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Self-organization: New James Shapiro paper on the Read-Write genome


From U Chicago’s James Shapiro at Pub Med:

Biological action in Read-Write genome evolution.

Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. In the most highly evolved multicellular organisms, biological complexity scales with ‘non-coding’ DNA content rather than with protein-coding capacity in the genome. Coincidentally, ‘non-coding’ RNAs rich in repetitive mobile DNA sequences function as key regulators of complex adaptive phenotypes, such as stem cell pluripotency. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read-Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations. (paywall) More.

A friend comments that this paper repackages Shapiro’s work for a different audience, but all the better if he even has a different audience.

See also: James Shapiro on intelligence in nature


Self-organization: Can we wring information from matter — shake the bit out of the it?

Challenging the Modern Synthesis Adaptation, Development, and Inheritance Edited by Philippe Huneman and Denis M. Walsh Overview:
Represents the most comprehensive and current survey of the various challenges to the Modern Synthesis theory of evolution. Incorporates a variety of theoretical and disciplinary perspectives, from evolutionary biologists, historians and philosophers of science. These essays constitute the state of the art in the current debate on the status of the Modern Synthesis.
Since its origin in the early 20th century, the Modern Synthesis theory of evolution has grown to become the orthodox view on the process of organic evolution. Its central defining feature is the prominence it accords to genes in the explanation of evolutionary dynamics. Since the advent of the 21st century, however, the Modern Synthesis has been subject to repeated and sustained challenges. These are largely empirically driven. In the last two decades, evolutionary biology has witnessed unprecedented growth in the understanding of those processes that underwrite the development of organisms and the inheritance of characters. The empirical advances usher in challenges to the conceptual foundations of evolutionary theory. The extent to which the new biology challenges the Modern Synthesis has been the subject of lively debate. Many current commentators charge that the new biology of the 21st century calls for a revision, extension, or wholesale rejection of the Modern Synthesis Theory of evolution. [see the link below]
Table of Contents:
[see the link below]
Author Information:
[see the link below]
https://global.oup.com/academic/product/challenging-the-modern-synthesis-9780199377176?q=modern%20synthesis&lang=en&cc=us Dionisio
Dionisio, Okay, no problem. Origenes
Origenes @18:
If you hold that the answer to my question is in there, please provide the relevant quote.
Did I ever say that the answer to your question was somewhere? @15 you brought up a very good point on Shapiro’s careless use of important terms. Your comment seems to complement gpuccio’s insightful analysis of that text. Dionisio
Origenes @19 correction @15 you brought up a very good point on Shapiro’s vague use of important terms. Your comment seems to complement gpuccio’s insightful analysis of that text. BTW, ET @282 in gpuccio's thread on spliceosomes just thickened the plot: https://uncommondescent.com/intelligent-design/the-spliceosome-a-molecular-machine-that-defies-any-non-design-explanation/#comment-647532 Dionisio
Origenes @18:
I happened to post my question right after I read GPuccio’s comment.
Which gpuccio's comment? 1. The comment gpuccio posted @2 in this thread? This comment was based on the abstract of the given paper*. 2. The comment gpuccio wrote in his own thread on Spliceosome, which is pointed to by the link posted @7 in this thread? This comment was based on the full text of the given paper*, which was made available to us by toza @6 in this thread. 3. All of the above? (*) the paper referenced in the OP that started this thread. [emphasis added] BTW, you brought up a very good point on Shapiro's use of important terms. Your comment seem to complement gpuccio's analysis of that text. Thanks. Dionisio
Dionisio @17 I happened to post my question right after I read GPuccio's comment. If you hold that the answer to my question is in there, please provide the relevant quote. Origenes
Origenes See the link @7 Dionisio
gpuccio's brief comment on paper @13: https://uncommondescent.com/intelligent-design/the-spliceosome-a-molecular-machine-that-defies-any-non-design-explanation/#comment-647504 Dionisio
What does Shapiro mean by "organism"? We all know what a consistent materialist means by that term: precisely nothing.. Does Shapiro hold that, distinct from e.g. 'mobile DNA elements' and ‘non-coding RNAs', there is also a causally effective *organism*? A real entity that can do things? It seems so when he writes stuff like:
Living organisms regularly facilitate their own evolution.
I would like to know, again, does Shapiro elucidate his position on "organisms" or are we supposed to guess what he means? Origenes
Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints Corinne N. Simonti, Mihaela Pavli?ev, John A. Capra? Molecular Biology and Evolution, Volume 34, Issue 11, 1 November 2017, Pages 2856–2869, https://doi.org/10.1093/molbev/msx219 Dionisio
On causal roles and selected effects: our genome is mostly junk. Doolittle WF1, Brunet TDP2,3. BMC Biol. 2017 Dec 5;15(1):116. doi: 10.1186/s12915-017-0460-9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718017/pdf/12915_2017_Article_460.pdf Dionisio
Human evolution: the non-coding revolution. Franchini LF1, Pollard KS2,3. BMC Biol. 2017 Oct 2;15(1):89. doi: 10.1186/s12915-017-0428-9. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625771/pdf/12915_2017_Article_428.pdf Dionisio
Two modes of targeting transposable elements by piRNA pathway in human testis. Gainetdinov I1, Skvortsova Y2, Kondratieva S2, Funikov S3, Azhikina T2. RNA. 2017 Nov;23(11):1614-1625. doi: 10.1261/rna.060939.117. Epub 2017 Aug 25. http://rnajournal.cshlp.org/content/23/11/1614.full http://rnajournal.cshlp.org/content/23/11/1614.full.pdf Dionisio
Exploring the read-write genome: mobile DNA and mammalian adaptation. Shapiro JA Crit Rev Biochem Mol Biol. 2017 Feb;52(1):1-17. doi: 10.1080/10409238.2016.1226748. Epub 2016 Sep 7. [paywall] Dionisio
Biological action in Read-Write genome evolution. Shapiro JA1. Interface Focus. 2017 Oct 6;7(5):20160115. doi: 10.1098/rsfs.2016.0115. Epub 2017 Aug 18. http://rsfs.royalsocietypublishing.org/content/7/5/20160115.full.pdf Dionisio
Living Organisms Author Their Read-Write Genomes in Evolution. Shapiro JA Biology (Basel). 2017 Dec 6;6(4). pii: E42. doi: 10.3390/biology6040042. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5745447/pdf/biology-06-00042.pdf Dionisio
toza @6: Thanks for providing the link to the full text of the paper. Here's an insightful review of the given paper: https://uncommondescent.com/intelligent-design/the-spliceosome-a-molecular-machine-that-defies-any-non-design-explanation/#comment-647392 Dionisio
Biological action in Read–Write genome evolution James A. Shapiro http://rsfs.royalsocietypublishing.org/content/7/5/20160115 http://rsfs.royalsocietypublishing.org/content/royfocus/7/5/20160115.full.pdf http://extendedevolutionarysynthesis.com/ https://pandasthumb.org/archives/2017/12/questioning-evolution.html#disqus_thread toza
If you want free access to the article, go to sci-hub.cc and enter the DOI. You will be able to read and download it. wsread
welcome back gpuccio. Mung
gpuccio, Very insightful comment, as usual. Thanks. "And who is the responsible for that “natural” engineering?" Well, obviously 'nature'*, isn't it? :) "...those evident design processes must be “natural” by definition, of course without giving any support to that idea." Isn't enough that it's said by a professor? Do you require more support than that? :) Here's an older paper by the same author that seems a little related: http://www.mdpi.com/2079-7737/5/2/27/htm BTW, note this: "Molecular Phylogenies Based on Core Information-Processing Systems" (*) whatever that means Dionisio
J-Mac: "Seems obvious Shapiro has not problem to butter his bread on both sides…" Absolutely! He's very clever at that. :) Unfortunately, there is no free access to the paper, so we can only guess his "arguments" from the abstract. I would say that he is clever in mixing two completely different types of arguments as thought they were one and the same thing: a) Symbiogenetic cell mergers, hybridizations and genome doublings: IOWs, information remixing. Of course such events took place, and they certainly have some importance, but the statement that they "generated new species" is a really bold one: is Shapiro so certain that the "symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes" can explain the shift from prokaryotes to eukaryotes, or even the simple functional acquisition of mytochondria? I can think of thousands of very strong objections to that simple statement! Shuffling existing information can be a part of a complex engineering process (whoever has done some software programming is well aware of that), but certainly is not enough to explain the process itself. Any complex engineering process is driven by conscious design, even if it reuses existing information as a part of the process itself. Well, that covers points (i), (ii) and (iii) I suppose. But then, strangely, and without even a (iv) label, the abstract goes on with something completely different: b) "Adaptive variations also involved horizontal DNA transfers..." OK, here we are still in the reshuffling argument, but wait, here comes the fun! c) "... and natural genetic engineering by mobile DNA elements to rewire regulatory networks". Wait, this is something completely different! Suddenly, and without any label, we get "natural" (always a very suspicious word :) ) "genetic engineering". Wow! That is a game changer, and it is introduced as smartly as possible, I would say... And who is the responsible for that "natural" engineering? "mobile DNA elements"!!!! :) IOWs, transposon activity that "rewires regulatory networks". So, what Shapiro is saying is: In evolutionary processes, there is some reshuffling of existing information (indeed, a very intelligent reshuffling and remodeling!), but the new information is really engineered by transposon activity. OK, that apparently a design process, but it is "natural", because I guarantee that, and you should well believe what I say. Now, all those who have read some of my posts here are certainly aware that I have been proposing guided transposon activity as the main tool for biological design for years. It seems that Shapiro agrees with me, except that he obviously declares that those evident design processes must be "natural" by definition, of course without giving any support to that idea. Talk about "butter his bread on both sides"! :) This is a very good example of what I call: trendy post neo-neo-darwinism. :) Beware, I consider Shapiro's work very, very interesting. He is really smart, and when he butters his bread on the right side, he can say very interesting things! gpuccio
Seems obvious Shapiro has not problem to butter his bread on both sides... J-Mac

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