Origin of Life: E...
Follow
2.3K views | +0 today
Origin of Life: Emergence, Self-organization and Evolution
A system-centered perspective on the origin and evolution of Life on Earth
Your new post is loading...
Your new post is loading...
Scooped by Davide De Lucrezia
Scoop.it!

On stochastic simulation of minimal cell models

On stochastic simulation of minimal cell models | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

If stochastic simulation of minimal cell models intrigues you, see may be interested in:

 

Carletti T, Filisetti A.

The stochastic evolution of a protocell: the gillespie algorithm in a dynamically varying volume.
Comput Math Methods Med. 2012;2012:423627.

 

Lazzerini-Ospri L, Stano P, Luisi P, Marangoni R.

Characterization of the emergent properties of a synthetic quasi-cellular system.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S9.

 

Zachar I, Fedor A, Szathmáry E.

Two different template replicators coexisting in the same protocell: stochastic simulation of an extended chemoton model.

PLoS One. 2011;6(7):e21380. Epub 2011 Jul 19.

 

Van Segbroeck S, Nowé A, Lenaerts T.

Stochastic simulation of the chemoton.

Artif Life. 2009 Spring;15(2):213-26.

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence

The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

One of the most puzzling questions about the origin of life is how the rich chemical landscape that makes life possible came into existence.

One idea is that groups of molecules can form autocatalytic sets as first suggested by S. Kauffman. These are self-sustaining chemical factories, in which the product of one reaction is the feedstock or catalyst for another (see topic's logo). The result is a virtuous, self-contained cycle of chemical creation. Now Kauffman and coworkers present new results from a detailed study of the structure of autocatalytic sets. They show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. They argue how this has important consequences for the evolvability, enablement, and emergence of autocatalytic sets.

 

Source:

The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence

Wim Hordijk, Mike Steel, Stuart Kauffman

(Submitted on 2 May 2012, last revised 4 May 2012)

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Stochastic simulations of minimal cells: the Ribocell model

Stochastic simulations of minimal cells: the Ribocell model | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Lipid compartments (liposomes, lipid-coated droplets) have been extensively used as in vitro "minimal" cell models to shed new light on the origin of life and the basic feature of living system as well. In this paper, Mavelli and Mirazo develop a comprehensive platform called ENVIRONMENT suitable for studying the stochastic time evolution of reacting lipid compartments. The software will allow the investigation of random fluctuations and stochastic events tha may lead an open system towards unexpected time evolutions.

 

Source:

Mavelli F.

Stochastic simulations of minimal cells: the Ribocell model.

BMC Bioinformatics. 2012 Mar 28;13 Suppl 4:S10.

 

Mavelli F, Ruiz-Mirazo K.

ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments.

Phys Biol. 2010 Aug 11;7(3):036002.

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Seven Theories on the Origin of Life

Seven Theories on the Origin of Life | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

A nice overview about the different mainstream theories on the Origin of Life...

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Noise, Stochasticity and Evolvability

Noise, Stochasticity and Evolvability | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Kuwahara and Soyer report about stochastic fluctuations in gene regulation that can lead to increased evolvability of biological systems by pushing "system parameters toward a nonlinear regime where phenotypic diversity is increased and small changes in genotype cause large changes in expression level".

These findings strongly suggest that stochasticity and noise are used by biosystems to increase plasticity and access new phenotypes.

 

Source:

Hiroyuki Kuwahara & Orkun S Soyer. Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology 8:564

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

How does innovation arise in biological systems?

How does innovation arise in biological systems? | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

How does innovation arise in biological systems? A typical example is the emergence of novel catalytic functions in enzymes.

Hereafter I report two studies that come to contradicting conclusions.

Axe and Gauger suggest that the number of simultaneous mutations required to convert a 2-amino-3-ketobutyrate CoA ligase (Kbl2) to 8-amino-7-oxononanoate synthase (BioF2) are so many changes that it becomes probable only “on timescales much longer than the age of life on earth”.

Conversely, Jez and Penning showed that a single mutation changes D4-3-ketosteroid-5b-reductase to 3a-HSD; where Sommerville and coworkers have proved that six substitutions are sufficient to convert a hydroxylase to a desaturase.

How do we account for such contradicting results?

Does evolvability inversely correlate with specificity and catalytic proficiency?

Shall an enzyme be suboptimal adapted to its function in order to evolve new functions?

Does this apply to whole organism?

 

By Davide De Lucrezia

 

Source:

Gauger AK and Axe DD. The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway. BIO-Complexity, Vol 2011

 

Jez JM and Penning TM. Engineering steroid 5b-reductase activity into rat liver 3a-hydroxysteroid ehydrogenase. Biochemistry 1998, 37:9695-9705.

 

Broun P, Shanklin J, Whittle E and Somerville C. Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids. Science 1998, 282:1315-1317.

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Evidence of non-random mutation rates suggests an evolutionary risk management strategy

Evidence of non-random mutation rates suggests an evolutionary risk management strategy | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

A central tenet in evolutionary theory is that mutations occur randomly in the genome, now Luscombe and co-workers show that “neutral mutation rate varies by more than an order of magnitude across 2,659 genes” and surprisingly this variation is not random. Researchers detected a lower rate in highly expressed genes and in those undergoing stronger purifying selection. These findings suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations. It seems like that bacteria have evolved a mechanism that protects important genes from random mutation, effectively reducing the risk of self-destruction.

 

Source:

Iñigo Martincorena, Aswin S. N. Seshasayee & Nicholas M. Luscombe

Evidence of non-random mutation rates suggests an evolutionary risk management strategy

Nature, 22 April 2012

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Tackling emergence in complex networks: is engineering possible?

Tackling emergence in complex networks: is engineering possible? | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Complex network engineering is a remarkable challenge due to non-linear interactions among variables, emergent properties that cannot be anticipated and inherent resilience to changes.

In his latest work prof. Motter addresses the issue of complex network analysis and engineering: “Many broadly significant scientific questions, ranging from self-organization and information flow to systemic robustness, can now be properly formalized within the emerging theory of networks”.

 

Are we anywhere close to develop a comprehensive complex network engineering theory?

 

Source:

Adilson E. Motter and Réka Albert, Networks in motion. Physics Today, Vol: 65, Issue 4, April 2012

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Synthetic DNA Created, Evolves on Its Own

Synthetic DNA Created, Evolves on Its Own | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Chaput and co-workers synthetized XNA by replacing the natural sugar component of DNA with synthetic chemical polymers.

In addition, researchers managed to engineer a XNA polymerase and XNA-to-DNA retro-transcriptase.

The bundle may allow the in vitro evolution of XNA

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Autopoiesis and Self-organization

Autopoiesis and Self-organization | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

The concept of autopoiesis was first introduced in 1972 by Maturana and Varela to describe one of the main feature of biological system as “a machine organized (defined as a unity) as a network of processes of production (transformation and destruction) of components which: (i) through their interactions and transformations continuously regenerate and realize the network of processes (relations) that produced them; and (ii) constitute it (the machine) as a concrete unity in space in which they (the components) exist by specifying the topological domain of its realization as such a network” [1]. Within this framework, autopoiesis relies on the concepts of operational closure and self-maintenance.

Conversely, an allopoietic system does not achieve self-maintenance though it may display operational closure. For example, a car factory is a defined unity in space which transform raw materials in organized structures (i.e. cars) within its own boundaries. However the resulting object is something other than the factory itself and does not contribute directly to the self-maintenance of the factory from within.

Since its introduction autopoiesis became a central concept in the origin of life research and for large number of researcher it embodies the fundamental feature that a chemical system shall have to be defined alive.

Autopoiesis has been repeatedly coupled to the notion of self-organization that can be defined as “a process in which pattern at the global level of a system emerges solely from numerous interactions among the lower-level components of the system. Moreover, the rules specifying interactions among the system's components are executed using only local information, without reference to the global pattern” [2].

However, it is commonly accepted that autopoietic systems are "structurally coupled" with their medium and that they change dynamically as the surrounding environment changes.

Within this framework, are self-organization and radical autonomy still compatible with the notion of autopiesis and structural coupling?

by Davide De Lucrezia

 

Reference

1. Maturana and Varela. Autopoiesis and Cognition. 1980

2. Camazine, Deneubourg, Franks, Sneyd, Theraulaz and Bonabeau. Self-Organization in Biological Systems. Princeton University Press, 2003.

 

Further readings

Cornish-Bowden A, Cárdenas ML. Self-organization at the origin of life. J Theor Biol. 2008.

Pulselli RM, Simoncini E, Tiezzi E. Self-organization in dissipative structures. Biosystems. 2009

Boiteau L, Pascal R. Energy sources, self-organization, and the origin of life. Orig Life Evol Biosph. 2011

Etxeberria A. Autopoiesis and natural drift and evolution revisited. Artif Life. 2004

Luisi PL. Autopoiesis: a review and a reappraisal. Naturwissenschaften. 2003.

Scott B. Organizational closure and conceptual coherence. Ann N Y Acad Sci. 2000.

Bertschinger N, Olbrich E, Ay N, Jost J. Autonomy: an information theoretic perspective. Biosystems. 2008.

Ruiz-Mirazo K, Moreno A. Basic autonomy as a fundamental step in the synthesis of life. Artif Life. 2004.

Damiano L, Luisi PL. Towards an autopoietic redefinition of life. Orig Life Evol Biosph. 2010

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Lee Cronin: Making matter come alive | Video on TED.com

Lee Cronin: Making matter come alive | Video on TED.com | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

TED Talks Before life existed on Earth, there was just matter, inorganic dead "stuff." How improbable is it that life arose? And could it use a different type of chemistry?

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Life as quantum-like property

Life as quantum-like property | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

A quite controversial/interesting definition of Life grounded on the quantum-like mathematical properties of living systems by use of the principle of extreme physical information (EPI).

 

Source:

B. Roy Frieden and Robert A. Gatenby

The Role of Information and Order in the Origin of  Life

Astrobiology, 2012, Volume 22, Part 3, 437-468, DOI: 10.1007/978-94-007-2941-4_24

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

No more lost in translation: ARS-like ribozymes

No more lost in translation: ARS-like ribozymes | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Transfer RNA (tRNA) is an essential component of the cell's translation apparatus. Aminoacylation, which occurs exclusively at one of the 3'-terminal hydroxyl groups of tRNA, is catalyzed by a family of enzymes called aminoacyl-tRNA synthetases (ARSs). In a primitive translation system, before the advent of sophisticated protein-based enzymes, this chemical event could conceivably have been catalyzed solely by RNA enzymes. Given the evolutionary implications, Suga and co-workers attempted in vitro selection of artificial ARS-like ribozymes, successfully uncovering a functional ribozyme (r24) capable of charging activated aromatic amino acids onto specific kinds of tRNA.

 

Source:

Morimoto J, Hayashi Y, Iwasaki K, Suga H.

Flexizymes: their evolutionary history and the origin of catalytic function.

Acc Chem Res. 2011 Dec 20;44(12):1359-68.

 

 

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Down to the roots...of Life

Down to the roots...of Life | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

"We have found an unknown branch of the tree of life that lives in this lake. It is unique! So far we know of no other group of organisms that descend from closer to the roots of the tree of life than this species". This is the bold statment of Shalchian-Tabrizi and co-workers who report about evolutionary origin of the poorly studied protist Collodictyon by cDNA and rDNA sequencing. Results suggest that Collodictyon constitutes a new lineage in the global eukaryote phylogeny.

 

Source:

Zhao S, Burki F, Bråte J, Keeling PJ, Klaveness D and Shalchian-Tabrizi K.

Collodictyon: An Ancient Lineage in the Tree of Eukaryotes.

Mol Biol Evol. 2012 Mar 21.

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Non-adaptive evolution

Non-adaptive evolution | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

A common tenet in biology is that complex traits, such as gene networks, are the result of natural selection. In this paper Lynch shows "that many of the qualitative features of known transcriptional networks can arise readily through the non-adaptive processes of genetic drift, mutation and recombination".

These findings raises the questions about whether natural selection is strictly necessary for the emergence of complex traits.

These findings highlight the importance of endogenous processes that lead to innovation, irrespective of exogenous constraints or environmental demands.

Within this framework, “the production of novelty” is not merely a reaction to environmental changes, it is rather a active exploration of the “possible and attainable” primarily grounded in the organizational structure of the biosystem as suggested by Varela and Maturana and later on by Stuart Kauffman

 

Source:

Lynch M. The evolution of genetic networks by non-adaptive processes. Nat Rev Genet. 2007 Oct;8(10):803-13.

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Teaching old dogs new tricks: Biological adaptaion and exaptation

Teaching old dogs new tricks: Biological adaptaion and exaptation | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Adaptation and exaptation are two fundamental mechanisms for evolutionary success which play a pivotal role as much as innovation. Baliga and coworkers describe Halobacterium salinarum adaptation to new environments by reprogramming general transcription factors TFBs. Researchers have investigated the “implications of TFB expansions by correlating sequence variations, regulation, and physical interactions of all seven TFBs in Halobacterium salinarum NRC-1 to their fitness landscapes, functional hierarchies, and genetic interactions across 2488 experiments covering combinatorial variations in salt, pH, temperature, and Cu stress”. This study reveals how archea can generate completely novel fitness landscapes “by gene conversion events that introduce subtle changes to the regulation or physical interactions of duplicated TFBs.”

 

Source:

Serdar Turkarslan, David J Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J Christopher Bare, Christopher L Plaisier & Nitin S Baliga. Niche adaptation by expansion and reprogramming of general transcription factors. Molecular Systems Biology 7 Article number: 554
more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Transition to multicellularity: it is all about regulation

Transition to multicellularity: it is all about regulation | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

The transition to multicellularity marks the most pivotal and distinctive events in life’s history on Earth and it only happened a few times in eukaryotes. Multicellularity implies a complex network of regulatory action to coordinate a large number of cell types. Prohaska and co-workers discuss how non-protein-coding RNA (ncRNAs) may have played a crucial role in the development of multicellularity paving the way to the emergence of organism complexity.

 

Source:

Irma Lozada-Chávez, Peter F. Stadler and Sonja J. Prohaska.

A pervasive Non-coding RNA-Based Genetic Regulation is a Prerequisite for the Emergence of Multicellular Complexity. Origins of Life and Evolution of Biospheres. Volume 41, Number 6 (2011), 587-607

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Measuring Biosystems structural distance and evolutionary relationship

Measuring Biosystems structural distance and evolutionary relationship | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

Most of the people would agree on the following definition of Evolution: “any change across successive generations in the heritable characteristics of biological populations”

However those “changes” occur in complex networks (e.g. metabolic, regulatory, ect ect), thus we shall study evolution as the evolution of the correspondent networks.

In his work Anirban Banerjee develops a method to quantify the topological distance to measure and retrace the evolutionary relation and distance between two evolving systems (i.e. population/organism) using normalized graph Laplacian.

This method may allow to measure the evolutionary mechanism that causes functional changes that forces complex systems to adopt new configurations of interaction pattern between their components.

 

Source:

Anirban Banerjee, Structural distance and evolutionary relationship of networks. Biosystems, Volume 107, Issue 3, March 2012, Pages 186–196

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Martin Hanczyc: The line between life and not-life

We are used to consider Life as a dichotomic variable, what if Life were a continous variable?

Prof. Hanczyc leads us through the boundary between living and non-living.

 

http://youtu.be/dySwrhMQdX4

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Damiano Luisa, Unità in dialogo. Milano, Bruno Mondadori, 2009.

Damiano Luisa, Unità in dialogo. Milano, Bruno Mondadori, 2009. | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it
more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

Operational Closure. A review

Operational Closure. A review | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

“The idea that life depends on the organization of the thousands of biochemical reactions that constitute metabolism was obvious [...]. The essential but often over-looked point is that enzymes, and all other proteins, are themselves products of metabolism, and thus metabolites”. The circular organization of living organisms was captured by Mettrie’s methaphor of ‘‘machine which winds its own springs’’

 

Source:

Juan-Carlos Letelier, Marıa Luz Cardenas, Athel Cornish-Bowden. From L’Homme Machine to metabolic closure. J Theor Biol. 2011.

 

more...
No comment yet.
Scooped by Davide De Lucrezia
Scoop.it!

From chaos to order: the emergence of Life

From chaos to order: the emergence of Life | Origin of Life: Emergence, Self-organization and Evolution | Scoop.it

"Living matter is solemnly perceived as an embodiment of ultimate order [...] yet, disorder is its necessary component in an intricate interplay between life’s actors from the highest level of populations, all the way to molecules" Ernesto Di Mauro, A. Keith Dunker and Edward N. Trifonov discuss the inteplay between order and disorder in the transition from non-living to living matter.

 

Source: 

Ernesto Di Mauro, A. Keith Dunker and Edward N. Trifonov

Disorder to Order, Nonlife to Life: In the Beginning There Was a Mistake

Cellular Origin, Life in Extreme Habitats and Astrobiology, 2012, Volume 22, 415-435.

 

more...
No comment yet.