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How patent trolls hijacked the building blocks of life
There were three great scientific horse races in the last century. The first two, the race to the moon and the race to split the atom have been widely reported. The race to sequence the human genome seems to remain slightly less well understood by the public, in spite of its critical importance to the world of medicine.
The starting pistol was fired in 1989 when the NIH, the Wellcome Trust and a number of other groups agreed to fund the $3 billion dollar Human Genome Project (HGP) which was forecast to take fifteen years to complete. The sample of DNA which contained 3.3 billion pairs was broken in to strips of 150,000 pairs. Bacteria were used to replicate the strips and they were sent to labs around the world to be painstakingly decoded. This was one of the most ambitious scientific projects in our history and at every step along the way the information was uploaded on to the internet for free for scientists the world over to research in whatever way they pleased. The project promised to provide the groundwork for the cures of countless diseases and the roadmap of the human genome was to be available for free, in full on the internet, with new data released every single day.
In 1998 Craig Venter, a disaffected NIH scientist broke away and announced that his firm, Celera, was going head to head with the HGP in a separate bid to sequence the genome, using his new method. He aimed to do this for a tenth of the price and within a fraction of the time by effectively shattering the genome in to tiny pieces and using a faster technique to fit the puzzle back together.
This created a bitter controversy. Many argued that the faster technique was to take full advantage of the freely available HGP data. It was argued that not only was Celera attempting to undercut the largest humanitarian operation of all time and beat it at its own game, with its own pack of cards, Celera intended to patent everything it found in the process. Once news of this leaked every bio-tech company, hedge fund and banking consortium under the sun wanted a slice of the pie.
The irony of the situation was the Venter had tried desperately for his project to be a part of the public project and fully intended his data to be made public. Unfortunately Venter was forced to resign to being funded by investors, who of course have the sole objective of turning a profit. Venter’s bitter fights with his peers and overlords are described in Venter’s autobiography:
“I still felt trapped by constant legal hassles as HGS blindly went on attempting to patent the data flooding from my institute, whether they had a use for it or not. This was crazy, something had to give”.
Pretty soon Celera had filed patent applications on 6,500 whole or partial human genes. The company was well on its way in the process of patenting a great number of the very building blocks that make us human and the possible keys to beating diseases and infections ranging from HIV to the common cold. Celera wasn't the only horse in the race however; patent trolls began filing DNA patents on a daily basis, based on publicly available data that was being released every night. Two other companies alone filed a further 6,300 patents each. Venter describes how “while my many critics were obsessed with the release of the Celera data, the publicly funded labs were heedlessly dumping sequences into public databases that the pharmaceutical companies were gleefully downloading nightly so they could file patents on them. This naïve policy… had precisely the opposite effect: Gene patents were filed sooner and faster, and almost all were based on government data, not Celera’s”.
Both Celera and the patent trolls had to duck for cover to escape the flack from all sides. All sides except the side of the banks that is. Celera’s stock price rapidly skyrocketed from $8 a share to $500 to share.
Things finally peaked when rumours surfaced that Celera was about to beat the HGP in the race to sequence the genome. Could it be possible that the whole genome was about to be reconstructed, only to be torn apart and patented bit by bit by one company? Wall Street went crazy, if this was true this would be the biggest, baddest, gamble in history and everyone wanted in. In the end President Clinton himself had to go on TV to tell everyone to calm down:
“in the strongest possible terms our genome, the book in which all human life is written, belongs to every member of the human race”
To sighs of relief from scientists and non-bankers everywhere Clinton asserted that no-one was going to patent the Genome. DNA was not for sale. Predictably enough, the bankers pulled out faster than a priest caught doing the bad thing. The Nasdaq experienced the second biggest crash in history losing a mammoth $50 Billion in 2 days on biotech stock alone. Celera tumbled from a listing of 47 to 142 on the New York Stock Exchange.
Unfortunately this was by no means the end of the battle, in reality little changed, patents on human genes continued to stand in the way of affordable access to treatment. Research recently published in the journal Genome Medicine found that at the very least 40% of the human genome was patented, note that the graph below is on a logarithmic scale, if this graph was on a linear scale, the line would appear to be pretty much vertical and you’d need a much bigger screen to fit it all in.
Finally, this month the US Supreme Court ruled unanimously against the patenting of human genes, reversing the decisions of previous courts. At long last we can now say that we all own the building blocks from which we are made. Though it's still unclear precisely how much we should rejoice. In the ruling (which had three errors in the first paragraph) the presiding judge both admitted he did not understand the science and left the door open with regard to more intricate cases than the one that brought the matter to court.
If it was news to you that something as fundamental as the building blocks of life, were until now patented material, then it’s worth investigating further the madness that is current patent law, This American Life recently conducted a fantastic report on the tragic state of affairs. According to the Federal Trade Commission, the majority of patent law cases are currently conducted by patent trolls. Obama has recently declared war on patent trolls, it will now be down to Congress to ensure the law is changed to make it harder for patent trolls to hold us to ransom. Today a leading patent troll was finally taken to the court, it'll be a case worth following. If the war against patent troll is to be won, it'll be down to all of us to get patent trolls into the public consciousness. Hopefully soon it won’t just be our DNA that is freed from their grip.
Mason C. (2013). Pervasive sequence patents cover the entire human genome,Genome Medicine, 5 (27) DOI: 10.1186/gm431
Image Credit: Composite created from images by doomu and iunewind (Shutterstock).
Evolution proves to be just about as ingenious as Nikola Tesla
- For the first time, scientists developed 3D scans of shark intestines to learn how they digest what they eat.
- The scans reveal an intestinal structure that looks awfully familiar — it looks like a Tesla valve.
- The structure may allow sharks to better survive long breaks between feasts.
Considering how much sharks are feared by humans, it is a bit of a surprise that scientists don't know much about the predators. For example, until recently, sharks were thought to be solitary creatures searching the seas for food on their own. Now it appears that some sharks are quite social.
Another mystery is how these prehistoric swimming and eating machines digest food. Although scientists have made 2D sketches of captured sharks' digestive systems based on dissections, there is a limit to what can be learned in this way. Professor Adam Summers at University of Washington's Friday Harbor Labs says:
"Intestines are so complex, with so many overlapping layers, that dissection destroys the context and connectivity of the tissue. It would be like trying to understand what was reported in a newspaper by taking scissors to a rolled-up copy. The story just won't hang together."
Summers is co-author of a new study that has produced the first 3D scans of a shark's intestines, which turns out to have a strange, corkscrew structure. What's even more bizarre is that it resembles the amazing one-way valve designed by inventor Nikola Tesla in 1920. The research is published in the journal Proceedings of the Royal Society B.
What a 3D model reveals
Video: Pacific spiny dogfish intestine youtu.be
According to the study's lead author Samantha Leigh, "It's high time that some modern technology was used to look at these really amazing spiral intestines of sharks. We developed a new method to digitally scan these tissues and now can look at the soft tissues in such great detail without having to slice into them."
"CT scanning is one of the only ways to understand the shape of shark intestines in three dimensions," adds Summers. The researchers scanned the intestines of nearly three dozen different shark species.
It is believed that sharks go for extended periods — days or even weeks — between big meals. The scans reveal that food passes slowly through the intestine, affording sharks' digestive system the time to fully extract its nutrient value. The researchers hypothesize that such a slow digestive process may also require less energy.
It could be that this slow digestion is more susceptible to back flow given that the momentum of digested food through the tract must be minimal. Perhaps that is why sharks evolved something so similar to a Tesla valve.
What is Tesla's valve doing there?
Above, a Tesla valve. Below, a shark intestine.Credit: Samantha Leigh / California State University, Domi
Tesla's "valvular conduit," or what the world now calls a "Tesla valve," is a one-way valve with no moving parts. Its brilliance is based in fluid dynamics and only now coming to be fully appreciated. Essentially, a series of teardrop-shaped loops arranged along the length of the valve allow water to flow easily in one direction but not in the other. Modern tests reveal that at low flow rates, water can travel through the valve either way, but at high flow rates, the design kicks in. According to mathematician Leif Ristroph:
"Crucially, this turn-on comes with the generation of turbulent flows in the reverse direction, which 'plug' the pipe with vortices and disrupting currents. Moreover, the turbulence appears at far lower flow rates than have ever previously been observed for pipes of more standard shapes — up to 20 times lower speed than conventional turbulence in a cylindrical pipe or tube. This shows the power it has to control flows, which could be used in many applications."
A deeper dive
Summers suggests the scans are just the beginning. "The vast majority of shark species, and the majority of their physiology, are completely unknown," says Summers, adding that "every single natural history observation, internal visualization, and anatomical investigation shows us things we could not have guessed at."
To this end, the researchers plan to use 3D printing to produce models through which they can observe the behavior of different substances passing through them — after all, sharks typically eat fish, invertebrates, mammals, and seagrass. They also plan to explore with engineers ways in which the shark intestine design could be used industrially, perhaps for the treatment of wastewater or for filtering microplastics.
It could fairly be said, though, that Nikola Tesla was 100 years ahead of them.
The non-contact technique could someday be used to lift much heavier objects — maybe even humans.
- Since the 1980s, researchers have been using sound waves to move matter through a technique called acoustic trapping.
- Acoustic trapping devices move bits of matter by emitting strategically designed sound waves, which interact in such a way that the matter becomes "trapped" in areas of particular velocity and pressure.
- Acoustic and optical trapping devices are already used in various fields, including medicine, nanotechnology, and biological research.
Sound can have powerful effects on matter. After all, sound strikes our world in waves — vibrations of air molecules that bounce off of, get absorbed by, or pass through matter around us. Sound waves from a trained opera singer can shatter a wine glass. From a jet, they can collapse a stone wall. But sound can also be harnessed for delicate interactions with matter.
Since the 1980s, researchers have been using sound to move matter through a phenomenon called acoustic trapping. The method is based on the fact that sound waves produce an acoustic radiation force.
"When an acoustic wave interacts with a particle, it exerts both an oscillatory force and a much smaller steady-state 'radiation' force," wrote the American Physical Society. "This latter force is the one used for trapping and manipulation. Radiation forces are generated by the scattering of a traveling sound wave, or by energy gradients within the sound field."
When tiny particles encounter this radiation, they tend to be drawn toward regions of certain pressure and velocity within the sound field. Researchers can exploit this tendency by engineering sound waves that "trap" — or suspend — tiny particles in the air. Devices that do this are often called "acoustic tweezers."
Building a better tweezer
A study recently published in the Japanese Journal of Applied Physics describes how researchers created a new type of acoustic tweezer that was able to lift a small polystyrene ball into the air.
Tweezers of Sound: Acoustic Manipulation off a Reflective Surface youtu.be
It is not the first example of a successful "acoustic tweezer" device, but the new method is likely the first to overcome a common problem in acoustic trapping: sound waves bouncing off reflective surfaces, which disrupts acoustic traps.
To minimize the problems of reflectivity, the team behind the recent study configured ultrasonic transducers such that the sound waves that they produce overlap in a strategic way that is able to lift a small bit of polystyrene from a reflective surface. By changing how the transducers emit sound waves, the team can move the acoustic trap through space, which moves the bit of matter.
Move, but don't touch
So far, the device is only able to move millimeter-sized pieces of matter with varying degrees of success. "When we move a particle, it sometimes scatters away," the team noted. Still, improved acoustic trapping and other no-contact lifting technologies — like optical tweezers, commonly used in medicine — could prove useful in many future applications, including cell separation, nanotechnologies, and biological research.
Could future acoustic-trapping devices lift large and heavy objects, maybe even humans? It seems possible. In 2018, researchers from the University of Bristol managed to acoustically trap particles whose diameters were larger than the sound wavelength, which was a breakthrough because it surpassed "the classical Rayleigh scattering limit that has previously restricted stable acoustic particle trapping," the researchers wrote in their study.
In other words, the technique — which involved suspending matter in tornado-like acoustic traps — showed that it is possible to scale up acoustic trapping.
"Acoustic tractor beams have huge potential in many applications," Bruce Drinkwater, co-author of the 2018 study, said in a statement. "I'm particularly excited by the idea of contactless production lines where delicate objects are assembled without touching them."
Australian parrots have worked out how to open trash bins, and the trick is spreading across Sydney.
Dumpster-diving trash parrots
In a study about these smart birds just published in Science, researchers define animal culture as "population-specific behaviors acquired via social learning from knowledgeable individuals."
Co-lead author of the study Barbara Klump of the Max Planck Institute of Animal Behavior in Konstanz, Germany says, "[C]ompared to humans, there are few known examples of animals learning from each other. Demonstrating that food scavenging behavior is not due to genetics is a challenge."
An opportunity presented itself in a video that co-author Richard Major of the Australian Museum shared with Klump and the other co-authors. In the video, a sulphur-crested cockatoo used its beak to pull up the handle of a closed garbage bin — using its foot as a wedge — and then walked back the lid sufficiently to flip it open, exposing the bin's edible contents.
Major has been studying Cacatua galerita for 20 years and says, "Like many Australian birds, sulphur-crested cockatoos are loud and aggressive." The study describes them as a "large-brained, long-lived, and highly social parrot." Says Major, "They are also incredibly smart, persistent, and have adapted brilliantly to living with humans."(Research regarding some of the ways in which wild animals adapt to the presence of humans has already produced some fascinating results and is ongoing.)
Clever cockie opens bin - 01 youtu.be
The researchers became curious about how widespread this behavior might be and saw a research opportunity. After all, says John Martin, a researcher at Taronga Conservation Society, "Australian garbage bins have a uniform design across the country, and sulphur-crested cockatoos are common across the entire east coast."
Martin continues, "In 2018, we launched an online survey in various areas across Sydney and Australia with questions such as, 'What area are you from, have you seen this behavior before, and if so, when?'"
Word Gets Around
Credit: magspace/Adobe Stock
Although the cockatoos' maneuver was reported in only three suburbs before 2018, by the end of 2019, people in 44 areas reported observing the behavior. Clearly, more and more cockatoos were learning how to successfully dumpster dive.
As further proof, says Klump, "We observed that the birds do not open the garbage bins in the same way, but rather used different opening techniques in different suburbs, suggesting that the behavior is learned by observing others." One individual bird in north Sydney invented its own method, and the scientists saw it grow in popularity throughout the local population.
To track individual birds, the researchers marked 500 cockatoos with small red dots. Subsequent observations revealed that not all cockatoos are bin-openers. Only about 10 percent of them are, and they are mostly males. The other cockatoos apparently restrict their education to a different lesson: hang around with a bin-opener, and you will get supper.
Thanks to the surveys, the researchers consider the entire project to be a valuable citizen-science experiment. "By studying this behavior with the help of local residents, we are uncovering the unique and complex cultures of their neighborhood birds."
The few seconds of nuclear explosion opening shots in Godzilla alone required more than 6.5 times the entire budget of the monster movie they ended up in.