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Proponent of nearly neutral evolution theory offers her views on Darwinism

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In “Q & A (with) Tomoko Ohta” (Current Biology,, Volume 22, Issue 16, R618-R619, 21 August 2012), famed Japanese geneticist Ohta, proponent of “nearly neutral” evolution, offers her views on today’s Darwinism:

The current orthodox theory in evolution is Neo-Darwinism, which is based on Mendelian genetics. However, recent progress in developmental biology, and especially in uncovering epigenetic mechanisms, tells us that Mendelian genetics is not enough for describing certain phenomena of inheritance. Also, genomics is expanding rapidly such that analyses at the genomic level are needed for understanding evolutionary processes. My ambition is to combine these new findings with the nearly neutral theory in which the interplay of drift and weak selection is thought to be most important.

What do you think are the big questions in your field?

If you look at systems biology papers, you are struck by extreme complexities of various interaction systems. To me, the biggest question is how such complex systems could have evolved? Once, a Japanese immunologist, Dr Tomio Tada, called the immune system an “immune super-system”. It now seems that super-systems exist at so many levels in the biological world. Shifting and modification of these systems are essential for their evolution and variation. (Paywall)

See also:

Michael Behe on the theory of constructive neutral evolution

This year’s wishful thinking?: “Constructive neutral evolution” can create complex processes like splicing and RNA editing …

BA77, thanks for the info.
But for me personally, the biggest surprise from epigenetic research has been the recent finding that ‘mental states’ may actually have epigenetic effects on genes:
This is definitely a stunner.
Needless to say Chance, if all this ‘mental epigenetics’ does indeed pan out in future research, it will leave the genetic reductionism model of neo-Darwinism so far back in the dust that future researchers will probably have to use shovels and metal detectors just find where it was last buried !
Yes but it could never disprove "evolution." :p Chance Ratcliff
Chance as to your question:
does not epigenetics in general challenge the central dogma?
Yes, the central dogma (DNA makes RNA makes Proteins: i.e. the Genetic Reductionism model of neo-Darwinism) is directly challenged by many recent findings in epigenetics. ,,, Some epigenetic information flow is found to be completely outside of DNA, whereas other epigenetic information, instead of merely being information that is added onto DNA, as was initially assumed in mainstream neo-Darwinian thought, is now found that this epigenetic information, in some instances, actually controls DNA information, thus completely contradicting the central dogma, genetic reductionism model, of neo-Darwinism. For instance this recent paper:
Histone-modifying proteins, not histones, remain associated with DNA through replication - August 23, 2012 Excerpt: "Essentially, all histones are going away during DNA replication and new histones, which are not modified, are coming in,",, "What this paper tells us," he continues, "is that these histone modifying proteins somehow are able to withstand the passage of the DNA replication machinery. They remained seated on their responsive binding sites, and in all likelihood they will re-establish histone modification and finalize the chromatin structure that allows either activation or repression of the target gene." http://phys.org/news/2012-08-histone-modifying-proteins-histones-dna-replication.html
A bit more detail on the insurmountable challenge this epigenetic information presents to the neo-Darwinian paradigm is discussed in this following video, and article:
The Mysterious Epigenome. What lies beyond DNA - Woodward - video http://www.youtube.com/watch?v=RpXs8uShFMo Epigenetics and the "Piano" Metaphor - January 2012 Excerpt: And this is only the construction of proteins we're talking about. It leaves out of the picture entirely the higher-level components -- tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players. http://www.evolutionnews.org/2012/01/epigenetics_and054731.html
The following paper, on page 22, has a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt: Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
But for me personally, the biggest surprise from epigenetic research has been the recent finding that 'mental states' may actually have epigenetic effects on genes:
Anxiety May Shorten Your Cell Life - July 12, 2012 Excerpt: These studies had the advantage of large data sets involving thousands of participants. If the correlations remain robust in similar studies, it would indicate that mental states and lifestyle choices can produce epigenetic effects on our genes. http://crev.info/2012/07/anxiety-may-shorten-your-cell-life/
The following site is not nearly as reserved in its claims, as the preceding site, that mental states can epigenetically effect genes:
Genie In Your Genes - video http://www.genieinyourgenes.com/ggtrailer.html Upgrade Your Brain Excerpt: The Research; In his book The Genie in Your Genes (Elite Books, 2009), researcher Dawson Church, PhD, explains the relationship between thought and belief patterns and the expression of healing- or disease-related genes. “Your body reads your mind,” Church says. “Science is discovering that while we may have a fixed set of genes in our chromosomes, which of those genes is active has a great deal to do with our subjective experiences, and how we process them.” One recent study conducted at Ohio University demonstrates vividly the effect of mental stress on healing. Researchers gave married couples small suction blisters on their skin, after which they were instructed to discuss either a neutral topic or a topic of dispute for half an hour. Researchers then monitored the production of three wound-repair proteins in the subjects’ bodies for the next several weeks, and found that the blisters healed 40 percent slower in those who’d had especially sarcastic, argumentative conversations than those who’d had neutral ones. http://experiencelife.com/article/upgrade-your-brain/ Genie In Your Genes - Book Book review: First of all, if you are a newcomer to Dawson Church's writing, you need to know that his facts are unimpeachable - they were stringently peer-reviewed before publication. What is more, when Church makes categorical statements, he provides research to corroborate them. http://www.amazon.com/gp/product/1604150114?ie=UTF8&tag=eliboo-20&linkCode=as2&camp=1789&creative=9325&creativeASIN=1600700225
Needless to say Chance, if all this 'mental epigenetics' does indeed pan out in future research, it will leave the genetic reductionism model of neo-Darwinism so far back in the dust that future researchers will probably have to use shovels and metal detectors just find where it was last buried :) ! Music and verse:
Mark Schultz - All Things Possible http://www.youtube.com/watch?v=Emj6O__05N4 Matthew 19:26 Jesus looked at them and said, “With man this is impossible, but with God all things are possible.”
BA77, thanks for reposting your comment on a thread authored by a non-diva. Sheesh! Wrt your post, does not epigenetics in general challenge the central dogma? Chance Ratcliff
OT: Central Dogma of neo-Darwinism challenged (yet again)
To cap or not to cap: Scientists find new RNA phenomenon that challenges dogma - August 27, 2012 by Emily Caldwell Excerpt: ,,, Until now, scientists have believed that once an mRNA is no longer needed to make protein, the cap comes off and the molecule is degraded, its job complete. But Schoenberg's lab discovered in 2009 that some mRNAs that were thought to be degraded were instead still present in the cell, but they were missing part of their sequence and had caps placed back on the newly formed ends. Because these mRNAs were in the cytoplasm, the changes had to happen there rather than inside the nucleus.,,, "We have always thought that one gene would give an mRNA for one kind of protein. But what we have found makes us wonder if multiple proteins could be made from each of the messenger RNAs that undergo decapping and recapping in the cytoplasm," Schoenberg said.,,, "It wasn't random. It was very specific," Schoenberg said. "There are specific families of mRNAs that are regulated in this way, and that has ramifications for how proteins are expressed and regulated.",,, For now, these scientists can only speculate about what this unexpected biological process really means.,,, http://phys.org/news/2012-08-cap-scientists-rna-phenomenon-dogma.html
The Current Biology article on Dr. Tomoko Ohta can be freely read here: http://www.sciencedirect.com/science/article/pii/S0960982212007075 Enezio E. De Almeida Filho
Is nearly neutral evolution a form of evolution so slight that it's indistinguishable from non-evolution? Mung

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