‘Nature’s Envelope’ – a simple device that reveals the scope and scale of all biological processes

All processes fit into a broad S-shaped envelope extending from the briefest to the most enduring biological events. For the first time, we have the first simple model that depicts the scope and scale of biology.

Arctic tern by Mark Stock, Schleswig-Holstein Wadden Sea National Park. License: CC BY-SA.

As biology is progressing into a digital age, it is creating new opportunities for discovery. 

Increasingly, information from investigations into aspects of biology from ecology to molecular biology is available in a digital form. Older ‘legacy’ information is being digitized. Together, the digital information is accumulated in databases from which it can be harvested and examined with an increasing array of algorithmic and visualization tools.

From this trend has emerged a 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, there will need to be an infrastructure that gathers information from ALL sources, reshapes it as standardized data using universal metadata and ontologies, and made freely available for analysis. 

That information also must make its way to trustworthy repositories to guarantee the permanent access to the data in a polished and fully suited for re-use state.

The first layer in the infrastructure is the one that gathers all old and new information, whether it be about the migrations of ocean mammals, the sequence of bases in ribosomal RNA, or the known locations of particular species of ciliated protozoa.

How many of these subdomains will be there?

To answer this, we need to have a sense of the scope and scale of biology.

With the Nature’s Envelope we have, for the first time, a simple model that depicts the scope and scale of biology. Presented as a rhetorical device by its 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 compiling information about the processes conducted by all living organisms. The processes occur at all levels of organization, from sub-molecular transactions, such as those that underpin nervous impulses, to those within and among plants, animals, fungi, protists and prokaryotes. Further, they are 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 system. 

Nature’s Envelope, in green, includes all processes carried out by, involving, or the result of the activities of any and all organisms. The axes depict the duration of events and the sizes of participants using a log10 scale. Image by David J. Patterson. License: CC BY.

In the Nature’s Envelope, information on sizes of participants and durations of processes from all levels of organization are plotted on a grid. The grid uses a logarithmic (base 10) scale, which has about 21 orders of magnitude of size and 35 orders of magnitude of time. Information on processes ranging from the subatomic, through molecular, cellular, tissue, organismic, species, communities to ecosystems is assigned to the appropriate decadal blocks. 

Examples include movements from the stepping motion of molecules like kinesin that move forward 8 nanometres in about 10 milliseconds; or the migrations of Arctic terns which follow 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 briefest and most enduring processes.

The briefest event to be included is the transfer of energy from a photon to a photosynthetic pigment as the photon passes through a chlorophyll molecule several nanometres in width at a speed of 300,000 km per second. That transaction is conducted in about 10-17 seconds. As it involves the smallest subatomic particles, it defines the lower left corner of the grid. 

The most enduring is the process of evolution that has been progressing for almost 4 billion years. The influence of the latter has created the biosphere (the largest living object) and affects the gas content of the atmosphere. This process established the upper right extreme of the grid.

All biological processes fit into a broad S-shaped envelope that includes about half of the decadal blocks in the grid. The envelope drawn round the initial examples is Nature’s Envelope.

Nature’s envelope will be a useful addition to many discussions, whether they deal with the infrastructure that will manage the digital age of biology, or provide the context for education on the diversity and range of processes that living systems engage in.

The version of Nature’s Envelope published in the RIO journal is seen as a first version, to be refined and enhanced through community participation,”

comments Patterson.

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Original source:

Patterson DJ (2022) The scope and scale of the life sciences (‘Nature’s envelope’). Research Ideas and Outcomes 8: e96132. https://doi.org/10.3897/rio.8.e96132

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Senckenberg Nature Research Society transfers three journals to ARPHA Platform

Arthropod Systematics & Phylogeny, Vertebrate Zoology and Geologica Saxonica are the latest historic titles to select the various services and advanced technology provided by the OA-born scholarly publishing platform

One of the largest natural research associations in Germany, the Senckenberg Nature Research Society moved three of its international, open-access scholarly journals to the publishing platform ARPHA, following a recent contract with the scientific publisher and technology provider Pensoft.

Having opted for the white-label publishing solution, the journals remain under the brand of the Society and the Senckenberg Natural History Collections Dresden, one of the oldest natural-science museums in the world. Despite transitioning to a new platform, the past volumes of the journals remain accessible from a link on their website homepages.

Following their recent move to the Pensoft-developed publishing platform, Arthropod Systematics & PhylogenyVertebrate Zoology and Geologica Saxonica have not only acquired their own glossy and user-friendly websites, but have also taken advantage from ARPHA’s signature fast-track, end-to-end publishing system, which is to benefit all journal users: authors, reviewers and editors alike. In addition, the journals are already using many of the unique services offered by ARPHA, including publication in PDF, semantically enhanced HTML and machine-readable XML formats; advanced data publishing; sub-article-level usage metrics; automated export of sub-article elements and data to key aggregators; web-service integrations with major indexing and archiving databases; and others.

In particular, to the appeal of the authors, editors and reviewers, the ARPHA’s collaboration-centred online environment takes care after each submitted manuscript during the review, editing, publication, dissemination and archiving stages, so that no one needs to deal with locally stored files and their transfer by email or third-party cloud storages. Additionally, the platform is designed to regularly notify the users about any required action, thus sparing the burden of unnecessary communication and ensuring the speedy processing of manuscripts.

All three journals operate a Diamond Open Access policy, thanks to the support of the Senckenberg Nature Research Society, making the journals free to publish for all authors.

Arthropod Systematics & Phylogeny

Arthropod Systematics & Phylogeny is the successor of the historical Entomologische Abhandlungen, formerly published by the Museum of Zoology at Dresden.

Its scope covers the taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of arthropod taxa, but excludes faunistics and research with a strong regional focus. Descriptions of new taxa are only welcome when embedded in a wider context, for example, a phylogenetic, evolutionary, or biogeographical framework.

Currently, the journal enjoys an Impact Factor of 1.51 and a continuously increasing Scopus CiteScore.

Vertebrate Zoology

Similarly, Vertebrate Zoology was preceded by Zoologische Abhandlungen, also formerly published by the Museum of Zoology at Dresden. Its first publications since the move to ARPHA Platform and part of the first journal volume for 2021 are already a fact.

The journal deals with research on taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of vertebrates. Again, descriptions of new taxa should be integrated into a proper context, for example, a complete revision of a taxon. To support accountability and reproducibility in science and academia, the journal requires that studied specimens have to be deposited in a public scientific collection.

Vertebrate Zoology’s Impact Factor is currently standing at 1.167, while its last Scopus CiteScore reached 2.1 (2019).

Geologica Saxonica

Geologica Saxonica – Journal of Central European Geology, began its life in distant 1876, when it was founded under the name Mitteilungen aus dem Königlichen Mineralogisch-Geologischen und Prähistorischen Museum by German geologist Hanns Bruno Geinitz, renowned for his work on the Carboniferous and Cretaceous rocks and fossils of Saxony.

The journal’s scope ecompasses geology, paleontology, stratigraphy, petrography, mineralogy and geoscience history with focus on Central Europe.

“At Pensoft, we are delighted to support a world-renowned natural history association like Senckenberg in carrying its legacy and treasure of knowledge into our days and well beyond. Now, with ARPHA’s white-label solution, we’re certain that the journals will simultaneously preserve their identity and enjoy all perks of modern and technologically advanced publishing,”

comments Pensoft and ARPHA’s founder and CEO Prof. Lyubomir Penev.

“We are very pleased to have found reliable partners in Pensoft and the ARPHA platform for our three publications to further increase their visibility. Senckenberg’s scientific publications have a long – almost 200-year tradition – and are now shown in a new and innovative design with unprecedented information retrieval options!”

says Prof. Dr. Uwe Fritz, Editor-in-Chief of the journal Vertebrate Zoology and head of the Department of Zoology at Senckenberg Natural History Collections in Dresden.

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Senckenberg is not the first prestigious German research institution to sign an agreement with Pensoft and ARPHA Platform. Since 2014, the Natural History Museum Berlin has trusted the publisher with its own historical titles in the Biology domain: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution. In 2017, Evolutionary Systematics by the University of Hamburg, another prominent journal with a legacy in the field of Zoology, followed suit. Last year, Zitteliana, a historical scholarly journal covering all fields of paleontology and geobiology by the State Natural History Collection of Bavaria (SNSB) also announced its joining the journal portfolio of Pensoft and ARPHA Platform.

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Recursive language and modern imagination were acquired simultaneously 70,000 years ago

The lion-man sculpture from Germany (dated to 37,000 years ago) must have been first imagined by the artist by mentally synthesizing parts of the man and beast together and then executing the product of this mental creation in ivory. The composite artworks provide a direct evidence that by 37,000 years ago humans have acquired prefrontal synthesis.
Image by JDuckeck
[Public domain, https://commons.wikimedia.org/wiki/File:Lion_man_photo.jpg, Wikimedia Commons]

A genetic mutation that slowed down the development of the prefrontal cortex (PFC) in two or more children may have triggered a cascade of events leading to acquisition of recursive language and modern imagination 70,000 years ago.

This new hypothesis, called Romulus and Remus and coined by Dr. Vyshedskiy, a neuroscientist from Boston University, might be able to solve the long-standing mystery of language evolution. It is published in the open-science journal Research Ideas and Outcomes (RIO).

Numerous archeological and genetic evidence have already convinced most paleoanthropologists that the speech apparatus has reached essentially modern configurations before the human line split from the Neanderthal line 600,000 years ago. Considering that the chimpanzee communication system already has 20 to 100 different vocalizations, it is likely that the modern-like remodeling of the vocal apparatus extended our ancestors’ range of vocalizations by orders of magnitude. In other words, by 600,000 years ago, the number of distinct verbalizations used for communication must have been on par with the number of words in modern languages.

On the other hand, artifacts signifying modern imagination, such as composite figurative arts, elaborate burials, bone needles with an eye, and construction of dwellings arose not earlier than 70,000 years ago. The half million-year-gap between the acquisition of the modern speech apparatus and modern imagination has baffled scientists for decades.

While studying acquisition of imagination in children, Dr. Vyshedskiy and his colleagues discovered a temporal limit for the development of a particular component of imagination. It became apparent that modern children who have not been exposed to full language in early childhood never acquire the type of active constructive imagination essential for juxtaposition of mental objects, known as Prefrontal Synthesis (PFS).

Dr. Vyshedskiy explains:

“To understand the importance of PFS, consider these two sentences: “A dog bit my friend” and “My friend bit a dog.” It is impossible to distinguish the difference in meaning using words or grammar alone, since both words and grammatical structure are identical in these two sentences. Understanding the difference in meaning and appreciating the misfortune of the 1st sentence and the humor of the 2nd sentence depends on the listener’s ability to juxtapose the two mental objects: the friend and the dog. Only after the PFC forms the two different images in front of the mind’s eye, are we able to understand the difference between the two sentences. Similarly, nested explanations, such as “a snake on the boulder to the left of the tall tree that is behind the hill,” force listeners to use PFS to combine objects (a snake, the boulder, the tree, and the hill) into a novel scene. Flexible object combination and nesting (otherwise known as recursion) are characteristic features of all human languages. For this reason, linguists refer to modern languages as recursive languages.”

Unlike vocabulary and grammar acquisition, which can be learned throughout one’s lifetime, there is a strong critical period for the development of PFS and individuals not exposed to conversations with recursive language in early childhood can never acquire PFS as adults. Their language is always lacking understanding of spatial prepositions and recursion that depend on the PFS ability. In a similar manner, pre-modern humans would not have been able to learn recursive language as adults and, therefore, would not be able to teach recursive language to their own children, who, as a result, would not acquire PFS. Thus, the existence of a strong critical period for PFS acquisition creates a cultural evolutionary barrier for acquisition of recursive language.

The second predicted evolutionary barrier was a faster PFC maturation rate and, consequently, a shorter critical period. In modern children the critical period for PFS acquisition closes around the age of five. If the critical period in pre-modern children was over by the age of two, they would have no chance of acquiring PFS. A longer critical period was imperative to provide enough time to train PFS via recursive conversations.

An evolutionary mathematical model, developed by Dr. Vyshedskiy, predicts that humans had to jump both evolutionary barriers within several generations since the “PFC delay” mutation that is found in all modern humans, but not in Neanderthals, is deleterious and is expected to be lost in a population without an associated acquisition of PFS and recursive language. Thus, the model suggests that the “PFC delay” mutation triggered simultaneous synergistic acquisition of PFS and recursive language.

This model calls for:

  • two or more children with extended critical period due to “PFC delay” mutation;
  • these children spending a lot of time talking to each other;
  • inventing the recursive elements of language, such as spatial prepositions;
  • acquiring recursive-conversations-dependent PFS;
  • teaching recursive language to their offsprings.

The hypothesis is named after the celebrated twin founders of Rome, Romulus and Remus. Similar to legendary Romulus and Remus, whose caregiver was a wolf, the real children’s caregivers had an animal-like communication system with many words, but no recursion. Their parents could not have taught them spatial prepositions or recursion; children had to invent recursive elements of language themselves. Such an invention of a new recursive language has been observed in contemporary children, for example among deaf children in Nicaragua.

“The acquisition of PFS and recursive language 70,000 years ago resulted in what was in essence a behaviorally new species: the first behaviorally modern Homo sapiens,” concludes Dr. Vyshedskiy. “This newly acquired power for fast juxtaposition of mental objects in the process of PFS dramatically facilitated mental prototyping and led to fast acceleration of technological progress. Armed with the unprecedented ability to mentally simulate any plan and equally unprecedented ability to communicate it to their companions, humans were poised to quickly become the dominant species.”

Humans acquired an ability to trap large animals and therefore gained a major nutritional advantage. As the population grew exponentially, humans diffused out of Africa and quickly settled in the most habitable areas of the planet, arriving in Australia around 50,000 years ago. These humans were very much like modern humans since they possessed both components of full language: the culturally transmitted recursive language along with the innate predisposition towards PFS, enabled by the “PFC delay” mutation.

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Original source:

Vyshedskiy A (2019) Language evolution to revolution: the leap from rich-vocabulary non-recursive communication system to recursive language 70,000 years ago was associated with acquisition of a novel component of imagination, called Prefrontal Synthesis, enabled by a mutation that slowed down the prefrontal cortex maturation simultaneously in two or more children – the Romulus and Remus hypothesis. Research Ideas and Outcomes 5: e38546. https://doi.org/10.3897/rio.5.e38546