BioHackers Podcast

BioHackers Podcast Ep. 2 - Chaos Theory featuring Reed Bender

June 21, 2022 David James Clarke IV and Alex Feltus featuring Reed Bender Season 1 Episode 2
BioHackers Podcast
BioHackers Podcast Ep. 2 - Chaos Theory featuring Reed Bender
Show Notes Transcript Chapter Markers

Welcome to Episode 2 of the BioHackers Podcast!

In this episode, David and Alex welcome Reed Bender to the show. Together, they discuss creative ways for science to help find order in life’s randomness, including chaos theory, yoga’s role in biosciences, single cell RNA sequencing, democratized compute, sonic brain interactions, and holistic approaches to cancer research. It is a lot of FUN! 

Watch the Video Podcast on YouTube: https://youtu.be/k6g3l8ZI-VM

Here is a list of topics: 

  • Welcome to Episode 2 (00:00)
  • What is Chaos Theory? (00:44)
  • The Order of Life’s Randomness (02:30)
  • Welcome Guest: Reed Bender (05:39)
  • Integrating Yoga and BioSciences (09:26)
  • BioHackathon (13:40)
  • Chaos Theory in BioSciences (14:45)
  • Can BioHackers Disintermediate Science and Medicine? (18:21)
  • What is Single Cell RNA Sequencing? (24:41)
  • How to Achieve Democratized Compute (31:52)
  • Is Compute a Fundamental Service? (35:08)
  • Is Discord a Good Model for Democratized Compute? (38:24)
  • Currency Mining and the Development of Compute-based Biology Research (43:43)
  • Holistic Perspective Toward Cancer Research (48:00)
  • Universe as a Cloud (50:10)
  • Sound and the Brain (52:57)
  • What is a Biohacker to You? (1:01:05)
  • Closing Comments (1:04:45)

Enjoy the Show! 

hi everybody and welcome back to the bio hackers podcast i'm your co-host david james clark iv here with uh my esteemed colleague dr alex feltes how you doing today alex pretty good david how you doing awesome awesome are you excited we this is podcast number two i'm very excited about our guest yes this is going to be a good one so cue the opening theme [Music] hey all right all right welcome back so before we bring on reed bender i want to talk a little bit about uh today's topic chaos theory and one thing i've noticed is the 80s and 90s are having a moment you know it's it's uh it's pretty crazy with all of the nostalgia flying around we just had a second top gun movie we've got a fourth jurassic park movie bell bottoms are back in um but i think that the key element the key connection to today's topic is jurassic park and that great character the jeff goldblum character ian mac malcolm who is the chaotician the the chaos theory mathematician kind of made chaos theory popular in the 90s you know as a pop culture reference and uh he talked about he had a great uh line in that movie that i wanted to get your take on um when he was trying to describe you know the dinosaurs were no matter how much we tried to control them they were going to break out of their confines they were going to break through you know the the controls the biological controls that were put in place and he said life will find a way and and i wonder what that means to you because that's a really cool line that stuck with me yeah this is like a i mean philosophical slash like genetics evolutionary science kind of blend for me but like everything that comes out of nature like from an original gene set however it got here on earth is just being uh drawn forward in time through randomness and selection like evolution is really simple you just you know have have changes in your your genes or recombinations of your genes and pass it on to your kids right your offspring and and that passes forward these traits and the ones that are better adaptive more fit can go go forward so everything in life is built around randomness but what's cool is there's some sort of organizing principles in the randomness that is in our universe that drives it forward this process so it's not like completely crazy and that's what chaos theory um really captures is that taking what appears to be random and having seeing repeating patterns in it at different scales and you can see it at you know looking at the um tree branches right you can go and look at how the bifurcating structure of trees and picture it like you know with no leaves on it on a on a winter day and see these patterns and you can see the same thing in your capillary beds inside you you can even like go way out into the cosmos and see dark matter have like the same kind of structure so there's something about the universe organizing principles that this randomness kind of rides on top of and i don't think anybody really knows what that is right i think we're their infancy and trying to understand this kind of stuff but to me that's what it's about and and i i like to look at biological systems from a systems perspective and not like breaking into little pieces and this this kind of chaos theory and other type of modeling techniques are really um i think the future of science and it will be interesting to get reid's take on that because i know you know he's uh one of your ex students uh former students and and a colleague who's participated in some of our bio hackathons and someone who's taking a very unique approach to uh to the study of genomics and computational biology to cancer and other things more at a systems level in our first podcast you know we did talk about reductionist versus systems you know approaches to science and chaos theories that really interesting kind of mathematical computational model for um helping try and find order in non-linear systems yeah um and so it you know be interesting to see his take i don't want to steal any of his thunder but he has a very unique you know perspective on it so um as you've been approaching your science and thinking about you know the new age of computational science do you feel like just having this ability to compute gigaflops and exascale data and the technology that exists today is giving us a more power to embrace chaos theory in systems biology where maybe in 20 years ago that wasn't the case oh yeah the the amount of data we're accumulating especially like at the molecular level and biology is just amazing and rich and very big it's very difficult to process it and so i i think that we have the ability to see the natural world and be in a way that is such high resolution that you have to have computers to be able to see the picture with that but i think i think we're on the verge of like maybe it's not this bad but going from alchemy to chemistry i think we're in that kind of a phased transition no pun intended i don't know if the alchemist would agree with me on that though yeah hey well that's a great segue let's phase transition into the guest portion of the show thank you and uh and welcome our friend uh reid bender yes welcome back biohackers we're very lucky to have our good friend reed bender with us today how you doing today reed doing great thank you guys so much for having me this is really cool oh absolutely and and uh we can't think of a better podcast number two topic than chaos theory and but you've got a really interesting angle on chaos theory before we get there um alex why don't you tell us how you know reed and give us a little bit of his background yeah i read reworked in my lab um at clemson university uh we met years ago i think it was like 2016 2017 in there and we've we've been collaborating ever since yeah yeah sometimes every day and now now a little less frequently but after about five years now through the praxis bio hackathon you guys have kind of reunited and now you know you're attending office hours i think you were just talking about chaos theory yesterday so yeah um here we are on the podcast so reid tell us a little bit about what it was like being in alex's lab yeah so i joined it um kind of towards the end of my sophomore year beginning of my junior year uh while i was working at clemson and i joined it basically by reaching out to a variety of genetics professors knowing i want to do research in the field but having very little introductions to the field and so i sent cold call emails to a bunch of professors um and pretty much got one response which was from alex which was really cool and so he offered me a spot in his lab beginning with my junior year which would have been 2017. and it was funny because at that point i had no computational experience i didn't know anything about systems genetics chaos theory coding in general and it was very much of an open invitation of if you're willing to learn and want to use these tools like come on in and so that's kind of where i got started with all of this stuff well it's a great story reid you know you just basically uh laid out the the whole vision plan for the biohacker community you know as as people from interdisciplinary backgrounds so where you were a biologist then i was uh so i was a bio engineer it was more engineering uh on the biology side before this um but that kind of does give some context for why i'm so gung-ho about this mission because it's quite literally how i got involved in it so i'm very much very much a fan of what you guys are doing here with praxis ai and happy to be a part of it thank you thank you and alex you know your mantra is always hey if you're willing to put in the work and learn how to you know learn learn how to use the command line learn true computation you know power then you know the sky's the limit yeah and also the reads distinction of like i i do genetics and basic science as the department i'm in but i whenev whenever an engineer is interested i'm i'm extremely interested because they think about problems in a much more holistic way much more practical let's actually make it work way it's fantastic to have them in the lab with basic scientists it's a great interdisciplinary mix love it yeah i learned a ton so and here i am because of it thank you yeah i know and the biohacker is the same and and and i know going through some of your journeys alex you know i i attended some of those bioinformatics classes i think read you might have been gone by then but the you know the the cross platform you know computer science meets wet science meets bio meets life science bioscience is a really interesting mix um and you kind of see the power of integrating synergy between you know disseparate seemingly disseparate systems i know that you've got another integration you're working on reid so why don't you tell us a little bit something surprising and interesting about yourself because i think the audience is going to love to hear about this this yeah that's a that's a cool way to tee it up so one thing people a lot of people are actually surprised because you know my engineering background i've always been very much of a rationalist very much of them following the scientific method and very interested in more of the much more rational discussion around science but kind of to balance that out one thing that surprises a lot of people is that i'm actually a certified yoga instructor and i've been studying that for about three or four years now and so that is really cool because one thing i love about yoga is the emphasis it places more on kind of as we were saying before the holistic aspect of it and it's more about incorporating um a larger array of your anatomy your your of your mental states consciously breathing so there's a lot of stuff about yoga that i think complements the scientific method very well but what's cool about yoga for me is that really it really is you know if you look back at the text from india and if you look back at the way it was depicted long ago you can really begin to pull it away from the religion of hinduism of india and yoga really does become a science and of its own right it's science of the body it's just a science of how the breath works and it's a science of how the energy and how energy moves around the body and how harmony and balance is maintained and so i think studying that and learning that kind of on my own in conjunction with more of the systems biology and base science and engineering curriculum i think have given um i've learned to see the world and see a lot of these more complicated complex system problems in a much more different light and so it's kind of cool to be able to come into a conversation like this um with a bit of a different background to see these kind of problems with maybe could you like give your your view on what it's what systems biology is because i think i'm a systems biologist i'm still not exactly sure what it is yeah so and i'm sure we'll get into this more as we begin to talk about chaos there i think this is a great segue into that because when i think about systems genetics i really begin to think about kind of again we we're going to overuse this word i'm sure but more of a holistic approach to the basic science of genetics most of science ever since you know the sequencing of the human genome even before that when you're doing simple knockout studies trying to identify um you know the needle in the haystack for various diseases various inheritable traits you know the central dogma has really been for a long time now let's find the key gene let's find a biomarker or let's find a gene that we know can correlate with a particular phenotype and then see maybe if we can find drugs that can perturb that or act on that or maybe we can look at inheritability inheritability studies and see how genes pass down through populations and all of that is very reductionistic it looks for a particular gene it's more looking for a needle in a haystack when in reality you know what we have with our dna is really about 23 000 protein coding genes and that's 23 000 different variables different knobs on the dial that are your body that you can tune and so genetics as a general field is having a really hard time right now understanding complex systems like we are by looking at single genes in isolation and so systems genetics really i think the purpose of it is to study the genes and study the transcriptome and study how your body is working without removing anything from the system it's looking at all of the pieces in conjunction with the part they play within the hole and so it's looking at the system as it as it actually operates you know it's like trying to study a car while the car is moving as opposed to stopping it and taking out the transmission it's like do it doing yoga just with your one finger yeah exactly there's there's a sense where you need to understand how it all works as a comprehensive system and that's really where the gold is going to be gleaned yeah i really like the way you're thinking about it that way and that brings you know that allows you to bring a new perspective to a lot of your science and and you know the bioscience genetic work you're doing i know that uh we've interacted a little bit on this bio hackathon with bill passman the past you know hackathon and you came at it kind of looking at a holistic it was interesting the different camps that came up you know the long code a long non-coding rna group you had the chaos theory group you had you know but but looking at it more from a systems perspective gave you a whole new you know insight into what might be going on with bill who has this rare kidney cancer but also now a brain tumor and you know are those things related well they're in the same body um and you know bill got super excited about as the patient about you know this new way of thinking about medicine um and in his particular case you know precision medicine one person uh so we were talking earlier about uh jurassic park which is making a big comeback and i you know i talked about chaos theory and that you know the jeff goldblum character and he talked about he had this great line life will find a way and you know and i asked alex you know what does that mean to him what does that mean to you when when you know you think about chaos theory in biosciences so i love that quote and i love the idea that life will find a way because i think at the root of that um you know this we can go as deep as we want into this because i think that really does open up into you can turn that into even a theological discussion of is there some greater ordering principle that is credit is giving rise to the complexity we see in living systems and i think that that quote of life will find a way is somehow trying to address this problem of how do complex ordered coherent systems arise out of a chaotic unpredictable entropy driven world you know in a world that is trending towards randomness and increasing disorder how do we get human bodies that are so coherent and so ordered and so i think that that quote is a really just um beautiful way of depicting that idea of somehow this ordering principle will always find a way to bring order out of that underlying chaos and i think that's that's the foundation that's really what chaos theory is getting at are you looking for that ordering principle so i think that's partly what has led me um down this road and down this whole um beginning with systematics it's one of those things i believe that my you know emailing you and your response to me and getting involved in the lab and pursuing a career in systems genetics and more of a his holistic biology approach um i think has been extremely synchronistic for that reason because it's largely been something that i've been searching for of you know just asking the question of how do complex systems arise out of something that should be random you know the universe is inherently chaotic we don't know what's happening we have zero idea how to make a seed sprout in the ground you know you plant a seed and you can say you can predict that a flower will grow out of it but in reality throughout two decades of you know rigorous searching and however long the scientific method whatever benchmark you want to place on it for where the really rigorous scientific method began we still don't know how a flower blooms we don't know what that ordering principle is that you know makes complexity and makes living systems arise out of dirt otherwise and so i think that that's largely what's gotten me interested in this is really just trying to understand that and it's a pipe dream because it's you know one thing that i think if we have a little bit of humility we can accept we probably never will understand and it's in its entirety um but that doesn't mean it's not something to strive for oh flying was a pipe dream not too long ago right yeah that's i love that analogy yeah yeah i'm because i'm excited what's going to happen and living on mars is elon musk's pipe dream for right now so we'll see how long it takes us to do that but um so you bring up a very interesting point about the the way that you know the scientific method the reductionist kind of process you know works and the power of crowd start you know you think about the world is flat and you know crowdsourcing and you know some of what we're doing right now with the podcast is our ability you know we're disintermediating the uh publishing industry by you know just posting our podcast and and getting the word out there um so you know is it possible for a crowd-sourced community like the biohackers using some of these computational tools and these theories chaos theory systems genetics like you're talking about to disintermediate maybe some of what's happening in the scientific and medical fields and you know in coordination right with them we don't want to blow up the world but the idea that i think we can maybe make some quantum leaps in discovery by doing that is that an is that an interesting path for you i definitely hope so um i'm encouraged when i look at the scientific field right now um i think on one hand there's a lot of reasons to be discouraged i think that it's becoming um increasingly niche i think more and more people are studying more and more um specialized nuanced nuances yeah exactly you're looking at a tighter and tighter sliver of the world and so i think that as you know that's just the medical field is moving in that direction the university system is moving in that direction and i think there's this push um for post docs and phds and you know this is something that i was really wrestling with when i was trying to decide do i want to go and pursue a phd or do i want to go and work in industry or do i want to pursue something else and one of the things that initially discouraged me about the prospect of pursuing a phd and getting really involved in that academia center of research the way that's working currently is that exactly that point of everybody is looking at increasingly complicated systems with z with blinders on to the other complex systems that fill the world around us and so i think that has led to a lot of issues where people are not seeing the whole picture and people are very narrow narrowed in into a particular way of seeing the world and it's kind of leading us in a position where a lot of people know a lot of things about fewer and fewer um pieces of our world and so i think that part of what the bio heart hacker this whole idea promises is a way to decentralize that and pull it out of these increasingly siloed institutions where individuals who just have passion and have interests have the tools at their own disposal to go and learn whatever they need and i think that you know even praxis ai and biohackers aside i think that this is just a trend in the world in a more general sense right now you know you can look at the publication industries and scientific publications and how those have been blocked behind a paywall for a very very long time now and the paywall is becoming increasingly expensive um but then you have things like scihub which are you know democratizing that and taking scientific publications and open sourcing them to the world where the high school student in rural america can access the most cutting edge of scientific research and computational tools and that same student if they were very curious could go on to aws and get a free trial membership and start using computational tools because the tutorials are available and i think that that's one thing that practice ai is doing a really cool job of is getting removing one of those barriers of friction where instead of having to go to aws they have the compute at their fingertips already with tutorials to tell them how to get started and so i'm really encouraged when i look at practice ai and i just look at the direction that the scientific field is moving in general because i do think it's moving more in that democratized decentralized open source framework and i think that once we get to that point and continue to move that direction we'll see much less of this siloing off into niche subjects and much more people who are approaching problems with a much more holistic mindset that's my hope at least do you think that we need compute to do this because i mean like you mentioned that and like is it because when we measure things like are we just gonna have to measure so many things that we need fast computers to analyze it i mean can you do it on a piece of paper um to date myself yeah so i think it's a great i mean to that point exactly i think that um you used to be able to do physics with a piece of paper and you can still do theoretical physics you know there's armchair physicists for sure um i think it's very difficult to conceptualize an armchair biologist just because of how complex the system is not to say that the universe and physical laws of nature are not complex but it's much more tangible we can see the world around us it's much more difficult to see the way a cell is working it's very hard to generate an intuition about the way that genes are being expressed in your cells because it's something that is so foreign if you haven't actually seen it in a computer or plotted on a um uh very like a new map plotter to sneak plot or various ways of displaying this complex um genomic or biological data and so i think that um while i do hope that there is much more theoretical work that goes into of people who just have wild ideas of maybe this is how the body works and then float those out there an open source way of just you know putting their ideas out there with zero compute necessary and let other people run with it but i do think for some of the more complex questions of actually understanding um how the body is working at a cellular level you know breaking it down to the resolution of looking at cells i think we have the technology now with all of this high throughput um all these new high throughput technologies like single cell rna sequencing um to actually answer those questions for the first time so i think to answer your question more pointedly that will require a lot of compute and i think that's why it's really neat that y'all are making those tools available but i'm also encouraged by the idea of potential armchair biologists who could who could just have wild intuitions that prove to be really leaps and bounds forward in the field but i guess so if you have the idea i mean if you're doing science you're gonna have to test it right if you have exactly i just wonder i wonder if you can even test it because it used to be you could go and just capture a few things capture a few dragonflies and you know see if they're different than the other dragonflies and that's great on a macroscope it is that molecular scale it just seems like it's getting the resolution is getting higher and higher the single cell can you this is a complicated thing for me i've been doing this for over you know 25 years like single cell rna sequencing can you kind of explain what that is in layman's terms yeah sure so single cell rna sequencing what what the way that technology works um and why it is such a resolution or um revolution is because in the past kind of giving the back story of what led up to single cell rna sequencing was primarily all the work was being done with bulk rna sequencing where you can take a tissue let's say you have a kidney because that's what you're working with in the context of bill passman and you can essentially remove the kidney or you can look at cell lines you can look at really any cellular or tissue system you have and if you have the tissue in hand what you do is essentially in a more complex manner you take the tissue you put it in a blender you extract the rna and then you look at the quantities of different genes that are transcribed and if you can say that one gene is transcribed at a significantly higher level than another based purely on the number of these transcripts you count inside of the hodgepodge of cells you've blended up you can get a general sense for how the tissue as a whole is expressing these genes and so you can say maybe there's a particular protein that we know to be an oncogene a cancer driver and if you s if you lyse a cancerous kidney and you do bulk rna sequencing sure enough what you'll find is up regulation of those oncogenes um if you know the right one to look for and that's happened to see what hap what is happening in the system so that's the way it's been working in the past but the resolution you're looking at is very coarse because all you can really see is at the general tissue level one thing that we know though about cancer in general and a lot of these various diseases is that there's a lot of heterogeneity within the cancers and so the cells on one end of the of the tissue might look completely different from another end of the tissue and this is particularly extreme in cases like cancer but even in a totally healthy tissue um this is going to be the case you know in the liver you have the portal vein in the central vein and you have this localization of the various cells on the liver and the cells on one end are going to express totally different patterns of genes than on the other and so this idea of blending up the entire tissue sequencing the genes and then trying to get some high level picture of what the tissue is doing is not really that realistic it can give you a very high level view of what's happening in a system but you don't have the resolution to look at what's happening across a time series or at particular cell types within the tissue so like you can't differentiate um the hepatocytes from the cell cells for example you know in the liver like if there's cell there's different cell types in each tissue and you need to be able to differentiate those and so single cell rna sequencing what it does is it basically does this process of cutting up the tissue but then it encapsulates every single cell as its own measurement essentially and so what you're doing is you are getting that same kind of gene expression measurements but you're getting it at the resolution of each individual cell and so all of a sudden with this new technology what we can do is is we can put an entire tissue into the sequencer and throughout these various methods you know it takes a molecular biologist who knows the science of actually how to do the sequencing but what you get is this resolution where you are now looking at the gene expression values of individual cells across a tissue and so what that does is it basically allows you to zoom in it's the genetics equivalent of looking with your eye versus looking with an electron scanning microscope um that's really what single cell sequencing has offered yeah i guess it's kind of i mean i've thought about this it's almost like the ultimate resolution right like because that now we can see we can take a bunch of people and we can go and sequence their dna from their blood right and we can go and see what their dna sequences is down to the exact nucleotide differences or the you know the atgc's the alphabet of dna between everybody and we could do look at the gene expression levels the output of that dna on on a bulk tissue perspective right to sequence the whole oasis yeah instead of like you know going into the croc looking at crocodiles and trying to understand crocodiles but then we could go that resolution if we i know we the tech is still not quite there to be able to to see like every gene expressed um and as we go deeper and look even further that's just a technology issue in my mind yeah biggest largely and that that plus cost and so i think this gets to your point you had made before about you know to what extent can computational biology and systems genetics be really made open source and do you need compute and i think that this kind of helps answer that question as well because in order to get this data in the first place you need extremely expensive sequencing technologies the kits that you use to then put into those technologies for just a single sample of sequencing are also extremely expensive and you need a well-trained molecular biologist who knows how to operate these sequencing machines and as a computational person you know i can study the biology and ask questions while i have the data in front of me but i couldn't tell you the first thing about how to actually go and generate this data and so you know that's i think a bottleneck here because it's very hard and i think i don't really see a clear path forward for this but i it's currently impossible to really decentralize or democratize something like molecular biology just because of the need to actually be sitting there in a wet lab with pipettes with the years of training behind you with all the expensive technology so that's really a bottleneck in this democratization of these tools but i think that the flip side of that is that the computational biology really can be democratized because once you've created these data sets and once you have the sequencing technology that's out on the web you know available for anybody to go and download i then can come in with a youtube tutorial on how to perform a genome alignment and 20 bucks on aws and do it myself just as an experiment and so i think that computational biology is really going to be one of the first steps forward in really making this a democratized platform and that's the hope that i have for it so do you think that um the democratized part of it's just so important i think for everybody i would just see that the people that have the really good ideas who aren't you know maybe in the system getting them some skills and access that's kind of what the whole bio hacker packer i think is all about but do you think that um he's going back and i'm kind of harping on the same issue but the computer like is aws that we're not calling out the commercial cloud providers are it's amazing what's going on but the costs go get out of hand pretty quick because you don't sometimes you can't predict how much it's actually going to cost to run a basic experiment because the data centers are so huge yeah like if we truly want to get you know i don't know high school students you know doing oncogenomics and trying to find cures for cancer and stuff like that they're going to need the compute and do you think it's like a in the is bringing the commercial cloud providers you know costs down for research purposes the way to do democratized computers is it just building out government systems you know and i just like i know it's kind of like boring and nerdy but it seems to be absolutely critical it's the fuel for discovery yeah i mean you can't do computational biology um on a desktop computer you'd need um you need something a little bit more robust and for a lot of these analyses um you know especially if you're going to incorporate machine learning tools you really need gpus and those get even more expensive you know and so a lot of this i think that it really is an unsolved problem right now and you know mentioning the bottleneck is not only the molecular biologists who can generate the data but it is also making the compute available and relatively cheap you know because 20 bucks on aws for a genome alignment that's pushing it you know it can get more expensive than that pretty quickly like you mentioned um and so i think that what we really need is compute platforms that are dedicated to this where and for people who don't understand this concept of a compute platform it's quite literally you from your own desktop computer open up a terminal or a web page and type in a couple of fancy commands and all of a sudden the hardware that you're connected to is located somewhere else entirely in the world and it's a server that's set up with these massive compute clusters with extremely robust and some of the most cutting edge technology that these computers can offer and so you can get much better performance much more storage much faster memory by remotely connecting to these external sources um so that's kind of the base ground the baseline we're talking about here but once if you can do that you know wherever it is whether it's aws or a government compute center or um a cluster that praxis ai has set up and has allowed access to for all the biohackers within the network you know whatever it looks like um that's that is necessary um the question just is what form will that take as this kind of idea of a democratized research um infrastructure grows and it's really interesting there's a big push for uh uh broadband access for everybody right around the planets here right there's the starlight satellites going up and to me there's tremendous opportunity to connect everybody on the planet right it doesn't matter who they are but that there is the compute part like the cost of doing compute is not like buying a laptop or a smartphone and then using it sure you're going to need more power and so like i just wonder like i know i'm going off on a little bit of a narrow subject here but um you know the road like the road system is incredibly important for like the u.s economy right and like i didn't pay for the roads you know myself i had some taxes go and do that and so like you know i guess the the the private sector could have built the the road system or the government could you know this is the same kind of thing like that they have the networks that scrape within the compute yeah is this a fundamental service of the government to give access you know we could build it people in other countries could use it right too so i think it's a really important question because it comes down to the central point of like you know we can talk about this all day until we're blue in the face but if there's no actual um way to deliver this compute you're dead in the water i mean there's no way to even get off the ground and so i think that that really needs to be addressed um this is one place where to answer your questions specifically about government infrastructure for these systems um i would argue certainly not i don't think that that's necessarily the best um way to move forward with this just because for i mean for several reasons because it's it's clunky it might not um have the best you know it's very difficult to update the bureaucracy i mean it just moves very slowly and getting users onboarded getting the clusters and the servers updated maintaining the most cutting edge compute you know if you have private servers like this this is one thing that makes aws um so powerful is that they are constantly updating their servers they're constantly putting in the newest and best computers and so i tend to be a little bit pessimistic about the ability of a centralized bureaucracy to maintain that kind of interesting constant update and this is where i actually am extremely interested in blockchain technologies um and kind of building off of the cryptocurrency idea where rather than having something like an aws or a government center that is hosting this compute from a centralized center what you really have and what becomes available if you can create the blockchain technology robust enough and create the create the infrastructure in place what you can have is basically you know a biohacker like myself with a series of raspberry pies that i hook together and link up um in my apartment and if you have 10 000 biohackers around the world that have some combination where let's say a third of them have their own form of compute and that can be anywhere from a raspberry pi to an nvidia gpu that they have in their house and if you have that range of biohackers that are actively contributing to the network um as a part you know as a part of being as a part of being in the network so part of i'm a biohacker i want to do this democratized compute i want to study gene expression and cancer across various time points i can basically have my own little computer that i connect to the network through a blockchain technology through a blockchain hash essentially and then that links up with all the other biohackers across the world and so what you have then is basically a democratized cloud um and i think that if you can get something like that in place you can really bring what makes cryptocurrencies so promising as economics as a technology and make that available to independent researchers as a platform and instead of validating transactions validating financial currency movement across the world what those compute clusters are doing is letting people study genetics wow i love it discord you know we do have a uh we do have an early stage analogy for that you know in the discord which we we've started using you know ourselves which is this you know cloud of servers that are free and open but you have this um this concept of of membership to a server and when you join that community you can nitro boost you know you so you can use you know tangible real money to purchase and effect a cryptocurrency a boost which is then donated to the server to increase the capabilities of the server and therefore enhance the experience for everybody who's a member of that community um and you know early early early days but you know love your vision it's very foundation ask if you've ever read the uh as a novel or watched the apple tv show but the idea that you know you do have this fully democratized um cloud where everybody's contributing and you know i bet if you counted up the usage analytics on a typical raspberry pi sitting in your apartment or an nvidia you know gpu it's probably only being used a third of the time maybe less you know but imagine if it was you know on if we were able to tap into that unused you know time and and resource and you think about a raspberry pi and you don't think about a very powerful compute um but you link up 10 raspberry pi's together and you can do some cool things with that and so i think that if this is not um this is not unreasonable you know it's definitely far-fetched it would take a lot to get to this realization but i do think it's definitely possible and part of the vision for this this is exactly how the um cardano blockchain specifically um that one is a i highlight that cryptocurrency out of the uh host of them for a particular reason because the way that the blockchain for cardano works is rather than like bitcoin where you have um operators who are basically mining and running very intense compute just to reveal new bitcoin essentially is how that works is you run these iterative operations on the computer and eventually you strike gold and a new bitcoin is minted that's not how cardano works cardano actually works by distributed stake pools and so the way that that works is i if i wanted to be a part of the cardano network could create my own stake pool and so that could be whether it's on a raspberry pi in my own apartment i could i could basically buy an aws compute server and host it myself i could do this in any of the cloud providers or if i have my own server so let's say i'm connected to a server um that i just happen to have access to maybe through um research universities probably not the best idea because you would have some legal issues there but however however you have access to the compute basically what i can do is spin up a um it's called a stake pool and what happens is once i have that that stake pool is running basically in a similar way to bitcoin nodes work and it's constantly validating the network and so what it's doing is it's reading all the transactions like the um the ledger basically across the across the cryptocurrency network and as it reiteratively updates it's validating the network and so it's basically the checks and balances to everybody else on the network but these are running all over the place so everybody across a whole host of operators across the world have stake pools up and running and if i as an independent owner of cardano want to then invest i can stake my cardano to that pool so it's basically it's still in my wallet but i contribute it it's like i tag it to a particular pool that i am i believe in or i think has a good mission because typically these pools have donations so each one of them will have their own cause so maybe one stake pool is donating um to the salvation army and i believe in that mission so i'm going to stake my cardano to this pool and i believe that this democratized compute within something like a practice ai system could work very similarly where if i as a biohacker wanted to run my own server i could host the raspberry pi's or the server in my own apartment i could put them onto aws and then other bio hackers in the network who are you know interested in the mission and believe that maybe what i'm researching maybe it's something that i can like post my research thesis on on the website on the front page of the pool and people can contribute it almost like a you know buy me a coffee or a gofundme where they're kind of helping to pay for the server costs um and as a result they then they then have access to it and so you can very much you can turn this into more almost like a game and kind of play with the incentives of people want to donate to good causes people want to be a part of cool research and if you incentivize that well enough and work with a psychology you can really grow a democratized platform very quickly i think cardano has shown great proof of work of that or proof of concept so we're off the rails here on the conversation totally off the rails but i don't think that's one way it could work but this is really good you know it's i think this is obvious what you're saying i didn't i've never thought about this but like cryptocurrency mining is about generating a currency of that a value something valuable but it's like it's an abstract value analogous to a dollar right attack to physical currency but if you were to take and you have to have compute systems to be able to do that that's what you're talking about but if you had every other calculation when one goes towards cryptocurrency one goes towards processing genomic data for some kid that's got cancer like you you created a whole interlaced value structure that goes far beyond this you know currency model of our our species that works great it's good right it abstracts things and it keeps us from having to barter allows us to go you know be add more people but that that's that's the i didn't really think about the compute is being driven by this i always think about you know gaming drives computing right drives a lot of technology right and then i've benefited you've benefited a lot of people benefited from graphics processing units gpus like you mentioned they're used just to throw you know better better frames per second on the screen so you can you can frag people or you know all the puzzle or tetrising or whatever yeah these are being now this those have been co-opted by the research computing you know market and people are making major discoveries that are very valuable for our species but it's from gaming which i'm not going to argue gaming's bad i'm a gamer i like to game but like you know there you can use it for two purposes and maybe there's a third purpose you know with currency mining and wow yeah the future is right very much so that was a total tangent we went way away from chaos theory but i do think to your point it's a really important question of how do you actually make this compute available because without it like i said you're dead in the water you know that's kind of any prior you need to solve and one of the one of the questions i've been trying to get to for half an hour um which is thank you guys it's actually a precursor so i'm going to do that thing that star wars did you know where they did the first uh the middle three movies first and then they went back to the prequels so i'm gonna go back to the prequel to that entire discussion which is you know why all of a sudden is chaos theory having a moment you know it was a in biology in bioscience it was around in the 90s you know and system genetics and systems biology you know was a way of seeing the world back then fast forward excuse me 20 years later now suddenly it's the way i think i mean you've made a really good case today read on this podcast that you know if you're if you're looking at if you're doing science right now bioscience uh you know in a sliver orientation you're doing it wrong um then is it is it the compute i mean is it the compute and the capabilities that we have now to run these gigantic exa scale you know data models etc in you know in full systems that is allowing us to embrace chaos theory and systems biology whereas maybe 20 years ago we couldn't i think there's definitely something to that i don't think that it's the whole story because even with all of the compute that we have available to us you could take the old paradigm of reductionist biochemistry and plug it into a recursive algorithm that is just you know searching for the again the needle in the haystack and you have this algorithm that is just burning through compute looking for the one mass regulator that's going to lead to cancer you know you could try and find a single gene that once it's turned on you have cancer and i i would argue that's a not as fruitful of an approach because even though you have the compute you have the wrong hypothesis going into it because i don't believe that's how the system is going to operate and so i think that along with the increase in compute and the increase in computational power and just a expansion of what's possible i think you need to couple that with the right way of thinking about the system you're trying to study i think if you take the old paradigm and just apply it to new technologies you're not going to get any further you're just going to be going in faster circles is that where your yoga background comes in i mean you're coming at it from a holistic you know perspective uh from the get-go i think that's part of it um i think that that's something that definitely trained me um it was funny because i was studying yoga and learning yoga at the same time i was really being introduced to systems biology those two really went hand in hand for me which is an interesting thing to reflect on um because i think i had two um very impactful movements in my life where both of those things really changed the trajectory that the light that my life was moving in and kind of the types of questions that i was interested in um and both of those highly um put a lot of emphasis on holistic thinking and thinking about the system rather than individual components you know the way that the way that i think about it i think a very clear distillation of it is a lot of science and a lot of you know the 1990s way of viewing the world was like a clock where you have everything is deterministic where if you know the starting state and if you know the conditions that you're working with and you know how each piece of the system works you can deterministically predict what will happen in the future and the way the system will operate moving forward into the future and it's very much like taking apart a clock if you have a grandfather clock that you is broken and is no longer ticking you can take it apart piece by piece find the tooth that is broken repair it put the clock back together and sure enough you have a functional grandfather clock and so i think that that's the paradigm that science has adopted in most of its work up to now you know chaos theory and a lot of quantum theory aside that have been much more fringe until until recently the bulk of science has been really focused on that reductionistic problem of let's break things down to their key pieces and if we can understand how each piece works on its own we can then put them back together and understand the whole and how it works but that leads to a completely deterministic world you know there's there's no room there for chaotic outcomes or for unexpected potentials and so i think that a better way to view the world and the way that you know i've kind of come to see it both through my research with systems genetics and through just studying yoga as a philosophy i think that the two of those kind of converge on this sense of we really need to view the universe as more like a cloud where you can you can think about a cloud as a system where you can ask you can ask the question is it going to rain in an hour looking at a cloud will that cloud drop rain in an hour and in order to understand that question to try and answer it you can cut the cloud in half and you can say okay well this cloud well this half wrangled this half and then you can keep breaking it down you can keep having it until you break it down to a single molecule of water and the reductionistic paradigm would say if i understand the behavior and the initial state of every single molecule in the cloud then i can with 100 confidence deterministically predict whether or not it will rain in an hour better not you could predict whether or not it will rain in a hundred years because it's that deterministic if it's truly a clockwork universe what we're seeing though in biology and in physics and in meteorology and in all of these disparate fields that have begun to take an appreciation of chaos theory is that's not how the world works fundamentally you cannot break it down to the key components and understand the state of the system really you need to understand how each water molecule is functioning within the context of every other water molecule so as soon as you pull one piece out of the puzzle the whole puzzle shifts it's like walking through a maze while the walls are moving around you it's impossible to get your bearings when you begin to take pieces out of the system because it's chaotically changing immediately and so where chaos theory comes in is really trying to understand the dynamic state of a system within the context it's operating um and i think that that's really the approach that yoga has taken to the body and to human physiology um i think this is the approach that more and more domains of science are beginning to move into then we're going kind of longer but i want to make sure that um reid can explain what your project is right now this this web service that you're building and maybe if you could fit into this crazy complex that we're talking about i can definitely segue this sense this is this is a huge tangent this is a bit moving away from chaos theory but it does relate in the way that i conceive of the human system um if you will i'm currently working on um a web application um and it's a subscription-based service um it's i'm going i want to make it very cheap like five bucks a month and make it highly available um for everybody um but really kind of adopting this paradigm and this mentality to mental well-being and psychological health one thing that has been proven over and over again and really has direct ties into chaos theory is that um sound has an incredible impact on the human mental state human psychology and just human health in general even the physical body is extremely receptive to sound they've actually they've done studies on musical ensembles and symphony orchestras and they found that the brainwaves of musicians that are playing in harmony with one another playing in a band together their brain waves actually synchronize and so what i mean by that and this is getting into what this website is offering um is that the way that the brain works we think of it and this is again tying it into the reductionistic paradigm of we think of the brain as a series of neurons that are firing and conducting information really though the way that it works is more like a network where each of these neurons is firing and then that leads to other networks other neurons that are firing and so you have these neurons that rather than operating like deterministic switches on or off it's more like a musical symphony where you have harmonies and coherence and you have discord in various parts and so if you if you begin to look at the brain and the firing of the human nervous system like a musical ensemble where there is harmony and discord and you need to find some kind of harmonic equilibrium well that's what your brain waves are doing so your brain waves are actually firing at certain frequencies and so you can have lower frequencies um in the two to five hertz range that correspond to deep sleep but then you have higher frequencies in the 30 hertz plus range that correspond to stress and anxiety and within there you have intermediate ranges that correspond to intense focus there's particular frequency bands that lead to deep deep meditative states there's frequency bands that lead to more creative introspection and kind of floating thoughts and so you can really tune your neurology in the same way that you tune a guitar string if you know the frequency band you're interested in entering into you can actually tune the way that your brain is firing to actually access that frequency band and you can do that with sound because your brain and the way that your brain responds to audio audio inputs basically um has a frequency following response is what it's called where if you play a certain frequency of music your brain will begin to synchronize at that same frequency and this is what leads to the musicians having synchronized brain waves when they play the same piece of music together and so that's kind of the the um scientific background for what i'm trying to offer with this website where it really is a combination of these various um audio tones and so offering within the website at you know you can click a drop-down box and play the tone directly within your web browser um i'm they're called binaural beats and it plays one tone in one ear and one in the other and your brain begins to synchronize to the delta between them so let's say you're trying to synchronize into a six hertz band maybe you can play 40 hertz in your right ear and 46 hertz in your left ear and this is the same mechanism that allows you to locate a sound if it's over your left shoulder you can point to exactly where it was even though you didn't see it or hear where the sound came from it's because you're able to essentially triangulate where that came from and so it's hacking into that mechanism within the brain to enshrine your brain waves this particular pattern so that you can enter into very easily these deep sleeps these deep meditations these intense focuses um or even like extroverted engaged awareness on the more stressful side of the spectrum and so that's what this is it's called a tuning mind the website is a tuning mind att you in ing mind dot com um it's still you know in in the works it's a it's a it's definitely in progress but the website is live you can go and check it out and see the progress as it develops for sure but that's what this is going to be and so i think that it definitely ties into chaos theory because really it's getting away from the paradigm of you have you're stressed out okay here's a drug you can't sleep well here's some melatonin getting away from more of this biochemical reductionism of you know you have something you need to fix here's a single drug a single pharmacological input that will affect it and it's much more of a holistic approach where really the way that we're viewing the way that i view the body in creating this is as a series of oscillations you know the body and the neurology is really just um an electrical harmony on a massive scale and you have um an infinitude of discordant and harmonious frequencies that are playing with and against one another and so by using sound and by using different frequencies of music to begin to bring those into a more coherent state you can radically shift your perception and so that's what i'm trying to offer through this website and this is all the mechanism of all this is happening at the molecular level yeah it says see that right you can't you can't drill into somebody's brain when they're doing yoga and and see what's gene expression patterns are changing but yeah exactly and this is this is kind of where i view the body as more um you know and more and more study of this and i think this is more directly correlated with yoga as well which has kind of given me a chance to see um the human machine and physiology a little bit differently because i really view the body as an electrical system more so than a chemical system and i think that that perception kind of opens up a new way of seeing you know because you can't think of the brain as music if you're thinking about it as a drug as chemicals if you think about it as a series of molecules it's very hard to conceptualize the idea that your music could be actually or your brain could actually be singing a harmony of tones what we think about it as electricity it's much easier because all that sound is is oscillating frequencies it's oscillating uh waves like a pendulum um electricity is the exact same thing and so you have these um alternating currents essentially running through your nervous system and it runs it runs through every single cell so every single cell in your body um is electrically active not just like ionic potential yeah so this is not just sodium potassium gas that lead to nerve impulses this is actual um conductive electricity that can be measured measured with a voltmeter and that's what surrounds every single cell and so i believe that is what this um harmony of sounds is beginning to tap into because if you stick with a given binaural beat long enough you will begin to see especially at more of the six to eight hertz range it's very strange because you'll actually begin to feel this if you give this a shot you try listening for you know more than 10 minutes if you sit with the sound for about 20 or 30 minutes yeah you will feel very quickly and very viscerally um vibrations begin to set in in your fingers and in your body and you will actually feel this oscillatory nature of your energy um and it will very quickly change the way you think about yourself um as a living system because there's really no other way to conceptualize it and it kind of forces you to open up your mind a little bit so i challenge all the biohackers out there who are listening to check out um reid's website and what what is again it was a it's a tuningmind.com.com and uh and make sure to uh zero in on the eight to six range before the next podcast so that you can be creatively attuned into all the the wisdom you'll get on the show so um last question we do we know we did talk about biohackers a little bit as we were going through and you're one of the original biohackers reed thank you very much you know for for getting badged for getting engaged for you've already attended and participated in you know our inaugural bio hackathon you're here on the podcast so what is a biohacker to you um i i love that you all have termed this as a biohacker like i think that that word um you know because you come from especially from the computational side when i really got into the computer science i got um exposed to the word hackathon it was like i had never heard of that before and this idea of you can collect what you can gather with a group of like-minded individuals who like solving problems and write code to try and come up with cool solutions and the idea of a hackathon i just got so excited about and started to do a lot more of them while i was in school and so now to hear you guys um kind of you know adopting this terminology of biohacker i i can't think of a term that better suits my own endeavors and my own approach to these problems um and so when i think about the word biohacker it really combines you know the idea of a hackathon in computer science with somebody who is in intricately invested and deeply interested in the idea of biology and physiology and really the key question is you can make it as broad as you want but really this all comes down to how does the body work you know this goes back to what i opened up the conversation with of how does order and complexity arise out of a world that is trending towards increasing entropy and disorder and chaos um you know the what chaos theory says is that the underlying infrastructure and the underlying foundation of our world is chaotic and probabilistic and it makes absolutely zero sense but then there is this complexity principle there's this ordering principle that comes in and gives shape to it and it almost like puts constraints around that chaos um and that is nature nature is what then brings the order around that chaos um and allows it to take form and become something beautiful like a human body or like a tree or like a flower and so that's how i see the world and that's how i see chaos theory as it relates to the world around me and so then to your question about what is a biohacker um i really think that a biohacker is somebody who takes it upon themselves to see the world in that light to see the world not as a deterministic um clock but as something that can be engaged with and can be inquired about you know we actually have the tools and have the ability now to ask questions about the universe that we live in and try and dive deeper into the mysteries of what makes a human body tick because it's infinitely more complex than we think it is right now and so i believe that a biohacker is somebody who takes it upon themselves to try and ask those questions and use the tools that are available through praxis ai and through compute and through youtube and through you know libraries and there's we have infinite resources available to us now any questions you want to learn about these types of fields you can go and ask you can ask any question and come up with an answer the question is just how much effort you're willing to put into it and how much thought and mental capacity you really want to invest into these questions and so the true nature of a biohacker is somebody even if you never touch a command line is somebody who takes it upon themselves to find the initiative to see the world in a different light and ask questions that are difficult but might reveal really beautiful answers and to do it in a community so we've got you know yeah exactly hackers.bio and and prxai.com and and we have a couple bio hackathons coming up so you know reach out to us and and sign up it's all free and and we're trying to get people engaged in that crowdsourcing approach to to bioscience research that's really cool closing comments alex oh just to go up on that you know a big thing that we're trying to do is is remove the gap between research and education and really trying to democratize research and you know our our perspective is or approaches that it's a computational approach is a big underlying component to it all just because you can't process a lot of this data without that help and you need help yeah there is nothing harder than what what the kind of stuff you're talking about but like i don't you know you might your ideas are fantastic and you might not figure them out in your lifetime but the tools are here now so maybe maybe we can maybe you will you know and maybe those drugs that you're taking melatonin is not working but you know maybe understanding the the pulse of of you know how these this through yoga and and changing you know sound waves in your in your brain will reveal how you're supposed to administer drugs that we know have some effect but we're just administering them wrong right we're putting we're not they're not in the right sequence and i'm going off so i'm going to be quiet now no that's not wonderful that was the that that was the uh the the vision the statement uh i don't know what that was it's it's it's highly relevant um because i think that that is what that sticking point and that friction that you just highlighted is really what led to um i think this mission that you all have really that's watched um and that i have enthusiastically joined as a part of thank you so i think that it's i think that you hit the nail on the head with that as the friction point that you are trying to alleviate find a need fill a need and you know and as we all know from physics you know anytime you uh you get friction it creates some sort of energy and that energy you know hopefully is positive in this case i think yes very positive and uh reid we're very very thrilled to have you on today's show thank you so much that was a brilliant conversation this has been really fun i've i've thoroughly enjoyed this um and really appreciate you guys having me on this has been cool well this will be the first of many uh so certainly where we'll go from here but thank you so much for your time and thank you alex and and everybody for listening and until next time cue the ending music [Music] [Applause] [Music] you

What is Chaos Theory?
The Order of Life’s Randomness
Welcome Guest: Reed Bender
Integrating Yoga and BioSciences
BioHackathon
Chaos Theory in BioSciences
Can BioHackers Disintermediate Science and Medicine?
What is Single Cell RNA Sequencing?
How to Achieve Democratized Compute
Is Compute a Fundamental Service?
Is Discord a Good Model for Democratized Compute?
Currency Mining and the Development of Compute-based Biology Research
Holistic Perspective Toward Cancer Research
Universe as a Cloud
Sound and the Brain
What is a Biohacker to You?
Closing Comments