Quantum biology: Algae evolved to switch quantum coherence on and off

Jun 16, 2014
A scanning electron microscope image of cryptophytes. A UNSW Australia-led team has discovered how cryptophytes that survive in very low levels of light are able to switch on and off a weird quantum phenomenon that occurs during photosynthesis. Credit: CSIRO

A UNSW Australia-led team of researchers has discovered how algae that survive in very low levels of light are able to switch on and off a weird quantum phenomenon that occurs during photosynthesis.

The function in the algae of this quantum effect, known as coherence, remains a mystery, but it is thought it could help them harvest energy from the sun much more efficiently. Working out its role in a living organism could lead to technological advances, such as better and quantum-based electronic devices.

The research is published in the journal Proceedings of the National Academy of Sciences.

It is part of an emerging field called quantum biology, in which evidence is growing that quantum phenomena are operating in nature, not just the laboratory, and may even account for how birds can navigate using the earth's magnetic field.

"We studied tiny single-celled algae called cryptophytes that thrive in the bottom of pools of water, or under thick ice, where very little light reaches them," says senior author, Professor Paul Curmi, of the UNSW School of Physics.

"Most cryptophytes have a light-harvesting system where quantum coherence is present. But we have found a class of cryptophytes where it is switched off because of a genetic mutation that alters the shape of a light-harvesting protein.

"This is a very exciting find. It means we will be able to uncover the role of quantum coherence in photosynthesis by comparing organisms with the two different types of proteins."

In the weird world of quantum physics, a system that is coherent – with all quantum waves in step with each other – can exist in many different states simultaneously, an effect known as superposition. This phenomenon is usually only observed under tightly controlled laboratory conditions.

So the team, which includes Professor Gregory Scholes from the University of Toronto in Canada, was surprised to discover in 2010 that the transfer of energy between molecules in the light harvesting systems from two different cryptophyte species was coherent.

The same effect has been found in green sulphur bacteria that also survive in very low light levels.

"The assumption is that this could increase the efficiency of photosynthesis, allowing the algae and bacteria to exist on almost no light," says Professor Curmi.

"Once a light-harvesting protein has captured sunlight, it needs to get that trapped energy to the reaction centre in the cell as quickly as possible, where the energy is converted into chemical energy for the organism.

"It was assumed the energy gets to the reaction centre in a random fashion, like a drunk staggering home. But quantum coherence would allow the energy to test every possible pathway simultaneously before travelling via the quickest route."

In the new study, the team used x-ray crystallography to work out the crystal structure of the light-harvesting complexes from three different species of cryptophytes.

They found that in two species a genetic mutation has led to the insertion of an extra amino acid that changes the structure of the protein complex, disrupting coherence.

"This shows cryptophytes have evolved an elegant but powerful genetic switch to control coherence and change the mechanisms used for light harvesting," says Professor Curmi.

The next step will be to compare the biology of different cryptophytes, such as whether they inhabit different environmental niches, to work out whether the effect is assisting their survival.

Explore further: Quantum effects help cells capture light, but the details are obscure

More information: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins , PNAS, www.pnas.org/cgi/doi/10.1073/pnas.1402538111

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EnricM
1.2 / 5 (5) Jun 17, 2014
It is part of an emerging field called quantum biology, in which evidence is growing that quantum phenomena are operating in nature,


My ESP powers preview the next wave of pseudoscience mumbo-jumbo "Healing through quantum biology"... and just wait that an idiot such as Deepak Chopra reads this.

Modernmystic
5 / 5 (3) Jun 17, 2014
It is part of an emerging field called quantum biology, in which evidence is growing that quantum phenomena are operating in nature,


My ESP powers preview the next wave of pseudoscience mumbo-jumbo "Healing through quantum biology"... and just wait that an idiot such as Deepak Chopra reads this.



Interesting take. I would think that something as fundamental to the nature of the universe and how it works (which has been shown over and over via scientific inquiry) as quantum mechanics would absolutely have a deep cause and effect relationship with biology which follows rules based on rules of quantum mechanics.
JVK
1 / 5 (8) Jun 17, 2014
De novo creation of olfactory receptor genes is only possible in the context of quantum mechanics, not mutations and evolution.
anonymous_9001
5 / 5 (9) Jun 18, 2014
De novo creation of olfactory receptor genes is only possible in the context of quantum mechanics, not mutations and evolution.


False dichotomy
johnhew
not rated yet Jun 18, 2014
How so JVK and anon??
supamark23
5 / 5 (9) Jun 18, 2014
How so JVK and anon??


JVK doesn't believe in evolution, and has a very wacky theory about how the various species got here. Basically, a total crackpot to be ignored.
anonymous_9001
5 / 5 (7) Jun 18, 2014
How so JVK and anon??


There's no reason mutation/NS and quantum effects are incompatible.
RealScience
5 / 5 (8) Jun 18, 2014
@johnhew: Since 'mutation' as commonly used and defined in biology means a change in genome base-pair sequence, new genes (whether de novo creations or alterations of existing genes) are BY DEFINITION 'mutations'.

JVK has had this pointed out to him many times, but acknowledging this would force JVK to admit that his statement that mutations are never selected for is wrong, and he's not honest enough to admit his mistakes.

Instead he ignores or insults anything that disagrees with him, whether it is experimental evidence, how words are used in a field that he claims to be an expert in, or other commenters.

And as far as quantum mechanics goes, JVK is so clueless that he thinks he needs quantum mechanics to understand the difference between changes in gene sequence and changes in gene expression. That's as silly as not understanding the difference between changing 'pray' to 'play' versus saying 'pray' three times instead of once without starting with Chomsky's universal grammar.
Captain Stumpy
5 / 5 (8) Jun 18, 2014
How so JVK and anon??
@johnhew
If you want to learn more, and learn about WHY jvk is wrong(whom I call jk, as he really is a joke)
and to learn about how jk reacts to people who prove him wrong... go here and read this article in Myers blog: http://freethough...s-place/

please pay special attention to how Myers (a biologist and professor) describes jk/jvk/kohl

there is another reason that I think you should consider carefully what jk says... His model that he posts about ad nauseum specifically causes mutations, and yet you will notice that he is extremely anti-mutation.
Follow jk's comments and watch how he posts... he is here to drum up support for his perfume "scent of eros" as well as push his model which he believes supports his creationist/xtian religion.

"If a man does not know what he is talking about with regard to his fields lexicon, then he doesn't know what he is talking about!"
OZGuy
4.8 / 5 (4) Jun 19, 2014
@JVK
At the end of the day it isn't what you believe to be true but what you can prove to be true. So far, despite writing thousands of lines of comments, you haven't proved anything other than you like to write comments ad nauseum.
JVK
1 / 5 (6) Jun 19, 2014
http://www.scienc...07/111/2 Progress in Biophysics and Molecular Biology

A quantum theory for the irreplaceable role of docosahexaenoic acid in neural cell signalling throughout evolution http://www.ncbi.n...23206328

PZ Myers and most evolutionary theorists want chromosomal rearrangements to be excluded and mutation-initiated natural selection to continue to be represented in the context of the evolution of biodiversity. Simply put, they want what we detailed in 1996 to be dismissed so that they can continue to tout pseudoscientific nonsense.

From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html "ZFX and ZFY are described as "DNA-binding proteins" and via their binding of sexually dimorphic proteins, chromatin structure and transcription could be modulated in sexually dimorphic ways as a result of females having only ZFX binding events..."
JVK
1 / 5 (6) Jun 19, 2014
New insights into the hormonal and behavioural correlates of polymorphism in white-throated sparrows, Zonotrichia albicollis http://www.scienc...14001869

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

Does anyone else read the current extant literature on cell type differentiation in species from microbes to man? Is it not nutrient-dependent and pheromone-controlled via epigenetic effects that enable ecological adaptations?

Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
http://www.ncbi.n...24693353
Captain Stumpy
5 / 5 (7) Jun 19, 2014
PZ Myers and most evolutionary theorists want chromosomal rearrangements to be excluded
@jk
assumption based upon conspiracy theory and stupidity
what we detailed in 1996
your model CAUSES MUTATIONS, per your own words. remember when we talked about mutations?I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
to which you answered
YES!
--Thanks for asking
so you only prove here that you are stupid because your model
Nutrient-dependent/pheromone-controlled adaptive evolution
is already accepted as part of evolution BECAUSE IT CAUSES MUTATIONS and you proved it already.

your conspiracy hypothesis above is based upon your creationist religious beliefs which are supported by ZERO SCIENCE

stick to the facts. Evolution Theory is true, and it works.

Your arguments are invalid as your denigration of mutation also denounces your own model.
JVK
1 / 5 (6) Jun 19, 2014
How so JVK and anon??


Thanks for asking, John

As you know, "The genetic and biophysical mechanisms by which new protein functions evolve is a central question in evolutionary biology, biochemistry, and biophysics."

http://www.pnas.o...abstract

"...explicit studies of protein structure and dynamics..." show how a "...shift in function was driven primarily by two historical amino acid changes..."

The amino acid substitutions are nutrient-dependent and pheromone-controlled in my atoms to ecosystems model, which cannot be discussed because anonymous fools and idiot minions of biology teachers like PZ Myers have no clue about what needs to happen with hydrogen bonds to achieve biophysically constrained thermodynamically controlled seemingly futile cycles of protein biosynthesis and degradation that enable organism-level thermoregulation manifested in biodiversity.

If you can eliminate the idiots here, progress might be made.
Captain Stumpy
5 / 5 (7) Jun 19, 2014
If you can eliminate the idiots here, progress might be made.
@jk
well, I know that some people ARE trying to get you banned, so... it would be much easier if you just left and stopped posting pseudoscience though! then all the idiots would be gone!
The amino acid substitutions are nutrient-dependent and pheromone-controlled in my atoms to ecosystems model, which cannot be discussed
it cannot be discussed because YOU don't know what you're talking about! remember when we talked about mutations?I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
to which you answered
YES!
--Thanks for asking
so continually talking about it, but denigrating mutations, only proves IN YOUR OWN WORDS that you are an idiot of the highest degree, and that you know less about biology etc than "any idiot minion" here
JVK
1 / 5 (6) Jun 19, 2014
Everything known about the photosynthetic, micronutrient, and macronutrient pathways that link ecological variation via base pair changes to ecological adaptations shows that mutations perturb the protein-folding that is required for niche construction to result in increasing organismal complexity via amino acid substitutions.

For example, see: http://www.scienc...14003403

"The origin of homochiral amino acids and sugars is assessed.
The integrated development of the Universal Genetic Code in shown in eight steps.
Mutation rates limited the sizes of early nucleic acid genomes to about 200 bases."

Achiral glycine links the nutrient-dependent pheromone-controlled stabilized genomes of yeasts and mammals via the conserved molecular mechanisms of amino acid substitutions.

See: http://figshare.c...s/994281
InterestedAmateur
5 / 5 (7) Jun 19, 2014
If you can eliminate the idiots here, progress might be made


Couldn't agree more, when are you leaving?
JVK
1 / 5 (6) Jun 19, 2014
If you can eliminate the idiots here, progress might be made


Couldn't agree more, when are you leaving?


Are you trying to tell others that achiral glycine does NOT link the nutrient-dependent pheromone-controlled stabilized genomes of yeasts and mammals via the conserved molecular mechanisms of amino acid substitutions that also link light as a nutrient source to the quantum biology of consciousness?

Have you read: "Molecular Vibration-Sensing Component in Human Olfaction" http://dx.doi.org....0055780 or the news version: 'Quantum smell' idea gains ground" http://www.bbc.co...21150046

Do you think that mutations and natural selection can somehow be used to explain anything about "Consciousness in the universe: A review of the 'Orch OR' theory" http://www.scienc...13001188

Or are you just someone's idiot minion?
RealScience
5 / 5 (6) Jun 19, 2014
"...explicit studies of protein structure and dynamics..." show how a "...shift in function was driven primarily by two historical AMINO ACID CHANGES..." (emphasis added)


Everything known about the photosynthetic, micronutrient, and macronutrient pathways that link ecological variation via BASE PAIR CHANGES to ecological adaptations shows that mutations perturb the protein-folding that is required for niche construction to result in increasing organismal complexity via AMINO ACID SUBSTITUTIONS. (emphasis added)


As has been pointed out to you numerous times, JVK, amino acid changes ARE MUTATIONS.
Base pair changes ARE MUTATIONS.
Amino acid substitutions ARE MUTATIONS.

We've been through the definition of 'mutation' before - do you need to have it explained to you yet again?
JVK
1 / 5 (6) Jun 19, 2014
RealScience apparently wants others to believe that light as a nutrient source causes mutations that somehow lead to natural selection and the evolution of biodiversity.

However, to believe in that pseudoscientific nonsense, you must discount what Dobzhansky wrote about nutrient-dependent pheromone-controlled amino acid substitutions that differentiate the cell types of primates in "Nothing in Biology Makes Any Sense Except in the Light of Evolution" http://img.signal...nsky.pdf

Clearly, Dobzhansky, who claimed to be a Creationist, may have been one of the first to "see the light" and to almost recognize it as a nutrient source that led from ecological variation in algae to the ecological adaptation of consciousness in the universe via the sense of smell.
He also noted that those who could not "see the light" were like bird watchers and butterfly collectors (Dobzhansky, 1964) http://icb.oxford...citation
JVK
1 / 5 (6) Jun 20, 2014
"This strong connection between structural biology and physics means that ultrafast light-harvesting functions are under genetic and evolutionary control."
http://www.pnas.o...abstract

However, what is currently known about biophysically-constrained ecological adaptations informs intelligent people that constraint-breaking mutations lead to perturbed protein folding, and the perturbations do not lead to the de novo creation of any novel receptors that could contribute to nutrient-dependent pheromone-controlled receptor-mediated behaviors.

For contrast: "The great diversity of solutions to light harvesting in the cryptophyte algae, in particular the combination of different chromophores and significantly different structural combinations, are quite extraordinary." Given the need for nutrients, the diversity of structural combinations cannot result from mutations that perturb stability via nutrient-dependent amino acid substitutions.
JVK
1 / 5 (5) Jun 20, 2014
"The ancestral cryptophyte alga acquired its chloroplast by engulfing and taming a red algal endosymbiont, which would have had at least a primitive phycobilisome (7, 24)."

That suggests a nutrient-dependent ecological adaptation to me. Who thinks "...engulfing and taming a red algal endosymbiont..." is an example of mutation-driven evolution? How can anyone be that ignorant when it comes to biologically based cause and effect?

You don't need to believe in the neo-Darwinian theories that were invented and defined to fit what RealScience thinks is known. You need only compare what people like that think to the biological facts.

See: Replace the Modern Synthesis (Neo-Darwinism): An Interview With Denis Noble
http://www.huffin...211.html

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

How else could quantum consciousness arise if not by ecological adaptations?
Surly
5 / 5 (2) Jun 20, 2014
>Clearly, Dobzhansky, who claimed to be a Creationist, may have been one of the first to "see the light" and to almost recognize it as a nutrient source that led from ecological variation in algae to the ecological adaptation of consciousness in the universe via the sense of smell.

You're saying that consciousness exists because we can smell light?
RealScience
5 / 5 (5) Jun 20, 2014
I'll explain your own references to you yet again, JVK.
Your reference "Nothing in Biology Makes Any Sense Except in the Light of Evolution" says:
The environment does not impose evolutionary changes on its inhabitants, ... the environment presents challenges to living species, to which the latter may respond by adaptive genetic changes. ... The entire evolutionary development of the living world has taken place not by invention of new "letters" in the genetic "alphabet" but by elaboration
of ever-new combinations of these letters.

The environment includes nutrients, and new combinations of DNA's 'letters' are mutations BY DEFINITION, so your Dobzhansky reference disagrees with your both your pet theory of controlled nutrient-dependent genetic changes AND your claim that mutations don't contribute to evolution.
Your reference goes further against you than anyone commenter here has, saying that ALL evolution is such sequence changes (it pre-dates epigenetics).

Checkmate.
JVK
1 / 5 (6) Jun 20, 2014
See the extended discussion of biological facts compared to the pseudoscientific nonsense of evolutionary theory. Join the group and try to comment intelligently in either of the two threads about how light acts as a nutrient to induce changes that lead to amino acid substitutions that differentiate cell types.

https://www.faceb...6109275/
RealScience
5 / 5 (5) Jun 20, 2014
@JVK - experimental evidence against your hypothesis that mutations are never selected for has been presented to you, and you have ADMITTED that you ignore such evidence. And you have also ADMITTED that you have no experimental evidence to support your hypothesis. To insist on something that goes against the evidence is pseudoscience.

Please stick with your facebook discussion and stop posting your pseudo-science on this science site.

otero
Jun 20, 2014
This comment has been removed by a moderator.
anonymous_9001
5 / 5 (6) Jun 20, 2014
light as a nutrient source


1. Light is an energy source, but not a nutrient. Why do you feel the need to keep redefining terms others have established?

2. I may have missed a citation somewhere, but what suggests light causes amino acid substitutions? If it somehow causes codon changes at the DNA level (although only UV light and above are able to cleave bonds), then it's still defined as a mutation.
Captain Stumpy
5 / 5 (4) Jun 21, 2014
...mutations that somehow lead to natural selection and the evolution of biodiversity
@jk
but YOU draw the same conclusions with your model, jk. YOUR OWN MODEL CAUSES MUTATIONS so when you say
the pseudoscientific nonsense of evolutionary theory
you are also specifically calling YOUR OWN MODEL PSEUDOSCIENCE
try to comment intelligently
we would ask the same of you but we've long given up on that! When you denigrate mutations and evolution, then say that your model explains it all... THAT is called PSEUDOSCIENCE, because, as ANYONE can plainly see, YOUR MODEL CAUSES MUTATIONS, and you even AGREED that it did! I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
So preach away, mensa boy. your model causes mutations and is a part of Evolution theory!
JVK
1 / 5 (5) Jun 21, 2014
"...a structural switch controlled by an amino acid insertion to modulate excitonic interactions and therefore the mechanisms used for light harvesting."

http://www.pnas.o...abstract

"The emergence of two forms appears to have been caused by a single insertional/deletional mutation in the new cryptophyte α subunit. A central biological question is whether the presence of longlived electronic coherence in the light-harvesting proteins results
in a selective advantage for the algae—for example, is coherence important for efficient light harvesting?"

Amino acids are fixed in the DNA of organized genomes if they benefit orgnanism-level thermoregulation. Mutations are typically eliminated if they perturb protein folding that benefits orgnanism-level thermoregulation. The mutations are linked to pathology; the amino acid substitutions are linked to increasing organismal complexity in species from microbes to man.
RealScience
5 / 5 (4) Jun 21, 2014

"The emergence of two forms appears to have been caused by a single insertional/deletional mutation in the new cryptophyte α subunit.


Great - I don't have to point out the the reference supports mutations being involved in evolution because you have done so yourself - maybe there's hope for you yet!

the amino acid substitutions are linked to increasing organismal complexity in species from microbes to man.

So much for hope. What part of the standard definition of mutation, "a change in DNA sequence" did you fail to understand? I'll repeat it for you again: amino acid substitutions are DNA sequence changes, and hence they ARE mutations, by definition.
JVK
1 / 5 (6) Jun 21, 2014
Please clarify this for me:

Are you saying that light-induced amino acid substitutions are evidence that the quantum physics of sunlight causes the quantum biology that links photosynthesis in plants to nutrient-dependent pheromone-controlled MUTATIONS that differentiate the cell types of all individuals of all species from microbes to man? I'm saying that serious scientists should substitute ECOLOGICAL ADAPTATIONS for "MUTATIONS."

If you do not agree, please tell us where to find the definition of mutation that you are using. I would like to know what kind of idiot encourages you to tout that pseudoscientific nonsense as if inventing a definition was the means to explain anything about quantum physics or the quantum biology of biophysically constrained ecological adaptations.
RealScience
5 / 5 (5) Jun 21, 2014
I'm saying that serious scientists should substitute ECOLOGICAL ADAPTATIONS for "MUTATIONS."

Serious scientists used mutations to mean "amino acid sequence changes".

Mutations and ecological adaptations are not synonymous:
Some mutations are ecological adaptations, but most are either non-adapative or maladaptive.
Some ecological adaptations are mutations, while others are epigenetic changes and others are temporary gene expression changes, and yet others are alternative splicing changes, etc.
RealScience
5 / 5 (5) Jun 21, 2014
please tell us where to find the definition of mutation that you are using.


Are you pretending that you haven't already be given this several times?

For example, in http://phys.org/n...ars.html you asked for the source of the definition and were given FOUR sources.

Here those sources are again:

NIH: A mutation is a change in a DNA sequence (http://ghr.nlm.ni...utation)

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

Biology Online: A permanent, heritable change in the nucleotide sequence in a gene or a chromosome (http://www.biolog...tation).

You really should read a good basic introduction to genetic mutations such as that by Nature's educational group: http://www.nature...tion-441
Note the definition: "a mutation is defined as any alteration in the DNA sequence"
JVK
1 / 5 (6) Jun 21, 2014
Thanks, I had forgotten how many citations attest to the pseudoscientific nonsense of population genetics.

Do any of the claims come with experimental evidence of how the mutations are linked to the evolution of biodiversity by natural selection or any other additional nonsense about biologically-based cause and effect?

I have a copy of the 2013 textbook by Nei:
Mutation-Driven Evolution
http://www.amazon...99661731

It was published on the same day as my most recent review:
Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...3960065/

Nei wrote that "Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation."

He did not write anything about how the type of DNA change was naturally selected.

I explained how ecological variation leads to ecological adaptations via amino acid substitutions.
anonymous_9001
5 / 5 (5) Jun 22, 2014
light-induced amino acid substitutions


What implies the substitution was caused by light?

He did not write anything about how the type of DNA change was naturally selected.


Mutations are selected based on how the phenotype they result in performs.
RealScience
5 / 5 (5) Jun 22, 2014

Thanks, I had forgotten how many citations attest to the pseudoscientific nonsense of population genetics.


These were examples of the definitions of mutations. If you use the term to mean something other what real scientist in biology and genetics mean, it is hardly surprising that those in the field dismiss you as a crackpot.

I happen to like non-mainstream thinking, but since you refuse to define what you mean by the term mutations, even I can't have a civil discussion with you.

Do any of the claims come with experimental evidence...?

Sure - Lenski is a good example of how this process starts.
In contrast, do you have any experimental evidence yet of your claim that mutations are NEVER selected for?

RealScience
5 / 5 (4) Jun 22, 2014
Nei wrote that "Selective advantage of the mutation is determined by the type of DNA change, and therefore natural selection is an evolutionary process initiated by mutation."


I've told you before, I disagree to some extent with Nei. Nei's statement sees one path that nature uses and ignores that there are other paths. For example:
1) there can be pre-existing variety, and a change in environment can initiate the natural selection from among that variety
2) epigenetic changes (as opposed to mutations, which are gene sequence changes) can also initiate natural selection

He did not write anything about how the type of DNA change was naturally selected.

That was explained by Darwin, Russel, and others over 150 years ago, although they did not know the molecular basis of what was being selected (which includes at least gene sequence variations, regulatory sequences variations heritable epigentic variations).
RealScience
5 / 5 (5) Jun 22, 2014
I explained how ecological variation leads to ecological adaptations via amino acid substitutions.

No you don't. You hypothesize THAT ecological variation leads to ecological adaptations via amino acid substitutions, but as *9001 and others point out, you don't explain HOW, in your comments or in any of your review articles.

Since our genomes use lots of tricks and this would be a useful trick, it wouldn't surprise me at all if there are numerous ways for this to happen. But as the Captain points out, such substitutions fall within the standard definition of mutations. And as I have pointed out, even if controlled sequence 'edits' are common, it would NOT mean that our genome don't ALSO use location-specific but non-deterministic sequence changes and even almost-random sequence changes.
JVK
1 / 5 (5) Jun 22, 2014
I included examples of conserved molecular mechanisms that link Darwin's 'conditions of life' to nutrient-dependent pheromone-controlled ecological adaptations and I have since included more details about thermodynamics and organism-level thermoregulation that reintroduce the quantum physics that link light to amino acid substitutions in plants to ecological variation that links amino acid substitutions to cell type differentiation in all individuals of all species.

The fact that I am still attempting to discuss the entirety of what is known about ecological adaptations with anonymous fools and idiot minions of biology teachers who taught them to believe in pseudoscientific nonsense attests to how pervasive that nonsense is. Clearly, it is easier to remain ignorant than to learn, which is why only the ignorant continue to challenge the facts I have detailed.

If ever you read a comment on my work by a serious scientist who is not anonymous, let me know.
JVK
1 / 5 (5) Jun 22, 2014
Lenski, and others, have since moved forward from their ridiculous misrepresentations of what others decided must be mutation-initiated natural selection that enabled the evolution of biodiversity.

See for example: http://phys.org/n...sis.html

Intelligent people realize how unlikely it is that these feedback loops would appear in the context of concurrent bottom-up (nutrient-dependent) and top-down (pheromone-controlled) ecological adaptations, which is why intelligent researchers are distancing themselves from us of the term mutations. What we see here is comment on my works from the unintelligent who don't read.
anonymous_9001
5 / 5 (5) Jun 22, 2014
Lenski and others are not denying mutations/NS like you keep insisting. Dobzhansky spent his entire career researching mutation/NS. He never denied it. I've pointed out ti you before that the majority of his publications concerned their role in evolution.
JVK
1 / 5 (5) Jun 22, 2014
Lenski and others are not denying mutations/NS like you keep insisting. Dobzhansky spent his entire career researching mutation/NS. He never denied it. I've pointed out ti you before that the majority of his publications concerned their role in evolution.


Please describe the role you think mutations play in the context of concurrent bottom-up (nutrient-dependent) and top-down (pheromone-controlled) ecological adaptations, or in the context of the evolution of biodiversity via natural selection.

Then try to support your description of biologically-based cause and effect with experimental evidence that does not assume that the organisms automagically evolved.

If Dobzhansky lived long enough, he would have recognized the difference between a mutation and an amino acid substitution that differentiates the cell types of all individuals of all species. Unlike you, he had the intelligence required to recognize the difference between
pseudoscientific nonsense and facts.
JVK
1 / 5 (5) Jun 22, 2014
"Our results demonstrate that mutant-HSC-driven niche damage critically contributes to disease manifestation in MPN and identify niche-forming MSCs and their neural regulation as promising therapeutic targets."
Neuropathy of haematopoietic stem cell niche is essential...
http://www.nature...383.html

This is the kind of thing that anonymous fools and idiot minions of biology teachers who taught them to believe in mutation-initiated natural selection think leads to the evolution of biodiversity. Ask them how that could be possible, and expect to get answers like "Lenski and others are not denying mutations/NS..." and "...the majority of his publications concerned their role in evolution."

What's worse is that the anonymous fool [anonymous_9001] got me banned from participation on the human ethology yahoo group by asking me about the role of RNA, which I have detailed in my published works.

Video link http://youtu.be/DbH_Rj9U524
JVK
1 / 5 (5) Jun 22, 2014
http://medicalxpr...ors.html

Links nutrient-dependent atomic-level interactions via quantum physics and quantum biology to the de novo creation of olfactory receptor genes and to glycine receptors that stabilize the body's response to stimuli such as light and pain. Those classically-conditioned responses link nutrient-stress and social stress to ecological adaptations perturbed by mutations that prevent protein folding from resulting in the creation of typically differentiated cell types.

Cell type differentiation is nutrient-dependent and pheromone-controlled via conserved molecular mechanisms in species from microbes to man -- as detailed in my atoms to ecosystems model of ecological adaptations:

Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems

http://figshare.c...s/994281
George_Rajna
Jun 23, 2014
This comment has been removed by a moderator.
JVK
1 / 5 (3) Jun 23, 2014
Thanks George. Have you tried to publish this in a peer-reviewed journal? In the context of discussion here, your information seems far to valuable to go un-cited or linked only to internet publication. Indeed, if you are familiar with the works of Luca Turin, something citable might lead to collaboration with others who understand the links from quantum physics to quantum biology, which suggests -- as you have -- that they lead to an understanding of quantum consciousness.
RealScience
5 / 5 (2) Jun 23, 2014
What's worse is that the anonymous fool [anonymous_9001] got me banned from participation on the human ethology yahoo group by asking me about the role of RNA, which I have detailed in my published works.


How would he get you banned by asking you a question?
It seems far more likely that YOUR ANSWER got you banned.
RealScience
5 / 5 (2) Jun 23, 2014
Clearly, it is easier to remain ignorant than to learn

You are a counter-example - you work really hard at remaining ignorant.

How many times have other commenters pointed out that amino acid substitutions ARE mutations? Well over 100 times, and you still ignore it. Or do you claim that amino acid substitutions are not DNA sequence changes?
JVK
1 / 5 (2) Jun 24, 2014
The ISHE group's moderator dictated the terms of my answer about RNA and made it impossible for me to address the anonymous fool's ridiculous question.

http://www.nature...146.html includes the involvement of amino acid substitutions that specifically seem to alter clathrin and its downstream effects on brain development. The brain development is thereby associated with the microRNA/messenger RNA balance and Alzheimer's disease.

That links light-activated amino acid substitutions to ecological, social, neurogenic, and socio-cognitive niche construction that is perturbed in neurodegenerative diseases associated with abnormal cell type differentiation -- and perhaps to quantum consciousness via perturbed learning and memory.

Evolutionary theorists might like to attribute the amino acid substitutions to mutations that somehow enable natural selection and the evolution of biodiversity. But their ideas lack experimental evidence.
JVK
1 / 5 (2) Jun 24, 2014
Re: amino acid substitutions ARE mutations

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... No, it wasn't dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact."
http://www.huffin...211.html

Most of the comments here are from people who refuse to address any aspect of how the theory they believe in was invented and defined. They assume that the initial assumptions of population geneticists were based on experimental evidence and continue to tout pseudscientific nonsense. They are scientifically illiterate idiot minions and/or anonymous fools.
RealScience
5 / 5 (2) Jun 24, 2014
The ISHE group's moderator dictated the terms of my answer about RNA and made it impossible for me to address the anonymous fool's ridiculous question.


So why did you try to blame your getting banned on _9001's question rather than owning that it was your answer that got you banned?
RealScience
5 / 5 (2) Jun 24, 2014
Re: amino acid substitutions ARE mutations

You didn't answer the question:
Or do you claim that amino acid substitutions are not DNA sequence changes?


You have previously said:
But they don't contribute to evolution -- no matter how you define 'mutation.'

You have been provided with multiple links that mutations are defined as DNA sequence changes.
And you have acknowledged that amino acid substitutions contribute to evolution
So either your previous statement is clearly wrong (in which case, let's see if you are honest enough to admit it), or you don't think that amino acid substitutions are DNA sequence changes.

Which is it - do you:

1: admit that your previous statement:
But they don't contribute to evolution -- no matter how you define 'mutation.'
is wrong when mutations are defined as DNA sequence changes,

or

2: think that amino acid substitutions are not DNA sequence changes.
JVK
1 / 5 (2) Jun 24, 2014
I wrote and "RealScience" confirmed that:

"Most of the comments here are from people who refuse to address any aspect of how the theory they believe in was invented and defined. They assume that the initial assumptions of population geneticists were based on experimental evidence and continue to tout pseudscientific nonsense. They are scientifically illiterate idiot minions and/or anonymous fools."

RealScience
5 / 5 (2) Jun 24, 2014
Trying to dodge the question, JVK?

Which is it - do you:

1: admit that your previous statement:
But they don't contribute to evolution -- no matter how you define 'mutation.'
is wrong when mutations are defined as DNA sequence changes,

or

2: think that amino acid substitutions are not DNA sequence changes.

JVK
1 / 5 (2) Jun 24, 2014
Again,

"Most of the comments here are from people who refuse to address any aspect of how the theory they believe in was invented and defined. They assume that the initial assumptions of population geneticists were based on experimental evidence and continue to tout pseudscientific nonsense. They are scientifically illiterate idiot minions and/or anonymous fools."
---
See also: Snf2h-mediated chromatin organization and histone H1 dynamics govern cerebellar morphogenesis and neural maturation http://dx.doi.org...omms5181
It is an open access refutation of what "RealScience" want's you to believe about mutations as amino acid substitutions. Cell type differentiation is correctly portrayed in the context of: ",.. findings [that] highlight the complexity and functional diversity of
Snf2h-containing CRCs during brain development, and their roles in controlling chromatin organization..." http://medicalxpr...tor.html
RealScience
5 / 5 (2) Jun 24, 2014
... people who refuse to address any aspect of how the theory they believe in was invented and defined...


How do you KNOW whether they REFUSE to discuss it, or whether, for example, they consider the origins of a theory less relevant than whether there is modern experimental evidence for that theory? Oh, you just ASSUMED it.

They assume that the initial assumptions of population geneticists were based on experimental evidence


How do you KNOW that that is what others assume when they haven't discussed their assumptions?
Oh, you just ASSUMED it.

So quit dodging the question.
Do you:

1: admit that your previous statement:

But they don't contribute to evolution -- no matter how you define 'mutation.'


is wrong when mutations are defined as DNA sequence changes,

or

2: think that amino acid substitutions are not DNA sequence changes.
JVK
1 / 5 (2) Jul 01, 2014
http://www.huffin...211.html

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... No, it wasn't dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact."

"Assumptions, made but not verified, were taught as fact."
"Assumptions, made but not verified, were taught as fact."
"Assumptions, made but not verified, were taught as fact."
"Assumptions, made but not verified, were taught as fact."
"Assumptions, made but not verified, were taught as fact."
"Assumptions, made but not verified, were taught as fact."
Captain Stumpy
5 / 5 (2) Jul 01, 2014
What's worse is that the anonymous fool [anonymous_9001] got me banned from participation on the human ethology yahoo group by asking me about the role of RNA
@jk
it is FAR more likely that your own stupidity got you banned because you cannot comprehend the lexicon of your chosen field, and because you are pushing a KNOWN pseudoscience as well as ignoring blatant and obvious studies and information that prove evolution while trying to argue against it, all the while your own model SUPPORTS EVOLUTION and anyone with a basic knowledge of BIOLOGY can see this for themselves, and can also see that you are a pseudoscience crackpot pushing a known fallacy
...mutations that somehow enable natural selection and the evolution of biodiversity. But their ideas lack experimental evidence
not only does Lenski support it, BUT YOUR OWN MODEL SUPPORTS IT

you dont answer RealScience because you know you are WRONG and you will look like a fool
again
and you call us idiot minions
RealScience
5 / 5 (2) Jul 02, 2014
"Assumptions, made but not verified, were taught as fact."

Once again, JVK, what you accuse others of is what you are actually guilty of yourself.
You ASSUME that mutations are never selected for, but you have not verified it (you have admitted that you have no experimental evidence to support this assumption), and yet you claim that it is a 'biological fact'.

Biology has recognized that mutations are not the only factor in evolution. You are the one who has fallen into the old way of thinking, that nature uses only one mechanism (your beloved nutrient/ pheromone hypothesis). And once again your own reference contradicts you - it says:
By "replacement" I don't mean to say that the mechanism of random change followed by selection does not exist as a possible mechanism. But it becomes one mechanism amongst many others...

Checkmate again - can't you at least find something new to be wrong about?
JVK
1 / 5 (2) Jul 02, 2014
Anyone who thinks there is anything wrong with my model of how ecological variation leads to ecological adaptations via nutrient-dependent pheromone-controlled reproduction should be able to tell me something about HOW mutations and natural selection lead to the evolution of biodiversity. The fact that no one can say anything except that random change might be a mechanism reveals how pitiful the pseudoscientific nonsense of neo-Darwinism still is -- more than 80 years after it was invented.
RealScience
5 / 5 (2) Jul 02, 2014
Anyone who thinks there is anything wrong with my model of how ecological variation leads to ecological adaptations via nutrient-dependent pheromone-controlled reproduction

No one here has disagreed with ecological variation leading to ecological adaptations via nutrient-dependent pheromone-controlled reproduction.
What is wrong with your model is that you seem to think that this is the ONLY thing involved, and close your mind to everything else in evolution.

The fact that no one can say anything except that random change might be a mechanism

That's from an article that YOU cited without even realizing that the article disagreed with you.
As for "no one can say anything except..." you are ignoring the other score or so of your own citations that I have pointed out ALSO disagree with you, as well as Lenski, malarial resistance, etc. that have been pointed out to you.
You even ADMIT that you ignore evidence that of mutations are selected for.
JVK
1 / 5 (2) Jul 03, 2014
"You even ADMIT that you ignore evidence"

What evidence? Why are you ignoring my request to tell me what is wrong with the evidence in my model but not offering experimental evidence of biologically based cause and effect for comparison? Do you prefer to ignore all evidence of epigenetic effects on cell type differentiation and continue to tout random mutations and natural selection -- while others also ignore the most important information on cause and effect that has ever been presented?

see for another example: Cesarean section may cause epigenetic changes
http://medicalxpr...tic.html
RealScience
5 / 5 (1) Jul 04, 2014
Why are you ignoring my request to tell me what is wrong with the evidence in my model

I have NOT ignored your request. For example, your model claims that mutations are never selected for, I have pointed out REPEATEDLY that you have not yet presented any evidence, experimental or otherwise, that mutations are never selected for. And I have repeatedly pointed out evidence against that part of your model, for example Lenski's results and the distributions of sickle-cell alleles.

You have asked for experimental evidence from everyone else. I'll give you another chance:
Do you have ANY experimental evidence that mutations are never selected for by natural selection? If not, then stop claiming that it is a 'biological fact' and admit that it is just a hypothesis of yours.

-continued-

RealScience
5 / 5 (1) Jul 04, 2014
Do you prefer to ignore all evidence of epigenetic effects on cell type differentiation and continue to tout random mutations and natural selection


I haven't seen anyone here ever claim that cell type differentiation is caused by 'random mutations and natural selection', OR argue against epigenetic effects.

You are the one who appears to thinks that nature only uses one technique, and that thus if nature uses controlled epigenetic changes for some things then it can't use mutations for other things.

And that is in addition to your lack of understanding of the basics of the field; for example, your confusion between epigenetics and genetics, plus your continued lack of understanding that the term 'mutations' as commonly used in the field includes all DNA nucleotide sequence changes (and on top of that you refuse to define what you mean when you use the term 'mutations').

Here's another chance: please define what YOU mean by 'mutation'.