My idea in a paragraph
I want a virtual body to facilitate research, teaching and general understanding of how we all work. The more we understand how we work the better prepared we are to maintain our bodies given the daily challenges we all face. I want to see a human body exercising, zoom in to see the heart pumping, zoom further to see the blood platelets rushing through, zoom further to see a blood cell. Then zoom inside to see the cell contents, then further, to the oxygen and carbon dioxide. So I could zoom in and out of cells, organs and even people to see what’s happening at every layer.
Here’s a bit more detail about the where, why, and how
Games already simulate human activities over time and I’d show how simple cellular mechanics have the big impact they do. You’d be able to zoom into the cell and see what happens, then zoom out again to see the wider implications. You can fast forward in time, go backwards, pause. And highlight cells or organs and change values. Because it’s digital you can save state and share it.
Now we’re getting to the creative aspect. A virtual laboratory. Your lecturer asks you to figure out why diabetes is occurring in a given population. You work on this tool that has the population and tweak their lifestyles looking for the answer. Reading the research you hear about glut4 a glucose transporter on the cell walls. They are activated by insulin and fit people have more of these than unfit. The transporters regulate carbohydrate flow from the blood to the cell. Hence you’ve found a reason why fitness could be directly related to diabetes risk. You experiment with the settings now you know what to look for. You set up your virtual experiment and get the results. You’ve now got your answer. You export your settings, send to a friend who confirms it. Then send to your professor and receive an A.
It surprises me that the means to build this exists yet it hasn’t yet been built. it’s the definition of good science. Repeatable, sharable, uses standards etc. Year on year it could improve with more knowledge etc. so you could test more.
I’m probably not the first to think of it, but I don’t see one on the market and I don’t see any reason, why it can’t be done. It’s incredibly difficult but it’s definitely possible. I might take the rest of my life and then some but it would be an amazing journey.
The best example I can find of an existing project is the Virtual Physiological Human program headed by Professor Denis Noble of Oxford. It is a very well funded programme that seems to be delivering at a fantastic rate.
The only problem with this is that it is a closed project delivering software and tools for health and medicine but not for everyday people. So I’m very happy to see the progress of the VPH project but I don’t feel it will help me or the average person any time soon.
I have a lot of research in this area which I will add to this post in time. For now I just want to start the topic and provide a place to relevant details as I go. This is one of the most core articles to this blog. I’ve been investigating this topic for almost a decade now and is why I will often cover wider topics like technology, programming, marketing, economics and other areas in detail. They become important when you consider such a lofty aim.
Of course the first goal is to build a virtual cell. My plans have always been to build something incredibly simple. Share it and go from there. I’ve already built a very simple cell in using Unity as my 3d software. I’ve searched around and tried many solutions including html 5 but found unity to be the best for what I need.
Until now I’ve very much been wondering where the best conversation are happening. Current topics include
- Computational Biology
- Synthetic Biology
- Systems biology: looking at biology as a holistic process. on linkedin systems biology
I have found so much research I will post it here and then start to organise it as I go.
- Is the cell really a machine? argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes
- Build a Virtual Body: Bacteria communicate with their hosts
- Twenty papers, five starred Denis Noble as the founder of the Virtual physiological human and the Cardiac Physiome project Professor noble has been pushing for Computational biology for decades
- Chemical Reactions Spark Life Into Self-Folding Micro Origami Machines
- Model the heart
- The don’t stop the beat talks about the preDiCt project which models the electrical activity of the heart.
- Modeling the HeartDenis Noblehttps://doi.org/10.1152/physiol.00004.2004
- Cardiac cell modelling: Observations from the heart of the cardiac physiome project
- A model for human ventricular tissue proposal for experimental and clinical possibilities for studying cardiac arrhythmias in human ventricular myocardium through modelling heart
- Model individual cells
- A very nice article on the potential of whole-cell modeling.
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- The Dawn of Virtual Cell Biology
- The mathematics of cell boundary ‘ruggedness’: Researchers have uncovered both the mathematical and biological mechanism behind the rugged structures at cell boundaries found in tissues such as the kidneys and nasal glands.
- Artificial organelles for sustainable chemical energy conversion and production in artificial cells: Artificial mitochondrion and chloroplasts: Recent advances in biotechnology have enabled this sustainable energy supply, especially the adenosine triphosphate (ATP), by mimicking the organelles, which are the core structures for energy conversion in living cells
- Exploring the self-organizing origins of life Catalytic molecules can form metabolically active clusters by creating and following concentration gradients giving an insight into how metabolic processes can form.
- Model a human
- Living Human Project: is developing a worldwide, distributed repository of anatomo-functional data and of simulation algorithms relative to the human musculoskeletal apparatus, fully integrated into a seamless simulation environment and directly accessible by any researcher in the world. This infrastructure will be used to create the physiome of the human musculoskeletal system.
- Living Human Digital Library : aims to create the technical infrastructure for the Living Human Project (LHP). LHP will create a silico model of the human musculo-skeletal apparatus which can predict how mechanical forces are exchanged internally and externally, from the whole body down to the protein level. This model will be designed as an infrastructure that can be updated and extended whenever new data and algorithms become available. LHDL aims to develop this infrastructure
- Virtual Physiological Human: a methodological and technological framework that, once established, will enable collaborative investigation of the human body as a single complex system. VPH: wikipediaon pubmed
- VPH-Share: An organisational and coordination framework for the virtual physiological human project. Run by the Open university
- Toward continuous Medical Education By Roni Zeiger, head of google health. Outlining ways in which lifelong learning via the web could vastly improve the quality of care we all receive by simplifying the continual development of medical practitioners.
- Lifelong learning, Self development and expression
- Jane McGonigal believes Gaming can make a better world and has an avant game blog where she’s launching gameful to help people make games to improve the world
- Modelling nerves and neurons
- CoreNEURON : An Optimized Compute Engine for the NEURON Simulator a neutron simulator and review of other computational models as something to log and research towards developing and neutron interactive.
- myelin repair foundation. Also using games to educate and promote their cause
- Motor simulation: Evaluating the role of mirror neurons in humans through ECOG and Lesion Studies
- Genetics in 3d by utah university Amazing collection of animations and tools about anything related to genetics. A lot of money was put into this and they might be worth trying to work with.
- a long 3D animation of the fight or flight response.
- project health design: is forging a new vision of personal health records (PHRs) by exploring practical ways to capture and integrate patient-recorded observations of daily living (ODLs) into clinical care
- Wolfson research institute: UK organisation that conducts research on human health and well-being.
- You make me sick. Excellent game about designing a pathogen (virus or bacteria) to infect a human host. Really fun and friendly game.
- WikipediaL Biological computing:A basic introduction to the topic
- What is biocomputing? he ultimate goal of biocomputing is to mimic some of the biological ‘hardware’ of bodies like ours — and to use it for our computing needs
- Parallel computation with molecular-motor-propelled agents in nanofabricated networks proof-of-concept of a molecular-motor-driven, protein filament based parallel computer solving a classical nondeterministic-polynomial-time complete (“NP-complete”) problem, the subset sum problem. Proc Natl Acad Sci U S A. 2016 Mar 8; 113(10): 2591–2596. Published online 2016 Feb 22. doi: 10.1073/pnas.1510825113
- De novo design of protein interactions with learned surface fingerprints: our surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling an approach for the de novo design of protein interactions and, more broadly, of artificial proteins with function.
- Researchers are making a single molecule valve for ion gates and channels like those in cell membranes. A joint research team led by Associate Professor Yan Xu of the Osaka Metropolitan University Graduate School of Engineering has succeeded in regulating the flow of single molecules in solution by opening and closing a nanovalve in a nanofluidic device by applying external pressure.
- DNA as software
- In silico biology: In Silico Biology is a scientific research journal for the advancement of computational models and simulations applied to complex biological phenomena
- Cellular automata model for human articular chondrocytes migration, proliferation and cell death: An in vitro validation: a cellular automata model, based on random-walk theory, was devised in order to predict articular chondrocyte behavior in monolayer culture during cell expansion
- Simulation of diffusion using a modular cell dynamic simulation system: a scalable and adjustable foundation for the simulation of natural systems. Based on neighborhood relations in graphs and the complex interactions in cellular automata
- Researchers use table tennis to understand human-robot dynamics in agile environment
- Insect-sized jumping robot adapts to compliant environments
- Noise-free Jellyfish-Bot could one day clean up our oceans: The artificial muscles contract and relax through periodic electric currents flowing through the wires, allowing the underwater robot to swim gracefully and create swirls underneath its body.
- Mathematics Behind Wiggly Worm Knots Could Inspire Shapeshifting Robotics
- An intuitive approach for understanding electricity: A great presentation explaining how electricity works and flows through a circuit in a surprisingly similar way to water flowing through pipes
- Excellent explanation of electricity flow at the same time as water flow and energy flow.
- It is a principle I can use to explain basics of the body and this guy explain it very well. I did not know ohms law explained parts of fluid dynamics.
- What I kept picturing when watching this I think of the heart pumping blood around its circuit. In this video the battery is the pump and the electrons just flow through the wire the Same way the water flows through the circulation.
- Visualizing electron flow motivates new nanoscale devices inspired by airplane wings
- Electric charge moves similarly to how air flows over the surface of an airplane wing,” said Gabor, a professor of physics and astronomy. “While it is easy to image the flow of air by using, say, streams of smoke or steam in a wind tunnel, as often seen in car commercials, imaging the streamlines of electric currents is far more difficult.”
- Ties in with the other video I saw on electrical flow being fluid dynamics.
- And a description of water flow matching electrical ion flow
- Does the future of medicine lie in space?: Earth’s gravity makes it harder to cultivate the proteins needed to study diseases and pathogens. And although the cost of space travel is high, private enterprise is stepping in
Useful Projects and Tools
- centre of the cell
- systems-biology.org cell designer.exe
- biomodels database curated set of models viewable online: BioModels Database is a repository of peer-reviewed, published, computational models. These mathematical models are primarily from the field of systems biology, but more generally are those of biological interest
- biopax (biological pathway exchange) a standard language for exchanging . BioPAX is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups
- Human protein atlas search for proteins or genes and find protein expression profuiles, subcellular localisation, transcript expression
- xvivo.net: david bolinsky presented the inner life of a cell on TED. They have a vision, along with harvard, to explore biology through immersive applications.
- The gadget show : a recent programme simulator challenge part 1 part 2 showed simulations helped the team pass real life challenges like learning to fly and achieve a high grade in martial arts entirely through simulations. The first time ortis flew a real plane was during his test which he passed. The first time jason met a real opponent was in his grading which he passed.
- wikipathways: In the new tradition of Wikipedia, WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community
- bigcat: turning heaps of data into biology. department of bio-informatics at Maastricht University
- Simulation-based textbook for Cancer Biology The textbook utilizes a dynamic simulation approach and software, Cell Collective (www.thecellcollective.org Mammalian Cell Cycle), that enables students to learn about biological systems from a systems and dynamical perspective rather than by memorizing static pictures of pathways in textbooks.
- Andrew Hessel: Programming Living Things – The Next Generation Of Computing a fascinating talk explaining how synthetic biology allows us to build DNA scripts and update bacteria like you write computer code or put lego together. I think that tied to Unity a lot of fun could be had.
- Artificial Cells – The Powerhouse of the Future
- Transmembrane signaling by a synthetic receptor in artificial cells
- How does RNA know where to go in the city of the cell? Using cellular ZIP codes and postal carrier routes
- Revolutionary Sensor Mimics Human Eye for Vivid Imagery Researchers have created a device that emulates the human eye’s ability to see color by using narrowband perovskite photodetectors and a neuromorphic algorithm.
- Researchers Invent E-skin That ‘Talks’ to the Brain Researchers have developed an artificial electronic skin (e-skin) capable of converting sensory inputs into electrical signals that the brain can interpret. This skin-like material incorporates soft integrated circuits and boasts a variety of sensory abilities, including temperature and pressure detection
- Scientists are growing animals in artificial wombs. Humans might be next: What if technology could eliminate the need for anyone to go through pregnancy and childbirth to have a baby?
- New “AI doctor” predicts risk of death with 85% accuracy: Some of its predictions were better than those made by a team of doctors. Artificial life and also shows that doctors notes are pretty good at predicting mortality which means we do have a good grasp of what keeps people alive. The challenge is translating that into our daily habits.
How to track your life and get data to analyse
- http://quantifiedself.com/self-tracking-links-to-get-you-started/list of sites and apps to track personal stuff.
- http://personalinformatics.org/ site dedicated to tracking yourself.
Software to Optimize the motion and control of musculoskeletal models. an open source software package that makes predicting new motions accessible to those without an optimal control background. Moco leverages the existing modeling tools offered by the OpenSim musculoskeletal modeling package and provides an easy-to-use interface that facilitates generating and sharing simulation pipelines.
Apis for each scientific discipline. What lots of us need are basic physical, chemical and biological processes coded as basic function calls of an API. Things like the Krebs cycle and photosynthesis, for biology and the Maillard reaction for chemistry, not sure what for physics. It really depends on what you want to achieve but long term wouldn’t it be nice if the equations had already be converted to code and you could just implement the appropriate API.
Could be modelled on jQuery. We need libraries and APIs that do standard calculations for each science. No sure if the jQuery approach fits Just create some basic examples first.
Synthetic biology is a related approach following attempts to make biological entities. How far this approached has pr
How life emerges from a simple particle motion law: Introducing the Primordial Particle System
The next article shows how simple self organising features can be by applying a simple rule to a set of autonomous tiles.
Each tile has the same simple rule – if you see a neighbour blink, then increase your urge to blink by 10%. From that simple rule comes such an amazing result!
Decoding natures maths. Bacteria using a flagella as a motor. Something I would like to model in software. The video notes include the related maths.
4D printing in this amazing video about self folding materials perfect for the engineering section and mimicking biology
This is a very nerdy but fascinating and thorough introduction to cells and biology in general in terms of their functionality for computing.
How a Bacteria Colony Outwitted Computers By Evolving
How bacteria are turing complete and can solve coomplex problems by working together. The following video goes into detail about how they solved one problem much faster than a computer.