Archive for April, 2012
Pattern recognition: How rational is that?
“Recently there’s been an emerging consensus among [researchers] … that a lot of religious beliefs are grounded in intuitive processes,” says Will Gervais, a graduate student at the University of British Columbia, Vancouver, in Canada and a co-author of the new study, published today in Science.
Pattern recognition is required of scientists who have changed the attitudes of their peers. It is also important when comparing analytical thinking to beliefs.
Here’s a pattern
Non-random mutation, as evidenced by ‘hot’ and ‘cold’ genes involved in amino-acid biosynthesis, energy metabolism , and catabolism of specific compounds (Martincorena, Seshasayee , & Luscombe, 2012) is conceptualized in a model for adaptive evolution where 1) nutrient chemicals calibrate intracellular signaling and stochastic gene expression, and 2) the metabolism of nutrients to pheromones standardizes and controls reproduction (Kohl, 2012).
The honeybee is the invertebrate model organism that extends the common molecular biology across species from microbes to man. The pattern is hard to miss, and additional support for that model can found in a recent report on a vertebrate model organism of speciation. Stickleback evolution is accelerated by the use of pre-existing genetic variation, not random mutation (Jones et al., 2012). Although random mutation may be involved, it is pre-existing genetic variation that allows a cell to adapt to changes in the availability of nutrients from its environment. This ability appears to be programmed into the first living cells. Receptor-mediated cellular changes in the intracellular metabolism of the nutrients enables cell to cell signaling that varies with the metabolism of nutrients to pheromones that control reproduction.
This pattern can be recognized by a general audience. All scientists need to say is that food odors cause us to eat food that metabolizes to pheromones that cause us to develop preferences for other people. For example, in placental mammals, in utero nutrient chemical exchange precedes nutrient chemicals provided though lacation. These nutrient chemicals are associated with the pheromones of the mother and result in social bonding. In this context, pheromones are social odors just as they are in bacteria, in the honeybees, in the sticklebacks, and all other species.
The ability to recognize patterns across species helps to ensure that at some point this common thread, which involves only only food odors and social odors, may allow analytical thinkers to use olfaction and odor receptors to follow a clear evolutionary trail from unicellular organisms to insects to humans.
Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., et al. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55-61.
Kohl, J. V. (2012). Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology , 2, 17338 – DOI: 17310.1340 2/snp.v1733 2i17330.173 38.
Martincorena, I., Seshasayee , A. S. N., & Luscombe, N. M. (2012). Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature, advance online publicatio n, doi:10.103 8/nature109 95.read more April 27, 2012 • 6:38 PM
Cultural processes are biologically based
“Courtiol is not certain how strong natural selection is today, particularly in the developed world. But he says that at the very least, the data show that even as recently as 200 years ago, it still played a role in shaping humans as a species. As such, he notes, biological and cultural processes should both be considered in understanding how humans are changing through time.”
Problem: Ignoring the molecular biology common to all organisms from microbes to man makes it appear that biological and cultural processes operate somewhat independen
Solution: In the past few years, the importance of sexual selection for chemosenso
Human Pheromones: extremely technical representation of the concept
For those interested in highly technical representations of the concept of human pheromones:
- B. Jesse Shapiro,
- Jonathan Friedman,
- Otto X. Cordero,
- Sarah P. Preheim,
- Sonia C. Timberlake,
- Gitta Szabó,
- Martin F. Polz,
- and Eric J. Alm
Science 6 April 2012: 336 (6077), 48-51. [DOI:10.1126/science.1218198]
Abstract (subscription required to read the full text of this article)
Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. Here, we show that in two recently diverged populations of ocean bacteria, ecological differentiation has occurred akin to a sexual mechanism: A few genome regions have swept through subpopulations in a habitat-specific manner, accompanied by gradual separation of gene pools as evidenced by increased habitat specificity of the most recent recombinations. These findings reconcile previous, seemingly contradictory empirical observations of the genetic structure of bacterial populations and point to a more unified process of differentiation in bacteria and sexual eukaryotes than previously thought.
My comment on the full text of this article is apparently not going to be published so I will add it here:
Isn’t it most likely that nutrient chemicals establish the ecological niche of different bacterial species and that nutrient calibrated receptor-mediated events link the metabolism of nutrients to pheromones that standardize and control speciation (e.g., via changes in intracellular signaling and stochastic gene expression)? This would link microbes to man via the origins of the olfactory and immune systems with a clear evolutionary trail that can be followed by the development of olfaction and odor receptors. I’m having difficulty opening up a dialogue in this regard, despite my publication history, and current position in microbiology. Can anyone advise me on errors in logic, basic principles of biology, or levels of biological organization
in this regard?
read more April 06, 2012 • 6:54 PM
Pre-existing genetic variability or random mutations: a matter of priorities and choices
“The study, published online today in Nature, shows that bacteria have evolved a mechanism
that protects important genes from random mutation, effectively reducing the risk of self-destruction.”
My comments on what the actual article tells us in: Evidence of non-random mutation rates suggests an evolutionary risk management strategy
Non-random mutation, as evidenced by ‘hot’ and ‘cold’ genes involved in amino-acid biosynthesis, energy metabolism, and catabolism of specific compounds is compatible with a model where 1) nutrient chemicals calibrate intracellular signaling and stochastic gene expression, and 2) the metabolism of nutrients to pheromones standardizes and controls reproduction.
This is the model detailed in Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. The honeybee is the invertebrate model organism that extends the common molecular biology across species from microbes to man, but additional support for my conceptualization can now be found in what was recently reported on threespine stickleback fish, a vertebrate model organism of speciation.
Evolutionary theorists have been loudly shouting for years that “[RANDOM] Mutations are the reason each of us is unique. These changes to our genetic material are at the root of variation between individuals, and between cells within individuals.” Indeed, it seems that the theorists may continue to focus on non-random mutations instead of the more obvious scientifically established fact that pre-existing genetic variation enables adaptive evolution, and random mutation does not.
For example, the pre-existing genetic variation that allows a cell to adapt to changes in the availability of nutrients from its environment appears to have be programmed into the first living cell(s). Receptor-mediated cellular changes in metabolism of the nutrients enable cell to cell signaling that varies with the metabolism of nutrients to pheromones.
This fact can be explained to a general audience by saying that food odors cause us to eat what causes us to produce pheromones that cause us to associate, or not associate, with other people. In this context, pheromones are social odors.
A matter of choices:
Pre-existing genetic variations across species makes food choice essential to individual survival, and it makes mate choice essential to species survival in species that sexually reproduce. An organism that eats the wrong food may not live to reproduce. Clearly, the pre-existing genetic variations make the effects of different foods on hormones that affect our behavior a key indicator of how pre-existing genetic variability can effect hormones and their metabolism to pheromones that cause changes in sexual behavior.
The allegorical representation of this newly established scientific truth occurs in Genesis with a story indicating that what Eve decided to eat epigenetically altered events across Creation (i.e., based on pre-existing genetic variability, not random mutations). Nevertheless, incorporating similar important choices into thoughts and decisions about what we eat and our mate choice may be easier for those who continue to think the development of their behavior was determined by random mutations. After all, who’s going to hold them accountable for not recognizing the truth about the difference between pre-existing genetic variations and random mutations?read more April 25, 2012 • 9:29 AM
Adam’s rib: Pheromones and the adaptive evolution of human sexuality
The article linked (above) may be of interest in the context of my comments and response to commentary linked below.
I don’t think ingestion of heterospecific DNA by microbes is widely known, and was reluctant to suggest it as a precursor to the self / non-self recognition that accompanies the adaptive evolution of sex differences in yeasts. But, I did in: Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
Here’s the section head and excerpted text from:
An epigenetic continuum from microbes to humans: from theory to facts
“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).”
My academic and commercial interest in this complex ability in bacteria that suppress reproduction with pheromones when insufficient nutrients are available led me to sponsor the video game “Bacillus.” One entitlement is that I get to name an organism and attribute to it a characteristic. If a named organism eats the DNA of other bacteria, I named it! If you want to encourage others to have some fun while learning about the molecular biology of sex differences, there is still time to contribute to the game’s development and get credit for doing so.read more April 23, 2012 • 8:27 AM
Creation vs Evolution? Pre-existing genetic variation, not random mutation
“…evolution is accelerated by the use of pre-existing genetic variation, instead of waiting for new, random mutations to arise…”
Full text is free: Jones, F. C. et al. Nature. http://dx.doi.org/10.1038/nature10944 (2012).
My Comment to the Nature site:
The honeybee is an invertebrate model organism that exemplifies the vertebrate molecular mechanisms detailed here. As noted by the authors, these molecular mechanisms are common to microbial species, which indicates the requirement for their ubiquitous and consistent use across life’s evolutionary continuum.
In the honeybee, what the queen eats determines her pheromone production and everything else about the colony, including the neuroanatomy of the worker bee’s brains. From this perspective on molecular biology, the honeybee model tells us that nutrient chemicals calibrate receptor-mediated intracellular signaling and stochastic gene expression associated with the metabolism of nutrients to pheromones in all species from microbes to man. The pheromones standardize regulatory control of receptor-mediated intracellular signaling and stochastic gene expression required for speciation. Reciprocal bottom-up / top-down relationships among chemicals associated with the “odors” of food are directly responsible for the formation of an ecological niche, which is maintained by the “social odors” / the pheromones that establish the social niche.
Changes in nutrient chemicals result in changes in the ecological niche that change the social niche by partial suppression of reproduction in individuals that don’t “smell” right because they are malnourished (or in bacterial colonies where reproduction is suppressed by pheromones and quorum sensing). The ability to acquire sufficient nutrient chemicals is genetically predisposed but also depends on conspecifics and stressors in the social niche (e.g., dominance in mammals) that might prevent access to changing supplies of existing nutrients. Individuals with genetic predispositions that allow them to adapt to changes associated with available nutrients will reproduce in microbial species like bacteria, or pheromonally signal their reproductive fitness in yeasts or in the multicellular organisms of all other species. These nutritional and social stressors are associated with immune system dysfunction in primates as they are with nutritional deficits or excess in other species.
In species from yeasts to primates, this model allows incorporation of social science theories of individual selection, kin selection, and group selection where nutrition and food odors are as essential to individual survival as they are to the production of pheromones and species survival. In this context, olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans.
Human Pheromones and Common Scents: Plants and Perfume
By Daniel Chamovitz
Botanists are getting a whiff of the ways that plants smell one another. Some plants recognize injured neighbors by scent; others sniff out a meal
Re: “other flora throughout our natural world respond to pheromones, just as we do. Plants detect a volatile chemical in the air, and they convert this signal (albeit nerve-free) into a physiological response. Surely this could be considered olfaction.”
The concept of human pheromones has been challenged — even by olfactory researchers like Richard L. Doty in his book “The Great Pheromone Myth.” Clearly, however, the concept is one of olfactory/pheromonal communication that must occur for any species of plant or animal to survive. Nutrient chemicals, for example, calibrate individual survival via their epigenetic effects on intracellular signaling. The nutrients metabolize to pheromones that standardize and control reproduction.
The common molecular mechanisms place the human pheromone-deniers in a category that could only be reserved for those who think that plant odors (as in food odors) do not have the same epigenetic effects on intracellular signaling as pheromones do in species from microbes to man. How (e.g.,on earth) could humans not produce and respond to pheromones. Are we evolutionarily adapted outliers due to random mutations, or is our behavior consistent with the epigenetic effects of nutrient chemicals and pheromones on pre-existing genetic variability across all species?read more April 24, 2012 • 9:38 AM
Human pheromones and your immune system
“Social stress affects immune system gene expression in monkeys.” April 9th, 2012. http://medicalxpress.com/news/2012-04-social-stress-affects-immune-gene.html
My comments: In Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors the epigenetic effects of nutrient chemicals on intracellular signaling and their metabolism to pheromones calibrates, standardizes, and controls individual and species survival. Nutrient-dependent and pheromone-determined changes in the brain of invertebrates and vertebrates are the most obvious of all environmental effectors of neuroendocrine and neuroimmune system changes directly linked to from the sensory environment. This makes the role of pheromones in the social regulation of stress in primates more difficult to deny since there is more than sufficient evidence from molecular biology that cause and effect must be the same in species from microbes to man. Note that Gene R. Robinson edited the article by Tung et. al., and that the role of mammalian pheromones in immune system modulation should be acknowledged as it has been in Robinson’s work on insect species.read more April 10, 2012 • 11:48 AM
Disclosure, or not
By Ruth Williams
Editors at PLoS Medicine suggest that merely disclosing conflicts of interest is insufficient and possibly even counterproductive.
“Whether or not journals adopt exclusion policies, Caplan suggests a possible improvement to the disclosure process. “We’ve got the internet. You should put your relationships and what you are doing online and explain what you are up to.”
Disclosure of Pheromones.com as my domain for information dissemination about human pheromones and the purchase of pheromone-enhanced products continues to be a thorn in my side when I expect interest in my published works, such as Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.
Nevertheless, the epigenetic effects of nutrient chemicals and pheromones that I detailed have since been indicated in reports of pre-existing genetic variations responsible for adaptive evolution, as compared to random mutations, which apparently are not involved in adaptive evolution. See: Evidence of non-random mutation rates suggests an evolutionary risk management strategy.
Taken together these two publications might be considered “game changers” that force evolutionary theorists and molecular biologists alike to reconsider whatever model they are using for therapeutic drug development, or whatever else they are doing. Clearly, epigenetic effects on the gene, cell, tissue, organ, organ system pathway must at least be considered before scientific progress can best be ensured.
But when the most important of these epigenetic effects appear to come from nutrient chemicals and their metabolism to pheromones instead of from “random mutations,” the fact so many people have intuitively “known that all along” may reflect badly on researchers who have not considered the facts, and who will therefore not respond favorably to disclosure or non-disclosure of commercial interests. With disclosure, or without it, the first rule of and scientific venture is to get the model right!
read more April 25, 2012 • 11:02 AM
People select specific fragrances that suit their individual body odor
“Our results indicate that people select specific perfumes that suit their individual body odor and they thus provide an insight into the highly individual nature of perfume choice.”
Fragrance enhances individual body odor and pheromones are the individual body odor that is enhanced. This is the concept of human pheromone-enhanced fragrances that I detailed in Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
Both of the research journal articles linked to the URLs above are available for free.
read more April 09, 2012 • 8:03 AM