaging insect-, and found out that clean plants connected to infected ones by the mycorrhizae built up their chemical defenses (i.e. release a chemical attractor for wasps, who feed on pesky aphids), whereas unconnected ones showed no chemical response.

There is also some evidence on airborne plant communication, i.e. veggie WiFi, so we can at least say that both Cameron and Konietzko did their homework right in this case.

Source: Ecology Letters

Ever wanted to grow your own TARDIS?

Breeding electronics is not a new idea in science fiction. Not only the Doctor’s most faithful companion is indeed a mix of organic and non-organic material that can be grown out of a piece of itself. Moya, in Farscape, is also a bio-mechanoid, in this case born from another Leviathan. And so are cylon raiders, from Galactica, the Shadows’ and Vorlons’ ships and the White Stars from Babylon 5. In Hyperion (1989), Dan Simmons also describes enormous tree-ships that are grown to move between the stars. And, actually, the trees in Cameron’s Avatar work like an enormous interconnected circuit.

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It’s no surprise, then, that people have been trying to grow, at least partially, their own circuits using bio-stuff. For example, Jean-Baptiste Labrune of Alcatel-Lucent Bell Labs came with the idea of Orgatronics, that combine transducers and microcontrollers with organic materials, mostly wood,

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Why would these circuits be interesting? First of all, you don’t build them, you grow them. They would be also way easier to recycle. Plus, according to their creators, they could use alternative power sources. Of course, we’ve got the sun, but let’s not forget that plants present potential differences that may provide some feeding to low power consumption electronics. For example, see how Texas MSP 430 microcontroller can be fed (up to a point) with almost any citric.

There have also been projects to feed conventional circuitry with, e.g. the potential difference created by tree root acidification, so, for example, trees could sense heat and trigger alarms in case of wildfires. However, electronics were conventional, even though they used the tree for power. It would be way better if the trees could grow just so, right?

This is, for example, the work of Andrew Adamatzky at the University of the West of England in Bristol. Based on studies about the electrical impedance of cucumbers and olive trees, he has focused on lettuce seedlings to create some sort of organic wire. The problem with organic stuff is that, unlike metals, it is typically not a good conductor for electricity. Adamatzky placed the seedlings across a 10 mm gap in a circuit, passed 1 uA current through it and measured impedance and potential over 10 minutes. Turns out his stuff behave like a 2.76 MOhms resistor, way higher than metals, but still well under the resistance of a body. He plans to use the seedlings to connect biosystems with silicon devices. The main challenge Adamatzky is facing is how to control the growth of the seedlings, which is in no way well structured. However, given that the resistance of materials change with factors like, for example, temperature, these thingies could be used to create fully organic sensors.

Still a long way to go, but moving in the right direction.

Source (partially): MIT Technology Review