Potential falsifications of the theory of evolution

That the paper expresses no doubts as to the existence of natural selection; also that the author is presumably neither retarded not insane.

And guess what, neo-Darwinism is in "the post-genomic era".If by "the Modern Synthesis" he means "what people knew about genetics in the 1920s", then the theory of evolution has indeed been improved by the accumulation of further knowledge since that time; and it seems otiose now to write an article urging that this should happen when it already has.

Eugene Koonin writes:"...a far cry from the orderly, rather simple picture envisioned by Darwin and the creators of the Modern Synthesis. The biosphere is dominated, in terms of both physical abundance and genetic diversity, by "primitive' life forms, prokaryotes and viruses. These ubiquitous organisms evolve in ways unimaginable and unforeseen in classical evolutionary biology."

Eugene Koonin writes:"Equally outdated is the (neo)Darwinian notion of the adaptive nature of evolution: clearly, genomes show very little if any signs of optimal design, and random drift constrained by purifying in all likelihood contributes (much) more to genome evolution than Darwinian selection."

He is wrong that the Modern Synthesis was written in stone in the 1960's and that no one is allowed to add anything to it. The health of the Modern Synthesis is exemplified in it's ability to absorb new knowledge which it is doing and continues to do.Besides, I don't see how Koonin helps the creationist argument. What Koonin is arguing for is a new theory of evolution

Again, you cannot discard the modern synthesis because it would mean ignoring the driving necessities that brought evolution and genetics together in the first place. We observe adaptive evolution (Darwinian evolution) everywhere, and genetics is the mechanism of adaptive evolution as demonstrated by the population geneticists of the 1920's. No matter how much evolution and genetics are enhanced and revised, the two of necessity must be combined. Koonin's proposal that we discard the modern synthesis, which would mean considering evolution and genetics as separate and independent, makes no sense.

The theory of evolution is, simply put, everything we know about genetics that is relevant to evolution. That's the neo in neo-Darwinism. Darwin knew that there was reproduction, variation, and selection. We know the details. Finding out more details helps to flesh out the theory, it doesn't controvert it.

razd writes:Are you expecting us to debate Dr. Koonin's work against a blank slate? Clearly you seem to be enamored of his work, and to fail to support it after claiming that you find it compelling is rather ... somewhat ... disappointing? Perhaps you are not qualified (undereducated) to speak on this topic but present it because it reinforces some beliefs you have, but are honest enough to realize that you do not have the expertize to discuss it from a scientific basis (which is okay with me).

razd writes:That kind of sums it up in a nutshell. We already have a web of life at the early stages from other sources, and we already have horizontal gene transfer between bacteria as a means of genetic exchange for single cellular life. These are not new, nor are they earth shaking revelations that shake the foundations of the science of evolution or rattle the walls of the ivory towers of the scientists that study evolution.

razd writes:Nor does the theory of common descent, that life is related to life by descent from common ancestor populations, fail if there is horizontal gene transfer that provides essentially the same contribution to descendants that sexual reproduction does in multicellular organisms. It just means that identifying the "mama" and "papa" may be a little more difficult, but that the process of changes in the frequency of hereditary traits in (gene exchanging) populations from generation to generation in response to ecological opportunities still occurs and is still subject to the trials and tribulations of survival, reproduction, drift, etc, within those ecologies.

razd writes:Rates of evolution change. Stunning. I fail to see any cause for a new synthesis nor any reason to say that current theory is in any jeopardy.

razd writes:This again is his opinion. Opinion is not fact, nor is it able to alter facts in any known way, whether "mind-action directed" or not.What will alter the theory of evolution is facts and objective empirical evidence of portions of evidence that the theory does not adequately explain -- that is how science works -- not by opinions.

Dr. Adequate writes:And if by "classical evolution theories" you mean everything we knew about genetics between 1850 and 1920, then what you say he is arguing is right. I for one would not roll the clock back on genetics 90 years.

Natural Genetic Engineering -- the Toolbox for Evolution: Prokaryotes
Dr. Jim Shapiro, Chicago
--------------------------------------------------------------------------------Interesting synopsis that is 10 years old.Once again this is an issue that is old news in evolution science ... nor does it mean that "many changes in the modern synthesis" will be needed: this is still the change in frequency of hereditary traits in breeding populations from generation to generation in response to ecological opportunities - where in this case the ecology includes the bacteria. The theory is still that evolution is sufficient to explain the diversity of life as we know it. Providing a more comprehensive accounting of the ecological factors is not a major rewrite of theory.

Mobile DNA and evolution in the 21st century
James A ShapiroCorrespondence: James A Shapiro jsha@uchicago.eduAuthor Affiliations
Department of Biochemistry and Molecular Biology, University of Chicago, Gordon Center for Integrative Science W123B, 929 E 57th Street, Chicago, IL 60637, USAMobile DNA 2010, 1:4 doi:10.1186/1759-8753-1-4The electronic version of this article is the complete one and can be found online at: Mobile DNA and evolution in the 21st century | Mobile DNA | Full TextReceived: 14 August 2009
Accepted: 25 January 2010
Published: 25 January 2010 2010 Shapiro; licensee BioMed Central Ltd.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (Creative Commons — Attribution 2.0 Generic — CC BY 2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Abstract
Scientific history has had a profound effect on the theories of evolution. At the beginning of the 21st century, molecular cell biology has revealed a dense structure of information-processing networks that use the genome as an interactive read-write (RW) memory system rather than an organism blueprint. Genome sequencing has documented the importance of mobile DNA activities and major genome restructuring events at key junctures in evolution: exon shuffling, changes in cis-regulatory sites, horizontal transfer, cell fusions and whole genome doublings (WGDs). The natural genetic engineering functions that mediate genome restructuring are activated by multiple stimuli, in particular by events similar to those found in the DNA record: microbial infection and interspecific hybridization leading to the formation of allotetraploids. These molecular genetic discoveries, plus a consideration of how mobile DNA rearrangements increase the efficiency of generating functional genomic novelties, make it possible to formulate a 21st century view of interactive evolutionary processes. This view integrates contemporary knowledge of the molecular basis of genetic change, major genome events in evolution, and stimuli that activate DNA restructuring with classical cytogenetic understanding about the role of hybridization in species diversification

"Although there remain many gaps in our knowledge, we are now in a position to outline a distinctively 21st century scenario for evolutionary change. This scenariio includes the following elements.(1) hereditary variation arises from the non-random action of built-in biochemical systems that mobilize DNA and carry out natural genetic engineering;(2) major disruptions of an organism's ecology trigger cell and genome restructurilng. The ecological disruptions can act directly, through stress on individuals, or indirectly, through changes in the biota that favour unusual interactions between individuals (cell fusions, interspecific hybridizations). Triggering events continue until a new ecology has emerged that is filled with organisms capable of utilizing the available resources;(3) ecologically-triggered cell and genome restructurings produce organisms which, at some frequency, will possess novel adaptive features that suit the altered enviroment. Novel adaptive features can be complex from the beginning because they result from processes that operate on pre-existing functional systems, whose components can be amplified and rearranged in new combinations. Competition for resources (purifying selection) serves to eliminate those novel system architectures that are not functional in the new ecology;(4)once ecological stability has been achieved, natural genetic engineerinig functions are silenced, the tempo of innovation abates, and microevolution can occur to fine-tune recent evolutionary inventions through successions of minor changes.This 21st century scenario assumes a major role for the kind of cellular sensitivities and genomic responses emphasized by McClintock in her 1984 Nobel Prize address.
Such a cognitive component is absent from conventional evolutionary theory because 19th and 20th century evolutionists were not sufficiently knowledgable about cellular response and control networks. This 21st century view of evolution establishes a reasonable connection between ecological changes, cell and organism responses, widespread genome restructuring, and the rapid emergence of adaptive inventions. It also answers the objections to conventional theory raised by intelligent design advocates, because evolution by natural genetic engineering has the capacity to generate complex novelties. In other words, our best defense against anti-science obscurantism comes from the study of mobile DNA because that is the subject that has most significantly transformed evolution from natural history into a vibrant empirical science."

I have mentioned it. I don't see how Koonin's argument helps the creationist argument. Do you?

This is why we do not use the neo-Darwinian Synthesis from the 1960's. We use the modern verison which incorporates everything that Koonin is talking about.

Koonin would certainly agree with Coyne and Dawkins that evolution is a fact. He treats it as a given in the paper you quoted from. There's nothing arrogant about stating this. It's true. And neither Coyne nor Dawkins think that we know everything about the processes by which evolution happens. Just like Koonin.

What neo-Darwinism states is that mutation and selection are independent of one another. That is, mutations are blind to what is good or bad for the individual. This is exactly what we see with mobile DNA elements. They insert all over the place, and the helpful ones are kept through natural selection.

james a. shapiro writes:The past five decades of research in genetics and molecular biology have brought us revolutionary discoveries. Upsetting the oversimplified views of cellular organization and function held at mid-century, the molecular revolution has revealed an unanticipated realm of complexity and interaction more consistent with computer technology than with the mechanical viewpoint which dominated the field when the neo-Darwinian Modern Synthesis was formulated. The conceptual changes in biology are comparable in magnitude to the transition from classical physics to relativistic and quantum physics.

I understand this to mean he is saying that major changes are the result of planned, engineered functions in the cell that do not rely on gradual, random changes.

Then you are jumping to a concussion.

Eh? I don't think he is saying that. Where are you even getting that from? From the "more consistent with computer technology" line? That doesn't mean that biology is a product of planned engineering. I agree with RAZD, you are reading too much into such a simple statement

Unfortunately, readers of Boston Review may remain unaware of this intellectual ferment because the debate about evolution continues to assume the quality of an abstract and philosophical "dialogue of the deaf" between Creationists and Darwinists. Although our knowledge of the molecular details of biological organization is undergoing a revolutionary expansion, open-minded discussions of the impact of these discoveries are all too rare. The possibility of a non-Darwinian, scientific theory of evolution is virtually never considered. In my comments, then, I propose to sketch some developments in contemporary life science that suggest shortcomings in orthodox evolutionary theory and open the door to very different ways of formulating questions about the evolutionary process. After a discussion of technical advances in our views about genome organization and the mechanisms of genetic change, I will focus on a growing convergence between biology and information science which offers the potential for scientific investigation of possible intelligent cellular action in evolution.