Natural genetic engineering (NGE) is a class of process proposed by molecular biologist James A. Shapiro to account for novelty created in the course of biological evolution. Shapiro developed this work in several peer-reviewed publications from 1992 onwards, and later in his 2011 book Evolution: A View from the 21st Century, which has been updated with a second edition in 2022. [1] He uses NGE to account for several proposed counterexamples to the central dogma of molecular biology (Francis Crick's proposal of 1957 that the direction of the flow of sequence information is only from nucleic acid to proteins, and never the reverse). Shapiro drew from work as diverse as the adaptivity of the mammalian immune system, ciliate macronuclei and epigenetics. The work gained some measure of notoriety after being championed by proponents of Intelligent Design, despite Shapiro's explicit repudiation of that movement.
Shapiro first laid out his ideas of natural genetic engineering in 1992 [2] and has continued to develop them in both the primary scientific literature [3] [4] [5] [6] and in work directed to wider audiences, [7] [8] culminating in the 2011 publication of Evolution: A View from the 21st Century (second edition in 2022. [9] ).
Natural genetic engineering is a reaction against the modern synthesis and the central dogma of molecular biology. The modern synthesis was formulated before the elucidation of the double-helix structure of DNA and the establishment of molecular biology in its current status of prominence. Given what was known at the time a simple, powerful model of genetic change through undirected mutation (loosely described as "random") and natural selection, was seen as sufficient to explain evolution as observed in nature. With the discovery of the nature and roles of nucleic acids in genetics, this model prompted Francis Crick's so-called Central Dogma of Molecular Biology: "[Sequential] information cannot be transferred back from protein to either protein or nucleic acid." [10] [11]
Shapiro points out that multiple cellular systems can affect DNA in response to specific environmental stimuli. These "directed" changes stand in contrast to both the undirected mutations in the modern synthesis and (in Shapiro's interpretation) the ban on information flowing from the environment into the genome.
In the 1992 Genetica paper that introduced the concept, Shapiro begins by listing three lessons from molecular genetics:
From these, Shapiro concludes:
[I]t can be argued that much of genome change in evolution results from a genetic engineering process utilizing the biochemical systems for mobilizing and reorganizing DNA structures present in living cells. [2]
In a 1997 Boston Review article, Shapiro lists four categories of discoveries made in molecular biology that, in his estimation, are not adequately accounted for by the Modern Synthesis: genome organization, cellular repair capabilities, mobile genetic elements and cellular information processing. [12] Shapiro concludes:
What significance does an emerging interface between biology and information science hold for thinking about evolution? It opens up the possibility of addressing scientifically rather than ideologically the central issue so hotly contested by fundamentalists on both sides of the Creationist-Darwinist debate: Is there any guiding intelligence at work in the origin of species displaying exquisite adaptations that range from lambda prophage repression and the Krebs cycle through the mitotic apparatus and the eye to the immune system, mimicry, and social organization? [12]
Within the context of the article in particular and Shapiro's work on Natural Genetic Engineering in general, the "guiding intelligence" is to be found within the cell. (For example, in a Huffington Post essay entitled Cell Cognition and Cell Decision-Making [13] Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criterion.) However, the combination of disagreement with the Modern Synthesis and discussion of a creative intelligence has brought his work to the attention of advocates of Intelligent Design.
Natural genetic engineering has been cited as a legitimate scientific controversy (in contrast to the controversies raised by various branches of creationism). [14] While Shapiro considers the questions raised by Intelligent Design to be interesting, he parts ways with creationists by considering these problems to be scientifically tractable (specifically by understanding how NGE plays a role in the evolution of novelty). [6]
With the publication of Evolution: A View from the 21st Century, Shapiro's work again came under discussion in the Intelligent design community. In a conversation with Shapiro, William Dembski asked for Shapiro's thoughts on the origins of natural genetic engineering systems. Shapiro replied that "where they come from in the first place is not a question we can realistically answer right now." [15] While Dembski sees this position as at least not inconsistent with Intelligent Design, Shapiro has explicitly and repeatedly rejected both creationism in general [16] and Intelligent Design in particular. [17]
While Shapiro developed NGE in the peer-reviewed literature, the idea attracted far more attention when he summarized his work in his book Evolution: A View from the 21st Century. [18] In part due to its discussion of the Intelligent Design movement, the book was widely and critically reviewed. [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] Criticism falls into two main categories:
Shapiro responded to the review in Evolutionary Intelligence. [32]
Evolution is the change in the heritable characteristics of biological populations over successive generations. Evolution occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, resulting in certain characteristics becoming more or less common within a population over successive generations. The process of evolution has given rise to biodiversity at every level of biological organisation.
Genetics is the study of genes, genetic variation, and heredity in organisms. It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene.
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.
Molecular biology is a branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions.
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA, which then may undergo error-prone repair, cause an error during other forms of repair, or cause an error during replication. Mutations may also result from insertion or deletion of segments of DNA due to mobile genetic elements.
Junk DNA is a DNA sequence that has no relevant biological function. Most organisms have some junk DNA in their genomes - mostly pseudogenes and fragments of transposons and viruses - but it is possible that some organisms have substantial amounts of junk DNA.
The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA, and RNA makes protein", although this is not its original meaning. It was first stated by Francis Crick in 1957, then published in 1958:
The Central Dogma. This states that once "information" has passed into protein it cannot get out again. In more detail, the transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein may be possible, but transfer from protein to protein, or from protein to nucleic acid is impossible. Information here means the precise determination of sequence, either of bases in the nucleic acid or of amino acid residues in the protein.
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.
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.
Molecular genetics is a branch of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens.
Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed on to their offspring. Some examples of evolution in species over many generations are the peppered moth and flightless birds. In the 1930s, the discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology.
The Weismann barrier, proposed by August Weismann, is the strict distinction between the "immortal" germ cell lineages producing gametes and "disposable" somatic cells in animals, in contrast to Charles Darwin's proposed pangenesis mechanism for inheritance. In more precise terminology, hereditary information moves only from germline cells to somatic cells. This does not refer to the central dogma of molecular biology, which states that no sequential information can travel from protein to DNA or RNA, but both hypotheses relate to a gene-centric view of life.
Gene editing may refer to:
In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. 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 non-coding genes.
Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will be lost or will replace all other alleles of the gene. That loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection.
James Alan Shapiro is an American biologist, an expert in bacterial genetics and a professor in the Department of Biochemistry and Molecular Biology at the University of Chicago.
The following outline is provided as an overview of and topical guide to genetics:
Evolutionary biology, in particular the understanding of how organisms evolve through natural selection, is an area of science with many practical applications. Creationists often claim that the theory of evolution lacks any practical applications; however, this claim has been refuted by scientists.
Aspects of genetics including mutation, hybridisation, cloning, genetic engineering, and eugenics have appeared in fiction since the 19th century.
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