Warmed over Dr. James Shapiro. These guys are years behind the good doctor, who has earned no respect from the usual suspects here.
Dr. Shapiro
http://shapiro.bsd.uchicago.edu/21st_Cent_View_Evol.html
A 21st Century View of evolution
The conventional view is that genetic change comes from stochastic, accidental sources: radiation, chemical, or oxidative damage, chemical instabilities in the DNA, or from inevitable errors in the replication process. However, the fact is that DNA proofreading and repair systems are remarkably effective at removing these non-biological sources of mutation. For example, consider that the E. coli cell replicates its 4.6 megabase genome every 40 minutes. That is a replication frequency of almost 2 kHz. Yet, due to the action of error-recognition and correction systems in the replication machine and in the cell to catch mistakes in already-replicated DNA, the error rate is reduced below one mistake in every 1010 base-pairs duplicated, and a similar low value is observed in mammalian cells (32). That is less than one base change in every 2000 cells, certainly well below the mutation frequencies I have measured in E. coli of about four mutations per every 100 to 1000 cells.
In addition to proofreading systems, cells have a wide variety of repair systems to prevent or correct DNA damage from agents that include superoxides, alkylating chemicals and irradiation (33). Some of these repair systems encode mutator DNA polymerases which are clearly the source of DNA damage-induced mutations and also appear to be the source of so-called "spontaneous" mutations that appear in the absence of an obvious source of DNA damage (34). Results illustrating the effectiveness of cellular systems for genome repair and the essential role of enzymes in mutagenesis emphasize the importance of McClintock?s revolutionary discovery of internal systems generating genome, particularly when an organism has been challenged by a stress affecting genome function (Fig. 4; 5).
McClintock recognized that genetic change is a cellular process, subject to regulation, and is not dependent on stochastic accidents. The idea of internally-generated, biologically regulated mutation has profound impacts for thinking about the process of evolution. Darwin himself acknowledged this point in later editions of Origin of Species, where he wrote about natural "sports" or "...variations which seem to us in our ignorance to arise spontaneously. It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure independently of natural selection." (6th edition, Chapter XV, p. 395).
See also: Genomes 2nd Ed 2002, T. A. BROWN, Department of Biomolecular Sciences, Manchester UK 14.1. Programmed mutations? Excerpt
In 1988 startling results were published suggesting that under some circumstances Escherichia coli bacteria are able to mutate in a directed way that enables cells to adapt to an environmental stress. The randomness of mutations is an important concept in biology because it is a requirement of the Darwinian view of evolution, which holds that changes in the characteristics of an organism occur by chance and are not influenced by the environment in which the organism is placed. In contrast, the Lamarckian theory of evolution, which biologists rejected well over a century ago, states that organisms acquire changes that enable them to adapt to their environment. The Darwinian view requires that mutations occur at random, whereas Lamarckian evolution demands that programmed mutations occur in response to the environment.BTW, I think Dr. James Shapiro may have suffered the ideational flu of hubris regarding the over-generaity of his findings on rates of mutants in single cell organizisms -- more complex organisms have even more magnitudes of layers to fight off mutations. AND while the bacteria are singleton cell organisms, in many ways the very environment in which they grow acts as a sort of super-organism, and with that super-organism more layers of mutation-resitance. Shapiro's studies perhaps may have provided the very type of unrealistic forced lab environment most condusive to permitting mutations and encouraging the vitality of mutants....< snip > ...
The results of Cairns et al. 1988 showed that when the lactose auxotrophs were plated onto a minimal medium containing lactose as the only sugar - circumstances that require that the bacteria must mutate into lactose prototrophs in order to survive - then the number of lactose prototrophs that arose was significantly higher than that expected if mutations occurred randomly. In other words, some cells underwent programmed mutation and acquired the specific change in DNA sequence needed to withstand the selective pressure.
Since 1988, a number of examples of what appear to be programmed mutations have been published, but the notion that bacteria, and possibly other organisms, can program mutations in response to environmental stress is by no means accepted by the scientific community. It is quite possible that these mutations will eventually be disproved or be shown to have an orthodox basis. However, until this happens we are left with the tantalizing possibility that even at this fundamental level our knowledge about genomes might be far from complete.