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origins13
Participant
Title
Abstract
Steven Benner
Chemical Paradoxes in
Origins and Possible
Geological Solutions
Four paradoxes obstruct current efforts to understand how life originated on Earth:
(a) The Tar Paradox. Organic molecules, given energy and left to themselves, devolve into complex mixtures, “asphalts” better suited
for paving roads than supporting Darwinian evolution. Any scenario for origins requires a way to allow organic material to escape this
devolution into a state that has Darwinian behavior, enabling replication with imperfections, where the imperfections are themselves
replicatable.
(b) The Water Paradox: Water is commonly viewed as essential for life. So are biopolymers, like RNA, DNA, and proteins. However,
contemporary terran biopolymers are corroded by water. Any scenario for origins must manage the apparent contractiction where life
needs a substance (water) this is inherently toxic to life.
(c) The Single Biopolymer Paradox. Even if we can make biopolymers prebioically, it is hard to imaging making two or three (DNA,
RNA, proteins) at the same time. This drives the search for a single biopolymer that "does" both genetics and catalysis. However,
genetics places very different demands on the behavior of a biopolymer than catalysis. Catalytic biopolymers should fold; genetic
biopolymers should not fold. Catalytic biopolymers should contain many building blocks; genetic biopolymers should contain few. Any
"biopolymer first" model for origins must resolve this paradox.
(d) The Probability Paradox. Some biopolymers, like RNA, strike a reasonable compromise between the needs of genetics and of
catalysis. However, experiments show that RNA that destroys RNA is more likely to be found in a pool of RNA sequences than RNA
that makes RNA.
This talk will review experimental data that suggest early planetary environments and mineralogy that might avoid, mitigate, and
possibly resolve these paradoxes. Key are the presence of minerals, including borates and molybdates, that interact with organic
species that are intermediates between atmospheric carbon dioxide and dinitrogen and RNA. Productive interaction also requires a
subaerial environment having only intermittent interaction with water. Recent data suggests that such environments might even be
found today on Mars.
Finally, we shall consider ways that synthetic biology might be able to address these issues, including approaches that construct
artificial life forms as a step towards understanding the relation between chemical diversity in biological macromolecules and their
functional behaviors.
Edwin Bergin
The origin of water in
terrestrial worlds
Tanja Bosak
The Meaning of Stromatolites
Dieter Braun
Nonequilibrium First: Towards
a thermally driven Darwin
Process
The origin of life is one of the fundamental, unsolved riddles of modern science. Life as we know it is a stunningly complex nonequilibrium process, keeping its entropy low against the second law of thermo-dynamics. Therefore it is straightforward to argue that first
living systems had to start in a natural non-equilibrium settings.
Recent experiments with non-equilibrium microsystems suggest that geological conditions should be able to drive molecular evolution,
i.e. the combined replication and selection of genetic molecules towards ever increasing complexity.
As a start, we explored the non-equilibrium setting of natural thermal gradients. Temperature differences across rock fissures
accumulate small monomers more than millionfold [1] by thermo-phoresis and convection [2]. Longer molecules are exponentially better
accumulated, hyperexponentially shifting the polymerization equilibrium towards long RNA strands [3]. The same setting implements
convective temperature oscillations which overcome template poisoning and yield length-insensitive, exponential replication kinetics [4].
Accumulation and thermally driven replication was demonstrated in the same chamber, driven by the same temperature gradient [5].
Protein-free, non-ligating replication schemes can be driven by thermal convection. For example, the hairpins of tRNA can be used for
reversible codon-sequence replication, bridging from replication of genes to the translation of proteins [6]. Non-templated polymerization
and hybridization-dependent degradation leads to replication-like information transmission [7]. Replication and trapping of DNA persist
over long time in a constant influx of monomers, closely approaching the criteria for an autonomous Darwin process.
Experiments using non-equilibrium conditions at the microscale are non-trivial. For example, molecules have to be detected selectively
with the most sensitive biochemical, optical and microfluidic approaches. Advances of biotechnology in this regime is very fruitful. Our
award winning NanoTemper spinoff company [8] demonstrated that basic research for the origin of life can lead to cutting edge
biotechnology [8][9].
Besides temperature gradients, many more non-equilibrium settings can be imagined and become increasingly accessible to
experimentation. For example, geological pH gradients, geological redox potentials or the optical excitation of geological nanoparticles
should drive metabolic reactions in a very peculiar way.
To be successful, an effort on the origin of life has to be embedded in a strong and very active inter-dis-cip-linary background of biology,
biochemistry, chemistry, astrogeology and not the least, theoretical modeling at various levels of abstraction.
[1] PNAS 104, 9346–9351 (2007)
[2] PNAS 103, 19678–19682 (2006)
[3] PNAS.1303222110 (2013)
[4] PRL 91, 158103 (2003)
[5] PRL 104, 188102 (2010)
[6] PRL 108, 238104 (2012)
[7] PRL 107, 018101 (2011)
[8] Nature Communications, 1, 100 (2010)
[9] PNAS, 106, 21649–21654 (2009)
John Chaput
On the Origin of Biomolecular
Function: From Artificial
Genetic Polymers to Novel
Protein Folds
Abstract.
Life presumably arose through a series of discrete steps in which molecular systems gave rise to unicellular organisms with DNA
genomes and protein enzymes. As we study the path from chemistry to biology, several interesting scientific questions arise that are
worthy of experimental investigation. One question that has captured our attention concerns the origin of our genetic material. According
to the RNA world hypothesis, earlier life forms were composed of RNA molecules that stored genetic information and catalyzed
chemical reactions. Although the chemical plausibility of the RNA world remains strong, it is not clear that RNA was the first genetic
material. One could imagine that whatever chemistry gave rise to RNA-based life would have produced other RNA analogues, some of
which could have preceded or competed directly with RNA. Threose nucleic acid (or TNA), an alternative genetic polymer in which the
natural ribose sugar found in RNA has been replaced with an unnatural threose sugar, has received considerable attention as a
possible RNA progenitor. Threose is chemically simpler than ribose and TNA polymers are able to exchange genetic information with
themselves and with other strands of RNA. However, to establish a primordial metabolism, TNA would also need to fold itself into
shapes that can catalyze important chemical reactions. To explore this possibility, we have developed a Darwinian evolution system that
makes it possible to evolve functional TNA molecules in response to external stimuli. In this talk, I will discuss our recent progress on
TNA replication and provide evidence to support the role of TNA as a primordial genetic material. A second question that has attracted
our attention concerns the origin and early evolution of functional proteins. Therefore, a portion of my talk will examine the evolution of
functional proteins from pools of random sequences.
Irene Chen
Evolution during early life in
the RNA World
The origin of life is believed to have progressed through an RNA World, in which RNA acted as both genetic material and functional
molecules. Understanding early evolution requires systematic knowledge of the relationship between RNA sequence and functional
activity. In particular, knowing the structure of the fitness landscape of RNA is critical to estimating the probability of the emergence of
functional sequences and the role of historical accident during evolution. Much theoretical work has been devoted to fitness landscapes,
but experimental maps have been relatively limited. We use in vitro selection on a pool of short RNA sequences that nearly saturates
sequence space to reconstruct the form of a comprehensive fitness landscape. We also study mutations during non-enzymatic
polymerization to understand how early RNA replicators would 'move' in sequence space.
Ralf Conrad
no talk
Peter Coveney
Theory, Modelling and
Simulation of Origins of Life
Processes
In this talk we consider the contributions made by theory, modelling and simulation to fundamental issues in the origins of life.
Theoretical approaches have had and continue to make major impact on the ''systems chemistry'' level, based on the analysis of the
properties of nonlinear catalytic chemical reaction networks, which arise due to the auto-catalytic and cross-catalytic nature of many of
the processes associated with self-replication and self-reproduction. We consider inter alia nonlinear kinetic models of RNA replication
within a primordial Darwinian soup, the origins of homochirality and homochiral polymerization. We also discuss approaches to the
numerical estimation of the rate parameters required as part
of such models. Finally, we take a look at computationally-based molecular modelling techniques that are currently being deployed to
investigate various scenarios relevant to the origins of life.
Georg Feulner
The evolution of Earth's
atmosphere and climate
through geological time
Long-term changes of Earth's atmosphere and climate are governed by physical and chemical interactions with the crust and the
biosphere. Powerful agents like plate tectonics and changes due to biological evolution have shaped Earth's climate history. In my
presentation I will review the evolution of the atmosphere and the climate since the formation of Earth, highlighting the processes
responsible for both gradual and drastic changes in the history of our planet, and the close interplay between the solid Earth, life and
climate.
Ulrich Gerland
Nonequilibrium effects that
facilitate the emergence of
self-replication and evolution
Christian Hallmann
Fossil sedimentary lipids and
the early evolution of life on
Earth
Thomas Henning
Convener
Kai-Uwe Hinrichs
The Subseafloor Biosphere
and the Limits of Life
later, not fully decided on content of talk
Birte Höcker
On the origin of complex
proteins
Proteins are the molecular machines of the cell. They fold into specific three-dimensional structures to fulfill their functions. Similarities
in protein sequence and structure suggest that the diverse set of modern proteins evolved from simpler and less specialized subunits.
The most common subunit is the protein domain, which refers to a segment of the polypeptide chain that is able to fold autonomously
and can be found in diverse protein architectures. Recombination of protein domains has led to the development of large multi-domain
proteins, whose domains evolved to interact and accomplish one or more functions together. Similarly, domains themselves are
hypothesized to originate from smaller subunits. Structural alignments between divergent pairs of protein domains suggest that nature
assembled these fragments to create the structural diversity we observe today.
To better understand the evolutionary mechanisms that generated this structural diversity, we applied the concepts of combinatorial
assembly and fragment recruitment to construct new well-folded protein domains. We combined stable fragments from different
topologies that are populated by thousands of proteins in all kingdoms of life to build new functional proteins, thereby demonstrating
how new proteins can quickly develop and be competitive in today’s protein world.
In addition to the synthetic biology approach that teaches us about possible evolutionary engineering pathways, we further elucidate
natural relationships between protein domains. We started by comparing the sequences of two ancient super-folds to find the most
closely related homologous groups between these two topologies. Further detailed analysis revealed a family of protein sequences that
is intermediate to homologous groups representing different super-folds. The determination of the first representative crystal structure of
one of its members supports the relationship and enables the development of a model explaining the evolutionary link.
Overall, it becomes apparent that the systematic approach for the detection of intermediate steps between known protein folds enables
us to cover missing areas of the protein universe and identify their origin. Additionally, further forays into uncharted protein structure
territory will help us to better understand how sequence defines structure and, thus, ultimately unravel the protein folding problem.
Lisa Kaltenegger
Modeling observables of
terrestrial exoplanet
atmospheres - Super-Earths
and Life
A decade of exoplanet search has led to surprising discoveries, from hot giant planets orbiting their star within a few days, to planets
orbiting two Suns, extremely hot, rocky worlds with potentially permanent lava on their surfaces due to the star's proximity all the way to
the first potential rocky worlds in the Habitable Zone of their stars. Observation techniques have now reached the sensitivity to explore
the chemical composition of the atmospheres as well as physical structure of some detected planets and find planets of less than 10
Earth masses (so called Super-Earths), among them some that may potentially be habitable.
A 'modern' Earth system has existed for about 500 million years, but this period covers only ~15 % of Earth history. The foundation for a
planet that is habitable by complex life has been laid during the preceding ~4 billion years. Ancient sediments hold clues to the nature of
this early Earth system, but the absence of skeletonized animals and a paucity of microfossils in rocks of such age necessitate the use
of sensitive chemical techniques. I will show how we can use the sedimentary hydrocarbon remnants of biological lipids to increase our
understanding of the early evolution of life, gradually changing environmental conditions and the reciprocal interaction between both.
Five confirmed planets orbit in the Habitable Zone of their host star. Observing mass and radius alone can not break the degeneracy of
a planet’s nature due to the effect of an extended atmosphere that can also block the stellar light and increase the observed planetary
radius significantly. Even if a unique solution would exist, planets with similar density, like Earth and Venus, present very different
planetary environments in terms of habitable conditions. Therefore the question refocusses on atmospheric features to characterize a
planetary environment. We will discuss observational features of rocky planets in the HZ of their stars that can be used to examine if our
concept of habitability is correct, different geochemical cycles as well as signs of life through geological times. Using data as well as
atmospheric models we will discuss how we can find the first habitable new worlds in the sky.
Eugene Myers
I would simply like to attend
and listen
I am a director at the MPI-CBG specializing in microscopy, image analysis, and DNA sequencing.
Ann Pearson
Molecular and Isotopic
Signatures of Early Life
(tba)
Matthew Powner
On the Divergent Origins of
Functional RNA
Recent progress towards understanding the chemical origins ribonucleotides will be discussed.
Sascha P. Quanz
Observational
characterization of extrasolar
planet atmospheres
Steen Rasmussen
Physicochemical and
computational protocall
assembly
We sketch our main experimental- and computational results and highlight our recent results and challenges in coupling information,
metabolism and container to form autonomous replicating protocells bottom up.
Rebecca Schulman
Robust information replication
via crystal growth and
scission
Understanding how a simple chemical system can accurately
replicate combinatorial information, such as a
sequence, is an important question for both the study of
life in the universe and for the development of evolutionary
molecular design techniques. During biological sequence
replication, a nucleic acid polymer serves as a template for the
enzyme-catalyzed assembly of a complementary sequence. Enzymes then separate the template and complement before the next
round of replication. Attempts to understand how replication could occur
more simply, such as without enzymes, have largely focused on developing minimal versions of this replication process. Here we
describe how a different mechanism, crystal growth and scission, can accurately replicate chemical sequences without enzymes.
Crystal growth propagates a sequence of bits while
mechanically-induced scission creates new growth fronts. Together, these processes exponentially increase the number of crystal
sequences. In the system we describe, sequences are arrangements of DNA tile monomers within ribbon-shaped crystals. 99.98% of
bits are copied correctly and
78% of 4-bit sequences are correct after 2 generations;
roughly 40 sequence copies are made per generation. In
principle, this process is accurate enough for 1000-fold
replication of 4-bit sequences with ~50\% yield, replication of
longer sequences, and Darwinian evolution. We thus demonstrate that neither enzymes nor covalent bond formation are required for
robust chemical sequence replication.
Petra Schwille
Towards a possible origin of
regulated cell division
Peter Stadler
Origins of Complex
Regulation: A Tale of RNA
and Chromatin
Peter F Stadler (U Leipzig)
joint work with Sonja J Prohaska, David C Krakauer, Christian Arnold, Lydia Steiner, Irma Lozada-Chaves
Modern organism rely on complex regulatory circuits that involve control at many different levels making use of a plethora of different
modes of molecular interactions. Despite the central role of the notion of ``regulation'' in modern biology, we still lack a deeper
theoretical understanding. Here, I will discuss the evolutionary history and properties of the epigenetic
layer of regulation with an emphasis on its computational aspects. Protein complexes that are capable of simultaneous reading and
writing of histone modification can be seen as physical instantiations of rewriting rules -- and thus of an essentially digitial computer. A
second aspect that will be discussed is the role of the many evolutionarily young non-coding RNAs that have been identified as
additional layers of regulation. It may not be surprising that they are tied to epigenetic phenomena in manifold ways.
Sonja J Prohaska, Peter F. Stadler, and David C. Krakauer. Innovation in gene regulation: The case of chromatin computation. J. Theor.
Biol., 265:27-44, 2010.
Irma Lozada-Chávez, Peter F. Stadler, and Sonja J. Prohaska. Hypothesis for the modern RNA world: a pervasive non-coding RNAbased genetic regulation is a prerequisite for the emergence of multicellular complexity. Orig. Life Evol. Biosph., 41:587-607, 2011.
John Sutherland
Origins of Life Systems
Chemistry
The lecture will cover recent advances in systems chemistry syntheses of the informational, catalytic and compartment–forming
molecules thought necessary for the emergence of life.
Tsvi Tlusty
Self-replication in a life full of
errors: the ribosome as a
molecular decoder
The origin of Life is associated with the emergence of molecular recognition systems that can convey, process and store information in
a noisy biochemical environment. This stochastic biophysical setting poses a tough problem: how to construct information processing
systems that are efficient and yet error-resilient?
We will discuss this challenge in the “modern” context of the ribosome, the molecular engine of the present self-replication machinery: In
order to synthesize proteins, ribosomes have to select the correct building blocks from a large pool of similar substrates, and inaccurate
or inefficient selection might be devastating to the organism. We will examine the performance of the ribosome in this task and the
possible role of its large conformational changes. The analysis suggests a simple generic mechanism that may be relevant also in the
context of more primitive molecular machinery.
Stéphane Udry
Super-Earths and Neptunemass planets: a window to
planetary-system diversity
Our understanding of planetary systems has tremendously changed over the past 15 years after the detection of exoplanets orbiting
other stars similar to the Sun. I will report on the results of a 10-year survey carried out at the La Silla Observatory with the HARPS
spectrograph to detect and characterise an emerging large population of exoplanets in the super-Earth and Neptune-mass regime, not
observed in the Solar System. The detection of a sufficiently large number of low-mass planets allows us to study the statistical
properties of their orbital elements, the correlation of host-star properties with the planet masses, as well as the occurrence rate of
planetary systems around solar-type stars. These results will be discussed in comparison with the recent findings of the Kepler satellite,
bringing light to our understanding of the formation and evolution of planetary systems, with a focus on the ones in the habitable zone of
their parent stars. Prospects for the future detection of Earth twins will be discussed as well.