Origin of the Eukaryotic cell: Part II - Cytoskeleton, membranes, and beyond

Origin of the Eukaryotic cell:  Part I - How to train your endosymbiont
Credit: Cold Spring Harbor Press

(Phys.org) —In Part I of our review of the new book "The Origin and Evolution of the Eukaryotic Cell" we talked about the acquisition of endosymbionts by cells. While there we focused on some of the genetic issues involved in acquiring mitochondria, here we want to focus on some of the other structural features that defined eukaryotic evolution. One approach that many of the chapter authors take is to examine the ways in which different bacterial and archaeal cells solve the universal problems of building membranes, organizing DNA, and constructing cilia or flagella to move things about. If prevailing intuitions are right, then once we are armed with sufficient knowledge regarding which primitive bacteria bear the rudimentary traces of the major innovations that define eukaryotic cells then the one true evolutionary path should be laid bare before us.

In the grand and timeless scheme of Cavalier-Smith, which we discussed in Part I, the original bacterial "cenancestor" (and all later Eukaryotes) have largely employed bilayer membranes constructed with fatty acid chains linked through ester bonds to a glycerol 3 phosphate backbone. The highly contentious eukaryotic sister clade, the Archaea, inhabit more extreme enviroments and therefore do membranes a little bit differently. It appears they split from the main evolutionary trunk around the time they began to substitute in membranes made from isoprenoid chains linked through ether bonds to a glycerol 1 phosphate (G-1-P) backbone. A major mystery is hiding in the dry details of which cells use G-1-P and which use it's mirror image, G-3-P—namely, where did glycerol come from in the first place? A good explanation for the spontaneous formation of glycerol here on earth is still lacking. Just to whet the appetite, we offer that one new idea hints at the possible origins of glycerol deep within electron-irradiated interstellar methanol ices.

One seeming paradox highlighted by Nick Lane's chapter is that while archaea and bacteria place similar values on fundamental issues like DNA transcription, ribosomal translation, and their ATP synthases, they differ in basic membrane-linked processes such as DNA replication. While the genetic, structural and phylogenetic data in general tends to address membrane or cytoskeletal homologies separately, the real story doesn't contain evolution of two structures in isolated cellular vacuums. Membranes of ever increasing flexibility and selective permeability are only useful when mated to an equaly nimble cytoskeletal apparatus that is capable of things like phagocytosis, or controlling organelle geometry, movement, and division.

Of central importance is the evolution of the cell is its centriole, which among other things serves as a cytoskeletal organizing center. The centriole conducts an orchestra that in many cells might still play flawlessly without it—at least through the first stanza. Over time however, cell harmony would inevitably be sacrificed if the cell can't quickly evolve sufficient compensations for the absent centrioles. In cells that have them, the centriole is intimately linked to the primary cilium or flagella, and much of the search for the ancestral eukaryote consists in defining how centrioles are controlled and replicated across successive cell cycles in different protists. Not only how many centrioles exist and where in the cell they are located, but also how many so-called "microtubule cones" each elaborates are important questions that need to be more fully defined.

A few key features of how cilia or flagella are built in bacteria, archaea and eukarytoes are probably worth mentioning here. The bacterial flagellum evolved not only to give creationists something to get worked up about, but also to give the origin of life sleuths a fascinating puzzle. Flagella on generally use two bearings in the lipid membrane while the gram negative versions have four bearings on account of the double membrane. All bacteria construct flagella by pumping individual flagellin protein subunits through a central bore out to the growing tip, but some are powered by hydrogen ions (proton motive force), while others instead by a sodium gradient. The unique forward and reverse motions of each these cellular appendages in space is yet another dimension to their character which seems to organize every aspect of their existence.

The archaea use their own archael flagellins (called archaellins), which are similar to bacterial type IV pilins. Archaea add successive protein subunits instead to the cell side of their growing flagellar chain, but power it using ATP just like the eukaryotes. The eukaryotes build their cilia from tubulin, an entirely different building block, and supply materials to the growing tip just like the bacteria do, except they use their own unique intraflagellar transport system to do it. The evolution of tubulins and actin from their hypothesized ancestral protein superfamilies —FtsZ and Mreb respectively—is an interesting tale that contains many life lessons for us here.

One thing that is seen over and over again is that freedom to evolve new sequence, structure and function, as typically created by gene duplication, relaxes many of the requirements on the original protein and can therefore facilliate the wholesale replacement of subcellular forms and organelle designs. One example in the duplication of tubulin genes would be in the selection of an actin ring vs a tubulin-based Z-ring in various species for maintaining cell geometry and controlling division. Although the role of FtsZ in division is analogous to that of actin (and the actin-myosin ring) in eukaryotes, there is no known motor associated with it.

In this absence the fertile imagination has readily supplied potential mechanisms for force generation. Chromosome pumps that behave like an osmotic contractile gel, expanding and constricting throughout mitosis, could be one such supplier of the mysterious "cytokinetic force" that researchers have previously shown must exist. With the case of FtsZ, a contractile force was found even in the absence of all other proteins. The use of an FtsZ ring in dividing chloroplasts and some mitochondria is suggestive of their deep their prokaryotic ancestry.

In the previous installment Torbjorn Larsson left us some insightful comments regarding the vertically inherited ATP importer of the premitochondrion, as opposed a horizontally descended ATP-exporter, noting its ability function in low oxygen environments. The various milestones in eukarytoic evolution still require accurate placement in time with respect to the background eco-physiology of the Earth. Undoubtedly its oxygenation is the big one. A recent paper gives a tantalyzing new hypothesis that would not only address these question but might also clear up doubts in our existing theories for the mitochondrion's origins.

The paper notes that although detailed images of the cellular structure of a class of alpha-protobacterial known as methaotrophs have been available for over half a century, apparently nobody has (until now) realized that they might be looking at actual mitochondrial cristae in living bacteria. I asked author Mauro Espostiif these unique inner membrane structures of Methylomonas might contain cristae junction proteins that would be analogous to those now found in our mitochondria, and he indicated that a refined sequence analysis has yet to be done for these creatures.

In his chapter, Cavalier-Smith uses the shape of mitochondrial cristae (either tubular or flattened), the structure of the golgi (absent or with stacked dictysomes), and the particular variety of intron splicing elements as important indicators of possible relatedness and ancestry in cells. Moving the field forward will undoubtedly require new links between these kinds of structures and the genetic sequence information that is now rapidly becoming available.


Explore further

Origin of the Eukaryotic cell: Part I - How to train your endosymbiont

More information: The Origin and Evolution of Eukaryotes: cshperspectives.cshlp.org/cgi/ … lution_of_eukaryotes

Part 1 of the story is here: phys.org/news/2014-12-eukaryot … ll-endosymbiont.html

© 2014 Phys.org

Citation: Origin of the Eukaryotic cell: Part II - Cytoskeleton, membranes, and beyond (2014, December 17) retrieved 18 October 2019 from https://phys.org/news/2014-12-eukaryotic-cell-ii-cytoskeleton.html
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Dec 17, 2014
The bacterial flagellum evolved not only to give creationists something to get worked up about, but also to give the origin of life sleuths a fascinating puzzle.
this sentence alone will keep kohlslaw posting for the next three months straight

i love seeing this
at least John Hewitt has a sense of humor!
THANKS

Dec 17, 2014
The bacterial flagellum evolved not only to give creationists something to get worked up about, but also to give the origin of life sleuths a fascinating puzzle.
this sentence alone will keep kohlslaw posting for the next three months straight

i love seeing this
at least John Hewitt has a sense of humor!
THANKS


I was thinking the same thing this morning. Surprised the jackass hasn't shown up yet.

Dec 17, 2014
I was thinking the same thing this morning. Surprised the jackass hasn't shown up yet.

Awww... you went and threw the gauntlet. Only a matter of minutes now, then....

JVK
Dec 17, 2014
These biologically uninformed idiot minions of the biology teacher PZ Myers think I am the only one who understands how RNA-mediated events link amino acid substitutions to cell type differentiation in species from microbes to man via the conserved molecular mechanisms of nutrient-dependent bio-physically constrained protein folding.

See also: One Plus One Equals One: Symbiosis and the evolution of complex life
http://www.amazon...9966059X

(p. 26) "The haemoglobin data supported the idea that protein sequences diverge from another at a constant rate: the more distantly related two species were--as inferred from the fossil record, for example--the more differences one would see in their amino acid sequences."

John Hewitt is one of few people who could potentially link quantum physics to quantum biology without use of de Vries definition of 'mutation.' Most others link mutations to increasing organismal complexity.

JVK
Dec 17, 2014
The ribosome as a missing link in the evolution of life
http://www.scienc...14006778

"We believe that our results provide tantalizing insights into evolution processes that bridge the RNA-world and compositional approaches to the origins of life with LUCA approaches to provide an intermediary state of organization that integrates self-replication with protein translation."

Those who think self-replication arose in the context of mutations should will not like this excerpt from an article, co-authored by co-editor of this book: Eugene Koonin.

"We cannot conceive of a global external factor that could cause... parallel evolution of amino acid compositions of proteins in 15 diverse taxa that... span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms."

Dec 17, 2014
These biologically uninformed idiot minions of the biology teacher PZ Myers,,,,


Cher, you are not any better at name calling then you are selling stinky love potions.

think I am the only one who understands how


Who told you that lie Skippy. Nobody around here thinks that.

RNA-mediated events link amino acid substitutions to cell type differentiation in species from microbes to man via the conserved molecular mechanisms of nutrient-dependent bio-physically constrained protein folding.


"nutrient-dependent-bio-physical-constrained-folded-gobbledygook" right back to you Cher.

Dec 17, 2014
John Hewitt is one of few people who could potentially link quantum physics to quantum biology without use of de Vries definition of 'mutation.' Most others link mutations to increasing organismal complexity.
john Hewitt or John Archibald?
because you say Hewitt after you linked a book by Archibald...

never mind... i will simply inquire to BOTH of them about the role of mutations in biology as well as the validity of Lenski and Extavour's publications or their claims regarding your interpretations of their work

Especially that part where you call them idiots because they said there was suck a thing as beneficial mutations and that you were wrong about their work

I will include all your posturings and rantings from here (on Phys.org) VERBATIM, like usual
ok?

great!
now we are getting somewhere!

JVK
Dec 17, 2014
Note: In part 1, John Hewitt wrote: "While horizontal, lateral and verticle gene flow among bacteria, archaea, and eukaryotes are constant confusers across species, the ribosomal RNA and riboproteins that exist in several unique cell-trafficking or inheritance scenarious in the organelles of single cell can be even more confounding."

This shows how quickly scientific progress can be made by dispensing with the pseudoscientific nonsense about mutations and the evolution of biodiversity. In the past two weeks alone, serious scientists have learned that everything comes down to RNA-mediated amino acid substitutions and protein folding that differentiates cell types via conserved molecular mechanisms in species from microbes to man.

See: A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping http://www.cell.c...)01497-4

See also: http://www.ncbi.n...24693353 for details on feedback loops.

Dec 17, 2014
This shows how quickly scientific progress can be made by dispensing with the pseudoscientific nonsense about mutations and the evolution of biodiversity.


Is that why after 20 years of writing this foolishment you are still the only Skippy buying it? They haven't made so much progress if everybody still thinks you are the bioque (that's coonass that means moron).

JVK
Dec 17, 2014
john Hewitt or John Archibald?


John Hewitt is one of the few people who may understand how "Molecular Vibration-Sensing Component in Human Olfaction" http://dx.doi.org....0055780
can be linked to John Archibald's representations of how amino acid substitutions differentiate cell types.

The link from light-induced amino acid substitutions in plants to nutrient-dependent pheromone-controlled cell type differentiation in animals will not be clear to anyone who accepts the role of "mutations" in ridiculous theories about evolution. Clearly, they have failed to realize the definition was an early attempt to explain ecological adaptations based on ecological variations in sources of energy that fuel the thermodynamic cycles of protein biosynthesis and degradation characteristic of differences between phosphorus and epigenetic effects linked to phosphorylation.

JVK
Dec 17, 2014
Watch the responses to part II of John Hewitt's review, which includes current information about cell type differentiation. The biologically uninformed will probably destroy any attempt to discuss bio-physically constrained nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species.

Wait to see if anyone else realizes that de Vries definition of 'mutation' was a feeble attempt to explain observable differences at a time when little was known about how energy was required to link physics to chemistry and biologically-based cause and effect.

Try not to judge too harshly the intelligence of evolutionary theorists based on what they were taught to believe in. They are the people your biology teacher should have warned you about, but your biology teacher may have been one of them.

see also: http://cshperspec...abstract

Dec 17, 2014
Great links, particularly the recent chromatin loops paper.
Good comments often tend to have good links, lets all keep it civil and learn from each what they have to offer.

JVK
Dec 17, 2014
Thanks. These folks are scared, John. They can almost sense what's coming, and they know they are not going to like it. If it does not support de Vries definition of 'mutation' and its use in defining neo-Darwinian theory, they will attack you, also.

But, as serious scientists know, de Vries definition led to Nei's 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." (p. 199) Mutation-Driven Evolution http://www.amazon...99661731

The fact that I have been attacked based on Nei's claim and the claims others have made about mutations, natural selection, and evolution leaves no 'wiggle room' for theorists whose beliefs have not been supported in the context of evidence that shows how ecological variation leads to ecological adaptation via RNA-mediated events, not evolutionary inferences.

I look forward to Part III and more.

JVK
Dec 17, 2014
The bacterial flagellum evolved not only to give creationists something to get worked up about...


this sentence alone will keep kohlslaw posting for the next three months straight


It's much worse than that. The differences between gram positive and gram negative organisms are linked to cell types that take up the crystal violet stain and those that can subsequently be decolorized and counter-stained.

Obviously, there are other differences in morphological phenotypes and behavioral phenotypes and in growth characteristics that include many other factors that differentiate species -- and even those strains that have been sub-cultured for long enough to slightly change their patterns of antibiotic resistance/sensitivity, as did Lenski's E. coli.

Those who have claimed the changes are evidence that beneficial mutations lead to evolution have not tried to understand the complexity of nutrient-dependent pheromone-controlled cell type differentiation.



Dec 17, 2014
For clarity: John Hewitt has been studying and publishing on behavioural genetics for 40 years. He does NOT support JVK's bogus pheromone-is-all-of-biology claims at all. Nobody in the science community does.

JVK is James V Kohl, a maker of fake pheromone perfume sex shop paraphernalia for the gullible.

It's all just self-serving commercial word salad for this scammer.

JVK
Dec 17, 2014
I am the author or co-author of a series of published works that link RNA-directed DNA methylation and RNA-mediated events from metabolic networks to cell type differentiation via amino acid substitutions.

I have been presenting and publishing on how the epigenetic landscape is linked to the physical landscape of DNA in organized genomes for 2 decades and do not care who supports me. The facts about cell type differentiation have not changed.

See for instance, the molecular epigenetics section of our 1996 review: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

The model of RNA-mediated cell type differentiation was extended by others to insects (2000) and to the life history transitions of honeybees (2005) before my most recent review was published.

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

JVK
Dec 17, 2014
Great links, particularly the recent chromatin loops paper.


Thanks. It was a game-changer. Those who have not followed the extant literature that links metabolic networks and genetic networks via protein folding may want to see the report on the journal article in The Scientist Magazine.

http://www.the-sc...e-Loops/

See also: http://www.scienc...4419.htm

"When you see genes turn on or off, what lies behind that is a change in folding. It's a different way of thinking about how cells work."

For additional attacks on my credibility by anonymous trolls, see: http://phys.org/n...tic.html

Excerpt: "Folding drives function,"said co-first author Miriam Huntley..."

Mutations perturb protein folding! They do not lead to the increasing organismal complexity manifested in biodiversity.


Dec 17, 2014
Good comments often tend to have good links, lets all keep it civil and learn from each what they have to offer.
@JohnHew
perhaps you can clarify this then, John
kohl says
Mutations perturb protein folding! They do not lead to the increasing organismal complexity manifested in biodiversity
even while promoting his model, which, by definition, causes mutations
I cite his previous comments when i asked him
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 kohl answered answered
YES!
--Thanks for asking
But beyond this, as shown in this comment thread: http://phys.org/n...firstCmt

[to be contd]

Dec 17, 2014
[ctd]
But beyond this, as shown in this comment thread: http://phys.org/n...firstCmt

kohl states that there are no beneficial mutations (and that Lenski and Extavour are idiots, per the thread) because Dr. Extavour stated
mutations, ALSO play a role in the evolution
So now can you specifically clarify this:

1. Do you believe in the role of Mutations in the Theory of Evolution?
2. Do you concur with Dr. Extavour when she stated
So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution

Simple questions & kohl cannot refute having said anything so, as he HAS put it
Are you one of the idiots who was taught to believe in the pseudoscientific nonsense about mutations, natural selection, and the evolution of biodiversity?
Simple and to the point... Please expound on your knowledge of MUTATIONS

thanks

Dec 17, 2014
For clarity: John Hewitt has been studying and publishing on behavioural genetics for 40 years. He does NOT support JVK's bogus pheromone-is-all-of-biology claims at all. Nobody in the science community does.

JVK is James V Kohl, a maker of fake pheromone perfume sex shop paraphernalia for the gullible.

It's all just self-serving commercial word salad for this scammer.


Wrong John Hewitt.
https://sciencex.com/authors/

Dec 18, 2014
@johnhew

Here's a link to what Khol is really all about. His "perfume" business based on pseudoscience.

http://pheromones...4NY.dpbs

Dec 18, 2014
@JohnHew
One last point for you to clarify: with regard to Kohls claims
Quotes from his past
mutations perturb protein folding...
Perturbed protein folding is never beneficial...
I refuse to accept definitions and assumptions about mutations...
Are you one of the idiots who was taught to believe in the pseudoscientific nonsense about mutations, natural selection, and the evolution of biodiversity?
care to comment on the above quotes from Kohl regarding mutations? (located here: http://phys.org/n...firstCmt )
attacks on my credibility by anonymous trolls
if you refute him in any way, he will simply turn on you as well, you can guarantee it... he USED to use Dr. Extavour to support his claims till i posted her reply
you [Captain Stumpy- (CS)] are right that we in no way claim that mutations in the heritable genome play no role in evolution.
I am awaiting your reply

JVK
Dec 18, 2014
His "perfume" business based on pseudoscience.


From the Science section of my commercial site there are links to:
166 Blog posts on RNA-mediated events
http://perfumingt...mit.y=19

Many also address protein folding, which is mentioned in 145 blog posts
http://perfumingt...bmit.y=0

Those who do not understand the attacks on my credibility need only wait until John Hewitt finishes his review of the book.

If any chapters provide experimental evidence of biologically-based cause and effect that can be linked from beneficial mutations and/or their natural selection to the evolution of increasing organismal complexity manifested in the diversity of morphological and behavioral phenotypes, the evidence can be compared to what is known about how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man.

Dec 18, 2014
The ribosome as a missing link in the evolution of life
http://www.scienc...14006778


That's funny. That's a major basis of support of the RNA world hypothesis and, as I demonstrated in my thesis, RNA enzymes, like the ribosome, are subject to Darwinian natural selection.

The link from light-induced amino acid substitutions


You mean those substitutions you can't prove were CAUSED by light? Many organisms are exposed to light. How can you differentiate the substitutions that are caused by light (which needs a mechanism, by the way) and those that are caused by nutrients (which also still needs a mechanism)? In your model, how do you know the substitutions in Lenski's E. coli weren't cause by light? They were exposed to light too.

You have absolutely no idea what causality is or how to determine it.

JVK
Dec 18, 2014
You have absolutely no idea what causality is or how to determine it.


You have only your belief in pseudoscientific nonsense, which is why you can't explain how mutations can cause the evolution of biodiversity. Serious scientists and intelligent journalists have you at a disadvantage.

Re: the "hydrogen hypothesis" mentioned in Part I of John Hewitt's book review

See: http://www.scienc...1127.htm
Excerpt: "...hydrogen-rich fluids host complex microbial communities that are nurtured by the chemicals dissolved in the fluids."

The link from quantum physics to quantum biology and ecologically adapted biodiversity appears to be energy, not the definition of 'mutation.'

@John Hewitt Let me know if I am interfering with your ability to convey a coherent message in your review of the book. As you can see, it's almost impossible to discuss the topics here, unless the pseudoscientist are forced to comply with basic courtesies.

Dec 18, 2014
Regarding causality, I'll simplify it for you, using an example I've presented to you multiple times and you still can't explain: Each of Lenski's 12 IDENTICAL populations were exposed to IDENTICAL environments. How would your model produce different adaptations in each if that's the case? If specific nutrients produced specific DNA changes, then there's no way they could be different.

Dec 18, 2014
While it is impossible to deny a role of mutations in evolution, it is greatly exaggerated compared to the more powerful mechanisms that are built into the system. For the higher animals, that is clearly mate selection. I have some thoughts about it is these articles below on a topic at the rough edges of the knowable. I have never been a huge pheromone fan myself, but have never come across someone in the business who is on top of the literature as JVK.
Even if you disagree with certain ideas, it is often worthwhile to watch shows about aliens building pyramids to get information about how humans actually built them.

http://www.extrem...ia-sperm

Dec 18, 2014
and this one on a similar follow up study: http://phys.org/n...nce.html
also a correction, Mauro's actual surname is Degli Esposti
http://scholar.go...mp;hl=en

JVK
Dec 18, 2014
While it is impossible to deny a role of mutations in evolution...


The role of odors is linked to the experience-dependent de novo creation of receptors that allow the entry of nutrients into the cell.

The metabolism of the nutrients to species-specific pheromones links genetic networks and metabolic networks via RNA-mediated events and cell type differentiation.

Mutations accumulate and eliminate receptors that are no longer required for organism-level genomic stability, which is enabled by amino acid substitutions in DNA.

Mutations perturb protein folding, which is why they do not contribute to increasing organismal complexity via natural selection that leads to biodiversity. Their contribution to ecological adaptation is via elimination of what's unnecessary.

If flagella were not needed for movement, nutrient-dependent cell type differentiation controlled by reproduction would eliminate them -- like unnecessary eyes in cave fish.

JVK
Dec 18, 2014
I have never been a huge pheromone fan myself, but have never come across someone in the business who is on top of the literature as JVK.


Thanks. Kudos to you for recognizing how important it is to have a model of biologically-based cause and effect.

To further probe these behavioral phenomena, Ziv suggests that olfactory processes could be blocked at various stages in the adults.


Leslie Vosshall's group recently showed how this works in experiments on life history transitions in mosquitoes.

(2014) Evolution of mosquito preference for humans linked to an odorant receptor
http://dx.doi.org...ure13964

(2013) orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET http://www.ncbi.n...3696029/

(2012) Amino Acid Residues Contributing to Function of the Heteromeric Insect Olfactory Receptor Complex http://www.ploson....0032372

JVK
Dec 18, 2014
Most serious scientists are one step away from realizing the importance of feedback loops to protein folding that links physics, chemistry, and conserved molecular mechanisms of cell type differentiation.

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

What we see here, except from John Hewitt, is how offensive ideas about mutations, which somehow lead to increasing organismal complexity and the evolution of biodiversity, can be. The biologically uninformed continue to yell: MUTATIONS!

Serious scientists ignore them, but their pseudoscientific nonsense has caused severe delays in scientific progress -- almost everywhere, except in Israel, where the theory of evolution is now taught as an example of nonsense at the same time students in middle school learn about ecology. http://www.educat...olution/

JVK
Dec 18, 2014
Biophysicists interested in cell type differentiation in health and disease will be interested in works by Eshel Ben-Jacob et al.

(2003) http://rsta.royal...abstract
Bacterial self-organization: co-enhancement of complexification and adaptability in a dynamic environment

(2009) http://dx.doi.org....05022.x Learning from Bacteria about Natural Information Processing

(2014) http://dx.doi.org...rep06449 The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition

(2014) Modeling putative therapeutic implications of exosome exchange between tumor and immune cells http://www.pnas.o...abstract "Fluctuations in energy sources and oxygen within a tumor contribute to malignant progression and cell phenotypic diversity (22, 23)."

Dec 18, 2014
For clarity: John Hewitt has been studying and publishing on behavioural genetics for 40 years. He does NOT support JVK's bogus pheromone-is-all-of-biology claims at all. Nobody in the science community does.

JVK is James V Kohl, a maker of fake pheromone perfume sex shop paraphernalia for the gullible.

It's all just self-serving commercial word salad for this scammer.


Thanks for the info, LOL, I though he/she/it was just your run-off-the-mill nutjob XD

JVK
Dec 18, 2014
For comparison to everything known by serious scientists, see Criticisms of the nutrient-dependent pheromone-controlled evolutionary model http://www.ncbi.n...24959329

Excerpt: "James Kohl presents an unsupported challenge to modern evolutionary theory..."

The author, Andrew Jones (aka anonymous_9001) -- see his comments above -- continues to ignore everything known about cell type differentiation, which I detailed with examples in my review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Rarely have I encountered his level of ignorance, which can be compared to the intelligence of others like John Hewitt and Eshel Ben-Jacob "Modeling putative therapeutic implications..."

Modeling based on nutrigenomics has led to pharmacogenomic profiles that differentiate between effects of mutations and RNA-mediated amino acid substitutions on metabolic networks and genetic networks.

JVK
Dec 18, 2014
John Hewitt:

have never come across someone in the business who is on top of the literature as JVK.


Re: It's all just self-serving commercial word salad for this scammer.

EnricM
Thanks for the info, LOL, I though he/she/it was just your run-off-the-mill nutjob XD


If the moderator is not going to rid us of this nonsense, there is no point to attempts to discuss facts.

JVK
Dec 18, 2014
http://en.wikiped...rylation
Oxidative phosphorylation (or OXPHOS in short) is the metabolic pathway in which the mitochondria in cells use their structure, enzymes, and energy released by the oxidation of nutrients to reform ATP. Although the many forms of life on earth use a range of different nutrients, ATP is the molecule that supplies energy to metabolism.


Evolutionary theorists take de Vries definition of 'mutation' and remove factors that don't fit their theories from consideration. For example: "...we will not consider geographical and ecological factors.... Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation...." (p. 813) http://gbe.oxford...abstract

Energy use that leads to perturbed protein folding is inefficient, which is why mutations are typically eliminated when they accumulate and prevent energy-dependent cell type functions.

Dec 18, 2014
While it is impossible to deny a role of mutations in evolution, it is greatly exaggerated compared to the more powerful mechanisms that are built into the system
@JohnHew
well, the point is NOT that there are more powerful mechanisms, as this is something that we all can see and agree on. The point was that, in your words
it is impossible to deny a role of mutations in evolution
and this is exactly what kohlslaw does
No one is claiming anything else except him. Even with your expertise, he continues his diatribe against ALL mutations
Mutations perturb protein folding, which is why they do not contribute to increasing organismal complexity via natural selection that leads to biodiversity
in the face of overwhelming evidence, kohlslaw refuses to acknowledge the science and clings to his creationist ideas

THAT is the point most people make when dealing with him (from Anon to myself)

Dec 18, 2014
[contd]
in the face of overwhelming evidence, kohlslaw refuses to acknowledge the science and clings to his creationist ideas
and nowhere is this set of facts more evident than here: http://phys.org/n...firstCmt

Read through his arguments with Anonymous9001 and you will see a creationist pseudoscience acolyte clinging to a belief, not to the science

Anon tries to show that there ARE such things as beneficial mutations, which kohlslaw completely ignores and disagrees with regardless of the information and evidence

By the way, you can also see that the evidence is NOT a model, but repeated experiments done by Lenski et. al. and Dr. Extavour, et. al.

This is therefore not a debatable subject, especially with regard to the comparison to a model

so he now floods with minute details meant to distract from the original conversation (beneficial mutations) demonstrated by his own model


Dec 18, 2014
[contd] and as for that last part
(beneficial mutations) demonstrated by his own model
kohlslaw cannot even accept that simple fact

not a denigration of any work, but a fact, proven by his own words

his model causes mutations, as it causes changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element

Which, for some reason, kohlslaw actually refutes
STOP TELLING PEOPLE THAT MY MODEL CAUSES MUTATIONS, YOU IDIOT!
his words, verbatim & you can find the quote here: http://phys.org/n...ell.html

So what do you say, JohnHew?
Is the definition of the word Mutation, used by biologists and geneticists the world over wrong?
are all the users of the word idiots, like kohlslaw points out?
do people with educations need to stop using the nomenclature/lexicon?
Are all biology teachers/prof's who use the word mutation idiots?

or is someone being just a tad ridiculous?


JVK
Dec 18, 2014
Is the definition of the word Mutation, used by biologists and geneticists the world over wrong?


The question that also arises in this context is: "Have you stopped beating your dog?"

Yes means you were beating your dog.
No means you will continue to do so.

Those who have based their beliefs about evolution on a definition and assumptions will not tell anyone how perturbed protein folding could lead to the evolution of biodiversity and they will not quit beating to death the horse they rode in on.

".de Vries discovered that in the offspring even of thoroughly pure-bred stocks... two or three in tens of thousands, turn up with small but 'jump-like' changes... a discontinuity... as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels."

JVK
Dec 18, 2014
Are all biology teachers/prof's who use the word mutation idiots?


Thanks for asking.

Only if they use it to infer that mutations lead to the evolution of increasing organismal complexity that is obviously nutrient-dependent and controlled by the physiology of reproduction in species from microbes to man by feedback loops that link food "odors" and the metabolism of nutrients to pheromone-controlled feedback loops.

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

Biology teachers/prof's who use the word mutation are science idiots if they use it in the context of evolutionary inferences now that serious scientists understand the role of RNA-mediated amino acid substitutions in cell type differentiation.

Dec 18, 2014
I am not sure there is a fundamental flaw with the basic concept of mutation any more than there is with the idea that, for example, an event of radioactive decay might be said to be random. The idea that good mutations can accumulate in the face of a preponderance of bad to drive evolution of new structure through natural selection is what I find preposterous at this point in the game.

Dec 18, 2014
in this context
you are wrong and this is your lack of education showing here

because you failed out of college, you think that everyone who is educated is an idiot, as shown by your contempt in other threads like: http://phys.org/n...ell.html
or here: http://phys.org/n...firstCmt

there is no way to be nice to you (proven in various threads when trying to discuss your model) and there is no way to disagree with you without being labeled an idiot because we are educated beyond you. If someone doesn't agree with you 100%, they are an idiot

it's your failing, kohlslaw, not ours

you should check that ego, because it is a primary reason that you refuse to acknowledge the science! and THAT is supported by your denigration of Dr. Extavour (whom you've cited as supporting you in the past until she refuted your comments directly under inquiry-now she is an idiot per your words)

JVK
Dec 18, 2014
The idea that good mutations can accumulate in the face of a preponderance of bad to drive evolution of new structure through natural selection is what I find preposterous at this point in the game.


Thanks. I've found that idea to be preposterous since the time I began my training as a medical laboratory scientist. Nothing beneficial was ever attributed to chemical imbalances or to perturbed protein folding.

From the perspective of the immune system and thermodynamic cycles of protein biosynthesis and degradation, benefits from mutations would be akin to those accumulated if frying enough eggs resulted in the functional protein structures and physiology of a live chicken.

What's preposterous is the beliefs that my antagonists have continued to tout in their attacks on everything currently known about physics, chemistry, and conserved molecular mechanisms of ecological adaptations sans fried eggs. They want to link the fried eggs to evolution of the chicken.

Dec 18, 2014
I am not sure there is a fundamental flaw with the basic concept of mutation any more than there is with the idea that, for example, an event of radioactive decay might be said to be random. The idea that good mutations can accumulate in the face of a preponderance of bad to drive evolution of new structure through natural selection is what I find preposterous at this point in the game.


Then I take it you are not the real John-Hewitt-Skippy? Maybe you are the JVK-not-John-Hewitt-Skippy? Is that right? He's done that before a couple of places.

Dec 18, 2014
The idea that good mutations can accumulate in the face of a preponderance of bad to drive evolution of new structure through natural selection is what I find preposterous at this point in the game.
This is interesting. Why? The vast preponderance of evidence supports the evolution of new structure through natural selection. Furthermore "bad" or "good" mutation is purely subjective - a "bad" mutation in one environment may be considered a "good" mutation in another. What exactly do you have a problem with?

Dec 18, 2014

For creating the planthopper's gears:
http://www.extrem...creature
and the firefly's mantle:
http://www.extrem...ogy-leds
the language of mutations and base pairs would be the last I would elect to describe how the species did it.

Read more at: http://phys.org/n...html#jCp

Dec 18, 2014
Waiting through an infinite progression of random and negative base pair substitutions IS the monkey banging on the Shakespearean typewriter problem in the absence of more powerful mechanisms like viral manipulation, epigenetics, duplication, inversion, reading frame adjustments, splice variant, subunit and exon selection, etc, which are operated by more direct mechanisms than UV radiation, chemical insult or just plane old natural (predictable) progression or clustering through the base pair modification mill.

Dec 18, 2014
Waiting through an infinite progression of random and negative base pair substitutions IS the monkey banging on the Shakespearean typewriter problem in the absence of more powerful mechanisms like viral manipulation, epigenetics, duplication, inversion, reading frame adjustments, splice variant, subunit and exon selection, etc, which are operated by more direct mechanisms than UV radiation, chemical insult or just plane old natural (predictable) progression or clustering through the base pair modification mill.


So I take it then you are another crankpot-Skippy? Quoting your own articles (if you really are the John-Hewitt-Skippy and not the JVK-not-John-Hewitt-Skippy) is what the JVK-crankpot-Skippy does, and he always puts in a plug for his stinky love potions. He also likes to put articles that disagree with him and says they agree (he's stupid like that.).

Dec 18, 2014
Do you want to continue to comment on physorg Ira? If so start you can start by saying something positive or worthwhile that conveys real information. If not then find somewhere else to deposit the insults and hate you have obviously accumulated in life

JVK
Dec 18, 2014
Re:
...the monkey banging on the Shakespearean typewriter problem...


This is what evolutionary theorists have been taught to believe in. It's all they have! It's why I wrote:
The biologically uninformed will probably destroy any attempt to discuss bio-physically constrained.... RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species."


They have not noticed that Dobzhansky (1973) attested to the role of amino acid substitutions in cell type differentiation more than 40 years ago. "...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

Instead, they fit the picture of monkeys banging on the Shakespearean typewriter who think that given enough time they will evolve into more intelligent beings.

Dec 18, 2014
Do you want to continue to comment on physorg Ira?


I come alone, and go alone. Nice try, but Ira-Skippy will for sure take you up on that Cher. Laissez les bons temps rouler P'tit-Boug-Skippy (that's the way a Cajun say bring it on little man.) Do your worst Skippy.
,

If so start you can start by saying something positive or worthwhile that conveys real information. If not then find somewhere else to deposit the insults and hate you have obviously accumulated in life


Oh, you mean as opposed to peoples calling anyone who disagrees with them idiots, ignorant, stupid, morons, fools, and such like of that? Especially when they are the one sole single only person in the world who has got it right, everybody is idiots, ignorant, stupid, morons fools and such like.

Dec 18, 2014
Au contraire mon frere, I just did - gave you two examples, either of which you are free at any time to tell us how you would build them by radiating your base pair strings

Dec 18, 2014
Do you want to continue to comment on physorg Ira?


I come alone, and go alone. Nice try, but Ira-Skippy will for sure take you up on that Cher. Laissez les bons temps rouler P'tit-Boug-Skippy (that's the way a Cajun say bring it on little man.) Do your worst Skippy.
,

If so start you can start by saying something positive or worthwhile that conveys real information. If not then find somewhere else to deposit the insults and hate you have obviously accumulated in life


Oh, you mean as opposed to peoples calling anyone who disagrees with them idiots, ignorant, stupid, morons, fools, and such like of that? Especially when they are the one sole single only person in the world who has got it right, everybody is idiots, ignorant, stupid, morons fools and such like.


You could have added he has admitted to being a creationist.

JVK
Dec 18, 2014
What does creationism have to do with accurate representations of biologically-based cause and effect? Please ban them both, along with Captain Stumpy.

My comment on: Understanding and accounting for relational context is critical for social neuroscience http://journal.fr...127/full

Across-species comparisons from insects to vertebrates... attest to the relative salience of sensory input from the rearing environment... Animal models affirm that food odor makes food either appealing or unappealing. Animal models reaffirm that it is the pheromones of other animals that makes them either appealing or unappealing.


Geroge F.R. Ellis responded: "This is absolutely correct and forms part of the larger concept that top-down causation is a key factor not just in the way the brain works but in broader contexts in biology and even physics. This is explored here: http://rsfs.royal.../2/1.toc "


Dec 18, 2014
@jvk

On another tread you said birds didn't evolve from dinosaurs. What is the common ancestor of birds?

Dec 18, 2014
For creating the planthopper's gears:
http://www.extrem...creature
and the firefly's mantle:
http://www.extrem...ogy-leds
the language of mutations and base pairs would be the last I would elect to describe how the species did it.
Interesting. Ok, so we know what you WOULDN'T use to describe how they arose. What would you use to describe how it arose then?

JVK
Dec 18, 2014
http://www.scienc...3606.htm

"...results showed the top reason for being abused was physical appearance, followed by sexual orientation and an inclination for non-mainstream interests."

My non-mainstream interests include a series of published works that explain how ecological variation leads to ecological adaptations via epigenetic effects of odors and pheromones on feedback loops linked to the nutrient-dependent pheromone-controlled physiology of reproduction.

The interests of every other person here besides John Hewitt are in denigrating anyone and any works that do not focus on the role of mutations and natural selection in the evolution of biodiversity. Each of my antagonists should long ago have been banned from participation at phys.org

Hopefully, that will happen now, so that phys.org can become a place for intelligent discussion.

Dec 18, 2014
Waiting through an infinite progression of random and negative base pair substitutions IS the monkey banging on the Shakespearean typewriter problem in the absence of more powerful mechanisms like viral manipulation, epigenetics, duplication, inversion, reading frame adjustments, splice variant, subunit and exon selection, etc, which are operated by more direct mechanisms than UV radiation, chemical insult or just plane old natural (predictable) progression or clustering through the base pair modification mill.


And yet, it is said that given enough time, those monkeys will write the complete works of Shakespeare. In that sense, there has certainly been enough time. Or, perhaps more precisely, there have been enough generations.

Are you suggesting that a random mutation that confers a beneficial result on a species will not be passed on to subsequent generations?

Dec 18, 2014
Each of my antagonists should long ago have been banned from participation at phys.org

Hopefully, that will happen now, so that phys.org can become a place for intelligent discussion.


Careful what you wish for Skippy, there might be a gator sleeping in that tall grass and you would hate he wake up because you stomping around making all that noise.


JVK
Dec 18, 2014
What is the common ancestor of birds?


Thanks for asking. See: Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes. http://www.pnas.o...abstract

They link the evolution of the two morphs to amino acid substitutions that appear to vary with uniparental or bi-parental feeding during a critical period of development. In this case, however, no experimental evidence suggests the white-throated sparrow morphs evolved from dinosaurs. I think they probably evolved from birds.

On another tread you said birds didn't evolve from dinosaurs


What evidence of biologically-based cause and effect suggests they did? I also said something about fried eggs not evolving into chickens. If you think I'm wrong about that, or anything else, support an alternative representation with experimental evidence of cause and effect.

JVK
Dec 18, 2014
Careful what you wish for Skippy, there might be a gator sleeping in that tall grass and you would hate he wake up because you stomping around making all that noise.


This is the kind of vague threat delivered several times before by this anonymous fool. Why is he still allowed to post on phys.org?

Dec 18, 2014
@jvk

" I think they probably evolved from birds."

In other words, birds just popped into existence without a link to a common ancestor, the work of a Creator.

Dec 18, 2014
Maggnus, those who would say that would be wrong, there is NOT enough time for blind unlearning monkeys or blind mutational noise in any conceivable universe.

Dec 18, 2014
This is the kind of vague threat delivered several times before by this anonymous fool. Why is he still allowed to post on phys.org?

I have, on numerous occasions, provided you opportunity to provide your version of why you don't consider the diverse adaptations taken by nature in response to environmental change, as mutation. As always, you wish to dispute Mr. Webster (and numerous others) and the concept of a fixed description of change.

Dec 18, 2014
This is the kind of vague threat delivered several times before by this anonymous fool. Why is he still allowed to post on phys.org?


I realize you are not the smartest couyon here, so I will be patient and try to tell you simply what it is. The real or the not real John-Hewitt-Skippy tells me to watch what I say. Then the real JVK-Skippy comes whining how I ought get the boot.

All I did is offer you some simple advice to be careful what you wish for. That was not the threat, it was the advice.

Because when you are whining about me, the nice peoples at the physorg, might notice how you use their interweb page to try to sell your stinky love potions. They might also notice how you always pushing crankpot stuffs and creation stuffs. If they take a particular notice of you, they might decide to enforce the laws about that and give you the boot.

JVK
Dec 18, 2014
In other words, birds just popped into existence without a link to a common ancestor


Koonin is the senior author of: "A universal trend of amino acid gain and loss in protein evolution" http://www.nature...306.html

Excerpt: "We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms."

I think what they are saying is that metabolic networks and genetic networks were linked before ecological variation first led from an amino acid substitution to an ecological adaptation.

Does anyone think they are claiming that birds evolved from dinosaurs?


Dec 19, 2014
@jvk

"Does anyone think they are claiming that birds evolved from dinosaurs? "

Considering neither birds or dinosaurs are mentioned thats a stupid question.

And their paper does nothing to support your "model".

Dec 19, 2014
Maggnus, those who would say that would be wrong, there is NOT enough time for blind unlearning monkeys or blind mutational noise in any conceivable universe.

WeIl seems there is enough actually - look around you. The diversity is astounding - yet all share basic DNA that links all life on the planet. How could that arise if not from slow, methodical change over the course of billions of generations? Some of the others here have already mentioned the work of Richard Lenski, and he only went through about 60,000 generations. Have you read his work or the multiple papers he has published on it?

I'm a little confused though johnhew - you have again stated what you don't think causes species diversification. I asked you to outline what you think does cause diversification. Did I not worded the question in a manner that you understood it? Have I asked it better this time?

I also asked you if you were suggesting that beneficial mutations wouldn't be passed onto offspring.

Dec 19, 2014
Thanks! I don't have so much to contribute here, except possibly that the latest ribosome phylogenies I know of order Archaea as split from Bacteria and Eukarya as split from Archaea. The ribosome preserved rRNA core growth is beautifully shown from a root of a P loop for phosphorylation* of peptide cofactors, then growing a tunnel for unordered nests (used for amyloid sheet membranes and metal site activities, presumably), then evolving an mRNA site and remaining tRNA sites for coding.

And that growth continues nicely from Bacteria through Archaea to Eukarya. ["Evolution of the ribosome at atomic resolution", Anton S. Petrov et al, PNAS, 2014; see the non-paywalled figure here: http://www.pnas.o...abstract ]

*Which could originally been a metal site when the emerging RNA nucleotides were cofactors for metals instead of vice versa, e.g. Russell et al's vent theory which seems to fit the phylogeny like a hand in a glove.

JVK
Dec 19, 2014
And their paper does nothing to support your "model".


What's needed is experimental evidence that supports an alternative model of biologically-based cause and effect. But first, another model that links physics, chemistry, and biology is needed.

I also asked you if you were suggesting that beneficial mutations wouldn't be passed onto offspring.


When told that there is no such thing as a beneficial mutation, this is typically the next question that arises.

You might as well tell someone who is biologically uninformed that the sickle cell hemoglobin variant is due to a mutation not due to a vitamin D-dependent amino acid substitution. They won't believe that fixed amino acids protect some populations from malaria. They've been taught to believe that the mutations that cause sickle-cell disease are beneficial.

They think that darker skin pigment and all other ecological adaptations also are due to mutations.

Evolution = racism = Scopes trial

Dec 19, 2014
Possibly also that the eukaryote vacuoles, golgi apparatus and nuclear membrane are related as far as I know, and the latter has the wrong topology to be derived from outer membranes. It is a doubled double layer membrane with membrane clad pores, very different pores than the special membrane protein assemblies used in outer membranes. (And possibly the many proteins used to regulate the nuclear pores and their traffic is independently rooted, I can't remember.)

One can see many attempts to predict the nucleus that do not recognize its peculiarities. My unsupported intuition, as it were, is that the nucleus evolution postdate the mitochondria and could have been prompted by escaped mitochondrial genes that could harm the eukaryote host. (Eventually such acquisition happened anyway and some of it benefited the host, of course.)

JVK
Dec 19, 2014
phosphorylation* of peptide cofactors


Is that like phosphorylation in the context of amino acid substitutions that link the "hydrogen hypothesis" from ecological variation to nutrient-dependent ecological adaptations via the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction in species from microbes to man?

If so, you've probably just added enough support for my model to forever eliminate any further discussion of the mutations, natural selection, evolution pseudoscientific nonsense.

If not, what are you talking about?

What's a peptide co-factor?

How does phosphorylation occur?

Is there any link to oxygenation and pH or CO2 levels that could be linked to hemoglobin variants in animal and human populations living at different elevations above sea level?

Try making sense in terms that are relevant to biological evolution if you think what you know about physics supports it.

JVK
Dec 19, 2014
My unsupported intuition, as it were, is that the nucleus evolution postdate the mitochondria and could have been prompted by escaped mitochondrial genes that could harm the eukaryote host.


In other words, you're saying that you are content to have no explanatory power whatsoever built into your theory, which may link the hydrogen hypothesis from physics to the chemistry of protein folding and stability of DNA via amino acid substitutions via phosphorylation.

You would rather jump into the thread and add theory to theory if only to completely eliminate the possibility that others might understand the foolishness of those who live in a world of physics that is meaningless to those who are interested in understanding biologically-based cause and effect from an atoms to ecosystems approach.

I don't have so much to contribute here, except possibly that the latest ribosome phylogenies...


(Eventually such acquisition happened...


Automagically?

Dec 19, 2014
As for the other ribosome reference, after a quick browsing (may read later) it looks to be an eager pattern search. Indications of eager pattern search is that they tweak and chose match programs until they get their desired result, and that they ignore the standard statistics tools. However, they do test that mRNA (iclduing old proteins) have less matches.

The problems I have with this pattern is that the rRNA has grown through time, both before (presumably) and after coding was established and there would have been a huge machinery supporting a huge assembly of replication strands besides rRNA. Their own data shows that their method gives false positives, the younger rRNA parts show the same patterns as the old and they find patterns of young proteins among the old (murein et cetera). In fact, they claim that the frequency of the pattern is irrelevant to their hypothesis since the core is preserved. But it is preserved due to the preserved coding machinery.

Dec 19, 2014
Other problems is that they refer to mitochondria for similar matching. But mitochondria are very derived, which means it is a problematic and not beneficial fact for their hypothesis.

No one denies that tRNA and the later rRNA did not have, and have preserved in its older parts, a generic enzymatic function that goes up to one-electron exchange otherwise seen only in proteins. But it emerges, outside of the modern rRNA function, only in a Hadean environment. (70+degC, anoxic, Fe rich solution.)

I'm fairly confident in the Petrov paper. This paper, not so much.

Dec 19, 2014
Re the crackpot creationist (non-evolutionary) discussion, I will opt out. Before commenting on the earlier article I had forgotten that Hewitt does not accept the existence of the biological process. It is even worse than denying the existence of gravity since it is the most evidenced process we have! E.g. Theobald could show that we have a UCA with a 10^2000 likelihood against creationist magical random species. [Nature, 2010]

So I will opt out from that. The references speak for themselves as everything else on basic biology from Darwin founding it and onward. It is meaningless to discuss uninteresting crackpotism (shown to be wrong two centuries ago). Besides, would it be interesting it can't be done: crackpots can't keep their trolling straight. Eg the Pheromone Troll thinks my intuition is part of biological theory and that I support the very idea I referenced counter-evidence on (hydrogen hypothesis) under the 1st article. Madness!

Dec 19, 2014
Tor, clearly I accept the biological process in full, I just point out that mates are generally not selecting base pair mutations, but rather the more obvious kinds of genetic rearrangements I indicated in comments above, and in the same way neither is the self selecting single mutants when synthesizing its differential palette of gametes across time and experience

JVK
Dec 19, 2014
Re the crackpot creationist (non-evolutionary) discussion, I will opt out.


The questions seemed simple enough.

What's a peptide co-factor?

How does phosphorylation occur?

Opting out makes it appear that you have no idea what you are talking about, which is why I asked the questions. Referring to me as the "crackpot creationist" suggests the same thing. Why not just answer the questions if you are not a crackpot theorist?

JVK
Dec 19, 2014
mates are generally not selecting base pair mutations


Pheromones control the physiology of reproductive sexual behavior; they are indicators of nutrient-dependent reproductive fitness.

neither is the self selecting single mutants


Self vs other recognition allows natural selection for nutrients that benefit self compared to "other" which is recognized as a nutrient source.

Nutrient uptake and metabolism to species-specific pheromones = Feedback loops link odor and pheromone signaling with reproduction.

Crackpot theorists seem largely unable to recognize biological facts. Rarely do we see one, like Torbjorn_Larsson_OM, who claims John Hewitt "...does not accept the existence of the biological process." Then, the crackpot theorist refuses to answer question about what he introduced in the context of peptide co-factors and phosphorylation.

He must think everyone here, including John Hewitt, does not recognize a crackpot by the content of their posts.

Dec 19, 2014
So, I like to keep things simple..

Are we saying that blue eyes and fair skin did NOT come as a result of a change to the genetic code via the overall lower sunlight in higher latitudes, but from something the Europeans ate?

It the converse true for Africans?

It's all nutrients and no environment/mutations? What EXACTLY did the Europeans eat that changed their eye, skin, and hair color/texture and HOW exactly did this happen biologically.

If we assume environmental pressures, selection, and mutation it's pretty straightforward and easy to understand...even if it has the "disadvantage" of dispelling supernatural myths which people cling to like their lives depended on it.

Dec 19, 2014
Lets see jvk use his "nutrient dependent' crap to explain this:
http://phys.org/n...ion.html

Dec 19, 2014
Viet, nice point, quite fascinating level of detail in that study - 5,040 possible pathways for the amino acid changes in the string of the 7 required for the change, and in the case of scabbardfish, simple UV sensitivity change with only 1 mutation.
Skin color is obviously more complex with many genes and processes involved, and gears, mantles, and lanternfish lures even more so. These require other behavioral downward pressures on the genome structure to be realized.

JVK
Dec 19, 2014
Thanks for "baiting" the theorists into discussion of facts like:
These require other behavioral downward pressures on the genome structure to be realized.


Therein lies the problem with the pseudoscientific nonsense of neo-Darwinism, which has never addressed the obvious need to link the mutations to changes in behavior that link top-down causation (re: George F.R.Ellis).

Instead, mutations automagically cause fixation of amino acid substitutions in the organized genomes of species from microbes to man because fixation is required for protein folding stability in the context of controlled organism-level thermoregulation.

That's what is examplified in epigenetic pharmacology when a single amino acid substitution links behavioral changes during human life history transitions from adolescence to adulthood.

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

JVK
Dec 19, 2014
If we assume environmental pressures, selection, and mutation it's pretty straightforward and easy to understand...


Indeed, that's why neo-Darwinism was invented in accord with the definition of "mutation" by de Vries. It's also why Nei, eliminated ecological factors and geographical factors that attest to the facts about how ecological variation leads to RNA-mediated ecological adaptations, and then 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

Pseudoscientific nonsense like that requires only the ability to convince others to believe in it, which is why teaching "evolution for dummies" has been incredibly effective. The "dummies" believe in it and teach others to believe in it. Only serious scientists require experimental evidence of biologically-based cause and effect.

JVK
Dec 19, 2014
Feynman on pseudoscience: https://www.youtu...X_0jDsrw

Mazur/Margulis on the Modern Synthesis:

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

Officials in Israel who refuse to raise children who are taught to be science idiots:

"...learning about evolution is not the primary function of the decision, but rather to use it as a building block for students to learn more about their ecology."
http://www.educat...olution/

Dec 19, 2014
So you do understand that you have a mutation (lighter skin) and then the environment helps reinforce and select for it.

There you go.

Only serious scientists require experimental evidence of biologically-based cause and effect.


Well we have the evidence that modern humans appeared in Africa 200,000 years ago, and then at some point after they migrated to Europe their DNA mutated, they acquired light skin, various eye colors, hair colors, and hair textures. We know this because...well there's billions of them running around on the planet today just as their "ancestors" who never left Africa and hence never had such mutations selected for.

In order to believe...well whatever the hell it is you believe...you'd have to be literally BLIND or have never met a white human being...

JVK
Dec 19, 2014
What's a peptide co-factor?

How does phosphorylation occur?


Who is John Galt?

JVK
Dec 19, 2014
So you do understand that you have a mutation (lighter skin) and then the environment helps reinforce and select for it.


No experimental evidence of biologically-based cause and effect suggests that is possible. Did you not read what John Hewitt said about the ridiculous proposal you just made, which is based on the pseudoscientific nonsense you were taught to believe in? What good is his book review, if you and others keep coming back with your theories, which explain nothing.

Well we have the evidence that modern humans appeared in Africa 200,000 years ago, and then at some point after they migrated to Europe their DNA mutated...


No. What we have is biologically uninformed anonymous participants who were taught to believe in pseudoscientific nonsense and have since refused to learn anything about biologically-based cause and effect.


Dec 19, 2014
No experimental evidence of biologically-based cause and effect suggests that is possible.


Except for the fact that there are people and some of them are white, and some are black. So despite your theory there's ample evidence it's false.

No. What we have is biologically uninformed anonymous participants who were taught to believe in pseudoscientific nonsense and have since refused to learn anything about biologically-based cause and effect.


The cause was mutation, the effect was white skin.

JVK
Dec 19, 2014
...some of them are white, and some are black.


"... 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!" Dobzhansky (1964) http://icb.oxford...citation

"Ingram and others found that hemoglobin S differs from A in the substitution of just a single amino acid, valine in place of glutamic acid in the beta chain of the hemoglobin molecule."

"... a previously under-appreciated property of gene regulation, namely widespread buffering of protein levels so that a cell can sustain some amount of RNA variation without it affecting proteins," Gilad said. "This appears to be a common phenomenon and motivates us to look for the mechanisms that can account for it."
http://phys.org/n...html#jCp

Mutations are not mechanisms of cell type differentiation.

Dec 19, 2014
OK kohl, since you apparently cannot comprehend modernmystic's question and line of reasoning, let's repeat anon's question.
Regarding causality, I'll simplify it for you, using an example I've presented to you multiple times and you still can't explain: Each of Lenski's 12 IDENTICAL populations were exposed to IDENTICAL environments. How would your model produce different adaptations in each if that's the case? If specific nutrients produced specific DNA changes, then there's no way they could be different.

Answer it.

Dec 19, 2014
Please ban them both, along with Captain Stumpy
kohlslaw only wants me banned because i use his own words against him!

I would like to add a cautionary post to yall:

I came here to learn, and to learn REAL science

jvk is pushing a KNOWN PSEUDOSCIENCE with his BS comments about mutations never being beneficial, and the science proves him wrong ( http://myxo.css.m...dex.html & http://www.oeb.ha...oeb.html )

Yall can make your anti-Evolution creationist diatribe all you want... i don't care

But there will ALWAYS be SCIENCE refuting the creationist movement, because, as even the Lawyers can see, there is NO science in their movement: https://en.wikipe...Arkansas

My recommendation: stick strictly to the site rules for your own sake, because a violation of those rules and pushing personal influence to violate those rules could cause a huge ugly nasty mess

some people take science serious
I am one

Dec 19, 2014
my antagonists should long ago have been banned
for what reason, jk? for promoting SCIENCE that you don't like? giving EVIDENCE you don't understand?
Hopefully, that will happen now
the only thing that will happen by banning those who refute you, jk, is that the site will be overcome by PSEUDOSCIENCE creationists

sorry, but ignoring ALL MECHANISMS of Evolution is PSUEDOSCIENCE, and having a belief that forces data to conform to a religion, is PSEUDOSCIENCE

your model is a SMALL part of the theory of Evolution, kohlslaw... it is a PART of it, regardless of your pontification and vilification of the Theory

There is evidence that supports the Theory of Evolution, and until YOUR model is PROVEN capable of supplanting ALL OTHER METHODS of known mutation in the Theory's playbook, then you are pushing pseudoscience

THAT is what science is all about... following the evidence
NOT banning everyone who follows the evidence

JVK
Dec 19, 2014
The biologically uninformed will probably destroy any attempt to discuss bio-physically constrained nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all species.


IT'S WHAT THEY DO! THEY'VE DONE IT, AGAIN.

No serious scientist is going to read through the amount of pseudoscientific nonsense touted here by everyone else besides John Hewitt.

His first two reviews of the book help to bring others current, and he has barely touched the surface of how they are integrated into a cohesive compendium about biologically-based cause and effect.

I look forward to what he has to say about "The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function" http://cshperspec...abstract

I do not look forward to any further discussion of biologically-based facts about cell type differentiation on phys.org

Dec 19, 2014
hey kohlslaw? about this: http://www.pnas.o...pdf+html
There is no place in this study WHATSOEVER that states that the sparrows did NOT come from dinosaurs... in fact, if anything it says that they are the possible product of two birds, but that simply shifts the question back to... where did THOSE birds evolve from?

we have evidence that birds come from dinosaurs: here are good articles
http://www.talkor...214.html
http://www.talkor...1_1.html
and studies are in the references sections, including relevant data proving my point as well as further reading

I would also like to point out that you are NOT answering my questions, JohnHew
You are dancing around them, trying to placate jk as well as mutations... why is that?

I think i should continue this next post
[to be contd]

Dec 19, 2014
[contd]
@JohnHew
No one doubts that jk's model is not beneficial in any way... however, you are dancing a little too much and not being a clear as i thought an author with your expertise should be, so

I will ask some SIMPLE yes or no questions, please bear with me:

Can mutations be beneficial?
Does Kohl's model cause mutations?
Which is more likely to be correct, The Theory of Evolution (which, by the way, Inclused Kohls model) or the creationist theory of evolution after creation? (Answer: Evolution or Creation to this one)

lastly, why would you defend Kohls creationist idealism but say that you believe in science? take all the time in the world to explain that one!

because on one hand, jk links valid science, but we've also shown where he misinterprets MUCH of what he links in the light of creationist ideals, which are decidedly NOT scientific... like his admonition about birds above, or his failure to accept his own model causes mutations, etc

I am CURIOUS


Dec 19, 2014
It is possible I think, just not likely.
Not really familiar with Kohl's model.
Of course evolution happens, but I put it at like 2% mutations, 98% higher processes
Mutation, genomes, and proteins have significant predictability.
is one engine of evolution in the same way that thermal motion is an engine of the cell

Koonin sums it up well in:
Calorie restriction à Lamarck.
http://www.cell.c...)00880-0
"Epigenetic inheritance of resistance to exogenous nucleic acids via small interfering (si) RNA is well established in animal models. Rechavi et al. demonstrate epigenetic inheritance of a starvation-induced pattern of gene silencing caused by endogenous siRNAs and resulting in an increased longevity in the third generation progeny. Combined with recent findings in prokaryotes, these results suggest that Lamarckian-type inheritance of acquired traits is a major evolutionary phenomenon."

Dec 19, 2014
Combined with recent findings in prokaryotes, these results suggest that Lamarckian-type inheritance of acquired traits is a major evolutionary phenomenon."


Well maybe you and maybe you are not the real John-Hewitt-Skippy but you just did the Zephir-Skippy act with that one. He's the one who is really fond of an old tired dis-proven theory about the aether stuffs. The theory you are pushing is even older and more dis-proven, that Lamarckian-type-stuffs.

I just read me a good book on the history of the sciences and that Lamarkian-worn-out-theory was in him.

Dec 19, 2014
mutation is of little positive value in the higher organisms. in viruses, bacteria, and endosymbiotic organelles of course it is, they are the lab & wellspring for the proteins of life, not us big organisms with huge loads of soma and germ mutations that some folks incredibly imagine could possibly be selected for idividually through natural means, let alone by the real, intelligent, & selective operators, the egg bearers

Dec 19, 2014
Of course evolution happens, but I put it at like 2% mutations, 98% higher processes
Ok, 3rd time I've had to ask this. What higher processes johnhew? You should take a read of Kohl's stuff, maybe you'll then understand why there is such skepticism of anyone defending him. He stands pretty much alone for a reason.

"Epigenetic inheritance of resistance to exogenous nucleic acids via small interfering (si) RNA is well established in animal models. Rechavi et al. demonstrate epigenetic inheritance of a starvation-induced pattern of gene silencing caused by endogenous siRNAs and resulting in an increased longevity in the third generation progeny. Combined with recent findings in prokaryotes, these results suggest that Lamarckian-type inheritance of acquired traits is a major evolutionary phenomenon."

The nurture vrs nature debate.

Dec 19, 2014
mutation is of little positive value in the higher organisms.


Well, that depends on the nature of the mutation doesn't it? Certainly one would not expect a cow to suddenly develop gills and go live in the ocean - and if that is what you consider evolution, you have a very bastardized idea of the theory.
in viruses, bacteria, and endosymbiotic organelles of course it is, they are the lab & wellspring for the proteins of life
But isn't that the whole point? To come at it from a different angle, a small change in a genome can confer a beneficial trait to a organism, be it a virus or a rhinoceros. I do not think the argument is, or was, that a cow can suddenly become a horse. But a cow that has a mutation that allows it to survive on slightly less water than its neighbors in a drying environment may certainly pass that mutation onto its offspring. Incremental changes are the key, be it a bacterium or a dinosaur. Don't you agree?

Dec 19, 2014
For that Maggnus, you need to imagine all the moleculo-physiological pathways that might exist to explain why the ladies would unanimously go for Tyson and not Leon Spinks after Tyson took him out in seconds. In addition to the surging hormone swaddle the gametes enjoy, consider something even more exotic, that the nervous system evolved to select and distribute mitochondria, and their associated nuclear protein, RNAs, and experience, to the body (and gonads). Not claiming that, but tabulating it here only as 1 among 100 that I might list for you where that came from.

Dec 19, 2014
not us big organisms with huge loads of soma and germ mutations that some folks incredibly imagine could possibly be selected for idividually through natural means, let alone by the real, intelligent, & selective operators, the egg bearers


For someone who claims to be the science writer, you sure don't seem to be very good at stating what it is you think.

Here is an easy question for you, one a six grader could answer, I just tried him out on the little-Ira-Skippy so I know a seventh grader can answer it.

Here's the easy question. "Ira-Skippy would like to know where the heck you think all the different kinds living things came from?" If not from evolution, then from what? Where it start?

Either answer it in normal language, or don't bother to answer it at all. If you can not bamboozle me with the gobbledygook, you for sure can not bamboozle the really smart peoples here.


Dec 19, 2014
For that Maggnus, you need to imagine all the moleculo-physiological pathways that might exist to explain why the ladies would unanimously go for Tyson and not Leon Spinks after Tyson took him out in seconds. In addition to the surging hormone swaddle the gametes enjoy, consider something even more exotic, that the nervous system evolved to select and distribute mitochondria to the body (and gonads). **SNIP**
That doesn't make any sense johnhew. There may be just as many ladies who spurn Tyson in that scenario and offer comfort to Spinks. If, however, Spinks was dead, then nothing of his would be passed on (well, assuming he hadn't fathered children before then).

Are you aware of the study where a red tracking band added to a male bird's leg accidentally shifted female mating preference? They liked the red band. But none of the offspring of those mating's was born with a red band on their leg. Doesn't that disprove Lamarkian evolution?

Dec 19, 2014
One does not disprove Lamark, Lamark disproves you. or was it Putin that said that?
The ladybirds liked what the red band represented, just like Lovelace loved his polyethylene 6-pack soda necklace talisman -- a touch with the higher. You need do better than that.

Dec 19, 2014
One does not disprove Lamark, Lamark disproves you. or was it Putin that said that?
The ladybirds liked what the red band represented, just like Lovelace loved his polyethylene 6-pack soda necklace talisman -- a touch with the higher. You need do better than that.


I'm not trying to disprove Lamark johnhew, I am trying hard to get an understanding of where you are coming from. There is a lot of evidence that suggests Lamark was right - and there is a lot of evidence that suggests he was wrong. I am not giving you my personal opinion here, I am looking at the claims you have made and trying to put them perspective. You said
The idea that good mutations can accumulate in the face of a preponderance of bad to drive evolution of new structure through natural selection is what I find preposterous at this point in the game.
And I asked you why. You have not answered. Instead you linked to 2 instances of complexity with a backhanded comment. So do I take you seriously?

Dec 19, 2014
@johnHew
It is possible
Are you in training to be a politician?
Not really familiar
he has linked already: http://www.ncbi.n...24693353
2% mutations, 98% higher processes
and would you please show supporting links so that we can review them?
you should also read this link after jk's model http://www.ncbi.n...4049134/

Perhaps we should back up and this point and we should also clarify something else:

@JohnHew- are you the same John Hewitt that wrote the above article?

Perhaps you think that the tap dancing is necessary, but it really isn't.

i am not trying to be politically correct, nor am i trying to force anyone to say something not backed by science...

i need specific answers and jk is already known for his tap dancing anti-science creationist word salads which have been noted here: http://freethough...s-place/

TIA

Dec 19, 2014
@JohnHew- are you the same John Hewitt that wrote the above article?


Good luck with that Captain-Skippy. I ask him my own self three or two times and that seems to be another question he don't want to answer. Since he disagrees with everybody here, and doesn't disagree with JVK-Skippy and finds a way to hint that JVK-Skippy is the most "informed in that area",,,, just saying me.

He's either a real crankpot pretending to be an open minded science writer or he's JVK-Skippy doing an act. I went back and read all his old postums, and he sure does throw out the goobledygook like JVK-Skippy. It caught my attention when up there he linked his own articles the way JVK-Skippy does. Then he give me the veiled threat, and really got my attention.

Dec 19, 2014
I don't really care if Kohl thinks the world is 6000 yrs old and just bought an indulgence to the promised land. I'm here to solve the problem of how we are here, how cells evolve new structure, and new species, and mutations ain't the the answer so wake up and lets find the biochemical pathways through cellulo-corporeal-environmental space that do it.

JVK
Dec 19, 2014
http://www.salk.e...p?id=552
The difference in the two types of nematodes (one with teeth) arises in the context of their nutrient-dependent pheromone-controlled reproduction via one nutrient-dependent amino acid substitution.

"Differences in the behavior of nematodes are determined by nutrient-dependent rewiring of their primitive nervous system (Bumbarger et al., 2013). Species incompatibilities in nematodes are associated with cysteine-to-alanine substitutions (Wilson et al., 2011), which may alter nutrient-dependent pheromone production." -- Kohl (2013) http://www.ncbi.n...3960065/

All other cell type differentiation in all cells of all individuals of all species also occurs via nutrient-dependent amino acid substitutions and pheromone-controlled species-specific reproduction, which is why I modeled cause and effect across species in my most recent review. Only the biologically uninformed believe in mutation-driven evolution.

Dec 19, 2014
I don't really care if Kohl thinks the world is 6000 yrs old and just bought an indulgence to the promised land. I'm here to solve the problem of how we are here, how cells evolve new structure, and new species, and mutations ain't the the answer so wake up and lets find the biochemical pathways through cellulo-corporeal-environmental space that do it.


Ah, so you really don't have an understanding of evolution. You could have just said that. Although, truly I suspected as much. No doubt Kohl loves you.

Mutations are the answer, actually, Even Kohl's work proves that, although he cries and stomps his feet when that is pointed out to him. Obviously, the idea of billions of generations of incremental change scares you.

Nice chatting with you though!

Dec 19, 2014
I don't make veiled threats Ira, you can disagree with me, and I can disagree with you, but the next time anyone on this forum disrespects another, I will see to it that it is the last comment they make here, myself included.

JVK
Dec 19, 2014
I don't really care if Kohl thinks the world is 6000 yrs old and just bought an indulgence to the promised land.


I don't know anyone who is selling them. How much does one cost?

Luca Turin was on the right track with quantum smell. Close enough for others to begin putting their heads together on links from the "hydrogen hypothesis" to nutrient odor-induced changes in H-bonds. They appear to lead to experience-dependent odor-induced de novo creation of olfactory receptor genes in mosquitoes, which is perturbed by mutations -- as shown by Leslie Vosshall's group in a series of published works.

Anna Di Cosmo et al have extended Luca's recent works on anesthesia in flies to octopuses via my model of GnRH-directed nutrient-dependent pheromone-controlled amino acid substitutions and cell type differentiation in all vertebrates, linked via GnRH receptors across what others report as 400-600 million years of vertebrate evolution -- excluding coelacanths.

Dec 19, 2014
Imagine a world where near nameless, avatar-less characters question the identity of the one with both

Dec 19, 2014
@jvk

These biologically uninformed idiot minions--



JVK
Dec 19, 2014
Rechavi et al. demonstrate epigenetic inheritance...


That's where the real action is. His group is the least academically subdued. http://onlinelibr...abstract

Excerpt: "Regulatory RNA exchange between different organisms could be an important component in the hologenome's genetics, since RNA is a 'universal language' which affects other epigenetic processes, and in certain cases can become heritable."

You'll see more about this in the book chapter by Brosius, which is the most comprehensive review I have read. Until September, Rechavi's lab statement of purpose read: Our principle aim in the lab is to attack scientific dogmas. http://www.odedre...out/cnec

Bottom line: Everything about typical cell type differentiation occurs downstream of the microRNA/messenger RNA balance, which is why I claim it is RNA-mediated by amino acid substitutions when others still tout their ridiculous theories.

Dec 19, 2014
I don't make veiled threats Ira, you can disagree with me, and I can disagree with you, but the next time anyone on this forum disrespects another, I will see to it that it is the last comment they make here, myself included.

As pointed out above by vietvet, the person on this thread who has cast the most stones is Kohl. So why aren't you taking him to task? Do you understand the term "hypocrisy"?

Dec 19, 2014
I don't make veiled threats Ira, you can disagree with me, and I can disagree with you, but the next time anyone on this forum disrespects another, I will see to it that it is the last comment they make here, myself included.


Well I see your "seeing to it" and raise you a "silly looking pointy cap to wear" for your very own.

You have a lot to say, but can't answer easy questions about you said. That is sort disrespectful to peoples you are writing to.

Are you some High-Pontiff-Skippy who can't be troubled to answer the questions put to you by the little peoples? Most people who tried that one on me got their feeling hurt really bad (I think it has something to do with the silly looking pointy cap I made them wear for being the bioque.)

Laissez les bons temps rouler Skippy (that's Cajun talk for it's your turn Skippy).

Dec 19, 2014
@Johnhew


Of course evolution happens, but I put it at like 2% mutations, 98% higher processes
Mutation, genomes, and proteins have significant predictability.

Sounds like personal conjecture, even if educated conjecture. Can we look forward to an article, or more likely a series of articles on your position? Of course it would require all relevant peer reviewed citations, hopefully more than just abstracts.


JVK
Dec 19, 2014
mates are generally not selecting base pair mutations, but rather the more obvious kinds of genetic rearrangements


http://www.pnas.o...abstract
Excerpt: "...our results illustrate a detailed chain of events linking a chromosomal rearrangement to changes in overt social behavior."

From the supplementary information: "The ZAL2 and ZAL2m alleles code for 597 amino acids, with two fixed differences driving a Val73Ile and Ala552Thr polymorphism in ZAL2m. valine to alanine substitution..."

Its an alanine to valine substitution in the mouse to human model I used as an example of amino acid substitutions and cell type differentiation in my 2013 review. However, the folks at Harvard still refer to the substitution as if it was a mutation.

https://www.youtu...PLsJI3GM

JVK
Dec 19, 2014
PZ Myers prefaced his attack on my credibility with: "Evolution was all due to chromosome rearrangements, which somehow are not mutations, and he also somehow ignored the existence of allelic differences between species" http://freethough...s-place/

He banned me on the same day I posted the information on chromosomal rearrangements in the behavioral and morphological traits of the white-throated sparrows.

In our 1996 Hormones and Behavior review, we wrote: "...structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the active X, the inactive X, and the Y chromosomes.... Increasingly the structure and timings within the nucleus are realized as contributing to gene expression regulation..." http://www.hawaii...ion.html

cont:

JVK
Dec 19, 2014
anonymous_9001 aka Andrew Jones, cites my posts to PZ Myer's blog in:

"Criticisms of the nutrient-dependent pheromone-controlled evolutionary model" http://www.ncbi.n...24959329 "...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."

He exemplifies how far others will go to attempt to silence anyone who dares to offer experimental evidence of biologically-based RNA-mediated cell type differentiation that Elekonich and Robinson (2000) extended to insects and Elekonich and Robertts (2005) extended to life history transitions of the honeybee. All this based on our 1996 of RNA-mediated pheromone-controlled sex differences in cell types.

Our model has consistently showed up, without citation, in the works of others who still want to deny all aspects of human pheromones and their epigenetic effects.

Dec 19, 2014
http://freethough...s-place/

Looks like PZ-Skippy nailed it. So glad you posted that because a lot of peoples have been trying to tell you that for as long as I've been around.

You should be thankful that the nice peoples at the physorg give you a place write all the silly things you write and for giving us some really big fun watching you do it.

Oh yeah, I almost forget. @ the John-Hew-Skippy, that's right, ol Ira-Skippy is being disrespectful to the JVK-Skippy. Unless he acts so silly on purpose just to give us something to laugh about. If he's doing that then I'm not being disrespectful, I'm complimenting him on his show. How you like the Cajun now Skippy?

JVK
Dec 19, 2014
http://www.donotl...ed?10666

"...Richard B. Goldschmidt [1940] presented the evidence that it is the chromosome, not the gene that is the unit of evolutionary change. While this was not then accepted by the evolutionary establishment, recent karyological studies fully support his perspective."

Someone is going to someday write about how any challenge to the dogma of evolutionary theory has been dismissed, no matter who it comes from: Goldschmidt, Schrodinger, Feynman, or our 1996 co-author Milton Diamond, who exposed John Money's widely touted "textbook" claims about nurture trumping nature.

I hope you plan to continue your book review and include comments on "Origins of Eukaryotic Sexual Reproduction" http://cshperspec...abstract and Origin of Spliceosomal Introns and Alternative Splicing http://cshperspec...abstract and other chapters that integrate what's been known since 1940.

Dec 20, 2014
I don't make veiled threats Ira, you can disagree with me, and I can disagree with you, but the next time anyone on this forum disrespects another, I will see to it that it is the last comment they make here, myself included.
Now John, technically speaking, you DID make a threat when you said
Do you want to continue to comment on physorg Ira? If so ...life
Now, i know you obviously have some pull, but i would ask you to seriously consider who you decide to exercise it upon for Various reasons:
- temps are already running HIGH between jk and most of the others
- this whole "disrespects another" thing started a long time back, which is why i linked those threads to you (did you read how he villified Lenski and Extavour yet?)
and jk is the worst offender, because he got caught pushing a lie
- lastly, it could seriously backfire on the SITE itself... if enough people get together, and the wrong element finds out (ie: the REAL Anon group)

[to be cont'd]

Dec 20, 2014
[cont'd]
so, whereas i see that being a mediator is a good thing, I would caution you and ask you to very seriously consider whom you push for a ban from here

Your actions should reflect ALL posts from the person and their actions, not just what is mentioned in THIS comment thread

case in point: if you read here http://phys.org/n...firstCmt
What you will see is kohl flying off the handle regularly while Anonymous9001 tries patiently to refute his creationist beliefs with science

Personally, i think he does a great job... and you really SHOULD read through the exchanges to get a handle on what is happening above here... because this is just round TWO

also, you may think people like Ira or Vietvet offer nothing, but they can spot a TROLL from a mile away, and they point out that you are dancing around more than nailing down any answers

regardless, be fair based on EVERYTHING
not just this comment thread

PEACE

Dec 20, 2014
disrespects another, I will see to it that it is the last comment they make here
@JohnHew

IF you are the author John Hewitt

I would also ask you to take into consideration the site rules, the status of the members, Longevity and their ranking as part of your bid for "ban" or "termination"

I know a LOT of people don't like Ira/VietVet... but a lot of us DO... because they bring a perspective that most scientists don't have
practical and down to earth

In conclusion... if you will notice jvk's rankings, you will see that a LOT of people do NOT like him... and you REALLY SHOULD be asking yourself WHY?

you should be doing homework, especially before threatening and banning people here

If you love science... follow the evidence
find out WHY jvk is regularly downrated

Creationists are NOT scientists
and labeling something as it is is NOT disrespect (like kohl's word salads AKA kohlslaw)

DO YOUR HOMEWORK
READ THOSE LINKS
& THE HISTORY HE HAS HERE

Dec 20, 2014
@johnHew
It is possible
Are you in training to be a politician?
Not really familiar
he has linked already: http://www.ncbi.n...24693353
2% mutations, 98% higher processes
and would you please show supporting links so that we can review them? Something NOT paywalled?
Personally, i think you should also read this link after jk's model http://www.ncbi.n...4049134/

Perhaps we should back up and this point and we should also clarify something else: @JohnHew- are you the same John Hewitt that wrote the above article?

Perhaps you think that the tap dancing is necessary, but it really isn't.
i am not trying to be politically correct, nor am i trying to force anyone to say something not backed by science, but i need specific answers
jk is already known for his word salads which have been noted here: http://freethough...s-place/

Dec 20, 2014
I'm here to solve the problem of how we are here, how cells evolve new structure, and new species, and mutations ain't the the answer so wake up and lets find the biochemical pathways through cellulo-corporeal-environmental space that do it
@John
so waht about this fauxpa from jk? he used Dr. Extavour to support his claims when he posted
Insulin signalling underlies both plasticity and divergence of a reproductive trait in Drosophila
http://www.oeb.ha...oeb.html
"Finally, we asked whether nutrition-dependent plasticity of this critical reproductive trait was linked to broader ecological patterns of ovariole number diversity, which may indicate an adaptive value of nutritional plasticity."
This is the kind of question not asked by idiot minions of biology teachers, like PZ Myers, who teach others to believe in mutation-driven evolution and never question why there is no model for that
[sic]

[to be continued]

Dec 20, 2014
[CNTD]
so we went to the source and inquired directly
I can clarify that although our work does, we hope, provide an example of how nutrition/ecology could affect the evolution of potentially adaptive traits, you [Captain Stumpy] are right that we in no way claim that mutations in the heritable genome play no role in evolution. Indeed, as you [Captain Stumpy] correctly state, just because we provide evidence that nutritional conditions play a role, this does not negate a role for mutations. Indeed, in that very same paper, we provide evidence that heritable differences in the genome sequences between Drosophila species, in other words, mutations, ALSO play a role in the evolution of the trait we are studying.

So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
[sic]
So i guess now it comes to YOUR thoughts, John
especially with your comment about 2% ??
care to elaborate?

Dec 20, 2014
so John, since you are saying
I'm here to solve the problem of how we are here, how cells evolve new structure, and new species, and mutations ain't the the answer so wake up and lets find the biochemical pathways through cellulo-corporeal-environmental space that do it.
and i am learning that your comment may not be as valid as it seems at first glance... maybe you should start showing a few links and explaining them to me so that i can see where exactly you are coming from...

because i happen to agree with what i have been reading with regard to Lenski and Dr Extavour.... but maybe you can see and explain something that i missed

Is there something in their studies that doesn't translate 100% and can you give me some proof so i can study it?

THANKS

and YES, i am biting my tongue with jk
he is a foolish child that should be banned already for his more outrageous claims and denigrations of GREAT scientists on PO

If you ban anyone, he should be #1

Dec 20, 2014
The idea that good mutations can accumulate in the face of a preponderance of bad to drive evolution of new structure through natural selection is what I find preposterous at this point in the game.


You're resembling Ren82 more and more. What you stated here is the thesis of genetic entropy, an idea used to "support" young Earth creationism by saying that DNA decays at such a rate that life couldn't possibly be more than 6000 years old and everything would have gone extinct from uncontrolled mutations if it were actually 3.something billion years old.

I posted a number of links in response to Ren82 showing how genetic entropy is a ridiculous proposition. Selection keeps detrimental mutations from running wild throughout populations.

Dec 20, 2014
So JVK the ONLY way you can get support within Physorg is by emulating Zephir and creating false accounts and use them to pretend you have supporters. Falsification and lies appear to be a comfortable way of life for both of you.

You calling for anyone to be banned is as hypocritical as you calling people frauds and pseudoscientists.

You are a stated creationist who sells scent to gullible fools as love potions.

BTW if your scent worked as you claim why would you be spending time posting on physorg, aren't women throwing themselves at you day and night.

Dec 20, 2014
a serious chink in jk's argument!
linked here: http://phys.org/n...firstCmt

According to the study
Small molecules that change the oligomeric state of proteins by binding to a site distant from the interface are called allosteric. They often act by taking advantage of intrinsic protein dynamics and stabilizing a particular conformation of the protein. Perica et al. show that mutations can similarly act at a distance to change protein conformation. They identified 11 mutations in an RNA- binding protein that determine whether it is stable as a dimer or a tetramer. Examination of ancestral sequences showed that the allosteric mutations are part of a downhill adaptation to lower environmental temperatures. This mechanism for modulating the oligomeric state is probably common in evolution.
[sic]editor's summary

So much for your ANTI-mutation diatribe, jk
http://www.scienc...346.full

Dec 20, 2014
I don't make veiled threats Ira, you can disagree with me, and I can disagree with you, but the next time anyone on this forum disrespects another, I will see to it that it is the last comment they make here, myself included.

Ahem. Was that an "un"veiled threat?

Dec 20, 2014
Ahem. Was that an "un"veiled threat?

Reads like a threat to shut down physorg. Given the current state of the world it is NOT a smart move to make such threats.

JVK I suggest clarify to physorg what you mean or Homeland Security may be interested in having a chat.

JVK
Dec 20, 2014
Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution


Captain Stumpy inferred that I made that claim. My claim can be placed into context because my 2013 review concluded:

"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

Nei's book was published on the same day and he concluded: "...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

Works by Luca Turin et al and by Anna Di Cosmo et al have since linked Extavour's insect work to my works via conserved molecular mechansims in the context of anesthesized flies and octopuses.


JVK
Dec 20, 2014
Selection keeps detrimental mutations from running wild throughout populations.


Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants http://dx.doi.org...ure11690
My comment: 86% of our potentially harmful alleles arose in the past 5,000 years.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication http://www.pnas.o...abstract
My comment: Mutations that negatively impact genes are not eliminated by selection. With domestication of horses, deleterious mutations can accumulate in the genome. This was shown for rice and dogs. Horses and humans are added examples that refute ridiculous claims.

The unstated claim is that mutations are naturally selected. The link to the evolution of biodiversity parallels Nei's conclusion about constraint-breaking mutation, but he links mutations to the magic of evolved biodiversity without natural selection.

JVK
Dec 20, 2014
My comment (above) : 86% of our potentially harmful alleles arose in the past 5,000 years.

The domestication of horses associated with inbreeding and an excess of deleterious mutations supposedly occurred across 5,500 years. See: http://esciencene...illennia

When placed into the context of chromosomal rearrangements in dog domestication, mutations that perturb protein folding can be linked to many deleterious traits across species via conserved molecular mechanisms that consistently link mutations to pathology via genetic networks and metabolic networks.

The understated aspect of epigenetic pharmacology is that it also links genetic networks and metabolic networks (i.e., pharmacogenomics) and nutrigenomics via the same conserved pathways of RNA-mediated cell type differentiation we detailed in our 1996 review. http://www.hawaii...ion.html

JVK
Dec 20, 2014
...allosteric mutations are part of a downhill adaptation to lower environmental temperatures. This mechanism for modulating the oligomeric state is probably common in evolution.


Again, this suggests adaptation to higher environmental temperatures also is due to allosteric mutations, which is similar to the claim that fried eggs lead to the evolution of chickens. I'm not sure how to address such claims in the context of everything known about thermodynamic cycles of protein biosynthesis and degradation, because what they infer ignores physics and chemistry and substitutes facts with definitions and assumptions.

It is common for evolutionary theorists to do that, which is why serious scientists claim that what is currently known about protein folding is important.

http://www.scienc...4419.htm
"More and more, we're realizing that folding is regulation..."

That's like saying that cell type differentiation is important.

Dec 20, 2014
@johnhew
If you follow the comments at:http://phys.org/n...firstCmt you'll see why all but one reader here have a difficult time taking jvk seriously, besides him calling everyone an idiot for not agreeing with him.

Dec 20, 2014
Captain Stumpy inferred that I made that claim
EXCEPT that the good Captain did NOT make ANY inferences at all

I copied and pasted your words Verbatim

I not only copied your words VERBATIM, but i also included a LINK so that what i copied could be VERIFIED by the reader

This is what i always loved about your delusional world, kohlslaw!
you want so desperately to believe in something that you are willing to completely ignore all the empirical data in front of you to believe your personal delusion

EVEN if it makes you look like a complete fool

And by the way... we've ALREADY discussed this more than once!

and i am not averse to posting your words VERBATIM again to prove that i inferred nothing

shall i post it so that everyone else can see how you are lying above?
how you are trying to make it sound like you simply made a small error or typo?

She read YOUR words, not MY interpretation of your words

Epic fail on your part

Dec 20, 2014
Ahem. Was that an "un"veiled threat? Reads like a threat to shut down physorg.
@Oz
That was JohnHew that made the threat, not jk

if you would like to talk to an authority about jk... why not talk to his local authorities and the local medical board for his previous claims of having "decades of experience in Diagnostic medicine" which he claimed a LOT not too long ago...

you can word search PO for it and get the exact wording, because he's claimed it often enough

(it is a violation of law to practice medicine without a license, and jk already admitted to failing out of college, so it is impossible for him to hold a medical license because he has not met the education requirements as per the federal gov't and local regulatory agencies directly involved in regulating medical personnel - this is punishable by fine & jail time)

I warned him off about it several times, but he ignored it then...

Dec 20, 2014
why not talk to his local authorities and the local medical board for his previous claims of having "decades of experience in Diagnostic medicine" which he claimed a LOT not too long ago.


He claims to be the pathological-society-certified-Scientist too. But to regular peoples that is only the lab bench tech that runs the blood checking machine in the hospital basement. But I don't think he still works in that hospital up there in Ewatta-Something Georgia, maybe he called the real doctor-Skippys a bunch of fools, idiots and morons too.

It cost a couple of dollars to the pathological-society interweb place to check him out. For them he is just the ordinary lab tech assistant sort of certified.

JVK
Dec 20, 2014
besides him calling everyone an idiot for not agreeing with him.


I don't care if anyone agrees with me. People who fail to recognize that protein folding is regulation are biologically uniformed (aka science idiots).

http://www.scienc...4419.htm "More and more, we're realizing that folding is regulation..." -- as detailed in our 1996 review.

For comparison, see:
http://www.scienc...abstract
"...mutations act by changing either protein conformation or conformational dynamics, analogous to the ways in which allosteric ligands introduce conformational change. Thus, we referred to the indirect mutations as allosteric mutations. "

Science idiots invent terms like allosteric mutations and use them in attempts to link natural selection for mutations to evolution, as in:
evolutionary plasticity; that is, "evolvability." Selection favors mutations of side-chain interactions..."

JVK
Dec 20, 2014
Claims that "selection favors mutations" can be placed into this context:

"The protein network can be interpreted as a collection of evolutionary paths in protein space," said Prof. Ben-Tal. "Paths in the major connected component of the network include many domains, and demonstrate the sequence and shape resemblance between them. The large number of paths within the major connected component suggest it is particularly easy to add and delete motifs in the continuous region of protein space without impeding stability. Apparently, evolution took advantage of this property to design new proteins with novel functions." http://phys.org/n...tml#nRlv

Added motifs are stabilized by nutrient-dependent amino acid substitutions. Deletion of unstable motifs typically occurs when accumulated mutations perturb cell type function (e.g., protein biosynthesis or degradation). If not, perturbed protein folding leads to pathology.

JVK
Dec 20, 2014
CAVEAT:
...evolution took advantage of this property to design new proteins with novel functions."
http://phys.org/n...tml#nRlv

This attribution to evolution attests to the problem with most theories about the de novo creation of new proteins with novel functions. If you accept that claim that "evolution took advantage..." of anything, you introduce selection for something that has already occurred outside the context of selection for nutrients. Nutrients enable the physiology of pheromone-controlled reproduction.

Selection for mutations or anything else that does not enable reproduction is a death sentence to individuals that may lead to extinction of a species as quickly as when the individuals of a species concurrently exhaust their food supply.

Eschel Ben-Jacob (2003) puts that fact into the perspective of Lenski's experiments.
http://rsta.royal...abstract

Dec 20, 2014
@JohnHew
hey John, where is your banning threat now?
You have painted yourself into a corner... you specifically stated
, but the next time anyone on this forum disrespects another, I will see to it that it is the last comment they make here, myself included
and now, JK is slamming an entire team of scientists because he doesn't like the terminology of their publication, nor the reasons that they chose to use the terminology that they did
Science idiots invent terms like allosteric mutations and use them in attempts to link natural selection for mutations to evolution
AND, to make matters worse, that team is NOT here to defend itself, nor will they likely stoop to arguing with a creationist on a Pop-sci site because they have real jobs

you should be talking to someone about Kohls denigration of an entire team with NO reason and getting him ousted

At least when he lies about ME
i can defend myself with his own words and prove him wrong

What say you, eh, John?

JVK
Dec 20, 2014
Re: Eschel Ben-Jacob (2003) and Lenski's experiments.

In many experiments, bacteria are exposed to lethal constraints in order to select mutants that happen to have the appropriate trait for surviving. The selective conditions are conceived as an imitation of the environmental action in natural selection. Usually, the effect of one specific selection factor is tested under uniform and constant conditions. The above-described approach is well developed and provides an efficient test bed for studying issues related to the selection for which they were designed. It is not suitable, however, for revealing the significant continuous role of the environment in bacterial `self-improvement' between the rare events of selection, due to a large sudden change in a specific factor.


A sudden shortage of a specific nutrient exemplifies a large change in an ecological factor.

Dec 20, 2014
A sudden shortage of a specific nutrient exemplifies a large change in an ecological factor.

causing multiple adaptation strategies - which, in turn, cause multiple "mutations". Some which survive and some don't...
AKA diversification.

JVK
Dec 20, 2014
JK is slamming an entire team of scientists because he doesn't like the terminology of their publication


I'm slamming them because they invented a term and used it to misrepresent what must occur for ecological variation to lead to nutrient-dependent pheromone-controlled ecological adaptations in the context of what is known about bio-physically constrained RNA-directed DNA methylation and RNA-mediated events that link amino acid substitutions from thermodyncamic cycles of protein biosynthesis and degradation to organism-level thermoregulation manifested in the biodiversity of morphological and behavioral phenotypes.

They ventured from biology into the area of physics, where others have set precedents for descriptions of their behavior. https://www.list....in-ince/

Robin Ince "Am I wrong to sometimes be scared of science idiots?"

Brian Cox "…my favoured response would be: 'you bunch of utter nob ends'.

Dec 20, 2014
Re: Eschel Ben-Jacob (2003) and Lenski's experiments.

A sudden shortage of a specific nutrient exemplifies a large change in an ecological factor.


That's natural selection. All you're doing is giving it a different name because you don't like the original for some reason. It's ecological adaptation via natural selection. The environment changes and a nutrient is limited. Some individuals die off because they're unable to utilize what's left. THAT'S the act of selection for those that CAN utilize what's left.

That's more or less what happened in Lenski's, except instead of one population dying off, another became able to use what was already there BETTER because of the translocation.

JVK
Dec 20, 2014
http://blogs.scie...olstice/

As a science journalist, I know that scientists don't have a clue how our universe sprang into being billions of years ago, or why it took this particular form out of an infinitude of possibilities, including nonexistence. Nor does anyone know how inanimate matter on our little planet coalesced into living creatures, let alone creatures that could invent reality TV. Science, you might say, has discovered that our existence is infinitely improbable, and hence a miracle.


Compare that approach to the most recent claim made here:

Some which survive and some don't...
AKA diversification.


--and thus mutations link natural selection to the evolution of creatures who invented reality TV. The same creatures who refuse to discuss the book review. Does anyone else recognize the pattern here?

The biologically uninformed will probably...

Dec 20, 2014
@jvk

Are you aware proteins evolved?

http://www.biomed...48/12/13

Dec 20, 2014
I'm slamming them ...
ok, for starters, they use the term very specifically, and also describe what they use it for and WHY
the second paragraph says
The most likely hypothesis is that these mutations act by changing either protein conformation or conformational dynamics, analogous to the ways in which allosteric ligands introduce conformational change. Thus, we referred to the indirect mutations as allosteric mutations
& i KNOW you can read the whole study, so i know you didn't miss that part in the 2nd paragraph (unless you didn't read it or you've been BANNED from there as well because of your lies and attacks)

Now, you've attacked an ENTIRE TEAM of scientists because you don't like their abstract terminology OR you didn't read the study
- AND WORST YET they can't defend themselves!

THIS is directly against the terms JohnHew set forth, therefore, because you broke the rules, you DESERVE to be banned

John?
Why are you waiting?

JVK
Dec 20, 2014
It's ecological adaptation via natural selection.


Is there a model for that? In my model of ecological adaptation, natural selection for nutrients leads from ecological variation to RNA-directed DNA methylation and RNA-mediated events that link amino acid substitutions to the pheromone-controlled physiology of reproduction via feedback loops and loops important to protein folding, which is perturbed by mutations.

Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353 Conclusion: "Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."

Why isn't anyone comparing my model to this claim: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." (p. 199) http://www.amazon...99661731

JVK
Dec 20, 2014
https://medium.co...81bc793a

Excerpt: "Information is similar to energy in this respect. It can be encoded using light, chemistry, electronics, smoke signals and so on, and all these things obey different laws of physics. However, the information itself is somehow separate from all this. It is substrate-independent. But the information itself is preserved, regardless of the laws in play."

"...there is a discontinuity inasmuch as there are no intermediate forms between the unchanged and the few changed. De Vries called that a mutation. The significant fact is the discontinuity. It reminds a physicist of quantum theory -no intermediate energies occurring between two neighbouring energy levels. He would be inclined to call de Vries's mutation theory, figuratively, the quantum theory of biology." Schrodinger (1944)

How could information loss lead to increasing organismal complexity?

JVK
Dec 20, 2014
Are you aware proteins evolved?


Koonin is one of two editors of the book that John Hewitt is reviewing. I can't imagine any author of any chapter claiming that proteins evolved because it would be like a science idiot claiming that Koonin's group was wrong when they claimed:

"We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms."
http://www.nature...306.html

See my second post in these attempts to discuss the book review. The universal trend is the RNA-mediated link between metabolic networks and genetic networks via amino acid substitutions.

JVK
Dec 20, 2014
http://medicalxpr...nes.html
"Whether changes in the microbial community arise directly from the altered nutrient environment in the gastrointestinal tract, or indirectly due to effects of altered diets on host physiology that are consistent across genotypes, remains a fascinating area for future inquiry."

"genetically identical human twins had gut microbiotas that were no more similar than those of fraternal twins, who share only half of their genes."

http://www.salk.e...p?id=552
The difference in the two types of nematodes (one with teeth) arises in the context of their nutrient-dependent pheromone-controlled reproduction via one nutrient-dependent amino acid substitution.

All other cell type differentiation in all cells of all individuals of all species also occurs via nutrient-dependent amino acid substitutions and pheromone-controlled species-specific reproduction.

Dec 20, 2014
@JohnHew
you directly threatened the entire forum to not disrespect one another and those who broke that would be banned
the next time anyone on this forum disrespects another, I will see to it that it is the last comment they make here, myself included
now it is time for you to act, becuase Kohl directly disrespected an entire scientific team because he doesn't like they way they typed up an abstract
He directly attacked the team against your threat, therefore, per your own post, you should be doing everything you can to make sure he cannot post here again... only problem is, he is now flooding the site with his backpedaling, as though it justifies his remarks against those who could not defend themselves
I KNOW he read the study, as he posted the SAME words i used above explaining WHY in THIS thread: http://phys.org/n...firstCmt

This is a direct SNUB to the scientists as well as PO, YOU and your threat

Dec 20, 2014
@JohnHew
you came into the thread and tried to make people play nice, but kohl has shown you that he feels all authority is contemptible to him

He displays these traits regularly everywhere, from ScienceMag to PO

So far, the bulk of the posters have tried to be as respectful as possible, regardless of their historical battles with Kohl

Now, Kohl is dragging a whole team into the fight who cannot defend themselves

he has directly insulted a team of reputable scientists while refusing to acknowledge the study OR its contents, which i posted as supporting evidence

the link in the last post i made PROVES that he was well aware of the contents, as he posted the same part himself- the same part i used as proof

you are the one who specified the rules of engagement

Kohl is ignoring you OR calling your bluff

it is upon YOUR shoulders now
you spelled out some consequences
are you, or are you NOT going to act upon your own threat?

Dec 20, 2014
Captain
Realise JohnHew posted that but without clear evidence to the contrary I'm of an opinion that the JohnHew posting here is JVK. If it writes JVK and acts likes JVK, then quack springs to mind.
If the writer is not JVK then that's two people physorg should ban, one for being a scam artist using pseudoscience to make money out of desperate and gullible people and the other for making open threats.

JVK
Dec 20, 2014
http://www.webmd....od-sugar

Here is information about the potential benefits of pharmacogenomic profiles, which link genetic networks to metabolic networks. It's about one of the prescription medications that showed up as an evidence level 1 alert due to my potential to rapidly metabolize Tramadol.

The alert was linked to the cytochrome P450 2D6 enzyme that is encoded by the CYP2D6 gene. CYP2D6 is responsible for the metabolism and elimination of approximately 25% of clinically used drugs. Variations in gene expression in the liver are associated with the enzymatic metabolism of drugs via RNA-mediated links between genetic networks and metabolic networks, not mutations.

The ability to link these networks to patient outcomes was established in a study of 10,000 patients that led the way to what is now available in the context of personalized evidence-based medical practice.

JVK
Dec 20, 2014
Medicare insurance typically pays for the pharmacogenomic profile and it is non-invasive testing (a cheek swab). Evidently, the US government realizes the importance of evidence-based personalized medicine in the context of prescription drugs.

Indeed, it seems likely that only science idiots will continue to ignore the obvious links between genetic networks and metabolic networks as they continue to tout their pseudoscientific nonsense about beneficial mutations.

What we've seen here is that some of them would rather see you dead than admit they don't know anything about biologically-based cause and effect. They're anonymous silent killers, like the types of cancers that cannot be identified by their cell types because evolutionary theorists want you to believe that beneficial mutations lead to cell type differentiation, not nutrient-dependent amino acid substitutions.

JVK
Dec 20, 2014
From the man who brought us the pseudoscientific nonsense of microbial evolution via mutations, we have: Coevolution Drives the Emergence of Complex Traits and Promotes Evolvability http://dx.doi.org....1002023 -- coauthored by Richard E. Lenski

http://www.scienc...4139.htm
"Even though we're basically studying computer viruses, we're able to address some of the oldest questions in evolutionary biology," Zaman said.

To address questions in evolutionary biology you first link physics to the chemistry of protein folding and protein folding from the availability of nutrients to the RNA-mediated amino acid substitutions that stabilize protein folding, which is required for ecological adaptation.

DNA Loop-the-Loops http://www.the-sc...e-Loops/ A new full-genome map indicates how DNA is folded within the nuclei of human cells.

JVK
Dec 20, 2014
Now, Kohl is dragging a whole team into the fight who cannot defend themselves


Agreed. There is currently no defense for their claims, which involve inventing a term and using it to misrepresent what everyone knows can only occur in the context of what is known about bio-physically constrained RNA-directed DNA methylation and RNA-mediated events that link amino acid substitutions to cell type differentiation in species from microbes to man.

For example, see this report: Brain structures devoted to learning, memory highly conserved in animal kingdom, suggesting common evolutionary origin http://phys.org/n...mal.html

There has never been any experimental evidence to support a theory involving mutations and/or natural selection compared to facts about conserved molecular mechanisms that link nutrient-dependent pheromone-controlled cell type differentiation via RNA-mediated events and amino acid substitutions in all species.


Dec 21, 2014
Captain
Realise JohnHew posted that but without clear evidence to the contrary I'm of an opinion that the JohnHew posting here is JVK. If it writes JVK and acts likes JVK, then quack springs to mind.
If the writer is not JVK then that's two people physorg should ban, one for being a scam artist using pseudoscience to make money out of desperate and gullible people and the other for making open threats.
@Oz
Well, that WOULD be a good reason for the complete lack of action as well as for the protection of jvk on the site

and perhaps explain some of the tap dancing done in the comments with regard to certain questions too...

Hmmm

Perhaps we should take this argument to the site managers and post it to the SITE?

I am sure that if enough posters pushed the issue the site would have to act... unless, of course he is being protected by THEM as well, due to some creationist tribal thing?

Dec 21, 2014
Captain
They banned Oliver fast enough, they banned Zephir and eventually the subsequent sockpuppet gets banned. Creationists do appear to be immune. Maybe the moderators are too busy rolling around the floor laughing at the creationist drivel to actually ban them.

Dec 21, 2014
Maybe they're so overwhelmed with reports that they won't deal with the crackpots and creationists?

Or maybe they just don't give a rat's ass.

JVK
Dec 21, 2014
The strategy is to let the biologically uninformed continue to ignore the content of phys.org posts, like those from John Hewitt. The focus of the ignorant is on attacking anyone who understands what they do not. See what's happened here. Learn why the efforts of the uninformed are predictable. They always have been.

Watch the responses to part II of John Hewitt's review, which includes current information about cell type differentiation. The biologically uninformed will probably destroy any attempt to discuss bio-physically constrained...


The anonymity of the ignorant fuels more ignorance. No attempt is made to address the content of the book that John Hewitt is reviewing. The discussion focuses on banning the reviewer and anyone who attempts to discuss his review.

If his review was not so threatening to the anonymous fools who participate here, and the idiot minions of biology teachers like PZ Myers, we would be discussing facts, not those who deliver them.

JVK
Dec 21, 2014
http://www.ncbi.n...4222338/
Changes in Methylation Patterns of Kiss1 and Kiss1r Gene Promoters Across Puberty

Changes are linked to GnRH but reportedly: "The data presented here serve as a starting point for further investigation of the role of epigenetics in the transcriptional modulation of these genes by sex steroids and other environmental factors."

In my model, GnRH is the link from the epigenetic landscape to the physical landscape of DNA in the organized genomes of all vertebrates. The starting point for this link was with cell type differentiation in yeasts in our 1996 Hormones and Behavior review article.

JVK
Dec 21, 2014
This is a direct SNUB to the scientists as well as PO, YOU and your threat


How could experimental evidence of biologically-based cause and effect that attests to the ignorance of biologically uninformed science idiots be considered to be a
SNUB to the scientists as well as PO
or to John Hewitt?

He's done his best to promote intelligent discussion on phys.org Perhaps he will make good on the threat and that will happen.

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

Life history transitions manifested in behavior are nutrient-dependent and pheromone-controlled in the honeybee. When others see the clear link from a single amino acid substitution (Val158Met) to human behavior, do they still believe mutations can be linked to biodiversity via natural selection or automagically occurring evolution?

Why wouldn't facts change their ridiculous beliefs?

Dec 21, 2014
Creationists do appear to be immune.
@OZGuy
it is far more likely that they are also creationists
sigh... so much for being a person of their word

Maybe they're so overwhelmed with reports that they won't deal with the crackpots and creationists?
Or maybe they just don't give a rat's ass.
@Sapo
Judging from the responses, the second is far more likely than the first

John was willing to threaten everyone so we behaved, but allows the creationist to attack a well known reputable team FOR NO REASON

so, it looks as though creationists are protected here at PO, and that they don't give a RA about his personal attacks

At this point, it is perfectly clear that creationists
and jk in particular
have the run of the site, no matter HOW much jeopardy he puts them into with his public attacks etc

even though it is painfully obvious there is NO science in creationists dogma and even the LAWYERS could spot THAT one!
https://en.wikipe...Arkansas

Dec 21, 2014
The focus of the ignorant is on attacking anyone who understands what they do not. See what's happened here
yes, kohl, you have (repeatedly) demonstrated this very well with your attacks: http://www.scienc...346.full

you obviously ignored their study and attacked them anyway, while putting them down even though you quoted the exact same part i did in another thread here: http://phys.org/n...firstCmt

Showing that you didn't understand what was written &

Since we can see that JohnHew is NOT going to keep his word with regard to making you behave
and likely his direct threat was simply a means to force prejudice on US and allow the site to protect you
then the only thing WE have left is to simply ignore you as a creationist TROLL, report your post and pass on your denigrations to the team with links to PO for proof

Maybe THEY will do something, eh?


Dec 21, 2014
John Hewitt writes for Extreme Tech http://www.extrem.../jhewitt and after reading several of his articles but more telling the his comments on his articles, he his not a creationist.
He does seem though to be highly tolerant of theistic evolutionists.

Until he responds we can only speculate why he hasn't yet. My speculation is that he is trying to craft something diplomatic, something that won't fully satisfy anyone but that will get him off the hook.

JVK
Dec 21, 2014
the only thing WE have left is to simply ignore you as a creationist TROLL


That's a great idea! Others can then proceed to discuss John Hewitt's book review in the context of what is known about bio-physical constraints on the chemistry of protein folding that link RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in all cell types of all individuals of all genera via conserved molecular mechanisms.

Biologically uninformed science idiots can find somewhere else to tout their pseudoscientific nonsense. There are plenty of science idiots like PZ Myers with blog sites and plenty of science idiots post to them. That's where you can find your peers.

I'm looking forward to discussion of the book chapter by Brosius: The Persistent Contributions of RNA to Eukaryotic Gen(om)e Architecture and Cellular Function http://cshperspec...abstract


JVK
Dec 21, 2014
highly tolerant of theistic evolutionists.


Like Francis Collins, perhaps. He is the director of the NIH and author of the book: The Language of God: A Scientist Presents Evidence for Belief http://www.amazon...43286391

The book John Hewitt is reviewing attests to what serious scientists have learned during the past decade or so, which is expressed in Jordan et al / co-author Koonin (2005): "We cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid compositions of proteins in 15 diverse taxa that represent all three domains of life and span a wide range of lifestyles and environments. Thus, currently, the most plausible hypothesis is that we are observing a universal, intrinsic trend that emerged before the last universal common ancestor of all extant organisms." http://www.nature...306.html

JVK
Dec 21, 2014
http://www.extrem...lly-work

Excerpt: "One such hybrid approach now getting a lot of attention is the OpenWorm project which simulates whole assemblies of cells within an entire behaving organism."

John Hewitt is not the only science journalist to know that "System-wide Rewiring Underlies Behavioral Differences in Predatory and Bacterial-Feeding Nematodes." http://linkinghub...12015000]http://linkinghub...12015000[/url]

He may be the only one that knows how to place that fact into the context of what's known about cell type differentiation in species from microbes to man:

"The patterns of synaptic connections perfectly mirror the fundamental differences in the feeding behaviours of P. pacificus and C. elegans", Ralf Sommer concludes. http://linkinghub...12015000]http://linkinghub...12015000[/url]

It would be great if he had less tolerance for science idiots.

Dec 21, 2014
My speculation is that he is trying to craft something diplomatic
@Vietvet
the threat was not diplomatic

John gave a direct threat and used his connection with the site as a power play

Thus, he gave his word

he is violating his own word, and thus cannot be taken seriously

The appearance here so far is:
he protects those who attack others as long as they conform to his personal set of beliefs

we can also extrapolate that to the site, as the site has allowed it to continue

in conclusion: we can only conclude by demonstration above that the site protects creationists and those who attack legitimate scientists as long as they are also uneducated creationists who make up definitions and condemn others for the same behavior

The only defense for people interested in science is:
downvote and report jvk- per site rules
post his rantings to the authors and hope they don't feel litigious
keep on posting actual science regardless of jk's TROLLING and SPAM

Dec 21, 2014
Biologically uninformed science idiots can find somewhere else to tout their pseudoscientific nonsense
and i have been telling you this for over a year, jk

you have continued to misrepresent other science and the important work, as demonstrated by the replies that i've been receiving regarding your DIRECT QUOTES about their work... this means, by definition, that you are NOT a serious scientist, nor are you "Biologically informed"

The saddest part about all this is that your continued ranting and misrepresentation spills over onto the SITE, making the PO site look like it is filled with idiots who can't even take the four-freakin-seconds needed to google a simple definition, let alone interpret science as it should be.

you used to LOVE linking Extavour as proof of your NO MUTATION idiocy till she slammed you and said you misinterpreted her work http://www.oeb.ha...oeb.html

Now you call her an idiot

how pathetic

Dec 21, 2014
So now we have not only that the commenter possinging an identity is an impostor, but the author who wrote, "The bacterial flagellum evolved not only to give creationists something to get worked up about, but also to give the origin of life sleuths a fascinating puzzle," is a creationist sympathizer."
What might the Sherlocks conclude next?


JVK
Dec 21, 2014
What might the Sherlocks conclude next?


They cannot conclude anything other than what they've been taught to conclude. "...we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation..." http://gbe.oxford...abstract

"...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

That means differences in bacterial flagella arise due to beneficial mutations. They need only ignore everything currently known about bio-physical constraints on the chemistry of protein folding and RNA-mediated events that link nutrient-dependent pheromone-controlled feedback loops in species from microbes to man via conserved molecular mechanisms of amino acid substitutions.

JVK
Dec 21, 2014
Extavour as proof of your NO MUTATION idiocy till she slammed you and said you misinterpreted her work...


Her works are among all others that link "...an ancestral ground pattern common to all investigated taxa: chemosensory afferents supplying thousands of intrinsic neurons, the parallel processes of which establish orthogonal networks with feedback loops, modulatory inputs, and efferents." http://www.scienc...1401358X

The "...ground pattern common to all investigated taxa..." is nutrient-dependent and pheromone-controlled via feedback loops that link RNA-mediated amino acid substitutions to the differentiation of cell types. Mutations lead to pathology because they perturb protein folding that is stabilized by the amino acid substitutions.

That's why Extavour does not claim that mutations CAN be linked to the evolution of biodiversity. She claimed her works do not prove mutations CANNOT be linked to biodiversity!

Dec 21, 2014
Did you really say "possinging"? Is that the name of a dish as baffling as the BS you waffle about?

You've taken folks to task and blustered for quite a while, but nothing has happened except gas.

Are you a JVK sock?

JVK
Dec 21, 2014
"Gene and genome duplication constitute major forces in evolutionary innovation. The variety of mechanisms by which such duplications occur, as well as the various means by which the duplicated segments are subsequently rearranged (and sometimes partially lost), requires careful analysis and consistent use of biologically informed terminology." http://dx.doi.org...2/846421

BIOLOGICALLY INFORMED TERMINOLOGY (Get it?) Extavour does.

Co-author Ferrier is co-author with Extavour of "The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede..."http://dx.doi.org....1002005

Both works are linked via conserved molecular mechanisms of cell type differentiation in co-author Extavour's "Insulin signalling underlies both plasticity and divergence of a reproductive trait in Drosophila" http://rspb.royal...abstract

Captain Stumpy is a science idiot!

JVK
Dec 21, 2014
http://phys.org/n...firstCmt
Captain Stumpy wrote:

Feel free to contact me at: http://saposjoint.net/
my profile there is the same: Truck Captain Stumpy

Is saposjoint also
1) Captain Stumpy?
2) And Vietvet?
3) And OZGuy?

Alternatively, were they all taught to be science idiots by the same biologically uniformed teacher?

JVK
Dec 21, 2014
The Origin of Species: Lizards in an Evolutionary Tree
http://www.hhmi.o...ary-tree

This video supports the snake-centric view of human brain evolution. It can be compared to what is known about "...all investigated taxa: chemosensory afferents supplying thousands of intrinsic neurons, the parallel processes of which establish orthogonal networks with feedback loops, modulatory inputs, and efferents." http://dx.doi.org...4.10.049

Theories based on definitions and assumptions can be discussed in the context of facts known to serious scientists about lizards that defy evolutionary theory via their bizarre patterns of ecological speciation sans mutations and/or natural selection. http://www.bioone.../MCZ17.1

Is their behavior more important than their genes?
http://sicb.org/m...p?id=124

Dec 22, 2014
"...we will not consider geographical and ecological factors because of space limitation. Our primary purpose is to clarify the roles of mutation and selection in the evolution of reproductive isolation..."


This will be news to you because you don't do experimental work, Kohl, but when you're trying to establish causality, you isolate variables. You identify independent variables that you can control or observe so that you can be sure they and nothing else control the resulting dependent variable. This is experimental design 101.

They need only ignore everything currently known about bio-physical constraints on the chemistry of protein folding


Who's ignoring that? I provided you multiple models integrating them.

"Gene and genome duplication constitute major forces...


I linked that paper initially as evidence against you when you stated that duplications are pheromone-controlled. They describe how duplications happen. You don't.

Dec 22, 2014
... impostor,...creationist sympathizer."
@JohnHew
well, considering you have not answered some very relevant questions... and you HAVE made threats while ignoring the obvious attacks, allowing jk to mouth off with free reign, but you cautioned everyone else

and you cannot dispute the "creationist sympathizer" label that is hung around the "Johnhew" profile posting here considering you made that threat, but you are now not doing ANYTHING AT ALL to make good on your threat?

If you observed this behavior in a police officer, you would likely conclude that the officer is either protecting the arrogant creationist or has orders from "on high" that say to protect them

This is what is OBSERVED above
it is not a matter of debate
it is a matter of observation

which is why people are challenging your moniker as the author

If you had no intentions of following through on your threat, why offer it?


Dec 22, 2014
@JohnHew
you are even ignoring his attacks that dragged in another site... calling all of us idiots because we learned biology in college, and because we challenge the greak jk college failure based upon his inability to wield the basic 4second dictionary search for supporting or relevant info regarding his chosen path
or we challenge him because he fails to interpret science correctly
or we challenge him because he doesn't understand a LOT of what he is talking about (See the arguments Anon9001 posts against him)

I posted a forum site that will allow me to share relevant information regarding SCIENCE becasue they cannot access it here due to a paywall

It is obvious by now that you are supporting and defending jk and his posts, regardless of content, therefore it is not likely to get us anywhere to push for you to actually keep your word

You would only apply that word to those threatening jk anyway, given the above demonstrations / posts


Dec 22, 2014
taught to be science idiots
why did you leave out the rest of the post, jk?
Allow me to add the rest
I can provide help with actual science, especially with regard to ScienceMag, like the one above that jk decided was wrong because he didn't like the wording of the study and that they support mutations, the nemesis that he forgets also defines his own work

There is an interesting study that jk decided to malign the authors because they used words he didn't understand... the same study argued in the following threads:
http://phys.org/n...firstCmt
http://phys.org/n...firstCmt

That second link is where John threatened us all to behave, but it APPEARS it is OK for jk to do whatever he likes because he is protected here at PO -IMHO

he must pay them BIG $$$$ for that
that place was chosen because of the HEAVY moderation
they do NOT allow pseudoscience or crackpots

Dec 22, 2014
What might the Sherlocks conclude next?
POST SCRIPT @JohnHew
You really should have read the interactions between kohl and Anonymous9001 (an ACTUAL biologist, not a pretend one playing as a lab tech and lying about his decades working in diagnostic medicine) in this thread here: http://phys.org/n...firstCmt

Those comments alone should have opened your eyes to WHY jk is considered a creationist troll here by most

It also should have opened your eyes about jk's inability to comprehend the science, and how he distorts everything based upon his religious perspective and delusion world view
It is OBVIOUS, not subtle or craftily hidden

I, personally, have no illusions as to you or your abilities at this point
your demonstrations have been adequate for the formation of an impression

protecting one pseudoscience acolyte only draws others to the flame
I sincerely hope that the site doesn't suffer for it


Dec 22, 2014
@jk says
BIOLOGICALLY INFORMED TERMINOLOGY (Get it?) Extavour does.
but apparently YOU do NOT
Dr. Extavour says
our work does, we hope, provide an example of how nutrition/ecology could affect the evolution of potentially adaptive traits, you [Captain] are right that we in no way claim that mutations in the heritable genome play no role in evolution. Indeed, as you [Captain] correctly state, just because we provide evidence that nutritional conditions play a role, this does not negate a role for mutations. Indeed, in that very same paper, we provide evidence that heritable differences in the genome sequences between Drosophila species, in other words, mutations, ALSO play a role in the evolution of the trait we are studying.

So Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
again, your "interpretation" FAILED to see clearly

I still have a hundred more inquiries outstanding

Dec 22, 2014
Captain Stumpy is a science idiot!
& where has this been demonstrated? because i spooted your failure to accept a defninition used by your chosen field when i pointed out that you yourself said your model causes mutations?
or was it when i queried Dr. Extavour and Lenski about your claims that their models supported your "anti-mutation" creationist drivel?
I simply forwarded your quotes VERBATIM and linked the pages... they are the ones that said you don't know what you are talking about
Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
so, again, you are attacking THEM with that statement, not i
as for these:
http://www.plosbi....1002005
http://rspb.royal...abstract

We've already established from the authors that you are not interpreting the studies correctly

[cntd]

Dec 22, 2014
[cont'd] @jk
and as for your SPECIFIC use of this particular link: http://rspb.royal...abstract
This is the link that YOU specifically used to support your anti-mutations rant which is what i forwarded to Dr. Extavour. In fact, this specific link, more than ANY link you have posted proves your inability to comprehend the studies you are posting, because it is the REASON that she gave the above quoted reply to me at my e-mail that i quoted above, adding in ONLY the part that notified the reader who she wasx referring to when saying "you:

She stated I was correct in my interpretation of her study, and that
Kohl is mistaken if he is claiming that my study (or Rich Lenski's work) provide evidence AGAINST the role of mutations in evolution
ALL of this is specific to the Drosophila studies she was doing, and to the linked one particularly

we are demonstrating jk's inability to see the SCIENCE for his religious delusion

Dec 22, 2014
Captain Stumpy is a science idiot!
this is also a strong demonstration of the protection afforded to jk and his anti-science trolling and creationist vilification of the scientists working hard on experimentation attempting to find answers
for more, we see
they all taught to be science idiots by the same biologically uniformed teacher?
It would be great if he had less tolerance for science idiots [meaning everyone who disagree's with jk as described in so many other threads]
There are plenty of science idiots like PZ Myers...That's where you can find your peers
idiot minions of biology teachers like PZ Myers
Science idiots invent terms like allosteric mutations and use them in attempts to link natural selection for mutations to evolution
I'm slamming them because they invented a term and used it to misrepresent what must occur
So PO and John protect the acerbic jk troll because...?
my guess is $$$$
or ...what?

truly a sad time for science on PO