Vendo a célula em uma dimensão totalmente nova: mero acaso, fortuita necessidade ou design inteligente?

sexta-feira, julho 29, 2022

Journal of Molecular Biology

Volume 434, Issue 2, 30 January 2022, 167351

Research Article

Building Structural Models of a Whole Mycoplasma Cell

Martina Maritan 1†Ludovic Autin 1†Jonathan Karr 2 Markus W.Covert 3 Arthur J.Olson 1 David S.Goodsell14

1 Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037 USA

2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA

3 Department of Bioengineering, Stanford University, Stanford, CA 94305, USA

4 RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA

Received 5 August 2021, Revised 4 November 2021, Accepted 5 November 2021, Available online 10 November 2021, Version of Record 22 November 2021.

Edited by Amy Keating 

Image of a 3D model of a Mycoplasma cell by Martina Maritan


• 3D whole cell modeling requires new bioinformatics and computational methods.

• Information for generating 3D cell models is gathered and curated with Mesoscope.

• A multi-step workflow generates structural models of an entire proteome.

• Entire bacterial cells are interactively modeled and visualized with CellPACKgpu.

• This work demonstrates the feasibility of building 3D models of an entire cell.


Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of integration between multiple sources of biological data and enhanced methods for computational modeling and visualization. Here, we present the first 3D structural models of an entire Mycoplasma genitalium (MG) cell, built using the CellPACK suite of computational modeling tools. Our model recapitulates the data described in recent whole-cell system biology simulations and provides a structural representation for all MG proteins, DNA and RNA molecules, obtained by combining experimental and homology-modeled structures and lattice-based models of the genome. We establish a framework for gathering, curating and evaluating these structures, exposing current weaknesses of modeling methods and the boundaries of MG structural knowledge, and visualization methods to explore functional characteristics of the genome and proteome. We compare two approaches for data gathering, a manually-curated workflow and an automated workflow that uses homologous structures, both of which are appropriate for the analysis of mesoscale properties such as crowding and volume occupancy. Analysis of model quality provides estimates of the regularization that will be required when these models are used as starting points for atomic molecular dynamics simulations.

FREE PDF GRATIS: Journal of Molecular Biology

Uma nova teoria da formação da Terra

Stochastic accretion of the Earth

Paolo A. Sossi, Ingo L. Stotz, Seth A. Jacobson, Alessandro Morbidelli & Hugh St. C. O’Neill 

Nature Astronomy (2022)

Artist’s impression of the forming Earth – from chondritic asteroids on the left, and from planetesimals on the right. Credit: Tobias Stierli /


Chondritic meteorites are thought to be representative of the material that formed the Earth. However, the Earth is depleted in volatile elements in a manner unlike that observed in any chondrite, and yet these elements retain chondritic isotope ratios. Here we use N-body simulations to show that the Earth did not form only from chondrites, but by stochastic accretion of many precursor bodies whose variable compositions reflect the temperatures at which they formed. Earth’s composition is reproduced when the initial temperatures of planetesimal- to embryo-sized bodies are set by disk accretion rates of (1.08 ± 0.17) × 10−7 solar masses per year, although they may be perturbed by 26Al heating on bodies formed at different times. Our model implies that a heliocentric gradient in composition was present in the protoplanetary disk and that planetesimals formed rapidly within ~1 Myr, consistent with radiometric volatile depletion ages of the Earth.

Subscription or payment needed/Requer assinatura ou pagamento: Nature Astronomy

Preprint available/Pre-impressão disponível: arXiv

A evolução química reimaginada

quarta-feira, julho 27, 2022

Chemical Evolution Reimagined


Moran Frenkel Pinter, Hebrew University of Jerusalem ,Kavita Matange, Georgia Institute of Technology, Vahab Rajaei, Georgia Institute of Technology, John T Costner, Georgia Institute of Technology, Adelaide Robertson, Georgia Institute of Technology, Jennifer Seoyoung Kim, Georgia Institute of Technology, Anton S Petrov, Georgia Institute of Technology, Jessica C. Bowman, Georgia Institute of Technology, Loren Dean, Williams Georgia Institute of Technology 

Image/Imagem: Chemistry World


Some of the most interesting open questions about the origins of life and molecular sciences center on chemical evolution and the spontaneous generation of new complex and functional chemical species. The spectacular polymers that underlay biology demonstrate an untapped, by modern science, creative potential. We hypothesized that prebiotic chemical evolutionary processes leading to biopolymers were not idiosyncratic one-off events. We have developed an experimental platform that accomplishes chemical evolution in the laboratory. In this paper we describe this platform and report empirical outcomes, some of which were not foreseen. We have constructed experimental platform to study evolution of chemical systems that: (i) undergo continuous recursive change with transitions to new chemical spaces while not converging, (ii) demonstrate stringent chemical selection, during which combinatorial explosion is avoided, (iii) maintain synchronicity of molecular sub-populations, and (iv) harvest environmental energy that is invested in chemical reactions. We have established general guidelines for conducting chemical evolution. Our results suggest that chemical evolution can be adapted to produce a broad array of molecules with novel structures and functions.

FREE PDF GRATIS: ChemRxiv Sup. Info.

A interpretação de embriões fósseis requer avaliação razoável da idade de desenvolvimento.

Interpretation of fossil embryos requires reasonable assessment of developmental age

Published online by Cambridge University Press:  20 July 2022

D. Charles Deeming and Martin Kundrát 

Figure 1. Three-dimensional mapping of real consectutive positioning and developmental geometry of cranial and postcranial elements in Crocodylus niloticus embryos. The incubation period is around 90 days. Note the position of the skull inside the egg, overall curling patterns, and in ovo space left unoccupied by 55- and 68-day-old embryos.


Dinosaur embryos cause a lot of excitement in the scientific literature and are often widely reported because of the general public's interest in dinosaur biology. Well-preserved, articulated oviraptorosaur embryos in eggs are usually interpreted as representing a stage of development close to hatching because of their large size and good level of skeletal ossification. Based on this evidence, a recent report suggested that the position of the one embryo's head was reminiscent of an avian-like hatching position. Here we explore how the developmental stage of well-preserved oviraptorosaur embryos can be estimated, rather than assumed. This will help in our understanding of their developmental biology and its evolutionary consequences. Using quantitative methods and comparison with modern crocodilian embryos, we show that all articulated oviraptorosaur embryos are small relative to the egg and most likely at a stage of development equivalent to around 50%–60% of the developmental period, that is, not even close to hatching. This conclusion is supported by the fact that many elements of the crocodilian skeleton are well ossified many weeks before hatching and the position of oviraptorosaur embryos’ heads was also comparable to a crocodilian embryo many days before hatching. Misunderstandings about the stage of the developmental biology of these well-preserved oviraptorosaur embryos hampers our understanding of the true nature of their reproductive biology. We urge a more conservative approach to their interpretation. This is important, because misunderstandings in the minds of the public about dinosaur biology are hard to counter once poorly evidenced ideas have been reported around the world.

FREE PDF GRATIS: Palaeobiology

Se o design na natureza é mera ilusão, por que procurar design na natureza?

terça-feira, julho 26, 2022

A DNA origami rotary ratchet motor

Anna-Katharina Pumm, Wouter Engelen, Enzo Kopperger, Jonas Isensee, Matthias Vogt, Viktorija Kozina, Massimo Kube, Maximilian N. Honemann, Eva Bertosin, Martin Langecker, Ramin Golestanian, Friedrich C. Simmel & Hendrik Dietz 

Nature volume 607, pages492–498 (2022)

Fig. 1: Motor design and experimental setup.


To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry1,2,3,4,5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6,7,8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. 3) and also in artificial molecular motors created by organic chemical synthesis9,10,11,12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14,15,16,17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20,21,22,23,24,25,26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F1F0-ATPase.

FREE PDF GRATIS: Nature Sup. Info. 

O desenvolvimento embrionário inicial diverso de vertebrados e implicações sobre sua ancestralidade

sábado, julho 23, 2022

The diverse early embryonic development of vertebrates and implications regarding their ancestry

David Swift

Image/Imagem: Nature Reviews Molecular Cell Biology 


It is well known that the embryonic development of vertebrates from different classes (e.g., fish, reptiles, mammals) pass through a “phylotypic stage” when they look similar, and this apparent homology is widely seen as evidence of their common ancestry. However, despite their morphological similarities, and contrary to evolutionary expectations, the phylotypic stages of different vertebrate classes arise in radically diverse ways. This diversity clearly counters the superficial appearance of homology of the phylotypic stage, and the plain inference is that vertebrates have not evolved from a common vertebrate ancestor. The diversity extends through all stages of early development—including cleavage and formation of the blastula, gastrulation, neurulation, and formation of the gut and extraembryonic membranes. This paper focuses on gastrulation, during which the germ layers originate and the vertebrate body-plan begins to form. Despite its key role in embryonic development, gastrulation occurs in fundamentally different ways in different classes of vertebrates. The inference against common ancestry becomes progressively stronger as more is discovered about the genetic and molecular mechanisms that implement development. It is increasingly evident that these are of such complexity that it is unrealistic to think that undirected variations (random mutations) could produce constructive changes to development, such as those required to account for a diversification of development from that of a common ancestor, especially while retaining a similar phylotypic stage.


Edição especial do PNAS sobre os 200 anos do nascimento de Gregor Mendel e suas descobertas científicas

quarta-feira, julho 20, 2022

Cronometragem e tomada de decisão em células vivas: mero acaso, fortuita necessidade ou design inteligente?

terça-feira, julho 19, 2022

Time-keeping and decision-making in living cells: Part I

John J. Tyson, Attila Csikasz-Nagy, Didier Gonze, Jae Kyoung Kim, Silvia Santos and Jana Wolf

Published:15 April 2022

Figure 1. Some components of the information-processing system (IPS) in a mammalian cell. 


To survive and reproduce, a cell must process information from its environment and its own internal state and respond accordingly, in terms of metabolic activity, gene expression, movement, growth, division and differentiation. These signal–response decisions are made by complex networks of interacting genes and proteins, which function as biochemical switches and clocks, and other recognizable information-processing circuitry. This theme issue of Interface Focus (in two parts) brings together articles on time-keeping and decision-making in living cells—work that uses precise mathematical modelling of underlying molecular regulatory networks to understand important features of cell physiology. Part I focuses on time-keeping: mechanisms and dynamics of biological oscillators and modes of synchronization and entrainment of oscillators, with special attention to circadian clocks.

FREE PDF GRATIS: Interface Focus

Darwin, nós temos um problema: o DNA lixo é funcional e faz uma grande diferença.

segunda-feira, julho 18, 2022

Not functional yet a difference maker: junk DNA as a case study

Joyce C. Havstad & Alexander F. Palazzo 

Biology & Philosophy volume 37, Article number: 29 (2022) 


It is often thought that non-junk or coding DNA is more significant than other cellular elements, including so-called junk DNA. This is for two main reasons: (1) because coding DNA is often targeted by historical or current selection, it is considered functionally special and (2) because its mode of action is uniquely specific amongst the other actual difference makers in the cell, it is considered causally special. Here, we challenge both these presumptions. With respect to function, we argue that there is previously unappreciated reason to think that junk DNA is significant, since it can alter the cellular environment, and those alterations can influence how organism-level selection operates. With respect to causality, we argue that there is again reason to think that junk DNA is significant, since it too (like coding DNA) is remarkably causally specific (in Waters’, in J Philos 104:551–579, 2007 sense). As a result, something is missing from the received view of significance in molecular biology—a view which emphasizes specificity and neglects something we term ‘reach’. With the special case of junk DNA in mind, we explore how to model and understand the causal specificity, reach, and corresponding efficacy of difference makers in biology. The account contains implications for how evolution shapes the genome, as well as advances our understanding of multi-level selection.

FREE PDF GRATIS: Biology & Philosophy

Darwin, nós temos um problema: a conectividade de áreas de linguagem são únicas no cérebro humano

sexta-feira, julho 15, 2022

Comparing human and chimpanzee temporal lobe neuroanatomy reveals modifications to human language hubs beyond the frontotemporal arcuate fasciculus

Joanna Sierpowska, Katherine L. Bryant, Nikki Janssen, +4 , Guilherme Blazquez Freches, Manon Römkens, Margot Mangnus, Rogier B. Mars, and Vitoria Piai

Edited by Marcus Raichle, Washington University in St. Louis, St. Louis, MO; received October 7, 2021; accepted May 11, 2022

July 5, 2022

119 (28) e2118295119

Image/Imagem: Time Magazine - Tim O'Brien


Communication through language is a great achievement of evolution. In humans, the arcuate fasciculus, white matter that extended dramatically during evolution, is known to subserve language. We investigated whether connections through critical language centers in the temporal lobe are uniquely human. We show that connectivity in the posterior temporal lobe via the arcuate fasciculus expanded bilaterally to frontal and parietal cortices in humans compared with chimpanzees. Concomitantly, the ventral tracts connect more strongly to posterior temporal regions in the chimpanzees than in humans. In the anterior temporal lobe, connections shared between both species and uniquely human expansions are present. Changes to human language streams extend beyond the arcuate fasciculus, including a suite of expansions to connectivity within the temporal lobes.


The biological foundation for the language-ready brain in the human lineage remains a debated subject. In humans, the arcuate fasciculus (AF) white matter and the posterior portions of the middle temporal gyrus are crucial for language. Compared with other primates, the human AF has been shown to dramatically extend into the posterior temporal lobe, which forms the basis of a number of models of the structural connectivity basis of language. Recent advances in both language research and comparative neuroimaging invite a reassessment of the anatomical differences in language streams between humans and our closest relatives. Here, we show that posterior temporal connectivity via the AF in humans compared with chimpanzees is expanded in terms of its connectivity not just to the ventral frontal cortex but also to the parietal cortex. At the same time, posterior temporal regions connect more strongly to the ventral white matter in chimpanzees as opposed to humans. This pattern is present in both brain hemispheres. Additionally, we show that the anterior temporal lobe harbors a combination of connections present in both species through the inferior fronto-occipital fascicle and human-unique expansions through the uncinate and middle and inferior longitudinal fascicles. These findings elucidate structural changes that are unique to humans and may underlie the anatomical foundations for full-fledged language capacity.

Subscription or payment needed/Requer assinatura ou pagamento: PNAS


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Darwin, nós temos um problema: novo método de datação destrói nossa compreensão da evolução humana!

quinta-feira, julho 14, 2022

THE PAST — JULY 7, 2022 

New dating method shatters our understanding of human evolution

Fossils of Australopithecus in a South African cave are one million years older than previously thought. This challenges the consensus that humans first evolved in East Africa.


- The Sterkfontein caves in South Africa are home to hundreds of fossils of early hominins in the genus Australopithecus. Original age estimates of these fossils suggested that they were no more than 2.4 million years old — younger than our genus, Homo. 

- Researchers used a new, more accurate technique to redate the fossils and made an important discovery: The fossils were much older than previously thought. They were deposited between 3.4 million and 3.7 million years ago. 

- The finding challenges our understanding of human evolution, including the consensus that we evolved in East Africa. 

Hominins link the great apes with modern humans on the evolutionary tree. Ancestral hominins mark a crucial transition in the story of human evolution, and they have fascinated paleoanthropologists for decades. 

In 1936, South African doctor and paleontologist Robert Broom made a historic discovery in the Sterkfontein caves in South Africa. Broom discovered the first adult specimen of the genus Australopithecus, a group of early hominins from which our own genus, Homo, emerged. 

Since 1936, the Sterkfontein caves have become ground zero for Australopithecus research and fossil finds. The complex cave system runs 60 meters deep, and it has revealed hundreds of Australopithecus fossils within its sediment. From these rocks emerged notable discoveries, such as the nearly complete skeletons of specimens dubbed “Little Foot” and “Mrs. Ples.”

Age is just a method

The cave features six areas, or members: Members 1 to 3 lie underground, while Members 4 to 6 are exposed to the air because of erosion in the cave roof. Most Australopithecus fossils are in Member 4. The Sterkfontein caves are one part of a World Heritage Site with a telling name — the Cradle of Humankind

The complex cave system still houses many secrets, but the discoveries already made retain mysteries of their own. Among the most debated issues is the age of the fossils found in Member 4. Researchers have estimated the age of Australopithecus in the lower Member 2 section at 3.7 million years, which jars with the estimated age of the fossils found higher in the cave. Researchers originally estimated the fossils in Member 4 to be between 2 million and 2.4 million years old. The geological peculiarities of the cave challenge traditional methods of aging fossils, casting further doubt on the accuracy of these estimations.

Purdue University’s Darryl Granger is among the researchers who questioned the age of the Member 4 Australopithecus. Recently, Granger and a team of scientists from France and South Africa endeavored to redate the famous fossils using a new method. They published their results in the Proceedings of the National Academy of Sciences


Read more here/Leia mais aqui: The Big Think.

A crise de irreprodutibilidade da ciência moderna - Causas, consequências e caminho para reforma

quarta-feira, julho 13, 2022

A crise de irreprodutibilidade da ciência moderna - Causas, consequências e caminho para reforma - Relatório (em inglês) da National Association of Scholars.


Perspectiva evolutiva sobre a origem e diversificação da vida celular e a virosfera

terça-feira, julho 12, 2022

 Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere 

Anja Spang, Tara A Mahendrarajah, Pierre Offre, Courtney W Stairs Author Notes

Genome Biology and Evolution, Volume 14, Issue 6, June 2022, evac034,

Published: 26 February 2022 Article history Accepted: 18 February 2022 Published: 26 February 2022 Corrected and typeset: 06 June 2022

The tree is a schematic representation of the relationship of the major domains of life, comprised of the primary domains of Archaea and Bacteria and the secondary domain of Eukaryotes. (Credit: Anja Spang)


The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.

Key words tree of life, viruses, archaea, bacteria and eukaryotes, eukaryogenesis, diversity and evolution, methodological progress


Our review provides a timely overview of how recent methodological progress has allowed an updated view on the tree of life and its connection to the virosphere. It covers topics ranging from last universal common ancestor to last eukaryotic common ancestor and the extant diversity of prokaryotic and eukaryotic life as well as viruses. Furthermore, we summarize current developments in the field that can help to make further progress in our understanding of deep evolution in the coming years.

FREE PDF GRATIS: Genome Biology Evolution

Desvendando as origens de LUCA e LECA na Árvore da Vida

Highlight: Unraveling the Origins of LUCA and LECA on the Tree of Life 

Casey McGrath

Genome Biology and Evolution, Volume 14, Issue 6, June 2022, evac072,

Published: 06 June 2022 Article history Accepted: 10 May 2022 Published: 06 June 2022

Tree of life. The tree of life contains three major branches—bacteria, archaea, and eukaryotes. Proposed locations for LUCA and LECA are shown. LUCA, last universal common ancestor; LECA, last eukaryotic common ancestor. Adapted from Spang et al. (2022).

The latest Virtual Issue from Genome Biology and Evolution highlights articles that provide new insight into the deep evolutionary relationships among extant organisms and the origin of eukaryotes from among archaeal lineages. All cellular organisms are descended from a shared ancestor, often referred to as LUCA—the last universal common ancestor. Relationships among these organisms can be depicted by an evolutionary network known as the “tree of life”, which for the past few decades has included three major forms of life—bacteria, archaea, and eukaryotes (fig. 1). Evolutionary biologists have long sought to understand the placement of LUCA within this framework, as well as the origin of LECA—the last eukaryotic common ancestor. Unfortunately, accurately inferring relationships among microbial lineages presents a major challenge due to the vast evolutionary distances involved, as well as the frequent lateral transfer of genetic material between lineages. Recently, however, new data and methods have resulted in profound changes to our understanding of the tree of life.


FREE PDF GRATIS: Genome Biology Evolution

Darwin, nós temos um grande problema: as pesquisas do genoma e proteoma do LUCA não concordam entre si!

quarta-feira, julho 06, 2022

The evolution of proteome: From the primeval to the very dawn of LUCA

MiryamPalacios-Pérez, Marco V.José

Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México CDMX, C.P. 04510, Mexico

First published: 03 June 2022

Image/Imagem: BioSystems


The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide-derived organic cofactors.

FREE PDF GRATIS: Ecology & Evolution



"We undertook this study with the hypothesis that the specific predictions of the various studies on the LUCA genome or proteome performed over the last two decades would largely agree with one another. We expected that each study should have some unknowable level of error because it is inherently difficult to infer specific details about life forms that existed at least 3.5 billion years ago. However, if the previously published LUCA genome or proteome studies are at all accurate, they should agree with one another and, because these studies have used largely independent approaches to infer features of the LUCA genome and proteome, agreement between them could be taken as support for this sort of approach."

Surprisingly, we found that studies of the genome or proteome of the LUCA do not uniformly agree with one another.”


Darwin, we got a huge problem!!! Over!!!

Uma relíquia de design: contra as funções próprias da biologia. Será?

segunda-feira, julho 04, 2022

A relic of design: against proper functions in biology

Emanuele Ratti & Pierre-Luc Germain 

Biology & Philosophy volume 37, Article number: 27 (2022)



The notion of biological function is fraught with difficulties—intrinsically and irremediably so, we argue. The physiological practice of functional ascription originates from a time when organisms were thought to be designed and remained largely unchanged since. In a secularized worldview, this creates a paradox which accounts of functions as selected effect attempt to resolve. This attempt, we argue, misses its target in physiology and it brings problems of its own. Instead, we propose that a better solution to the conundrum of biological functions is to abandon the notion altogether, a prospect not only less daunting than it appears, but arguably the natural continuation of the naturalisation of biology.

FREE PDF: Biology & Philosophy

Alguns problemas abertos em Biologia Matemática

sexta-feira, julho 01, 2022

Open Problems in Mathematical Biology

Sean T. Vittadello, Michael P.H. Stumpf

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the extent to which our hypotheses agree with reality. But doing so in a systematic way is becoming increasingly challenging as our hypotheses become more detailed, and our data becomes more complex. Mathematical methods are therefore gaining in importance across the life- and biomedical sciences. Mathematical models allow us to test our understanding, make testable predictions about future behaviour, and gain insights into how we can control the behaviour of biological systems. It has been argued that mathematical methods can be of great benefit to biologists to make sense of data. But mathematics and mathematicians are set to benefit equally from considering the often bewildering complexity inherent to living systems. Here we present a small selection of open problems and challenges in mathematical biology. We have chosen these open problems because they are of both biological and mathematical interest.

Comments: 31 pages, 2 figures, 115 references

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (

Cite as: arXiv:2206.09516 [q-bio.QM]

  (or arXiv:2206.09516v1 [q-bio.QM] for this version)

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Submission history

From: Michael Stumpf [view email]

[v1] Mon, 20 Jun 2022 00:31:27 UTC (1,210 KB)