Natural genetic engineering

Last updated

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.

Contents

Concept

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]

Relation with Intelligent Design

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]

Criticism

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:

  1. That the theory crosses the line into teleology , a line exemplified by the review written by Larry Moran. [19] The form of Shapiro's argument has points of resemblance to several creationist arguments to the effect that observed biology cannot be explained by a combination of "random" (undirected) mutation and natural selection. One of the many standard responses to these arguments is that biology can be sufficiently explained without invoking higher causes. Shapiro's view differs significantly from that of creationists, not the least because his higher causes exist only at the level of cellular machinery. However, to a critic unpersuaded of the need for higher causes, it is not persuasive to substitute material higher causes for the supernatural.
  2. That Shapiro does not give a fair reading of the central dogma. Shapiro's reading of the central dogma requires that only random mutations can be the root of evolutionary change. If this reading is correct, then, ignoring the looseness of such an application of the term "random", the several mechanisms identified by Shapiro (e.g., epigenetics) do indeed falsify this theory. However, Crick and geneticists in general had long been well aware of the existence of mutagens at the time of the formulation and restatement of the central dogma, and in fact before the discovery of the mechanisms of biological heredity. [29] A more conservative interpretation, in the words of Marshall Nirenberg, is simply that "DNA makes RNA makes protein." [30] Under this reading, proteins would not be expected to modify DNA, but Shapiro provides multiple examples of where this occurs, including histone modification, mutagenic subclasses of excision and repair enzymes, extensive regulation of mobile genetic elements, and various classes of RNA regulation, and direct modification of nucleotides via cytosine methylation and enzymatic deamination. [31]

Shapiro responded to the review in Evolutionary Intelligence. [32]

See also

Related Research Articles

<span class="mw-page-title-main">DNA</span> Molecule that carries genetic information

Deoxyribonucleic acid is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.

<span class="mw-page-title-main">Evolution</span> Change in the heritable characteristics of biological populations

Evolution is the change in the heritable characteristics of biological populations over successive generations. It 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.

<span class="mw-page-title-main">Genetics</span> Science of genes, heredity, and variation in living organisms

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.

<span class="mw-page-title-main">Genetic code</span> Rules by which information encoded within genetic material is translated into proteins

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.

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.

<span class="mw-page-title-main">Mutation</span> Alteration in the nucleotide sequence of a genome

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 known 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 deals with 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 describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.

<span class="mw-page-title-main">Molecular genetics</span> Scientific study of genes at the molecular level

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. 

<span class="mw-page-title-main">Evolutionary biology</span> Study of the processes that produced the diversity of life

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.

<span class="mw-page-title-main">Weismann barrier</span> Distinction between germ cell lineages producing gametes and somatic cells

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.

The gene-centered view of evolution, gene's eye view, gene selection theory, or selfish gene theory holds that adaptive evolution occurs through the differential survival of competing genes, increasing the allele frequency of those alleles whose phenotypic trait effects successfully promote their own propagation. The proponents of this viewpoint argue that, since heritable information is passed from generation to generation almost exclusively by DNA, natural selection and evolution are best considered from the perspective of genes.

<span class="mw-page-title-main">History of genetics</span>

The history of genetics dates from the classical era with contributions by Pythagoras, Hippocrates, Aristotle, Epicurus, and others. Modern genetics began with the work of the Augustinian friar Gregor Johann Mendel. His works on pea plants, published in 1866, provided the initial evidence that, on its rediscovery in 1900's, helped to establish the theory of Mendelian inheritance.

Gene editing may refer to:

<span class="mw-page-title-main">Gene</span> Sequence of DNA or RNA that codes for an RNA or protein product

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.

<span class="mw-page-title-main">James A. Shapiro</span> American biologist

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:

Bacterial recombination is a type of genetic recombination in bacteria characterized by DNA transfer from one organism called donor to another organism as recipient. This process occurs in three main ways:

References

  1. ↑ "21st_Cent_View_Evol.shtml". shapiro.bsd.uchicago.edu. Retrieved 2023-01-16.
  2. 1 2 Shapiro, James A. (1992). "Natural genetic engineering in evolution" (PDF). Genetica. 86 (1–3): 99–111. doi:10.1007/BF00133714. PMID   1334920. S2CID   5983884.
  3. ↑ Shapiro, James A. (1997). "Genome organization, natural genetic engineering and adaptive mutation" (PDF). Trends in Genetics. 13 (3): 98–104. doi:10.1016/S0168-9525(97)01058-5. PMID   9066268.
  4. ↑ Shapiro, James A. (January 2005). "A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering" (PDF). Gene. 345 (1): 91–100. doi:10.1016/j.gene.2004.11.020. PMID   15716117.[ permanent dead link ]
  5. ↑ Shapiro, James A. (1999). "Transposable elements as the key to a 21st century view of evolution" (PDF). Genetica. 107 (1–3): 171–179. doi:10.1023/A:1003977827511. PMID   10952210. S2CID   7952900.
  6. 1 2 Shapiro, James A. (2002). "Genome Organization and Reorganization in Evolution: Formatting for Computation and Function" (PDF). Annals of the New York Academy of Sciences. 981: 111–134. doi:10.1111/j.1749-6632.2002.tb04915.x. PMID   12547677. S2CID   5296727.
  7. ↑ Shapiro, James A. (May 1999). "Genome System Architecture and Natural Genetic Engineering in Evolution". Annals of the New York Academy of Sciences. 870 (1): 23–35. Bibcode:1999NYASA.870...23S. doi:10.1111/j.1749-6632.1999.tb08862.x. PMID   10415470. S2CID   21506885.
  8. ↑ Shapiro, James A. (December 2007). "Bacteria are small but not stupid: cognition, naturalgeneticengineering and socio-bacteriology" (PDF). Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. 38 (4): 807–819. CiteSeerX   10.1.1.371.1320 . doi:10.1016/j.shpsc.2007.09.010. PMID   18053935. Archived from the original (PDF) on 2011-07-27.
  9. ↑ "21st_Cent_View_Evol.shtml". shapiro.bsd.uchicago.edu. Retrieved 2023-01-16.
  10. ↑ Crick, F.H.C. (1958): On Protein Synthesis. Symp. Soc. Exp. Biol. XII, 139-163. (pdf, early draft of original article)
  11. ↑ Crick F (August 1970). "Central dogma of molecular biology" (PDF). Nature. 227 (5258): 561–3. Bibcode:1970Natur.227..561C. doi:10.1038/227561a0. PMID   4913914. S2CID   4164029.
  12. 1 2 Shapiro, James (February–March 1997). "A Third Way". Boston Review . Archived from the original on 2012-03-04. Retrieved 2012-09-29.
  13. ↑ Shapiro, James A. (19 March 2012). "Cell Cognition and Cell Decision-Making". Huffington Post.
  14. ↑ Koperski, Jeffrey (June 2008). "Two bad ways to attack intelligent design and two good ones" (PDF). Zygon. 43 (2): 443–449. doi:10.1111/j.1467-9744.2008.00926.x.[ permanent dead link ]
  15. ↑ Dembski, William (12 January 2012). "Is James Shapiro a Design Theorist?". Evolution News and Views.{{cite web}}: Missing or empty |url= (help)
  16. ↑ Shapiro, James A. (16 April 2012). "What Is the Best Way to Deal With Supernaturalists in Science and Evolution?". Huffington Post.
  17. ↑ Shapiro, James A. (8 January 2012). "Evolutionary Lessons From Superbugs". Huffington Post.
  18. ↑ Shapiro, James A. (2011). Evolution: A View from the 21st Century. FT Press. p. 272. ISBN   978-0132780933.
  19. 1 2 Moran, Laurence A (May–June 2011). "(Review) Evolution: A View from the 21st Century". Reports of the National Center for Science Education. 32.3 (9): 1–4. Archived from the original on 2013-09-15. Retrieved 2012-08-16.
  20. ↑ Seoighe, Cathal (2012). "(Review) Evolution: A View from the 21st Century". Trends in Evolutionary Biology. 4 (e6): 32–33. doi: 10.4081/eb.2012.e6 .
  21. ↑ Bezak, Eva (2011). "(Review) Evolution: A View from the 21st Century". Australasian Physical & Engineering Sciences in Medicine. 34 (4): 643–645. doi:10.1007/s13246-011-0110-4. S2CID   30635367.
  22. ↑ Penny, David (June 2012). "(Review) Evolution: A View from the 21st Century". Systematic Biology. 61 (4): 709–710. doi: 10.1093/sysbio/sys006 .
  23. ↑ Wilkins, Adam S. (January 2012). "(Review) Evolution: A View from the 21st Century". Genome Biology and Evolution. 4 (4): 423–426. doi:10.1093/gbe/evs008. PMC   3342868 .
  24. ↑ Buratti, Emanuele (2012). "Evolutionary Lessons for 21st Century Molecular Biotechnologists". Molecular Biotechnology. 52 (1): 89–90. doi:10.1007/s12033-011-9472-9. S2CID   85337691.
  25. ↑ Li, Haipeng (December 2011). "Beyond our naked eyes". Journal of Molecular Cell Biology. 4 (1): 63. doi: 10.1093/jmcb/mjr048 .
  26. ↑ Yu, Xiaobo (2012). "A provocative view of evolution in the genomic age". Frontiers in Biology. 7 (2): 93–95. doi:10.1007/s11515-012-1203-5. S2CID   45141312.
  27. ↑ Ussery, David W. (2011). "Natural Genetic Engineering: Intelligence & Design in Evolution?" (PDF). Microbial Informatics and Experimentation. 1 (11): 11. doi: 10.1186/2042-5783-1-11 . PMC   3372291 .
  28. ↑ Kutschera, Ulrich (September 2012). "(Review) Evolution: A View from the 21st Century". In Höttecke, Dietmar (ed.). Newsletter of the International History, Philosophy and Science Teaching Group. Vol. 21.{{cite book}}: External link in |chapter= (help)
  29. ↑ Morgan, Thomas Hunt. The mechanism of Mendelian heredity New York, Holt, 1915
  30. ↑ Leavitt, Sarah A.; Marshall Nirenberg (June 2010). "Deciphering the Genetic Code: Marshall Nirenberg". Office of NIH History.
  31. ↑ Shapiro, James A. (July 2013). "How life changes itself: The Read-Write (RW) Genome" (PDF). Physics of Life Reviews. 10 (3): 287–323. Bibcode:2013PhLRv..10..287S. CiteSeerX   10.1.1.371.35 . doi:10.1016/j.plrev.2013.07.001. PMID   23876611.
  32. ↑ Shapiro, James A. (2012). "Response to Pauline Hogeweg's review of my book, "Evolution: a view from the 21st century"". Evolutionary Intelligence. 5 (3): 211. doi: 10.1007/s12065-012-0074-7 .
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.