All Biological life on earth is possible because of a discrete digital mechanism of preservation and replication.

The mechanism of signaling between the superorganism we know of as bacteria and its ongoing war against viruses is through a digital mechanism.
The source of innovation in biology is in this milieu of microbiome and viromes that are ubiquitous in every complex multicellular organism on earth. Humans are walking ecologies and cannot survive stripped of these ecologies.
We can picture this as a cloud of digital interaction that surrounds all of us.
The cells of multicellular creatures however do not communicate in the same way as bacteria. The DNA of mammals are sequestered from daily activity so as to prevent wear and tear.
The lifespan of mammals are related to their metabolism. The faster a mammal's heart beats the less time it has to live. A multicellular creature degrades like an analog system with each iteration error is accumulated.
Death is inevitable for multicellular creatures because our bodies have similar dynamics as non-linear systems found in chaos theory. The attractors that lead to our existence can lead to chaos and thus death.
Fortunately, evolution has gifted us with some of the digital mechanisms that bacteria have. The immune system is digital in nature. The same system that protects us from bacteria and viruses is also the same system that corrects for errors in our bodies.
At higher scales, evolution creates species that are more analog. But there is a constant tension between the drive to become analog and the need for preservation and replication.
All biological creatures balance these opposing forces by leveraging what is known as code duality. Every system has both an analog part that meets with the world and a digital part that preserves itself against the world.
In biology, the stuff that interprets the digital code of RNA are analog devices. More specifically, mechanical and electrical nano-machines.
The molecular machinery that converts energy into motion and energy into sensing are a consequence of biological innovation happening at bacteria and viral level.
But what meets the reality of physics and chemistry are analog machines. Living things require analog machinery to interpret and act within the world. The language of reality at higher scales is an analog language.
But to scale in size any organism requires digital mechanisms. Therefore this code duality must exist at many scales in a complex organism.
A common idea about the brain is that it is a dynamical system. A dynamical system is unlike a digital system like a computer. Brains have evolved to make sense of and move within their environments. They can only do so if they meet with the analog environment.
This idea however is an incomplete picture in the framing of code duality. The brain should have a digital component as predicted by this hypothesis of code duality. That digital component shares the same origin as our immune system.
Our immune system has the fascinating capability of recalling all the pathogens that have attempted to infect the body. What is the mechanism of this incredible memory system?
I've mentioned earlier that the human cognitive system consists of 3 'brains'. The nervous system, the endocrine system and the immune system. It's a very different triune brain that people conventionally think of.
The difference with biology and things that we design is that the latter has a designer that organizes things. So in a computer, the common currency is electrons. In biology, there is no common currency but a bureaucracy of transactions between different incompatible coins.
RNA has a surprisingly common currency (i.e. nucleotides). It is universal across earth originating living things. The power of digital systems come from a multitude of possible combinations. This only comes from standardization that leads to compatibility.
So evolution despite not having a designer with a mind, it has arrived at a strategy that acts like it has a mind!
@threadreaderapp unroll

More from Carlos E. Perez

It's a very different perspective when we realize that our bodies consist of an entire ecology of bacteria and viruses that are also passed to our ancestors. Mammals rear their young and as a consequence transfer the microbiome and virome to their offspring.


What does it mean to treat our individuality as ecologies? We are all ecologies existing in other ecologies. Nature is constantly performing a balancing act across multiple scales of existence.

There are bacteria and viruses that are unique to your ancestry as that of your own DNA. They have lived in symbiosis with your ancestor and will do so for your descendants.

It is an empirical fact that the microbiome in our stomach can influence not only our own moods but also our metabolism and thus our weight and health.

It is also intriguing to know that brains evolved out of stomachs and that our stomachs contain hundreds of millions of neurons. Humans can literally think with their gut.

More from Science

https://t.co/hXlo8qgkD0
Look like that they got a classical case of PCR Cross-Contamination.
They had 2 fabricated samples (SRX9714436 and SRX9714921) on the same PCR run. Alongside with Lung07. They did not perform metagenomic sequencing on the “feces” and they did not get


A positive oral or anal swab from anywhere in their sampling. Feces came from anus and if these were positive the anal swabs must also be positive. Clearly it got there after the NA have been extracted and were from the very low-level degraded RNA which were mutagenized from

The Taq.
https://t.co/yKXCgiT29w to see SRX9714921 and SRX9714436.
Human+Mouse in the positive SRA, human in both of them. Seeing human+mouse in identical proportions across 3 different sequencers (PRJNA573298, A22, SEX9714436) are pretty straight indication that the originals

Were already contaminated with Human and mouse from the very beginning, and that this contamination is due to dishonesty in the sample handling process which prescribe a spiking of samples in ACE2-HEK293T/A549, VERO E6 and Human lung xenograft mouse.

The “lineages” they claimed to have found aren’t mutational lineages at all—all the mutations they see on these sequences were unique to that specific sequence, and are the result of RNA degradation and from the Taq polymerase errors accumulated from the nested PCR process

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