As biology moves into a digital age, it creates new opportunities for discovery.
Increasingly, information from research on aspects of biology, from ecology to molecular biology, is available in digital form. Old “legacy” information is being digitized. Together, digital information is accumulated in databases from which it can be harvested and examined with an increasing range of algorithmic and visualization tools.
From this trend emerged a vision that one day we should be able to analyze all aspects of biology in this digital world.
However, before this can happen, it will take 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.
This information also needs to be routed to trusted repositories to ensure that the data is always available in a neat state that is well suited for reuse.
The first layer of the infrastructure is that which brings together all the information old and new, whether it is the migrations of marine mammals, the sequence of ribosomal RNA bases or the known locations of particular species of protozoans. ciliates.
How many of these subdomains will there be? To answer this question, we need to have some idea of the scope and scale of biology.
With Nature’s Envelope, we have, for the first time, a simple model that describes the scope and scale of biology. Presented as a rhetorical device by its author, Dr. David J. Patterson (University of Sydney, Australia), the envelope of nature is described in a Forum Paper, published in the open scientific journal Research Ideas and Outcomes (RIO).
This is achieved by compiling information about the processes carried out by all living organisms. Processes occur at all levels of organization, from submolecular transactions, such as those underlying nerve impulses, to those within and between plants, animals, fungi, protists, and prokaryotes. Moreover, 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 for the biosphere as a whole.
In the envelope of nature, information about the size of participants and the duration of processes at all levels of organization is plotted on a grid. The grid uses a logarithmic (base 10) scale, which is approximately 21 orders of magnitude in size and 35 orders of magnitude in time. Information about processes ranging from subatomic processes to ecosystems, molecules, cells, tissues, organisms, species and communities are assigned to the appropriate decadal blocks.
Examples include the motions of the stepping motion of molecules like kinesin that advance 8 nanometers in about 10 milliseconds; or arctic tern migrations that follow routes of 30,000 km or more from Europe to Antarctica in 3-4 months
The extremes of life processes are determined by the smallest and largest entities to participate in, and the briefest and most enduring processes. The briefest event to include is the transfer of energy from a photon to a photosynthetic pigment when the photon passes through a chlorophyll molecule several nanometers wide at a speed of 300,000 km per second. This transaction is completed in approximately 10 to 17 seconds. As these are the smallest subatomic particles, it defines the lower left corner of the grid.
The most enduring is the evolutionary process that has been progressing for almost 4 billion years. The influence of the latter created the biosphere (the largest living object) and affects the gas content of the atmosphere. This process established the uppermost right of the grid.
All biological processes fit within a broad S-shaped envelope that encompasses approximately half of the decadal blocks of the grid. The envelope drawn around the initial examples is the envelope of nature.
“The Nature Wrap will be a useful addition to many discussions, whether they’re discussing the infrastructure that will manage the digital age of biology, or providing the context for education about diversity and nature. “range of processes that living systems engage in. Nature’s version of the envelope published in the journal RIO is considered an early version, to be refined and improved through community input,” comments Patterson.
Patterson DJ (2022) The Scope and Scale of the Life Sciences (“The Envelope of Nature”). Research ideas and results 8: e96132. https://doi.org/10.3897/rio.8.e96132
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