DNA-grabbing bacteria

October 7, 2013 | James Kohl

DNA-grabbing bacteria hint at early phase of evolution New Scientist: 26 September 2013 by Michael Marshall [subscription required]

Excerpt: ‘By absorbing snippets of DNA that float in the environment, bacteria can access a junk shop of genetic material – some of which may no longer be in circulation in living things. What’s more, the mechanism requires hardly any cellular machinery, suggesting it may be left over from the earliest forms of life. Long before the advent of sex, the first cells may have randomly scavenged stray bits of DNA to survive and evolve.”

My comment: I look forward to more coverage on this topic because of its obvious relevance to nutrient-dependent pheromone-controlled adaptive evolution (sans mutations) in species from microbes to man.

In my 2012 published work, in the section titled: “An epigenetic continuum form microbes to humans: from theory to facts,”  I wrote about DNA uptake among different bacterial species and linked to “epigenetic feeding” and speciation via conjugation, which indicates that reproduction began with an active nutrient uptake mechanism that evolved into symbiogenesis in asexual organisms and pheromone-controlled sexual reproduction in all species that sexually reproduce. I’ve since read something that made me less sure about methylation in microbes, but this news article solidifies the importance of DNA uptake. I’ve had no luck getting information from someone who claims a background in biophysics, and welcome feedback from anyone who can address any aspect of how DNA uptake alters the thermodynamic stability of intercellular signaling in microbes.

Addendum: Clearly all aspects of nutrient uptake are at least somewhat dependent on self  vs non-self recognition and receptor mediation that enables the snippet of DNA to enter the microbial cells. In my  model, DNA uptake occurs in conjunction with the de novo creation of what are commonly called olfactory receptor genes.

I wrote:  “Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically ‘fed’ interspecies methylation and speciation via conjugation (Fall et al., 2007; Finkel & Kolter, 2001; Friso & Choi, 2002). This indicates that reproduction began with an active nutrient uptake mechanism in heterospecifics and that the mechanism evolved to become symbiogenesis in the conspecifics of asexual organisms (Margulis, 1998). In yeasts, epigenetic changes driven by nutrition might then have led to the creation of novel cell types, which are required at evolutionary advent of sexual reproduction (Jin et al., 2011). These epigenetic changes probably occur across the evolutionary continuum that includes both nutrition-dependent reproduction in unicellular organisms and sexual reproduction in mammals. For example, ingested plant microRNAs influence gene expression across kingdoms (Zhang et al., 2012). In mammals, this epigenetically links what mammals eat to changes in gene expression (McNulty et al., 2011) and to new genes required for the evolutionary development of the mammalian placenta (Lynch, Leclerc, May, & Wagner, 2011) and the human brain (Zhang, Landback, Vibranovski, & Long, 2011).

The entirety of this approach to the involvement of de novo olfactory receptor genes leads to their experience-dependent presence in mammals, which I exemplified in the context of “A gene that codes for the mammalian olfactory receptor, OR7D4, links food odors to human hunger, dietary restraint, and adiposity (Choquette et al., 2012). OR7D4 exemplifies a direct link1 from human social odors to their perception (Keller, Zhuang, Chi, Vosshall, & Matsunami, 2007) and to unconscious affects2 on human behavior associated with human olfactory-visual integration (Zhou, Hou, Zhou, & Chen, 2011); human brain activation associated with sexual preferences (Savic, Heden-Blomqvist, & Berglund, 2009), human learned odor hedonics; and motor function (Boulkroune, Wang, March, Walker, & Jacob, 2007). Insect species exemplify one starting point along an evolutionary continuum from microbes to humans that epigenetically links food odors and social odors to multisensory integration and behavior.”

I then proceeded to show how adaptive evolution occurs sans mutations theory, and have since staunchly advocated the obvious fact that natural selection must first occur for nutrients for evolution to occur at all. This fact seems to somehow have escaped from inclusion in the knowledge base of those who have been touting mutation-driven evolution since the idea was first proposed by Haldane in 1924 without any experimental support. I think we’ve been stuck with Haldane’s theory for far too long and this article represents a way to move forward using the common molecular mechanisms of nutrient-dependent pheromone-controlled adaptive evolution and dispatching most of evolutionary theory to the dustbin of experimentally unsubstantiated bizarre thoughts about biologically based cause and effect.

See Natural transformation of bacteria by fragmented, damaged and ancient DNA  to find new information from someone who is obviously interested in substantiating his ideas via a model of biologically based cause and effect (sans ridiculous theories). I hope you are inclined to compare mutation-driven evolution and nutrient-dependent pheromone-controlled adaptive evolution in the context of results from experiments, since no experimental evidence has ever supported mutation-driven evolution.

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James Vaughn Kohl

James Vaughn Kohl

James Vaughn Kohl was the first to accurately conceptualize human pheromones, and began presenting his findings to the scientific community in 1992. He continues to present to, and publish for, diverse scientific and lay audiences, while constantly monitoring the scientific presses for new information that is relevant to the development of his initial and ongoing conceptualization of human pheromones.