The idea that a human could be fully defined digitally on a
Smartphone, the thesis of the Digital Human Book, just got a little nearer. But
only a little.
NVIDIA an American advanced chip designer previously focussed
upon graphics processing chips and now entering the artificial intelligence
marketplace has released their DGX A100 AI chip containing 54 billion
transistors with a 5 petaflops performance. They are in the same marketplace as
the other major chip designers and manufacturers Intel, AMD, Qualcomm and ARM.
It uses their Ampere architecture which is a single micro
architecture for its Graphics Processing Unit’s (GPU) supporting both
commercial AI and consumer graphics usage. Their specialist capabilities in
support of graphics processing have now been applied to the broader
capabilities required by artificial intelligence (AI) processing. At the end of
the day it is all about the processing of on-off switches be they used for
graphics or AI.
The DGX A100 is a 7 nanometer chip produced to this higher
concentration of transistors but still on a 2D wafer. Significantly the current
Apple A12 chip fitted to the iPhone XS, XS Max and XR and the 2019 iPad Air and
5th Generation iPad Mini is also a 7 nanometer chip produced by the
Taiwan Semiconductor Manufacturing Company (TSMC) for Apple in Taiwan. But this
only has 6.9 billion transistors. But it does show how near to the leading edge
chip technologies your smartphone is getting in terms of its capabilities. When
applied to a Smartphone these can be in your pocket now.
But to emulate a Digital Human on a Smartphone we are still
probably a factor of several 1000’s if not millions off the processing power
that will be needed. But it does show how amazing the biological human is in
terms of sheer digital processing power. Unless how we humans actually do it
takes us beyond digital (just on-off) into another dimension. Certainly we are
also not limited to a 2D wafer like current chips with our storage running to
three dimensions (3D) as per the brain. But our digital world is progressing
although no doubt in 50 year’s time (2070) we will look back amazed at how
crude our digital technologies were in 2020. We will be asking what’s a chip? What’s
a Smartphone?
Today we need to leave the biological sciences to zoom
upwards and take a much higher perspective. Or oddly enough in this case zoom
down to a much lower perspective. All will be revealed.
The book title A Digital Human already eludes to this way of
thinking. It looks at the biological human as a digital device. In fact
consilience means a unity of knowledge. In truth this is an old word that has gone
out of fashion in the 21st Century belonging more to the 19th
Century when the sciences were racing ahead establishing their credibility. But
it turns out that the book A Digital Human is really about consilience. Maybe a
more relevant term maybe consolidation. It is the consolidation of everything
to the digital foundation. Put simply the consolidation of everything to the on-
off switches that are the building blocks of all things electronic. So why the
shift towards the digital?
It is necessary for me as the author of this book, currently a
work in progress, to stop and remind myself of the book’s objectives. To me the
clear objective of a book is to take you as the reader and lead you through a
number mental change processes so by the end of the book you think differently
on the subject covered. To do this here I want to briefly consider three
authors who cemented in my mind the subject of consilience. They changed my
thought processes let us see if they change yours.
Firstly Edward O. Wilson an American biologist born 1929. He
published a book called “Consilience” (1998). He quotes from William Whewell in
his 1840 synthesis “The Philosophy of Inductive Sciences” as the first to speak
of consilience.
To quote:-
“The Consilience of Inductions takes place when an Induction,
obtained from a class of facts, coincides with an Induction, obtained from
another different class. This Consilience is a test of the truth of the Theory
in which it occurs.” Replace the word “induction” with “experiment” to appreciate
a 21st Century interpretation.
Then to quote from Wilson’s book:-
“Disciplinary boundaries within the natural sciences are
disappearing, to be replaced by shifting hybrid domains in which consilience is
implicit. These domains reach across many levels of complexity, from chemical
physics and physical chemistry to molecular genetics, chemical ecology and
ecological genetics.”
Secondly Bruce F.Katz with his book “Neuroengineering The
Future” (2008) in which he quotes William of Occam in the 11th
Century where “entities should not be multiplied beyond necessity”. He also quotes
Einstein’s famous dictum that a theory should be as simple as possible, but no
simpler.
Then to quote fromKatz’s book:-
“…the simpler the theory, the greater its ability to
generalise to new phenomena. Complex theories arise because they tend to have
many special cases, each encompassing a disparate set of results. Each aspect
of the theory covers one and only one such set. However, if a commonality can
be found that ranges over these results, it will often be the case that it also
explains as yet unseen empirical data.”
This is where Artificial Intelligence (AI) is going to be
able to take us once everything is successfully transformed into their digital
foundations.
Thirdly William Sims Bainbridge with his book “Nanoconvergence”
(2007) brings it all together with the quote in the book taken from his 2000
report “Societal Implications of Nanoscience and Nanotechnology” edited by Mike
Roco and himself :-
“A revolution is occurring in science and technology, based
on the recently developed ability to measure, manipulate and organise matter on
a nanoscale – 1 to 100 billionths of a meter. At the nanoscale, physics,
chemistry, biology, materials science and engineering converge toward the same
principles and tools. As a result progress in nanoscience will have a very far
reaching impact.”
Followed by a more comprehensive statement in a 2003
Converging Technologies for Improving Human Performance Report:-
“We stand at the threshold of a new renaissance in science
and technology, based on a comprehensive understanding of the structure and
behaviour of matter from the nanoscale up to the most complex system yet
discovered, the human brain. Unification of science based unity in nature and its
holistic investigation will lead to technological convergence and a more
efficient societal structure for reaching human goals. In the early decades of
the twenty-first century, concentrated effort can bring together nano-technology,
biotechnology, information technology and the new technologies based upon
cognitive science. With proper attention to ethical issues and societal needs,
the result can be a tremendous improvement in human abilities, new industries
and products, societal outcomes, and quality of life.”
So as an author have I started to change your thinking
processes towards everything moving towards a digitally based foundation where
artificial intelligence (AI) can be used to seek out many of the unknowns spanning
the different scientific disciplines? Will it all dissolve down to some simple
rules as Einstein predicted. Or not?
As the armchair biologist reading all manner of resources on
genetics you soon keep coming across codes like FMR1, CCR5 and FOXP2 referred
to in many of the articles. What is going on? These are what I have termed Human Gene Codes.
Well this is how all the genes within the human genome have
been named individually. They are little bits of coherent code that define how
something is finally made in your body. But just to set the context correctly
these types of codes are also used for other genomes not just humans. They
exist for mice, fruit flies and peas in fact for any living organism. Anything
where DNA exists defining the master plan for making that organism. Mice, fruit
flies and peas have been listed because, believe it or not, most of the early
genetic research focussed on these three living things. Mainly because all
three reproduced quickly best supporting this type of research that needed to
be undertaken over many of the living thing generations.
Now just deviating slightly off from the subject of Gene
Codes we need to just give ourselves an appreciation of how small everything is
in the world of genetics. Watching an ant running around a paving slab in the
hot sun measuring between 2-3 mm in length reminds you that stored within all
his living cells is DNA that defines the building of the ant. In fact the ant
has all the same capabilities as a human. Head, brain, nervous system,
digestive system, legs, eyes and so forth. The majority of the DNA will be identical
to that of a human except in the process of evolution the DNA went down the
insect branch rather than the mammal branch so some differences will exist. So
this should allow you to better visualise how big a gene is since in the ant
and the human the actual gene is the same size.
So what about the documentation of genes that go across all
species. This is a specialist area in bioinformatics called Gene Ontology (GO).
So let us just confirm at bioinformatics is the interdisciplinary field that
develops methods and software tools for understanding biological data. So
bioinformatics is the study of the Digital Human in an informal way. Gene
Ontology (GO) looks to maintain and develop a controlled vocabulary (the FMR
letter codes) of genes and gene products attributes. Now just to complicate
matters the Gene Ontology (GO) is part of a larger classification effort, the
Open Biomedical Ontologies, being one of the initial Candidate Members of the
Open Biological and Biomedical Ontologies (OBO) Foundry. Currently there are
more than hundred ontologies that follow the OBO Foundry principles. (http://obofoundry.org) .
Now do not get too confused by all these names of bodies
looking to mark up biological data. Firstly the term ontology is not anything
to do with biology. It is more to do with philosophy. It is about defining
entities (ie things) that exist by giving them a name or label. The grouping of
like things is part of the process then often establishing hierarchies of related
things. So for the terms used say in banking or retailing or manufacturing or
logistics you could create an ontology. Think of it being like an index or
glossary. Now the fact biology is now getting around to drawing up ontologies
is significant because it is a prerequisite to establishing data processing,
information processing and artificial intelligence processing. It is getting
the building blocks of data analysis in place. But with the biological sciences
it is much more complex than anything in the commercial computing world.
So next time you see say “FOXP2” can I suggest you use the
Genetics Home Reference site search to look it up at http://ghr.nlm.nih.gov . So try looking at FM03
which causes Trimethylaminuria the genic disorder that makes you smell like a
fish. This site contains a huge list of these Gene Codes. So next time you read
something and a code like “FREM2” comes up use this website to look up the
details.
It is very important that when you are trying to understand
something that you first establish in your mind a simple model that you can
then drill down from to more detailed lower level models. You can call these
models, diagrams, frameworks or process flows. To support understanding the
best ones are hierarchical because at the top level it is like a summary or
precise which is then linked to lower models which serve to expand on the
detail. The author is from a professional computer background where the design
of computer systems has always been dependent on the use of such modelling or
process design techniques. From the top level Enterprise Architectures (EA) down
through to the Unified Modelling Language (UML) these are the established
techniques for designing and building computer systems. Now being only an
armchair biologist and chemist for me to understand these subjects I have to
apply my digital methodologies to them. This is why it is called the Digital
Human.
So being an armchair biologist and chemist I have a
preference for locating models that have been created by experts within these
professions that coincide with the types of model I would have been familiar
with or created in my digital profession. So I have located just such a diagram
below which is copyrighted to Nature Education (2014).
So in this one diagram it at a high level establishes the
process flow from DNA through RNA and to Protein creation. The protein is the
living cell. It does not go into the detail of DNA transcription to RNA nor the
Translation from RNA to the Proteins. At this stage we do not want any more
detail or complexity (eg mRNA). We just want simplicity. So in simple terms the
DNA which is like a roadmap is transcriped into a simpler linear sequences of
RNA which become the recipes for making proteins by sequencing the amino acids
within these proteins. It is important that you get this very simple model
understood. We will enlarge on the detail as we drill down into this model
later in the book.
Is
coronavirus like a computer virus?
So is coronavirus like a computer virus? Well obviously
not. Coronavirus is obviously biological in that it consists of living
bits of chemical called proteins. Whilst a computer virus is a non-living object. Now the thesis of this Digital
Human Book is that everything biological and living can be represented in
digital code. Essentially thousands of bits (like light bulbs) that are either
switched on or off in the computer’s memory. Now if you projected all these
bits on to the side of a building you could see many different patterns in it.
When these small patterns look the same you have within these masses of bits identified
a common object. It could be the digital representation of your face used in
face recognition. Or for coronavirus it would be the digital pattern that has
been identified firstly in China and subsequently at many locations throughout
the world. In fact all the current coronavirus testing takes the test swab and
through a process called the “polymerase chain reaction test” detects the virus
genetic information. Now the interesting challenge would be to reverse engineer
the process where this genetic digital information could be generated back into
a biological virus. From computer code back to a living thing.
What a changed world we now live in with the internet now
supporting global networking and data sharing. It allows anyone to become
involved in what would have previously been hidden areas of research. Coronavirus
is the best example to date of the benefits that the internet offers in terms
of instant internet networking and data sharing. The openness now applied to
this type of “save the human race” research with the removal of all commercial and
governmental secrecy (as far as I know) has allowed the ordinary individual to
become party to these events in real time. Now it is accepted that what you get
to read and research being “first hand” is often far too technical to
understand. This in my opinion is a good thing since it is not always good for
you to only read what the media have decided to simplify for your consumption.
The simplification detracts from the complexity which allows social media
pundits to draw very simplified conclusions and propose their own direction of
travel without knowing the underlying detail.
So in the case of coronavirus what can we get access to
that may have been previously kept away from the public view?
One of my popular websites on viruses is http://virological.org
where I can gather around the coffee machine with the world’s virologists for a
morning chat. Unfortunately like many a chat what I get to read one day maybe
gone the next. Best to remember the internet has its own fluidity. Someone on
the other end is always moving things around to confuse you. Always look to
capture it on own your own digital hardware. I am not even a full convert to
the Cloud Architecture. Remember they are businesses running them. Sorry for about
the gripe. But it is a blog !!!. So moving on with the subject in hand.
So I got to see the original posting from edward_holmes
as introduced below :-
“10th January 2020. This posting is
communicated by Edward C. Holmes, University of Sydney on behalf of the
consortium led by Professor Yong-Zhen, Fudan University, Shanghai.”
It opens with “The Shanghai Public Health Clinical &
School of Public Health, in collaboration with the Central Hospital of Wuhan etc
etc …………is releasing a coronavirus genome from a case of respiratory disease
from the Wuhan outbreak. The sequence has also been deposited on GenBank
(accession MN908947 20.2k) and will be released as soon as possible.”
So this was post by Professor Edward Holmes working at
the University of Sydney. He is an expert on infectious diseases particularly RNA
viruses that jump boundaries to infect humans. He can be located on http://scholar.google.com.au giving you
a link to his paper published in 2020 “A new coronavirus associated with human
respiratory disease in China” with excellent links to published articles based
upon the paper.
Now the link on the post lead to go to http://ncbi.nlm.nih.gov
so then follow the path NCBI>DNA7RNA>Nucleotide Database where you can
actually view the complete underlying genome code for “Severe acute respiratory
syndrome coronavirus 2 isolate Wuhan-Hu-1 complete genome”.
This site is the
National Centre for Biotechnology Information in the USA. Now GenBank is the
NIH genetic sequence database of publicly available DNA sequences. GenBank is
part of the International Nucleotide Sequence Database Collaboration with Japan
and Europe. These international centres process such data on a daily basis so it is real time research.
Now if you like searching through data that that means
nothing to you this is the place to visit. Maybe it is my computer background
but I enjoy just searching through data and the less I understand it the
better. The internet now allows you to become involved in any subject and at
any level of research. So today I am an amateur virologist. But what it does
achieve is to make you aware of the complexity that the normal media looks to
avoid in their published stories. In my case it always triggers me to want to
learn more so once again the internet becomes invaluable. Just Google or
Wikipedia every word you do not understand. Even buy a book or even if you are
digitally dependant an eBook off Amazon. But alongside this information the key
difference these days is you can have access to the first hand sources on the
subject and in real time see how things are unfolding. In fact it pays to pick
a few experts to follow where their bio and writings make you want to make them your
new best research friend.
The big difference is with coronavirus as the current subject
matter under the spotlight it is uncharted and things are unfolding in real
time. This along with it being relevant to everyone, because anyone can catch
it and die, makes it currently the ideal subject to have access to this inside
information over the internet. Fortunately the scientists working on solving the problems are adopting currently a none commercial open systems approach freely sharing their information on open access websites. Within 12 days of the Chinese sharing the digital genome of coronavirus over the internet an American team had shared an analysis showing the mechanism by which the coronavirus entered human cells. Then within 12 hours scientists in China had shown there analysis was correct. The speed of data interchange about the virus was starting to match the speed at which the virus was spreading. But unfortunately developing the solutions would take a lot longer.
