Natural genetic engineering
Natural genetic engineering (NGE) is a class of process proposed by molecular biologist James Shapiro to account for novelty created in the course of biological evolution. Shapiro developed this work in several peer-reviewed publications and later in his book Evolution: A View from the 21st Century. He uses NGE to account for several proposed counterexamples to the central dogma of molecular biology (the subsequently partly rejected proposal of 1970 that the direction of the flow of sequence information is only from DNA to DNA or DNA to RNA 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 and has continued to develop them in both the primary scientific literature and in work directed to wider audiences, culminating in the 2011 publication of Evolution: A View from the 21st Century.
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."
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:
- there is a surprising amount of genetic conservation across taxonomic boundaries,
- the mosaic structure of the genome results in multiple nonlocal genes having multiple phylogenic effects, and, drawing on the work of his friend and collaborator Barbara McClintock,
- the existence of multiple cellular mechanisms (including mobile genetic elements) that can restructure DNA.
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.
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. 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?
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 Shapiro defines cognitive actions as those that are "knowledge-based and involve decisions appropriate to acquired information," arguing that cells meet this criteria.) 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). 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).
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." While Dembski sees this position as at least not inconsistent with Intelligent Design, Shapiro has explicitly and repeatedly rejected both creationism in general and Intelligent Design in particular.
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.  In part due to its discussion of the Intelligent Design movement, the book was widely and critically reviewed. Criticism falls into three main categories:
- The theory crosses the line into teleology, a line exemplified by the review written by Larry Moran. 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.
- 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. A more conservative interpretation, in the words of Marshall Nirenberg, is simply that "DNA makes RNA makes protein." 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.
- Shapiro does not address how natural genetic engineering systems might have arisen. Shapiro's position is that we cannot yet know how these systems came about. However, critics point out that we have no reason to think that anything more than random mutation and natural selection would be required. If this is the case then there is not an obvious argument why these systems should be treated differently from any other system that resulted from Darwinian evolution.
Shapiro responded to the review in Evolutionary Intelligence.
- Shapiro, James A. (1992). "Natural genetic engineering in evolution". Genetica 86 (1-3): 99–111. doi:10.1007/BF00133714.
- Shapiro, James A. "Genome organization, natural genetic engineering and adaptive mutation". Trends in Genetics 13 (3): 98–104. doi:10.1016/S0168-9525(97)01058-5.
- Shapiro, James A. "A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering". Gene 345 (1): 91–100. doi:10.1016/j.gene.2004.11.020. PMID 15716117.
- Shapiro, James A. "Transposable elements as the key to a 21st century view of evolution". Genetica 107 (1-3): 171–179. doi:10.1023/A:1003977827511. PMID 10952210.
- Shapiro, James A. (2002). "Genome Organization and Reorganization in Evolution: Formatting for Computation and Function". Proceedings of the New York Academy of Sciences (981): 111–134.
- Shapiro, James A. (May 1999). "Genome System Architecture and Natural Genetic Engineering in Evolution". Annals of the New York Academy of Sciences 870: 23–35. Bibcode:1999NYASA.870...23S. doi:10.1111/j.1749-6632.1999.tb08862.x.
- Shapiro, James A. (December 2007). "Bacteria are small but not stupid: cognition, naturalgeneticengineering and socio-bacteriology". Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 38 (4): 807–819. doi:10.1016/j.shpsc.2007.09.010. PMID 18053935.
- Shapiro, James A. (2011). Evolution: A View from the 21st Century. FT Press. p. 272. ISBN 978-0132780933.
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- Shapiro, James A. (19 March 2012). "Cell Cognition and Cell Decision-Making". Huffington Post.
- Koperski, Jeffrey (June 2008). "Two bad ways to attack intelligent design and two good ones". Zygon 43 (2): 443–449. doi:10.1111/j.1467-9744.2008.00926.x.
- Dembski, William (12 January 2012). "Is James Shapiro a Design Theorist?". Evolution News and Views.
- Shapiro, James A. (16 April 2012). "What Is the Best Way to Deal With Supernaturalists in Science and Evolution?". Huffington Post.
- Shapiro, James A. (8 January 2012). "Evolutionary Lessons From Superbugs". Huffington Post.
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- Li, Haipeng (December 2011). "Beyond our naked eyes". Journal of Molecular Cell Biology 4 (1): 63. doi:10.1093/jmcb/mjr048.
- 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.
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- Morgan, Thomas Hunt. The mechanism of Mendelian heredity New York, Holt, 1915 
- Leavitt, Sarah A.; Marshall Nirenberg (June 2010). "Deciphering the Genetic Code: Marshall Nirenberg". Office of NIH History.
- Shapiro, James A. (July 2013). "How life changes itself: The Read-Write (RW) Genome". Physics of Life Reviews 10: 287–323. doi:10.1016/j.plrev.2013.07.001.
- Shapiro, James A. (2012). "Response to Pauline Hogeweg’s review of my book, "Evolution: a view from the 21st century"". Evolutionary Intelligence. doi:10.1007/s12065-012-0074-7.