24,325 research outputs found
Evolvability signatures of generative encodings: beyond standard performance benchmarks
Evolutionary robotics is a promising approach to autonomously synthesize
machines with abilities that resemble those of animals, but the field suffers
from a lack of strong foundations. In particular, evolutionary systems are
currently assessed solely by the fitness score their evolved artifacts can
achieve for a specific task, whereas such fitness-based comparisons provide
limited insights about how the same system would evaluate on different tasks,
and its adaptive capabilities to respond to changes in fitness (e.g., from
damages to the machine, or in new situations). To counter these limitations, we
introduce the concept of "evolvability signatures", which picture the
post-mutation statistical distribution of both behavior diversity (how
different are the robot behaviors after a mutation?) and fitness values (how
different is the fitness after a mutation?). We tested the relevance of this
concept by evolving controllers for hexapod robot locomotion using five
different genotype-to-phenotype mappings (direct encoding, generative encoding
of open-loop and closed-loop central pattern generators, generative encoding of
neural networks, and single-unit pattern generators (SUPG)). We observed a
predictive relationship between the evolvability signature of each encoding and
the number of generations required by hexapods to adapt from incurred damages.
Our study also reveals that, across the five investigated encodings, the SUPG
scheme achieved the best evolvability signature, and was always foremost in
recovering an effective gait following robot damages. Overall, our evolvability
signatures neatly complement existing task-performance benchmarks, and pave the
way for stronger foundations for research in evolutionary robotics.Comment: 24 pages with 12 figures in the main text, and 4 supplementary
figures. Accepted at Information Sciences journal (in press). Supplemental
videos are available online at, see http://goo.gl/uyY1R
Evolution of Biological Complexity
In order to make a case for or against a trend in the evolution of complexity
in biological evolution, complexity needs to be both rigorously defined and
measurable. A recent information-theoretic (but intuitively evident) definition
identifies genomic complexity with the amount of information a sequence stores
about its environment. We investigate the evolution of genomic complexity in
populations of digital organisms and monitor in detail the evolutionary
transitions that increase complexity. We show that because natural selection
forces genomes to behave as a natural ``Maxwell Demon'', within a fixed
environment genomic complexity is forced to increase.Comment: LaTeX 19 pages, incl. 4 fig
Robust monomer-distribution biosignatures in evolving digital biota
Because organisms synthesize component molecules at rates that reflect those
molecules' adaptive utility, we expect a population of biota to leave a
distinctive chemical signature on their environment that is anomalous given the
local (abiotic) chemistry. We observe the same effect in the distribution of
computer instructions used by an evolving population of digital organisms, and
characterize the robustness of the evolved signature with respect to a number
of different changes in the system's physics. The observed instruction
abundance anomaly has features that are consistent over a large number of
evolutionary trials and alterations in system parameters, which makes it a
candidate for a non-Earth-centric life-diagnosticComment: 22 pages, 4 figures, 1 table. Supplementary Material available from
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A Limited Habitable Zone for Complex Life
The habitable zone (HZ) is commonly defined as the range of distances from a
host star within which liquid water, a key requirement for life, may exist on a
planet's surface. Substantially more CO2 than present in Earth's modern
atmosphere is required to maintain clement temperatures for most of the HZ,
with several bars required at the outer edge. However, most complex aerobic
life on Earth is limited by CO2 concentrations of just fractions of a bar. At
the same time, most exoplanets in the traditional HZ reside in proximity to M
dwarfs, which are more numerous than Sun-like G dwarfs but are predicted to
promote greater abundances of gases that can be toxic in the atmospheres of
orbiting planets, such as carbon monoxide (CO). Here we show that the HZ for
complex aerobic life is likely limited relative to that for microbial life. We
use a 1D radiative-convective climate and photochemical models to circumscribe
a Habitable Zone for Complex Life (HZCL) based on known toxicity limits for a
range of organisms as a proof of concept. We find that for CO2 tolerances of
0.01, 0.1, and 1 bar, the HZCL is only 21%, 32%, and 50% as wide as the
conventional HZ for a Sun-like star, and that CO concentrations may limit some
complex life throughout the entire HZ of the coolest M dwarfs. These results
cast new light on the likely distribution of complex life in the universe and
have important ramifications for the search for exoplanet biosignatures and
technosignatures.Comment: Revised including additional discussion. Published Gold OA in ApJ. 9
pages, 5 figures, 5 table
Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss.
Many genes can be deleted with little phenotypic consequences. By what mechanism and to what extent the presence of duplicate genes in the genome contributes to this robustness against deletions has been the subject of considerable interest. Here, we exploit the availability of high-density genetic interaction maps to provide direct support for the role of backup compensation, where functionally overlapping duplicates cover for the loss of their paralog. However, we find that the overall contribution of duplicates to robustness against null mutations is low ( approximately 25%). The ability to directly identify buffering paralogs allowed us to further study their properties, and how they differ from non-buffering duplicates. Using environmental sensitivity profiles as well as quantitative genetic interaction spectra as high-resolution phenotypes, we establish that even duplicate pairs with compensation capacity exhibit rich and typically non-overlapping deletion phenotypes, and are thus unable to comprehensively cover against loss of their paralog. Our findings reconcile the fact that duplicates can compensate for each other's loss under a limited number of conditions with the evolutionary instability of genes whose loss is not associated with a phenotypic penalty
Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations.
Protein stability is widely recognized as a major evolutionary constraint. However, the relation between mutation-induced perturbations of protein stability and biological fitness has remained elusive. Here we explore this relation by introducing a selected set of mostly destabilizing mutations into an essential chromosomal gene of E.coli encoding dihydrofolate reductase (DHFR) to determine how changes in protein stability, activity and abundance affect fitness. Several mutant strains showed no growth while many exhibited fitness higher than wild type. Overexpression of chaperonins (GroEL/ES) buffered the effect of mutations by rescuing the lethal phenotypes and worsening better-fit strains. Changes in stability affect fitness by mediating the abundance of active and soluble proteins; DHFR of lethal strains aggregates, while destabilized DHFR of high fitness strains remains monomeric and soluble at 30oC and forms soluble oligomers at 42oC. These results suggest an evolutionary path where mutational destabilization is counterbalanced by specific oligomerization protecting proteins from aggregation
Quiescence: a mechanism for escaping the effects of drug on cell populations
We point out that a simple and generic strategy to lower the risk for
extinction consists in the developing a dormant stage in which the organism is
unable to multiply but may die. The dormant organism is protected against the
poisonous environment. The result is to increase the survival probability of
the entire population by introducing a type of zero reproductive fitness. This
is possible, because the reservoir of dormant individuals act as a buffer that
can cushion fatal fluctuations in the number of births and deaths which without
the dormant population would have driven the entire population to extinction.Comment: 18 pages and 9 figure
Differences in Thermal Tolerance Between Two Thermally Isolated and Genetically Indistinct Populations of \u3ci\u3eParagnetina Media\u3c/i\u3e (Walker) (Plecoptera: Perlodidae)
The critical thermal maximum (CTM) of Paragnetina media (Walker) (Plecoptera: Perlodidae) was studied at two sites of the Big Sable River in northwestern Lower Michigan during summer 2013. The sites were separated by ~8 km and differed in temperature by ~1°C in the early spring to ~5°C in mid-summer. Individual P. media specimens from the warm site had consistently higher CTM when acclimated to the mean temperature of the two sites for 3 days prior to experimental trials during May, June, and July. When acclimated for an additional 3 days to a higher or lower temperature, this thermal disadvantage disappeared. Groups of individuals from both sites simultaneously acclimated to both site temperatures for 3 days exhibited similar CTMs, except that cold site specimens acclimated to the cold temperature had a lower CTM than the other treatments. Sequencing of the CO1 gene revealed that nearly 75% of specimens shared a single haplotype, which was found in both warm and cold site individuals. Our results suggest that both long term and short term thermal history can influence thermal tolerance within populations of the same species that do not appear genetically distinct
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