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Evolutionary robots with on-line self-organization and behavioral fitness.

We address two issues in Evolutionary Robotics, namely the genetic encoding and the performance criterion, also known as the fitness function. For the first aspect, we suggest to encode mechanisms for parameter self-organization, instead of the parameters themselves as in conventional approaches. We argue that the suggested encoding generates systems that can solve more complex tasks and are more robust to unpredictable sources of change. We support our arguments with a set of experiments on evolutionary neural controllers for physical robots and compare them to conventional encoding. In addition, we show that when also the genetic encoding is left free to evolve, artificial evolution will select to exploit mechanisms of self-organization. For the second aspect, we shall discuss the role of the performance criterion, als known as fitness function, and suggest Fitness Space as a framework to conceive fitness functions in Evolutionary Robotics. Fitness Space can be used as a guide to design fitness functions as well as to compare different experiments in Evolutionary Robotics.

Evolution, Molecular↗
PubMed2000

Endogenous retroviruses and the human germline.

The human genome is rife with the proviral remains of many ancient retroviruses. The past year has seen significant progress in understanding the structure, distribution and potential function of many of these elements. Although hypotheses concerning the potential effects of these elements are common, however, incisive experiments to test any functions remain much less so.

Animals↗
PubMed1997

Molecular evolution and optimization.

Microbial populations (and life) not only evolve, they optimize. The transition from a random, unorganized, lifeless Earth to the present situation, where the Earth is virtually covered with nucleic acids and diverse and complex species, required numerous molecular changes and the integration of metabolic pathways over billions of years. Primitive prokaryotic life was dependent on and constrained by the physical-chemical conditions on the Earth, while slowly reshaping conditions present. In this review, molecular evolution and molecular optimization are examined with an emphasis on the order in which evolutionary events occurred.

Cells↗
PubMed2003

A research proposal on the origin of life.

This paper describes some experiments the author would have liked to carry out if he had started earlier in the origin-of-life field. The proposal is preceded by a hypothetical outline of the main events in the origin of life. According to this outline, the emergence of life amounts to the transition between two kinds of chemistry: 1) cosmic chemistry, which is beginning to be understood and most likely provided the building blocks with which life was first constructed; and 2) biochemistry, the well-known set of enzyme-catalyzed metabolic reactions that support all living organisms today and must have supported the universal common ancestor, or LUCA, from which all known forms of life are derived. The pathway leading from one to the other of those two chemistries may be divided into three stages, defined as the pre-RNA, RNA, and protein-DNA stages. A brief summary of the events that may have occurred in these three stages and of the possible underlying mechanisms is given. It is emphasized that these events were chemical in nature and, especially, that they must have prefigured present-day biochemical processes. Protometabolism and metabolism, it is argued, must have been congruent. With congruence as the underlying working hypothesis, three problems open to experimental investigation are considered: 1) the involvement of peptides and other multimers as catalysts of early biogenic chemistry; 2) the participation of thioesters in primitive energy transactions; and 3) the influence of amino acids on the molecular selection of RNA molecules.

Amino Acids↗
PubMed2000

Exiting an RNA world.

The RNA world hypothesis gains support from the in vitro evolution of a bifunctional ribozyme that can recognize an activated glutaminyl ester and subsequently aminoacylate a tRNA molecule.

Acylation↗
PubMed1997

Ykt6p, a prenylated SNARE essential for endoplasmic reticulum-Golgi transport.

Vesicular transport between secretory compartments requires specific recognition molecules called SNAREs. Here we report the identification of three putative SNAREs, p14 (Sft1p), p28 (Gos1p), and a detailed characterization of p26 (Ykt6p). All three were originally isolated as interacting partners of the cis Golgi target membrane-associated SNARE Sed5p, when Sec18p (yeast NSF) was inactivated. YKT6 is an essential gene that codes for a novel vesicle-associated SNARE functioning at the endoplasmic reticulum-Golgi transport step in the yeast secretory pathway. Depletion of Ykt6p results in the accumulation of the p1 precursor (endoplasmic reticulum form) of the vacuolar enzyme carboxypeptidase Y and morphological abnormalities consistent with a defect in secretion. Membrane localization of Ykt6p is essential for protein function and is normally mediated by isoprenylation. However, replacement of the isoprenylation motif with a bona fide transmembrane anchor results in a functional protein confirming that membrane localization, but not isoprenylation per se, is required for function. Ykt6p and its homologues are highly conserved from yeast to human as demonstrated by the functional complementation of the loss of Ykt6p by its human counterpart. This is the first example of a human SNARE protein functionally replacing a yeast SNARE. This observation implies that the specific details of the vesicle targeting code, like the genetic code, are conserved in evolution.

Amino Acid Sequence↗
PubMed1990

An improved distribution of codon frequencies allowing for inhomogeneity of DNA's primary-structure evolution.

This is a sequel to the paper, where a model which describes ranged series of codon frequencies was proposed. The model was tested against the empirical distributions obtained for the best studied species and was on the whole found to be in fairly good agreement with the available data. The few deviations from the model's predictions were found to have a monotypic regularity. In the present paper we proceed on the assumption that the deviations are due to inhomogeneous conditions of molecular evolution within a genome. This approach makes it possible to elaborate the theory presented earlier. An improved model is derived for the ranged distribution of codon frequencies, which is then tested against the experimental data.

Base Sequence↗