Blog

In this issue, we will discuss the reasons for welcoming Mr. Matsumotori as Director and CTO, and what we are aiming for.

Many of the Earth's and man's problems are bio

As life is realized through art (man-made systems) such as language, religion, education, finance, transportation, communication, and entertainment, art stands for nature (natural things) such as energy, life, food, and material materials. Sunlight is the only source of energy that can replenish the earth, and photosynthesis is an excellent mechanism for fixing light energy. Fossil fuels are made of carbon from ancient plants and animals, and since photosynthesis and CO2 are buffers of solar energy, it is only natural that they are directly related to the fate of the earth. Hence, many of the natures that are important for human survival, both food and energy, can be said to be bio-issues. When humans expand into space, bio-issues may be more important than rocket development. However, human beings have had difficulty in understanding the mysterious system called "life. COGNANO is challenging the 3-billion-year-old history of life on Earth by using the code of antibody genes.

On the other hand, the Web was a world (art) created by man, but now it seems to be evolving into a world where the Web itself has autonomy and reality (it is no longer virtual). In Matsumotori's eyes, the Web world is becoming more and more alive. It seems that the Web, which used to be art, is now moving toward nature (or something like that). If the Web is a living organism, it has already undergone a major evolution in the 30 years since its emergence, and "witnessing its evolution in real time," which is something that cannot be seen in biotechnology, should be a normal routine for IT engineers. I am sure that the image that came to my mind 25 years ago was a very important one.

Twenty-five years ago, I had an image in my head. The question was: Is it possible to look at a million bio-cities from the top of a hill and figure them all out?

View of Kyoto City from Mt.

We can now answer yes to that question. So now, what is the vision we should aim for with IT engineers?

Methodology for recognizing vast and diverse bio-information

I believe it is a "evolutionary" world where bio-awareness is auto-generated.

VHH antibodies are not only material but also "huge information". There are 10 million species of organisms in this world, each expressing 10 to 10 million different proteins. million different proteins are expressed, there are 1 to 100 trillion different proteins on earth (1,012 to 15), that is, 1 to 100 trillion different kinds of proteins. If we assume that there are 10 to 10 million different types of proteins expressed by 10 to 10 million different organisms, then there are 1 to 100 trillion types of proteins, or antigens, on earth. By the way, there are at least 205 possible combinations of antibody sequences encoded by 20 different amino acids (just within the range of sequences that can be deciphered by next-generation sequencers). This is already enough for an "ultra-server" that covers the molecular information of all organisms. For example, if we inductively decode all VHH antibody sequences covering mutations α, δ, and ο of the new corona, we can deductively understand "the composition of acquired immunity corresponding to viral mutations". In this pandemic, many useful antibodies have been reported, but COGNANO, from a unique perspective, has reported antibodies that reach deductive recognition against mutating viruses and continue to work against omicrons. The following is a preprint of the paper.

Nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants | bioRxiv
We are in the midst of the historic coronavirus infectious disease 2019 (COVID-19) pandemic caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Although countless efforts to control the pandemic have been attempted—most successfully, vaccination[1][1]–[3][2]—imbalances in accessibility to vaccines, medicines, and diagnostics among countries, regions, and populations have been problematic. Camelid variable regions of heavy chain-only antibodies (VHHs or nanobodies)[4][3] have unique modalities: they are smaller, more stable, easier to customize, and, importantly, less expensive to produce than conventional antibodies[5][4], [6][5]. We present the sequences of nine alpaca nanobodies that detect the spike proteins of four SARS-CoV-2 variants of concern (VOCs)—namely, the alpha, beta, gamma, and delta variants. We show that they can quantify or detect spike variants via ELISA and lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays[7][6]. The panel of nanobodies broadly neutralized viral infection by pseudotyped SARS-CoV-2 VOCs. Structural analyses showed that a P86 clone targeted epitopes that were conserved yet unclassified on the receptor-binding domain (RBD) and located inside the N-terminal domain (NTD). Human antibodies have hardly accessed both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins undetected by conventional antibodies and maintains activity against spike proteins carrying escape mutations. ### Competing Interest Statement The authors have declared no competing interest. [1]: #ref-1 [2]: #ref-3 [3]: #ref-4 [4]: #ref-5 [5]: #ref-6 [6]: #ref-7
iconhttps://www.biorxiv.org/content/10.1101/2021.10.25.465714v1
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Our style of recognition is the product of a catch-all between (inductive) antibody sequence information that springs from alpacas and can be linked to viral mutations, and deductive theory discovery of molecular interactions through machine learning. This recognition unit is the engine of COGNANO. In practical use, COGNANO will be able to quickly predict drug discovery in silico, instead of responding to each theory when the next mutation comes along. In conventional biotechnology, it is often the case that the "results" of each theory are sufficient. This is because to arrive at a deductive theory requires a huge amount of standardized data, which is impossible to obtain.

COGNANO's life recognition engine

COGNANO is also building up recognition units such as "discovering unknown cancer markers" through computational science, and COGNANO's machine learning team believes that the day will come when machines will predict optimal solutions without inductive data as a result of multiple unit operations. Emergence, akin to the human "abduction," or "I know what I'm doing even though I haven't experienced it (or experimented on it individually)! will occur.

In addition, if VHH antibodies are used as a detection tool, various personal monitoring such as viral infections and myocardial infarctions will become possible and useful as IoT. What this means is that molecular data, rather than information from medical records, questionnaires, or images, will be used for direct services. In practical use, VHH antibodies will become a useful commodity, taking advantage of their superiority in mass production and standardization. In other words, VHH antibodies can be used as useful materials (hardware) as well as huge information (software), which is a rare case in biotechnology.

Now, in this pandemic, we had to line up at PCR laboratories and hospitals, even though we just wanted to "make the right decision" not to treat, ...... outpatient clinics were filled with patients who were not sure if it was corona or not... ...didn't you feel somewhat uncomfortable? Perhaps it was harder to complain, even if it was inconvenient, "because it was wartime." Maybe safety and medical information got mixed up somewhere in the inspection flow line.

In the late 21st century, humans can now check their own health (infectious diseases, cancer, genetics, fatigue, life expectancy, mental health, etc.) that they used to leave to hospitals. Even difficult bio-knowledge can now be taught by smart speakers. Information acquired by small devices is now collected anonymously via smartphones, and data from 7 billion people is analyzed simultaneously, increasing the intangible asset of human health.

The scenario described here is still based on a "wisdom and ingenuity create the future" type of worldview. In the future, the handling of health information will shift even more to the individual, and the growing amount of user information will bring deeper and more accurate feedback. This is the way it should be, and it is certain that a big business will be created there.

New perceptions go to create new worldviews.

But what we are trying to do with Matsumotori and others is a longer range vision. We feel that a autogenous transformation of consciousness will occur. Our generation has experienced a pandemic, and we can no longer just dismiss it as a natural disaster like the "Spanish flu. We have the probes to understand life, and we already know that both viruses and humans exist on a common life principle. If we change our perspective on biotechnology, money, consumption, and the environment may look a little different. Even now, humans are fragile beings who feel that health and life come first when they fall ill. I found myself talking about this with Matsumotori-san and other IT engineers who are gathering at COGNANO.

Just as capital and energy change the way of the world, biotechnology changes the way of the world. VHH data is nature itself. Since its inception, COGNANO has been able to learn from Nature, draw in the direction of Art, and extract deductive value. We are now entering an era in which new worldviews will emerge that are faithful to Nature, but also go beyond it. Our view of life will evolve and may become what could be called digital nature. The web should be the space where such a perception is born. We are ready.

Stay tuned for the future of COGNANO!

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Not only will we be a biotech but IT company, we'll be a team that can do biotech despite being IT! On-going fusion of biotechnology and IT through digitization of biological information