man person flying arm

How could you build a virtual human body?

Colin Chambersbiology, DNA, ecosystems, Virtual body Leave a Comment

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. 

Virtual Cell

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. 

Conversations

Until now I’ve very much been wondering where the best conversation are happening. Current topics include

Useful Reading

I have found so much research I will post it here and then start to organise it as I go.

Useful Projects and Tools

Personal informatics

How to track your life and get data to analyse

Existing informatics

Simulation

Computational biology

OpenSim moce

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.

https://opensim-org.github.io/opensim-moco-site/

PLOS review article, open sim moc github

Simulating the effect of ankle plantarflexion and inversion-eversion exoskeleton torques on center of mass kinematics during walking

Science libraries in javascript

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. 

jPhysics, jChemistry or jChem, jBiology

Synthetic biology

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

How life emerges from simple beginnings. A simulation.
A wonderful example of the potential of synthetic biology
Programming artificial life 

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!

Complex behaviour from emergent properties

My aim is to replicate this experiment on the web using javascript. The emitted light would simply need to be a value that other tiles could read when they are near.

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

The cell as a computer: Turing complete and massively parallel – Andy Thomason [ACCU 2019]

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.

How a Bacteria Colony Outwitted Computers By Evolving

Javascript resources

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