As someone outside of mainstream biological research this whole subject of how biological things are coded remains very confusing to this Digital Human. It does appear to be evolving but at the same time there appears many competing establishments looking to establish some standards for the coding of these biological entities. The term establishments is used in the broadest possible sense since there appear to be a number of these attempting to establish their standards as defacto. It has to be accepted that this is a very broad subject with each of the biological entities under constant change either due to deeper scientific analysis or biological evolution itself. For example consider the deeper identification of protein structures along with the annual mutation of flu viruses. So the depth of scientific investigation and analysis runs deeper whilst running in parallel with forever ongoing biological evolution. Against this is the variety of the biological entities covering genes, bacteria, viruses, hormones and antibodies for a start. Combine this with projecting these entities across species from human, monkey, mouse, bird to plants and algae you can just imagine the complexity.
Here I just want to touch the surface of this whole subject
of biological, meaning living, entity definition. This whole subject has been
called bioinformatics. In defining the Digital Human this is going to form one
of the major foundations. It is probably no surprise that much of this work has
been focussed upon understanding diseases since this gives the research a
defined objective rather than it being just pure research. It also supports
funding initiatives particularly when aligned with the commercial objectives of
the pharmaceutical industry. Medicines and drugs themselves require their own entity
definitions and classifications in parallel to the work on living entities. So
just consider one database covering gene diseases.
So just take a look at the link below for a Gene Disease Database
https://en.wikipedia.org/wiki/Gene_Disease_Database
Now you can appreciate reading my Digital Human blogs that
many of my links are to Wikipedia. Being an “amateur biologist” but “professional
information expert” outside of the research, academic and pharmaceutical spheres
of knowledge I find the simple way things are described in Wikipedia really
beneficial. But you have to note that many people engaged in these establishments
object strongly to the “open” nature of contributions to this Wikipedia resource
where strong “peer” review and validation processes are not applied by
biological academia or research experts. Being honest when I read the academic
and scientific research papers that can to be easily found these days on the
internet I am often confused by the content. This in in no way intended to
undermine this critical and valuable work. Only to say the words written don’t
steer my personal Digital Human consciousness in any sort of constructive way. I
just don’t understand them. Consider this
old posting (July 2008) since it does provide a good beginners insight into the
subject of the Gene Wiki.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2443188/
The plan is not to spend too much time on this subject here since this is one of the last Digital Human blogs of 2020 and these are areas of bioinformatics that are going to be investigated more deeply in 2021. But I wanted to include, more for myself than for your benefit, a few pointers that require further investigation by me the Digital Human in 2021.
Covid-19 has been a big driving force in terms of this
Digital Human’s consciousness during 2020 and I am sure this will apply to
2021. Now wearing my Information Analyst’s hat back in March 2020 I always referred
to it as the Coronavirus then the media started to label it Covid-19 which has
remained its popular identifier for the last 9 months. Now this is the name of disease
caused by the virus whilst the virus itself has been labelled as SARS-CoV-2.
Now a new mutant variant of this has been detected on the 20th
September 2020. For some reason this has been labelled VUI-202012/01. It has
been initially based upon statistical evidence which appears to show it is more
easily transmitted.
For details of this use the link below.
https://en.wikipedia.org/wiki/Variant_of_Concern_202012/01
So what trains of thought did it set off in this Digital
Human’s thinking? So to be more transmittable it must be more effective at
entering the human cells. It propagates itself making more of itself within the
cell it has entered before moving out of the destroyed cell to enter into more
human cells. It repeats the propagation through the digital human body. It
appears the human cells in the respiratory system are the first targets and
most easily entered. But that is because these are the most easily got out
having entered the nose and mouth. But once inside the lungs with access to
blood circulation and the heart systems it can penetrate the gastrointestinal
tract then finally to muscles, bones and joints. It becomes a true Digital
Human invader. Now the body provides anti-bodies to neutralise this attack. Hopefully
these successfully defeat the invader. Unfortunately the “flood” of these
anti-bodies being called for by the immune system can become a problem itself.
They have to have precise instructions on what to attack. If they get a set of
incorrect instructions they can incorrectly identify normal human cells as
being the enemy so destroying perfectly good living cells with this impacting
the body’s ability to sustain life. Anti-bodies are called glycoproteins and
they are a complex subject in their own right.
Now it is well publicised that it is the spikes on the SARS-CoV-2 virus that are the tools whereby they force entry into the human cell. Now the question to be answered - Is this entry by a chemical or a mechanical process? Does the spike touch the cell with a chemical that results in the human cell wall dissolving so the virus can gain access into the cell? Or is the spike equipped at its end with the equivalent of a “beak” where by it can mechanically beck its way into the cell membrane to gain access. To make it more transmittable either the attack chemical has been made more potent or the mechanical beak has been redesigned to make it cut into the cell more effectively. These are evolutionary changes. The digital code within the virus must have changed to allow these changes to be implemented. But there is no intelligence within a virus to trigger this redesign. Does it just happen randomly? If random a change could be for the better or it could be worse. A random decision making it worse could lower transmission rates and the virus could then just die out.
You sort of enter the discipline
of game theory. When to innovate against when to remain unchanged. Innovation
could improve success or lead to failure. Remaining unchanged would uphold the
status quo. This is against a backdrop of anti-bodies choosing to make similar
decisions with hopefully vaccines improving the odds for the success of
anti-bodies. The intellectual issue remains. What triggers the decision by the
virus to change and how is the process undertaken to establish the new DNA code
to support the change. One line of thought could be a battle raging inside someone with Covid-19 with the virus fighting the anti-bodies whilst trying to gain access to a human cell. In this battle the Covid-19 virus by chance effects a change that allows it to succeed in battle. The virus RNA is modified to reflect this change. Then reproduction is based upon this these new RNA instructions. These new mutant versions then proceed to succeed in all future battles thereby becoming the new dominant virus whilst the old virus just dies away. This is life played out at its very basic lower level almost emulating the basics that lead to the very start of life.These basic processes are what we need to understand if we are tio fully define the Digital Human.
From an
Information Analysts perspective (rather than a biologists) it is going to be
vital that a standardised global resource is established so we can effectively
deal with future global pandemics as well as all other diseases effecting our
lives. Just as the internet has established local and global standardised communication
networks (5G,Wifi, IP,Bluetooth etc) and the world wide web (WWW) has
established global standardised information processing (HTML,XML,CSS,JS etc) along
with all the supporting digital file structures (eg PDF,JPEG, MPEG etc) to
define what goes on in the silica. Then similarly bioinformatics have to go
through a process of establishing in a similar way all the biological standards
necessary covering the living part of our world. It will be a lot more
complicated that our current Information Technologies (IT) based upon silica
but it is these technologies we will be using to get started.
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