Biologists describe mechanism promoting multiple DNA mutations

DNA mutations—long known to fuel cancer as well as evolutionary changes in a living organism—had been thought to be rare events that occur randomly throughout the genome.

However, recent studies have shown that cancer development frequently involves the formation of multiple mutations that arise simultaneously and in close proximity to each other. These groups of clustered mutations are frequently found in regions where chromosomal rearrangements take place.

The discovery, published in the journal Cell Reports, may one day lead to new cancer therapies, according to a University of Iowa biologist and her colleagues, and a group of researchers from the National Institute of Environmental Health Sciences led by Senior Associate Scientist Dmitry Gordenin.

The formation of clustered mutations may result from the process of DNA repair.

Anna Malkova, associate professor of biology in the UI College of Liberal Arts and Sciences, notes that the DNA repair pathway, known as break-induced replication (BIR), can promote clusters of DNA mutations.

"Previously, we have shown that double-strand DNA breaks, which can result from oxidation, ionizing radiation and replication errors, can be repaired by BIR," says Malkova.

"During BIR, one broken DNA end is paired with an identical DNA sequence on another chromosome and initiates an unusual type of replication, which proceeds as a migrating bubble and is associated with the accumulation of large amounts of single-strand DNA," she says.

In the Cell Reports study, researchers subjected yeast cells undergoing BIR to alkylating (cancer cell-killing agents) damage. "We found that the single-stranded DNA regions that accumulate during BIR are susceptible to damage that leads to the formation of mutation clusters," explains Cynthia Sakofsky, postdoctoral fellow at the UI and one of two co-first authors on the paper. "These clusters are similar to those found in human cancer," she says.

Importantly, say the researchers, the paper provides a mechanism to potentially explain how genetic changes form in human cancers. Thus, it will be critical for future research to determine whether BIR can form clustered mutations that lead to in humans. If this turns out to be true, it may lead to the discovery of new targets for developing therapies against human cancers.

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JVK
1 / 5 (1) Jul 31, 2014
Excerpt from above: "DNA mutations—long known to fuel cancer as well as evolutionary changes..."

Evolutionary theorists have touted the pseudoscientific nonsense of mutation-driven evolution for decades. Are we now supposed to simply believe those whose obvious bias puts what is known about nutrient-dependent pheromone-controlled chromosomal rearrangements into a ridiculous proposal that perturbed protein folding somehow results in the evolution of biodiversity via disease?

Biophysical constraints prevent mutations from resulting in functional proteins. For example, a fried chicken's egg does not morph into a chicken. However, this report indicates that the egg from a white-throated sparrow might somehow mutate and become an adult of some other species.

For comparison, see: http://www.pnas.o...abstract It details the involvement of nutrient-dependent pheromone-controlled amino acid substitutions and chromosomal rearrangements in biodiversity.
anonymous_9001
5 / 5 (1) Jul 31, 2014
Biophysical constraints prevent mutations from resulting in functional proteins.


Mutagenesis studies resulting in new or altered protein functions directly refute this.

Mutagenesis resulting in blue fluorescence instead of green:

http://onlinelibr...0467/pdf

Resulting in increased antibiotic specificity:

http://www.jbc.or...abstract
JVK
1 / 5 (1) Jul 31, 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.
anonymous_9001
5 / 5 (1) Jul 31, 2014
Is that supposed to be refutation of the articles I posted? It has nothing to do with them, in case you didn't notice.
JVK
1 / 5 (1) Jul 31, 2014
Your pseudoscientific nonsense about mutation-initiated natural selection and evolution of biodiversity has nothing to do with anything that is currently known about cell type differentiation in any species. The fact that you referenced blog posts by atheist blogger PZ Myers in your review of my published work attests to my claims that you will never be more than an anonymous fool named Andrew Jones.

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

"A multitude of misconceptions and misunderstandings can be seen in his comments on Dr. PZ Myers' blog, Pharyngula (Kohl, 2014b)."

More than 1000 blog posts to Pheromones.com (see the "Science" section) and nearly everything on my FB page: https://www.faceb...bookmark attests to the accurate representations in my published and unpublished works.
anonymous_9001
5 / 5 (1) Jul 31, 2014
Another irrelevant post in which you refuse to address the citations I provided above. You're so predictable.

You made the claim that mutations never result in functional alterations. I provided 2 of the countless examples of experiments demonstrating that and you refuse to acknowledge them or point out how they don't refute you.
JVK
1 / 5 (1) Jul 31, 2014
From the link provided by the anonymous fool: Andrew Jones:

Re: "...evolution events that result from the insertion and excision of transposons in nature is discussed." http://www.jbc.or...abstract

Does anyone else, besides PZ Myers, not realize that the insertions and excisions are nutrient-dependent and pheromone-controlled, which links the epigenetic landscape to stabilization of the physical landscape of DNA in the organized genomes of species from microbes to man? Mutations perturb protein folding and destabilize the genome, which is why they are manifested in pathology, not in ecological adaptations manifested in the morphological and behavioral phenotypes of all individuals of all species.
anonymous_9001
5 / 5 (1) Jul 31, 2014
You're still ignoring the mutagenesis studies I posted. They directly refute your opinion that all mutations are detrimental amd destabilizing.
JVK
1 / 5 (1) Jul 31, 2014
Can anyone who is not an anonymous fool or idiot minion of a biology teacher like PZ Myers understand why anyone else might think that my detailed representations of biologically-based cause and effect should be considered as if I had an "...opinion that all mutations are detrimental..." because they destabilize protein folding?

Ecological variation can only lead to ecological adaptations if nutrient-dependent protein folding is stabilized by the fixation of amino acid substitutions. How could mutation-initiated natural selection lead to the evolution of biodiversity unless the mutations that perturb the thermodynamics of protein folding also stabilized the organized genome of a species that then somehow mutated into another? But, why would a species with a stable "mutated" genome mutate into another species? And, how might that be possible?

Are the questions above intelligent questions in the context of theories about mutagenesis. If so, why haven't they been asked and answered.
JVK
1 / 5 (1) Jul 31, 2014
Increased organismal complexity is manifested in the morphological and behavioral phenotypes that are closely linked to organism-level thermoregulation after the thermodynamic cycles of protein biogenesis and degradation have occurred.

Mutations perturb biophysically-constrained thermodynamic cycles of protein biogenesis and degradation that are required for organism-level thermoregulation. However, a textbook that was published on the same day of my 2013 review article claimed that "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." http://www.amazon...99661731

Given the details of biologically-based cause and effect that I provided in my review, http://www.ncbi.n...4693353/ why hasn't anyone told others HOW constraint-breaking mutations lead to evolution, for comparison to nutrient-dependent pheromone-controlled ecological adaptations?
anonymous_9001
5 / 5 (1) Aug 01, 2014
I give you 2 examples of mutation leading to new functional traits and you continue blathering on with your usual nonsense. If you don't have a rebuttal to the 2 papers I posted, just say so.
JVK
1 / 5 (1) Aug 01, 2014
If no one can tell me
HOW constraint-breaking mutations lead to evolution
I have no rebuttal to the suggestion that they can. What makes you think that your examples are meaningful to any serious scientist. You're simply saying nothing of importance because you can't back it up with experimental evidence that validates your simple-minded opinion.

http://www.scienc...11.short
"This epigenetic information has the potential to elucidate regulatory changes underlying species divergence and population adaptation."

Lenski's experiments have served only to confuse anonymous fools and idiot minions of biology teachers like PZ Myers. All experimental evidence of biologically-based cause and effect continues to support my detailed explanation of how cell type differentiation occurs via nutrient-dependent amino acid substitutions.
JVK
1 / 5 (1) Aug 01, 2014
https://www.faceb...0825553/ is the current discussion of

Flaws emerge in RNA method to build tree of life
http://www.nature...-1.15625

This is the most recent attack on Dobzhansky (1964/1973) and on subsequent works, including those I have authored or co-authored since 1996.
anonymous_9001
5 / 5 (1) Aug 01, 2014
You're simply saying nothing of importance because you can't back it up with experimental evidence that validates your simple-minded opinion.


And the papers I posted aren't evidence because...?

Amino acid substitutions are not regulatory nor epigenetic in nature if they're the result of DNA changes.
JVK
1 / 5 (1) Aug 01, 2014
The anonymous fool: Andrew Jones continues to drive me away from discussions here because he seems to have no knowledge of cell type differentiation.

Anyone interested in discussion of biologically-based cause and effect may want to see the discussions elsewhere, so I again recommend: https://www.faceb...0825553/
anonymous_9001
5 / 5 (1) Aug 03, 2014
I repeat:

And the papers I posted aren't evidence because...?


I took a look at that facebook page. I noticed you haven't learned a damn thing about physics over the past few years (remember when I had to inform you that cells are not closes systems? hilarious).

You said on FB:

Since I am not a virologist or physicist,I'm not sure that the laws of physics apply to viruses and their replication.


The laws of physics apply to EVERYTHING. Why on Earth wouldn't they apply to viruses?

If the Second Law of Thermodynamics does not apply to viruses, which means the chemical bonds that enable the amino acid substitutions can form at random and somehow be naturally selected


All the laws of physics apply to everything in biology, as they do in every other field. Where are you getting the idea that the second law prevents mutations?
JVK
1 / 5 (1) Aug 03, 2014
Thanks. I needed the anonymous fool (i.e., Andrew Jones) to admit that the laws of physics apply. Does anyone else realize how the biophysical constraints of nutrient-dependent energy prevent mutation-initiated natural selection from causing the evolution of biodiversity.

See: http://onlinelibr...abstract
"We regard the basic unit of the organism, the cell, as a complex dissipative natural process functioning under the second law of thermodynamics.... Organisms are conglomerates of information bearing cells that optimise the efficiency of energy (nutrient) extraction from its ecosystem. Dissipative processes, such as peptide folding and protein interaction, yield phenotypic information from which form and function emerge from cell to cell interactions within the organism. Organisms... interact to minimise the free energy of their ecosystems. Genetic variation plays no role in this holistic conceptualisation of the life process."
JVK
1 / 5 (1) Aug 03, 2014
Discussion of entropy on the geneticist Ricki Lewis' blog site:
http://blogs.plos...aterial/

PZ Myers even offered his ridiculous opinion. It was intelligent discussion except for Myers' opinion, which was immediately dismissed.

I mentioned "DNA as a Nutrient: Novel Role for Bacterial Competence Gene Homologs" cited in "Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors." http://www.socioa...38/20758

When biology teachers like PZ Myers realize all organisms must eat and that all species must reproduce, they may begin to teach others, like his idiot minion, Andrew Jones, that evolution is biophysically constrained, which is why only ecological variation can lead to the ecological adaptations manifested in the complexity of morphological and behavioral phenotypes.

How can anyone not know that organisms must eat?
JVK
1 / 5 (1) Aug 03, 2014
How can anyone claim that "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." --Mutation-Driven Evolution http://www.amazon...99661731

Why doesn't everyone admit that ecological adaptation is nutrient-dependent and pheromone-controlled. -- Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...3960065/

My review was published on the same day as "Mutation-driven evolution"

My conclusion: "...the model represented here is consistent with what is known about the epigenetic effects of ecologically important nutrients and pheromones on the adaptively evolved behavior of species from microbes to man. Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."

Do constraint-breaking mutations fit into any model?
anonymous_9001
5 / 5 (1) Aug 03, 2014
Does anyone else realize how the biophysical constraints of nutrient-dependent energy prevent mutation-initiated natural selection from causing the evolution of biodiversity.


You have never explained this [opinion] in any appreciable detail. You make the claim that biophysical constraints prevent mutations from contributing to evolution, but you never say WHY.
JVK
not rated yet Aug 03, 2014
Your comments on my model were addressed by the editor of Socioaffective Neuroscience & Psychology.

"Based on his writings, both published and unpublished, James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published." -- from Criticisms of the nutrient-dependent pheromone-controlled evolutionary model
http://www.ncbi.n...4959329/

Editor's note
"The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers."

Andrew Jones (aka anonymous_9001) simply refuses to accept the refutation of pseudoscientific nonsense in my model and hopes to convince others I have nothing more than an opinion.
anonymous_9001
not rated yet Aug 03, 2014
The editorial team let yours through because they obviously needed your errors pointed out to them in retrospect. I assume you're aware none of them are evolutionary biologists or biophysicists. If they were, your "model" would not have been published. Why don't you accept the challenge I gave you a while back and try to get it published in a journal that focuses on evolution or biophysics or try to present it at a relevant conference?

I have refuted your refutation through pointing out your numerous misinterpretations and unsupported statements and had my refutation published in the journal you're in. Either Mouras accepts the validity of my arguments or he let it through as a joke as you stated before, which would make yours a joke as well. I'm going to go with the first option. Mouras' disclaimer means they thought your model was valid *at the time*, not that they think it's still valid *in spite of* my published refutation.
JVK
not rated yet Aug 03, 2014
I cannot imagine anyone more ignorant than those like you who attribute nutrient-dependent pheromone-controlled cell type differentiation to anything other than the amino acid substitutions that differentiate the cell types of all animals species, and probably all plants, given the fact that amino acid substitutions differentiate proteins associated with viral virulence.

That you now attack the editor of the journal and the reviewers is more than enough to convince others of your ignorance. However, why don't you tell us how you think cell type differentiation occurs and leads to the morphological and behavioral phenotypes manifested in species from microbes to man, so everyone can have an even bigger laugh about you and your brainless, spineless, anonymous comments on my published work with references to the comments by the most uniformed biology teacher I have ever encountered: PZ Myers (and his idiot minions).
anonymous_9001
not rated yet Aug 04, 2014
Attack? Your misrepresenting isn't limited to papers, I see. All I'm saying is that evolutionary biology isn't their specialty and I wouldn't expect them to be as rigorous with publications in that field. I wouldn't try to publish an article about evolution in the Astrophysical Journal.
JVK
not rated yet Aug 04, 2014
What articles have you published, Andrew Jones? What articles that link epigenetic cause and effect via de novo Creation of olfactory receptor genes have you read?

Not so pseudo anymore: pseudogenes as therapeutic targets http://www.ncbi.n...4068744/

Do you think that others do not know about the "Epigenetic Trap" that Dobzhansky (1973) set for evolutionary theorists who ignored the fact that "...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."?

Alternatively, if you think that the amino acid substitutions that differentiate the cell types of all cells in all individuals of all species are the result of mutation-initiated natural selection, please tell us why you are ignorant enough to think such ridiculously pseudoscientific thoughts.

Explain your inexplicable nonsense, or quit challenging my explanation of biological facts.
anonymous_9001
not rated yet Aug 04, 2014
Do you think that others do not know about the "Epigenetic Trap" that Dobzhansky (1973) set for evolutionary theorists who ignored the fact that "...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."?


What are you implying here? The difference in hemoglobin between gorillas and the other apes is a genetic difference. It does not stem from epigenetics. Why don't you want to tell everybody why the two papers I posted are invalid? They're clear examples of mutation leading to novel, functional traits.
anonymous_9001
not rated yet Aug 04, 2014
What articles have you published, Andrew Jones?


Just the one that refutes yours and is published in the very same journal, subject to the very same peer review.
anonymous_9001
not rated yet Aug 04, 2014
What articles that link epigenetic cause and effect via de novo Creation of olfactory receptor genes have you read?


I think you're still terribly confused regarding this whole "gene creation" thing. From your site:

The alternative splicings are obviously nutrient-dependent and they lead to 1) de novo gene creation and 2) chromosomal rearrangements


Splicing does not lead to new genes. What citation suggests it does? Splicing occurs at the level of the mRNA following transcription. It makes changes to the mRNA. It does not do anything to the DNA. It does not have the ability to affect the DNA.

JVK
not rated yet Aug 04, 2014
Andrew Jones referenced three works other than mine. See: http://www.ncbi.n...4049134/

The article he thinks he "published" that refutes my refutation of evolutionary theory is akin to a child saying "Nuh-uh" to any serious claim, like mine, which supported by approximately 100 citations to published works by others who have provided details on cell type differentiation via nutrient-dependent amino acid substitutions.

Add this one: http://www.cell.c...)00806-X
"We show that these starvation-induced small RNAs are transmitted transgenerationally, providing a mean for starved worms to control the expression of relevant genes in consecutive generations."

Can anyone else besides the anonymous fool not grasp the fact that alternative splicings of pre-mRNA occur only in organisms that have not already starved to death? Can anyone else grasp the magnitude of ignorance Andrew Jones continues to display?
anonymous_9001
not rated yet Aug 04, 2014
Alternative splicing:

1. Does not occur in prokaryotes, so your model has no explanatory power for bacteria or archea
2. Does not alter the genome, so saying splicing is responsible for de novo gene creation is absolutely false

The article he thinks he "published" that refutes my refutation of evolutionary theory is akin to a child saying "Nuh-uh"


Instead of going through and pointing out what he thinks my mistakes were, Kohl can merely say this over and over.

Add this one: http://www.cell.c...)00806-X
"We show that these starvation-induced small RNAs are transmitted transgenerationally, providing a mean for starved worms to control the expression of relevant genes in consecutive generations."


EXPRESSION of relevant genes. Evolutionary changes concern both expression and SEQUENCE changes, which your model cannot explain due to it being based on epigenetics alone.
JVK
not rated yet Aug 04, 2014
Prokaryotes, on the other hand, splice rarely and mostly non-coding RNAs. http://en.wikiped...splicing

I can draw from the lowest level of knowledge about biologically based cause and effect and use it to counter the anonymous fool's claim that

"Alternative splicing:

1. Does not occur in prokaryotes, so your model has no explanatory power for bacteria or archea "

In addition, light-induced amino acid substitutions differentiate the cell types of plants and animals, which links the phrase "Let there be light" from nutrient-dependent amino acid substitutions in the influenza virus that determine its seasonal virulence, to pheromone-controlled ecological adaptation in species from microbes to man. I have no doubt that these facts, or any other facts will never influence the comments of Andrew Jones, who obviously will continue to believe that atheist blogger PZ Myers knows everything anyone else needs to know about biology because Myers is a biology teacher.
anonymous_9001
not rated yet Aug 04, 2014
The exceedingly rare self-splicing that occurs in prokaryotes is not common enough to be a means for generating significant polypeptide variety. The vast majority is self-splicing of tRNA rather than mRNA as in eukaryotes.

light-induced amino acid substitutions


I seem to recall the citation you used for this not indicating that the substitutions were caused by light, but rather that the substitutions (mutations) changed the resulting protein so that it was better at gathering energy from the light. This is the same mistake you made when trying to explain Lenski's E. coli, which underwent a translocation mutation rather than a change in splicing (oh, and the citrate didn't cause the translocation, or else all of his other populations would have done the same thing).
JVK
not rated yet Aug 04, 2014
The exceedingly rare self-splicing that occurs in prokaryotes, which you claimed did not ever occur is more than sufficient for nutrient-dependent pheromone-controlled ecological adaptations to occur in organism that reproduce at such a rapid rate.

You insist on putting everything into terms of mutations, which continues to attest to your ignorance about how cell type differentiation occurs, which is via amino acid substitutions.

You excel and revel in your ignorance, please stop ignoring biological facts.

"It has been shown previously that the majority of expressed non-ribosomal transcripts are non-coding. We now conclude that differential expression triggered by signaling pathways gives rise to a similar abundance of non-coding content. It is thus unlikely that the prevalence of non-coding transcripts in the cell is a trivial consequence of leaky or random transcription events."
http://genomebiol...15/3/R48
anonymous_9001
not rated yet Aug 04, 2014
http://www.ncbi.n...BK21132/

Bacterial mRNAs do not undergo any significant forms of processing: the primary transcript that is synthesized by the RNA polymerase is itself the mature mRNA, and its translation usually begins before transcription is complete


Doesn't sound sufficient to me. Can you provide a citation quantifying and showing that the rare occurrences of prokaryote splicing are enough to explain their phenotypic variety?
JVK
not rated yet Aug 04, 2014
Of course I can.

Why would I?

Is there a model in which mutation-initated natural selection leads to the evolution of biodiversity in morphological and behavioral phenotypes in species from microbes to man, or only a ridiculous theory based on the pseudoscientific nonsense of population genetics?

A model could be compared to my model, which would make the information on alternative splicings in prokaryotes something to consider. Otherwise, the fact that amino acid substitutions differentiate the cell types of viruses and whales is proof of the concept supported by experimental evidence in model organisms.

Isn't it?
anonymous_9001
not rated yet Aug 04, 2014
99% of making a scientifically valid argument is backing it up with data and proper logic. I offered a paper showing that "Bacterial mRNAs do not undergo any significant forms of processing" and all you can say is
Of course I can (offer data contrary to yours, but) why would I?


The entire point of scientific debate is to bring forth citations and you refuse to.

http://rstb.royal...411.full

Clearly, the root source of quantitative genetic variation is mutation. The rate of input of new variation can be measured by the increase in variance in an inbred line. The effect of spontaneous mutation is typically measured in inbred lines, and thus measures only homozygous effects. This type of experiment gives reliable estimates of Vm, the (steady-state) per generation increase in variance owing to mutation. For many traits, Vm falls in the range 10−3 VE to 10−2 VE (reviewed by Lynch 1988; Lynch & Walsh 1998, ch. 12).
anonymous_9001
not rated yet Aug 04, 2014
http://mbe.oxford...04.short

http://www.ncbi.n.../713.pdf

Recently published, comprehensive book on evolutionary biology. It seems to cover a lot of bases, including Dobzhansky, so you may like it.

http://books.goog...;f=false

http://www.ncbi.n...25080100

http://www.jbc.or...91.short

http://onlinelibr...284/full

This one is a deeper look into the molecular basis of Lenski's cit+ population and how it evolved that trait:

http://www.pnas.o...56.short
JVK
not rated yet Aug 04, 2014
I'm done with this anonymous fool (Andrew Jones) here. Anyone interested in biologically-based cause and effect can follow my posts on

https://www.faceb...0825553/ or on

https://www.faceb...bookmark

There is no point to reading "dated" literature and trying to explain anything to anonymous fools. Although evolutionary theorists may continue to tout mutation-driven evolution, serious scientists know about biophysical constraints and epigenetic effects that have established the fact that:

"Genetic variation plays no role in this holistic conceptualisation of the life process."
http://onlinelibr...abstract
anonymous_9001
not rated yet Aug 04, 2014
Dated? The book and 5 of the 7 articles I posted are from this year! What on Earth are you talking about?

8. 8 relevant citations and you dismiss them all without even a cursory glance (which I know for a fact considering you called them "dated").

JVK
not rated yet Aug 04, 2014
"Genetic variation plays no role in this holistic conceptualisation of the life process."

That means epigenetic effects of nutrients and their metabolism to species-specific pheromones control the life processes of organisms from microbes to man. It also means that any mention of mutations and/or natural selection in the context of the evolution of biodiversity is dated and probably made by someone who doesn't understand the basic principles of biology or levels of biological organization required to link sensory input to cause and effect and biodiversity.

But, the real question here is why you did not mention any of these works in your comments on my 2013 review article http://www.ncbi.n...3960065/

or in the discussion that led to me being banned from participation on the ISHE's human ethology group.

What kind of anonymous fool continues attacking in different venues but never offers an alternative explanation that includes how mutations do anything?
anonymous_9001
not rated yet Aug 05, 2014
That's not at all what that quote means.

Never offer an explanation? When's the last time you had your eyes checked? I only ask because I could have sworn I posted 8 links a little while ago and 2 more a couple days ago talking about mutations resulting in novel traits and how they're involved in evolution.
JVK
not rated yet Aug 05, 2014
I posted 8 links... talking about mutations resulting in novel traits and how they're involved in evolution.


No, like others you simply continue to make ridiculous assumptions about how they're involved in evolution.

"[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

I reiterate: "Assumptions, made but not verified, were taught as fact." -- to anonymous fools and idiot minions of biology teachers like PZ Myers who believe in assumptions.
anonymous_9001
not rated yet Aug 05, 2014
No, like others you simply continue to make ridiculous assumptions about how they're involved in evolution.


10 papers plus the countless others I've posted before are merely assumptions?
JVK
not rated yet Aug 05, 2014
...are merely assumptions?


How could they be anything else. You can't start with the assumptions made by population geneticists and turn them into biological facts without experimental evidence of biophysically-constrained biologically plausible,cause and effect.

I reiterate (redundantly): "Assumptions, made but not verified, were taught as fact." -- to anonymous fools and idiot minions of biology teachers like PZ Myers who believe in assumptions.
anonymous_9001
not rated yet Aug 05, 2014
All those papers are experimental evidence! Did you even read them? They're all about investigating evolution at the molecular level, especially the one about Lenski's bacteria. In what way is that paper not direct insight into what was going on in the genome of that E. coli population?
JVK
not rated yet Aug 05, 2014
Biologically-based: NO MUTATIONS! http://www.scienc...14000495
"The organization of chromatin within the nucleus and the regulation of transcription are tightly linked. Recently, mechanisms underlying this relationship have been uncovered. By defining the organizational hierarchy of the genome, determining changes in chromatin organization associated with changes in cell identity, and describing chromatin organization within the context of linear genomic features (such as chromatin modifications and transcription factor binding) and architectural proteins (including Cohesin, CTCF, and Mediator), a new paradigm in genome biology was established wherein genomes are organized around gene regulatory factors that govern cell identity. As such, chromatin organization plays a central role in establishing and maintaining cell state during development, with gene regulation and genome organization being mutually dependent effectors of cell identity."
JVK
not rated yet Aug 05, 2014
"The Modern Synthesis - the evolutionary theory to which EP is entirely wed - almost exclusively invokes natural (including kin and sexual) selection as the driving force, genetic mutations as the creative force and genetic transmission as the only mechanism of heredity." http://journal.fr...abstract

However, in "Mutation-driven evolution" Nei wrote "...natural selection is an evolutionary process initiated by mutation. It does not have any creative power..." and concluded that "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." http://www.amazon...99661731

In my model, ecological variation and the nutrient-dependent pheromone-controlled physiology of reproduction is the source of all the biodiversity in the world. http://www.ncbi.n...3960065/

There is no other model for that!
JVK
not rated yet Aug 05, 2014
"Strictly speaking the modern synthesis can be understood as a theory of genes, which arguably is poorly equipped to provide a more fully-fledged explanation of the transformation of form, other than the occurrence of genetic mutations and recombinations, which somehow translate into phenotypic modifications." http://journal.fr...abstract

That's why the anonymous fool and other idiot minions of biology teachers cannot explain anything or link the conserved molecular mechanisms of biologically-based cause and effect to the morphological and behavioral phenotypes manifested in the increasing organismal complexity of biodiversity. They have no model and no concept of conserved molecular mechanisms -- so, even after the molecular mechanisms become clear, which makes it clear mutations and natural selection are not involved, those who have been taught to believe in the pseudoscientific nonsense of evolutionary theory can think of nothing else.
JVK
not rated yet Aug 05, 2014
"Specificity turns out to be not inherent in any single biomolecule in these large networks but induced by regulated recruitment and combinatorial control (Ptashne and Gann 2002). And it is here that we will find that the networks cannot be reduced to DNA sequences and gene products..."

http://www.fronti...14.00908

That fact led serious scientists to determine what can lead from ecological variation to nutrient-dependent pheromone-controlled ecological adaptations after abandoning the pseudoscientific nonsense Andrew Jones (aka anonymous_9001) still believes in.
JVK
not rated yet Aug 05, 2014
'...even the determination of the primary sequence of gene products is a creative process of 'molecular epigenesis' that cannot be reduced to the information encoded in the genome alone (Stotz 2006b; Griffiths and Stotz 2013)."

http://journal.fr...abstract

Molecular epigenetics (from our 1996 Hormones and Behavior review)
Yet another kind of epigenetic imprinting occurs in species as diverse as yeast, Drosophila, mice, and humans and is based upon small DNA-binding proteins called "chromo domain" proteins, e.g., polycomb. These proteins affect chromatin structure, often in telomeric regions, and thereby affect transcription and silencing of various genes... (citations). Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and by this mechanism, contribute to sexual differentiation..." of cell types that are obviously differentiated by nutrient-dependent amino acid substitutions.
anonymous_9001
not rated yet Aug 05, 2014
Biologically-based: NO MUTATIONS! http://www.scienc...14000495


You obviously didn't read that paper. That's about the processes that drive cell differentiation DEVELOPMENTALLY within an organism, not over evolutionary timescales. It concerns how stem cells specialize into different tissues and organs using the same genome. Cell differentiation is not analogous to evolution and adaptation.
JVK
not rated yet Aug 05, 2014
Cell differentiation is not analogous to evolution and adaptation.


Nutrient-dependent pheromone-controlled cell type differentiation links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via the conserved molecular mechanisms manifested in the amino acid substitutions that exemplify how biological diversity arises across all genera.

See: Extended evolutionary psychology: the importance of transgenerational developmental plasticity http://journal.fr...abstract

The only thing she does not do to refute the pseudosciefic nonsense of the "Modern Synthesis" is provide details of the molecular epigenetics like I did in my 2013 review, and we did in our 1996 review.
http://www.ncbi.n...3960065/ (2013)
http://www.hawaii...ion.html (1996)
JVK
not rated yet Aug 05, 2014
"... a new paradigm in genome biology was established wherein genomes are organized around gene regulatory factors that govern cell identity." -- A mechanistic link between gene regulation and genome architecture in mammalian development.

The new paradigm in genome biology should have been established when we detailed the mechanisms of molecular epigenetics in our 1996 review. The anonymous fool, and others like him, seem instead to think that cell type differentiation during development within an organism has nothing to do with cell type differentiation over evolutionary time. They're right, cell type differentiation is nutrient-dependent and pheromone-controlled which means it has nothing to do with the evolution of biodiversity, because biodiversity is the manifestation of how ecological variation results in ecological adaptations.

Ecological variation that results in ecological adaptations is not mutation-initiated and does not involve natural selection of anything except food.
JVK
not rated yet Aug 06, 2014
http://www.the-sc...Plans%2F

Re: "They are starting to become two different species on a genetic basis—and on a behavioral basis," says Yawata.

The refutation of claims that E.coli are mutating into a different species are invalidated by what an example of ecological speciation, which is nutrient-dependent and pheromone-controlled in species from microbes to man. The pseudoscientific nonsense touted by ignorant biology teachers like PZ Myers and his idiot minions, or anonymous fools continues to be attacked with experimental evidence of biologically-based cause and effect.

At some point, we will hear no more from the anonymous fool (aka Andrew Jones). Having never made a significant contribution to any discussion, he will crawl back under the woodwork and hopefully never be heard from again.

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