Seeing the (UV) light: Previously undetected difference in human mutation rate unique to Europeans

Differences in transcriptional strand bias
Differences in transcriptional strand bias. Each point in A and B represents a mutation type with an A or C ancestral allele. The x coordinate of each point in A is the PAf strand bias minus the PE strand bias; similarly, the x coordinates in B describe the PAf strand bias minus the PAs strand bias. The y coordinate of each point is the χ2 P value of the strand bias difference. The P values in A and B were computed from contingency tables C and D, respectively, using a χ2 test. At the P = 0.01 significance level (gray dashed line), only TCC → T has a significant strand bias difference between Europe and Africa, whereas no mutation type significantly differs in strand bias between Asia and Africa. E shows the variance of strand bias in each population across 100 bootstrap replicates. Similarly, F shows the distribution across bootstrap replicates of the ratio between genic f(TCC) and intergenic f(TCC). Credit: Harris K (2015) Evidence for recent, population-specific evolution of the human mutation rate. Proc Natl Acad Sci USA 112:11 3439-3444.

(Phys.org)—Although humans are a single species, not all genetic variation is shared between populations – and the ability to sequence our entire genome has allowed scientists to catalogue mutations that occur in one ethnic group alone. These so-called population-private mutations give researchers a unique window into recent human history. Recently, graduate student Kelley Harris – a scientist at University of California, Berkeley – revealed a previously undetected difference between Europeans and other ethnic groups by comparing population-private mutation frequencies from Europe, Asia, and Africa, finding that Europeans experience higher rates of a specific mutation type that has known associations with UV light exposure. Harris concludes that while it is unclear whether the excess mutations are harmful or directly related to the UV sensitivity of light skin, her results demonstrate that the human mutation rate has evolved on a much faster timescale than previously believed, with implications for cancer genetics, anthropology and other fields of inquiry.

Harris discussed the paper she published in Proceedings of the National Academy of Sciences with Phys.org, first addressing the challenge of revealing a previously undetected difference between Europeans and other ethnic groups contrasting frequencies of private to Europe, Asia, and Africa. "A question that's pretty hot in human genetics right now is whether the human mutation rate has changed over time. The idea that motivated me to do this project is that there are many different ways that DNA can mutate (an A base can change to G, a C to A, and so on), and I reasoned that if some biochemical force had changed the mutation rate at some point during human history, it was likely to have affected certain mutation types more than others," Harris tells Phys.org. However, she adds, while she assumed that if a difference did exist it would be subtle, she was surprised to find such a large difference between the mutational spectra of different populations. In fact, she notes that the pattern described in her paper was observed in the results of the first simple test she performed (although additional effort was needed to show that this pattern was valid and not simply a genome sequencing artifact). "There are hundreds of cryptic data quality problems that can affect genome sequences, and it was challenging to show that so many potential sources of error weren't creating the illusion of a biologically significant finding."

A more specific challenge was determining that Europeans experience higher rates of a specific mutation type that has known associations with UV light exposure. "When I performed a broad screening test for mutation frequency differences between populations," Harris explains, "the excess of the mutation type TCC->TTC in Europe immediately jumped out as hugely significant." The TCC->TTC mutation is the most common somatic mutation present in melanoma skin cancers, as well as the mutation most frequently induced in vitro by UV. "I didn't know at the time that this mutation type had associations with UV exposure, but these associations turned up pretty quickly in the course of further online research."

The paper also described how Harris had to account for the possibility that mutation rates might have changed owing to recent regional adaptations affecting DNA repair. "The possibility of local adaptation affecting DNA repair wasn't so much a challenge as a motivating factor for doing the analysis," Harris says, adding that her strategy was to describe how real differs from idealized models of mutation as a simple process that doesn't change over time. "That being said, while I was really excited to find evidence that DNA replication fidelity appears to differ between populations, we're still a long way from knowing the mechanism behind this difference or whether it affects human health."

One question that Harris hopes will generate some excitement among experimentalists who know how to grow yeast or culture cells concerns the prospects of determining that folate depletion could cause some of the mutations observed in UV-irradiated cells, and that these same mutations might appear in the germ line of a light-skinned individual rendered folate-deficient by sun exposure. "I'd love to be able to compare nutrient-deficient cell populations to control cell populations and test whether cells deprived of folate or other DNA synthesis cofactors experience different patterns of mutation than cells grown without nutrient deficiencies." She points out that while counting new mutations requires a lot of DNA sequencing, but this sort of experiment should become cheaper and more feasible as the cost of DNA sequencing continues to decline.

The paper also notes that differences in metabolic rate can drive latitudinal gradients in the rate of molecular evolution. "Several previous studies observed that organisms with high metabolic rates appear on average to have higher mutation rates than organisms with low metabolic rate. I'm not sure if those observations have any relationship to my observations about humans, since they deal with much more highly diverged organisms that have much more metabolic rate diversity than exists within the human species, but it would be really interesting if that were the case."

Overrepresentation of 5’-TCC-3’ → 5’-TTC-3’ within Europe
Overrepresentation of 5’-TCC-3’ → 5’-TTC-3’ within Europe. (A and B) The x coordinate of each point in gives the fold frequency difference (fPE(m) - fPAf(m)/fPAf(m)) [respectively (fPAS(m) - fPAf(m))/ fPAf(m))], and the y coordinate gives the Pearson’s χ2 P value of its significance. Outlier points are labeled with the ancestral state of the mutant nucleotide flanked by two neighboring bases, and the color of the point specifies the ancestral and derived alleles of the mutant site. (C and D) The χ2 contingency tables used to compute the respective P values in A and B. (E) The distribution of f(TCC) across bins of 1,000 consecutive population-private SNPs. Only chromosome-wide frequencies are shown for chromosome Y because of its low SNP count. Credit: Harris K (2015) Evidence for recent, population-specific evolution of the human mutation rate. Proc Natl Acad Sci USA 112:11 3439-3444.

Harris explains an idea from the scientific literature that the hypothesized hominoid evolutionary slowdown1 might be related to lengthening generation time. "It's important to know the rate per year at which mutations accumulate to use DNA to answer questions related to human history," Harris tells Phys.org. To estimate this rate, she explains, researchers usually compute the fraction of sites at which two DNA sequences differ and divide this by an estimate of how long ago the sequences shared a common ancestor. However, she points out that although this estimation procedure seems straightforward, mutation rate estimates tend to be lower when they're based on differences between parents and children than those between a human sequence and a chimp sequence. "One possible explanation for this is that the mutation rate was higher at the time closer to that when the human/chimp common ancestor lived."(This phenomenon is referred to as the hominoid slowdown because it postulates that the mutation rate slowed down as hominoids evolved into anatomically modern humans.)

"The reason this might be a consequence of lengthening generation time," she says, "is that mutations occur most often during cell divisions – and the older humans are when they reproduce, the more cell divisions occur along the lineage between when one human child is conceived and when his or her own child is eventually conceived ."

That said, Harris continues, the hominoid slowdown is just one hypothesis to explain the observed discrepancy between different human mutation rate estimates; another posits that DNA sequencing errors interfere with accurately estimating the small numbers of differences between parents and offspring. "Since DNA sequencing quality issues potentially make it so difficult to count mutations and estimate their absolute rates, I decided to try an indirect approach to shed light on whether the human mutation rate has recently changed, reasoning that if some populations had higher frequencies of specific mutation types than other populations, it probably indicated that the absolute rates of those mutation types had recently changed – a more parsimonious explanation than a zero-sum event where some mutation types increased in rate and other mutation types simultaneously decreased in rate. Using this approach, I was able to infer that the mutation rate has been evolving without relying on any possibly inaccurate numerical rate estimates."

Relatedly, Harris' approach presents a caveat to the standard molecular clock2 assumption – the idea that mutations accumulate over time at a constant rate, like clock ticks. "This supposition predicts that the number of differences between two DNA sequences is linearly proportional to the amount of time they have been diverging since their last common ancestor. The molecular clock assumption is usually assumed to be false when you're comparing really distantly related organisms like humans and flies, since DNA replication and error correction has had a lot of evolutionary time to change, but it's usually assumed to be true when comparing organisms as close together as humans and chimps. When you assume that the molecular clock assumption is true and that you know the mutation rate per year, you have a lot of power to use DNA sequences to infer historical dates. This is one reason that my finding of mutation rate change in Europeans is significant: To some extent, it contradicts an assumption that human geneticists usually take for granted – and that's important for applying genetics to anthropology."

There are also the apparent differences in the distribution of de novo mutations between human and chimpanzee male and female germ lines, as well as between different mutation types. Regarding the human/chimpanzee differences, Harris notes that this is an observation from the scientific literature. "A recent study at Oxford3 sequenced families of chimps and found that many more mutations were transmitted from fathers to children than from mothers to children. This makes sense given that sperm undergo many more cell divisions than do eggs, and thus accumulate mutations faster. This same trend is thought to hold in humans – but in humans, the difference between male and female mutation rates appears less extreme."

Variation of f(TCC) within and between populations
Variation of f(TCC) within and between populations. This plot shows the distribution of f(TCC) within each 1000 Genomes population (i.e., the proportion of all derived variants from PA, PE, and PAf present in a particular genome that are TCC→T mutations). There is a clear division between the low f(TCC) values of African and Asian genomes and the high f(TCC) values of European genomes. The slightly admixed African Americans and more strongly admixed Latin American populations have intermediate f(TCC) values reflecting partial European ancestry. Credit: Harris K (2015) Evidence for recent, population-specific evolution of the human mutation rate. Proc Natl Acad Sci USA 112:11 3439-3444.

Harris also refers to the Oxford study when discussing differences in the distribution of de novo mutations between different mutation types, pointing out that a high percentage of the mutations they found in the chimp family they sequenced were so-called CpG mutations – that is, a mutation in which a C nucleotide separated by a phosphate (p) from, and located next to, a G nucleotide, to a T nucleotide. "This mutation type has a different chemical mechanism than do most mutations where a C changes to a T," Harris explains. "In most organisms, C nucleotides located next to G nucleotides have higher than most sites in the genome, and this difference in mutability looks like it might be more extreme within chimp genomes than within human genomes. This is an example of a scenario where one mutation type – in this case, CG->TG – might have increased in rate along the chimp lineage relative to the rates of other mutation types."

Harris has several plans for her continued and future research, one being to analyze whether the mutagenic spectrum might have changed numerous times during great ape evolution and beforehand given that it was able to change during the last 60,000 years of human history. "This is a question I hope to address by applying the techniques I developed in this paper to new datasets. For example," she illustrates, "a large dataset of great ape genomes was published last year, and I'm looking forward to searching for differences between the mutation spectra of great ape species the same way I looked for differences between human populations for this paper. This should give us a better idea of whether the observed difference between Europeans and Africans/Asians was a real anomaly that had functional significance, or whether it was just one of many random mutation rate changes that are more frequent than we've assumed them to be." Harris also plans to investigate DNA from anatomically modern humans who died thousands of years ago, since an increasing number of these ancient DNA sequences are starting to be produced at high quality and released for public use.

Another goal in Harris' calendar is pinpointing finer-scale mutation rate changes and other avenues of research. "The statistical analysis techniques I used in this paper are really simple – I used the same chi-square test taught in high school biology class because the signal of TCC->TTC mutations being more frequent in Europeans than in other groups is so strong that more sophisticated techniques weren't needed to detect it. However, now that I know that the mutational process can differ between human populations, I'm going to develop more robust statistical tools that will be intended to have higher power to detect interpopulation differentiation signals that might be weaker than the dominant signal I studied in this paper, but still be real and thereby important." A key question she'd like to answer is how frequently and routinely mutational processes do change – and she sees detecting smaller differences between populations as important step toward achieving that.

In addition, Harris in interested in determining whether the TCC->TTC excess in Europeans is a trait with a simple genetic basis – that is, if it might be the result of a causal mutation in a single gene associated with DNA replication or repair. "Scientists have mapped the locations of a lot of that are associated with variation in traits like height or disease risk, and knowing the genetic basis of the variation in some trait can help you test whether or not that variation was likely driven by natural selection," Harris tells Phys.org. "Usually, we think about a person's DNA sequence encoding a trait that's external to the DNA – but my question is unusual in that I'm interested in a trait that is itself a feature of the DNA sequence." Harris acknowledges that this intertwining presents some technical challenges, but states that if she can develop new techniques for overcoming those challenges, those techniques could allow researchers to study variations in other traits that are endogenous, rather than exogenous, to DNA.

In closing, Harris notes that other areas of research might benefit from her study. "Cancer genetics is an area that I've recently started reading about because of the association of melanoma with the mutation type TCC->TTC that jumped out in the results of my study. Although I'm far from being an expert on cancer genetics at this point, I'm hopeful that that field could have something to gain from a better description of how mutational processes can vary in a benign way between human populations."


Explore further

Study finds increased DNA mutations in children of teenage fathers

More information: Evidence for recent, population-specific evolution of the human mutation rate, Proceedings of the National Academy of Sciences (2015) 112:11 3439-3444, doi:10.1073/pnas.1418652112

Related:

1Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid–cercopithecoid divergence, Proceedings of the National Academy of Sciences (2004) 101(49):17021–17026, 10.1073/pnas.0407270101

2The molecular clock runs more slowly in man than in apes and monkeys, Nature (1987) 326:93-96, doi:10.1038/326093a0

3Strong male bias drives germline mutation in chimpanzees. Science (2014) 344(6189):1272–1275, doi:10.1126/science.344.6189.1272

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Mar 28, 2015
""(Phys.org)—Although humans are a single species, not all genetic variation is shared between populations – and the ability to sequence our entire genome has allowed scientists to catalogue mutations that occur in one ethnic group alone.""

that sounds very much like the concept of race in humans, something that many scientist say does not exist.

if ethnic groups have different DNA then they are indeed a separate race.

Mar 28, 2015
""(Phys.org)—Although humans are a single species, not all genetic variation is shared between populations – and the ability to sequence our entire genome has allowed scientists to catalogue mutations that occur in one ethnic group alone.""

There's the problem...we ARE different species.

Mar 28, 2015
@zangetsu: Not really. Said mutations aren't fixed by population, and there's still more variation within continental populations than between them.

@joerocker: Nope. Humans are very homogenous by animal standards. There's more genetic variation in chimps than in humans worldwide. While the biological species concept (can produce fertile offspring = same species) is an oversimplification of how taxonomists actually distinguish species, all humans are very definitely the same species.

JVK
Mar 28, 2015
Excerpt: "These so-called population-private mutations..."

I am reminded of Dobzhansky (1973) "...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla" (p. 127). http://www.jstor..../4444260

Apparently, some theorists still haven't learned the difference between a mutation and an amino acid substitution. For example, nutrient-dependent RNA-directed DNA methylation leads to RNA-mediated amino acid substitutions that are fixed in the organized genomes of all genera via their physiology of reproduction.

Mutations perturb protein folding and are linked to pathology, which means they are not beneficial. UV light-induced amino acid substitutions in plants and animals may confuse some theorists who link excess exposure to mutations but do not link the sun's anti-entropic biological energy to ecological adaptations.

Mar 28, 2015
UV light-induced amino acid substitutions in plants and animals may confuse some theorists who link excess exposure to mutations but do not link the sun's anti-entropic biological energy to ecological adaptations.


What's the threshold at which UV-induced substitutions become UV-induced mutations?

JVK
Mar 29, 2015
Thanks for asking. No one seems to know. That's why others are trying to treat physiopathology after-the-fact.

Until theorists recognize the difference between amino acid substitutions, which stabilize the organized genomes of all genera, and mutations that perturb protein folding, millions more people will die -- at the same time serious scientists are Combating Evolution to Fight Disease http://www.scienc...8.short.

See also:
New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis http://www.scienc...14001869

System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes http://linkinghub...12015000

Feedback loops link odor and pheromone signaling with reproduction
http://www.scienc...05009815

http://rna-mediated.com/

Mar 29, 2015
No one seems to know


If it's impossible to tell, how can you distinguish them then? UV light breaks bonds. It can't discriminate beforehand between good and bad breaks. What's different at the molecular level between breaks you claim lead to substitutions and breaks you claim lead to mutations?

smd
Mar 29, 2015
Mutations perturb protein folding and are linked to pathology, which means they are not beneficial.

@JVK: Mutations themselves are neither good nor bad, but are the fundamental evolutionary mechanism by which speciation and adaptation occur, whether de novo or in response to environmental factors, respectively.

Moreover, I hope you realize that it appears to be a mutation in a ancestral single gene (i.e., that made an incomplete copy of itself) that gave rise to a unique human gene responsible for the rapid evolution of the H. sapiens neocortex (http://www.scienc...9/1465), which ironically has allowed you to make your (incorrectly one-sided) point.

You also mischaracterized the Combating Evolution to Fight Disease paper: it is a call to integrate molecular and evolutionary biology to better address disease, not a call to combat (as in try to halt) evolution as your phrasing implied. (Hmm...are you a Creationist in scientific language clothing?)

JVK
Mar 29, 2015
What's different...
Thanks for asking.

The balance of viral microRNAs to nutrient-dependent microRNAs is the determinant of controlled vs perturbed cell type differentiation in all cells of all individuals of all genera.

Cell type differentiation is biophysically constrained by the nutrient-dependent chemistry of RNA-mediated protein folding, which is perturbed by mutations. That's why uncontrolled mutations lead to pathology that is typically prevented by nutrient-dependent DNA repair. Fixed amino acid substitutions link the molecular mechanisms of repair to metabolic networks and genetic networks via everything currently known about nutrigenomics and pharmacogenomics.

2 minute video: https://www.youtu...G_9EEeeA
5.5 minute video: https://www.youtu...youtu.be

Anyone interested in preventing the suffering and deaths of others should see:
http://www.scienc...88.short

smd
Mar 29, 2015
UV light-induced amino acid substitutions in plants and animals may confuse some theorists who link excess exposure to mutations but do not link the sun's anti-entropic biological energy to ecological adaptations.

@JVK: Biological negentropy (as well as the emergence of life from non-living matter) is a response to energy, not a property of a given energy source itself. For example, there are cave-dwelling organisms that ingest rock formation-bound minerals and others that ingest the sulfur contained in ocean floor so-called smoking vents.

JVK
Mar 29, 2015
it appears to be a mutation in a ancestral single gene (i.e., that made an incomplete copy of itself) that gave rise to a unique human gene responsible for the rapid evolution of the H. sapiens neocortex


Caveat: It appears that way to a biologically uniformed science idiot who is participating anonymously in this discussion. Thank God, for intelligent serious scientists who refuse to accept ridiculous theories and, instead, provide experimental evidence of biologically-based cause and effect like this:

Convergent microRNA actions coordinate neocortical development
http://link.sprin...ml#Sec20

Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs http://nar.oxford...abstract

MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains
http://dx.doi.org....1002327

JVK
Mar 29, 2015
there are cave-dwelling organisms that...


...also exemplify eye regression, which appears to be antithetical to the ridiculous concepts linked to Mutation-driven evolution via the pseudoscientific nonsense attributed to people like Masatoshi Nei.

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements" (p. 199). http://www.amazon...99661731

For comparison, see: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

The nutrient-poor environment of the caves forces cave fish to focus their efforts on foraging and finding mates. Their eyes become unnecessary energy drains, and regress due to the entropic effects of viral microRNAs on cell type differentiation.

JVK
Mar 29, 2015
...negentropy (as well as the emergence of life from non-living matter) is a response to energy, not a property of a given energy source itself.


For an example of how much scientific progress has been prevented by that pseudoscientific nonsense see: Characterisation of two Neurogenin genes from the brook lamprey Lampetra planeri and their expression in the lamprey nervous system http://dx.doi.org...dy.24273

Ricardo Lara-Ramirez thinks publishing an article about the differentiation of two cell types in two different species is more important that publication of articles like this:

Role of olfaction in Octopus vulgaris reproduction http://www.scienc...14004006

Excerpt: "...we propose a model in which the olfactory organ and the olfactory lobe of O. vulgaris could represent the on–off switch between food intake and reproduction." Citations include (Kohl, 2013; Elekonich and Robinson 2000)

Mar 29, 2015
Their eyes become unnecessary energy drains


That was the assumption for a long time, but experimental evidence has disproved it.

http://icb.oxford...531.full

Therefore, cavefish eye degeneration does not appear to be an economic process: considerable metabolic energy must be expended by the continuous generation of new retinal cells that are eventually bound to die. These results appear to be inconsistent with any theory of cavefish eye regression that assigns a positive selective value to energy conservation.



JVK
Mar 29, 2015
the emergence of life from non-living matter


That was an assumption for a long time, and no experimental has disproved it. Indeed, many theories have been based on the assumption because "...the emergence of life from non-living matter..." is not something that can be disproved.

See: Was ribosome the first self-replicator? http://matpitka.b...tor.html

Excerpt: "Can one tell whether it was pro-cell or bio-molecules that emerged first? It seems that all these structures could have emerged simultaneously. What emerged was dark matter and its emergence involved the emergence of all the others. Hens and eggs emerged simultaneously."

My comment: I can't disprove the claim that "Hens and eggs emerged simultaneously."

That's the problem. No one can disprove pseudoscientific nonsense, so biologically uninformed science idiots are taught to accept it as if it were supported by experimental evidence of cause and effect.

smd
Mar 29, 2015
there are cave-dwelling organisms that...

...also exemplify eye regression, which appears to be antithetical to the ridiculous concepts linked to Mutation-driven evolution via the pseudoscientific nonsense attributed to people like Masatoshi Nei.

Incorrect (although it is no great challenge to find ideas that one can disagree with). Organisms with mutations that express as phenotypical characteristics that in turn provide an adaptive advantage - including energy efficiency - over time either replace those who do not or occupy a differential ecological niche.

smd
Mar 29, 2015
No one can disprove pseudoscientific nonsense, so biologically uninformed science idiots are taught to accept it as if it were supported by experimental evidence of cause and effect.

Your sleight-of-hand is showing. Generalizing from a single extreme case, or even multiple cases, to form a deductive conclusion is not science - it's belief-based and thereby more akin to religion. Speculation is just that - and anyone who claims that speculation is proven fact, as you seem to be doing regarding your position, is practicing pseudoscience as well.

Of course scientific "facts" change with greater knowledge, as should be clear to anyone who is familiar with and understands the history of science. However, you present an alternative view that is speculative in the same way as are those you denounce - the fundamental problem being that you position yours as correct and others' as idiotic. Again, this is indicative of belief-based, not scientific method-based, thinking.

JVK
Mar 29, 2015
The full text of this 2015 article is available for download:

Epigenetic regulation of mammalian sex determination Makoto Tachibana PDF http://medical.me...x_1.html

See also the molecular epigenetics section of our 1996 Hormones and Behavior review, which was extended by others to insects and the life history transitions of the honeybee model organism. http://www.hawaii...ion.html

Others have also addressed the fact that "Feedback loops link odor and pheromone signaling with reproduction" http://www.scienc...05009815

Unfortunately, no one can prove the chickens and eggs did not simultaneously emerge. On the other hand, only biologically uninformed science idiots believe that the molecular mechanisms of the biophysically constrained chemistry of nutrient-dependent protein folding vary across species.

JVK
Mar 29, 2015
Organisms with mutations that express as phenotypical characteristics that in turn provide an adaptive advantage - including energy efficiency - over time either replace those who do not or occupy a differential ecological niche.


No experimental evidence of biologically-based cause and effect supports that nonsense. It's the word-play of population geneticists, as is "population-private mutations."

See instead: Tracking niche variation over millennial timescales in sympatric killer whale lineages http://rspb.royal...81.short

Excerpt: "Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4]."

Also, "If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based" (p 1014). http://jp.physoc....007.full

smd
Mar 29, 2015
]"If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based"/q]

Again, misdirection: In , the focus is, broadly speaking, to correctly point out that anthropomorphisms such as "Attributes like 'selfish' and 'cooperative' have different meanings when applied to objects or ensembles at different levels....The concept of level in evolutionary theory requires careful analysis....Concepts and mechanisms do not necessarily carry through from one level to another – an important point to bear in mind also in multi-level physiology."

In short, he is calling for a more integrative, complex system approach to physiology and genetics than is often practiced. I, as any interdisciplinary systems thinker should, no argument there. What he is not doing is giving blanket support to your rather extreme position.

JVK
Mar 29, 2015
I thank smd and anonymous_9001 for once again showing to everyone that the biologically uninformed science idiots of the world will never become anything else.

No matter how much experimental evidence of biologically-based cause and effect links ecological variation to ecological adaptation in all genera via the conserved molecular mechanisms of the biophysically constrained RNA-mediated chemistry of protein folding, the pseudoscientific nonsense touted by theorists will prevail among those too ignorant to learn about anything else.

I've linked this discussion to a blog post at http://rna-mediat...heory-2/

I hope to encourage discussion among the biologically informed and eliminate the pseudoscientific nonsense, but participants here do not seem interested in intelligent discussion anywhere else.

Mar 29, 2015
JVK=James Vaughn Kohl...who spent 30 years researching pheromones. To date, scientists have collected evidence for possible pheromone effects but have not definitively identified a single human pheromone. He provides links to his own "sciencey" website full of reposts of his own debates, to which no one has ever replied. His supposed "award winning" article from 2007 on pheromones is being used by all manner of snake oil salesmen on the web, to sell fake human pheromone sprays to the desperate.

Continued....

Mar 29, 2015
Continued...SMD, you are correct in your assumption that he is a creationist in scientists clothing. Direct excerpts from his article: "Rarely do sex researchers address the ongoing philosophical debate between canonical neo-Darwinism and Biblical creation."; "Integration of Science and religion might be achieved by recognizing that the key components of this olfactory/pheromonal model appear to be as irreducibly complex as the basic tenets of evolution and the basic tenets of religion."; "From a religious perspective, these signaling mechanisms dictate that the creation of life, which begets life, also allows for the creation of diversified life through the same mechanisms."; "Since all life does not beget diversified life, those who judge sexual preferences that do not seem to result in diversified life may be judging creation itself."

And he has the gall to come here and call people idiots.

JVK
Mar 29, 2015
Thanks also to "Monkey Butt" for joining the other anonymous fools who, with no discussion of experimental evidence that links nutrient-dependent RNA-mediated biologically-based cause and effect from sexual orientation in yeasts to human sexual orientation, dismisses my review in its entirety--as is expected by all who are biologically uninformed science idiots.

http://phys.org/n...tml#nRlv How genes are permanently silenced by small RNAs

See also: Charge separation and charge delocalization identified in long-living states of photoexcited DNA http://www.pnas.o...abstract

See also: Can genetic information be controlled by light? http://phys.org/n...091.html

In my model, light-induced amino acid substitutions link RNA-mediated cell type differentiation of all cell types in all genera via anti-entropic effects linked to the physiology of reproduction and fixation of the substitutions.

JVK
Mar 29, 2015
Excerpt from this news article: "...there are many different ways that DNA can mutate (an A base can change to G, a C to A, and so on), and I reasoned that if some biochemical force had changed the mutation rate at some point during human history, it was likely to have affected certain mutation types more than others..."

"Life is physics and chemistry and communication" http://dx.doi.org...as.12570

If you start with a biochemical "force" without first linking it to the sun's biological energy, you set yourself up to fail. Typically, the failure involves de Vries definition of "mutation" and assumptions made by evolutionary theorists about how long it takes for accumulated mutations to cause a species to become another species.

Excerpt from this news article: ... DNA replication fidelity appears to differ between populations, [but] we're still a long way from knowing the mechanism behind this difference or whether it affects human health."

Who is WE?

smd
Mar 30, 2015
CORRECTION: The first line in my previous post should have read
Again, misdirection: In Combating Evolution to Fight Disease, the focus is, broadly speaking, to correctly point out that anthropomorphisms such as "Attributes like 'selfish' and 'cooperative' have different meanings when applied to objects or ensembles at different levels....


smd

smd
Mar 30, 2015
@Monkey_Butt,

Yes, JVK is quite a piece of work. In response to my post
...a mutation in a ancestral single gene (i.e., that made an incomplete copy of itself)...gave rise to a unique human gene responsible for the rapid evolution of the H. sapiens neocortex (http://www.scienc...465)....


@JVK wrote
Caveat: It appears that way to a biologically uniformed science idiot who is participating anonymously in this discussion....


However, he misleadingly omitted the link I provided to the peer-reviewed paper - but he apparently thought this was the way to publicly justify another juvenile ad hominem attack instead of addressing the paper on its merits. Moreover, this criticism (http://www.socioa...w/24367) of his paper that he cited above (at its original location of http://www.socioa...1_20553) is well worth reading.

Mar 30, 2015
@jk
well, if you say
Mutations perturb protein folding and are linked to pathology, which means they are not beneficial
but then you also say your own model causes mutations...
remember when I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
so LOGICALLY...NOW you are saying YOUR OWN MODEL causes perturbed protein folding that is linked to pathology and it is NOT beneficial... so why do you keep posting it?

TROLLING?
i will tell you why: it is PSEUDOSCIENCE

you don't even know WTF you are talking about... proven by ABOVE!

Mar 30, 2015
You also mischaracterized the Combating Evolution to Fight Disease paper: it is a call to integrate molecular and evolutionary biology to better address disease, not a call to combat (as in try to halt) evolution as your phrasing implied. (Hmm...are you a Creationist in scientific language clothing?)
@smd
he is not a SCIENTIST in creationist clothing, he is a CREATIONIST pretending to play scientist trying to support his religious ideas

Notice that he intentionally MISREPRESENTS almost everything he links too
He also has a 100% fail rate for "interpreting" studies and the science within them

when proven wrong, he then will lash out at the authors who refute him with various ad hominem attacks
Take Dr. Extavour, for example: he used to use her as "proof" that he was right, until i asked her to explain, using his own words verbatim
she said he was wrong, so now he will attack HER (and Lenski) every chance he gets

so much for his mensa claims, eh?

Mar 30, 2015
Moreover, this criticism (http://www.socioa...w/24367) of his paper that he cited above (at its original location of http://www.socioa...1_20553) is well worth reading.
@smd
your links are broken and only go to the title page and his original article link... not to the refute of his paper
it IS listed on the page you first linked, though
I thought i would share the link here: http://www.socioa...ew/24367

that is the link to the criticism of his paper

Thanks for continuing to present logical scientific arguments against the trolling of jk
he is not known for his acceptance of science, though
only for his creationist beliefs

Which he spreads around like herpes in a brothel

smd
Mar 30, 2015
@Captain Stumpy - thanks for catch the link issues...it's odd because I copied the URLs from the respective pages...

JVK
Mar 30, 2015
he is a CREATIONIST pretending to play scientist trying to support his religious ideas


EVOLUTIONISTS cannot support their ridiculous ideas. Dobzhansky (1973) wrote: the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla" (p. 127). http://www.jstor..../4444260

"...I am convinced that the sciences are being imprisoned by the outmoded ideology of materialism. I show how each of the 10 dogmas of materialism can be turned into a question, treated as a scientific hypothesis, and evaluated scientifically. None of these dogmas turns out to be valid or persuasive. In every case, new questions open up, along with new possibilities for scientific research." -- Rupert Sheldrake http://www.thebes...terview/

What does that suggest to intelligent people about use of definitions and assumptions?

JVK
Mar 30, 2015
2014 http://news.scien...te-brain
Excerpt: "the first neuroscientific support" for her snake-centric evolutionary theory."

See also:
2015 Cerebral hierarchies: predictive processing, precision and the pulvinar http://rstb.royal...169?etoc
'... if the brain transcribes causal structure from the world, then this (hierarchical) structure should be embodied in cortical architectures. Predictive coding provides a particular process theory for this transcription and calls for an understanding of microscopic (laminar-specific) message passing in canonical microcircuits—that is consistent with macroscopic cartography defined by extrinsic connections. The particular contribution of this paper is to highlight the context-sensitive and dynamic aspects of functional anatomy—distinguishing between the neuronal processing of (first-order) content and (second-order) context."

cont.

JVK
Mar 30, 2015
Compare what is currently known about snake-centric evolution of the human brain to what is known about nutrient-dependent pheromone-controlled cell type differentiation via the RNA-mediated chemistry of protein folding that links food odors and pheromones to reproduction in all vertebrates via conserved molecular mechanisms.

2005 Feedback loops link odor and pheromone signaling with reproduction http://www.scienc...05009815

2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353

See also:
2005 Dairy milk is singled out as the biggest dietary cause of osteoporosis http://www.news-m...120.aspx
"These microscopic organisms get fed calcium and phosphorus from the bloodstream and then secrete calcium phosphate to cause calcification."

2015 http://ethicalfoo...est.html

cont.

JVK
Mar 30, 2015
The title of this news article is: "Seeing the (UV) light: Previously undetected difference in human mutation rate..."

What level of intelligence can we assume that evolutionary theorists possess who use de Vries definition of "mutation" in the context of their ridiculous theories about snake-centric evolution of the human brain, while also attributing differences in mutation rates to UV light AND to dairy milk?

I assume that theorists are biologically uninformed science idiots who have failed to link the sun's biological energy to cell type differentiation associated with ecologically adapted changes in skin pigmentation and vitamin-D. Many different vitamins are essential to the stability of organized genomes in human populations, like vitamin D -- where malaria is endemic.

Is there one intelligent serious scientist who still reports that the hemoglobin S variant linked to sickle cell disease is a mutation? Or is it only evolutionary theorists who do that?

JVK
Mar 30, 2015
Robert Karl Stonjek (moderator of the Evolutionary Psychology Yahoo group) and Jay R. Feierman (moderator of the International Society for Human Ethology's yahoo group) have both posted links to this news release.

Both moderators banned me from participation in their groups. See why: Human pheromones: integrating neuroendocrinology and ethology (2001) -- an award-winning review http://www.nel.ed...iew.htm.

We linked nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation to hormone-organized and hormone-activated behaviors. In 2005 Elekonich and Roberts linked the model to the life history transitions of the honeybee model organism. http://www.ncbi.n...15925525

In 2014 the conserved molecular mechanisms of the biophysically constrained chemistry that links metabolic networks and genetic networks via protein folding was extended to human life history transitions: http://dx.doi.org...4-0895-5

JVK
Mar 30, 2015
Re:
...extended to human life history transitions:


Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults http://dx.doi.org...4-0895-5

Biologically uninformed science idiots must put this amino acid substitution and its affect on behavior into the context of their ridiculous theories. They can then attempt to make other science idiots continue to believe in the pseudoscientific nonsense of "Mutation-driven evolution." http://www.amazon...99661731

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements" (p. 199).

Alternatively, my "...model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."

Mar 30, 2015
@Captain Stumpy - thanks for catch the link issues...it's odd because I copied the URLs from the respective pages...
@smd
i found that it happens sometimes when quoting multiple links on PO...
Always glad to help when someone points out the stupidity of jk!

EVOLUTIONISTS cannot support
@jk
except that you are WRONG again, like usual
Evolution is based upon the scientific method

your creationist ideas are based upon a KNOWN FALLACY for starters (your historical comic)
secondly: it is NOT authored by who it says it is authored by
third: it does NOT represent reality (obvious from GEN to REV)

most importantly...
and i have pointed this out to you before time and again...
when you try to fit the data to the philosophy, that is called PSEUDOSCIENCE

there is NO science in the creationist movement
THAT is also well known... shall i link those references AGAIN?

you keep posting your pseudoscience
we will continue to point out your lies

Mar 30, 2015
Both moderators banned me from participation in their groups
you get BANNED because you cannot support your conclusions with SCIENCE
you are pushing a KNOWN PSEUDOSCIENCE and you can't admit that
wanna know why?
because your religious BELIEF will not allow you to SEE the SCIENCE
http://www.ploson...tion=PDF

This is OBVIOUS to EVERYONE who watches how you try to interpret the science and studies of others... ALWAYS with the light of creationist stupidity

that is NOT science following the evidence
that is religion trying to justify it's existence...
you are scrambling for anything that will justify your faith because the world is learning how stupid that lack of logic is
2013 Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
this is DEBUNKED here: http://www.socioa...ew/24367

JVK
Mar 30, 2015
Criticisms of the nutrient-dependent pheromone-controlled evolutionary model http://www.ncbi.n...4049134/

Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published.


Captain Stumpy
we will continue to point out your lies


No, you won't. You will only complain that you don't like my model, which clearly links RNA-mediated amino acid substitutions to cell type differentiation of all cells in all genera.

My conclusion was "...this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."

It can be compared to Nei's conclusions about constraint-breaking mutations and biodiversity. Quit complaining, start comparing.

Use facts! I did.

Mar 30, 2015
Use facts! I did
No, you are using your INTERPRETATION of facts to promote your RELIGION... and THAT IS A KNOWN FACT

your historical record for interpretation of studies is 100% FALSE
you also like to misrepresent, blatantly LIE and compare apples to frogs in the hopes that the distraction as well as confusion will somehow explain the stupidity of your religion

https://en.wikipe...Arkansas

i don't CARE about your model, so it is not a matter of like or dislike
it is a matter of being scientifically valid, and as this link points out: http://www.socioa...ew/24367
YOUR MODEL IS NOT SCIENTIFICALLY VALID

epic fail

you should have stayed in school and actually learned a little something instead of counting on your belief in creationist ideas to get you through the night
you can't even empirically prove pheromones, yet you are basing your entire model on them

EPIC FAIL

JVK
Mar 30, 2015
I got banned from the SICB FB group despite starting my 2013 review with mention of their annual meeting.

This report comes from their 2015 annual meeting: "... Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes." My comments: http://comments.s...6219.220

Excerpt: "...they've learned that the same set of microRNAs controls expression of the genes for rate-limiting enzymes that control the hormone production of different hormones in insects and crustaceans."

In my 2013 review, I wrote: "...the epigenetic 'tweaking' of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance..."

...BANNED because you cannot support your conclusions with SCIENCE


My RNA-mediated model supports their conclusions.

JVK
Mar 30, 2015
Re:
My RNA-mediated model supports their conclusions.


The model was extended across species by other serious scientists, after we first included a section on the molecular epigenetics of RNA-mediated cell type differentiation in our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

The fact that no intelligent serious scientist has offered a model for comparison and that only biologically uninformed science idiots (e.g., PZ Myers) have continued to denigrate my works, attests to the importance of understanding how physics and chemistry are linked from molecular biology to biophysically constrained biodiversity.

Simply put, serious scientists know that "Life is physics and chemistry and communication" http://dx.doi.org...as.12570 because that fact has been detailed in everything they have published during the past two decades.

JVK
Mar 30, 2015
Re:
... know that "Life is physics and chemistry and communication" http://dx.doi.org...as.12570 because that fact has been detailed in everything they have published during the past two decades.


Even Greg Bear, an English major and science fiction novelist understood the importance of molecular epigenetics. He incorporated our model and Luis Villarreal's model of virus-driven ecological adaptations in Darwin's Radio (1999) and Darwin's Children (2003). He exemplifies what can be done by anyone who is intelligent enough to examine and integrate what is known about biological facts.

See: https://www.youtu...NcMR_-RU When Genes Go Walkabout
and see: Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation http://youtu.be/DbH_Rj9U524

See also: http://www.gregbe...ture.cfm "Review in Nature" Excerpt: "...happenings at the periphery of Mendelian genetics, at the edge of neo-Darwinian theory.."

JVK
Mar 30, 2015
See also: Female Brain Maintained by Methylation http://www.the-sc...ylation/

Wrangling Retrotransposons http://www.the-sc...sposons/

The anti-entropic epigenetic effects of light-induced amino acid substitutions on cell type differentiation in plants and animals links viral microRNAs and nutrient-dependent microRNAs from respective roles in maintaining entropic elasticity to the nutrient-dependent pheromone-controlled biodiversity of species from microbes to man via the conserved molecular mechanisms of the biophysically constrained chemistry of RNA-mediated protein folding.

Vosshall's group has showed what happens when mutations perturb protein folding in female mosquitoes compared to what happens when de novo olfactory receptor gene creation occurs in the context of nutrient-dependent RNA-directed DNA methylation.

JVK
Mar 30, 2015
you are using your INTERPRETATION of facts to promote your RELIGION... and THAT IS A KNOWN FACT


Feedback loops link odor and pheromone signaling with reproduction http://www.scienc...05009815

That's a known fact. Everything ever expressed by your atheistic idol, PZ Myers, and other theorists is pseudoscientific nonsense.

One crank dies, another rises to take his place http://freethough...s-place/

Nutrient-dependent chromatin remodeling and RNA-mediated cell type differentiation link the pheromone-controlled biodiversity of all vertebrates via the conserved molecular mechanisms of their biophysically constrained chemistry of protein folding to chromosomal rearrangements.

Sex-biased chromatin and regulatory cross-talk between sex chromosomes, autosomes, and mitochondria http://www.bsd-jo...nt/5/1/2

smd
Mar 30, 2015
Both moderators banned me from participation in their groups
you get BANNED because you cannot support your conclusions with SCIENCE
you are pushing a KNOWN PSEUDOSCIENCE and you can't admit that
wanna know why?
because your religious BELIEF will not allow you to SEE the SCIENCE
http://www.ploson...tion=PDF

Don't forget the motivation of money: JVK sells so-called pheromone-based products at http://pheromones.com/ - and when clicking the "Science" menu link redirects to http://perfumingthemind.com/, where the religious visual and other implications are obvious.

JVK
Mar 30, 2015
Academics are supported by the evolution industry and "big bang" cosmology industry, which is why they have stayed decades behind serious scientists who are not as readily constrained by institutions and dogma.

Claims that money is the motivator almost always apply, but they do not explain why 1200 blog posts at http://perfumingthemind.com/ preceded 200 at http://rna-mediated.com/ and the fact that everything we reported in our 1996 review has now been integrated into the lastst report from Nugent et al on sex differences in cell type differentiation.

Obviously, I'm not paying them to report what I have detailed during the past two decades in the context of this article: http://www.the-sc...ylation/

The only explanation for why they are finally doing it is because they can no longer ignore the facts about RNA-mediated amino acid substitutions and cell type differentiation.

Mar 30, 2015
That's a known fact. Everything ever expressed by your atheistic idol, PZ Myers, and other theorists is pseudoscientific nonsense
spoken like a true creationist
ONLY a CREATIONIST who denies actual science could IGNORE all the empirical data given in support of a scientific theory and then be stupid enough to propose a FALLACIOUS model, WHICH ALSO REQUIRES SUPPORTS AND PROMOTES MUTATION DRIVEN EVOLUTION to replace mutation driven evolution

Are you stupid, mensa boy? we've already pointed out that your "model" causes and promotes MUTATIONS, and that is using YOUR OWN WORDS
VERBATIM

just because YOU don't understand it doesn't mean it is not understandable
see Lenski, Dr. Extavour and MORE for proof of that

here is a serious question: you once used Extavour to "support" your model, but once she DIRECTLY REFUTED your claims which i copied pasted to her, you started maligning her and her work...
WHY IS THAT?

your Dunning-Kruger, EGO or religion?

Mar 30, 2015
Don't forget the motivation of money: JVK sells so-called pheromone-based products at http://pheromones.com/ - and when clicking the "Science" menu link redirects to http://perfumingthemind.com/, where the religious visual and other implications are obvious.
@smd
thanks for pointing that out!

jk caught in a LIE AGAIN!

that is his primary motivator... money
but it walks hand in hand with his RELIGION
because his religious folk are STUPID and cannot comprehend the lies he talks or decipher the kohl-slaw word salads which usually say nothing

Glad he linked Myers site
it is the BEST descriptor of jk's stupidity yet!
http://freethough...s-place/


Mar 30, 2015
"Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published."

Thanks for this link SMD, I always like to start my day off with a laugh!

JVK
Mar 30, 2015
James Kohl presents an unsupported challenge to modern evolutionary theory ...


http://www.the-sc...ylation/

"...evolutionarily, this evolved a lot differently than we thought," said study author Margaret McCarthy, a professor of pharmacology at the University of Maryland School of Medicine."

"Using whole-genome RNA sequencing, the authors also showed global differences in not only RNA levels but in the expression of male and female-specific splice variants and differential promoter usage. These differences accounted for more variability between males and female mice compared to differences in gene expression, said McCarthy."

http://www.hawaii...ion.html
"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation..."

JVK
Mar 30, 2015
With participants like Captain Stumpy, Monkey Butt, and idols like PZ Myers and Andrew Jones (aka anonymous_9001) as your leaders/experts, how can you help but fail miserably in any attempts to learn anything about biologically-based cause and effect in any species.

Like all theorists, you are doomed to remain biologically uninformed science idiots.

Meanwhile, the death toll mounts as both suffering and death continue to be attributed to the pseudoscientific nonsense touted by those who cannot understand how cell type differentiation occurs and how it is perturbed by mutations linked to pathology.

Mar 30, 2015
With participants like Captain Stumpy, Monkey Butt, and idols like PZ Myers and Andrew Jones (aka anonymous_9001) as your leaders/experts, how can you help but fail miserably in any attempts to learn anything about biologically-based cause and effect in any species
@jk
hey.. lets actually look at some statistics side by side regarding that issue

actual science that is proven with studies and correctly linked with accurate representation of data within - IOW:
INTERPRETATION OF STUDIES
Capt/ANON/Myers (CAM et al) etc jk
100% accurate 100% WRONG

how about linked PSEUDOSCIENCE
CAM et al jk
0% pseudoscience 50% PSEUDOSCIENCE/50% misinterpretation of science

LIES
CAM et al jk
NONE REGULARLY

.
.
speaks VOLUMES about who the idiot is around here
that is YOU jk
diagnose anyone lately?


Mar 30, 2015
how it is perturbed by mutations linked to pathology
again? really?
lets go through this again for the IDIOT jk
remember when I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
so YOUR OWN MODEL CAUSES MUTATIONS

therefore, PER YOUR OWN WORDS, mensa boy, YOUR MODEL CANNOT BE ANYTHING BUT DANGEROUS AND WRONG

again, YOUR WORDS
YOUR FAILURE to comprehend the science
so, your own words are ironically ONLY applicable to YOU
you are doomed to remain biologically uninformed science idiots.

Meanwhile, the death toll mounts as both suffering and death continue to be attributed to the pseudoscientific nonsense touted by those who cannot understand

SCIENCE follows the evidence
YOU HAVE NONE
you still cannot provide empirical evidence of pheromones
EPIC FAIL

JVK
Mar 30, 2015
SCIENCE follows the evidence


http://www.the-sc...ylation/
"This is the first study to identify a molecular component of sexual differentiation that appears to be part of the causal change of testosterone masculinizing the male brain," Marc Breedlove who studies sexual differentiation of the developing brain at the Michigan State University told The Scientist in an e-mail. "The idea that testosterone might be acting by decreasing methylation, thereby releasing many genes from epigenetic repression, is an important contribution, and is likely to spur a lot of new research lines," wrote Breedlove, who was not involved in the research."

"...this evolved a lot differently than we thought," said study author Margaret McCarthy..."

http://dx.doi.org...ne.12072 "Less well known are the microRNAs and transposed and transposable elements."

JVK
Mar 30, 2015
Re: "Less well known are the microRNAs and transposed and transposable elements."

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281

"This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and..."

smd
Mar 30, 2015
@JVK, You first post cites http://www.the-sc...ylation/ and http://onlinelibr....f02t04. The first is your comment; the second discusses the known factor of epigenetics but makes no mention of pheromones. In your following post you cite your own paper http://figshare.c.../994281.

The unethical bit is that you again tried to misdirect readers into accepting a falsity - i.e.,that the first two necessarily imply the validity of the third.

The consensus (for example, http://www.ncbi.n...K200980/ and http://medicalxpr...ne.html) is that there is as yet no demonstrable factual evidence that human pheromones exist.

Cue @JVK's "idiot" chorus...

JVK
Mar 30, 2015
The consensus is based on definitions and ridiculous assumptions that humans should exhibit a stereotypical response, like insects. That is pseudoscientific nonsense.

If you don't want to learn how top-down cause is linked to nutrient-dependent RNA-directed DNA methylation and RNA mediated amino acid substitutions that differentiate cell types via the biophysically constrained chemistry of protein folding, feel free to continue supporting the evolution industry.

Signaling Crosstalk: Integrating Nutrient Availability and Sex http://www.ncbi.n...3932994/ "The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.

The molecular mechanisms that enable the coordinated response are conserved in all genera.

Feedback loops link odor and pheromone signaling with reproduction http://www.scienc...05009815

JVK
Mar 30, 2015
Regulation of gonadotropin-releasing hormone neurons by glucose http://www.ncbi.n...21855365

Metabolic control of GnRH pulsatility has been demonstrated primarily by measuring LH pulses as a surrogate for GnRH release [6]. These studies have found that food deprivation suppresses pulsatile LH secretion in rats [7–9], sheep [10,11], monkeys [12] and humans [13], consistent with inhibition of pulsatile GnRH release.


Identified GnRH neuron electrophysiology: A decade of study http://www.ncbi.n...2992586/
The gonadotropin-releasing hormone (GnRH) neuronal system is the final common pathway for central regulation of fertility.


"Indications that GnRH peptide plays an important role in the control of sexual behaviors suggest that pheromone effects on these behaviors might also involve GnRH neurons." p 683. http://www.scienc...05009815

????NO HUMAN PHEROMONES????

JVK
Mar 30, 2015
Human pheromones and nutrient chemicals: epigenetic effects on ecological, social, and neurogenic niches that affect behavior. http://f1000.com/.../1092668

http://f1000.com/.../1089879 ISHE Powerpoint

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Life is physics and chemistry and communication http://dx.doi.org...as.12570

If you missed that fact throughout a career in academia, would you admit it? No one else is going to tell the truth, until they can make it seem like that is what they have been claiming all along.

Epigenetic Contributions to Hormonally-Mediated Sexual Differentiation of the Brain
http://dx.doi.org...ne.12072
"...research is still in its early days and these studies reflect the promise of what is to come rather than comprising a genuine determination of how epigenetic changes impact or maintain sexual differentiation."

smd
Mar 30, 2015
Signaling Crosstalk: Integrating Nutrient Availability and Sex http://www.ncbi.n...3932994/

At first glance this seems better...except that:
(1) "Pheromones are thought to be detected predominantly by the accessory olfactory ("vomeronasal") system." The operational phrase is "thought to be" (i.e., "it's speculated that").
(2) "Female mice were exposed to α-farnesene, a pheromone in male mouse urine that induces estrus in group-housed females." Again, the links I posted illustrate the consensus that [i]human[/i] pheromones have not yet been identified. (In fact, the terms "human" or "H. sapiens" appear nowhere in the paper.) Also, whether you give the link to Cell or Science Direct, it's the same paper...but nice try.

However, if you has a link to a paper that explicitly identifies a human pheromone chemical that has been shown in an experimental setting to act as such by corroborating relevant neural activity, please present it. Really.

smd
Mar 30, 2015
Sorry for the "However, if you has a link..." typo. Obviously it should have been "However, if you have a link..."

SMD

Mar 30, 2015
However, if you have a link to a paper that explicitly identifies a human pheromone chemical that has been shown in an experimental setting to act as such by corroborating relevant neural activity, please present it. Really.
@smd
yeah... i've been waiting for that paper myself
he has linked his stinky love potion site numerous times after this request
he has said that the papers he links show definitive proof
he has made LOTS of claims that pheromones are real...

but nowhere else except within his pseudoscience clan and the creationists is there ANY other evidence of this
and it appears that NO ONE has been able to repeat his "experiments" successfully and without bias
i would say his "experiments" are designed to prove the point and are biased to begin with... there are NO double blind experiments that he's listed that show anything at all

and that is MY point to him... but he will ignore it and flood us with stinky-love potions for teens anyway

JVK
Mar 31, 2015
...explicitly identifies a human pheromone chemical that has been shown in an experimental setting to act as such by corroborating relevant neural activity...


Thanks for again demonstrating how deeply convicted you are to your ongoing belief about ridiculous theories.

Despite evidence from all animal species that the nutrient-dependent physiology of their reproduction is controlled by the metabolism of nutrients to pheromones, which link metabolic networks to genetic networks via everything known about nutrigenomics, pharmacogenomics, and personalized medicine, you want evidence that the conserved molecular mechanisms of biophysically constrained RNA-mediated protein folding extend to humans.

If I told anyone that there was more than one person who was that ignorant, they would not believe me. Now we have smd, monkey butt, captain stumpy, anonymous_9001 and several others.

https://www.youtu...G_9EEeeA

JVK
Mar 31, 2015
http://phys.org/n...rgy.html

Excerpt: "...up until now, it has been believed that real quanta, such as real photons of light, are the only carriers of information from the early Universe."

There is a clear link from the light-induced de novo creation of amino acids to their anti-entropic epigenetic effect on cell type differentiation in plants and animals. Cell type differentiation is controlled by the biophysically constrained chemistry of RNA-mediated amino acid substitutions and protein folding.

Inventing a theory of information transfer sans energy transfer is required now that serious scientists have focused on the fact that "Life is physics and chemistry and communication" http://dx.doi.org...as.12570

Pseudoscientists are forced to fight against the facts by inventing new theories that disassociate energy and information.

http://www.nature...-1.16535

JVK
Mar 31, 2015
What is Life?: The Intellectual Pertinence of Erwin Schrödinger http://www.amazon...07604664

with forward Roger Penrose who has co-authored with George F.R. Ellis and Stephen Hawking

Excerpt: "How often do we still hear that quantum effects can have little relevance in the study of biology, or even that we eat food in order to gain energy?"

Inventing a new theory of information transfer without energy transfer serves the "big bang" cosmology industry and evolution industry. But there will always be people like George F.R. Ellis to tell the theorists they must support their ridiculous claims with experimental evidence.

"...what potential observational or experimental evidence is there that would persuade you that the theory is wrong and lead you to abandoning it? If there is none, it is not a scientific theory."

http://www.nature...-1.16535

JVK
Mar 31, 2015
"...a very small number of individuals, say two or three in tens of thousands, turn up with small but 'jump-like' changes, the expression 'jump-like' not meaning that the change is so very considerable, but that there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries's mutation theory, figuratively, the quantum theory of biology. We shall see later that this is much more than figurative. The mutations are actually due to quantum jumps in the gene molecule"(p. 33-34) http://www.amazon...07604664

Theorists must now change the definition of mutation to break the link between energy and information.

Apr 02, 2015
Thanks for again demonstrating how deeply convicted you are to your ongoing belief about ridiculous theories
you mean like YOUR refusing to accept the definition of MUTATION, denigrating MUTATIONS and stating without ANY evidence (and directly CONTRADICTORY to AVAILABLE STUDIES and evidence) that ALL mutations are negative while at the SAME TIME PROMOTING MUTATIONS IN YOUR OWN MODEL????
the irony of your statement is completely off the charts!

I thought you were being satirical, but you honestly believe your own diatribe, which makes you a Pseudoscience idiot, not a comedienne

and i can prove it... because EVERYTHING you try to "interpret" in the studies you link are all INTERPRETED in the light of CREATIONIST dogma, which has been PROVEN to not have ANY scientific validity
https://en.wikipe...Arkansas
that is why you have a 100% FAIL rate interpreting evidence from studies when authors are queried

Apr 02, 2015
If I told anyone that there was more than one person who was that ignorant
@jk
ONLY a PSEUDOSCIENCE poster would argue that they are capable of understanding the SCIENCE and then post that anyone who argues against it WITH THE ACTUAL SCIENCE is ignorant or not able to comprehend science
LMFAO

you are that PSEUDOSCIENCE poster!

or did you forget about when i asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
so we can PROVE that you post PSEUDOSCIENCE simply by linking your own model
PLUS, you've given NO empirical irrefutable evidence supporting your pheromones position (sans double blind experimentation)

PROVING you a liar with ONE LINK:
http://www.socioa...ew/24367

Apr 02, 2015
@CaptianStumpy
You could added Kohl is a prolific spammer.

https://sciencex....K/?v=act

JVK
Apr 02, 2015
DNA can't explain all inherited biological traits, research shows
http://phys.org/n...its.html

Unraveling a mystery in the 'histone code' shows how gene activity is inherited
http://phys.org/n...tml#nRlv

Excerpt: They have discovered that a single amino acid difference in the structure of histone H3.3 enables it to serve as a kind of memory device for the cell, marking genes that need to remain active.

Apr 03, 2015
Imagine error correction alleviating all mutagenic changes.
In other words a mutation-free organism.
Will this organism undergo evolution?

If your answer is yes, then whatever your new placeholder for mutation is, that will become the fundamental driver of evolution.

What exists to replace the holiest of all to genetics - that of mutation?
Don't postulate nutrients and odor.

JVK
Apr 04, 2015
The balance of viral microRNAs and nutrient-dependent microRNAs is the placeholder.

Serious scientists have been approaching that obvious conclusion for more than 18 years. Once they learned about RNA-mediated cell type differentiation, it became clear that nutrient-dependent pre-mRNAs must be involved. Only biologically uninformed science idiots have continued to claim that mutations and natural selection lead to the evolution of biodiversity.

Elekonich and Robinson (2000) extended our model to insects and Elekonich and Roberts (2005) extended it to the life history transitions of the honeybee model organism.

Don't postulate nutrients and odor.
Why not? All intelligent researchers do it. See: Feedback loops link odor and pheromone signaling with reproduction http://www.scienc...05009815




Apr 04, 2015
Genomes change over subsequent generations. This is readily observable. miRNAs do not make changes to the genome, so that is not at all an explanation for what we observe.

JVK
Apr 04, 2015
miRNAs are currently the only explanation for what we observe

MicroRNAs silence the noisy genome
http://www.scienc...41.short

"Schmiedel et al. ascribed intrinsic noise reduction to enhanced transcription that presumably compensates for the mRNA degradation (which maintains a given expression level). Recent reports on the "circular" nature of gene expression—namely, that mRNA degradation feeds back to elevate transcription (8)—may thus provide an intriguing potential mechanism that explains the intrinsic noise reduction effect. And the story need not end with miRNAs. A most profound revolution in genomics is the realization that there are many additional types of RNA. For instance, "antisense" RNAs may also act in noise filtration, especially when coregulated with their corresponding sense transcript (9). Perhaps some long noncoding RNAs (10), too, contribute to fine tuning of gene expression programs."

http://rna-mediated.com/

Apr 04, 2015
DNA repair make changes to the genome. Even sequences having undergone successful repair changes the expression of the sequences. Where repair falls short mutations result.
Those are the claims. The research to prove these claims is unfinished.

JVK
Apr 04, 2015
The research to prove these claims is unfinished.


No, it's just unpublished. Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems http://figshare.c...s/994281

In my invited review of nutritional epigenetics, I cited: Fall, S., Mercier, A., Bertolla, F., Calteau, A., Gueguen, L., Perriere, G., . . . Simonet, P. (2007). Horizontal Gene Transfer Regulation in Bacteria as a "Spandrel" of DNA Repair Mechanisms. PLoS ONE, 2(10), e1055. doi: 10.1371/journal.pone.0001055

The review was invited after publication of Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...3960065/

That publication has been viewed ~15,000 times since January 2014. The invited review was returned because no one would review the submission.

Apr 04, 2015
Mutations are not only the result of unsuccessful repair changes, but can also be induced by systems like SOS.

miRNAs are currently the only explanation for what we observe


You're aware that miRNAs control post-transcriptional regulation and silencing, yes?

JVK
Apr 04, 2015
You're aware that miRNAs control post-transcriptional regulation and silencing, yes?


I'm aware that you know nothing about the biological basis of cell type differentiation because you were either taught to be a biologically uniformed science idiot by the folks at Carthage College, or became one on your own.

Actually, it is hard to imagine how anyone with a degree in biology could know nothing about cell type differentiation, so maybe Carthage College is not responsible. Maybe you are simply the most unintelligent student who has ever attended, and they felt they must grant your degree anyway, since you paid for it.

Apr 04, 2015
Deflection. Typical.

You're aware that miRNAs control post-transcriptional regulation and silencing, yes?

JVK
Apr 04, 2015
What are you claiming about the role of microRNAs in cell type differentiation?

Apr 05, 2015
I just told you. They modify mRNAs, leading to differential gene expression and modification of transcripts through processes like silencing, RNA interference, methylation, etc.

As an example, these processes are the reason only your pancreas produces insulin. The INS gene is controlled by a number of different factors, including methylation and translational repression via miRNA.

http://www.ncbi.n...24722187
http://www.nature...076.html

JVK
Apr 05, 2015
I just told you. They modify mRNAs, leading to differential gene expression and modification of transcripts...


What do you think I've claimed in a series of published reviews, beginning with a section on molecular epigenetics in 1996 and most recently in the 2013 review http://www.ncbi.n...24693353

You claimed that review was: "...an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research."

Now you claim that to be telling me about what I have detailed as if you "knew all along" that it was an accurate representation of biologically-based cause and effect.

This is the worst kind of nonsense that serious scientists are subjected to by the biologically uninformed science idiots like you. After the paradigm shift, the science idiots claim they knew everything all along.

http://www.scienc...41.short MicroRNAs silence the noisy genome

JVK
Apr 05, 2015
Re: http://www.scienc...41.short MicroRNAs silence the noisy genome

See: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

"...the epigenetic 'tweaking' of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution. The role of the microRNA/messenger RNA balance (Breen, Kemena, Vlasov, Notredame, & Kondrashov, 2012; Duvarci, Nader, & LeDoux, 2008; Griggs et al., 2013; Monahan & Lomvardas, 2012) in adaptive evolution will certainly be discussed in published works that will follow."

That fact has never been "...an unsupported challenge to modern evolutionary theory." My model destroys neo-Darwinian theory with examples of facts.

Apr 05, 2015


That fact has never been "...an unsupported challenge to modern evolutionary theory." My model destroys neo-Darwinian theory with examples of facts.


Repeating your delusional claims doesn't make them true.

JVK
Apr 05, 2015
Repeating your delusional claims doesn't make them true.


Agreed. Why didn't anyone check to see if this claim was true?

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements" (p. 199). http://www.amazon...99661731

If they had checked, it would be perfectly clear that my claims are true.
Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Even biologically uniformed science idiots would recognize the difference between a ridiculous theory and a model of biologically based cause and effect. If they did, I would not need to repeat my claims and conclude:

"...this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."

Apr 05, 2015
Why didn't anyone check to see if this claim was true?
because YOU are the one making the claim... the responsibility for providing justification or supporting evidence is YOURS, not ours

Another deflection and known fallacy of yours
that is why you choose to REPEAT everything... because you've learned, from religion, that substance is meaningless and that repetition is the fastest way to establish a perspective as being in line with a tenet or codified set of rules...

unfortunately for you, the Scientific Method requires EVIDENCE as well as validation (meaning OUTSIDE validation) of results

THAT is why people trained in the scientific method call you a PSEUDOSCIENCE poster and those who accept religion hang on your every word

NO PHEROMONE PROOF: http://rspb.royal...full.pdf

your model DEBUNKED: http://www.socioa...ew/24367

you're a failure, jk

Apr 05, 2015
I would not need to repeat my claims and conclude:
and again, let me reiterate the scientific method is NOT about repetition, but evidence

your Dunning-Kruger aside: you STILL haven't been able to demonstrate or VALIDATE... or find anyone else to validate, your claims... your model is DEBUNKED: http://www.socioa...ew/24367

your ASSumption of pheromones is NOT substantiated by scientific evidence: http://rspb.royal...full.pdf

but you want people to ASSume that you are correct ... based upon what?
your word?
you've lied about experience and so much more, but NOW you are being truthful?

respect and knowledge is EARNED, not given
you've EARNED NOTHING... nor have you given evidence

only FALSE CLAIMS

THAT is the biggest reason you are considered a PSEUDOSCIENCE poster

Apr 05, 2015
Here's what you need to understand- just because you say one valid thing doesn't mean everything you say is valid. Your 1996 paper was fine, but over the years, you began drawing conclusions so far removed from your citations that in some cases you began making claims that were completely contrary to what your citations said. Paabo et al. ring any bells? You claimed they showed a lack of fixation, but that's clearly untrue and anyone that can read the graphs in that paper could tell that you were full of it.

JVK
Apr 05, 2015
Here's what all serious scientists already understand.

Our 1996 Hormones and Behavior review linked all aspects of nutrient-dependent cell type differentiation to pheromone-controlled RNA-mediated events. Our accurate representation of biologically-based cause and effect was extended to insects in 2000; to the life history transitions of honeybees in 2005 and to humans in 2014. See: Clinically Actionable Genotypes Among 10,000 Patients With Preemptive Pharmacogenomic Testing http://www.medsca...24253661

The only researchers who remain unaware of how metabolic networks and genetic networks are linked via RNA-directed DNA methylation and RNA-mediated amino acid substitutions are those who were taught to believe in the pseudoscientific nonsense touted by evolutionary theorists. Unlike the biologically uninformed science idiots here, those researchers are not commenting on the data that proves their theories are based on assumptions and definitions.

JVK
Apr 05, 2015
Paabo et al. ring any bells?


Yes. He is the senior author of "Natural Selection on the Olfactory Receptor Gene Family in Humans and Chimpanzees" http://linkinghub...07620138

Even he knew -- more than a decade ago -- what we detailed in 1996. Mutations are not naturally selected.They perturb protein folding and cause pathophysiology. Natural selection on olfactory receptor genes links the nutrient-dependent pheromone-controlled physiology of reproduction in species from microbes to insects to humans.

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. http://www.ncbi.n...24693349
Conclusion:" Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans (Keller et al., 2007; Kohl, 2007; Villarreal, 2009; Vosshall, Wong, & Axel, 2000)."

...just because you say one valid thing...

Apr 05, 2015
The only researchers who remain unaware blah blah blah are those who were taught to believe in the pseudoscientific nonsense ....
i guess your Dunning Kruger missed the above post?
you are making unsubstantiated conjectures again without evidence!

ANON says it best...
Here's what you need to understand- just because you say one valid thing doesn't mean everything you say is valid. Your 1996 paper was fine, but over the years, you began drawing conclusions so far removed from your citations that in some cases you began making claims that were completely contrary to what your citations said. Paabo et al. ring any bells? You claimed they showed a lack of fixation, but that's clearly untrue and anyone that can read the graphs in that paper could tell that you were full of it.
a bad literacy day like most other interpretations you've made?

i will simplify it for you:
just because you published once doesn't mean you are infallible or even CORRECT!


JVK
Apr 05, 2015
Re:
...just because you say one valid thing...


I said " Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans..."

That is not "one valid thing." It is the only valid thing that has consistently been supported by two more decades of experimental evidence (since I published my book in 1995). The Scent of Eros: Mysteries of Odor in Human Sexuality http://www.amazon...9523383X

MicroRNA control of protein expression noise http://www.scienc...abstract

--attests to the other accurate representations of biologically-based cause and effect that I have made per Lewis Thomas (1980): "I should think we might fairly gauge the future of biological science, centuries ahead by estimating the time it will take to reach a complete comprehensive understanding of odor." http://www.nejm.o...73021307

Apr 05, 2015
Human pheromones and food odors
there is no definitive proof that human pheromones exist: http://rspb.royal...full.pdf

just like you have never provided a model to support your conclusions that evolution is somehow in doubt... for that, you would need evidence as well as validation of said evidence
and considering your model not only required mutations, but it also is debunked... ( http://www.socioa...ew/24367 )
that makes you posting known pseudoscience

the whole reason you post HERE is because it is not moderated for content and you can make all the spurious pseudoscience claims that you do while being protected

you don't have to produce evidence for your claims or validation
just like your arguments are based almost entirely of your interpretations (which are 100% wrong to date)

IOW- pseudoscience

Apr 05, 2015
Edit: Chelo et al. ring any bells? I'm sure you remember that paper. They tested and very clearly confirmed Haldane's assumptions and you directly contradicted their results and said they confirmed the complete opposite. They demonstrated fixation and you said they demonstrated a LACK of fixation.

JVK
Apr 05, 2015
Also co-authored by Paabo:
MicroRNA-Driven Developmental Remodeling in the Brain Distinguishes Humans from Other Primates http://dx.doi.org....1001214

Excerpt: "... tissue-specific changes in the expression of trans-regulators, such as miRNA, rather than sequence changes in cis-regulatory regions, are the driving force underlying developmental remodeling across hundreds of genes."

you began drawing conclusions so far removed from your citations that in some cases you began making claims that were completely contrary to what your citations said. Paabo et al. ring any bells?


Anything is better than drawing conclusions based on the pseudoscientific nonsense that biologically uninformed science idiots believe in.

I wrote: "Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'." http://www.ncbi.n...3960071/

JVK
Apr 05, 2015
Also co-authored by Paabo: "Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan"

Conclusion: "We hope that the differences in methylation discovered here will help to uncover the epigenetic basis for phenotypic differences between present-day and archaic humans and shed light on the role of epigenetics in the recent evolution of our lineage."

See my comments to Science: http://comments.s....1250368

Is there any intelligent Phys.org discussion participant that has not seen repeated examples from biologically uninformed science idiots that attest to their inability to grasp any aspect of biologically-based cause and effect?

If so, I could cite more literature that makes them look like the anonymous fools they are. If not, I encourage intelligent discussants to also begin "Combating Evolution to Fight Disease" http://www.scienc...88.short

Your loved ones will suffer if you don't.

JVK
Apr 05, 2015
Widest possible photosynthesis, absorbing any color of sunlight, from oranges through near-infrared http://www.scienc...1337.htm

"...scientists were surprised to discover a film of photosynthesizing microbes on the underside of the squirts as well. They turned out to be full of chlorophyll d, a rare variant of the chlorophyll molecule that absorbs near-infrared light."

"...evolution had managed to contrive a version that soaks up the last bit of sunlight, adapting the bacteria to life in perpetual shade. It is an astonishing feat, but one achieved by nature's traditional method of trial and error."

Here we have other biologically uninformed science idiots who want to place the light-induced de novo creation of amino acids and amino acid substitutions that differentiate all cell types in all genera into the context of natural selection and evolution by trial and error.

Who will die next due to their ignorance?

JVK
Apr 05, 2015
...clearly confirmed Haldane's assumptions...


"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... Assumptions, made but not verified, were taught as fact." http://www.huffin...211.html

Who is willing to join the troops that Andrew Jones apparently intends to lead? I think Captain Stumpy is currently an officer (the bomb blast that claimed his leg and brain left him still able to comment on phys.org and support Andrew Jones /aka anonymous_9001.)

Obviously, however, Jones seems to encourage those who are brain damaged to accept his ridiculous beliefs about fixed mutations and evolution -- because no one else will.

Apr 05, 2015
It seems you need a refresher. Reread Chelo's paper because you obviously don't understand the implication of his results.

http://www.nature...417.html

JVK
Apr 05, 2015
I understand the implications of your pseudoscientific nonsense. It led others to write:

Combating Evolution to Fight Disease http://www.scienc...88.short

I addressed your mention of Paabo, and you failed to acknowledge that he and I are claiming the same thing about natural selection for olfactory receptor genes.

If you were capable of understanding what's claimed about fixation in Chelo or by any other serious scientist, you would see that all of us are claiming the same thing and only biologically uninformed science idiots, like you, are saying Nuh-uh!

"If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based" (p 1014). http://jp.physoc....007.full

Apr 05, 2015
You've cited the Chelo paper many times in the context of statements like "Since we now know that mutations are never "fixed" ..." when, in fact, Chelo DID experimentally demonstrate fixation and how it complied with Haldane's hypotheses.

Paabo does not share your views at all. He studies mutation and natural selection, whereas you deny its contribution to evolution.

http://www.bbc.co...29649499
http://www.eva.mp...dex.html

A PhD thesis he advised- Mutation and selection as inferred by the comparison of the human and the chimpanzee genomes
http://humangenet...dex.html

JVK
Apr 05, 2015
You don't know the difference between a mutation and an amino acid substitution, which means you cannot know why mutations are not fixed in the organized genomes of any species.

Paabo knows that mutations lead to loss of function and that includes loss of olfactory receptor genes that are no longer required for species survival. Like eye regression in cave fish, mutations cause loss. They do not link the sensory environment to increasing organismal complexity because they perturb protein folding.

Mutation and selection as inferred...


That's because the mutations lead to loss of function. They are never fixed in organized genomes. RNA-directed DNA methylation and RNA-mediated amino acid substitutions differentiate all cell types in all genera. Mutations don't. Anyone who claims otherwise is a biologically uniformed science idiot. Stop the pseudoscientific nonsense about inferences. It's killing people.

JVK
Apr 05, 2015
Why do you think Kelly Harris said (in this article)

I'd love to be able to compare nutrient-deficient cell populations to control cell populations and test whether cells deprived of folate or other DNA synthesis cofactors experience different patterns of mutation than cells grown without nutrient deficiencies.


Why do you think the same science journalist wrote this:
In the complex, somewhat rarified world of interactions between various flavors of RNA, one elusive goal is to understand the precise regulatory relationships between competing endogenous RNA (ceRNA), microRNA (miRNA), small interfering RNA (siRNA) and messenger RNA (mRNA).

http://phys.org/n...tic.html

Kelly and Stuart are not biologically uniformed science idiots. Both probably understand that the regulatory relationships between competing endogenous RNAs are nutrient-dependent even if they don't know how they are controlled by feedback.

JVK
Apr 05, 2015
See also: "Nutrient-dependent microRNAs control cell types"
http://rna-mediat...l-types/

I included a link to Paabo's "The Human Condition—A Molecular Approach" (2014)
---------------------------
I am happy to see that Paabo's group finally discovered the works on the EDAR variant (a single amino acid substitution). I used the companion reports cited above as the link from nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in species from microbes to man in my 2013 review:

Excerpt: "Two additional recent reports link substitution of the amino acid alanine for the amino acid valine (Grossman et al., 2013) to nutrient-dependent pheromone-controlled adaptive evolution.
-----
Paabo wrote: "...one has to rely on comparing the numbers of substitutions likely to have functional consequences, for example by causing an amino acid substitution..."

Apr 05, 2015
You don't know the difference between a mutation and an amino acid substitution


I know you're making up a difference that nobody subscribes to but you.

mutations are not fixed in the organized genomes of any species


Directly contradicted by Chelo. You're blatantly and absolutely wrong. I've provided direct counterevidence, so I'm not going to address this again.

Why do you think Kelly Harris said...


What facets of Neo-Darwinism are those at odds with? Needing precursor molecules is not limited to your model.

JVK
Apr 06, 2015
...you're making up a difference that nobody subscribes to...


Biologically uninformed science idiots don't know that serious scientists have continued to echo everything we first detailed about RNA-directed DNA methylation and cell type differentiation in our 1996 review: http://www.hawaii...ion.html

See my comment on "Inching toward the 3D genome" http://comments.s....6217.10

Cell type differentiation is nutrient-dependent. RNA-directed DNA methylation links RNA-mediated amino acid substitutions to cell type differentiation via protein folding during life history transitions. Amino acid substitutions stabilize protein folding...


See also: Vast Complexity of Chromatin 3D Shapes http://jonlieffmd...d-shapes

Your ignorance of RNA-mediated amino acid substitutions and cell type differentiation is overwhelming.

JVK
Apr 06, 2015
What facets of Neo-Darwinism are those at odds with?


Your question was re-phrased: "Neo-Darwinism, the Modern Synthesis and selfish genes: are they of use in physiology?" http://jp.physoc....007.full

Serious scientists do not care about any "facets of Neo-Darwinism." What's been learned about epigenetic links between metabolic networks and genetic networks makes the pseudoscientific nonsense of the Modern Synthesis irrelevant.

That's why Denis Noble said: "If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based" (p 1014).

It's why Dobzhansky (1964) said: "...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." http://icb.oxford...citation

It's why I refer to you as a biologically uninformed science idiot.

Apr 06, 2015
As I've told you many times, Noble is not wholly rejecting mutation and selection, he's merely advocating for a more complete integration of it with physiological processes. If you actually read Noble's stuff, you'd know that. It's clear as day.

What's also clear as day is that you're still purposefully taking that Dobzhansky quote out of context.


Apr 06, 2015
Most amino acids have more than one code.
Q. Has any correlation been seen between how protein folds and what code is used for the same amino acid?

Just point me in the right research direction. Thanks

JVK
Apr 06, 2015
Noble is not wholly rejecting mutation and selection, he's merely advocating for a more complete integration of it with physiological processes.


He has not linked physics and chemistry to the conserved molecular mechanisms of RNA-mediated amino acid substitutions and cell type differentiation in all genera. I have!

...you're still purposefully taking that Dobzhansky quote out of context.


His work from 1973 was cited in "Combating Evolution to Fight Disease." See my comments published to Science http://comments.s....1247472

He is not advocating the pseudoscientific nonsense of your ridiculous approach based on your mutagenesis experiments. You are!

The difference is that Denis Noble and I are not biologically uninformed science idiots.

Apr 06, 2015
Most amino acids have more than one code.
Q. Has any correlation been seen between how protein folds and what code is used for the same amino acid?

Just point me in the right research direction. Thanks


Yep.

http://en.wikiped..._folding

JVK
Apr 06, 2015
Just point me in the right research direction.


That's what I've been doing for more than two decades.

What have you learned so far?

Who did you learn it from?

Have you cited my works?

See, for example, others who have: Role of olfaction in Octopus vulgaris reproduction http://www.scienc...14004006
"...we propose a model in which the olfactory organ and the olfactory lobe of O. vulgaris could represent the on–off switch between food intake and reproduction."

"...olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000)."

Elekonich and Robinson (2000) cited our 1996 Hormones and Behavior review before Elekonich and Roberts (2005) extended the model, without attribution to the honeybee model organism and life history transitions.

JVK
Apr 06, 2015
Kelly Harris: "... there are many different ways that DNA can mutate (an A base can change to G, a C to A, and so on), and I reasoned that if some biochemical force had changed the mutation rate at some point during human history, it was likely to have affected certain mutation types more than others"

Q. Has any correlation been seen between how protein folds and what code is used for the same amino acid?


Kelly Harris: "I'd love to be able to compare nutrient-deficient cell populations to control cell populations and test whether cells deprived of folate or other DNA synthesis cofactors experience different patterns of mutation than cells grown without nutrient deficiencies."

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Apr 09, 2015
a model. http://www.ncbi.n...24693353
this "model" is refuted with the following link:
http://www.socioa...ew/24367
there is also this cogent study: http://rspb.royal...full.pdf
Over the last 45 years, some scientists have claimed that a number of molecules are human pheromones but, as I explain in this review, these claims have little scientific validity
in order to prove yourself, you should back up and do what the study suggests
we will need a new approach, applying the rigorous techniques that have been effective in the discovery of pheromones in other mammals
until yu can provide validated evidence
then EVERY post you make WRT pheromones is nothing more than personal conjecture based upon self aggrandizement

you were NOT referenced in that study which shows that you do NOT have irrefutable evidence
only CLAIMS with little scientific validity

JVK
Apr 09, 2015
Role of olfaction in Octopus vulgaris reproduction http://www.scienc...14004006

I am referenced, and so is the work that extended our 1996 review to insects

"...olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000)."

Your claim that Andrew Jones refuted my model is ridiculous. All he did was tell others that he didn't like my model. That's the typical response from all pseudoscientists. That's why serious scientists are "Combating Evolution to Fight Disease" http://www.scienc...88.short

For the latest refutation of pseudoscientific nonsense, see what is known about nutrient-dependent pheromone-controlled biodiversity in Bacillus. http://phys.org/n...ria.html

Their ability to adapt is clearly linked to an amino acid substitution.

Apr 09, 2015
I am referenced
@jk
so has other pseudoscience
you were NOT referenced in the study i linked- my point is simple: you are making a CLAIM

the scientific community and especially Biologists etc, have NOT chosen to accept your information as definitive, clear, concise proof that pheromones exist
therefore, the study i linked stands as evidence that you are simply positing a suggestion based upon your faith in something, not empirical evidence
http://rspb.royal...full.pdf
In the absence
of sound reasons to test the molecules,positive results in studies need to be treated with scepticism as these are highly likely to be false positives. Common problems include small sample sizes, an overestimate of effect size (as no effect can be expected),positive publication bias and lack of replication
focus on that last sentence, jimmie
it defines you to a T from what you've presented to date

JVK
Apr 09, 2015
Others are making ridiculous claims outside the context of what is known to serious scientists, which is this:

Feedback loops link odor and pheromone signaling with reproduction http://www.scienc...05009815

See also: The Brain Is Broadly Wired for Reproduction http://www.hhmi.o...oduction

Olfactory System Detects Pheromones that Control Reproduction
http://www.hhmi.o...oduction

When experimental evidence from a Nobel Laureate and a Harvard geneticist/neuroscientsist fails to convince others that the same GnRH-modulated pathway links food odors and pheromones in all vertebrates to all invertebrates, one must ask "What would it take to convince a pseudoscientist like Trystam Wyatt or Richard Doty?"

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

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