As biology advances into the digital age, it creates new opportunities for discovery.
Increasingly, information from investigations into aspects of biology from ecology to molecular biology is available in digital form. Old, “old” information is being digitized. Digital information is pieced together into databases that can be harvested and examined using a growing suite of algorithms and visualization tools.
From this direction emerged the vision that, one day, we should be able to analyze any and all aspects of biology in this digital world.
However, before this can happen, an infrastructure will be needed that collects information from all sources, reshapes it as unified data using global metadata and ontology, and makes it freely available for analysis.
This information should also make its way to trustworthy repositories to ensure that the data is always accessible in a polished state that is well suited for reuse.
The first layer in the infrastructure is the one that collects all the old and new information, whether it has to do with the migration of ocean mammals, the sequences of bases in ribosomal RNA, or the known locations of certain types of ciliated protozoa.
How many such subdomains will there be? To answer this, we need to understand the scope and scale of biology.
With Nature’s Envelope we have, for the first time, a simple model that depicts the scope and scale of biology. The envelope of nature was introduced as a rhetorical device by its author, Dr. David J. Patterson (University of Sydney, Australia), in a forum paper, published in the open science journal Research Ideas and Outcomes (RIO).
This is achieved by accumulating information about the processes conducted by all living organisms. Processes occur at all levels of organization, from sub-molecular transactions, such as those that support nerve impulses, to those within and between plants, animals, fungi, protists, and prokaryotes. Moreover, they are also the actions and reactions of individuals and societies; but also the sum of the interactions that make up an ecosystem; And finally, the consequences of the biosphere as a whole system.
In the envelope of nature, information on participant sizes and durations of processes from all levels of organization is plotted on a grid. The network uses a logarithmic (base 10) scale, which has about 21 orders of magnitude and 35 orders of magnitude greater. Information on processes ranging from subatomic, through molecular, cellular, tissue, organisms, species, and communities to ecosystems is allocated to the appropriate nodal clusters.
Examples include motions from the stepwise motion of molecules such as kinesin that move forward 8 nm in about 10 ms; or migrations of Arctic terns that follow routes of 30,000 km or more from Europe to Antarctica over a period of 3 to 4 months
The extremes of life processes are determined by the smallest and largest entities involved, and the shortest and most enduring processes. The shortest event involved is the transfer of energy from a photon to a photosynthetic pigment as the photon passes through a chlorophyll molecule several nanometers wide at a speed of 300,000 kilometers per second. This transaction takes about 10-17 seconds. Since it includes the smallest subatomic particles, it defines the lower left corner of the lattice.
The most enduring is the process of evolution that lasted for nearly 4 billion years. The influence of the latter creates the biosphere (the largest living organism) and affects the gas content in the atmosphere. This process created the far upper right of the grid.
All biological processes fit into a wide, S-shaped envelope that includes about half of the network’s nodal masses. The cover drawn around the prime examples is Nature’s Envelope.
“The Nature’s Hardcover will be a useful addition to many discussions, whether it is dealing with the infrastructure that will run the digital age of biology, or providing context for education about the diversity and range of processes in which living systems are involved. Nature’s hardcover published in the journal RIO is seen as the first edition , to be refined and improved through community involvement,” Patterson comments.
Patterson DJ (2022) Scope and Scale of Life Sciences (“Nature Envelope”). Research Ideas and Findings 8: e96132. https://doi.org/10.3897/rio.8.e96132