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Marcello Barbieri (born 1940) is an Italian theoretical biologist at the University of Ferrara whose main interest is the origin of novelties in macroevolution. He has been one of founders and first editor-in-chief of the journal Biosemiotics until 2012; currently, he is an editor of the journal BioSystems . His research field is code biology, the study of all codes of life from the genetic code to the codes of culture. His major books are The Semantic Theory of Evolution (1985), [1] The Organic Codes (2003), [2] and Code Biology. A New Science of Life (2015). [3]
Barbieri graduated in 1964 from the Science Faculty of Bologna University. [4] In 1965, he was employed by the Medical Faculty of the same University as a researcher in molecular biology and teacher of biophysics for medical students. He conducted research at the Medical Research Council in Cambridge, the National Institutes of Health in Bethesda, and the Max Planck Institute of Molecular Cell Biology and Genetics in Berlin. Since 1992 he is professor of embryology at the Medical Faculty of Ferrara University. In 1997, he founded the Italian Association for Theoretical Biology [5] (Associazione Italiana di Biologia Teorica) and in 2012 he founded the International Society of Code Biology. [6]
At the Max-Planck-Institut in Berlin, Barbieri obtained the largest microcrystals of eukaryotic ribosomes that have ever appeared in the scientific literature. [7] At the Medical Research Council in Cambridge, and at the National Institutes of Health in Bethesda, he developed mathematical models for the reconstruction of structures from incomplete information and has shown that a convergent increase in complexity is possible if the reconstructions are performed with iterative methods that make use of memories and codes. [8] He has proposed that the existence of organic codes is revealed by the presence of adaptors and has shown that such codes exist in signal transduction, in the cytoskeleton and in cell compartments. [2] This adaptor-dependent definition of code has been used by Kühn and Hofmeyr [9] to show that the histone code is a true organic code, whereas Gérard Battail has argued that "Barbieri's organic codes enable error correction of genomes". [10] He has been described as one of 'key figures' in biosemiotics by Donald Favareau in Essential Readings, [4] by Liz Else in New Scientist [11] and by Nigel Williams in Current Biology. [12]
Barbieri underlined that copying and coding are two fundamentally different mechanisms of molecular change and suggested that there are two distinct mechanisms of evolutionary change: evolution by natural selection, based on copying, and evolution by natural conventions, based on coding. This in turn implies that many organic codes appeared in the history of life after the genetic code, and Barbieri proposed that the greatest novelties of macroevolution were associated with the origin of new codes. These ideas have been developed in the course of a thirty-year period in the books: The Semantic Theory of Evolution (1985), [1] The Organic Codes (2003) [2] and Code Biology (2015). [3]
Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. According to modern evolutionary biology, all living beings could be descendants of a unique ancestor commonly referred to as the last universal common ancestor (LUCA) of all life on Earth.
Francis Harry Compton Crick was an English molecular biologist, biophysicist, and neuroscientist. He, James Watson, Rosalind Franklin, and Maurice Wilkins played crucial roles in deciphering the helical structure of the DNA molecule.
The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection, gene flow and genetic drift. This change happens over a relatively short amount of time compared to the changes termed macroevolution.
Macroevolution usually means the evolution of large-scale structures and traits that go significantly beyond the intraspecific variation found in microevolution. In other words, macroevolution is the evolution of taxa above the species level.
In biology, epigenetics is the study of stable changes in cell function that do not involve alterations in the DNA sequence. The Greek prefix epi- in epigenetics implies features that are "on top of" or "in addition to" the traditional genetic basis for inheritance. Epigenetics most often involves changes that affect the regulation of gene expression, and that persist through cellular division. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors, or be part of normal development. It can also lead to diseases such as cancer.
Molecular evolution is the process of change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes. Major topics in molecular evolution concern the rates and impacts of single nucleotide changes, neutral evolution vs. natural selection, origins of new genes, the genetic nature of complex traits, the genetic basis of speciation, the evolution of development, and ways that evolutionary forces influence genomic and phenotypic changes.
The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory assumes that most mutations that are not deleterious are neutral rather than beneficial. Because only a fraction of gametes are sampled in each generation of a species, the neutral theory suggests that a mutant allele can arise within a population and reach fixation by chance, rather than by selective advantage.
Sydney Brenner was a South African biologist. In 2002, he shared the Nobel Prize in Physiology or Medicine with H. Robert Horvitz and Sir John E. Sulston. Brenner made significant contributions to work on the genetic code, and other areas of molecular biology while working in the Medical Research Council (MRC) Laboratory of Molecular Biology in Cambridge, England. He established the roundworm Caenorhabditis elegans as a model organism for the investigation of developmental biology, and founded the Molecular Sciences Institute in Berkeley, California, United States.
Biosemiotics is a field of semiotics and biology that studies the prelinguistic meaning-making, biological interpretation processes, production of signs and codes and communication processes in the biological realm.
Medical cybernetics is a branch of cybernetics which has been heavily affected by the development of the computer, which applies the concepts of cybernetics to medical research and practice. At the intersection of systems biology, systems medicine and clinical applications it covers an emerging working program for the application of systems- and communication theory, connectionism and decision theory on biomedical research and health related questions.
Dr Lee M. Spetner is an American and Israeli creationist author, mechanical engineer, applied biophysicist, and physicist, known best for his disagreements with the modern synthesis. In spite of his opposition to neo-Darwinism, Spetner accepts a form of non-random evolution outlined in his 1996 book "Not By Chance! Shattering the Modern Theory of Evolution".
In biology, the word gene can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes.
Temple Ferris Smith is an emeritus professor in biomedical engineering who helped to develop the Smith-Waterman algorithm with Michael Waterman in 1981. The Smith-Waterman algorithm serves as the basis for multi sequence comparisons, identifying the segment with the maximum local sequence similarity, see sequence alignment. This algorithm is used for identifying similar DNA, RNA and protein segments. He was director of the BioMolecular Engineering Research Center at Boston University for twenty years and is now professor emeritus.
The adaptor hypothesis is a theoretical scheme in molecular biology to explain how information encoded in the nucleic acid sequences of messenger RNA (mRNA) is used to specify the amino acids that make up proteins during the process of translation. It was formulated by Francis Crick in 1955 in an informal publication of the RNA Tie Club, and later elaborated in 1957 along with the central dogma of molecular biology and the sequence hypothesis. It was formally published as an article "On protein synthesis" in 1958. The name "adaptor hypothesis" was given by Sydney Brenner.
Jesper Hoffmeyer was a professor at the University of Copenhagen Institute of Biology, and a leading figure in the emerging field of biosemiotics. He was the president of the International Society for Biosemiotic Studies (ISBS) from 2005 to 2015, co-editor of the journal Biosemiotics and the Springer Book series in Biosemiotics. He authored the books Biosemiotics: An Examination into the Signs of Life and the Life of Signs and Signs of Meaning in the Universe and edited A Legacy for Living Systems: Gregory Bateson as Precursor to Biosemiotics.
Edward Nikolayevich Trifonov is a Russian-born Israeli molecular biophysicist and a founder of Israeli bioinformatics. In his research, he specializes in the recognition of weak signal patterns in biological sequences and is known for his unorthodox scientific methods.
The internal measurement refers to the quantum measurement realized by the endo-observer. Quantum measurement represents the action of a measuring device on the measured system. When the measuring device is a part of measured system, the measurement proceeds internally in relation to the whole system. This theory was introduced by Koichiro Matsuno and developed by Yukio-Pegio Gunji. They further expanded the original ideas of Robert Rosen and Howard Pattee on the quantum measurement in living systems viewed as natural internal observers that belong to the same scale of the observed objects. According to Matsuno, the internal measurement is accompanied by the redistribution of probabilities that leave them entangled in accordance with the many-worlds interpretation of quantum mechanics by Everett. However, this form of quantum entanglement does not survive in the external measurement in which the mapping to real numbers takes place and the result is revealed in the classical time-space as the Copenhagen interpretation suggests. This means that the internal measurement concept unifies the alternative interpretations of quantum mechanics.
Howard Hunt Pattee is an American biologist, Professor Emeritus at Binghamton University and Fellow of the American Association for the Advancement of Science. He graduated at Stanford University in 1948 and completed a Ph.D. there in 1953.
Theory of language is a topic from philosophy of language and theoretical linguistics. It has the goal of answering the questions "What is language?"; "Why do languages have the properties they have?"; or "What is the origin of language?". In addition to these fundamental questions, the theory of language also seeks to understand how language is acquired and used by individuals and communities. This involves investigating the cognitive and neural processes involved in language processing and production, as well as the social and cultural factors that shape linguistic behavior.
Marcello Barbieri, a molecular biologist at the University of Ferrara in Italy, another key figure, echoes Favareau. He brings yet another perspective to the field – a "code model" that he has applied to the genetic code, splicing and other cellular codes.