20 - 023 Sonic Hedgehog Protein

 No you have not suddenly come across a gaming blog post nor have I as the author of this post lost the plot. Believe it or not it is one of the processes that occurs in what has been termed the hedgehog signalling pathway. The Hedgehog signalling pathway is a signalling pathway that transmits information to embryonic cells in support of cell differentiation. The cell signalling pathway is the communication between cells. The importance of the term signal is that it is potentially digital information. It’s a message transmitted from one cell to another. This message is generated by a Biological Programming Language. So let us first make it clear that this is a real chemical mixture which has been defined by the SHH gene. Just to complicate matters there is the Desert Hedgehog protein defined by the DHH gene and the Indian Hedgehog protein defined by the IHH gene that also exist within the hedgehog signalling pathway.

Firstly these were not derived from studying hedgehogs but flies. But because the larvae used in the experimentation looked like a hedgehog it acquired this name. So let us look briefly at the Sonic Hedgehog Protein.

The Sonic Hedgehog Protein is called a morphogen. Now the author as an Information Technologist gets really excited by the fact that Alan Turing in his paper “The Chemical Basis of Morphogenesis” predicted a chemical mechanism for biological pattern formation decades before research showed this to be a real physical biological process. To the author the building up of the embryo from a single cell and the ongoing maintenance of the human body had to have some design plans. How else would you know to put five fingers on the end of the palm within the design of a hand. Or an ear on each side of the face. Being a cell at the end of a palm how do I know the next cell will be part of a finger and not another bit of palm. Somehow these patterns have to be stored and progress in the making of these patterns recorded so you know how far you have got in the construction process. So I am the last palm cell now make a finger cell. This applies to the bone structure, artery structure, muscle structure and the skin wrapped over them. There must be coordination between them to build things in the right sequence. Sequence is indicative of a time element with this step having to be completed before that the next step. So the bone creation step by step. Then possibly around it the muscle creation step by step. This interwoven with the laying down of the blood pipework (arteries) outgoing and the return pipework with these inclusive of their own pumping muscles. Finally for this to be wrapped with a layer of skin.

This as a subject goes beyond the realms of just analysing the chemical make up of a human body. It moves us into the process of how the human body is made and then maintained. 

References

Read up on Sonic Hedgehog

https://en.wikipedia.org/wiki/Sonic_hedgehog

Read up on Desert Hedgehog

https://en.wikipedia.org/wiki/Desert_hedgehog_(protein)

Read up on Indian Hedgehog

https://en.wikipedia.org/wiki/Indian_hedgehog_(protein)

Read up on the Hedgehog signaling pathway

https://en.wikipedia.org/wiki/Hedgehog_signalling_pathway

Read up on the Cell signaling

http://en.wikipedia.org/wiki/Cell_signaling

Read up on Morhogen

https://en.wikipedia.org/wiki/Morphogen

Read up on the Chemical Basis of Morphogenesis

https://en.wikipedia.org/wiki/The_Chemical_Basis_of_Morphogenesis

 

 

20 - 022 Biological Programming Language

 

So here I sit with all my biological components made up of cells put together to make me a Digital Human. Each of these components can be defined in terms of their cells and chemically analysed. Each of these chemicals making up a cell can be digitally defined. Cells are continually being reproduced (or not in some cases) so a defined process has to from within a cell decide to make a new copy with all the instructions for doing so included. This instructions are called a transcription process. These instructions can go wrong so we have cancerous cell reproduction. The transcription instructions have to be digitally defined (or possibly something similar to digital) to create a Biological Programming Language.

Now if we consider that this Biological Programming Language exists in the stem cells where the stem cell is the outstanding source of all these instructions. From this one cell type embryos grow every other cell type from muscles to neurons. Each cell type being made up of a different digital gene code structures designed to achieve the specific purpose of the cell type.

So if you gain control over this Biological Programming Language you have the capability to control cell reproduction through a transcription mechanism. So you can reprogram stem cells to make any human cell required. But doing so is not that straightforward because they have not got all the genes in the newly created cell work properly. So the current version of this Biological Programming Language is not fully controlling these transcription processes. Although it would seem that a new company called Bit.Bio may have developed some further technology that solves this problem.

Read the article below in the Times on the 271020 :-

Then go look at the www.bit.bio website for more information.

20 - 021 3D Manufacturing Process leading to Digital Treatments

 

So in nanometer (nm) terms we want to discuss here something very large but it can still potentially float down the inside of a human hair. It is a tug boat, yes because it has been made to look like a tug boat, which measures 0.03 mm long. That is 30,000 nm so it is enormous compared with the things we normally view at an atomic scale like viruses or a helium atom at 0.06 nm.

What is really significant was it was created using 3D printing. So it was manufactured. Significantly it has been designed to propel itself along using a chemical reaction.

The Times article (281020) by Tom Knowles describes the detail below.

 This article does not focus upon what I see as the real significance of the boat, which is not so much the size because this has been achieved before by many research laboratories, but the fact that it is manufactured by a computer program. Not by the manual manipulation of tiny atoms but by a manufacturing process. The computer code defines this process linked to a 3D printer manufacturing machine. The computer code has been written to drive the 3D Printer to build the boat up in defined layers using an advanced 2PP (two-photon polymerisation) process utilising extremely accurate lasers. The other significant step is the inclusion in this process of a chemically driven “engine” to propel the boat along. Be it just a chemical reaction it is still generating power. It is not static and inert but a dynamic creation obviously like a battery with a finite life. This along with the tiny walking robots produced by Cornell University in America mark the trend towards developing “machines” that can operate within our bodies undertaking removal or repair work.

So not only will be defined fully as a “digital human” but all the processes to care for us will be defined as “digital treatments”. The tool kit is repair us will be written up in digital program code driving specialist devices to manufacture and install them. Although these devices would initially be hospital laboratory based it does not take much imagination it envisage home based devices with the code to drive them downloaded from the internet.

20 - 020 Making things smaller than Coronavirus 2 (SARS-CoV-2)

 Now with the latest advanced chips having digital switch sizes down to 5 nanometers (nm) you can appreciate how much progress has been made in the miniaturisation of electronics. It is worth on Wikipedia looking up the “International Technology Roadmap for Semiconductors” or ITRS to see the progress on miniaturisation from 1971 getting down to 5 nm in 2020 for the size of these digital switches.

Use this link to see the Wikipedia page for ITRS

https://en.wikipedia.org/wiki/International Technology Roadmap for Semiconductors

Now you realise these digital switches are now smaller than the Coronavirus 2 Virus which has a range between 60 nanometers (nm) to a maximum diameter of 140 nanometers (nm). Whilst the length of the spikes that surround the coronavirus sphere can vary from 9 to 12 nm. So we are now able to successfully manufacture something smaller that the virus. But in both cases it is very difficult to comprehend how small both these switches and the virus are in the real world. Now both of these can be viewed using electron microscopes along with many other small pieces of matter. This is called science undertaken at a nanoscale level. The exciting aspect to viewing the world at a nanoscale level is everything in our world starts to look exactly the same. So both inorganic and organic (life supporting) structures start to look identical. At the nanoscale level we move down to seeing the smallest building blocks of our world. Importantly to this author it will start to unify all the separate sciences under the one heading of Nanosciece and its application through Nanotechnology. Nanotechnology is focussed upon using real things that measure between 1 to 100 nanometers. Without a doubt it will be information technology that proves the most effective technology for the unification of the other sciences which has evolved its own name as Nano Convergence. But before we consider this unification or convergence it is important to get an appreciation of the size of a nanometre.

A nanometer is a unit of length equal to one billionth of a meter. (0.000 000 001 m) and is used to express dimensions on an atomic scale. For example a helium atom is 0.06 nm which is a reminder that you can have many things that are even smaller than a nanometer. Now everybody appreciates a nanometer is very small but it is difficult for us to picture exactly how small. To give you some perception note a coin like a penny is roughly 1 millimeter thick so imagine you could shrink yourself down to being just 1 nanometer tall then that 1 millimeter coin sat alongside you would look like it was a 100 miles tall.

Now in the organic or living world the DNA in the cells of our bodies is between 2 to 3 nanometers thick but up to several millimetres long so it has the proportions of a long piece of fine thread curled up inside the chromosomes. Atoms and water molecules are smaller than a nanometer. Whilst the wavelength of visible light ranges from approximately 400 nanometers at the violet end of the spectrum to approximately 700 nanometers at the red end.

So in terms of the size of what we can manufacture we are not far off being able to make digital life but establishing the digital patterns that can generate the chemical patterns to make us humans it is going to require far more complex digital processing. This is where the use of Artificial Intelligence (AI) processing techniques is going to accelerate our progress.

For a  more detailed analysis of SARS-CoV-2 read this excellent PDF

https://docs.google.com/document/d/1MoJ4T32z3ZLPDEQDawxzUf3A43ZWXfBbrCTv_HvaKqo/edit?usp=sharing