Biology’s Path to the Future

by Mike Van Schoiack | Mar 31, 2018

Biology Today – Headed Down the Wrong Path?

It would have been logical to assume chemistry governed biology before the realization that molecular machines built proteins, DNA, RNA and physical structures within the cell. But enzymes are still called catalysts, and catalysts are called chemicals that speed up a chemical reaction.

Chemical reactions are a different paradigm compared to molecular machines. Machines require embedded intelligence and continual energy consumption while running. Chemical reactions can occur without intelligence and its energy requirement. Could the materialist ideology that permeates the field of biology be the reason it views life through a chemical lens sans engineering?

Biologists have made great progress nevertheless. The ability to observe and measure what is actually happening in the cell was (and still is) very limited due to the microscopic size, 3-D, non-homogeneous envirnoment. Non-biological chemists do chemistry in bulk quantities which has limited use in biology due to its dependency upon highly specified complex, dynamic arrangements of matter/energy. These qualities makes reverse engineering life next to impossible.

The failure of biology to accept life being engineered results in wasted resources, time, energy and lives.

Life Needs to be Reverse Engineered

It is this engineer’s opinion that reverse engineering life is possibly the most significant advancement that mankind should now be pursuing. The benefits of having a detailed understanding of life are obvious, especially in the field of medicine. We could be better stewards of the world. It will help us adapt to changing conditions and to space travel. This may be the reason we exist!

Here are some thoughts about how this project might be organized.

Give the Project a Name

This project would be mankind’s biggest undertaking to date, far bigger than the human genome and ENCODE projects, and even bigger and more challenging than putting a man on the moon, Hubble and the Hadron Collider. An exaggeration? Life is far more complex than anything mankind has encountered, and we do not have means to directly observe the life process in detail. A project of this importance deserves a great name.

Define Goals

Defining the goals is the obvious start of any project. Here are a few straw-man ideas.

Explicitly Define the Knowledge to be Pursued, and the Form it is Documented

The main, high-level goal is to have complete, “know all there is to know” knowledge of life. This should also include understanding the functionality in terms of what each entity is doing, how it is doing it, why it is doing it, and how the process actions relate to each other. There needs to be a top-down (coherency of all functionalities) as well as a bottom-up understanding.

The proposal here is to think of life as a process with thousands of process tasks, to identify each of these tasks, diagram how these tasks relate to each other (linkage notation system) and identify the inputs, signaling means, the logic processing means, and the actuator means of each task.

And there should be a method of cataloging and referencing supporting information such as books, papers, studies, videos, educational materials, medical links, etc.¹

A possibility would be a cross between a Wikipedia format with a biology Dewey Decimal system.

Form a Standards Committee Consisting of Qualified Engineers and Biologists

The first task would be to assemble highly qualified people to design the process to be followed and organize the effort. Thousands of contributors will very quickly become involved once standards have been established. This group could morph into the role of on-going maintenance and management.

Develop Research Tools and Methods

The development of methods and tools for doing research would be a needed parallel effort. Because of the theoretical limitations of observing molecules, computer simulation can become a method of analyzing molecular machine function. For example, it seems that the natural folding of a protein has been successfully modeled, and it seems that this method could be expanded to simulate molecular machine operation. Again, forming a group to study and promote such efforts, and to provide a database for best practices, tools and methods would be worthwhile.

Since this was first written, Ann Ganger directed me to PDSsum which is a database of protein 3D structures, plus information how the information was gathered, and the KEGG Pathway database, which is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction, reaction and relation networks. Part of what I am thinking could be accomplished by adding to these tools. The details of how the protein works could be added to the PDSsum database, and an identification method for the pathways in the pathway maps with a database of information of how each of these pathways was implemented could be added to the KEGG Pathway database.