Scientists create purple-winged butterflies in six generations

Aug 05, 2014 by Marcia Malory weblog
After six generations of artificial selection, Bicyclus anynana developed violet ground scales in its wings while the cover scales remained brown. Credit: Antónia Monteiro

(Phys.org) —Scientists have used selective breeding to create purple wings on the normally brown-winged butterfly Bicyclus anynana. Antonia Monteiro and her colleagues selected butterflies with wing scales that reflected light closest to the wavelengths that produce the color violet and bred them. After six generation of breeding, the researchers produced butterflies with wings that had changed structurally to reflect violet light. The research appears in the Proceedings of the National Academy of Sciences.

Living things can produce color chemically or structurally. Those that produce chemical color create pigments that absorb certain and reflect others. Organisms that produce structural color experience changes in their bodies, at the nanoscale level, that enhance the reflection of particular wavelengths.

Butterfly wings have structural color. To understand how this color evolves, Monteiro and her team selectively bred B. anynana, a butterfly that normally has brown wings, in an attempt to create purple wings. Two close relatives of this butterfly, B. sambulos and B. medontias, have purple scales on the backs of their front wings. However, until now, no one has ever reported seeing any purple-winged B. anynana.

To create purple wings, the team measured the wavelengths of light reflected from the wings of B. anynana specimens. They then selected and bred those butterflies whose wings reflected light closest to the violet spectrum. They performed this process six times in eight consecutive generations. As the breeding process continued, reflected wavelengths moved further toward the violet spectrum. By the sixth time, the butterflies had purple wings.

The butterfly Bicyclus anynana before artificial selection to alter wing color. Credit: William Piel.

The butterfly Bicyclus medontias displays violet-colored wing scales that evolved through natural selection. Credit: Antónia Monteiro

When the researchers examined the wings that had changed color, they discovered that the thickness of some of the scales had changed. This altered the wavelengths of light the wings reflected. They studied the wings of B. sambulos and B. medontias, which naturally have that reflect violet light, and found that some of their wing scales were similar in thickness to those that had changed in the purple-winged B. anynana. However, the types of scales that reflected violet light in B. sambulos and B. medontias were different from the type of scale that had changed in B. anynana.

Monteiro's team believe their experiment shows that butterfly wing colors can evolve very quickly and that natural selection could play an important role in the development of wing color. For example, butterflies could use wing color to identify other of the same species or to influence mate choice.

Bicyclus anynana before (left) and after (right) artificial selection efforts to produce butterflies with violet wing scales. After selective breeding, the butterflies displayed more violet color in the ground scales of their wings. Credit: Antónia Monteiro

The team says engineers could use these findings when designing devices that tune , trap light or steer light beams.

Explore further: Wing design proves a key factor in determining migration success of Monarch butterflies

More information: Artificial selection for structural color on butterfly wings and comparison with natural evolution, PNAS, Bethany R. Wasik, DOI: 10.1073/pnas.1402770111

Abstract
Brilliant animal colors often are produced from light interacting with intricate nano-morphologies present in biological materials such as butterfly wing scales. Surveys across widely divergent butterfly species have identified multiple mechanisms of structural color production; however, little is known about how these colors evolved. Here, we examine how closely related species and populations of Bicyclus butterflies have evolved violet structural color from brown-pigmented ancestors with UV structural color. We used artificial selection on a laboratory model butterfly, B. anynana, to evolve violet scales from UV brown scales and compared the mechanism of violet color production with that of two other Bicyclus species, Bicyclus sambulos and Bicyclus medontias, which have evolved violet/blue scales independently via natural selection. The UV reflectance peak of B. anynana brown scales shifted to violet over six generations of artificial selection (i.e., in less than 1 y) as the result of an increase in the thickness of the lower lamina in ground scales. Similar scale structures and the same mechanism for producing violet/blue structural colors were found in the other Bicyclus species. This work shows that populations harbor large amounts of standing genetic variation that can lead to rapid evolution of scales' structural color via slight modifications to the scales' physical dimensions.

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JVK
1.3 / 5 (16) Aug 06, 2014
"In Ostrinia moth species, substitution of a critical amino acid is sufficient to create a new pheromone blend (Lassance et al., 2013). In the 'peppered moth' example of rapid response to human-induced environmental changes, which were heretofore considered to be driven by selective predation, some evidence now suggests the migration pattern of 2 km per evening is consistent with the male moth's ability to detect the nutrient-dependent pheromones of the female from 2 km upwind (see for review Cook & Saccheri, 2013)." -- excerpt from http://www.ncbi.n...3960065/

"Monteiro's team believe their experiment shows that butterfly wing colors can evolve very quickly and that natural selection could play an important role in the development of wing color. For example, butterflies could use wing color to identify other butterflies of the same species or to influence mate choice."

The team must believe in the theory of evolution even though they report biological facts.
evolution3
5 / 5 (13) Aug 06, 2014
The team must believe in the theory of evolution even though they report biological facts.


even when evolution is punching you in the face you are ignoring it...
antialias_physorg
5 / 5 (13) Aug 06, 2014
The team must believe in the theory of evolution even though they report biological facts

Weird. Evolution is mutation an selection. And that's exactly what they did in this experiment.

So yeah: They're pretty spot on believing in evolution, don't you think?
animah
5 / 5 (10) Aug 06, 2014
The team must believe in the theory of evolution even though they report biological facts

Says JVK - James V Kohl, purveyor of sex paraphernalia, thus great peddler of Sin and the destruction of Christian morality.

In any case your product, "scent of Eros" is snake oil and cannot possibly work. As Rob van den Hurk (a pheromone specialist) noted, pheromones work "in concentrations of nanograms to picograms. When administered in higher concentrations, pheromones often result in no or a repulsive behavioral effect. "

This kind of concentration is not consistently achievable in a consumer product. A user is also likely to over-apply. So At best it has no effect, and there is a good chance it is actually repulsive to women.

So for you to pretend science supports your self-serving commercial aims is beyond the pale.
JVK
1.4 / 5 (11) Aug 06, 2014
See also: http://www.ncbi.n...=Kohl+jv
Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
Kohl JV.
Socioaffect Neurosci Psychol. 2012 Mar 15;2:17338. doi: 10.3402/snp.v2i0.17338. eCollection 2012.
PMID: 24693349 [PubMed] Free PMC Article
Related citations

Human pheromones: integrating neuroendocrinology and ethology.
Kohl JV, Atzmueller M, Fink B, Grammer K.
Neuro Endocrinol Lett. 2001 Oct;22(5):309-21. Review.
PMID: 11600881 [PubMed - indexed for MEDLINE]

From fertilization to adult sexual behavior.
Diamond M, Binstock T, Kohl JV.
Horm Behav. 1996 Dec;30(4):333-53.
PMID: 9047261 [PubMed - indexed for MEDLINE]

and the accurate representation of ecological speciation published as

Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans
http://www.cell.c...)00806-X

Any attempts to address the biological facts are welcome so that we can dispense with the nonsense.
JVK
1 / 5 (11) Aug 06, 2014
Butterflies do not use wing color to identify other butterflies of the same species although wing color may indirectly influence mate choice via hormone-organized and hormone-activated responses associated with olfactory/pheromonal input.

Behavior is nutrient-dependent and controlled by the nutrient-dependent production of species-specific pheromones, which control the physiology of reproduction in species from microbes to man via conserved molecular mechanisms.

See for example: Pheromones: a new term for a class of biologically active substances http://www.ncbi.n...13622694 and please attempt to deal with your Fear of Pheromones http://dx.doi.org...22850708 without denigrating my works or the works of others who have detailed biologically-based cause and effect.

Feedback loops link odor and pheromone signaling with reproduction
http://www.ncbi.n...16290036
JVK
1 / 5 (11) Aug 06, 2014
http://www.odedre...out.aspx

"Our principle aim in the lab is to attack scientific dogmas. Mainly, we aim to use powerful genetic tools to discover novel biological principles by which RNA affects formation and inheritance of complex traits."

The dogmas of evolutionary theorists are not scientific dogmas; they are pseudoscientific nonsense based on the bastardization of Darwin's ecological approach that put 'conditions of life' before natural selection and the evolution of biodiversity.

Although he was not aware of the conserved molecular mechanisms, unlike the population geneticists who tweaked his theory to fit their ridiculous explanations, Darwin must have somehow "just knew" that organisms must eat to reproduce, or realized that organisms that starved to death really were an evolutionary dead end. He did not offer any "Just-So" stories to support his theory and tried but failed to prevent others from doing so.
JVK
1 / 5 (10) Aug 06, 2014
Sex pheromone biosynthetic pathways are conserved between moths and the butterfly Bicyclus anynana http://dx.doi.org...omms4957

"Functional consequences of sequence variation in the pheromone biosynthetic gene pgFAR for Ostrinia moths" link the nutrient-dependent pheromone-controlled physiology of reproduction to ecological adaptations manifested in the morphological and behavioral characteristics of species from microbes and insects to elephants via conserved molecular mechanisms. http://www.pnas.o...abstract

That fact has been known to serious scientists since 1996. See: Insect pheromone in elephants http://www.ncbi.n...8602213. Facts about "...biological principles by which RNA affects formation and inheritance of complex traits" also were detailed in 1996 in our Hormones and Behavior review article. From Fertilization to Adult Sexual Behavior
http://www.ncbi.n.../9047261
supamark23
5 / 5 (13) Aug 06, 2014
@JVK - we get it, you don't believe in evolution... so quit spamming your pseudo science crap already.
JVK
1 / 5 (10) Aug 06, 2014
Thanks supamark23. Which of the cited articles are you claiming is "pseudo science crap."

"Feedback loops link odor and pheromone signaling with reproduction" was co-authored by a Nobel Laureate, and Gene Robinson's group has just confirmed the assertions the researchers made in another published work: Socially responsive effects of brain oxidative metabolism on aggression. http://www.pnas.o...abstract

It's reported here: http://www.scienc...249.htm, which means that you can also help others understand what you are calling "pseudo science crap" by commenting on their experimental evidence of biologically-based cause and effect that links microbes to insects and mammals, including human, via conserved molecular mechanisms.
RealScience
5 / 5 (13) Aug 06, 2014
@JVK -
Did you even read the article, or did you merely fail to understand it?

The article says nothing about the researchers changing the nutrients that they fed the butterflies, and since the scientists selectively bred the butterflies rather than letting the butterflies chose their own mates, pheromones are irrelevant, too.

So why did you bring up nutrients and pheromones?
Oh, that's right, you try to explain everything with nutrients and pheromones.

You really should open your mind to all of the other things that evolution uses.
This experiment is an example of selection from pre-existing genetic variety:
They then selected and bred those butterflies whose wings reflected light closest to the violet spectrum


Captain Stumpy
5 / 5 (11) Aug 06, 2014
Any attempts to address the biological facts are welcome so that we can dispense with the nonsense
@jk
If they are welcome, WHY DO YOU IGNORE THEM?
The team must believe in the theory of evolution even though they report biological facts
YOUR MODEL supports the THEORY OF EVOLUTION but you seem to think mutations are a bad thing... YOUR OWN MODEL SUPPORTS MUTATIONS and yet you always say there is NO PROOF for mutation driven evolution... so... YOU ALSO SUPPORT THE THEORY OF EVOLUTION
remember.. 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 try to pull your head out, mensa boy! WHICH IS IT?
is mutation BAD or GOOD? you SAY you are against it BUT YOU'VE PROVEN IT IS REAL AND BENEFICIAL...

HOW ABOUT THOSE BIOLOGICAL FACTS?
WHY DO YOU CONTINUALLY IGNORE THEM?
JVK
1 / 5 (10) Aug 06, 2014
The researchers demonstrated that variation in the organized genome led from existing nutrient-dependent amino acid substitutions to morphological changes manifested in color via the pheromone-controlled physiology of reproduction in 6 generations. They did not artificially inseminate the butterflies!.

Thus, they refuted evolutionary theory, which actually refutes itself each time morphological and behavioral differences (the response to pheromones) outpace what you and others typically believe is the result of mutation-initiated natural selection during millions of years.

What don't you understand about "...the first evidence of conservation and sharing of ancestral genetic modules for the production of FA-derived pheromones over a long evolutionary time-frame thereby reconciling mate communication in moths and butterflies."
http://dx.doi.org...omms4957 compared to the changes in 6 generations?

Gene duplication is nutrient-dependent and reproduction is pheromone-controlled.
JVK
1 / 5 (10) Aug 06, 2014
http://www.nature...20120410

"The study also shows that stickleback evolution is accelerated by the use of pre-existing genetic variation, instead of waiting for new, random mutations to arise, Wray explains."

The link from ecological variation in invertebrates (moths and butterflies) to ecological adaptations and biodiversity in the sticklebacks: 500 species of the Lake Victoria species diverged in the same lake in ~15,000 years ...

http://www.fishec...index_EN

...screams IDIOT MINION at those who think mutation-initiated natural selection led to the evolution of biodiversity in one species in ~15,000 years or color variation in a species of butterfly in 6 generations.

And the idiot minions reply is YES, I am one and always will be.
supamark23
5 / 5 (13) Aug 06, 2014
@JVK - stupid is as stupid does, or says... and you've said quite a lot of stupid here.
RealScience
5 / 5 (11) Aug 06, 2014
The researchers demonstrated that variation in the organized genome led from existing nutrient-dependent amino acid substitutions to morphological changes manifested in color via the pheromone-controlled physiology of reproduction in 6 generations.


Amino acid substitutions are caused by gene sequence alterations which are MUTATIONS as the term is generally used in biology and genetics, so your claim that this selection was for nutrient dependent amino acid substitutions ADMITS that mutations, as commonly defined, play a role in selectable features such as wing color.

Also, in http://phys.org/n...lts.html you denied that selection from existing variety happens, so you are disagreeing with yourself.

Checkmate again!
JVK
1 / 5 (10) Aug 06, 2014
...you denied that selection from existing variety happens


Context is important. Existing variety cannot select; it represents the history of nutrient-dependent pheromone-controlled ecological adaptations via the amino acid substitutions that differentiate the cell types of species from microbes to man.

Again, let me remind you that this is not a game. Evolutionary theorists are killing people with their pseudoscientific nonsense and ridiculous theories about mutations, which are now referred to as epimutations, since there is no experimental evidence of fixation of a mutation in the organized genome of any species.

Thus, no matter how you define "mutation" there is no such thing as mutation-initiated natural selection in the context of the evolution of diversity. That's why theorists cannot explain HOW biodiversity arose -- even though they know it did, and also know that it is nutrient-dependent. They're missing the control of reproduction by pheromones.
anonymous_9001
5 / 5 (13) Aug 06, 2014
Existing variety cannot select


With this, you've shown you don't understand the concept of selection at all. Selection acts on variety. Variety doesn't select. You word things so strangely sometimes and it makes me wonder if you use terms regardless of whether you understand them.
Captain Stumpy
5 / 5 (11) Aug 06, 2014
Thus, no matter how you define "mutation" there is no such thing as mutation-initiated natural selection in the context of the evolution of diversity
@jk
therefore, it is impossible for your own model to explain diversity as your own model utilizes mutation. so when you say
and also know that it is nutrient-dependent
you specifically are referring back to your own model, which you have also said CAUSES mutations!

you can't have it both ways...

and THIS is the reason you are classified as a PSEUDOSCIENCE TROLL and spammer
you THINK you know what you are talking about, but you are just throwing out a word salad, like Myers said: you obfuscate!

this is so that the overage person does not know you are an idiot!
give a person a little knowledge and you are completely transparent though.
You should have gone back to school, or at least purchased a dictionary, mensa boy
JVK
1 / 5 (10) Aug 07, 2014
Selection acts on variety.

That ridiculous idea can be compared to facts in the context of biophysical constraints on amino acid substitutions in a virus and the "ordered" existence of life.

http://www.pnas.o...abstract
"In conclusion, we have presented a minimally frustrated all-atom model to explore the extensive conformational rearrangement of influenza HA2. The interplay between the energetic stability of the S5I trimer and the entropic barrier toward S1F creates a quasi-stable kinetic intermediate..."

The stability of protein folding is enabled by nutrient-dependent amino acid substitutions at the atomic level in my model.

http://www.scienc...abstract
"The molecular basis of antigenic drift was determined for the hemagglutinin (HA) of human influenza A/H3N2 virus. From 1968 to 2003, antigenic change was caused mainly by single amino acid substitutions..."

How has variety selected atoms to evolve?
JVK
1 / 5 (9) Aug 07, 2014
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 socio-cognitive niche construction are manifested in increasing organismal complexity in species from microbes to man...
xstos
4.3 / 5 (6) Aug 07, 2014
By replying to JVK's nonsensical posts one simply validates his point of view. Debating with crazy people is futile. Just ignore him.
JVK
1 / 5 (9) Aug 07, 2014
...you are just throwing out a word salad, like Myers said: you obfuscate!


Anything not understood by Myers or his idiot minions can be labeled word salad.

What we see here is evidence that "Nothing in Biology Makes Any Sense Except in the Light of Evolution" http://www.jstor..../4444260

We also see that the basic principles of biology and levels of biological organization that link sensory input to cause and effect via conserved molecular mechanisms in species from microbes to man, make no sense to Myers or his idiot minions. There is not a serious scientist among them according to Dobzhansky (1964).

"...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!" http://icb.oxford...citation

The story about purple-winged butterflies is unworthy of scientists who understand molecular biology.
anonymous_9001
5 / 5 (10) Aug 07, 2014
How has variety selected atoms to evolve?


I point out that your first statement about variety selecting makes no sense and then you go ahead and essentially repeat it.
JVK
1 / 5 (9) Aug 07, 2014
Variety has not selected anything to evolve. Ecological variations (variety) enable the selection of nutrients by cells and the nutrients metabolize to species-specific pheromones that control the physiology of reproduction, which is responsible for ecological adaptations.

You have pointed out nothing about anything, and nothing you were taught to believe is true.

Why not just admit that you know nothing and avoid further embarrassment now that others know who you are: Andrew Jones?

Masquerading as the anonymous_fool here and in other discussions does no one any good. Anyone can read my published review and your ridiculous comments on it.

http://www.ncbi.n...3960065/ (My review)

http://www.ncbi.n...4959329/ (the anonymous fool's comments)
anonymous_9001
5 / 5 (8) Aug 07, 2014
Variety has not selected anything to evolve.


Duh! Variety doesn't do the selecting. Variety is what's acted upon by selection.

Anyone can read my published review and your ridiculous comments on it.


Don't mind the fact that my "ridiculous" comments were approved and published by the same editorial team that published your review.
supamark23
5 / 5 (11) Aug 07, 2014
@JVK - here's the problem, there's a veritable Mt. Everest of data and proof for mutation driven evolution, and less than a mole hill of evidence for your theory. Why might that be? Is it because you're simply wrong? That would be the logical, and sane, and objectively correct way to interpret it. You're like the Alex Jones of evolutionary biology, but without his winning personality... <- sarcasm, Alex Jones is a Grade A asshole and batcrap insane on top of it.
JVK
1 / 5 (9) Aug 07, 2014
proof for mutation driven evolution
There is none.

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. 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.... No, it wasn't dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact."
http://www.huffin...211.html
JVK
1 / 5 (8) Aug 07, 2014
Variety is what's acted upon by selection.


How? I've asked that question repeatedly and you will not answer. Neither does anyone else and most have given up. Even Carl Zimmer has noticed that fact.

"Scientists are exploring how organisms can evolve elaborate structures without Darwinian selection."

"Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed "the blind watchmaker." To some extent, it just happens."

Anyone who thinks selection acts on variety but who can not claim anything more than increasing organismal complexity "just happens,' exemplifies the fact that idiots were taught to believe in what teachers who were idiots believed and never questioned. Generations of idiots thought they knew something about biology, but never did.
JVK
1 / 5 (8) Aug 07, 2014
Zimmer: http://www.scient...plexity/

Robinson (with others): "Here we demonstrate that the relationship between brain metabolism and aggression is causal, conserved over evolutionary time, cell type-specific, and modulated by the social environment." http://www.pnas.o...abstract

Elekonich and Robinson (2000) linked our 1996 model of cell type differentiation (Diamond et al, 1996) to insects from microbes and to mammals via what was known about hormone-organized and hormone-activated insect and mammalian behaviors. Robinson's group has continued to help lead the way and help to link atoms to ecosystems by providing experimental evidence of nutrient-dependent pheromone-controlled biodiversity in insects.

My focus has been the similarities across species that eliminate mutations from any further consideration as should have been done in 1996 via information on alternative splicings.
supamark23
5 / 5 (10) Aug 07, 2014
@JVK - You've yet to show *any* proof of your theorum. Not a lick. I suspect you don't even really understand genetics and biochemistry. Neither does Suzan Mazur, by the way.

If mutations don't drive evolution and speciation, why don't we all share the same DNA? Even the genes themselves differ in sequence (both DNA and amino acid), how do you explain that through phermones and whatever else you made up? How do you explain differing numbers of chromosomes from species to species? You can't, and that's why we all laugh at your ignorance.
Captain Stumpy
5 / 5 (9) Aug 07, 2014
proof for mutation driven evolution
There is none.
except of course for Lenski and even your own model, mensa boy!
YOUR OWN MODEL is PROOF of MUTATION DRIVEN EVOLUTION
remember.. 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... supamark23 is ABSOLUTELY CORRECT... there is PLENTY of evidence... INCLUDING your own work!
Anything not understood by Myers or his idiot minions can be labeled word salad
only problem with this comment is that your "WORD SALAD" is confusing and obfuscating to EVEN ALL THE TRAINED BIOLOGISTS

and when you dissect it, it gets WORSE because you fail miserably regarding the use of words in the lexicon of your field, words like : MUTATION

Sorry... MYERS has it right, and you hate that he pegged you so succinctly, mensa boy

RealScience
5 / 5 (9) Aug 07, 2014
Variety is what's acted upon by selection.


How? I've asked that question repeatedly and you will not answer. Neither does anyone else and most have given up.


This has been answered many times, but you simply ignore answers that disagree with you.

In the context of this article, it was the researchers that selected for wing color, which is an example of selecting from variety. While researchers are not typical natural selection, natural selection can similarly act on variety to favor colors that better camouflage a butterfly, or make it look more like a toxic butterfly.

An example that has been pointed out to you repeatedly is people in malarial areas who have hemoglobin variants that confer malarial resistance being more likely to live long enough to breed. This is natural selection from among pre-existing gene variants.
mooster75
5 / 5 (8) Aug 07, 2014
By replying to JVK's nonsensical posts one simply validates his point of view. Debating with crazy people is futile. Just ignore him.

I can understand your view; these back and forth things get very tiresome when one of the participants is a dishonest raving lunatic, but on the other hand, allowing such people to spout their nonsense unchallenged on a science site doesn't sound like a good idea either.

And really, I don't think anything could validate his point of view...
JVK
1 / 5 (7) Aug 07, 2014
In our 1996 Hormones and Behavior review article "From Fertilization to Adult Sexual Behavior" we detailed the molecular epigenetics of cell type differentiation in species from yeasts to mammals. http://www.ncbi.n.../9047261

In 2000 Elekonich and Robinson extended our model of hormone-organized and hormone-activated behaivor, and Elekonich and Roberts (2005) extended the model to life history transitions in the honeybee model organism.

If the scientifically illiterate theorists denigrating my published works had ready any of them, they would already know the importance of Gene Robinson's group's latest publication, which links our model and his model organism via experimental evidence to nutrient-dependent pheromone-controlled ecological adaptation in all species without the pseudoscientific nonsense of mutation-initiated natural selection and inexplicable EVOLUTION of biodiversity.

http://www.pnas.o...abstract
JVK
1 / 5 (7) Aug 07, 2014
Molecular epigenetics http://www.ncbi.n.../9047261
Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes. (p. 337)

http://www.scienc...1249.htm "Their study, of fruit flies and honey bees, shows a direct, causal link between brain metabolism -- how the brain generates the energy it needs to function -- and aggression."

If you don't understand the direct link from nutrient-dependent morphology to pheromone-controlled behavior in insects, you can't understand it in humans. If you don't understand human behavior outside the context of evolution, you're not a serious scientist.
JVK
1 / 5 (7) Aug 07, 2014
...people in malarial areas who have hemoglobin variants that confer malarial resistance being more likely to live long enough to breed. This is natural selection from among pre-existing gene variants.


The hemoglobin S variant is nutrient-dependent and arose with vitamin D-dependent lactose persistence due to ingestion of fermented milk products and grains that allow the human gut microbiome to produce more vitamin D. There are more than 1180 hemoglobin variants that are also nutrient-dependent. The hemoglobin variant that differentiates our cell types from those of gorillas is not the result of any mutation. "...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." http://www.jstor..../4444260

All of the variants are due to amino acid substitutions. How can anyone here be so ignorant as those who comment based only on what they believe?
JVK
1 / 5 (7) Aug 07, 2014
While researchers are not typical natural selection, natural selection can similarly act on variety to favor colors that better camouflage a butterfly, or make it look more like a toxic butterfly.


Variation in an evolutionarily conserved sexual-differentiation gene, doublesex, has been found to explain how females of one species of butterfly mimic the colour patterns of several toxic species to avoid predation. http://dx.doi.org...ure13066

Mimicry is nutrient-dependent and pheromone-controlled via epigenetic effects on morphology and behavior. Anyone who wants natural selection to occur via another species (bird predation) or for visual cues (wing color/mimicry) is living in denial of the biological fact that "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)." http://www.ncbi.n...24693349
JVK
1.1 / 5 (8) Aug 07, 2014
Clarence 'Sonny' Williams is the most uninformed theorist I have encountered. He just posted this to another group where his nonsense is tolerated:

"Evolution of wing color in just 6 generations. You might think, "Wow," but you'd be wrong. This is an excellent example of "standing variation." Butterflies carry many "silent mutations" (a.k.a. "standing variation" or "hidden variation") which are not under strong negative (purifying) selection (for various reasons), and thus they remain in the population. When encountering the "right" environment, these silent mutations quickly increase in frequency or go to fixation. So, what looks like a case of saltation (sudden evolution) is not really that at all, but is rather good, old fashioned, Darwinian mutation."

There is no such thing as "Darwinian mutation." Darwin knew nothing about Mendel's work (i.e., nothing about genes).

Evolution evolves: physiology returns to centre stage http://jp.physoc....37.short
ViperSRT3g
5 / 5 (5) Aug 08, 2014
@JVK With your idea of nutrient driven evolution, how do you explain the yearly battle against viruses that cause the flu? They are clearly evolving at a brief enough timescale easily noticeable to humans. And yet they don't need pheromones nor nutrients to reproduce or evolve. They have no sex-specific characteristics! We technically don't even consider viruses to be living things, and yet here they are!

If that is the case, how do they select their mutations to change their own structure and become resistant to our vaccines from a year prior?

How do new strains of virus arise from the current variety?

Why do certain strains of virus become virtually eradicated even though they are still capable of evolving?
supamark23
5 / 5 (7) Aug 08, 2014
All of the variants are due to amino acid substitutions. How can anyone here be so ignorant as those who comment based only on what they believe?


How can someone, like you JVK, be so ignorant as to not understand that those amino acid substitions are due to mutations in the DNA, not phermones and nutrients. Seriously, do you even have a science degree (a bachelor's at minimum)? You sound about as scientifically literate as that crazy haired Ancient Aliens guy Giorgio A. Tsoukalos (whose degree is actually in sports information and communication). In fact, are you he? You make about as much sense...
JVK
1 / 5 (7) Aug 08, 2014
Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution http://www.scienc...abstract

Reported as: http://medicalxpr...ity.html

"...every two or three years the outer coat of seasonal flu (made up of amino acids) evolves...",

supamark23: "...those amino acid substitions are due to mutations..."

My comment to the Science site: http://comments.s....1244730

My comment to the anonymous fool "supamark23" The amino acid substitutions are glucose-dependent but not controlled by the metabolism to species-specific pheromones so far as is known, which may be the differentiating characteristic that defines living organisms from non-living viruses.

My response to ViperSRT3g: Thanks for asking. See also: "Glycolytic control of vacuolar-type ATPase activity: A mechanism to regulate influenza viral infection"
Whydening Gyre
4.2 / 5 (5) Aug 08, 2014
By replying to JVK's nonsensical posts one simply validates his point of view. Debating with crazy people is futile. Just ignore him.


It also raises his "search" standing...
supamark23
5 / 5 (6) Aug 08, 2014
Just repeating that the amino acid substitutions are glucose dependant does not make it true. Because it is not true. You really need to go back to school and take a genetics course before running your fool mouth again. Pay particular attention to translation, where the RNA transcript is translated into a protein. That transcript is based 100% on the DNA sequence it was transcribed (and in eukaryotes subsequently edited) from. In order to change the sequence, you have to change the DNA it was transcribed from.

Since the same translation process happens in both prokaryotes (no RNA editing, none) and eukaryotes, your whole stupid theory falls apart with even basic biological knowledge. In other words, how is mRNA in prokaryotes altered to change proteins without actually, you know, altering it? You have yet to provide a shred of proof for your theory, and frankly, if you were correct you'd have a Nobel prize instead of continual ridicule.
supamark23
5 / 5 (6) Aug 08, 2014
By replying to JVK's nonsensical posts one simply validates his point of view. Debating with crazy people is futile. Just ignore him.


It also raises his "search" standing...


Anyone who searches for his stuff and winds up here will see nothing but 1 star comments and ridicule from everyone. Not likely to help his cause...
JVK
1 / 5 (6) Aug 08, 2014
how is mRNA in prokaryotes altered to change proteins without actually, you know, altering it? You have yet to provide a shred of proof for your theory, and frankly, if you were correct you'd have a Nobel prize instead of continual ridicule.


Nutrient-dependent microRNAs alter the microRNA/messenger RNA balance, which is how experience-dependent de novo creation of olfactory receptor genes links the epigenetic landscape - via amino acid substitutions - to the physical landscape of DNA in the organized genomes of insects and mammals. However, the molecular mechanisms are conserved in species from microbes to man.

You have yet to provide a shred of proof for your theory


It's a model of biologically-based cause and effected supported by experimental evidence from every discipline that provides anything more than a theoretical approach.

http://www.cell.c...)00806-X

The Nobel Prize committee where to find me, my model, and the proof.
supamark23
5 / 5 (6) Aug 08, 2014
lol JVK, there is no evidence that supports your fantasy. Especially in prokaryotes. You don't even know how to use the language correctly - olfactory receptor genes that create themselves out of nothing? Really? That's like creationist bull, really stupid. where's the evidence? Where are the actual, brand new genes? If they can be created by scent (ignoring that not every organism has the ability to perceive scent molecules), you should be able to experimentally prove your thesis - where's your new genes? Where's your new proteins? Where's your proof? Until then, seriously, just shut the fuck up and stop spamming.
JVK
1 / 5 (6) Aug 08, 2014
Evidence is accumulating in prokaryotes, but they typically reproduce too rapidly to identify links between nutrient availability and the de novo creation of receptors that allow nutrients to enter the cell, which of course they must do. What the cells do not need to do is mutate into another species when their food supply is running out. There is no experimental evidence that suggests that is what happens in any species. For contrast, see:

http://www.jneuro...abstract

"In total, these results indicate that postnatal exposure to odorants can induce plasticity in OSN populations at the cellular level and that this plasticity is reversible and olfactory receptor–ligand specific."
anonymous_9001
5 / 5 (6) Aug 08, 2014
If the mere presence of a nutrient causally and reliably prompted the genetic changes necessary to take advantage of said nutrient, then more than 1/12 of Lenski's populations would have acquired the promoter shift mutation they observed.
JVK
1 / 5 (6) Aug 08, 2014
Whatever you think you about bilologcallu based case and effect is wrong. If you not going to look at the experimental evidence offerred by serious scinentists you shoud stick with the pseudoscientic nonsense you were taught to believe in,
Whydening Gyre
5 / 5 (6) Aug 08, 2014
Whatever you think you about bilologcallu based case and effect is wrong...

See what sniffin' pheromones will do to ya?
anonymous_9001
5 / 5 (5) Aug 09, 2014
Whatever you think you about bilologcallu based case and effect is wrong. If you not going to look at the experimental evidence offerred by serious scinentists you shoud stick with the pseudoscientic nonsense you were taught to believe in,


1/12 does not constitute cause and effect. This is simple logic. If the input doesn't result in the output 11/12 of the time, then how could it possibly be causally linked?
JVK
1 / 5 (5) Aug 09, 2014
http://www.scienc...2009.htm

"...backcrossed strains of laboratory mutant mice that had a specific mutation..."

"managed to reinstate traits typical of wild mice... including those pertaining to behavior, body structure, hormones, various biological processes and genetic functions."

They reversed what they thought was a fixed mutation by backcrossing for 10 generations, which means the mutation was not fixed. That means the diversity did not evolve via natural selection. It means a nutrient-dependent pheromone-controlled variant initially changed from the bottom up via nutritional epigenetics and the change was reversed from the top down via the pheromone-controlled physiology of reproduction.

Lenski's experiments show a few organisms have the ability to adapt. In organisms that reproduce rapidly, only a few are required for the nutrient-dependent change to be inherited by all the others, which explains why they didn't mutate into another species
JVK
1 / 5 (6) Aug 09, 2014
"...multi-generational selections in ecologically irrelevant contexts have generated mouse strains with anatomical, physiological and pathological characteristics that are best adapted to domestic environments" http://dx.doi.org...omms5569

As I recall, Neisseria spp exemplify the fact that no mutational mechanism biased toward amino acid substitutions (e.g., in mice) has been described. Since amino acid substitutions differentiate cell types and the substitutions are obviously nutrient-dependent and pheromone-controlled, it seems silly to keep looking for a mutational mechanism. Doesn't it?

It also seems silly to me that researchers are still reporting results in terms of mutation-initiated natural selection and the evolution of biodiversity because the conserved molecular mechanisms I have detailed across species have much more explanatory power. The pseudoscientific nonsense of ridiculous theories is no longer required.
JVK
1 / 5 (6) Aug 09, 2014
Does the fact there is no mutational mechanism that is biased towards amino acid substitutions, which differentiate the cell types of all individuals of all species, compare favorably -- in any model of biologically based cause and effect -- to theories about the mutation-driven evolution of biodiversity, which is obviously nutrient-dependent?

I think my examples of amino acid substitutions linked to species diversity should have been sufficient http://www.ncbi.n...3960065/

But the anonymous fool (Andrew Jones) thinks PZ Myers is teaching students to believe what is true.

Myers did not like the fact that nutrient-dependent chromosomal rearrangements in white-throated sparrows are the obvious cause of differences in morphological and behavioral phenotypes, so he made an excuse to ban me from further discussion on the same day I mentioned: http://www.pnas.o...abstract

But banning me from discussion doesn't change the facts
anonymous_9001
5 / 5 (8) Aug 09, 2014
They reversed what they thought was a fixed mutation by backcrossing for 10 generations, which means the mutation was not fixed.


The mutation was fixed in the lab mice, which is why they needed to undergo recombination with the wild mice.

That means the diversity did not evolve via natural selection.


Non sequitur

It means a nutrient-dependent pheromone-controlled variant initially changed from the bottom up via nutritional epigenetics and the change was reversed from the top down via the pheromone-controlled physiology of reproduction.


You have 2 fundamental misunderstandings here. The first is that nutrients caused the allele change. Since nutritional EPIgenetics does not have the capability of making deterministic DNA changes, that one's out the window. The second is that it was reversed by pheromones. This is also completely wrong because it wasn't reversed at all. All they did was introduce another wild type allele through breeding with a new population.
anonymous_9001
4.5 / 5 (8) Aug 09, 2014
Lenski's experiments show a few organisms have the ability to adapt. In organisms that reproduce rapidly, only a few are required for the nutrient-dependent change to be inherited by all the others


That whole 'causality' thing still escapes you, doesn't it. Do you have any evidence that the presence of citrate CAUSED the promoter translocation?

the fact there is no mutational mechanism that is biased towards amino acid substitutions


We can't read your mind, Kohl. What are you referring to here? What do you mean by mutational mechanism biased toward amino acid substitutions and how has Neisseria shown that?

I think my examples of amino acid substitutions linked to species diversity should have been sufficient


None of the citations in your paper concerning amino acid substitutions show any sign that they were nutrient-induced. You just tacked on that descriptor even though the sources did not indicate that it's factual.
antigoracle
1 / 5 (5) Aug 09, 2014
Hmmm... I wonder if their predators would develop a taste for this new item on the menu.
If not, it's going to be a very gay world, not that there's anything wrong with that.
https://www.youtu...VphK9AMk
JVK
1 / 5 (6) Aug 09, 2014
None of the citations in your paper concerning amino acid substitutions show any sign that they were nutrient-induced.


Thanks, that's like telling everyone that you know nothing about gene duplication, which explains why you cannot grasp the fact that Lenski's E.coli did not mutate, they ecologically adapted to ecological variation just like every other extant species has done. They did not mutate into another species, and no other species has ever done that. All have ecologically adapted or become extinct.

Try to read my mind, now. What do you think I am thinking about the presence of an anonymous fool (Andrew Jones) in any discussion of biologically-based cause and effect?

Does anyone else understand what it means when I say:
there is no mutational mechanism that is biased towards amino acid substitutions, which differentiate the cell types of all individuals of all species
anonymous_9001
5 / 5 (6) Aug 09, 2014
I repeat:

Do you have any evidence that the presence of citrate CAUSED the promoter translocation?


And there's still this word salad to sort through:

mutational mechanism that is biased towards amino acid substitutions


I can't find anything indicating what this is supposed to mean. A mechanism biased toward substitutions as opposed to what?

And you have yet to refute:

None of the citations in your paper concerning amino acid substitutions show any sign that they were nutrient-induced. You just tacked on that descriptor even though the sources did not indicate that it's factual.

Characterization of beta lactam resistance mutations:

http://www.scienc...11.short

A book concerning mechanisms and models involved in codon evolution:

books.google.com/books?isbn=019960116X

Another good book:

books.google.com/books?isbn=0199692599

anonymous_9001
5 / 5 (6) Aug 09, 2014
Fantastic review of biophysics literature and a biophysical model of protein evolution involving mutations (so yeah, in response to your favorite question to ask of all time, there IS a model for that):

http://www.readcu.../nrg1672

Book all about gene duplication:

books.google.com/books?isbn=1118148096

http://www.geneti...255.full

Tracking mutations and their adaptive effects in Pseudomonas:

http://www.pnas.o...39.short

Accounts
5 / 5 (4) Aug 10, 2014
This is so that the overage [sic] person does not know you are an idiot!

Uh, I kinda figured that out as soon as he revealed himself to be anti-evolution and thus denied - not theories - but facts right in front of his apparently impaired vision.

Anyone know a good ophthalmologist for him?
RealScience
5 / 5 (7) Aug 10, 2014
Does the fact there is no mutational mechanism that is biased towards amino acid substitutions...


JVK, you are showing your ignorance again.
Many mutations are biased towards amino acid substitutions. UV light, for example, so frequently causes thiamine for cytosine to be replaced by thymine that this is considered a signature of UV-induce damage. In over half of the 'C's in the 64 codons this causes an amino acid substitution. For example, if this occurs in the leading 'C' of CTT or CTC of a gene, it results in the amino acid phenylalanine substituting for leucine in the resulting protein.

Spontaneous depurination is another common type of mutation that is biased towards amino acid substitutions.

So what you state as a 'fact' is, in fact, NOT true.

You should at least learn the basics of the field that you claim to be an expert in.
RealScience
5 / 5 (8) Aug 10, 2014
The Nobel Prize committee where to find me, my model, and the proof.


ROFLMAO.

You are a good example of Einstein's dictum on ego:
"Ego=1/Knowledge", or The more the knowledge the lesser the ego, the lesser the knowledge the more the ego.
JVK
1 / 5 (5) Aug 10, 2014
I wrote: "no mutational mechanism that is biased toward amino acid substitutions has been described" and provided the citation.

The most ignorant of all possible responses to that clear statement is
Many mutations are biased towards amino acid substitutions.


No mutational mechanism has be described. Stating that mutations are biased towards amino acid substitutions is an admission akin to these statements:

1) Who cares about evidence of molecular mechanisms?
2) I have a theory!
3) All you have is a model of biologically-based cause and effect via conserved molecular mechanisms in species from microbes to man.

Besides, light-induced amino acid substitutions have already been detailed in the context of quantum physics that is clearly linked to biophysical constraints in the context of how ecological variations lead to ecological adaptations.

http://www.pnas.o...abstract "This strong connection between structural biology and physics..."
JVK
1 / 5 (6) Aug 10, 2014
You are a good example of Einstein's dictum on ego:


Thanks for mentioning him. I guess I forgot to mention the connection before that links quantum physics to quantum biology and quantum consciousness via amino acid substitutions that differentiate all cell types in all individuals of all species.

Or maybe, I mentioned it and your response was "Nuh-uh." I hope that intelligent discussion may someday occur here, but it can't when the same people keep coming back with claims that mutations do something they cannot do, without mention of HOW mutations could cause increasing organismal complexity.
RealScience
5 / 5 (6) Aug 10, 2014
I wrote: "no mutational mechanism that is biased toward amino acid substitutions has been described" and provided the citation.

The most ignorant of all possible responses to that clear statement is
Many mutations are biased towards amino acid substitutions.


No mutational mechanism has be described.


Again you ignore evidence that you are wrong.
I clearly described a mutational mechanism (ultraviolet light) that is biased toward creating amino acid substitutions:
Many mutations are biased towards amino acid substitutions. UV light, for example, so frequently causes thiamine for cytosine to be replaced by thymine that this is considered a signature of UV-induce damage. In over half of the 'C's in the 64 codons this causes an amino acid substitution.


So your statement that no mechanism has been described is full of bull.
Did you fail to read the description, or fail to understand it?
JVK
1 / 5 (5) Aug 11, 2014
'RealScience' is horribly confused about what is required to describe a mutational mechanism compared to what's required to point to a mutation and claim that the mechanism that causes the thiamine replacement associated with the mutation has been described.

Although the mechanism might someday be described in the context of quantum physics, which could link the mechanism to quantum biology and to quantum consciousness, such descriptions are not likely to come from those who say: "Look at this proof of cause and effect."

Descriptions of the molecular mechanisms of cause and effect will come from serious scientists, not anonymous fools and idiot minions of biology teachers who have been taught to believe in theories about cause and effect, and to ignore experimental evidence that ecological adaptations are nutrient-dependent and pheromone-controlled via amino acid substitutions that differentiate cell types.
anonymous_9001
5 / 5 (8) Aug 11, 2014
http://symposium.....extract

http://scholar.go...t=0%2C14

Kohl is even more horribly confused than he claims RealScience is because he's unaware that thousands of studies over the years have focused on mutation assays that isolate the molecular machinery to see how and how often they mess up and produce all the different kinds of mutations.

JVK
1 / 5 (6) Aug 11, 2014
What's interesting is that these anonymous fools and idiot minions continue to attest to what mutations do at the same time serious scientists are trying to put mutations into the context of epigenetically-effected amino acid substitutions that differentiate all cell types of all individuals in all species via conserved molecular mechanisms.

Its' as if they do not realize that changing the term from mutations to epimutations will only attest to the fact that nutrient-dependent pheromone-controlled ecological adaptations are not manifestations of mutations and natural selection in the context of evolved biodiversity.

The morphological and behavioral differences are manifestations of transgenerational epigenetic inheritance via conserved molecular mechanisms. The transgenerational epigenetic inheritance explains why there is no biologically-based experimental evidence of one species mutating into another. (No molecular mechanism has been described that would allow that possibility.)
supamark23
5 / 5 (8) Aug 11, 2014
No fools here but you JVK, and insulting others instead of providing evidence of your fantastic claims just cements that label - you are nothing but a wing nut with a poor understanding of genetics and general biology.
JVK
1 / 5 (7) Aug 11, 2014
Re: β-thalassemia mutations

http://www.the-sc...er-Gene/

1180+ hemoglobin variants attest to nutrient-dependent pheromone-controlled ecological adaptations. None of them appears to be the result of a mutation that leads to an amino acid substitution that differentiates the cell types that enable information about the microRNA/messenger RNA balance to be transmitted to every cell in every organism with a circulatory system.

However, if the experimental evidence of biologically-based cause and effect seems insufficient to anyone who thinks they know something more than serious scientists know about how ecological variation leads to ecological adaptations via conserved molecular mechanisms in species from microbes to man, they can comment on my review article as did Andrew Jones in: http://www.ncbi.n...4959329/

Please help establish cause and effect by showing that you know nothing about it.
Captain Stumpy
5 / 5 (8) Aug 11, 2014
What's interesting is that these anonymous fools and idiot minions continue to attest to what mutations do
what is even MORE interesting is that a FAILED college student not capable of even passing the BASICS on biology became a lab tech, LIED about being a diagnostician and his experience therein (which is being passed on to the BOARD, just FYI) now comes to a pop-sci site to call others idiots!
So... if we are educated and actually UNDERSTAND what is going on, we are idiot minions, but we can ONLY be smart if we agree with a moron that can't even comprehend the definition of the word mutation!
WOW

At least Anon, RealSci and others are presenting evidence that supports their conclusions... YOU keep linking evidence that UNDERMINES your own claims!
in more than this thread to boot!

Sorry minion mensa boy, per Anon's link
you are an EPIC FAILURE
http://scholar.go...t=0%2C14

(I love that link LMFAO)
JVK
1 / 5 (8) Aug 11, 2014
"The hemoglobinopathies, or Hb variants, are attributable to amino acid substitution(s) in either globin chain. Currently, 1,179 total hemoglobin variants have been characterized.2"

http://www.mlo-on...tems.php

"Countries with the highest incidence of diabetes also tend to have high incidence of Hb variants in the population.14"

Correlations are not proof of causation, but the correlations between amino acid substitutions that differentiate the cell types of all cells in all individuals of different species suggests that the amino acid substitutions that differentiate cell types with hemoglobin variants and those that somehow contribute to diabetes are nutrient-dependent.

However, the amino acid substitutions are not likely to become fixed in the absence of their effect on DNA stability in the organized genomes of species with circulatory systems that also produce pheromones.
JVK
1 / 5 (7) Aug 11, 2014
Not only in DNA's hands: Epigenetics has large say in blood formation
http://medicalxpr...ion.html

The role of mutations is clarified for those who are anonymous fools and idiot minions of biology teachers like PZ Myers.

http://www.scienc...abstract

Excerpt: Chromatin regulation has a central role in hematopoiesis: mutations or loss of chromatin factors lead to hematopoiesis defects and diseases (10).

See also: http://www.hawaii...ion.html

"The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the..."
RealScience
5 / 5 (7) Aug 12, 2014
'RealScience' is horribly confused about what is required to describe a mutational mechanism compared to what's required to point to a mutation and claim that the mechanism that causes the thiamine replacement associated with the mutation has been described.


Gosh, JVK, since you claim to be an expert I figured for sure you'd know something so basic as a common mutation from UV light.

But since you obviously don't, here is a link: http://www.nature...tion-441

Among other things it describes UV damaging cytosine bases and causing the bases to be replaced by thymine, and refers to this as a "UV-inducedC-to-T fingerprint-type mutation in genes".

And more than half of C-to-T changes in gene codons substitute one amino acid for another.

Note that the link is from Nature Education's BASIC primer on mutations, a link that I have posted for you before. You really should learn the basics of a field before you claim to be an expert.
JVK
1 / 5 (7) Aug 12, 2014
more than half of C-to-T changes in gene codons substitute one amino acid for another.


What are you claiming is the difference between a light-induced base pair change and amino acid substitution compared to a UV damaged base pair change and a mutation that leads to an amino acid substitution?

You seem to be saying that amino acid substitutions are mutations, which is ridiculous, but also typical of anonymous fools and idiot minions of biology teachers like PZ Myers.

Thanks for the link, which states "A change in a single amino acid in one of the hemoglobin proteins is responsible for causing the abnormal sickle shape of this red blood cell."

In my model the change is nutrient-dependent and pheromone-controlled like all other human hemoglobin variants (~1180 of them).

How many of them were you taught to believe are mutations? Did you ask why the variations occur in the context of vitamin D production or just assume they were random mutations (~1180) caused by UV light?
RealScience
5 / 5 (7) Aug 13, 2014
What are you claiming is the difference between a light-induced base pair change and amino acid substitution compared to a UV damaged base pair change and a mutation that leads to an amino acid substitution?


@JVK - do you still not understand that a light-induced base pair change IS A MUTATION as the term 'mutation' is most commonly used in genetics and in biology in general?
(You've been provided links to standard definitions of 'mutation' before, so by now you should understand how the term is used.)

You seem to be saying that amino acid substitutions are mutations

No, 'amino acid substitutions' are NOT mutations. Base pair changes are changes in DNA sequence and hence ARE mutations as the term is commonly used in genetics and biology.

SOME base pair changes CAUSE amino acid substitutions (more than half in the case of C-to-T mutations in genes).

Do you even understand how base pair changes in genes can cause amino acid substitutions?
JVK
1 / 5 (7) Aug 13, 2014
Do you even understand how base pair changes in genes can cause amino acid substitutions?


Yes, thanks for asking, but only from the perspective of biophysical constraints that prevent mutation-driven evolution. Nutrient-dependent base pair changes link ecological variation to amino acid substitutions and cell type differentiation that is perturbed by mutations.

Do you understand how mutations cause changes in base pairs that lead to amino acid-dependent protein folding and stability of DNA in organized genomes? If so, you should explain it to people like me who have found no biologically-based experimental evidence that suggests mutated base pairs lead to anything but pathology via perturbed protein folding.

Do you understand how the pseudoscientific nonsense of definitions used by population geneticists to invent neo-Darwinism prevent you from understanding how ecological variation leads to ecological adaptations?
JVK
1 / 5 (7) Aug 13, 2014
Base pair changes are changes in DNA sequence and hence ARE mutations as the term is commonly used in genetics and biology.


Nutrient-dependent base pair changes lead to amino acid substitutions that stabilize DNA in organized genomes.

Mutations cause base pair changes that perturb the beneficial changes in protein folding enabled by nutrients. That's why perturbed protein folding does not lead to amino acid substitutions that stabilize DNA.

Population geneticists could not explain how mutation-initiated natural selection led to the evolution of biodiversity, so they decided to tout the idea that some mutations in base pairs were beneficial. That led biology teachers like PZ Myers to claim that some mutations may somehow lead to the evolution of biodiversity. That led anonymous fools and his idiot minions to claim the same thing.

Is that what you're claiming? I'm claiming nutrient-dependent amino acid substitutions link ecological variation to ecological adaptations.
anonymous_9001
5 / 5 (9) Aug 14, 2014
Nutrient-dependent base pair changes


That occur by what mechanisms?

Here's a question for you- what are the functional differences between a nutrient-dependent base pair change and an identical change caused by a mutation? How could they be differentiated in otherwise identical organisms and the same environment?
RealScience
5 / 5 (5) Aug 14, 2014
Do you even understand how base pair changes in genes can cause amino acid substitutions?


Yes, thanks for asking, but only from the perspective of biophysical constraints that prevent mutation-driven evolution. Nutrient-dependent base pair changes link ecological variation to amino acid substitutions and cell type differentiation that is perturbed by mutations.


I'm not asking about the results of the amino acid substitutions (or alternative splicings or other editing). I'm asking if you understand the BASIC principle of how triplets of nucleic acids in a gene are translated into specific amino acids in a protein produced from the gene.
JVK
1 / 5 (6) Aug 14, 2014
I'm asking if you understand...


Again, thanks for asking. My co-authors and I detailed how triplets of nucleic acids in a gene are translated into specific amino acids in proteins produced from genes in the section on molecular epigentics in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

Now, see the culmination of 4 years of research reported yesterday that links olfactory/pheromonal input from epigenetic effects on SNPs and alternative splicings of pre-mRNA to amino acid substitutions and human behavior.

http://medicalxpr...ses.html

what are the functional differences...


Thanks for asking. Mutations perturb protein folding; amino acid substitutions stabilize it.

See: http://www.ncbi.n...3960065/ for examples of how stability is achieved in a animals.
RealScience
5 / 5 (5) Aug 14, 2014
My co-authors and I detailed how triplets of nucleic acids in a gene are translated into specific amino acids in proteins produced from genes in the section on molecular epigentics in our 1996 Hormones and Behavior review.


You are really confused, JVK.
The translation of triplets of nucleic acids is genetics rather than epigenetics, and your review does not even mention triplets, nucleic acids, translation or amino acids, let alone go into the details of the process.

So I'll ask again:

Do you even understand how base pair changes in genes can cause amino acid substitutions?
JVK
1 / 5 (6) Aug 14, 2014
Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this EPIGENETICALLY-EFFECTED MECHANISM, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans. That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes. (SEE p. 337) http://www.hawaii...ion.html

If anyone thinks that cell type differentiation occurs in any other context IN ANY CELL, they are welcome to detail how it occurs.

Telling others that it somehow occurs in the context of mutations, natural selection and the evolution of biodiversity is pseudoscientific nonsense, and it always has been.

The evolutionary origin of form and function http://onlinelibr...abstract
"Genetic variation plays no role..."
anonymous_9001
5 / 5 (6) Aug 14, 2014
Thanks for asking. Mutations perturb protein folding; amino acid substitutions stabilize it.


"Identical" was the key word in my question. Example: in one organism, an AGA triplet is changed to ATA by whatever unnamed mechanism makes base changes in your model. In another organism of the same species, the same triplet is changed by a mutation. How can you tell the difference?

The evolutionary origin of form and function http://onlinelibr...abstract
"Genetic variation plays no role..."


Include the full context of that excerpt next time. Don't be deceived by Kohl's quote here. It doesn't mean what he's trying to portray it as meaning.
Captain Stumpy
5 / 5 (6) Aug 14, 2014
Thanks for asking. Mutations perturb protein folding; amino acid substitutions stabilize it
@jk
so that means you have no mechanism for a stable mutation per your own model then, as you claim Mutations perturb protein folding
remember when I asked you
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 by your own words, either you dont know what you are talking about or you are seriously saying that your own model cannot be viable because it causes mutations... WHICH IS IT?
Telling others that it somehow occurs in the context of mutations, natural selection and the evolution of biodiversity is pseudoscientific nonsense, and it always has been
but this is EXACTLY what your OWN MODEL DOES....

WHY NOT ANSWER ANON and RS????
WHY SO EVASIVE?
JVK
1 / 5 (6) Aug 14, 2014
...an AGA triplet is changed to ATA by whatever unnamed mechanism makes base changes in your model.


Your misrepresentation of my accurate representation of biologically-based cause and effect in the context of my model, begins in my title:

Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...3960065/

How much clearer could it be that what you refer to as "whatever unnamed mechanism" is what I detailed in the context of a model of ecological variation that links the epigenetic landscape to the physical landscape of DNA in organisms from microbes to man via the conserved molecular mechanisms of nutrient-dependent cell type differentiation, which is controlled by the nutrient-dependent physiology of reproduction?

Don't be deceived by Kohl's quote here. It doesn't mean what he's trying to portray it as meaning.


It means:
Mutations perturb protein folding; amino acid substitutions stabilize it.
JVK
1 / 5 (6) Aug 14, 2014
Include the full context of that excerpt next time.


Is anyone else too ignorant to use the link I provided to find the quote in the abstract and read the article if they wish to challenge my representation of the facts it contains? If so, here's a link to the full text of the article:

The evolutionary origin of form and function http://onlinelibr...775/full

Concluding sentences: "The information that gives rise to form and function is dispersed throughout the organism in the constituent cellular phenotypes and derives mainly from the interactions between information bearing proteins. The concept of a gene, beyond a means of specifying the amino acid sequences of the peptides from which the proteins are formed, is both mostly unnecessary and possibly misleading."

The concept of a gene, as anything but what the authors just described, appears to have made anonymous fools and idiot minions of most who were taught ridiculous theories.
anonymous_9001
5 / 5 (7) Aug 14, 2014
How much clearer could it be that what you refer to as "whatever unnamed mechanism" is what I detailed in the context of a model


You didn't detail anything along those lines in your paper. You give a general scheme that nutrient and pheromones make epigenetic changes and then make the claim that they also make deterministic gene sequence changes, which you never support with anything.

Concluding sentences...


You're being misleading again.

From the discussion:

that is not to say that evolution has not taken advantage of mutational events, but that genetic variation is not rate limiting.
JVK
1 / 5 (5) Aug 14, 2014
You're being misleading again.


You're not telling anyone what the statements mean to you. They are meaningless to me outside the context of a model. That means they are more than misleading.

Outside a model of biophysically-contrained biologically-based nutrient-dependent pheromone-controlled reproduction, all theoretical claims are pseudoscientific nonsense, yet the anonymous fool (Andrew Jones) thinks I am being misleading.

Try this, put the theoretical claims into the context of "The Tree of Sex" database. http://www.nature...ta201415

Which organisms exhibit morphological and behavioral phenotypes that are not nutrient-dependent and pheromone-controlled? How could any of the organisms with nutrient-dependent pheromone-controlled morphological and behavioral phenotypes mislead anyone into thinking that the phenotypes arise via mutations and natural selection?
Uncle Ira
5 / 5 (5) Aug 14, 2014
@ JVK-Skippy. I got the serious question for you Cher. What the heck do stinky love potions have to do with purple butterflies? Just curious me.

Oh yeah, I almost forget. Where in the heck did you find that pink and purple striped silly looking pointy cap you wearing? I got some peoples in mind I'd like to give one to if they don't cost much more than the regular silly looking pointy caps that I been giving out.
JVK
1 / 5 (5) Aug 14, 2014
What the heck do stinky love potions have to do with purple butterflies?


Thanks for asking.

The nutrient-dependent pheromone-controlled physiology of reproduction was first detailed in moths (1959), which are like butterflies.

Since then, serious scientists have learned how ecological variation is linked to ecological adaptations in the context of the nutrient-dependent pheromone-controlled physiology of reproduction. It is difficult to explain the biological facts of how controlled cycles of protein biosynthesis and degradation lead to ecological adaptations manifested in morphological and behavioral phenotypes in species from microbes to man.

To begin with, theorists must understand the complexities of protein folding that they believe allows mutation-initiated natural selection to lead to the evolution of biodiversity (i.e., pseudoscientific nonsense).

Scientists fold RNA origami from a single strand http://www.scienc...2346.htm
Uncle Ira
5 / 5 (6) Aug 14, 2014
Thanks for asking.

The nutrient-dependent pheromone-controlled physiology of reproduction was first detailed in moths (1959), which are like butterflies.

Since then, serious scientists have learned how ecological variation is linked to ecological adaptations in the context of the nutrient-dependent pheromone-controlled physiology of reproduction. It is difficult to explain the biological facts of how controlled cycles of protein biosynthesis and degradation lead to ecological adaptations manifested in morphological and behavioral phenotypes in species from microbes to man.

To begin with, theorists must understand the complexities of protein folding that they believe allows mutation-initiated natural selection to lead to the evolution of biodiversity (i.e., pseudoscientific nonsense).

Scientists fold RNA origami from a single strand http://www.scienc...2346.htm


Yeah, psuedoscientific nonsense, and not one word about purple butterflies.
JVK
1 / 5 (5) Aug 15, 2014
The first post (here):

"In Ostrinia moth species, substitution of a critical amino acid is sufficient to create a new pheromone blend (Lassance et al., 2013). In the 'peppered moth' example of rapid response to human-induced environmental changes, which were heretofore considered to be driven by selective predation, some evidence now suggests the migration pattern of 2 km per evening is consistent with the male moth's ability to detect the nutrient-dependent pheromones of the female from 2 km upwind (see for review Cook & Saccheri, 2013)." -- excerpt from http://www.ncbi.n...3960065/

"Monteiro's team believe their experiment shows that butterfly wing colors can evolve very quickly and that natural selection could play an important role in the development of wing color. For example, butterflies could use wing color to identify other butterflies of the same species or to influence mate choice."

The team must believe in the theory of evolution even though they report biological facts.
rockwolf1000
5 / 5 (5) Aug 15, 2014
@JVK

The team must believe in the theory of evolution even though they report biological facts.


Well since evolution IS a biological fact I guess the team did the right thing didn't they?

The biggest question is "How does a certified autoclave operator (JVK) come to the conclusion that he knows more than thousands of brilliant scientists?"

or

How did ecological variation that links the epigenetic landscape to the physical landscape of DNA in organisms from microbes to man via the conserved molecular mechanisms of nutrient-dependent cell type differentiation, which is controlled by the nutrient-dependent physiology of reproduction cause your brain to shrivel and wither?

JVK
1 / 5 (4) Aug 15, 2014
Thanks.
...cause your brain to shrivel and wither?


Comments like yours attest to the overwhelming ignorance of biophysically-constrained biologically-based cause and effect that I detailed in my model (in a series of publications starting in 1995). What's remarkable is that these comments never address the content of any of my published works, and continue to denigrate me personally. It's as if each one is an attempt to display greater ignorance than all the others.

Please see: Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection http://www.pnas.o...abstract

Only you can help to end the vicious cycle of ignorance propagated by anonymous fools and idiot minions of biology teachers like PZ Myers. And all that's required is for you to realize that ecologcal adapations require thermodynamically-controlled cycles of protein biosynthesis and degradation.

Thanks again if you cannot do that.
anonymous_9001
5 / 5 (5) Aug 15, 2014
Please see: Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection http://www.pnas.o...abstract


First line of the abstract:

Natural protein sequences, being the result of random mutation coupled with natural selection


Shouldn't you be telling the authors about how mutation and natural selection is a myth?
rockwolf1000
5 / 5 (6) Aug 15, 2014
@JVK

continue to denigrate me personally


Are you effing serious?

You take it upon yourself to insult EVERYONE who doesn't fall into line with your thinking.

Does "idiot minions" ring a bell? While you cry and whine have a fit over insults directed at you personally, you offer up blanket insults towards literally millions of people over and over and over and over, again and again and again.

If I had a dollar for every time you called people "idiot minions" I would be able to use that money to buy this website and ban you and your lunacy from here permanently.

Your hypocrisy knows no bounds does it JVK?

No I haven't read your works. Why you ask? You've wasted enough of my time already quite frankly and as I've stated before I only infrequently allocate tiny portions of time to read the gobbledygook you post here. Occasionally it is quite amusing. In a pitiful fashion.

Generally you get 1 star and I continue scrolling down after ignoring your comments.
rockwolf1000
5 / 5 (5) Aug 15, 2014
@JVK
I just checked out your Eros website for desperate and unlovable people whom you victimize into purchasing your snake oil potions.
Are you aware of the many errors and mistakes on that site? Is this possibly a reflection of the quality of your other work Mensa boy?
For instance: On the "Women" page it states the following;
"Pheromones Can Help You Attract Men"

and then;

"allowing you to poses (sp) an unfair advantage in attracting men"

and then;

"because most women have some basic level of appeal, pheromones can help give you an unfair advantage in capturing the interest of men – and who doesn't want that?" (notice the double space? They're everywhere Mensa boy)

and finally;

"Finally, get the attention you want from women without any risk!"

What a monumental error! That you could allow such an error on your own website serves to demonstrates the quality of your work (or lack thereof). It certainly calls into question your integrity and subjects your other work to scrutiny.
rockwolf1000
5 / 5 (5) Aug 15, 2014
@JVK

I could proofread your other work if you want. But it'll cost you a fortune Mensa boy!
JVK
1 / 5 (4) Aug 15, 2014
Pheromones.com is a marketing site, which has helped me to fund my research.

My last two reviews were published in Socioaffective Neurscience & Psychology

Nutrient-dependent/pheromone-controlled adaptive evolution: a model
http://www.ncbi.n...3960065/

Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors.
http://www.ncbi.n...24693349

See also:
Human pheromones: integrating neuroendocrinology and ethology.
http://www.ncbi.n...11600881

From fertilization to adult sexual behavior.
http://www.ncbi.n.../9047261
RealScience
4.4 / 5 (7) Aug 15, 2014
In Ostrinia moth species, substitution of a critical amino acid is sufficient to create a new pheromone blend (Lassance et al., 2013).


@JVK - the study you cite SUPPORTS MUTATIONS as the cause of the new pheromone blend. Its summary says:
Altogether, this study identifies the reduction step as a potential source of variation in pheromone signals in the moth genus Ostrinia and suggests that selection acting on particular mutations provides a mechanism allowing pheromone reductases to evolve new functional properties that may contribute to variation in the composition of pheromone signals.


Once again you cite a study that actually conflicts with your position.
rockwolf1000
5 / 5 (5) Aug 15, 2014
Pheromones.com is a marketing site, which has helped me to fund my research.

My last two reviews were published in Socioaffective Neurscience & Psychology

Nutrient-dependent/pheromone-controlled adaptive evolution: a model
http://www.ncbi.n...3960065/


Perhaps you meant: Socioaffective Neuroscience & Psychology

Your attention to detail is terribly lacking. What does this say about your research??
Uncle Ira
4.2 / 5 (5) Aug 15, 2014
@ JVK-Skippy. Cher, I don't want to hurt your feelings no. But podna, you need to take that picture on your profile down. You ain't never going to sell any of those stinky love potions here if peoples start thinking they going to end up looking like that. You look like somebody is tickling your toes while you are getting your picture took. I take it that the stinky love potions don't help much with the hair falling out, eh? Or maybe they cause the hair to fall out.

You want one of the silly looking pointy caps to wear for your next picture? He won't help the face much but he will keep peoples from thinking about their hair maybe falling out from the stinky love potions.
JVK
1 / 5 (5) Aug 15, 2014
....suggests that selection acting on particular mutations provides a mechanism


Thanks for commenting on the citation.

Biophysical constraints on the thermodynamic cycles of protein biosynthesis and degradation eliminate any possibility that mutations provide that mechanism.

"...kinetic traps might appear on the folding landscape during evolution if a random mutation was to stabilize a conformation distinct from the functional one, leading to unviability. In this way, evolution and physical dynamics are coupled. A funneled, minimally frustrated landscape can be achieved if the sequence of the protein evolves to stabilize the native state..."

http://www.pnas.o...abstract
anonymous_9001
5 / 5 (6) Aug 15, 2014
Biophysical constraints on the thermodynamic cycles of protein biosynthesis and degradation eliminate any possibility that mutations provide that mechanism.


No they don't and nothing you cite suggests that in the slightest. All you did was read Nei's sentence about biophysics constraining mutations and blew it way out of proportion and misinterpreted it as meaning biophysics prevents mutations contributing to evolution completely.

Read through this and get back to us. It's a complete integration of biophysics in the context of mutations, selection, and protein folding:

http://onlinelibr...071/full

Here's one I think you'll really like, actually:

Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics
JVK
1 / 5 (4) Aug 15, 2014
CONCLUSIONS:Our results show that site-specific miRNA editing is an evolutionarily conserved mechanism, which increases the functional diversity of mammalian miRNA transcriptomes.

http://genomebiol...15/6/R83

The microRNA/messenger RNA balance is nutrient-dependent and pheromone-controlled in the context of thermodynamic cycles of protein biosynthesis and degradation, which enables organism level theromoregulation in species from microbes to man.

Evolutionary theorists do not understand physics, chemistry, or molecular biology. They insist that people who do understand the difference between experimental evidence of cause and effect look at information on theories, because they can't understand facts. If they could understand scientific facts, they would not believe in the pseudoscientific nonsense of evolutionary theories.

You do not merge molecular mechanisms in the context of population genetics; the merger comes from understanding biologically-based facts.
anonymous_9001
5 / 5 (6) Aug 15, 2014
Evolutionary theorists do not understand physics, chemistry, or molecular biology.


The paper in the second link was written by biophysicists! Serohijos has a PhD in physics and Shakhnovich has one in theoretical biophysics and molecular biology and is head of Harvard's chemistry and chemical biology department. I dare you to go toe to toe with those two and tell them precisely what's wrong with their paper. Did you even read it?

RealScience
5 / 5 (6) Aug 15, 2014
Biophysical constraints on the thermodynamic cycles of protein biosynthesis and degradation eliminate any possibility that mutations provide that mechanism.


Thank you for being polite in your response.

All base pair changes, regardless of their cause, are mutations by the standard definition of mutations (changes in DNA nucleotide sequence). Thus your acceptance that some base pair changes stabilize proteins and contribute to evolution is acceptance that some mutations (under the standard definition of mutations) stabilize proteins and contribute to evolution.

Even if you personally define mutations as only random changes, a random base-pair change that happens to be the same as what you call a nutrient-dependent base pair change will also stabilize the protein because it will produce the same change to the resulting protein.

JVK
1 / 5 (5) Aug 15, 2014
Nutrient-induced changes to base pairs are not mutations. They are the link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man. The amino acid substitutions that arise in the context of nutrient-dependent changes to base pairs stabilize DNA via conserved molecular mechanisms that link ecological variation to thermodynamic cycles of protein biosynthesis and degradation in all organisms.

The metabolism of nutrients to species-specific pheromones, which control the physiology of reproduction ensures that the stability of the genome is transgenerationally epigenetically inherited along with the plasticity of the genome that allows organisms to ecologically adapt to changes in their ecological, social, neurogenic, and socio-cognitive niches, which are nutrient-dependent and pheromone-controlled in the context of increasing organismal complexity.

WHAT PART OF BIOLOGICALLY-BASED CAUSE AND EFFECT IS DUE TO MUTATIONS?
anonymous_9001
5 / 5 (6) Aug 15, 2014
Nutrient-induced changes to base pairs are not mutations.


What nutrient caused the promoter shift in Lenski's bacteria and by what enzymatic pathway did it occur?
JVK
1 / 5 (5) Aug 15, 2014
I dare you to go toe to toe with those two and tell them precisely what's wrong with their paper.


I just told everyone what's wrong with papers that continue to frame their explanations in terms of mutation-initiated natural selection and the evolution of biodiversity.

The explanations don't work for butterflies or for any model organism because mutations perturb protein folding, which destabilizes the organized genomes of species from microbes to man. Nutrient-dependent pheromone-controlled ecological adaptions via amino acid substitutions stabilize the genomes of species from microbes to man.

I politely invited anyone to try to explain what's wrong with my model in my conclusion:

"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...24693353

I'm still waiting for that comparison after 14 months of criticisms based on belief in theory.
JVK
1 / 5 (5) Aug 15, 2014
What nutrient caused the promoter shift in Lenski's bacteria and by what enzymatic pathway did it occur?


Do your own homework, Andrew Jones. Only then can you escape from the clutches of ignorant biology teachers like PZ Myers who trains anonymous fools and idiot minions like you to be what they are.

JVK
1 / 5 (5) Aug 15, 2014
"On the level of genes or alleles, there is no inclusive fitness: Mathematical descriptions of the evolutionary dynamics of genetic mutations do not require a partition of fitness effects (which usually is impossible anyway) or any other aspect of inclusive fitness theory."

Finally, a comparison to my model. There is no need for discussion of the thermodynamic cycles of protein biosynthesis and degradation. There is no need for nutrient-dependent amino acid substitutions to differentiate cell types. There is no need for the pheromone-controlled physiology of reproduction or any aspect of nutrient-dependent pheromone-controlled reproductive fitness.

With a mathematical model, everything that has happened or ever will happen in the context of biophysically-constrained ecological adaptations is attributed to mutations.

But first see: http://bfg.oxford...050.long
Epigenomics and the concept of degeneracy in biological systems
Captain Stumpy
5 / 5 (5) Aug 16, 2014
The paper in the second link was written by biophysicists! Serohijos has a PhD in physics and Shakhnovich has one in theoretical biophysics and molecular biology and is head of Harvard's chemistry and chemical biology department. I dare you to go toe to toe with those two and tell them precisely what's wrong with their paper
@Anon
why not just forward his arguments here against them directly to them?

I've done that with a LOT of his posts...
So far, the NIH called him an idiot (not those exact words, but pretty much said he doesn't know squat... and SURELY doesn't realize that his own model actually creates mutations)
I forwarded his arguments to Lenski and a few others too...
awaiting replies...

I think they are of the opinion that he is too stupid to deal with

Myers had it right... he spouts off with pseudoscience word salads and doesn't know what he is talking about
Mensa is gonna hear about this, jk
I am cancelling my membership for letting you in
RealScience
5 / 5 (6) Aug 16, 2014
Nutrient-induced changes to base pairs are not mutations.


When you have asked for the definition of mutations before, you have been given the following definitions (with links):

NIH: A mutation is a change in a DNA sequence

Wikepedia: In genetics, a mutation is a change of the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element

Biology Online: A permanent, heritable change in the nucleotide sequence in a gene or a chromosome

Nature's educational group: "a mutation is defined as any alteration in the DNA sequence"

By ALL of these definitions "Nutrient-induced changes to base pairs" ARE mutations.

You may not LIKE the way real biologists and geneticists use the term 'mutation', JVK, but that's your problem (especially if you refuse to define what you personally mean by 'mutation').

JVK
1 / 5 (5) Aug 16, 2014
By ALL of these definitions "Nutrient-induced changes to base pairs" ARE mutations.


Thanks for confirming your belief in definitions used in the context of biologically based cause and effect. It is a clear difference between your perspective on evolution as it was defined, and my perspective, which is based on biological facts.

"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.... No, it wasn't dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact."
http://www.huffin...211.html

Everyone not capable of grasping biologically-based facts will continue to define their terms, while serious scientists make progress by learning how ecological variation leads to ecological adaptations in species from microbes to man.
JVK
1 / 5 (5) Aug 16, 2014
...the NIH called him an idiot


"If these are based on fundamental physical laws, then it may be reasonable to treat the model as 'predictive', in the sense that it is not subject to falsification and we can rely on its conclusions. However, at the molecular level, models are more often derived from phenomenology and guesswork." http://www.biomed...07/12/29

My model incorporates biophysical constraints, which predict two obvious facts

1) mutations that perturb protein folding will not be beneficial to species survival

2) nutrient-dependent amino acid substitutions benefit the stability of DNA in organized genomes

If anyone at NIH thinks either of these two facts are not accurately represented in my model of nutrient-dependent pheromone-controlled ecological adaptations they should review it and comment on my published work.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
JVK
1 / 5 (5) Aug 16, 2014

RealScience
5 / 5 (6) Aug 16, 2014
It is a clear difference between your perspective on evolution as it was defined

I have made no comments on the definition of evolution.

... and my perspective, which is based on biological facts.


Facts? You have ADMITTED that you throw out results that appear to attest to mutations as the cause of adaptive evolution, and you have also ADMITTED that you have no experimental evidence that mutations are never selected for.

Everyone not capable of grasping biologically-based facts will continue to define their terms


Real experts in the field will continue to use the standard definitions, or define how they are using a term if using it in a non-standard way, to communicate effectively.

Do you agree that under the Nature Education Group's definition of a mutation: "a mutation is defined as any alteration in the DNA sequence", that base pair changes, whether or not nutrient dependent, are mutations?
JVK
1 / 5 (5) Aug 16, 2014
If cell type differentiation did not occur via the conserved molecular mechanisms we detailed in our 1996 Hormones and Behavior review, we would not be seeing reports like these from a Special Issue "Chemosignals and Reproduction":

http://www.scienc...14001585 (primates)
http://www.scienc...14001603 (mammals)
http://www.scienc...14001172 (birds)

Eventually, our model in "From Fertilization to Adult Sexual Behavior" http://www.hawaii...on.html, which was extended to invertebrates in "Organizational and activational effects of hormones on insect behavior," http://www.ncbi.n...10980296 will be viewed by all serious scientists as the link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all species because that's what the model predicted and detailed nearly 18 years ago.
Uncle Ira
5 / 5 (6) Aug 16, 2014



Now you are making sense with this one Skippy, you should put this one up where your picture is.
JVK
1 / 5 (6) Aug 16, 2014
Real experts in the field will continue to use the standard definitions...


Anyone who uses standard definitions to explain how quantum physics and quantum biology lead to quantum consciousness via ecological, social, neurogenic, and socio-cognitive niche construction with increasing nutrient-dependent pheromone-controlled organismal complexity should continue discussion of this topic with the other anonymous fools and idiot minions of biology teachers like PZ Myers who have defined-away the common sense of generations of those who might otherwise have become serious scientists.

...base pair changes, whether or not nutrient dependent, are mutations?


Has "Nature Education Group's definition" ever been placed into the context of what is currently known about "Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans" http://www.cell.c...)00806-X

Does anyone else know how starvation leads to adaptations sans mutations?
JohnGee
5 / 5 (7) Aug 16, 2014
Yes, yes, blame real scientists for your inability to hack it as a scientist.
JVK
1 / 5 (5) Aug 16, 2014
Now you are making sense with this one...


Hi, Uncle Ira:

You are one of the last people I want to ever have tell anyone who is making sense.

Your criticisms of those you think do not make sense are based on the pseudoscientific nonsense of your beliefs, which are manifested in your "twisted" posts as an anonymous fool each time you comment about things you will never understand.

Thank you for continuing to provide an example of ignorance that I wish was unparalleled, but continue to see is not. You will remain only one example from several generations of fools who allowed themselves to be taught to believe in the pseudoscientific nonsense of ridiculous theories.
JVK
1 / 5 (5) Aug 16, 2014
...blame real scientists for your inability to hack it as a scientist.


Watch this 5.5 minute video from my 2013 ISHE presentation and explain yourself.
https://www.youtu...youtu.be

I've studied the role of epigenetic effects on alternative splicings of pre-mRNA for more than two decades and presented a model that links them to amino acid substitutions that differentiate all cell types in all individuals of all species.

I CAN hack it!
RealScience
5 / 5 (6) Aug 16, 2014
Has "Nature Education Group's definition" ever been placed into the context


JVK, I did not ask whether you agreed with the Nature Education Group's definition.
I asked whether you agree that UNDER THAT DEFINITION: "a mutation is defined as any alteration in the DNA sequence", that base pair changes, whether or not nutrient dependent, are mutations?

So please give a straight forward answer rather than trying to change the subject.

Captain Stumpy
5 / 5 (6) Aug 16, 2014
I CAN hack it!
LMFAO
IF YOU COULD HACK IT, you would be trying to convince biologists and the like of your creationist bull snot... you are HERE on a pop-sci site BECAUSE you can't hack it!
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 TAKEN FROM THE NIH SITE
to which you answered
YES!
--Thanks for asking
IOW - you are a LIAR, and a hack, sorry charlie... grab your crayons and plastic helmet and run faster, little buddy!

So please give a straight forward answer rather than trying to change the subject.
YEAH! get back to the subject!
JVK
1 / 5 (5) Aug 16, 2014
I asked whether you agree that UNDER THAT DEFINITION: "a mutation is defined as any alteration in the DNA sequence", that base pair changes, whether or not nutrient dependent, are mutations?

So please give a straight forward answer rather than trying to change the subject.


"Scientists create purple-winged butterflies in six generations" is the subject. Trying to place what is described into the context of mutation-initiated natural selection and the evolution of biodiversity (e.g., in six generations) is the feeble attempt made by those who know nothing about biologically-based cause and effect.

Like you, they try to show their belief in pseudoscientific nonsense can be justified. Like you, they think their belief in definitions is more important than biological facts are when it comes to details of biophysically-constrained biologically plausible epigenetic links from the sensory environment to the physical landscape of DNA in organized genomes.

Like you, they are fools.
Captain Stumpy
5 / 5 (5) Aug 16, 2014
they think their belief in definitions is more important than biological facts are
@jk
it's almost comical watching you post anymore...
THEY establish the definition of words to form a lexicon so that people in the field can utilize a set word structure and series to portray what they want to say in order to facilitate the spread of information and ease communication between individuals...

basically, what you are saying, jk, is that you are just going to make sh*t up as you go, make your own definitions, ignore the ENTIRE biological and medical community (maybe THIS is why you stupidly claimed to have experience as a diagnostician?) and just create a new lexicon BECAUSE YOU DON'T LIKE THE WAY SOME WORDS ARE IN THE CURRENT ONE

not how that works, dork. in fact, had you even TRIED to pass college, you might have learned a few things that would be useful now, like how to research the definition of certain WORDS so that you don't look like an IDIOT

lol
Uncle Ira
5 / 5 (5) Aug 16, 2014
Now you are making sense with this one...


Hi, Uncle Ira:

You are one of the last people I want to ever have tell anyone who is making sense.

Your criticisms of those you think do not make sense are based on the pseudoscientific nonsense of your beliefs, which are manifested in your "twisted" posts as an anonymous fool each time you comment about things you will never understand.

Thank you for continuing to provide an example of ignorance that I wish was unparalleled, but continue to see is not. You will remain only one example from several generations of fools who allowed themselves to be taught to believe in the pseudoscientific nonsense of ridiculous theories.


@ JVK-Skippy, well okayeei with me. Apology accepted and I am glad I was able to help you. We can start over again now. Sorry me too for making the fun of your picture, but you really ought to take him down, it ain't good for business if you want to sell those stinky love potions.
JVK
1 / 5 (5) Aug 16, 2014
from a Special Issue "Chemosignals and Reproduction":

http://www.scienc...14001585 (primates)
http://www.scienc...14001603 (mammals)
http://www.scienc...14001172 (birds)



http://bfg.oxford...050.long (bees) and systems biology.

Anyone interested in learning about the birds and the bees in the context of systems biology, which refutes the pseudoscientific nonsense of mutation-initiated natural selection and the evolution of biodiversity need read only a few review articles about nutrient-dependent pheromone-controlled ecological adaptations before they stop believing in the pseudoscientific nonsense -- or continue to believe in it because they lack the ability or motivation to learn.
Captain Stumpy
5 / 5 (5) Aug 16, 2014
which refutes the pseudoscientific nonsense of mutation-initiated natural selection
so you are saying this directly REFUTES YOUR MODEL?
WOW!

remember.. 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 PER EVERYONE IN BIOLOGY (except maybe you) to which you answered
YES!
--Thanks for asking
YOUR OWN WORDS jk

basically, you are saying above that you are an idiot and don't know what you are talking about!

RealScience
5 / 5 (5) Aug 16, 2014
I asked whether you agree that UNDER THAT DEFINITION: "a mutation is defined as any alteration in the DNA sequence", that base pair changes, whether or not nutrient dependent, are mutations?


So please give a straight forward answer rather than trying to change the subject.


...Like you, they think their belief in definitions is more important than biological facts are ...


So you again refused to answer a straight-forward question.

That's not surprising, since if you answer 'no' you are obviously wrong because base pair changes are DNA nucleotide sequence changes and hence ARE mutations by that definition, while if you answer 'yes' you are admitting that your earlier statement that mutations "don't contribute to evolution -- no matter how you define 'mutation.'" is false.

Let's see if you have the guts to admit that under the standard definition of mutations, mutations DO contribute to evolution, or whether you try to change the subject again.

JVK
1 / 5 (5) Aug 16, 2014
...under the standard definition of mutations, mutations DO contribute to evolution...

HOW?
you are admitting that your earlier statement that mutations "don't contribute to evolution -- no matter how you define 'mutation.'" is false.


RealScience demonstrates the magnitude of trickery used by population geneticists who throw their pseudoscientific nonsense out so anonymous fools and idiot minions of biology teachers like PZ Myers can eat it up and then regurgitate it, which is what they have been doing for decades.

He wants to define mutation out of context so that the term appears to have meaning in the context of natural selection and the evolution of biophysically-constrained biodiversity.

This removes the constraints of nutrient-dependent amino acid substitutions that stabilize DNA in organized genomes, and replaces those constraints with the nonsense of constraint-breaking mutations as the source of all biodiversity. http://www.amazon...99661731
RealScience
5 / 5 (5) Aug 16, 2014
...under the standard definition of mutations, mutations DO contribute to evolution...

HOW?


Even you have admitted that base pair changes happen (you claim that they are 'nutrient-dependent') and that they contribute (through amino acid substitutions) to ecological adaptation and increasing increasing organismal complexity, both of which are hallmarks of evolution. Since under the standard definition of mutations (whether or not you agree with that definition), base pair changes (regardless of whether nutrient dependent) are mutations, then under the standard definition mutations contribute to evolution.

So your earlier statement that mutations "don't contribute to evolution -- no matter how you define 'mutation.'" is false. Let's see if you have the guts to admit it.

RealScience
5 / 5 (5) Aug 16, 2014
RealScience demonstrates the magnitude of trickery used by population geneticists who throw their pseudoscientific nonsense out...

He wants to define mutation out of context so that the term appears to have meaning in the context of natural selection and the evolution of biophysically-constrained biodiversity.


Bull - I'm not defining mutations, I'm pointing out to you how the term IS defined by experts in the field.

You are the one who is refusing to use the standard definition. You are using it to mean something other than its standard meaning, so YOU are the one re-defining the term. And then you refuse to even state what you mean by the term, so YOU are the one being 'tricky'.
JVK
1 / 5 (5) Aug 16, 2014
Mutation-Driven Evolution http://www.amazon...99661731

Use of the term by experts like Nei, led others to believe in pseudoscientific nonsense about constraint-breaking mutations. No matter how the term is used, there is no experimental evidence of biologically-based cause and effect that links mutations via natural selection -- or anything else-- to the evolution of biodiversity, which is obviously nutrient-dependent.

Since biodiversity is obviously nutrient-dependent, I have modeled it in the context of ecological variation and the conserved molecular mechanisms of biologically-based cause and effect that link nutrient-uptake to pheromone-controlled reproduction in species from microbes to man, via amino acid substitutions that differentiate cell types (in 6 generations).

I have no need for the term mutation in the context of an accurate representation of biophysically-constrained cause and effect, and yet you insist I should use the standard definition. Why would I?
JVK
1 / 5 (5) Aug 16, 2014
...ecological adaptation and increasing increasing organismal complexity, both of which are hallmarks of evolution.


Increasing organismal complexity arises from nutrient-dependent pheromone-controlled ecological, social, neurogenic, and socio-cognitive niche construction via conserved molecular mechanisms that link cell type differentiation in species from microbes to man.

You seem to be confusing the result, which is ecological adaptation, with something that somehow evolved. Please tell me how it evolved so we can compare what you think happens via evolution to what I have detailed in my model of biophysically-constrained cause and effect, which links ecological variation to ecological adaptations without any pseudoscientific nonsense or belief in ridiculous theories.

Do you really believe that starving nematodes evolve? Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans http://www.cell.c...)00806-X

Does anyone?
JVK
1 / 5 (5) Aug 16, 2014
A critical appraisal of the use of microRNA data in phylogenetics http://www.pnas.o...abstract

They note that evolutionary theory has no explanatory power then examine 1/2 the nutrient-dependent microRNA/messenger RNA balance, which changes with nutrient uptake during development. By examining only half of the systems complexity, they conclude that models of microRNA-induced changes in morphological and behavioral traits are flawed.

Their representation resolves nothing presented in the context of evolution, but it may make people think that my model does not put an end to the pseudoscientific nonsense of mutation-initiated evolution because levels of microRNAs explain nothing.

My model integrates what is known about how nutrient-dependent changes in microRNAs lead to alternative splicings and amino acid substitutions that differentiate cell types in the context of the pheromone-controlled microRNA/messenger RNA balance .
RealScience
5 / 5 (4) Aug 17, 2014
No matter how the term is used, there is no experimental evidence of biologically-based cause and effect that links mutations via natural selection -- or anything else-- to the evolution of biodiversity, which is obviously nutrient-dependent.

YOUR OWN POSTS link base-pair changes, which are DNA nucleotide sequence changes, to the evolution of biodiversity. So if the term 'mutations' is used to mean 'changes to DNA nucleotide sequence' then YOUR OWN ARGUMENTS link mutations to the evolution of biodiversity.

So either your own arguments are wrong or your 'no matter how the term is used' statement is wrong. Checkmate again!
RealScience
5 / 5 (4) Aug 17, 2014
... you insist I should use the standard definition.

I have asked you many times before how you are using the term 'mutation', but you have refused to define it.

The standard definition of mutations is very broad, and I have even offered qualifiers for the term that would distinguish controlled DNA edits from semi-controlled (e.g., location-specific accelerated changes, for which I even provided you a link to a great example), and on to the quasi-random atomic decay mutations. But you refused to qualify what you mean by mutations.

If you post comments on a science-oriented comments board, and you use a term without making it clear what you mean by the terms, it is SILLY for you to complain when others interpret the term using the standard definition in the relevant field of science

So define what YOU mean by the term mutations, or quit complaining.
JVK
1 / 5 (4) Aug 17, 2014
YOUR OWN POSTS link base-pair changes, which are DNA nucleotide sequence changes, to the evolution of biodiversity. So if the term 'mutations' is used...


I don't use it in the context of explaining how ecological variation leads to ecological adaptations manifested in biodiversity.

If you post comments on a science-oriented comments board, and you use a term without making it clear what you mean...


My comments are directed towards people like you, who use a term I don't use. Like you, they think I should help them make sense of the way they use the term.

I don't use it because it makes no sense in the context of anything known about biological facts. Biological facts clearly link the epigenetic landscape to the physical landscape via amino acid substitutions, not mutations.

Facts explain the color change in the butterflies in 6 generations. Ridiculous theories about mutation-initiated natural selection and evolution of biodiversity explain nothing.
RealScience
5 / 5 (5) Aug 17, 2014
My comments are directed towards people like you, who use a term I don't use.

Bull. You often are the FIRST to use the term mutation in a comments thread.

For example:
http://phys.org/n...ark.html
http://medicalxpr...mes.html]http://medicalxpr...mes.html[/url]
http://medicalxpr...ion.html
http://medicalxpr...mes.html]http://medicalxpr...mes.html[/url]
http://phys.org/n...ars.html
http://phys.org/n...ces.html

Like you, they think I should help them make sense of the way they use the term.

You really are confused, JVK.
I do NOT think that you should help me make sense of how I use the term.
I have said If you wish to communicate effectively, and YOU use a term in a non-standard way, then you should define how YOU use the term.
JVK
1 / 5 (4) Aug 17, 2014
You often are the FIRST to use the term mutation in a comments thread.


I wrote: "I don't use it in the context of explaining how ecological variation leads to ecological adaptations manifested in biodiversity."

Commenting on incorrect use of a term in contexts that show the term has no explanatory power is the only means to attempt to teach others why use of "mutation" is incorrect, which is because it has no explanatory power compared to what is known about nutrient-dependent amino acid substitutions that differentiate cell types in all cells of all individuals of all species via conserved molecular mechanisms of pheromone-controlled ecological adaptations.

My first comment on this report included: "Monteiro's team believe their experiment shows that butterfly wing colors can evolve very quickly and that natural selection could play an important role..."

Please explain why you think they did not use the term mutation in the context of natural selection and evolution.
JVK
1 / 5 (4) Aug 17, 2014
Artificial selection for structural color on butterfly wings and comparison with natural evolution
http://www.pnas.o...abstract

There is no mention of "mutation" in the entirety of the article.
The authors represent: the Department of Ecology and Evolutionary Biology at Yale University, the Department of Applied Physics, Yale University, the Department of Nano and Electronic Physics, Kookmin University and the Department of Biological Sciences,
National University, and eYale-NUS College, Singapore

Anyone who still believes in the pseudoscientific nonsense they were taught about mutation-initiated natural selection and the evolution of biodiversity may want to ask if any of the students or researchers in any department at any of these Universities still believes in that pseudoscientific nonsense.

If anyone can be found who believes in a ridiculous theory ask why they don't believe in biological facts, like serious scientists do.
JVK
1 / 5 (4) Aug 17, 2014
article: http://medicalxpr...den.html
Excerpt: "...mutations cause the protein sentence to become unintelligible. Loss of a single protein can have devastating effects for cells, leading to dysfunction and sometimes to serious diseases."

My comment: Mutations that cause the protein sentence to become unintelligible do not lead from ecological variation to nutrient-dependent ecological adaptations controlled by the physiology of reproduction in the context of cell type differentiation of all cells in all individuals of all species by amino acid substitutions in my model.

I think that's why the pseudoscientific nonsense about mutation-initiated natural selection and the evolution of biodiversity attributed to constraint-breaking mutations is no longer considered by serious scientists who understand how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man.
RealScience
5 / 5 (4) Aug 17, 2014
Please explain why you think they did not use the term mutation in the context of natural selection and evolution.


I already did.
In my first comment on this article, I explained that it is an example of selection from pre-existing variety:

@JVK -
Did you even read the article, or did you merely fail to understand it?

The article says nothing about the researchers changing the nutrients that they fed the butterflies, and since the scientists selectively bred the butterflies rather than letting the butterflies chose their own mates, pheromones are irrelevant, too.

So why did you bring up nutrients and pheromones?
Oh, that's right, you try to explain everything with nutrients and pheromones.

You really should open your mind to all of the other things that evolution uses.
This experiment is an example of selection from pre-existing genetic variety:
They then selected and bred those butterflies whose wings reflected light closest to the violet spectrum


RealScience
5 / 5 (3) Aug 17, 2014
Artificial selection for structural color on butterfly wings and comparison with natural evolution
http://www.pnas.o...abstract

There is no mention of "mutation" in the entirety of the article.


As I already pointed out, this experiment is an example of selection from pre-existing variety (which you have also denied happens in natural selection).

And PNAS article you link to agrees that it is an example of selection from pre-existing variety. It says:
This work shows that populations harbor large amounts of standing genetic variation that can lead to rapid evolution


I have even told you at least twice that this is where I disagree with Nei.
While Nei only acknowledges evolution being triggered by mutation creating new variety, evolution can ALSO be triggered by environmental changes causing selection from pre-existing variety (and ALSO by epigenetic changes creating new variety, etc.).

Evolution is not a one-trick pony.
RealScience
5 / 5 (3) Aug 17, 2014
My comment: Mutations that cause the protein sentence to become unintelligible do not ...

First, many mutations are silent, not changing proteins at all.
Second, even many that change a proteins do not change the binding site and make relatively little difference.
Third, even some of those mutations that change the binding site are still intelligible, leading to only single amino acid substitutions.

And fourth, although most mutations that cause a protein sequence to become unintelligible are harmful, some are not.
For example, after a gene duplication event there may be too much of a protein. If ONE copy of the gene is mutated to become unintelligible, that can reduce the amount of that protein back to the original level.

Open your eyes, open your mind.
There are far more things in evolution, JVK, than are dreamt of in your philosophy.

JVK
1 / 5 (2) Aug 17, 2014
There are far more things in evolution, JVK, than are dreamt of in your philosophy.


Please put whatever you think those things are into the context of a model that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms so we can compare your philosophy to my model of how ecological variation leads to ecological adaptation.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353
Captain Stumpy
5 / 5 (2) Aug 18, 2014
There are far more things in evolution, JVK, than are dreamt of in your philosophy.


Please put whatever you think those things are into the context of a model that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms so we can compare your philosophy to my model of how ecological variation leads to ecological adaptation.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353
Lets see... considering your model CREATES MUTATIONS...
http://myxo.css.m...dex.html

but then again, you will argue against it... too bad YOU SAID YOURSELF that your model causes mutations

See above posts for proof

RealScience
5 / 5 (3) Aug 18, 2014
There are far more things in evolution, JVK, than are dreamt of in your philosophy.


Please put whatever you think those things are into the context of a model that links the epigenetic landscape to the physical landscape of DNA...


Since you ask nicely, I'll answer politely:
Many environmentally-caused epigenetic changes (including nutrient-dependent ones) do indeed change the physical landscape of DNA, often regulating gene expression in the process. However, with only a few exceptions known to date (e.g. the bacterial immune system's insertion of viral genes via CRISPR), environmental effects do not directly change the DNA sequence.

So far I have not seen any experimental evidence of any epigenetically-controlled base pair substitutions, but nature is broad enough that it would not surprise me if some examples exist.

- continued -
RealScience
5 / 5 (3) Aug 18, 2014
- continued -

I have asked you for examples of nutritionally-controlled DNA sequence edits, even telling you that finding them would be a significant contribution to the field, but so far you have not provided any. The closest I have seen is the Sasaki paper on the specifically-enhanced substitution rate that can restore a defective DMS-4 gene (without an increase in the substitution rate in the rest of the genome) that I sent you a link to in previous comments.

But even if you can find an example of nutrient-CONTROLLED edits to DNA sequences, that would not mean that that is the ONLY way DNA sequences change. Background DNA base pair substitution rates are known for many species, and even truly random base pair substitutions would occasionally make the same change as a controlled edit would.

- continued -
RealScience
5 / 5 (3) Aug 18, 2014
- continued -

Lenski's experiments provide a good example.

If the DNA sequence changes in Lenski were tightly controlled (by nutrients or other factors), they would happen rapidly across multiple colonies. However the DNA changes only occurred sporadically, indicating that they are not controlled. Also the rate at which they occurred matched the background change rate across the entire genome, indicating that they were essentially uncontrolled changes.

This does not conflict with the basic principle of ecological variation leading to ecological adaptation, but this conflicts with nutritionally-controlled changes (or even controlled changes in general) being the ONLY mechanism.

So while I agree with epigenetic control of gene expression being a dominant factor, I disagree with nutritionally-controlled changes (or even controlled changes in general) being the only class of factors. Our genomes have learned to use even quasi-random changes over the long term.

JVK
1 / 5 (3) Aug 18, 2014
I wrote: "Please put whatever you think those things are into the context of a model that links the epigenetic landscape to the physical landscape of DNA..."

There is no point to attempts to discuss models of biologically-based cause and effect with those who respond with comments about their ridiculous beliefs in pseudoscientific nonsense that lead them to claim.

... environmental effects do not directly change the DNA sequence.


Who indicated epigenetic effects directly change the DNA sequence?

Our genomes have learned to use even quasi-random changes over the long term.


Is there a model for that? The changes in morphology (i.e., color) of these butterflies occurred in 6 generations. What model of biologically-based cause and effect suggests they became different species after subsequent generations arose?

Lenski's experiments provide a good example.


Of what? Did the E. coli later become a different species of microbial life?
RealScience
5 / 5 (3) Aug 18, 2014
... environmental effects do not directly change the DNA sequence.


Who indicated epigenetic effects directly change the DNA sequence?


I said 'environmental effects' (such as nutrients), and you substituted 'epigenetic' for environmental. And in this very thread you have said:

Nutrient-induced changes to base pairs ... are the link from the epigenetic landscape to the physical landscape of DNA ...


To be clear about the term direct: by 'direct' in my comment I mean CAUSING the specific changes, as opposed to causing general changes that are then selected among to leave the specific change, and as opposed to causing selection among general changes to leave the specific change.

- continued -
RealScience
5 / 5 (4) Aug 18, 2014
Our genomes have learned to use even quasi-random changes over the long term.

Is there a model for that?

Certainly. As I have pointed out before, it is the standard model of evolution, so while you may disagree with the model, you can hardly pretend to be an expert in the field if you don't even know that that model exists.

The changes in morphology (i.e., color) of these butterflies occurred in 6 generations.

As I pointed out twice already in this thread, that is because it is an example of selection from pre-existing variety, rather than of de novo mutations being selected for.

Lenski's experiments provide a good example.


Of what?


Of genomes using quasi-random changes over the long term.

anonymous_9001
5 / 5 (5) Aug 18, 2014
Who indicated epigenetic effects directly change the DNA sequence?


You do every time you say things like "epigenetically-effected amino acid substitutions" or "Epigenetically-effected thermodynamic cycles of protein biosynthesis and degration result in fixation of amino acid substitutions that stabilize organism-level thermoregulation".

Since AA substitutions are the result of codon changes, you're saying codon changes are the result of epigenetic processes.

Did the E. coli later become a different species of microbial life?


Technically, yes.

The inability to use citrate as an energy source under oxic conditions has long been a defining characteristic of E. coli as a species (35, 36).

http://www.pnas.o...899.long

JVK
1 / 5 (3) Aug 18, 2014
"Non‐coding RNAs as the bridge between epigenetic mechanisms, lineages and domains of life" http://jp.physoc....abstract

Not some domains of life; all of them -- from microbes to man, via nutrient-dependent pheromone-controlled cell type differentiation. There's a model for that!

There's also a ridiculous theory that the different domains of life somehow evolved via mutations and natural selection. People who believe that seem to be not that bright, which may be why they comment anonymously, except for anonymous_9001, who reviewed my most recent published work as Andrew Jones.

http://www.ncbi.n...4959329/ Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

http://www.socioa...ew/20553
RealScience
5 / 5 (2) Aug 18, 2014
"Non‐coding RNAs as the bridge between epigenetic mechanisms, lineages and domains of life" http://jp.physoc....abstract


It is a very interesting paper, and well worth re-reading.

But it is concerned with changes in gene expression and not changes in DNA sequences (such as base-pair substitutions). Are you confusing gene expression changes and with gene sequence changes again? Since the paper does mention quantum mechanics, and you have said that you can only understand the difference by starting from quantum mechanics, I can see how you would be confused.
JVK
1 / 5 (2) Aug 29, 2014
Are you confusing gene expression changes and with gene sequence changes again?


No. You are again confusing your thought processes with those of serious scientists who understand that conserved molecular mechanisms link the epigenetic landscape to the physical landscape of DNA manifested in the morphological and behavioral diversity of invertebrates and vertebrates (like zebrafish).

http://www.scienc...2752.htm
"These findings inform our way of thinking about colour pattern formation in other fish, but also in animals which are not accessible to direct observation during development such as peacocks, tigers and zebras," [and butterflies]
RealScience
5 / 5 (1) Aug 30, 2014
You are again confusing your thought processes with those of serious scientists

Coming from someone who ADMITS to throwing out experimental evidence that disagrees with his hypothesis, that's hilarious.
JVK
1 / 5 (1) Aug 30, 2014
"Finally, we were able to build a single model that could predict transcription in all three organisms from upstream histone marks using a single set of parameters for both protein-coding genes and non-coding RNAs. Overall, our results underscore the importance of comparing divergent model organisms to human to highlight conserved biological principles (and disentangle them from lineage-specific adaptations)."

http://dx.doi.org...ure13424

Evolutionary theorists compare divergent model organisms and tout mutations and natural selection as an explanation for their nutrient-dependent pheromone-controlled ecological adaptations like those manifested in the coloration of the butterflies in 6 generations. The theorists aren't very bright, are they?
RealScience
5 / 5 (1) Aug 31, 2014
The theorists aren't very bright, are they?

ROFLMAO.
JVK, you have ADMITTED that you have no experimental evidence to support your HYPOTHESIS that mutations are never selected for in evolution. That makes you a theorist - checkmate again!

But while it is acceptable to speak for yourself, you really shouldn't speak about other theorists that way. Most theorists are bright enough not to throw out experimental results that disagree with their pet hypothesis. In contrast you have ADMITTED to this:
I can throw out results that appear to attest to mutations as the cause of adaptive evolution...


Ignoring experimental evidence against a pet hypothesis that you have no experimental evidence for is the hallmark of a FAILED THEORIST.

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