As biology moves into a digital age, new opportunities for discovery arise.
Information from studies on aspects of biology, from ecology to molecular biology, is increasingly available digitally. Older ‘legacy’ information is being digitised. Together, the digital information is collected into databases from which it can be harvested and explored with an increasing array of algorithmic and visualization tools.
This trend has spawned a vision that one day we should be able to analyze all aspects of biology in this digital world.
Before this can happen, however, there must be an infrastructure that collects information from ALL sources, transforms it into standardized data using universal metadata and ontologies, and makes it freely available for analysis.
That information must also find its way into trusted repositories to ensure permanent access to the data in a polished and fully reusable state.
The first layer in the infrastructure is the one that collects all the old and new information, whether it be the migrations of marine mammals, the sequence of bases in ribosomal RNA, or the known locations of certain species of ciliated protozoa.
How many of these subdomains will there be? To answer this, we need to have an idea of the scope and scale of biology.
With the Nature’s Envelope we have for the first time a simple model that represents the scope and scale of biology. Presented as a rhetorical device by author Dr. David J. Patterson (University of Sydney, Australia), the Nature’s Envelope is described in a Forum Paper published in the open science journal Research Ideas and Outcomes (RIO).
This is achieved by collecting information about the processes carried out by all living organisms. The processes occur at all levels of organization, from submolecular transactions, such as those that support nerve impulses, to those in and between plants, animals, fungi, protists, and prokaryotes. Furthermore, it is also the actions and reactions of individuals and communities; but also the sum of the interactions that make up an ecosystem; and finally the consequences of the biosphere as a whole.
In the Nature’s Envelope, information about the size of the participants and the duration of processes from all organizational levels is plotted on a grid. The grid uses a logarithmic (base 10) scale, which has approximately 21 orders of magnitude and 35 orders of magnitude of time. Information about processes ranging from subatomic, via molecular, cellular, tissue, organism, species, communities to ecosystems is assigned to the appropriate decadal blocks.
Examples include step motion motions of molecules such as kinesin that move forward 8 nanometers in about 10 milliseconds; or the migrations of arctic terns following routes of 30,000 km or more from Europe to Antarctica over 3 to 4 months
The extremes of life processes are determined by the smallest and largest entities to participate, and the shortest and most enduring processes. The shortest event to be recorded 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 km per second. That transaction is executed in about 10-17 seconds. Since it is the smallest subatomic particle, it defines the lower left corner of the grid.
The most sustainable is the evolutionary process that has been going on for almost 4 billion years. The influence of the latter has created the biosphere (the largest living object) and influences the gas content of the atmosphere. This process has created the top right corner of the grid.
All biological processes fit into a wide S-shaped envelope that encompasses about half of the decadal blocks in the grid. The envelope drawn around the first examples is Nature’s Envelope.
“The envelope of nature will be a useful addition to many discussions, whether they are about the infrastructure that will manage the digital age of biology, or provide the context for education about the diversity and range of processes by which living systems The version of the Nature Envelope published in the RIO magazine is seen as a first draft, which should be refined and improved through community participation,” said Patterson.
Patterson DJ (2022) The scope and scale of the life sciences (‘Nature’s envelope’). Research Ideas and Results 8: e96132. https://doi.org/10.3897/rio.8.e96132