The vital question: Why is life the way it is?

April 1, 2015 by John Hewitt, Phys.org report
The Vital Question: Why Is Life the Way It Is?
The Vital Question. Credit: Nick Lane

The Vital Question: Why is life the way it is? is a new book by Nick Lane that is due out on April 23rd. His question is not one for a static answer but rather one for a series of ever sharper explanations—explanations that apply at different resolutions to specific increments in the continuous chain of life, to the whole, and to generalizations of the process to other instances. For example, we might now boldly assert that an explanation for whether life evolved, or could have evolved, in the same way more than once on our own planet might also describe the same for any other planet. In reading Nick's staggeringly broad and indelible new synthesis, we reach the conclusion that in it's most rough top-level form this explanation must be that any sufficiently advanced chemiosmotic geochemistry is indistinguishable from life.

Chemiosmosis refers to the movement of ions down an electrochemical gradient and across a selectively permeable membrane. This process was there at the begining in what is now widely held to be 's most diffuse state, the alkaline hydrothermal vent. The incidentals of a chemiosmotic lifestyle have continued to exert their influence at every major subsequent induction of new form since, each time further encapsulating both the primal elements of, and various substitutions in the original geochemistry. The explanation for why all life conserves energy in the form of proton gradients across membranes contains within itself the reason why one bacterium was ultimately able to get comfortable living inside another.

As Nick details, the constraints imposed on the evolution of life by chemiosmotic coupling ultimately dictate what he calls the greatest paradox in biology: that all life on earth is divided into prokaryotes, which lack morphological complexity, and eukaryotes, which
share a massive number of perplexing traits never found in bacteria or archaea, including genome-wide sex, two sexes, and ageing. The gulf between the two families, and also among individual prokaryotic domains accordingly had less to do with adaptations for unique or extreme environments and more to do with the divergence of a group whose 'membranes were obliged to remain leaky for bioenergetic reasons.'

The main idea here is that without leaky membranes, the accumulation of protons inside a cell (or on the relavent side of a vent system operating at a specific pH) would quickly lead to a buildup of positive charge that opposes the influx of more H+. In this seemingly trivial description at least, activity across primitive membranes would eventually grind to a halt. In recent times Lane and his group have taken to the computer to provide insight into some of these effects, running all kinds of simulations to vet their hypotheses. We might mention here that these same simplistic intuitions apply to ATP accumulation in mitochondria. If ATP is generated at a higher rate than it is used, respiration grinds to a halt through the action of various inhibitory feedbacks. Low ATP consumption drives higher membrane potentials to higher levels making it even harder to pump protons. The respiratory complexes therefore gradually back up with excess electrons and leak away free radicals.

Any planet with rock, water, and CO2 has a more-or-less completed shopping list for life. Between 25 and 125°C biomass formation from H2 and CO2 is actually exergonic, ie. it should spontaneously be generated according to chemistry and geology provided two important kinetic barriers can be overcome. The trick for life is to clear the first barrier to get to formaldehyde or methanol without running the reaction straight through all the way to methane. If the latter happens, you miss the sweet spot where you score on life's shuffleboard, and all your efforts are dispersed away as methane gas.

Lane prefers to think of CO2 as a lego brick that can be plucked from the air carbon-by-carbon to build up strongly bonded molecules (at least stronger than silicon). Oxygen, by the same token, is an ideal photosynthetic waste product since it can simply diffuse away as a gas. Anoxygenic photosynthesis, on the other hand, may use 'easier' electron donors than water, however, it begets cells that ultimately get encased in their own waste.

A key insight into chemiosmotic coupling of proton pumping to ATP generation is that, as Nick observes, it transcends chemistry. Other than the occasional fermentation, it's really the only game in town. For a cell, simple biochemical accounting tells us that from any single reaction 1 whole ATP must be spent to generate fewer than 2 whole ATPs for growth based on H2 and CO2. If it takes an ATP to make an ATP, normal chemistry gets you nowhere. The beauty of chemiosompsitc coupling is that it allows the cell to save up the fractional ATPs, the loose change, and put it all to good use.

It may not be surprising that bacteria typically respire on average about three times faster (per gram) than single-celled eukaryotes. What might be more surprising is that according to Lane's calculations, the average eukaryote has over 1200 times more energy available to it per gene than does the average prokaryote, and in some cases as much as 200,000 times as much. We might think of an organsim's characteristic 'Lane number"—its energy per gene—to be a kind of scale-free descriptor of its general behavior, perhaps in the way engineers use the so-called 'Reynold's number' to describe abstracted aerodynamic flow conditions.

When you take a look at the largest bacteria, you find that rather than evolving themselves a gigantic nuclear genome what they usually do is simply hoard thousands of copies of their standard-issue tiny bacterial genome. This situation is much different than for eukarytotes which instead use a larger nuclear genome while retaining the services of thousands of copies of minimal respiratory genomes stashed in their mitochondria. One major side effect in the transition to eukaryotes that is important for understanding differences in genome organization was their acquisition of tens of thousands introns. Just to note, by comparison, a typical circular bacterial genome may have just 30 mobile introns spread across some 4000 genes.

We have taken stock of some of the recent research on the origins the in a previous two part post. Namely, part I dealing specifically with endosymbionts and part II dealing with membranes and nuclear structure. Lane's grand synthesis of the issue, which is detailed throughout the second part of his book, is simply stunning in its reach.

It begins with the realization that the only practical way to explain the chimeric mix of bacterial- and archeael- derived structural proteins that now create the modern nucleus (the nuclear pores, lamins, and nucleolus) is to assume that the nucleus evolved after the acquisition of mitochondrial precursors and their subsequent bombardment of the host with new DNA. The nuclear pore complexes appear to have created the double nuclear membrane by flattening and riveting together the internalized lipid bags that would have spontaneously precipitated out of the cytoplasm after excess bacterial-style lipids were synthesized by the still unregulated genes that were transferred along from the newly endocytosed endosymbionts.

These new genes would have been made available for integrating into the host (presumably of archeal origin) along with rogue introns similarly transferred when the endosymbionts expired. In order to splice out these aquired introns (which eventually proved to be a feature rather than a bug) the relatively slow-operating spliceosomal machinery that had evolved from earlier bacterial precursor versions needed to buy some time to work. This was achieved by fencing out the ribosomes that were standing by ready to grab onto any newly transcribed RNA. This fence, conveniently, was the nuclear membrane.

While that description is obviously condensed and storified, the truth can not now be so far off. Many of the larger implications for organisms with mitochondrial symbionts were explored years ago by Lane in his book 'Power, Sex, Suicide, Mitochondria and the Meaning of Life." New insights gained since that time have profound implications for new technologies currently being bandied-about, like for example, mitochondrial transfer in the creation of three-parent embryos. In particular, this work highlights a central challenge in all higher endosymbiotic life: the need to get the right match between the nuclear and mitochondrial encoded protein subunits that make up the respiratory chain.

As mosaics built from two genomes, any changes to protein sequences that increase the distance through which electrons must travel to get to the next membrane reaction center in the respiratory chain will have predictable negative effects on fitness, or even fertilization outcome. Lane notes that beyond separations of about 14 angstroms, quantum tunneling of electrons gets becomes unlikely. For each angstrom increase between redox centers the speed of electron transfer will fall approximately 10-fold.

One of the more intriguing connections made in the book is when Lane revisits the older ideas on sex and gender originally laid out in the work of Ursula Mittwoch in light of what is now known about mitochondria. Whereas we usually imagine the Y chromosome as the main determinant of our gender, the Y might be better described as a transitory reservoir of genetic keys. In other words, a controller of an even more fundamental trigger of gender, namely, temperature and/or energy. Mittwoch describes gender determination across different species where it is independent of chromosomes and relies instead on direct thermal effects, or specific molecules and other environmental cues. In this view, mitochondria function in gender specification becomes more important, and reports of the imminent demise of the 'Y' may might not give us too much pause for concern.

Mittwoch also convincingly portrays several less commonly observed phenomena regarding lateralized growth retardation (or acceleration) during early development according to gender and successfully predicts the related effects seen in hermaphroditism. Today we regularly hear incredible stories that defy traditional understanding of gender genetics. One recent example was a woman walking around with 95% of her cells in possession of an XY male karyotype. With the aid of specific drugs to fast-track the maturation of her proto-uterus into a functional organ she was able to bear healthy child.

Birds have figured into the mitochondria picture in many unique ways by virtue of their genetic arrangement of having homozygous males and heterozygous females. The vibrancy of their colored plumage, among other things, can in some sense be viewed as a direct map of their mitochondrial function, particularly with regard to the pigments that are synthesized within them. Birds also are a prime species to look at the above mentioned problem of mitonuclear coadaptation. In specific instances there are other names applied here, names like mitonuclear mismatch, mitonuclear breakdown, or even hybrid breakdown. The latter, a subject to which we will hopefully return to say more about later, generates specific mitochondrial ills in the first generation which can be predictably cured in the second by backcrossing with an appropriately matched mitochondrial mate.

The influence of on nearly every imaginable function, and dysfunction, of the cell now permeates new research. The primary determinants in many metabolic diseases, cancers, aging, and death are increasingly described in terms of specific energetic and respiratory behaviors of the cell. Nick leaves us with a simpler answer to the riddle of life, a quote from biophysicist Albert Szent-Györgyi "Life is nothing but an electron looking for a place to rest."

Explore further: The energetic origins of life

More information: The Vital Question: Energy, Evolution, and the Origins of Complex Life: www.amazon.com/The-Vital-Quest … -ebook/dp/B00OD8Z4JW

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orti
1 / 5 (4) Apr 01, 2015
"Life is nothing but an electron looking for a place to rest."
And Albert Szent-Györgyi is nothing but a tired electron.
johnhew
4.2 / 5 (5) Apr 01, 2015
then cancer must be an electron looking for a transport chain
jburchel
2.7 / 5 (9) Apr 01, 2015
"Relavent" is a misspelling. Does anybody even spell check these articles before publishing? The red squiggly line is pretty hard to miss for even a casual reviewer... Can I trust the high level content of somebody who doesn't bother to spell check before publishing? See a lot of these, not very professional. Maybe a policy to review before publishing is lacking or something...
johnhew
3 / 5 (6) Apr 01, 2015
Spot on jburchel, that is in fact the the vital question. Will do better using the guidance of the spell checker. As far as trusting high level content your question answers itself, without a high level content checker we are probably doomed. if you have found one please forward along and I will begin using it at once.
JVK
1.3 / 5 (12) Apr 02, 2015
Excerpt: "...any sufficiently advanced chemiosmotic geochemistry is indistinguishable from life."

If the differences between viruses and cellular life are removed, the link from viral microRNAs to the anti-entropic epigenetic effects of nutrient-dependent microRNAs limits explanations of how the nutrient-dependent microRNA/messenger RNA balance leads to the pheromone-controlled biodiversity of species from microbes to humans via RNA-mediated amino acid substitutions that differentiate all cell types in all individuals of all animal species.

See for example: Feedback from Network States Generates Variability in a Probabilistic Olfactory Circuit http://www.cell.c...)00184-1

Excerpt: "The integration of sensory information with network states may represent a general mechanism for generating variability in behavior."

My comment: The variability in behavior exemplified in C. elegans and P. pacificus is clearly due to dietary differences.
JVK
1.4 / 5 (11) Apr 02, 2015
??Shared without attribution to John Hewitt at: http://hackandtor...-is.html

The beauty of chemiosompsitc coupling is that it allows the cell to save up the fractional ATPs, the loose change, and put it all to good use.


See also: http://www.jneuro...abstract The link from atoms to ecosystems seems clearer in the context of the Kainate receptors (KARs). They "...act as ion channels as well as potentially activating G-proteins..."

That link from the light-induced de novo creation of amino acid and amino acid substitutions to receptors, metabolic networks, and genetic networks in different cell types of the CNS, also appears to link the nutrient-dependent pheromone-controlled ecological adaptations of C. elegans to biodiversity manifested in the morphological and behavioral types of the predatory nematode P. pacifica. http://linkinghub...12015000
johnhew
2.6 / 5 (5) Apr 02, 2015
Thanks for the comments JVK and links.
Surprised that hack website couldn't find another review to use. I guess the big time writers that get sent complimentary copies in the mail were not that interested.
If I ever think that someone copying something I write is a bad thing that will be the last thing I write. It's only worth $30.00 the first time so I can't imagine there is much value after that.
Captain Stumpy
4.5 / 5 (8) Apr 02, 2015
Will do better using the guidance of the spell checker
@Johnhew
you can also modify your own spell-check to include commonly used jargon words and add to it scientific words
there are likely databases that you can use that can be uploaded to your computer spell-check library but it is always best to input them yourself after checking and re-checking with a proper lexicon reference for the intended subject you are writing about
as you know, words and terms can be malleable and subject to change but are under far stricter control in professional environments (as in a biological nomenclature)
a high level content checker
it is called the peer review process as well as validation of said study, not always within the lifetime of the original author
when scientists compete, then it is the scientists themselves who are the high level content checkers
why scientists compete to find each other wrong: https://www.youtu...bQIlu4mk
johnhew
2.5 / 5 (8) Apr 03, 2015
Stumpy, knowledge doesn't come from, nor is fungible with, wealth, or for that matter with power, but from dissatisfaction with the known, and a curious fear of the unknown
JVK
1.4 / 5 (10) Apr 03, 2015
...the big time writers that get sent complimentary copies in the mail were not that interested.


I'm glad you follow the data. It will be interesting to note whether anyone else recognizes the paradigm shift.

"Watching a paradigm shift in neuroscience"
http://bjoern.bre...science/

Re:
why scientists compete to find each other wrong


Brembs and I were drawn to the same SFN 2012 poster session. It linked differences in pollen and fructose to neuronal activation in the honeybee model organism of nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation and ecological adaptation.

Earlier in the week I presented this poster at S4SN: Human pheromones and nutrient chemicals: epigenetic effects on ecological, social, and neurogenic niches that affect behavior. http://f1000.com/.../1092668

That came from dissatisfaction with the known, not competition.
Vietvet
4.1 / 5 (13) Apr 03, 2015
Stumpy, knowledge doesn't come from, nor is fungible with, wealth, or for that matter with power, but from dissatisfaction with the known, and a curious fear of the unknown


Says the man who is a fan of Steve Goddard and Sen. Ted Cruz.

https://twitter.com/jhewitt123
johnhew
1.4 / 5 (9) Apr 03, 2015
says the man who say what I say
Vietvet
4.2 / 5 (10) Apr 03, 2015
Time to put the bottle down John.

Vietvet
4.1 / 5 (14) Apr 03, 2015
@johnhew

Your tweets and re-tweets clearly show you are a AGW denier (science denier). You've made homophobic, racists and misogynistic comments on your twitter feed. When you sober up you may cancel your Twitter account or delete the comments I've referred to but I do hope you get help for your drinking problem.
johnhew
1.7 / 5 (12) Apr 03, 2015
yeah, you're good you

at least you could have offered some spell checker tips. or maybe you run your own high level checker on the back end, when you first read posts here?
johnhew
2 / 5 (12) Apr 03, 2015
I think you may be done here sir. Do you know Greg Laden? I think you must because you guys are all the same. I disagreed with him about global warming and in return he attempted to slander me in the same way you are. He contacted physorg and told them I was not scientifically qualified to write for them. You know what that is? A crime. You want to try smear me because you disagree with me too, try to threaten my livelihood too? Do you have a lawyer?
johnhew
2.1 / 5 (11) Apr 03, 2015
You want to publicly accuse me of being a drunk Vietvet without ever having met me, and do that from behind an anonymous mask? You can apologize or take your slander to another forum.
JVK
1.6 / 5 (13) Apr 03, 2015
Vietvet is Steven Taylor. See his comment here:
http://www.gregbe...?id=8064

From: Steven Taylor
Location: United States
Date: 01/28/2015
James V. Kohl claims you incorporated his model of nutrient dependent, pheromone ecological adaptation in your Darwin novels. Any truth to that?
---------------------------
Greg also incorporated Luis Villarreal's works on virus-driven evolution, which I have since integrated into my model of how the balance of viral microRNAs and nutrient-dependent micro
RNAs drives cell type differentiation.

If not for the participation of anonymous fools, like Steven Taylor aka Vietvet and Captain Stumpy, discussions might contribute to scientific progress -- as would be expected from people who follow the data and/or report on it. Instead, we have biologically uniformed science idiots cluttering up the space and driving intelligent participants away.
Vietvet
4 / 5 (12) Apr 03, 2015
I've never heard of Greg Laden but I've read your tweets. I don't think you should be fired but readers here should be aware you hold views that many here would find "controversial" to be kind.

Stumpy, knowledge doesn't come from, nor is fungible with, wealth, or for that matter with power, but from dissatisfaction with the known, and a curious fear of the unknown
?

says the man who say what I say


yeah, you're good you

at least you could have offered some spell checker tips. or maybe you run your own high level checker on the back end, when you first read posts here?


Rather incoherent and maybe not caused a little to much of the good stuff but it does bring back embarrassing memories of decades ago when I was guilty of drunk dialing.

Have a good evening.
Vietvet
4.2 / 5 (10) Apr 04, 2015
From: Greg Bear
Date: 01/29/2015

"There's more than a hint of pheromone-HERV and cortico-steroid interaction in DARWIN'S RADIO. And James is certainly a pioneer in the pheromone world! We've corresponded for years on these subjects. I'm not sure about the nutrient angle, however. Interesting to follow that track as well!"

@JVK
You left out the part that Bear was unaware "about the nutrient angle", meaning he was unaware of your model even if he incorporated pheromones in his novel. You're taking credit were none is due.
Captain Stumpy
4.2 / 5 (11) Apr 04, 2015
Stumpy, knowledge doesn't come from, nor is fungible with, wealth, or for that matter with power, but from dissatisfaction with the known, and a curious fear of the unknown
@Johnhew
first off, where do you suppose that i am making this claim?

I mentioned that you can add data to your library re: spell check and that the peer review process is one of the features that keeps data at a high level and the content real
I also say that science and the scientific method is most effective because scientists compete to keep each other honest as well as validate claims, etc.
FUNGIBLE: being of such a nature that one part or quantity may be replaced by another equal part or quantity in the satisfaction of an obligation
please demonstrate or quote my reference (or even allusion) where i make the claims which you are somehow attributing to me

you will not find it anywhere
to be cont'd
Captain Stumpy
4.3 / 5 (11) Apr 04, 2015
@John cont'd
lets talk about your above arguments and threats
I think you may be done here sir
considering that Vietvet is posting his opinion and assessment of the situation, then it is a perspective, and he is entitled to it. THere does seem to be some substantiating evidence that you are not fully cognizant.
this is evident in your reply to me, which is based upon what? there is NOTHING in my post that is anything other than a helpful hint for downloading (or purchasing) professional lexicons to expand your spell-check (something easily done in most word processors) as well as identifying the "high level content checker" of science

that is SCIENCE (as in the scientific method), not writing or science writing

2 B continued
Captain Stumpy
4.6 / 5 (10) Apr 04, 2015
@Johnhew cont'd
There does seem to be a lot of "misinterpretations" in science writing, or in certain peoples ability to comprehend the scientific data presented in a study

This is painfully evident in the original author feedback with regard to kohl's interpretations of biology and studies involving biology

I am NOT including his interpretations of physics or other studies because he has made far more outlandish claims WRT physics and QM than even his own "specialty" in biology

And i am not even going to bring up his own problems with justifying his pheromones claims WRT empirical evidence and the failure of the scientific community to validate his claims there
He contacted physorg and told them I was not scientifically qualified to write for them. You know what that is? A crime
it is NOT a crime if he has justification for said complaint
2 b continued
Captain Stumpy
4.6 / 5 (11) Apr 04, 2015
@Johnhew
it is NOT a crime if there is justification, and not knowing the argument, i can't speak
HOWEVER, if you are anti-AGW considering the overwhelming amount of scientific evidence and the consensus of the scientists and science, then it DOES question your ability to comprehend the studies or the science within them

And then there is your blatant support of kohl and his CREATIONIST dogma, which has been not only debunked in science and with science, it is also proven to NOT BE SCIENCE or SCIENTIFIC
https://en.wikipe...Arkansas

If you are going to start making threats to delete someone, you should consider your own self just for professing to be a science writer but supporting non scientific topics and religious dogma from kohl alone (that is called pseudoscience, NOT science)

so before you start trying to kill off the opposition, re-check your own commentary and posts
Captain Stumpy
4.6 / 5 (10) Apr 04, 2015
Do you have a lawyer?
@john
before you enlist your lawyers, you had better warn them of your public support of known pseudoscience like far too many of kohl's posts, because ANY decent defense lawyer will eat you alive and your lashing out with the legal system will definitely backfire

Science is not a toy, nor is it something that you can use to prove whatever you wish: it is about following the evidence
When jk uses science to try to justify his own religion and you accept this and do nothing to mitigate the stupidity being spread
-especially when the blatant lies or the misinterpretations of information are so horrendously wrong & anyone who disagrees is then also slandered, but you allow it and support it without interference-
Then you are undermining any future argument that you are somehow an infallible science writer

it also leads others to believe that either you are "currently unable to function" OR a pseudoscience promoter

Captain Stumpy
4.5 / 5 (10) Apr 04, 2015
That came from dissatisfaction with the known, not competition.
@jk
no, your "dissatisfaction comes from your attempts to prove your RELIGION

Before you can be dissatisfied with the known, you must first KNOW
and you already self admitted to failing out of college, you ALSO have demonstrated the complete failure to interpret or comprehend most studies in biology
You are also trying to promote anti-evolution pseudoscience while at the same time pushing a mutation driven method of evolution in your own model

you continually attempt to post supporting studies except almost all that are NOT to your personal site are misinterpreted, and that is demonstrated by author feedback when they have returned our requests for clarification

you also are not capable of accepting new evidence, from Dr. Extavour to Lenski
You've tried to lie about one (Dr. Extavour) and dismiss the other without cause

that is pseudoscience
NOT SCIENCE
Captain Stumpy
4.6 / 5 (9) Apr 04, 2015
Instead, we have biologically uniformed science idiots cluttering up the space and driving intelligent participants away.
@jk
TRUE
the question is: when are you either LEAVING or getting an education so that you can comprehend what is being discussed?

your support of and posting creationist dogma is NOT SCIENCE
it is religion
There is NO science in the creationist movement, & even the COURT will attest to that
https://en.wikipe...Arkansas

you have repeatedly misinterpreted other studies and then tried to lie about said authors (John says that is SLANDER as well as grounds for litigation)

you've posted that Dr. Extavour supported your stupidity re: anti-mutations etc
until she specifically stated that you were wrong, then she was the brunt of your vilification

Your interpretation rate is 100% WRONG thus far when feedback occurs
IOW- you push pseudoscience

irony?
or stupidity?
it's not ignorance if you've been taught otherwise
jsdarkdestruction
4.6 / 5 (9) Apr 04, 2015
Sorry for the four rating captain stumpy. It was supposed to be a 5.
bluehigh
2.5 / 5 (11) Apr 04, 2015
.. is posting his opinion and assessment of the situation, then it is a perspective, and he is entitled to it.
- Captain Stumpy

With respect CS, you and your little gang often operate in violation of your statement. In fact not just often but you consistently attack others perspectives, demanding empirical evidence to support posters opinions. Furthermore you become abusive and denigrate those that do not agree with you. Rather than using a spell checker, perhaps CS, invest in a dictionary and search for 'hypocrisy'.

Captain Stumpy
4.6 / 5 (9) Apr 04, 2015
With respect CS, you and your little gang often operate in violation of your statement
@bluehigh
not if it is stated as their opinion
i don't downvote people when they point out that something is IMHO, therefore opinion or a belief
i will argue the point, but i don't care what someone believes

it is when people promote and support a known fallacious set of comments that re directly against the proven, supported, validated science that i argue against most often
Such as: the eu, anti-evolution claims like the BS that jk posts, etc

And i WILL ask for evidence when someone starts to present an OPINION but promote it as fact or science
like verkle, ren and jvk when they start pushing creationist diatribe as science
it is NOT SCIENCE
2-b continued
Captain Stumpy
4.6 / 5 (10) Apr 04, 2015
invest in a dictionary
@blue
this is a SCIENCE site, not a religions site, nor a political activist site, nor a conspiracy theory site... there are NO aliens in area 51, there is NO worldwide conspiracy regarding AGW and global warming

your attempts to suggest that supporting SCIENCE on a SCIENCE SITE is somehow hypocrisy just supports my previous contentions that you are here to TROLL and not discuss actual science

there is a difference between science that is supported by studies and pseudoscience

pseudoscience makes claims or conjecture,iot does NOT utilize the scientific method

case in point: jvk claims mutations are always bad
but then promotes a model that causes mutations because he doesn't comprehend the basic definition of the word
he also ignores the empirical evidence of beneficial mutations (Lenski, Dr. Extavour, etc)

Like a lot of your own claims-
CONJECTURE is NOT SCIENCE

perhaps you are the one who needs the dictionary?
bluehigh
2.3 / 5 (6) Apr 04, 2015
@CS - thank you for your reply. I will take your feedback on board and clarify when I'm expressing a point of view or an opinion.

I did not suggest that supporting science is in someway hypocritical. I simply mentioned, that IMHO, your statement was at odds with your behaviour. I did not in my comment refer to supporting any particular poster nor did I refer to Aliens, Climate change or mutations.

If you choose to label other posters as 'trolls' then you may want to review the lack of content and negative tendency, inciting conflict, of your posts. Another use of the dictionary?

Captain Stumpy
4.4 / 5 (9) Apr 04, 2015
IMHO, your statement was at odds with your behaviour
@blue
and i am telling you that i support actual science, not pseudoscience
This seems like a contradiction to those who cannot relate to science because of a set of internal or other behavior or beliefs, such as religion

those people chose the answer and are seeking only confirmation, which excludes their ability to recognize science
http://www.ploson...tion=PDF

When you make supposition or claims without evidence, it is not science
Trolls and those who argue pseudoscience predominantly make unsupported conjecture and consider it equivalent to the scientific method
this is fallacious and it is also a large problem with the scientifically illiterate of society
Thus there is a huge problem with people not only being scientifically illiterate,but lacking in critical thinking and analytical skills

cont'd
Captain Stumpy
4.4 / 5 (9) Apr 04, 2015
you may want to review the lack of content and negative tendency, inciting conflict, of your posts
@blue
and when you step into an ongoing argument that is over a year long while ignoring the historical posts then you are not getting the whole picture, are you

WRT jk and i, this argument is well over a year old and he has YET to justify his pseudoscience
WRT your comment quoted: if i provided back story for every troll posting, then it would flood the site with far too many posts that are likely OT and irrelevant

you can continue to argue the point, but you are simply arguing because you have been labeled as a troll in the past and you've been known to post pseudoscience as well

This is purely defensive reaction on your part and (again) attempts to justify your opinion over that of proven modern science (at least to yourself)
see the link above for more on that

the CONFLICT only comes when people ASSume pseudoscience/unsubstantiated conjecture is reality
Captain Stumpy
4.4 / 5 (9) Apr 04, 2015
@blue
I did not in my comment refer to supporting any particular poster nor did I refer to Aliens, Climate change or mutations
did i say that you specifically did?
negative tendency, inciting conflict, of your posts
let me point out something specific here: the BULK of those getting angry or feeling that i am inciting conflict are themselves trolls and/or those who post unsubstantiated conjecture and ASSume that this is somehow equivalent to posting scientific evidence or studies which are supported with empirical evidence

i always try to be respectful at first, even to blatantly wrong or other claims

but when a troll/pseudoscience poster shows their true colors and demonstrates their fear of knowledge/science
then there is no reason to assume the other wants scientific discourse, nor are they looking for knowledge
therefore they are the aggressors in the fight against science
viko_mx
1 / 5 (9) Apr 04, 2015
If the author had read the Bible, it would know what is life and what is its purpose, and would not waste his time in silly philosophizing, demonstrating senceless darvinian cynicism. For such people feelings prevent to be adequate to reality and to accept the truth that there is nothing accidental in this world and life exist thanks to God's love and mercy. Because they want to take the place of God. Too difficult for their frail shoulders. But this is the reason they do not like the throught and prefer the comfortable delusion.
johnhew
1.9 / 5 (13) Apr 04, 2015
yes Stumpy creating and spreading lies to destroy someone is slander, and you are guilty. making up falsehoods about my background, my college, saying I am a religious creationist, all lies. I thank JVK when he reads my posts and gives thoughtful comment and because you can't, you hate me for it. even if I didn't have a degree from Drexel in physics class of 1991, that would hardly matter for writing science here, or for several other places I successfully write for.
If you and your bullies find that you can't comment here any longer, thanks yourselves. I did not ask for anyone to be banned, and have done all I can keep the forum open, but I do know that the editors are now aware of your and others continued violations and slanders
JVK
1.4 / 5 (11) Apr 04, 2015
You left out the part that Bear was unaware "about the nutrient angle", meaning he was unaware of your model even if he incorporated pheromones in his novel. You're taking credit were none is due.


Bear credited me in his 2004 acknowledgements. He was unaware of the link from viral microRNAs and nutrient-dependent microRNAs to RNA-mediated cell type differentiation. The model he incorporated was detailed in our 1996 Hormones and Behavior review and other reviews published before his 2004 sequel. Our assumption was that most people would realize cell type differentiation is nutrient-dependent.

See the review of Darwin's Radio (1999) http://www.gregbe...ture.cfm

Why would a sci-fi novel author be expected to keep up with the latest research that links nutritional epigenetics and pharmacogenomics via RNA-mediated metabolic networks and genetic networks.

Only biologically uniformed science idiots fail to realize there must be a "nutrient angle."
Uncle Ira
4.2 / 5 (10) Apr 04, 2015
He contacted physorg and told them I was not scientifically qualified to write for them.


He sounds like a real smart Skippy.

You know what that is?


I will take a really wild guess me. I guess that is really good advice.

A crime.


Since when is calling a couyon a "couyon" a crime?

You want to try smear me because you disagree with me too, try to threaten my livelihood too?


If your livelihood is writing foolishment I doubt anybody could threaten it more than you do.

Do you have a lawyer?


Hooyeei, I bet that Vietvet-Skippy is running scared now. Choot em, choot em quick before he disappears into the tall grass.
Uncle Ira
4.2 / 5 (10) Apr 04, 2015
@ Vietvet-Skippy.

I think you may be done here sir.


Don't worry so much about that. He gave me the boot too about three or two months ago. The nice peoples at Physorg just keeps him around to write silly stuffs so more people will stop in and laugh and have a good time.
Uncle Ira
4.2 / 5 (10) Apr 04, 2015
@ Captain-Skippy.

@John cont'd
lets talk about your above arguments and threats
I think you may be done here sir


And I was thinking he wasted that one on me three or two months ago.

johnhew
1.7 / 5 (11) Apr 04, 2015
luv that speech-to-text converter you gots, they didn't have them when I lived in cajunland
Uncle Ira
4.3 / 5 (12) Apr 04, 2015
luv that speech-to-text converter you gots


It's called fingers. You can find your very own one just about anywhere.
Captain Stumpy
4.6 / 5 (10) Apr 04, 2015
making up falsehoods about my background, my college, saying I am a religious creationist, all lies
@john
show me where i made up a falsehood about your background, college or said you are a creationist
i HAVE said you supported creationist dogma, and that is truth which can be shown in another thread http://phys.org/n...ton.html
you also made the claim in that thread
it is often worthwhile to watch shows about aliens building pyramids to get information about how humans actually built them
did you perhaps MISS the engineering shows that explain and demonstrate this?
i prefer SCIENCE to fiction
because you can't, you hate me for it
1- jk gives RELIGIOUS feedback, which is not thoughtful
2- i can give better feedback, but i will NOT argue religion with anyone
to be continued
Captain Stumpy
4.6 / 5 (11) Apr 04, 2015
If you and your bullies
@johnhew
let me make something perfectly clear
i don't BULLY anyone... i WILL, however, passionately defend SCIENCE...something that i thought would be a good thing, especially for someone who makes a living writing science and publishing it

Secondly: i am sure the editors are aware that there is an OVERWHELMING amount of trolling, spamming and PSEUDOSCIENCE being posted in the comments sections too
I have regularly argued that the site needs moderation as the trolls/pseudoscience posters (especially the more confusing ones like jvk) be taken off the site and perma-banned

jvk and those who support his diatribes are no better than the anti-vaxxers, the alien/area 51 conspiracy nutters or those like them

When you allow them to overrun the site with their PSEUDOSCIENCE, then there is no real reason for science discourse
Already too many actual scientists left here for moderated sites due to the stupidity of trolling/pseudoscience
Captain Stumpy
4.6 / 5 (11) Apr 04, 2015
creating and spreading lies to destroy someone is slander
@johnhew
one last point: show me where i have lied at all
you will NOT find any lies
any mistakes i HAVE posted i apologized for, even to those trolls/idiots/pseudoscience posters that i dislike and who regularly spam the site, including rc

All you have to do is check my history
and you are guilty. making up falsehoods about my background, my college, saying I am a religious creationist, all lies
So when you blatantly lie here, that means i have legal recourse, right?
i have talked about jvk's education and background, but only things he SELF ADMITTED, never yours

before you sick the site or lawyers on anyone, you had better get your facts right

i have no problems fighting back, and plenty of experience in court as a professional witness
i don't mind standing up to anyone making threats... especially unfounded threats to me

better re-read my posts above for clarity
johnhew
1.9 / 5 (11) Apr 04, 2015
my science speaks for itself, if you have another writer that you follow closer than me, and the several hundred original scientific articles I put out in the last year or so that I have been at this, on various sites to decode life and the operation of the brain then I suggest you troll them. however it seems like you prefer my insights, even if they don't always conform to your warmist views. unfortunately when you take snippet out of context, and threaten me, and make slanderous accusations about personal habits (which as you admit above are actually projections of your own past deficiencies), then you show yourself to be exactly the kind of pseudoscience monger that you so fervently claim to decry.
gkam
3.8 / 5 (10) Apr 04, 2015
OOOps, I gave vietvet a one when I meant a five, since there are no tens.
gkam
3.7 / 5 (9) Apr 04, 2015
"It's called fingers. You can find your very own one just about anywhere."
------------------------------------------

That's true.

My girlfriend found mine.
johnhew
2 / 5 (12) Apr 04, 2015
or perhaps yes, the particular comment above was from vietvet or one the other trolls in your team making the accusations about drinking problems etc.
Either way the pattern is same. hurl labels, insults, out of context lies, and try to purge anyone saying something true that threatens your agenda.
Captain Stumpy
4.5 / 5 (10) Apr 04, 2015
however it seems like you prefer my insights
@john
SHOW me ONE example
just one! prove your point right here, because i can show and prove where you have defended kohls creationist posts, and i did above
i don't follow you at all, i read PO and comment... especially when jk decides to present his skewed non-reality based interpretations of studies or science, anti-agw or blatantly debunked physics of things like the eu clan
and now i can add that you don't comprehend the physics or science behind AGW and global warming to that list with your comment here
even if they don't always conform to your warmist views
i follow the science and the evidence
i don't take a perspective and then try to validate it with political, religious or other site references

posting about your refusal to acknowledge climate science only undermines your credibility WRT science and your comprehension of the subject
Captain Stumpy
4.3 / 5 (11) Apr 04, 2015
when you take snippet out of context, and threaten me, and make slanderous accusations about personal habits
@john
by all means, QUOTE where i have done this above
i offered advice WRT Vietvet as well as your anger in that issue, and i offered opinion WRT to the subject... even said i was not aware of the whole argument (had you actually read what i posted)
Where have i said anything that i cannot prove, or validate the claim with your actual posts?
your own past deficiencies
i've not mentioned anything here to you at all, so you will have to be more specific
you show yourself to be exactly the kind of pseudoscience monger that you so fervently claim to decry
show me ONE POST where i have posted, supported or claimed ANY pseudoscience to be real or legit

just one
the particular comment above was from
oh, NOW you read for comprehension?
after your assault?
nice

Captain Stumpy
4.6 / 5 (10) Apr 04, 2015
Either way the pattern is same. hurl labels, insults, out of context lies, and try to purge anyone saying something true that threatens your agenda
@johnhew
the ONLY problems i have had with ANYONE on this site are with the trolls and the people who have a difficult time defining reality for whatever reason, and i will include THIS in the latter group.
Prove where i have lied
prove where i take out of context lies, purge anyone saying something TRUE...

i don't
and by TRUE, you better mean scientifically valid or supported by scientific evidence, not some idiot political blog, philosophy, unsubstantiated personal conjecture or anything else (IOW- the anti-AGW or anti-global warming crowd and their non-scientific approach to the issue)

I am a fervent supporter of SCIENCE and the scientific method because i am passionate about it and have a love for it

all you gotta do is prove yourself
i can prove MY comments to date
johnhew
2.1 / 5 (11) Apr 04, 2015
again, I don't know what JVKs religious beliefs are and I don't care. I do know that by recognizing him for an interesting link and commenting with some appreciation on my work, I have led a team of hateful trolls with nothing better to do then glorify him, around on a nose ring ever since. some advice, ignore him if you don't like his pheromones. news flash, I don't think humans are much controlled by them either, but he doesn't need pheromones to control you guys, and that is embarrassing.
Captain Stumpy
4.6 / 5 (10) Apr 04, 2015
some advice, ignore him if you don't like his pheromones
@John
are you not reading what i wrote?
1- it is not about belief at all, it is about provable science
2- MOST of what i am doing here is collecting data for a study involving people exactly like jk and his pseudoscience friends, so it requires that i interact from time to time, not only to get him to discuss what he thinks he sees in the studies and his own work, but also how he attempts to interpret the studies to others who are far more well versed in science than he is (Like Anon, Real, and others)

So again, i defend science, and i will point out pseudoscience whenever i can
ESPECIALLY since PO refuses to actually do any real moderation of pseudoscience

scientifically illiterate people that cling to those posts to validates their delusions
http://www.ploson...tion=PDF
Captain Stumpy
4.6 / 5 (10) Apr 04, 2015
he doesn't need pheromones to control you guys, and that is embarrassing
@john
see the post above
perhaps you might gain some "insight" as to why there are a group of people here trying to combat the PSEUDOSCIENCE being posted on the site

i will simplify it:
the site has very little moderation, which allows the trolls, pseudoscience and others free reign
the site has lost incredibly talented physicists, engineers and more because of this, and as such a lot of the credibility of the commenters has dropped because anyone promoting science is flooded with pseudoscience and derision

now that there are a group of people promoting actual science, the trolls are up in arms because they are being proven wrong

that is not "controlling" us

it is all about the science and the evidence
and jk has very little actual science on his side

until there is site moderation which will promote actual science and delete the pseudoscience, it is up to a select few to push SCIENCE
TheGhostofOtto1923
2.8 / 5 (5) Apr 04, 2015
"Relavent" is a misspelling. Does anybody even spell check these articles before publishing? The red squiggly line is pretty hard to miss for even a casual reviewer... Can I trust the high level content of somebody who doesn't bother to spell check before publishing? See a lot of these, not very professional. Maybe a policy to review before publishing is lacking or something...
uh burchel your zippers down-
JVK
1.7 / 5 (11) Apr 04, 2015
Ren82 echoes the sentiments of Rupert Sheldrake in this interview: http://www.thebes...terview/

John Hewitt echoes my sentiments:
I don't think humans are much controlled by them either


My published works have been placed into the context of "Role of olfaction in Octopus vulgaris reproduction" http://www.scienc...14004006

This links them to what John Hewitt understands about Luca Turin's works. For example: "Electron spin changes during general anesthesia in Drosophila" http://www.ncbi.n...4151765/

Criticizing John Hewitt, or me, without learning what is currently known about physics, chemistry, and the conserved molecular mechanisms of cell type differentiation is typical of what biologically uninformed science idiots must do.

They simply aren't intelligent enough to do anything else but complain that others who cite evidence or report it are wrong.
TheGhostofOtto1923
4 / 5 (12) Apr 04, 2015
Dark personalities make permanently compromise with the truth, but never with their interests. Unfortunately many of the "scientists" nowadays belong to the category of dark personalities
Ahaahaaaa its funny that ren uses john 18-21 to categorize scientists. Using bible wisdom to parse between science you agree with and that which you do not, and then equating that disagreeable science with sin, is quite a stretch dont you think?

Especially when you use the bible to define 'truth'. The truth, as we know, is that the bible stories never happened. And I suppose the scientists who proved this to you can also be relegated to the 'dark' category, which is one of the reasons you love the book so much... they may not suffer in this life, but they will sure as hell suffer in the next.
TheGhostofOtto1923
4 / 5 (12) Apr 04, 2015
Darwinism stands behind instant interest and denies the moral standards given to us by God in the Bible, which define what is good and what is bad for people
So if darwinism is evil why did your god go to so much TROUBLE to leave SO MUCH evidence to make it look as if it were real?? The more we learn, the more real it looks. Conversely, the less believable are creation and the rickety theories of its proponents.

But we know god doesnt know history because he wrote a book full of stories about people we know never existed and events which we know never happened. The evidence he left (or ignored) is conclusive and incontrovertible.

And as we also know, science is a lot harder than history.
TheGhostofOtto1923
4 / 5 (12) Apr 04, 2015
In this case these are my personal observations
-And your personal observations cannot be separated from scripture. Where is the line? You read about science you do not agree with and your only way of judging it is to gloss it over with bible verse.

Your god says in his book that the earth is flat and the sun and all the planets revolve around it. Yes it does, in so many words, and people were murdered for hundreds of years for questioning it.

And it says that rabbits chew the cud, and something wrong about camel hooves, I forget what. Its in the little details like these where your god screws up.

It also says that its ok to stone apostates, insolent children, and wayward women, and that slavery is a foregone conclusion. It also says that bigotry is mandated by god, that those who dont ascribe to the first 3 commandments are incapable of following the rest.

And so I would be very careful about using the term 'morality' in the context of the bible if I were you.
JVK
1.4 / 5 (10) Apr 04, 2015
From 2012: http://www.abc.ne...7620.htm
"The concordance of the findings of a scientific study and an ancient myth is a striking example of how traditional ecological knowledge can inform and enhance scientific research."

From 2013: Ecological variation is the raw material by which natural selection can drive evolutionary divergence [1–4].

The differences in amino acid composition among different tissues can lead to large differences in trophic discrimination [38]. http://rspb.royal...81.short

From 2014: "...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/

Does anyone remember when theorists stopped touting the pseudoscientific nonsense about mutations and evolution?
JVK
1.4 / 5 (10) Apr 04, 2015
The truth, as we know, is that the bible stories never happened.


The truth is that the textbook stories are misrepresentations of biologically-based facts.

http://www.abc.ne...7620.htm
"We've just demolished a textbook story," says team member, Professor David Bowman an environmental change biologist at the University of Tasmania.

"Even in the conservative case that we used the slower mutation rate, the divergence is estimated to have occurred about 32 852 years ago (90% HPDI: 13 632–63 529; table 2), which decisively rules out both the relic hypothesis (15 Ma; [13]), and the Pliocene river connections hypothesis (5–2 Ma; [16])." http://rspb.royal...738/2652

http://www.the-sc...st108489

http://www.scienc...2306.htm This latest study is one of only a few well-documented examples...
Captain Stumpy
4.4 / 5 (9) Apr 04, 2015
denies the moral standards given to us by God in the Bible
@ren
1- there is NOT truth in the bible that can be verified or validated as legitimate using the scientific method: MORALS are a cultural phenomenon and are as diverse as religion
2- you are YOURSELF saying that your own sky faerie is a blatant liar when you quote your bible and say what you do... after all, your own bible quotes the 2nd covenant very differently than you do: JER 31:31 - 34
you are now in the realm of promoter of blatant lies of your own book, which makes you a teacher of sin James 3:14
you yourself say that your deity is a part of the universe, but then deny his reality, therefore you are simply a liar looking for attention with a fallacies comic and your personal interpretations of it's contents...
did you sell your daughters and put to death all who are not godly around you as well?
JVK
1.4 / 5 (9) Apr 04, 2015
...he doesn't need pheromones to control you guys, and that is embarrassing.


Most of the biologically uninformed science idiots aren't intelligent enough to be more than puppets on a string. I've enjoyed being the puppeteer, despite having to repeatedly pull the same strings.

We can always count on people like Steven Taylor (aka Vietvet) and Captain Stumpy for comic relief. But when they finally realize the level of foolishness they've exemplified, there will always be more science idiots to take their place.

Let's give a warm welcome to the science idiot: "TheGhostofOtto1923" as we wait for Torbjorn_Larsson_OM and others to arrive.
Captain Stumpy
4.3 / 5 (11) Apr 04, 2015
Criticizing John Hewitt, or me, without learning what is currently known about physics, chemistry, and the conserved molecular mechanisms of cell type differentiation is typical of what biologically uninformed science idiots must do.
Except that modern PHYSICS, as well as CHEMISTRY and BIOLOGY (not to mention CONSERVED molecular mechanisms) state that you are not only wrong, but you are quoting from a scripture of creationist dogma, not SCIENCE

for instance: http://www.socioa...ew/24367

http://rspb.royal...full.pdf

so why should we accept you as some sort of authority in the subject matter when you cannot even get the basic science correct?

this means that you are wanting people to believe that you've somehow usurped Evolution when THE EVIDENCE says otherwise

appeal to self authority and Dunning-Kruger on your part
Captain Stumpy
4.3 / 5 (11) Apr 04, 2015
The truth is that the textbook stories are misrepresentations of biologically-based facts.
and @jk., you have NO empirical evidence supporting this argument other than your word

Most of the biologically uninformed science idiots aren't intelligent enough to be more than puppets on a string. I've enjoyed being the puppeteer, despite having to repeatedly pull the same strings.

We can always count on people like Steven Taylor (aka Vietvet) and Captain Stumpy for comic relief
i've made more money betting on what you will say and how you will respond ... the funny thing is that you, in your egotistical delusional world, actually think you are the Mensa master puppeteer...
you should re-read the entire last year and a half of posts if you want to learn more

but then again, that would cause you to challenge your version of reality
and your pseudoscience and religion could not survive that

keep on posting jk
JVK
1.4 / 5 (9) Apr 04, 2015
My other puppets should see this:

Understanding and accounting for relational context is critical for social neuroscience
http://journal.fr...127/full See the comments:

James Kohl: "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."

George FR Ellis: "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"

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

Life as physics and chemistry: A system view of biology http://www.scienc...12000922
JVK
1.4 / 5 (9) Apr 04, 2015
See also:

A Spectroscopic Mechanism for Primary Olfactory Reception http://chemse.oxf...abstract

Molecular Vibration-Sensing Component in Human Olfaction http://dx.doi.org....0055780

Electron spin changes during general anesthesia in Drosophila http://www.ncbi.n...4151765/

Dose-Dependent Effects of the Clinical Anesthetic Isoflurane on Octopus vulgaris: A Contribution to Cephalopod Welfare http://www.tandfo...uMckXI6I

John Hewitt may be the only journalist/scientist I know who can link the four works cited above from my published works to "Role of olfaction in Octopus vulgaris reproduction" http://www.scienc...14004006
Excerpt: "...olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000)."
JVK
1.4 / 5 (9) Apr 04, 2015
in your egotistical delusional world, actually think you are the Mensa master puppeteer...


Puppets never recognize who is pulling their strings.

More than 1000 others can also do it. No need to be a Mensa member. Join the RNA Society instead. http://www.rnasociety.org/

We're a non-profit, international scientific society with more than 1000 members dedicated to fostering research and education in the field of RNA science.


Or, see http://rna-mediated.com/
Here you will find information that links physics, chemistry, and molecular epigenetics via RNA-mediated events such as the de novo creation of olfactory receptor genes in order to encourage a public discussion of a paradigm shift.


Captain Stumpy
4.6 / 5 (9) Apr 04, 2015
Puppets never recognize who is pulling their strings.
@jk
true
you still haven't figured it out yet

http://rspb.royal...full.pdf

http://www.socioa...ew/24367

http://freethough...s-place/

http://sci-ence.o...-flags2/
(you've given me more than 20 bingo's in the past 6 months, btw)
Join the RNA Society instead
I prefer the AAAS ( http://www.aaas.org/ )
American Association for the Advancement of Science
http://www.sciencemag.org/

it talks about REAL science
not pseudoscience
JVK
1.4 / 5 (10) Apr 04, 2015
I prefer the AAAS

Sciencs is publishing works that are catching up to what we reported in 1996 about RNA-mediated cell type differentiation. For example, see:
http://www.scienc...abstract MicroRNA control of protein expression noise "Combinatorial miRNA regulation may thus be a potent mechanism to reinforce cellular identity by reducing gene expression fluctuations that are undesirable for the cell."

What you have learned from people like PZ Myers for comparison to this?

"This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements."
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281
Captain Stumpy
4.6 / 5 (10) Apr 05, 2015
What you have learned from people like PZ Myers for comparison to this?
@jk
tell you what, jk, lets do a nice tidy experiment to see just how much your interpretations of those studies reflects that actual conclusions or findings of the studies and their content, ok?

YOU post in as much detail as you can the full explanation of what you think the study says as well as how this applies SPECIFICALLY to your pheromones and your work... be as specific as possible and make sure you put all your "catch phrase kohl slaw" word salad in there so that you can get your point across about the findings and your interpretations
I will give you 48 hours and then post ALL your content verbatim and inquire to the authors as well as biologists in the education system as to the accuracy of your claims

care to try it? or will you back out and run away like you did the last 4 times i've requested you do it?

fear of being outed again by yet ANOTHER author?
Captain Stumpy
4.6 / 5 (10) Apr 05, 2015
example, see:
http://www.scienc...abstract MicroRNA
Oh, jk... don't forget to also add in your study and how it all relates to the linked AAAS study

Make sure that you tie it all in there together as well, so that the author can make a comment and you are not making more unsubstantiated claims about your own verbatim comments, like you did with Dr. Extavour and so many of the others...

make sure it all ties together and that all your claims are represented... no cheating and making assumptions after the fact, or saying the author didn't understand something because it is all in YOUR hands to demonstrate YOUR knowledge as well as provide the same level of expertise to the authors for perusal of your comments

failure to clearly state something is only more evidence of most of my previous claims anyway... and it will not go away any time soon with you

but i am giving YOU the chance here...
take it or leave it
viko_mx
1 / 5 (8) Apr 05, 2015
The theory of evolution holds that it is a slow process which need milion or bilion of years, but do not undertake to explain the reason why mankind for the last several millennia suddenly start to develop in unprecedent high temps than before this period in technological pace. This theory does not rely on scientific facts so its supporters never give meaningful scientific explanation supported by irrefutable evidence. It relies on the ignorance of the some people and the emotional needs of others who have no desire to take responsibility for their actions, by offering them a convenient excuse. I do not know whether luci is behind this theory, but would certainly appreciate this deception which lulls the conscience of the wicked.
JVK
1.4 / 5 (9) Apr 05, 2015
Oh, jk... don't forget to also add in your study and how it all relates to the linked AAAS study


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

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

One of the works that followed is: MicroRNA control of protein expression noise http://www.scienc...abstract
JVK
1.4 / 5 (9) Apr 05, 2015
See also: Search Results for 'microRNA' http://rna-mediat...microRNA

http://rna-mediat...-memory/

http://rna-mediat...actions/

http://rna-mediat...-agents/

http://rna-mediat...ulation/]http://rna-mediat...ulation/[/url]

http://rna-mediat...herited/

http://rna-mediat...ulation/]http://rna-mediat...ulation/[/url]

http://rna-mediat...onships/

http://rna-mediat...balance/

...and other posts that link nutrient-dependent microRNA controlled protein expression from the biophysically constrained chemistry of protein folding to biodiversity via amino acid substitutions, which differentiate all cell types in all genera via the physiology of reproduction.
Vietvet
4.2 / 5 (10) Apr 05, 2015
There he goes again. JVK spamming with links to his inane blog site.
JVK
1.4 / 5 (9) Apr 05, 2015
Steven Taylor doesn't like the fact that RNA-mediated.com is currently the only source of information that integrates physics, chemistry, and the conserved molecular mechanisms of RNA-mediated cell type differentiation in all genera.

"...Jerome Hui of the Chinese University of Hong Kong found that in both insects and crustaceans, the same set of micro RNAs control expression of the genes for those enzymes." http://www.scienc....summary

Others have since published "MicroRNA control of protein expression noise" http://www.scienc...abstract
Excerpt: "Combinatorial miRNA regulation may thus be a potent mechanism to reinforce cellular identity by reducing gene expression fluctuations that are undesirable for the cell."

That supports every claim I have ever made, including the most recent claims about links from the balance of viral microRNAs and nutrient-dependent microRNAs to cell type differentiation.
Captain Stumpy
4.6 / 5 (9) Apr 05, 2015
@jk

still collecting the data from your posts... don't forget to be as wide ranging as well as clear and concise as you possibly can so that the author can comprehend what you are saying

I will add the comments you made on SciMag into the letter of request as well, since you are linking it

anything and everything referenced, linked to and posted in this thread

if you would like a copy of the e-mail when i send it, you will have to provide an e-mail address for me to forward it to
JVK
1.4 / 5 (9) Apr 05, 2015
Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems
http://figshare.c...s/994281

"This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled changes in the microRNA / messenger RNA balance and chromosomal rearrangements. The nutrient-dependent pheromone-controlled changes are required for the thermodynamic regulation of intracellular signaling, which enables biophysically constrained nutrient-dependent protein folding; experience-dependent receptor-mediated behaviors, and organism-level thermoregulation in ever-changing ecological niches and social niches. Nutrient-dependent pheromone-controlled ecological, social, neurogenic and socio-cognitive niche construction are manifested in increasing organismal complexity in species..." cont.
JVK
1.4 / 5 (9) Apr 05, 2015
... from microbes to man. Species diversity is a biologically-based nutrient-dependent morphological fact and species-specific pheromones control the physiology of reproduction. The reciprocal relationships of species-typical nutrient-dependent morphological and behavioral diversity are enabled by pheromone-controlled reproduction. Ecological variations and biophysically constrained natural selection of nutrients cause the behaviors that enable ecological adaptations. Species diversity is ecologically validated proof-of-concept. Ideas from population genetics, which exclude ecological factors, are integrated with an experimental evidence-based approach that establishes what is currently known. This is known: Olfactory/pheromonal input links food odors and social odors from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man during their development."
JVK
1.6 / 5 (7) Apr 06, 2015
if you would like a copy of the e-mail when i send it, you will have to provide an e-mail address for me to forward it to


jvkohl@RNA-mediated.com

Re: "...the epigenetic 'tweaking' of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution."

Viral microRNAs perturb protein folding, which is how they cause physiopathology. They prevent the nutrient-dependent ecological adaptations manifested in the increasing organismal complexity of morphological phenotypes and behavioral phenotypes. The complexity of phenotypes exemplifies the fact that amino acid substitutions stabilize the organized genomes of all genera via fixation in the context of their nutrient-dependent physiology of reproduction.
JVK
1.6 / 5 (7) Apr 06, 2015
The biologically uninformed science idiot known on phys.org as Captain Stumpy, previously claimed he was emailing ~100 of those whose works I cited, in an attempt to determine whether I correctly interpreted their works in the context of my model. I suspect he did not email anyone, or that those he asked to comment on my representations claimed I was correct. The fact that I have been correct for 2 decades has now been established. I provided the links.

if you would like a copy of the e-mail when i send it, you will have to provide an e-mail address for me to forward it to


jvkohl@RNA-mediated.com

I welcome correspondence from anyone willing to discuss what is currently known about physics, chemistry, and the molecular biology of cell type differentiation, but wonder why no one comments to my blog site.

http://rna-mediated.com/
PeterKinnon
2.3 / 5 (3) Apr 06, 2015
It is sad to see so much of-topic silliness among these comments regarding what promises to be one of the most significant interpretations of biological evolution of recent times.

Lane has an excellent pedigree in this respect. His popular science works are well-informed but at the same time not seriously hampered by prevailing dogma. Lane is not always right, of course, non of us are! I have my points of disagreement, particularly on issues such a consciousness where, rather surprisingly in his case, he does tend to wax a little metaphysical.

However, within the realm of biology, there are many points of contact with my own more far-reaching model which is explored in "The Intricacy Generator: Pushing Chemistry and Geometry Uphill". Now available as 336 page illustrated paperback from Amazon, etc.

JVK
1.7 / 5 (6) Apr 06, 2015
Excerpt:
In recent times Lane and his group have taken to the computer to provide insight into some of these effects, running all kinds of simulations to vet their hypotheses.


Within the realm of biology, ecological variation and ecological adaptations are linked without the pseudoscientific nonsense about effects in the context of biological evolution.

Metabolic networks and genetic networks are 1) nutrient-dependent; 2) RNA-directed via 3) DNA methylation and 4) amino acid substitutions that 5) differentiate cell types via their 6) fixation in the context of the physiology of reproduction.

http://rna-mediat...entists/

Feel free to compare your model to mine: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
JVK
2.1 / 5 (7) Apr 06, 2015
Energy at life's origin http://www.scienc...92.short

What is the source of all biological energy? In my model, it is the sun.

A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria http://dx.doi.org....1001926

What is the source for membrane divergence and cell type differentiation in all genera?

In my model, the anti-entropic epigenetic effect of the sun's biological energy is linked from the light-induced de novo creation of amino acids to nutrient-dependent RNA-mediated amino acid substitutions that differentiate cell types by preventing virus-induced entropy, but also by ensuring entropic elasticity until nutrient-dependent epistasis is achieved in the organized genomes of any and all species via the physiology of reproduction.

If Lane is well-informed and not seriously hampered by prevailing dogma, what do you think he will tell us about the link from energy to cell type differentiation?
Captain Stumpy
4.3 / 5 (6) Apr 07, 2015
power and internet problems in the area... i will be gathering those posts when possible and forwarding the comments to the author for reply
@kohl... the copy of the e-mail will be sent to you
i will include all links and posts to this point as well as anything that is posted and linked on my last check before sending
Your verbose flooding will be largely attached as a reference (and linked it the source for validation, as i always do when arguing against your interpretations) and i will be having to pick specifics for the request for clarification from the author
Should you take umbrage at what is copied to you, feel free to bring it up and give a reason why
be specific in all your arguments for the sake of clarity

It should be ready by tomorrow, barring any unforeseen circumstances
Captain Stumpy
4.3 / 5 (6) Apr 07, 2015
Captain Stumpy, previously claimed he was emailing ~100 of those whose works I cited, in an attempt to determine whether I correctly interpreted their works blah blah blah
@the idiot kohl
actually, i have not received a single reply yet
Most likely because i have noticed that a LOT of actual scientists don't think replying to obvious wrong interpretations of science are worth the time...
Why?
as i was told one WRT another pseudoscience idiot like jk-
"when you do not have the education foundation to make a logical interpretation of the actual science involved, then it is not likely going to clarify or even help the situation when the actual science is presented.
Pseudoscience posters follow their own religious-like beliefs for a reason, and neither logic nor education have anything to do with their adherence to their dogma.
no matter how much science you throw at them, they will claim conspiracy, use circular logic or any myriad of other reasons to ignore it"
JVK
1.7 / 5 (6) Apr 07, 2015
Re: Captain Stumpy's efforts to show I am misinterpreting the works of others and Peter Kinnon's model.

See: Haozhe Zhang, Robert Sinclair. Namibian fairy circles and epithelial cells share emergent geometric order. Ecological Complexity, 2015; 22: 32 DOI: 10.1016/j.ecocom.2015.02.001

This suggests Peter Kinnon's model might explain how the light-induced de novo creation of amino acids that links nutrient-dependent amino acid substitutions to cell type differences in all genera might also explain the geometric order of Namibian fairy circles.

If the pattern suggests nothing more than coincidence to Peter Kinnon, his model may be as useless as other models that explain nothing about biologically-based cause and effect.

http://www.ncbi.n...24693353 Nutrient-dependent/pheromone-controlled adaptive evolution: a model. CONCLUSION: "Minimally, this model can be compared to any other factual representations of epigenesis and epistasis..."
Captain Stumpy
4.3 / 5 (6) Apr 07, 2015
@jk
per the above agreed upon request as well as for clarity -
all the collected comments above as well as the sci-mag comments will be sent as a request for clarification of your model compared to the work as well as to validate your interpretations of the following study: http://www.scienc...128.full

you have until noon NY Time APR 08 to lodge any further data to be sent off... any and all data posted will be added to the reference page verbatim, as i always have done

i will post replies when and if they are presented
Captain Stumpy
4.4 / 5 (7) Apr 07, 2015
misinterpreting the works of others
jk's interpretations of Dr. Extavour's work, which he CLAIMED supported his anti-mutation posts
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 [CPT S] are right that we in no way claim that mutations in the heritable genome play no role in evolution. Indeed, as you [CPT S] 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.
your fail, jk

why don't you link her as support anymore?
viko_mx
1 / 5 (4) Apr 07, 2015
Functional synchronization between the various structural parts of a biological system could not be attributed to evolutionary principle of randomness. A muscle has no physiological value, if the nerve did not set it in motion. But muscle and nerve have not physiological value without complex management system in the brain that coordinate muscle movements. Without harmonious synchronization between these three entities have their existance is pointless. How is it possible in a random evolutionary process three parts to reach simultaneously optimal functional ability in coordinating their actions by random mutations? Not to mention that they belong to tissue systems having different gifts and embryonic development.
viko_mx
1 / 5 (4) Apr 07, 2015
Let's look at the structural - functional perfection of the eye and brain. Their function depends on the complex synchronization of the various tissue structures. Reduction or elimination of the only part of this complex chain makes impossible the realization of the specific function. The human eye is made up of 100 million light-sensitive cells. Collection from these data are sent to the brain via the optic nerve consists of about one million nerve fibers. In the brain, the resulting information is analyzed and becoming understandable to create picture. The whole process is carried out by multiple interconnected components, operating with extraordinary synchronicity and incredible speed. But the visual ability of the brain is only part of its exclusive functional complexity.
JVK
1.7 / 5 (6) Apr 07, 2015
you have until noon NY Time APR 08 to lodge any further data to be sent off...


I have published a model of RNA-mediated biologically-based cause and effect that links the microRNA/messenger RNA balance to amino acid substitutions and cell type differentiation in all genera. Do not presume to tell me what I have time to add after others have already confirmed that the basis of cell type differentiation is microRNAs.

why don't you link her as support anymore?


She never linked the microRNA/messenger RNA balance to cell type differentiation via RNA-mediated amino acid substitutions.

You and other biologically uninformed science idiots used her works to support your ridiculous claims about mutations and evolution.

You told her I claimed her works did not prove mutations did not lead to evolution and she confirmed that fact. No one can prove that the definition of "mutation" and assumptions about evolution link biologically-based cause and effect.
JVK
1.7 / 5 (6) Apr 07, 2015
Let's look at the structural - functional perfection of the eye and brain.


Accumulated mutations lead to loss of function and eye regression in cave fish due to their nutrient-poor environment and no further need to create receptors for visual input. Only the de novo creation of olfactory receptor genes is required for ecological adaptation linked to vertebrate and invertebrate biodiversity.

That is the fact I have detailed in a series of published works.

The whole process is carried out by multiple interconnected components, operating with extraordinary synchronicity and incredible speed.


Evolutionary theorists hate that fact. It makes them look more foolish each time another published work refutes their ridiculous theories.

See: http://www.the-sc...ewiring/

viko_mx
1.8 / 5 (5) Apr 07, 2015

"Evolutionary theorists hate that fact. It makes them look more foolish each time another published work refutes their ridiculous theories."

They are subordinate to their feelings and are immune to the truth.
JVK
1.8 / 5 (5) Apr 07, 2015
Most intelligent people and serious scientists cannot be taught to believe in pseudoscientific nonsense.

If that happened, eventually there would be no one left alive and no one would currently be "Combating Evolution to Fight Disease" http://www.scienc...88.short

Only biologically uninformed science idiots fail to question reports on the evolution of the flagellum over the weekend compared to reports like this one:

http://www.scienc...4131.htm "The greatest absence of evolution ever reported...: a type of deep-sea microorganism that appears not to have evolved over more than 2 billion years. But the researchers say that the organisms' lack of evolution actually supports Charles Darwin's theory of evolution."

...because we provide evidence that nutritional conditions play a role, this does not negate a role for mutations.


What does the difference between 4 days and 2 billion years tell us?
JVK
1.8 / 5 (5) Apr 07, 2015
our work does, we hope, provide an example of how nutrition/ecology could affect the evolution of potentially adaptive traits


Thanks for the reminder from my Captain Stumpy puppet of what Extavour hopes could "affect" potentially adaptive traits. She may not realize that the epigenetic effects of nutrient uptake are linked via hormone-organization and hormone-activation to the affects of hormones on behavior, which is how the physiology of nutrient-dependent reproduction links feedback loops to chromatin loops and biodiversity.

When people see someone claim they "...provide an example of how nutrition/ecology could affect the evolution..." outside the context of epigenetic EFFECTS on hormones linked to AFFECTS on behavior, most intelligent people realize that theorists don't understand the difference between EFFECT and AFFECT.

I was taught the difference was essential to any model of cause and effect and to start with gene activation not mutations.
JVK
1.8 / 5 (5) Apr 07, 2015
COLLOQUIUM Correction for "Brain on stress: How the social environment gets under the skin," by Bruce S. McEwen, which appeared in supplement 2, October 16, 2012, of Proc Natl Acad Sci USA (109:17180–17185; first published October 8, 2012....

Excerpt: ...on page 17184, right column, first paragraph, line 4, "effect" should instead appear as "affect."

http://www.pnas.o...1.2.full

See also: Gonadotropin releasing hormone and human sexual behavior http://books.goog...AAAAMAAJ

Induction of FOS immunoreactivity in central accessory olfactory structures of the female rat following exposure to conspecific males http://www.ncbi.n...19912880

25 years ago, I learned that induction of FOS is due to an epigenetic effect of odor on gene activation in hormone-secreting nerve cells of the mammalian brain that link epigenetic effects to affects on behavior.
JVK
1.8 / 5 (5) Apr 07, 2015
Vast Complexity of Chromatin 3D Shapes http://jonlieffmd...d-shapes

Anyone who is not yet convinced that Captain Stumpy and anonymous_9001 (aka Andrew Jones) are not among the most biologically uninformed science idiots they could ever expect to encounter should ask themselves: What would it take to convince me of that fact?

See the thesis by Jones and his criticisms of my review. If you need anything more convincing than those two things, you are probably also a biologically uninformed science idiot.

Lipid Encapsulation of Self Replicating Ribozymes https://www.scrib...s#scribd

Criticisms of the nutrient-dependent pheromone-controlled evolutionary model. http://www.ncbi.n...24959329
anonymous_9001
5 / 5 (5) Apr 07, 2015
I love the free publicity. I couldn't pay someone to be a better advertiser than you.
PeterKinnon
3.7 / 5 (3) Apr 08, 2015
@JVK

"If Lane is well-informed and not seriously hampered by prevailing dogma, what do you think he will tell us about the link from energy to cell type differentiation?"

We will have to wait until his work is unveiled before we can answer that.

Re :"A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria http://dx.doi.org....1001926" Your proposal if an intermediary sodium-proton antiporter for the membrane is interesting and ingenious.

However the incremental approach that I adopt for membrane evolution
within the matrix of hydrothermal vents has, I believe, more parsimony and is consistent with known physics and chemistry. It also brings the probability issue within reasonable bounds.

"What is the source of all biological energy? In my model, it is the sun."

Well, actually, the source of all energy, biological or otherwise, is, as underlined in "The Intricacy Generator", actually appears to be gravity.
Vietvet
3.4 / 5 (5) Apr 08, 2015
"Well, actually, the source of all energy, biological or otherwise, is---
---actually appears to be gravity."

Just what this site needs, another crank.
JVK
2 / 5 (4) Apr 08, 2015
... incremental approach that I adopt for membrane evolution within the matrix of hydrothermal vents has, I believe, more parsimony and is consistent with known physics and chemistry.


The latest from Koonin's group puts the EVOLUTION of leaky membranes into the context of the de novo CREATION of receptors that allow the entry of nutrients into cells and also allow viruses to establish virulence via amino acid substitutions.

http://www.biolog.../10/1/12
Excerpt: "...a remarkable case of transfer of viral hallmark genes between widely different RNA viruses and together with similarly striking examples of gene exchange between viruses with RNA and DNA genomes [34]-[36], emphasize the ultimate modularity of the virosphere."
JVK
2 / 5 (4) Apr 08, 2015
I love the free publicity. I couldn't pay someone to be a better advertiser than you.


Is there something that your ridiculous mutagenesis experiments told us about biologically-based cause and effect? Most biologically uninformed science idiots would rather not be exposed. I'm glad you enjoy it.

Re: http://www.biolog.../10/1/12 Koonin's group puts the EVOLUTION of leaky membranes into the context of the de novo CREATION of receptors

So far as I know, no serious scientist has provided any details about how mutations lead to the creation of receptors. Vosshall's group has shown that mutations lead to loss of olfactory receptor genes, and that amino acid substitutions lead to the de novo creation of olfactory receptor genes.

Koonin's group (2005) http://www.nature...306.html "...cannot conceive of a global external factor that could cause, during this time, parallel evolution of amino acid..."
JVK
2 / 5 (4) Apr 08, 2015
I love the free publicity. I couldn't pay someone to be a better advertiser than you.


What kind of biologically uninformed science idiot revels in his exposed ignorance.

Excerpt from my review: http://www.ncbi.n...24693353
"...the epigenetic 'tweaking' of the immense gene networks that occurs via exposure to nutrient chemicals and pheromones can now be modeled in the context of the microRNA/messenger RNA balance, receptor-mediated intracellular signaling, and the stochastic gene expression required for nutrient-dependent pheromone-controlled adaptive evolution."

See: "...microRNA are pleiotropic, synaptically located, tightly regulated, and function in response to synaptic activity. The potential impact of microRNA on LTP maintenance as regulators of gene expression is enormous."
http://journal.fr...w15-2015
JVK
2 / 5 (4) Apr 08, 2015
"...the strategy of signal integration, which was previously found in decision-making behaviors of animals, is adopted at the cellular level to reduce noise and minimize uncertainty." http://elifescien...4/e03977

In our 1996 review, we linked this strategy from nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in yeasts to cell type differentiation in mammals via the conserved molecular mechanisms of the biophysically constrained chemistry of protein folding.

See our section on molecular epigenetics in: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

It helps to explain why I was able to link the microRNA/messenger RNA balance to the amino acid substitutions that differentiate all cell types in all genera, while theorists continue to tout their pseudoscientific nonsense about mutations and evolution.
JVK
2 / 5 (4) Apr 08, 2015
"The T->G base pair change we have identified near EDA provides a rare example in vertebrates of a particular non-coding base pair change contributing to repeated adaptive evolution."

"These results provide a new example of a specific regulatory change linked to morphological evolution in natural populations (Martin and Orgogozo 2013), and add to growing evidence that regulatory changes are a predominant mechanism underlying adaptive evolution in sticklebacks (Jones et al. 2012) and other organisms (Wray 2007, Carroll 2008)."

The regulatory changes, like all regulatory changes in all genera, are perturbed by mutations, which is why mutations cannot lead to increasing organismal complexity via the creation of anything. Accumulated mutations are eliminated when thermodynamic cycles of protein biosynthesis and degradation lead from nutrient-dependent amino acid substitutions to the stability and flexibility of organism-level thermoregulation.
JVK
2 / 5 (4) Apr 08, 2015
A problem with my Bibliographic references led me to review the above cited works and this one.

"This deterministic mechanism of selection, acting on the ecological and social traits of individuals and operating simultaneously across species, is believed to contribute to pervasive macroevolutionary patterns, including the tree-like structure of trait divergence over entire radiations10,13,14 and the non-random morphological differences found almost universally among co-occurring lineages14,15."
http://www.nature...874.html

I love the free publicity. I couldn't pay someone to be a better advertiser than you.


See his review of my most recent published work: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model. http://www.ncbi.n...24959329

There has never been any EVOLUTIONARY MODEL! Ecological variation leads to ecological adaptation via biologically based facts, not theory.
JVK
2 / 5 (4) Apr 08, 2015
http://perfumingt...toddart/

Excerpt: "Our sense of smell evolved to make human pheromones undetectable"

The link from ecological variation to ecological adaptation requires the RNA-mediated de novo creation of olfactory receptors. Mutations lead to loss of function, not from natural selection to the evolution of our sense of smell.

Twenty-five years after "The Scented Ape" and 20 years after "The Scent of Eros: Mysteries of Odor in Human Sexuality" Michael Stoddart puts everything known about ecological adaptation into the context of conscious detection of human pheromones.

[W]hat Haldane... 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
Whydening Gyre
4.2 / 5 (5) Apr 11, 2015

"Evolutionary theorists hate that fact. It makes them look more foolish each time another published work refutes their ridiculous theories."

They are subordinate to their feelings and are immune to the truth.

Man, does THAT sound like the pot calling the kettle black....
JVK
2.3 / 5 (3) Apr 11, 2015
What does this sound like: Beyond Genetic Evolution. A Conversation With Eva Jablonka ?
https://evolution...ablonka/

How does it compare to what this sounds like: "...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

It has been clear to me for more than 2 decades that the definition of "mutation" and the assumptions about the link to biodiversity is pseudoscientific nonsense. That's why I have detailed the links from physics and chemistry to molecular biology and ecological adaptation in a series of published reviews.

Your response is: Man, does THAT sound like the pot calling the kettle black....
If that does not sound like it came from a biologically uninformed science idiot, perhaps Captain Stumpy can help.
JVK
2.3 / 5 (3) Apr 11, 2015
"DSW: ..talk to you about the definition of evolution and the need for it to go beyond genetic evolution." https://evolution...ablonka/

"EJ: I did a PhD in genetics and molecular biology; in fact, on DNA methylation and chromatin structure. ... I did a Masters thesis in microbiology."

During my 40-year career as a medical laboratory scientist, the testing I performed on patients led to my reviews and claims about RNA-directed DNA methylation and RNA-mediated amino acid substitutions. The substitutions link the epigenetic landscape to the physical landscape of DNA via the nutrient-dependent pheromone-controlled physiology of reproduction, which I learned links microbes to man via fixation of the amino acid substitutions.

Why has it taken more than 40 years for theorists to learn enough about cell type differentiation to realize their ideas about "evolution" exemplify only their ignorance?
Whydening Gyre
4.2 / 5 (5) Apr 11, 2015
Your response is: Man, does THAT sound like the pot calling the kettle black....
If that does not sound like it came from a biologically uninformed science idiot, perhaps Captain Stumpy can help.

To start, my response was in regard to being subordinate to feelings and immunity to the truth.
Truth is, your response is indicative of an uninformed idiot without regard for the chosen language definitions of this forum or science in general.
While we're at it - please explain the mechanism of "pheromones" prior to the advent of sexual reproduction... How did they control the leap from cell division to cell "addition"?
JVK
2 / 5 (4) Apr 11, 2015
indicative of an uninformed idiot without regard for the chosen language definitions...


DSW and EJ discuss changing the definition of evolution, which suggests only biologically uninformed science idiots will continue to use "...the chosen language definitions of this forum or science in general."

Science is supported by experimental evidence, not by definitions that are subject to change when the experimental evidence forces them to change.

please explain the mechanism of "pheromones" prior to the advent of sexual reproduction...


There are too many articles about quorum sensing that are readily available. They preclude the need for me to explain what is still unknown to biologically uninformed science idiots who do not understand nutrient-dependent cell type differentiation in species of microbes or any other species.
JVK
2 / 5 (4) Apr 11, 2015
"A systematic, RNAi-mediated knock down of most of the predicted transcription factors identified an essential function of acj6, E93, Fer1, onecut, sim, xbp1, and zf30c in the regulation of more than 30 ORs. These regulatory factors are differentially expressed in antennal sensory neuron classes and specifically required for the adult expression of ORs."
http://dx.doi.org....1001280

Reported in 2012 as: "Few genes control neuronal function." March 14th, 2012.
http://medicalxpr...ion.html

"Genetic variations of chemoreceptors caused by single nucleotide polymorphisms (SNPs) that result in an amino acid change (S201F; A229D), were described for VN1R1 (Rodriguez et al., 2000)." http://www.scienc...15002116

Reported last week as http://medicalxpr...one.html "Delicate magnolia scent activates human pheromone receptor"
JVK
2 / 5 (4) Apr 11, 2015
What kind of biologically uninformed science idiot refuses to look at the review article that concludes: "Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans..." -- but comments here on what he knows nothing about?

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

please explain the mechanism of "pheromones" prior to the advent of sexual reproduction...


Is there even one anonymous fool here who can explain how sexual reproduction "evolved" so that the explanation can be compared to compared to what is known about physics, chemistry, and molecular biology by serious scientists? That's what I included in my model:
http://www.ncbi.n...24693353 Nutrient-dependent/pheromone-controlled adaptive evolution: a model.
JVK
2 / 5 (4) Apr 11, 2015
"Well, actually, the source of all energy, biological or otherwise, is------actually appears to be gravity."


Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins http://www.pnas.o...abstract

See also: Search Results for 'light-induced' http://rna-mediat...-induced
Whydening Gyre
4.2 / 5 (5) Apr 11, 2015
There are too many articles about quorum sensing that are readily available. They preclude the need for me to explain what is still unknown to biologically uninformed science idiots who do not understand nutrient-dependent cell type differentiation in species of microbes or any other species.

Quorum sensing is not "pheromone controlled"...
Whydening Gyre
4.2 / 5 (5) Apr 11, 2015
There are too many articles about quorum sensing that are readily available. They preclude the need for me to explain what is still unknown to biologically uninformed science idiots who do not understand nutrient-dependent cell type differentiation in species of microbes or any other species.

Please respond. How did "pheromones" control the leap between cell division and cell procreation...
JVK
2 / 5 (4) Apr 12, 2015
Quorum sensing is not "pheromone controlled"...


http://www.scienc...14004602
Recent progress in the chemistry and chemical biology of microbial signaling molecules: quorum-sensing pheromones and microbial hormones

Excerpt: "Communication among microorganisms is mediated by secretion and detection of microbial signaling molecules such as quorum-sensing pheromones and microbial hormones. The molecules elicit the regulation of important genes necessary for microbial survival and often play important roles in interspecies or even inter-kingdom communication."

...explain the mechanism of "pheromones" prior to the advent of sexual reproduction... How did they control the leap from cell division to cell "addition"?


How did "pheromones" control the leap between cell division and cell procreation...


"The molecules elicit the regulation of important genes necessary for microbial survival..."
Whydening Gyre
4.2 / 5 (5) Apr 12, 2015
"The molecules elicit the regulation of important genes necessary for microbial survival..."

Sooo... what controls pheromone secretion? Their must be some mechanism involved in regulating that, as well...
JVK
2 / 5 (4) Apr 12, 2015
...what controls pheromone secretion?


Thanks for asking. Does the title of this review provide you with any indication of what controls nutrient-dependent pheromone-controlled ecological adaptations in species from microbes to man?

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

If not, does the conclusion from the abstract?

CONCLUSION:
"An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates."

----------
If not, what kind of biologically uninformed science idiot asks the questions that you ask? That was a rhetorical question.
Whydening Gyre
4.2 / 5 (5) Apr 12, 2015
CONCLUSION:
"An environmental drive evolved from that of nutrient ingestion in unicellular organisms to that of pheromone-controlled socialization in insects. In mammals, food odors and pheromones cause changes in hormones such as LH, which has developmental affects on pheromone-controlled sexual behavior in nutrient-dependent reproductively fit individuals across species of vertebrates."

----------
If not, what kind of biologically uninformed science idiot asks the questions that you ask? That was a rhetorical question.

You completely side-stepped my question as to what mechanism is responsible for "pheremone" (quorum sensed or otherwise) production?
As to your question - an artist trying to view the process in a larger picture...
JVK
2 / 5 (4) Apr 12, 2015
... an artist trying to view the process in a larger picture...


Telling me I'm wrong.

Quorum sensing is not "pheromone controlled"...


Then asking

...what mechanism is responsible for "pheremone" (quorum sensed or otherwise) production?


What mechanism is responsible for the creation of biologically uninformed morons who think they are artists capable of asking intelligent questions or making intelligent comments?
Whydening Gyre
4.2 / 5 (5) Apr 12, 2015
... an artist trying to view the process in a larger picture...


Telling me I'm wrong.

Nope was legitimately asking you to explain why you are right in understandable verbage

Quorum sensing is not "pheromone controlled"...


Then asking

...what mechanism is responsible for "pheremone" (quorum sensed or otherwise) production?

A legitimately asked question. I am attempting to understand a process after perusing your link.

What mechanism is responsible for the creation of biologically uninformed morons who think they are artists capable of asking intelligent questions or making intelligent comments?

Stop being an egotistical dick...
and - answer the question. What mechanism is responsible for the initiation of production of pheromones or which ones to produce?
In plainer language, please.
JVK
2 / 5 (4) Apr 12, 2015
What mechanism is responsible for the initiation of production of pheromones or which ones to produce?


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

The fact that you are a biologically uninformed science idiot does not make me an egotistical dick. It makes those who have touted their nonsense about mutations and evolution egotistical pseudoscientists who have taught science idiots to believe in ridiculous theories.
Whydening Gyre
4.2 / 5 (5) Apr 12, 2015
http://phys.org/n...ria.html

Admittedly, an interesting read, but still leaves many information holes to be filled.

It makes those who have touted their nonsense about mutations and evolution egotistical pseudoscientists who have taught science idiots to believe in ridiculous theories.

Why aren't these other researchers having a problem with mutation driven evolution? Surely, if they see the same sequences you do, they must be biologically un-informed science idiots as well...
The fact that you are a biologically uninformed science idiot does not make me an egotistical dick.

Oh. That's right. You don't need any help with that one...
JVK
2 / 5 (4) Apr 12, 2015
Why aren't these other researchers having a problem with mutation driven evolution?


What is the basis of that ridiculous claim?

Eva Jablonka is trying to redefine "evolution" to make it appear that she and Lamb have been including what is known about RNA-mediated links from the epigenetic landscape to the physical landscape of DNA while touting the pseudoscientific nonsense about mutations and natural selection.

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

You still seem to think my ego is the issue when many others are "Combating Evolution to Fight Disease."
JVK
2 / 5 (4) Apr 12, 2015
Combating Evolution to Fight Disease http://www.scienc...88.short

The issue is the ignorance of evolutionary theorists.

Israeli Middle Schools School to Include Theory of Evolution http://www.educat...olution/

Excerpt: "...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."

While intelligent researchers learn about ecology and it is taught to some students, Jablonka's textbook is still used to teach pseudoscientific nonsense.

http://www.amazon...62525844

"The reality is that biologists know so little about how the RNAi system works that it is premature to speculate at al ... (p. 327)
Whydening Gyre
4.2 / 5 (5) Apr 14, 2015
You still seem to think my ego is the issue when many others are "Combating Evolution to Fight Disease."

Gotta start somewhere...
Still pondering your assertions and why you might be having such a hard time making headway...

Mike_Massen
3 / 5 (4) Apr 14, 2015
Ren82 claimed
.. quoted Bible because it is the most popular book in the world and every person with interest can read from the source of God's wisdom and truth
Really ?

Is bible a really GREAT parenting example ?

Your child rejects your authority so you punish her children for ever ?

"Wisdom" ?

Ren82, haven't you noticed, the activities & attributes of Moses' god is FAR more consistent with that of an egotistical cheating insane devil than any loving god !

ie. God is a supreme punisher of everyone for ever because he allowed a powerful angel to manipulate a girl who trusted all of god's creations & was Never educated in Guile.

And ALL the time Moses' god KNEW this was going to happen & Never educated the girl in how to deal with deception & was Never warmed ever her children would suffer for ALL time ?

Completely nuts Ren82

Your god has NO Wisdom or Truth, Bible writings of men; drawn from bad dreams !

Truth is chemistry ie. Nature: Eat & be Eaten !
JVK
2.3 / 5 (3) Apr 14, 2015
why you might be having such a hard time making headway...


Most people prefer to believe in pseudoscientific nonsense. That way, they don't need to learn anything.

Scientists identify an oncogene regulated by nutrients
http://www.eureka...1315.php

See for comparison: http://rna-mediat...ference/
and http://rna-mediat...eg-bear/

Truth is chemistry ie. Nature: Eat & be Eaten !


That's not nature; it's the de novo creation of amino acids and nutrient-dependent pheromone-controlled ecological adaptation via amino acid substitutions in all genera.
See http://www.ncbi.n...24693353

The chemistry of protein folding is biophysically constrained by the energy from food, which controls the physiology of reproduction.
Whydening Gyre
4 / 5 (4) Apr 14, 2015
Why are links to your OWN sites considered valid resources? Show others....
Vietvet
4 / 5 (4) Apr 14, 2015
Why are links to your OWN sites considered valid resources? Show others....


@Whydening Gyre
If history is a guide jvk might provide some links he claims supports him. They do no such thing, he is a flat out liar.
JVK
2 / 5 (4) Apr 14, 2015
František Baluška: Evolutionary Science 'Stuck' on Wrong Track, Situation 'Out of Control'
http://www.huffin...592.html

Combating Evolution to Fight Disease http://www.scienc...88.short
jburchel
5 / 5 (1) Apr 15, 2015
I was a bit acerbic unnecessarily to be harsh on grammar and spellcheck. Sorry. I do love your site for many years and want to help make it better, but your point is well taken. My criticism was only superficial, and only to help improve content presentation, but not really material either. You are a good science writer and I've come to enjoy your style in fact.

Spot on jburchel, that is in fact the the vital question. Will do better using the guidance of the spell checker. As far as trusting high level content your question answers itself, without a high level content checker we are probably doomed. if you have found one please forward along and I will begin using it at once.


Whydening Gyre
4.2 / 5 (5) Apr 15, 2015
THIS is what I found interesting....
František Baluška: "We are very far away from understanding the complexity of the whole system. It is dangerous to say we know because we've found all the genes there are to be found in humans and sequenced them. It is dangerous to say we know everything when we know almost nothing. The basis of disease is much more complex. Our cells are so complex. There is much more information stored in structures, in membranes... There's a lot of information stored in carbohydrates. The genome is not the whole story. "
JVK
2 / 5 (4) Apr 15, 2015
What I find interesting is the amount of pseudoscientific nonsense that people would rather believe in, despite 18 more years of details about nutrient-dependent RNA-mediated cell type differentiation. See for example our 1996 section on molecular epigenetics in: http://www.hawaii...ion.html

Then see this claim by Jablonka and Lamb in the most recent edition of their textbook.
"...where there were networks of RNA-mediated interactions, natural selection could have led to some RNA molecules responding to changes in conditions in a way that inhibited the activities of other molecules with a similar sequence. They might have modified the structure of these molecules by base-pairing with them...
What we have just said is very vague and speculative, and based on no evidence whatsoever."
http://www.amazon...title_bk

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