The possibility of creating a the Digital Human just got very
much closer with the DeepMind artificial intelligence research organisation,
owned by Google, managing to digitise the protein folding process. So what does
this all mean?
The human body is made of real tangible things. At an organ
level (eg heart, liver, brain etc) these are easily visualised and you have
probably seen the equivalents in animals at the local butcher. Now imagining
zooming into these using an electron microscope which has the power to make a
human hair look a mile wide. You going to come across structures made up from
atoms and molecules so tiny they could never be handled by us as humans but
they exist in the same way that organs exist but they are just a whole lot smaller.
These are the components that make up your human body. All be
it very small components. They can be viewed under an electron microscope at
the lowest level as tiny spheres, tubes and random three dimensional shapes
that wriggle and move around. Importantly they have structures so they maybe
strips that are straight or folded or tubes that are straight or bent or blobs
that are any shape. They can float independently or have differing attachments
to each other. They make up a very random and surreal world and to say it is
abstract would be an understatement. Now to represent this real moving world of
the body digitally has become the objective of DeepMind. It’s a case of getting
what you can view under an electron microscope to be created digitally. Just
like digital games reflect real life situations then DeepMind maps digitally represent
the working of these really tiny biological components.
You are going to zoom down from human body to a human organ
to cluster of human cells to a human cell and then to the molecules and atoms
within this cell. Then no doubt in the future into the atom itself. It is the
clusters of human cells forming their own unique structures where many new facets
of life are to be uncovered. Being real physical structures the way they move
and interact within the body can be investigated. Even using Computer Aided Manufacture
(CAM) vastly enlarged models can be made of these structures. These can be
handled and the way they lock together with other cell structures can be assimilated
to learn how things work. By applying the same techniques to humans suffering
illness and disease the faulty structures can be examined to determine how the
condition is causing illness. But possibly most significantly the same
processes can be applied after the introduction of medical interventions (eg
drugs) to determine how they change these structures. Dismantling the human
body, all be it digitally, like you would dismantle a car to locate the
component that is the root cause of a medical problem. Digitisation is the key
to this approach.
So let us try and visualise how this digitisation is
achieved. There are similarities to computer gaming and computer aided design
(CAD). So think of large rectangular box that the human body can be placed
inside possibly lying down flat like being in a coffin but not coffin shaped being
just rectangular box shaped. Now visualise ruler markings along the edges of
this rectangular box. Using three of these edges with their marking points can
allow you to locate any point within this box. So the tip of your nose can have
an X reading and a Y reading and a depth from the top of the box being the Z
reading. The classic three co-ordinates necessary to locate anything in space.
Now image the ruler markings going down to the thousandth of a hair width so
you can locate a point to a very exact molecular and even lower atomic level.
You can define a living cell at the end of your nose. A large number of
co-ordinates can define the shape of this cell as each point on the surface of
the cell are defined by X-Y-Z co-ordinates. You can even define things within
the cell itself along with their location and shape. The outer cell membrane
can be defined by both its inner and outer surfaces thereby defining its thickness
or even variations in this thickness over its surface. Now you can zoom both in
and out. Out from a cell to the part of an organ, then the organ itself and
then the organs place within the human body. It is Google Maps for the human
body. This covers what I term the physical mapping. Now at every one of these
points the chemical makeup of the point can be defined based upon the Periodic
Table so you achieve chemical mapping. This allows you to create a chemical map
if you like layered over the physical like in Google maps viewing something as
a map or a satellite image. The same thing viewed in a physical and a chemical
dimension. This creates the fact that within the physical shape the chemical
makeup may adopt a different pattern. Seeing the human body in this layered way
makes investigating the body’s changes and processes a multi-dimensional
experience. The physical shape might change whilst the chemical makeup does
not. Whilst the chemical makeup maybe changing whilst the physical remains
unchanged. One of the commonest processes, a process representing change, would
be for the chemical makeup within a cell to change with this subsequently
resulting in a physical change. The key medically would be to spot theses
chemical changes early with possibly a drug intervention before the problem
presents itself as a physical change. True preventative medicine. It is
important to reiterate the fact that the physical structures are created as a
digital map and the chemical makeup is recorded as a separate digital map.
These are then overlaid over each other. Now this overlaying of different what
I have termed dimensions is important. The physical dimension and the chemical
dimension. This lends itself to the addition of other dimensions if they can be
scientifically be defined by capturing data on them. So for example the
electrical activity within the body or other dimensions not previously
scientifically identified. These maybe considered unreal at present but
subjects like radiesthesia and telepathy come to mind being what I and others
(but only a few of us) term the “wireless aspects of life”. Subjects to be
explored later in this book.
But what becomes really important is when you can run these
digital maps over time so you can view all the changes in the human body both
physically and chemically. You can watch tumours grow and drugs destroy them digitally.
This leads to the important ability to re-run scenarios over and over again
with this forming one of the important tenets of artificial intelligence (AI).
The ability to build up digital pathways that can represent reality.
Adjustments can be made to data along these pathways and the changes can be
recorded. This approach can then be used to build up a whole holistic view as
thousands of different pathways are simulated and stored. So intelligence on a
subject is grown until it shown to accurately represent a reality.
So what you can see under a digital microscope can now be
digitally represented with the human body emulating a moving computer game. These
are digital 3D shapes all interacting like they would within a real living
biological body. In fact what you get to see digitally is a visual
representation of what you would see under a powerful digital microscope. The
significance of it being digital is that it can be analysed in terms of its
internal structures then by using artificial intelligence processing different
scenarios can be run through thousands of times with various adjustments being
made to the objects under scrutiny. Essentially you can make changes, possibly
by applying a drug, into the equation and then run through a sequence to
determine the impact of the drug. Like playing strategy games where decision
tree style thinking is important where at each node new decisions can be made
about the way forward based upon new data. These biological digital models
allowing for many thousands if not millions of different scenarios to be tested
leading to different final results. Once a positive result is achieved you can
reverse back over the decision tree to analyse all the different node point
inputs.
Whilst being really comfortable with these digital models
essentially replicating what can be seen using a digital microscope it is when
it comes to the underlying chemistry of the model where this adds a new very
powerful scientific dimension. Think of hovering a pointer over a particular
point within the digital model and then the chemical makeup is displayed at a
molecular level. Essentially the elements as defined in the Periodic Table.
These can be painted as colours within the digital model so you can visually
see the chemical makeup and importantly changes to this make up over time. You
can see things going wrong both visually and chemically at the same time. A new
tumour developing with cell multiplication with these cells changing in their
chemical makeup. Then hopefully the reverse effect after the application of
treatments. The thought that one day you could see all this happening in your
body real time on your smartphone. Possibly the most significant aspect being
the very early identification of these changes so they can be treated well
before the patient is aware of any symptoms.
DeepMind is applying both Gaming and Computer Aided Design (CAD)
principles to biological components down at a nanometre sizes. The CAD is
important because it is simple step to Computer Aided Manufacture (CAM) where
the three dimensional printing of components has become a standardised
industrial practice. So it is a simple step to create physical three
dimensional models of these biological components. Now significantly there is a
school of thought that being able to create physical models of these tiny
biological components will give us a totally new insight into how our bodies
are assembled from the very smallest building blocks of atoms and molecules up
to cells and cellular structures up to organs. So this is true biological
engineering. The creation of these tiny cells, viruses and bacterium as real
models produced through Computer Aided Manufacturing (CAM) but in sizes where
they can be handled which allow us to see how they interact manually. The way
viruses gain entry into human cells can be witnessed through the workings of
these enlarged models. It is important to appreciate that although many of the
processes within a human body are chemical it is also the mechanical designs
that evolve from these chemical processes that undertake purely mechanical
activities. They are interlocking mechanical processes like keys opening a lock
or pick axes breaking into the wall of a cell. These are real mechanical activities
taking place within the human body and their assessment as such it important as
a tenet of medical investigation.
So why is this suddenly so significant in respect of the work
at DeepMind on proteins?
Life is dependent on proteins. Proteins are made up from
chains of organic compounds known as amino acids. These bond together into long
chains to make proteins, which in turn create different types of tissue that
perform all sorts of functions within the human body. Proteins, the building
blocks of life, adopt complex three-dimensional shapes which determine what
they do and how they do it. They make up good cells, bad cancer cells, viruses,
bacteria and antibodies. If something is alive it will be made up of proteins.
Proteins are the machinery of both life and unfortunately death. Failures in
the production of these proteins will lead to death. Proteins which are
collections of compounds called amino acids are the machinery of life.
Machinery is the right term to use because it implies they are physical, which
they are, so we need to know what they look like. They cannot just be
considered as a chemical compound listing the molecules that make them up since
life is about movement and this is the machinery that supports this movement. It
is about biological engineering and not pure chemical engineering. At the
atomic level biology works by the interlocking structures of atoms in a
physical way. We need to know how the one dimensional sequence of atoms we get
from chemistry “folds” in a 3D image. Into a real physical component.
Protein molecules can coil around themselves in all sorts of
different ways. They can be tangled in a normal way. But also they can be
tangled in a way that is abnormal leading to conditions like Alzheimer’s and
Parkinson’s. Tangling is a really strong force in natural for good and for bad.
I think of how the Christmas tree lights or power cables to electrical
appliances or water hoses or blind cords can get so horrendously tangled
together. There seems to be some natural forces of nature that sit behind the
tangling of rope or strip like materials particularly if they have protrusions
like the lights on Christmas tree lights. Going back to the primeval soups of
life it is these tangling processes that allowed the build-up of more complex
life forms. Algae deposits and damp algae twisting and turning until by chance
something more sophisticated is created. The complexity of sperm swimming to
the egg to penetrate it to generate the start of a cell reproduction cycle.
These basic building blocks of life need to be digitally analysed both
physically and chemically to understand when and how life itself sparks into a
continuous process of growth and decay. In the case of decay protein
malformation and malfunction maybe behind many of the unpleasant conditions
associated with the aging process.
Now deriving the chemical formula of a protein is
scientifically relatively straightforward but determining its physical
appearance was a long laborious process called crystallography. Prior to this
digital break by DeepMind this was the standard way of “seeing” a protein by a
process of crystallisation. That is lock it in a stasis in a repeating pattern
then you fire x-rays at it in all different directions and from the image they
form you can infer its shape. What DeepMind did was create some specific
chemical knowledge and then apply this to those proteins where x-ray images
existed from the above crystallography process. By constantly adjusting the
underlying algorithm they started to get the protein chemical makeup to equal
the created x-ray images. So the model was built upon crystallised protein
x-ray pictures. So having trained the algorithm to link the protein amino acid
structure to the corresponding specific crystallographic image it could then be
applied to tens of thousands of proteins that had never been mapped using
crystallography. Some of these previously unmapped proteins could then have the
crystallographic process applied and this could be compared to the DeepMind
image. The success rate of this DeepMind mapped image against the actual
crystallographic image showed that the process was a real success. But
importantly the algorithm could continue to be adjusted as new crystallographic
images became available further refining its accuracy. To the point that the
digital only processes were deemed as accurate as crystallography. But the
digital approach had another major advantage.
Now in the body proteins are not crystallised but they are
free moving structures that warp and bend continually. This makes the modelling
of this real world behaviour a lot more difficult. But real success will follow
on from when the digital modelling mirrors real life. The computer model equals
what you can see under an electron microscope. But then significantly digital
model will have captured the underlying logic to these biological processes.
Once this structure is a “calculated” one based upon this logic we can then run
in a “live” model emulating life within the human body. Knowing this we can go
onto design the experiments that make drugs and enzymes and all the molecular
tools we need to improve the human condition. These medical interventions can
also be modelled real time so we can monitor how they interact with the faulty
proteins. So create a sick digital human then test the best medical
interventions to make it better.
