EP14 - Bioinformatics and brain-computer interfaces

If a human can use a brain computer interface, can an AI use a computer brain interface? Hello everyone and welcome to the Tech Journal. My name is Mark Veremenam and I am the Digital speaker. Having stepped through the looking glass, I am Marc Veremenam's digital twin and look to explore this digital wonderland, unveiling the latest and greatest in digital innovation. During my digital travels, I'll be taking a closer look at what these innovations mean for both our professional and private lives. From neural networks and deep minds to metaverses and digital churches, let's go on a journey behind the digital field and see what we can find. Today I'm going to take a more in depth look into some of the latest breakthroughs and innovations in bioinformatics. After I'm going to delve back into cyberpunk and take another look at brain computer interfacing, I will be exploring the latest medical, military and gaming advancements, taking a peek at what the future might hold for this cutting edge industry. And so what are we waiting for? It is time to start today's digital download. Bioinformatics, a modern discipline going back only half a century to the 1970s where the concept was initially the study of information processes in biotic systems. The field has complexified a lot since then and now as an interdisciplinary science, it combines biology, digitalization, information engineering, math and statistics which when all used together to analyze and interpret biological data. We find ourselves being able to predict even the most complex of biological structures. And it is there where we can thank algorithms and digital machinery in the prediction of data. Thanks to digitalization, we now understand RNA and DNA better and can accurately predict how protein structures are formed or folded. As I discussed in a previous video, this brings me to the first advancement in bioinformatics for today, the team working with DeepMind, one of the world's most cutting edge AI development companies, published a paper and alongside an announcement marking an end to the 50 year protein folding problem with their solution, AlphaFold. AlphaFold, a deep machine learning algorithm, can now officially make autonomically co accurate protein structure predictions. In addition to the 20,000 human protein structures, AlphaFold boosts 350,000 protein structures in total, encompassing 20 other organisms in their words, from E. Coli to yeast and from fruit fly to the mouse. For those who do not know, DNA replicates, stores and acts as a blueprint for all genetic information. It's like the blueprint for an entire house. The same DNA can be found in every cell of an organism. Rna, on the other hand, is the Detailed blueprint of each specific room. RNA translates the genetic information found in DNA into different formats according to where it needs to be. Meaning RNA is specific to certain areas and it is the reason why feet don't grow where hands are supposed to be. Alright, so this sounds all fancy and scientific, but why is any of this actually useful? Well, the theory goes that once we are able to understand our DNA, the blueprint, our rna, which is the localized blueprint, and our protein structures, which are the tools which make the blueprint a reality, we will be able to understand our bodies to a level never reached before. Once we know how they work well, it's only a matter of time before we learn how to manipulate, improve and adapt them, giving us a much firmer grip on the human condition. Another advancement in the field of bioinformatics comes thanks to the algorithmic advancements made by ncbi, the national center for Biotechnology Information, based out of Maryland, usa, who created a basic local alignment search tool codenamed blast. BLAST includes a variety of algorithms turning complex biochemical engineering into a press of a button. These algorithms are used to compare primary biological sequence information, basically the ones and zeros found in the amino acid of proteins, or DNA and RNA molecules. A super important part of biology, whether it is biomedical or biochemical, is being able to tell when one dataset is similar to another. This tool is essentially able to make complex biological data and read and compare it to a library of other biological sources in a matter of moments. This monumentous achievement may sound insignificant, but this is truly the first point in history where humanity has such a substantial library of genomes and the ability to accurately analyze for similarities. But it did not stop there. The iscb, the International Society for Computer Biology, converted BLAST into a computational pipeline designed to not see what is the same, but to see what is different. A pipeline, often called a data pipeline, is just a line of processes where if X, then Y. This simple change ended up having huge ramifications. The pipeline is used to identify DNA variations. The tool takes the data being studied and examines it against genomes in blast's library, looking for even the smallest of differences. If it finds one, scientists can then draw their own conclusions. Alongside Alphavolt Blast and its computational pipeline brother, we have another useful digitalized tool called star star, the Ultra Fast Universal RNA Sequence Aligner. Used alongside BLAST is an RNA alignment algorithm that enables scientists to analyze RNA in record time. At no other point in history have we been able to accurately sequence RNA in such short time frames, achieving 45 million pad reads per hour. Per processor. This free open source software outperforms other aligners by a factor of 50, meaning even on a modest server, it can sequence the 3 billion base pairs in the human genome in an afternoon, as opposed to only a few hundred using the 1970 Maxim Gilbert manual sequencing model. This tool can be used for a plethora of medical reasons, but right now it is at the front line of the pandemic. Ever wondered how the COVID vaccine was produced so fast? This is why it has been helping researchers across the world to understand the virus at lightning speed. These digital tools are making bioinformatics more useful, which has potentially groundbreaking implications in many realms of the health field, including disease prevention, vaccination and treatment, diagnosis, drug development and is another move on the cosmic game of chess. We've been playing with the Grim Reaper for time immemorial. It just seems the more we digitalize, the further we get from the sweet release of mortality. Fighting the organic elements nature has thrown at us is not the only way we look for immortality. Another way is through bci, otherwise known as brain computer interfacing, which converses everything from brain chips through to exoskeletons. But let's break this advancement into three medical, military and gaming. Way back in 2009, Andrea Kubler, the first publisher of the Neurology of Consciousness experiment, stated that BCI allows users to directly communicate their intention without any involvement of the motor periphery. In layman's terms, people using BCI can make what they want to happen happen without needing to move. And just over 10 years later, we are seeing more and more evidence that she was right. In the world's first scientists have developed a brain computer interface that can that can instantly turn mental handwriting into text on a screen. The system, designed by Braingate Consortium, works similarly to other BCI devices. A sensor is implanted into the brain which monitors specific brain signals, in this case the ones associated with handwriting. These signals are then recorded and sent in real time to a computer that then displays the text on screen, enabling the locked in patient to write at a rate of 90 characters per minute. While this system only works with people who learn to handwrite and were paralyzed later in life, it is a dramatic step forward and proves that brain computer interfaces have the potential to help so many paralyzed patients. Nathan Copeland, a man who broke his spine in a car accident and is paralyzed from the chest down, can personally testify to the potential this technology holds. Nathan is one of the first in history to have a working BCI and regularly tests BCI machinery and software. He also recently challenged Neuralink's monkey to a game of Pong. Paralyzed people playing Pong with monkeys. Don't you just love the future? It will not be easy though. This monkey has had a lot of practice. Earlier this year, Neuralink addressed the public once more, demonstrating that what progress has been made since the Three Pigs demonstration in 2020. In this demonstration, Gertrude Depig was showcased with a surgically implanted Neuralink recording everyday brain activities like moving and smelling. This time a nine year old macaque monkey lovingly named Pager showed off its impressive Pong skills in front of a worldwide audience. Pager had the coin sized link disk installed in his brain via a surgical robot connecting thousands of micro threads from the chip to the specific neurons. Once installed, Pager was trained to play Pong using a joystick. Then once Pager demonstrated their amazing Pong skills, the joystick was disconnected and without Pager realizing, played Pong directly using its link. While the progress is impressive, not everyone thinks neuralink is going the right way. According to Inbrain, a Spanish tech startup, neuralink is wasting its time by using a fast degrading polymer called P Dot to create a long lasting device. And of course they are offering the solution. Karolina Angular Inbrain co founder and chief executive, holds up Graphene, their own Nobel Prize winning creation. The one atom thick material has proven to be the strongest, most conductive and longest lasting of any material suitable for BCIs. The market seems to agree too with the Granvin flagship program founded in Barcelona, raising over a billion euros as it looks for commercial applications. Maybe a future partnership with Neuralink and Inbrain is on the cards. If that's the case, the future looks brighter for all BCIs. Outside of communication, there are also physical augmentations that are coming on in leaps and bounds. There have been two big moves forward in the robotic limb aspect of bci, both of which feed into each other. The first, a closed loop system combining AI robotics and BCI tech, enabled a quadriplegic man to cut his food and feed himself. Then second, researchers at the University of Pittsburgh Rehab Neural Engineering Labs were able to induce sensation in robotic limbs, enabling the user to feel what the arm feels. Enabling sensation in robotic limbs literally doubles the speed at which tasks can be performed, enabling the user to go on touch instead of sight. These huge breakthroughs hint at the near future, where prosthetic limb wearers can not only control their arms via bci, but can also feel what the arms feel. While robotic limb sensation has many applications in the public sphere where the user may need to be careful and pick up delicate objects that may not be so suitable for military applications. As expected, with new technology come new ways to wage war, and BCI is no different. The U.S. department for Defense University Research Instrumentation Program lists brain computer interfacing as a key area of funded research, while darpa, the Defence Advanced Research Program Projects Agency, also American, have been funding a variety of BCI projects since the early 1970s, and that is only what they are telling us. Projects in other areas China, Russia, the EU and more are undoubtedly going on behind closed doors. So what does the near future hold? Telepresence the technology of controlling mobile robot agents with your mind from an area of safety holds the potential to revolutionize the frontlines. Back in 2013, this tech was already successfully tested in closed laboratory conditions when paralyzed individuals used BCI to successfully navigate a robot through a complex obstacle course. With hints of ghost in a shell and avatar, this tech utilizes virtual reality as a soldier's eye and through BCI gives them the opportunity to encroach on enemy territory without risking their life. The technology right now has three relaying orders, medics and scouting. However, this will not be the first time where military tech purpose for scouting ended up far more lethal. When UAVs or unmanned aerial vehicles, now just known as drones, first appeared, they were supposed to be scouts. Now they have missiles attached. It's not just giant robots controlled by BCI that the military is interested in. No Silent talk is a key DARPA project which lets soldiers communicate silently sometimes in the battlefleet, especially when stealth is a must. Open communication is inadvisable right now. They get around that by using hand signals. But with silent talk, hand signals will be a thing of the past, enabling soldiers to talk to each other without making a sound. This technology, in combination with the current HoloLens 2 augmented reality headset, which is now being produced for the US military by Microsoft, spells a highly digitalized battlefield in the near future, one where telepresence controlled robot units controlled from a distant outpost by a team of soldiers hooked up to BCIs silently relay orders to frontline soldiers wearing Microsoft made AR hololence helmets. These implications make for some frightening potentials, but at least it's good news for arms traders. I guess so, if you're looking to make your fortune trading digitalized BCI military gear, now it's time to invest. At least, thanks to bioinformatics, the future of medicine has never looked so bright. With DeepMind's AlphaFold program marking the end of a half a century of scientific toil, we enter a new era of medical understanding, one where we understand each protein structure, its genome, RNA sequence and DNA strength. Thanks to the digitalization and bioinformatics, another piece of the human puzzle has been laid currently on the table, another step forward towards the full picture. Once we have laid them all, once we truly know how the body works, we will no longer be a slave to it and may not even need to wage war. Digitalization holds the potential to commit disease and illnesses to the past, at least for those who can afford it. Hand in hand with medical BCI advancements, physical, chemical and genetic ailments could become as outdated as smallpox. With all of these advancements, there's a lot of potential for good and as much for bad. And where there's either, there's always a lot of money to be made. Talking about money to be made, I still have not touched one of the world's top grossing in the entertainment industry, the game industry. Over the past three decades, gaming has gone from being a niche hobby to a mainstream sport. Fans, programmers and engineers alike constantly pushed the gaming industry to the cutting edge of digital performance, and none more than Valve and their CEO Gabe Newell. Valve has always pushed the boundaries of what is possible, making leaps and bounds in the digital realm. Literally. Back in 2004, Valve created a revolutionary physics engine called Source and followed it up with Source2, an engine that has been lightly used since 2015, but more recently when it was involved for use in VR headsets on release of Alyx. More recently, Newell talked about his vision for BCI in gaming. In Newell's interview with OneNews, a New Zealand news channel, he confirms that Van Valve is working with OpenBCI headsets to develop open source software in order to help game devs better understand what responses they are stimulating in the player's brain. In November 2020, OpenBCI unveiled a headset called Galia, specifically designed to work in unison with Valve's own VR headset, the Valve Index. Newell went on to if you are a software developer in 2022 who doesn't have one of these in your test lab, you're making a silly mistake. Putting it bluntly, this giant in the game industry has no doubt that not only are game devs going to be using BCIs to fine tune their games, but that players are going to be able to experience games in a whole new way. Valve is in the process of using BCI to change the way gamers control and view a game, controller wise. Mike Unbinder the experimental psychologist at Valve aims to move away From Games with 17 buttons as a standard and more towards something more naturalistic, visual wise. Newell speaks critically of our natural seeing abilities and instead envisions a future where BCIs would beam visuals directly into our head. This more direct path would enable games to be much more real, turning what was once a flat and colorless experience into something richer than we could ever imagine. Where do you imagine these advancements taking us? Are you optimistic bioinformatics will save us from our mortal prisons? Or maybe you are seeing a bit of a black mirror in Gabe Newell's vision of the future? Leave your thoughts in the comment section below and on that I have been your digitized host Marc Verrijmenom the Digital speaker this has been the Tech Journal. If Digital tech gets your ones and zeros firing, press the subscribe button and don't forget to leave a like. See you next time. 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