Scientists create world's largest protein map to reveal which proteins work together in a cell

Tree of life study unveils inner workings of a cell
Scientists have uncovered tens of thousands of new protein interactions, accounting for about a quarter of all estimated protein contacts in a cell. Credit: Jovana Drinkjakovic

A multinational team of scientists have sifted through cells of vastly different organisms, from amoebae to worms to mice to humans, to reveal how proteins fit together to build different cells and bodies.

This tour de force of protein science, a result of a collaboration between seven research groups from three countries, led by Professor Andrew Emili from the University of Toronto's Donnelly Centre and Professor Edward Marcotte from the University of Texas at Austin, uncovered tens of thousands of new protein interactions, accounting for about a quarter of all estimated protein contacts in a cell.

When even a single one of these interactions is lost it can lead to disease, and the map is already helping scientists spot individual proteins that could be at the root of complex human disorders. The data will be available to researchers across the world through open access databases.

The study comes out in Nature on September 7.

While the sequencing of the human genome more than a decade ago was undoubtedly one of the greatest discoveries in biology, it was only the beginning of our in-depth understanding of how cells work. Genes are just blueprints and it is the genes' products, the proteins, that do much of the work in a cell.

Proteins work in teams by sticking to each other to carry out their jobs. Many proteins come together to form so called molecular machines that play key roles, such a building new proteins or recycling those no longer needed by literally grinding them into reusable parts. But for the vast majority of proteins, and there are tens of thousands of them in human cells, we still don't know what they do.

This is where Emili and Marcotte's map comes in. Using a state-of-the-art method developed by the groups, the researchers were able to fish thousands of protein machineries out of cells and count individual proteins they are made of. They then built a network that, similar to social networks, offers clues into protein function based on which other proteins they hang out with. For example, a new and unstudied protein, whose role we don't yet know, is likely to be involved in fixing damage in a cell if it sticks to cell's known "handymen" proteins.

Today's landmark study gathered information on protein machineries from nine species that represent the tree of life: baker's yeast, amoeba, sea anemones, flies, worms, sea urchins, frogs, mice and humans. The new map expands the number of known protein associations over 10 fold, and gives insights into how they evolved over time.

"For me the highlight of the study is its sheer scale. We have tripled the number of protein interactions for every species. So across all the animals, we can now predict, with high confidence, more than 1 million protein interactions - a fundamentally 'big step' moving the goal posts forward in terms of protein interactions networks," says Emili, who is also Ontario Research Chair in Biomarkers in Disease Management and a professor in the Department of Molecular Genetics.

The researchers discovered that tens of thousands of protein associations remained unchanged since the first ancestral cell appeared, one billion years ago (!), preceding all of animal life on Earth.

"Protein assemblies in humans were often identical to those in other species. This not only reinforces what we already know about our common evolutionary ancestry, it also has practical implications, providing the ability to study the genetic basis for a wide variety of diseases and how they present in different species," says Marcotte.

The map is already proving useful in pinpointing possible causes of human disease. One example is a newly discovered molecular machine, dubbed Commander, which consists of about a dozen individual proteins. Genes that encode some of Commander's components had previously been found to be mutated in people with intellectual disabilities but it was not clear how these proteins worked.

Because Commander is present in all animal cells, graduate student Fan Tu went on to disrupt its components in tadpoles, revealing abnormalities in the way brain cells are positioned during embryo development and providing a possible origin for a complex human condition.

"With tens of thousands of other new interactions, our map promises to open many more lines of research into links between proteins and disease, which we are keen to explore in depth over the coming years," concludes Dr. Emili.


Explore further

New map uncovers the traffic of life in a cell

More information: Panorama of ancient metazoan macromolecular complexes, Nature, DOI: 10.1038/nature14877
Journal information: Nature

Citation: Scientists create world's largest protein map to reveal which proteins work together in a cell (2015, September 7) retrieved 15 October 2019 from https://phys.org/news/2015-09-scientists-world-largest-protein-reveal.html
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JVK
Sep 07, 2015
... tens of thousands of protein associations remained unchanged since the first ancestral cell appeared, one billion years ago (!), preceding all of animal life on Earth.


They discovered that the light-induced de novo creation of nucleic acids links the RNA-mediated de novo creation of G protein-coupled receptors and Darwin's "conditions of life" to the nutrient-dependent physiology of reproduction via amino acid substitutions that stabilize the organized genomes of species from microbes to man via the experience-dependent creation of olfactory receptor genes.

If they claimed all life on earth was evidence that ecological variation is linked to ecological adaptations via the conserved molecular mechanisms of biophysically constrained protein folding chemistry, they would reveal the fact that they were, until now, biologically uninformed.

See also: http://phys.org/n...tml#nRlv

JVK
Sep 07, 2015
The researchers discovered that tens of thousands of protein associations remained unchanged since the first ancestral cell appeared, one billion years ago (!), preceding all of animal life on Earth.


Note: This implies that the first ancestral cell automagically appeared one billion years ago.

See also: http://www.nature...306.html

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

My comment: No parallel evolution of amino acid compositions of proteins means NO EVOLUTION of proteins or RNA-mediated cell types.

JVK
Sep 07, 2015
... tens of thousands of protein associations remained unchanged since the first ancestral cell appeared, one billion years ago (!), preceding all of animal life on Earth.


See also: "Scientists discover organism that hasn't evolved in more than 2 billion years"
http://phys.org/n...ars.html

The claim that "....the first ancestral cell appeared, one billion years ago..." is unsupported by experimental evidence of biologically-based cause and effect and the fossil record dating is unsupported by claims that "....the first ancestral cell appeared, one billion years ago..."

Could the problem be that only serious scientists have considered the role that viruses play in preventing ecological adaptation?

"The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis..." -- Eugene Koonin

Sep 07, 2015
5 / 5 (4) Aug 05, 2015
Statement directly from Eugene Koonin to me:

"I certainly have never even thought about "rejecting" neo-Darwinism. All I said, in this interview and many previous publications, is that neo-Darwinsim Is a rather narrowly constrained theoretical framework that, for various reasons, leaves out many key evolutionary processes. One of the primary reasons for that is simply that at the time neo-Darwinism took its shape (1950s), the salient theory and especially observations were unavailable."

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

A reply to anonymous9001 when he queried Koonin about statements made by JVK.

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

JVK
Sep 08, 2015
phys.org/news/2015-08-reveals-human-body-stages-evolution.html

It is the de novo creation of G protein-coupled receptors that links Darwin's "conditions of life" to the nutrient-dependent physiology of reproduction in all living genera.


No amount of pseudoscientific nonsense will change that fact. Evolutionary theorists are biologically uninformed science idiots, as are all theoretical physicists. If they were not biologically uninformed, they would have linked the sun's biological energy to RNA-mediated cell type differentiation in all cell types of all living genera soon after Schrodinger suggested that the link from top-down causation was required (1943).

Instead, they ignored Dobzhansky (1973) and
"Amino Acid Difference Formula to Help Explain Protein Evolution" (1974)
http://www.scienc...abstract

JVK
Sep 08, 2015
"The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis..." -- Eugene Koonin

"I certainly have never even thought about "rejecting" neo-Darwinism." -- Eugene Koonin

What kind of biologically uninformed science idiot refuses to reject pseudosceintific nonsense?

http://www.huffin...450.html

"...when we eat food nucleic acids can get into our cells. Also, there is a theory that our cells in the body keep sending out nucleic acids and one theory has it that it seems to correct the mistakes that other cells have suffered from mutations. . . ."

"...evolutionary science has now "moved on to such an extent" that she and Peter Saunders don't really care anymore about "trying to convince the neo-Darwinists."

Summary: All neo-Darwinists are ignorant theorists.

Sep 08, 2015
What kind of biologically uninformed science idiot refuses to reject pseudosceintific nonsense?
this one is EASY to answer!.. the answer is: JVK!
pseudoscience
[all] Mutations perturb protein folding
Except the evidence says: NOT -Lenski, Extavour, Whittaker
In the past two years I've learned enough about physics to link the speed of light on contact with water to the de novo creation of amino acids...
Except the evidence says: NOT (no evidence at all)
I am a serious scientist (medical laboratory scientist) with 40 years experience in diagnostic medicine
Evidence says: NOT- self admitted to failing out of college; can't practice medicine without a license; NO LICENSE ON FILE [FELONY]
my model
Evidence says: DEBUNKED!
http://www.socioa...ew/24367

so, apparently, as everyone can see for themselves... only JVK is idiot enough to NOT "reject pseudosceintific nonsense"!

JVK
Sep 08, 2015
Excerpt: "Central to life is the faithful replication, inheritance, and maintenance of genomic DNA. The MRE11/RAD50/NBS1 (MRN) complex andATMplay a critical role in this biological mandate (Ciccia and Elledge, 2010). Cellular double-strand breaks (DSBs) are sensed by MRN and trigger the assembly of DNA damage response (DDR) foci that amplify global ATM signaling to induce cell-cycle arrest and DNA repair (Polo and Jackson, 2011). DNA viruses are an ancient and persistent threat to both cellular genome integrity and viability." http://dx.doi.org...5.07.058

Viruses perturb the faithful replication, inheritance, and maintenance of genomic DNA. Without nutrient-dependent microRNAs, which epigenetically effect RNA-mediated gene duplication and RNA-mediated amino acid substitutions that differentiation the cell types of all individuals of all living genera via the physiology of reproduction, genomic entropy would already have ended life on this planet.

Sep 08, 2015
http://dx.doi.org/10.1016/j.cell.2015.07.058
1- linking a paywalled study in no way supports your conclusions, especially with your historical failure to interpret studies

2- your entire post in NO WAY WHATSOEVER disproved my last post

in fact, it actually reinforced my last post
only JVK is idiot enough to NOT "reject pseudosceintific nonsense"
you cannot refute the claims, nor can you provide empirical evidence supporting your pseudoscience claims

therefore, by definition, you post PSEUDOSCIENCE and misguided "interpretations" of scientific studies because of your delusional religious dogma goggles which don't allow you to perceive actual science

your posts validate the following study WRT religion and conspiracy ideation (dueled by your Dunning-Kruger)

http://www.ploson...tion=PDF


JVK
Sep 08, 2015
I quoted:
Central to life is the faithful replication, inheritance, and maintenance of genomic DNA.


1- linking a paywalled study in no way supports your conclusions


Those are the conclusions of all serious scientists.

2- your entire post in NO WAY WHATSOEVER disproved my last post


Nothing you have ever claimed needs to be disproved. It is all pseudoscientific nonsense and every serious scientist knows that.

Sep 09, 2015
Nothing you have ever claimed needs to be disproved. It is all pseudoscientific nonsense and every serious scientist knows that.
those words [pseudoscientific nonsense ] define every post you have made to date, and especially prove you post pseudoscience

case in point: above

i am NOT CLAIMING ANYTHING

I HAVE PROVEN that you are a liar, pseudoscience poster, creationist, trolling, baiting, flaming, intellectually deficient, illiterate religious acolyte proselytizing on PO for attention and acolytes

that is not a matter of pseudoscience: it is PROVEN
it is not nonsense: most of it is YOUR OWN WORDS

as for serious scientists: you are NOT one
serious scientists do not debate trolls and liars like you
they also follow the evidence: something you've proven you WON'T do, regardless of it's validity!!

JVK
Sep 09, 2015
Preventing chromosomal chaos: Protein-based genome-stabilizing mechanism discovered
http://phys.org/n...tml#nRlv

Nutrient-dependent microRNAs stabilize organized genomes in my model of how ecological variation is linked from metabolic networks to genetic networks in all living genera via their physiology of reproduction.

I HAVE PROVEN that you are a liar, pseudoscience poster, creationist, trolling, baiting, flaming, intellectually deficient, illiterate religious acolyte proselytizing on PO for attention and acolytes


You have shown that you are nothing more than a biologically uninformed science idiot and that you never will be.

So has PZ Myers and every one of his idiot minions.
http://scienceblo...-aliens/
http://freethough...s-place/

Sep 09, 2015
Nutrient-dependent microRNAs stabilize organized genomes in my model


How do they go about doing that? miRNAs don't interact with the genome once they're transcribed. They interact with mRNAs.

Sep 09, 2015
microRNAs
@jk
When the researchers examined the stomach milk content of the juvenile mice raised in this way, they found high concentrations of miR-375. "MicroRNA molecules are relatively resistant to gastric acids," explains Stoffel.
http://phys.org/n...bed.html

see: anyone can link random quotes
just because you think it supports you, doesn't mean it does... shall we discuss your historical links to Dr. Extavour and your claims which were REFUTED when we queried the authors?
You have shown that you are nothing more than a biologically uninformed science idiot and that you never will be
Uhhhmmm
WOW
so i prove you are a liar, pseudoscience poster, creationist, trolling, baiting, flaming, intellectually deficient, illiterate religious acolyte proselytizing on PO for attention and acolytes...

and your reply is to stick your fingers in your ear and call me names?
the "i'm rubber, you're glue..." argument?
REALLY?

Sep 09, 2015
and perhaps you should go back and learn a little about English, Grammar and literacy: you posted
You have shown that you are nothing more than a biologically uninformed science idiot and that you never will be.

So has PZ Myers blah blah boohoo whine cry
so...
i never will be WHAT?
...and that you never will be
i never will be a "biologically uninformed science idiot"??? I know i will never be
I follow the evidence and the validated science... i don't make sh*t up and promote religious beliefs, like you!
or is it I never will be like you? (this is just plain old common sense and logic, and MY MENSA membership)

or is it i never will be a notorious religious fanatic posting to science sites (whoops, covered that with "being like you" - sorry)

you can complain all you want, the point really is: it is (and always has been) about evidence... not "your interpretations" of it... but the reality of it

when you look through religious goggles, you see a skewed world

JVK
Sep 09, 2015
Protein-based genome-stabilizing mechanism discovered http://phys.org/n...tml#nRlv

Excerpt: "According to Garini, this protein-mediated mechanism is fundamental to the stability of life as we know it."

The epigenetic landscape is linked to the physical landscape of DNA and the stability of all organized genomes of all individuals of all living genera by RNA-mediated protein biosynthesis and degradation. As exemplified across all living genera in my 2013 review, nutrient-dependent RNA-mediated amino acid substitutions are linked to cell type differentiation. http://www.ncbi.n...24693353

The chromosomal rearrangements linked to morphological and behavioral diversity in one species of white-throated sparrow are proof that my model links atoms to ecosystems via the biophysically constrained chemistry of nutrient-dependent protein folding.

Sep 09, 2015
Protein-based genome-stabilizing mechanism discovered http://phys.org/n...tml#nRlv


Proteins are not miRNAs. What point of mine is this a response to? Are you trying to refute something we've said with this?

JVK
Sep 09, 2015
What point of mine is this a response to?


In http://www.ncbi.n...24959329 you wrote: "...James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published."

What have you said about mutations and genomic stability that might make sense to a serious scientist?

See: Exosomes Role in the Future of Medicine http://www.thermo...52065786

JVK
Sep 10, 2015
What kind of biologically uninformed science idiot claims that
Proteins are not miRNAs.
and then disappears into the wood-work like any other cockroach never to be seen or heard from again?

Sep 10, 2015
What kind of biologically uninformed science idiot claims that

Proteins are not miRNAs.


That's not a claim. That's a fact. Do you not know the difference between polypeptides and nucleic acids?

Sep 11, 2015
That's not a claim. That's a fact. Do you not know the difference between polypeptides and nucleic acids?
@Anon
either the silence is a resounding "NO"
OR
he is about to flood the site with his irrelevant posts with random quotes from articles and studies that he "interprets" and can't comprehend ... that also don't support his perspective.

PS- i bet he also throws in a pseudoscience link from his personal site at least once

in 5...
4...
3...

JVK
Sep 11, 2015
Do you not know the difference between polypeptides and nucleic acids?


Do you know anything about nutrient-dependent RNA-mediated amino acid substitutions and cell type differentiation in the context of the physiology of reproduction?

See my 2013 review and tell me what I got wrong: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Excerpt: "Nutrients are metabolized to pheromones that condition behavior in the same way that food odors condition behavior associated with food preferences. The epigenetic effects of olfactory/pheromonal input calibrate and standardize molecular mechanisms for genetically predisposed receptor-mediated changes in intracellular signaling and stochastic gene expression in GnRH neurosecretory neurons of brain tissue. For example, glucose and pheromones alter the hypothalamic secretion of GnRH and LH. A form of GnRH associated with sexual orientation in yeasts..."

Sep 11, 2015
You are so oblivious. I asked you about how miRNAs stabilize the genome and you gave me a paper about proteins that do so. Can you not understand how your responses to me have made no sense?

Copying and pasting part of your abstract is not a sensible or direct response to anything said here.

JVK
Sep 11, 2015
I asked you about how miRNAs stabilize the genome and you gave me a paper about proteins...


You know nothing about cell type differentiation. Stop complaining that I am not providing you with enough information to begin examining what is known to serious scientists about biophysically constrained RNA-mediated protein folding, which I placed into the context of atoms to ecosystems in an invited review of nutritional epigenetics.

Excerpt: "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."

Sep 12, 2015
So... Anon asks
Do you not know the difference between polypeptides and nucleic acids?
and jk replies
Do you know anything about ...
why didn't you just say NO, jk? because you sure didn't answer the question! and that was obvious! which is why Anon replied
You are so oblivious. I asked you about how miRNAs stabilize the genome and you gave me a paper about proteins that do so. Can you not understand how your responses to me have made no sense?
there is a reason i am repeating this... because when you paste SPAM/TROLLING bs like
You know nothing about cell type differentiation. Stop complaining that I am not providing you with enough information...
this is called a misdirection, redirection, red-hering, etc...
it essentially means: NO! i don't know the answer, so i will throw out a lot of techno-babble and confuse the issue!

this is why you aren't considered a serious scientist

your creationist beliefs are why you're considered a PSEUDOSCIENTIST

Sep 12, 2015
another point
You know nothing about cell type differentiation. Stop complaining that I am not providing you with enough information to begin examining what is known to serious scientists...
Anon has proven, time and again, that he knows FAR MORE about "cell type differentiation" than you do

Why is this important?
just because you think your mensa membership allows you to throw out large words (which you've proven you don't fully understand) doesn't mean that you are a serious scientist any more than owning a spell-check program makes you an editor

why are you so fearful to demonstrate knowledge here on PO in a logical discussion with ANON????

is it because ANON has already proven you a liar and wrong? or is it because your sociopathic controlling nature and Dunning-Kruger will not allow you to admit defeat, lose control or acknowledge you are wrong?

take your pick!

JVK
Sep 12, 2015
GnRH is the decapeptide that links cell type differentiation from yeasts to mammals via the nutrient-dependent pheromone-controlled physiology of RNA-mediated reproduction, which we placed into the context of molecular epigenetics in our 1996 Hormones and Behavior review.

From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

See the section on molecular epigenetics.

Sep 12, 2015
so... that's another NO

imagine that


JVK
Sep 12, 2015
Anon has proven, time and again, that he knows FAR MORE about "cell type differentiation" than you do


You have proved you are a much bigger biologically uninformed science idiot than he is.

Andrew Jones (aka anonymous_9001) wrote: http://www.scribd...s#scribd

"Despite their challenges, ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered."

Sep 12, 2015
...and?
by all means, jvk!
spell out specifics about Jones post! state, with hearty abandon, what is specifically wrong with his post!

you've never minded posting absolutely wrong quotes in the past (see Extavour, Lenski arguments) so by all means, BE VERY SPECIFIC and tell the world what is wrong with Jones comments!

thanks!

JVK
Sep 12, 2015
BE VERY SPECIFIC and tell the world what is wrong with Jones comments!


He is like every other biologically uninformed science idiot who thinks in terms of abiogenesis. He cannot link biologically-based cause and effect, but speculates that it is only a matter of time until someone else does -- in this case by discovering his ribozyme.

In my model, for comparison, microRNAs are the most likely source of "Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles" http://onlinelibr...4.f01t04

Reported as: Amazing Food Science Discovery: Edible Plants 'Talk' To Animal Cells, Promote Healing http://news360.co...0380784#

See also: Another slap in the face for evolutionary theorists http://perfumingt...eorists/

Sep 12, 2015
"He thinks in terms of..." is not a refutation of facts/reasoning that support me/contradict you. Just more nonspecific nonsense from Kohl.

In my model, for comparison, microRNAs are the most likely source of "Interspecies communication between plant and mouse gut host cells through edible plant derived exosome-like nanoparticles" http://onlinelibr...4.f01t04


This contradicts what part of Neo-Darwinism/Modern Synth.?

See also: Another slap in the face for evolutionary theorists


In the moths, there was a change in the genes themselves, not a change in the EXPRESSION of the genes. We've identified the DNA changes that occurred. The wild type to melanic type change was not because of miRNA changes nor was it due to a new olfactory receptor. The loci responsible have been identified and they are not genes coding for olfactory receptors.

http://jhered.oxf.../95/2/97

JVK
Sep 12, 2015
In the light of what not to do if you want to maximize potential growth via cell type differentiation, see. http://discoverma...-success

"It turns out the agar is the problem...

The standard recipes require mixing agar and phosphate solution before sterilizing them via intense heat. But Kamagata and his team realized this sequence creates hydrogen peroxide, which destroys most of the cells. Sterilize the ingredients separately, and voila, a roughly tenfold increase in cell survival rates."

This shows why understanding nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation is important enough to challenge evolutionary theorists who claim that natural selection leads to evolution because they don't understand anything about the biophysically constrained links from the epigenetic landscape to the physical landscape of DNA in species from microbes to man.

In the moths, there was a change in the genes...

Sep 12, 2015
"De novo gene creation is considered by evolutionary biologists to be their "holy grail." As it turns out, it's proof of God's creation manifested in every cell of every individual of every species in the context of everything currently known by serious scientists about physics, chemistry, and molecular biology."
jvkhol at:http://christiann...reation/

I found that little gem when I googled:" nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation".

Surprise! JVK is the only one to ever use his pet phrase.


Sep 12, 2015
This shows why understanding nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation is important enough to challenge evolutionary theorists


Uh, what? That has absolutely nothing to do with the validity of evolutionary theory. What is that supposed to invalidate and how?

Sep 12, 2015
Uh, what? That has absolutely nothing to do with the validity of evolutionary theory. What is that supposed to invalidate and how?


That's what JVK does when he's cornered, he changes the subject.

Sep 13, 2015
who thinks in terms of
@jk
1- this is not a refute, this is a personal opinion about his thought process
2- you are not actually being specific, nor are you showing any problems with Jones argument, let alone proving any of Jones post to be scientifically incorrect
In my model, for comparison
you still haven't given any specifics - but throwing in your model is worse
You can't prove where Jones is scientifically incorrect in his refute of your model
//perfumingt...eorists/
linking a PSEUDOSCIENCE SITE to argue a scientific point is like offering the bible as proof of a scientific point: THERE IS NO SCIENTIFIC CREDIBILITY
your perfuming site mixes creationist dogma with your interpretations of science (proven to be 100% incorrect here on PO alone)
so it is PSEUDOSCIENCE
if you can't link a reputable science site for support, you've lost the argument out the gate

PS: for linking your personal pseudoscience site-
reported

Sep 13, 2015
This shows why understanding
ok, lets be perfectly clear: so far, you've been asked to actually answer a few questions... as well as to substantiate your continued personal claims against Jones (and therefore every educated biologist or medical professional in the world)

they are:
1- PROVE Jones is scientifically incorrect (as noted above: what is specifically wrong with his post???)

2- Do you not know the difference between polypeptides and nucleic acids?

so far, considering all your posts, you have:
continued complaining
used misinformation & pseudoscience
lied about content (and not being able to prove ANY of it)
redirection/strawman/red-herring
argument from ignorance
linking pseudoscience sites with known creationist/7th day adventist dogma

what you haven't done:
provide ANY proof
answer the questions

care to actually provide proof that Jones is wrong or actually answer the questions?
or are you having a literacy problem, mensa boy?


Sep 13, 2015
@Captain Stumpy

I seriously wonder if JVK is suffering from dementia. His comments about an article on Gulf War Syndrome is a real head scratcher---and another reading comprehension fail.

http://medicalxpr...ion.html

JVK
Sep 13, 2015
That has absolutely nothing to do with the validity of evolutionary theory.


Excerpt: "...the new understanding of evolution needs to integrate what we now know about viruses and virus-host interactions which, from my own perspective, has been absolutely one of the key factors of all evolution since the emergence of cells -- well, actually even before the emergence of cells." http://www.huffin...216.html

For comparison, Andrew Jones (aka anonymous_9001) wants us to believe this: "The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection. Based on progress in current research, it is only a matter of time before that ribozyme is discovered." http://www.scribd...s#scribd

JVK
Sep 13, 2015
The onslaught of irrelevant comments made by biologically uninformed science idiots continues to prevent intelligent discussions of biologically-based cause and effect.

Others can wait for discovery of Andrew Jones' ribozyme, or look elsewhere for intelligent discussions of nutrient-dependent cell type differentiation, which is perturbed by the effect of viruses on protein folding.

Sep 13, 2015
The onslaught of irrelevant comments made by biologically uninformed science idiots continues to prevent intelligent discussions of biologically-based cause and effect.
@jk
the ONLY way this will stop is if you stop posting "biologically uninformed science idiot" comments that are only substantiated by your delusional religious belief.

the questions above are VALID and also ON TOPIC
why aren't you ANSWERING THE QUESTIONS?
they are:
1- PROVE Jones is scientifically incorrect (as noted above: what is specifically wrong with his post???)

2- Do you not know the difference between polypeptides and nucleic acids?

JVK
Sep 13, 2015
Nucleic acids link the sun's biological energy to the de novo creation of RNA and to the de novo creation of olfactory receptor genes via nutrient-dependent amino acid substitutions in the context of the physiology of reproduction.

The polypeptide, GnRH, which is a decapeptide hormone that also appears to act as a neurotransmitter, links cell type differentiation in yeasts to cell type differentiation in mammals in our model of RNA-mediated cause and effect -- published in 1996 as From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

1- PROVE Jones is scientifically incorrect (as noted above: what is specifically wrong with his post???)


How can anyone prove that a biologically uninformed science idiot is scientifically incorrect?

Sep 13, 2015
This comment has been removed by a moderator.

JVK
Sep 13, 2015
The uncertainty principle does not appear to link anything to anything else in the context of biophysically constrained nutrient-dependent protein folding chemistry, which links the light-induced de novo creation of nucleic acids to RNA-mediated cell type differentiation via metabolic and genetic networks in the context of the physiology of reproduction in all living genera.

I'm surprised that you would try to link what is not known to anything that might otherwise be discussed by intelligent scientists in the context of protein folding, which certainly is nutrient-dependent.

I can't be certain whether you (docile) are simply biologically uninformed or if you are a biologically uninformed science idiot unless you tell us how the uncertainty principle can be linked to what is known about cell type differentiation.

...Just sayin'...

Sep 13, 2015
Genome stability, the means to resist mutations and rearrangements, is covered in some detail here:

http://www.nature...dex.html

and some more here:

https://en.wikipe...tability
http://www.scienc...05001029
http://e-collecti...9-02.pdf
http://www.ncbi.n...1831843/

You claimed that miRNAs stabilize the genome.

Here's a great paper covering the functions of miRNA:

http://www.nature...40a.html

The evidence shows that miRNAs are responsible for stabilizing transcripts, but not the DNA itself like you claim.

JVK
Sep 13, 2015
The evidence shows that miRNAs are responsible for stabilizing transcripts, but not the DNA itself like you claim.


How did you suddenly become an expert on what "the evidence" shows, or anything that you claim I claimed?

http://www.ncbi.n...24693353
I wrote: "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."

http://www.ncbi.n...4049134/ You wrote: "James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published."

Sep 13, 2015
How can anyone prove that a biologically uninformed science idiot is scientifically incorrect?
@jk
you do it the same way that Jones, Myers and everyone else has proven you to be incorrect and scientifically illiterate:
you prove it by proving that he said something that is factually incorrect and not supported by evidence, using clear concise language that is typical for Biology, attach links that support your claims, and then show where the fallacious comments are distinctly wrong...

problem is... you cannot do that!
the reason you can't do it is because:
creationist dogma is RELIGION, not science
your evidence draws upon creationist dogma
you don't understand BIOLOGY
you refuse to accept the lexicon

these things are not assumptions about your posts, they're proven... and i can link your continued fallacious comments after being shown evidence that directly refutes you

IOW- you lie, and it can be proven
thus, your credibility is negligible

Sep 13, 2015
How did you suddenly become an expert on what "the evidence" shows, or anything that you claim I claimed?
because he has continued to refute your religions claims on PO giving him experience

he is not making anything up... you are the one who posts dogma over science
and considering he is actually educated in biology whereas you flunked out of college because you don't like definitions and can't accept that religion is not science... then he is FAR more qualified to post about evidence and biology than you are

that is evident in your 100% fail rate interpreting other studies
wanna talk about that again?

Sep 14, 2015
I'm not claiming anything about what you claim. It's easy enough to show you using EVIDENCE:

Nutrient-dependent microRNAs stabilize organized genomes


Those are you exact words. The link I provided demonstrates what microRNAs actually do. Nothing in it suggests they stabilize the genome. There are proteins that act in that manner, like histones, but not microRNAs. You're misrepresenting their function.

JVK
Sep 14, 2015
The link I provided demonstrates what microRNAs actually do.


You know nothing about the microRNA/messenger RNA balance; about cell type differentiation; or about how the stability of organized genomes is maintained.

Stop telling others that I am misrepresenting everything known about nutrient-dependent biologically-based cause and effect, or tell them how your mutagenesis experiments help to explain anything to intelligent, serious scientists.

See also: http://rna-mediat...-dnarna/

Sep 14, 2015
You know nothing about the microRNA/messenger RNA balance; about cell type differentiation; or about how the stability of organized genomes is maintained.


You can shout it until your voice is hoarse. It doesn't make it true. The literature does not support you and that's the only thing that matters.

JVK
Sep 14, 2015
The literature does not support you and that's the only thing that matters.


The literature that is immediately available in results of a google search for "RNA mediated' support everything I have ever claimed since the time we published our 1996 review in Hormones and Behavior.

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

and these search results: https://www.googl...mediated

Sep 14, 2015
What in particular supports your specific claim that miRNAs stabilize the genome? I've provided very clear evidence to the contrary of that claim.

Sep 14, 2015
//rna-mediat...-dnarna/
PSEUDOSCIENCE PHISHING SITE
as long as you use this link and can't actually find reputable science journals to post to, you will always be MISREPRESENTING SCIENCE
your personally owned site mixes creationist dogma with science, therefore it PROMOTES PSEUDOSCIENCE
reported
Stop telling others that I am misrepresenting
WHY?
it's TRUE... you misrepresent it! you also blatantly LIE about it!(see above)
you link PSEUDOSCIENCE site links to support your claims because you can't find LEGITIMATE SCIENCE that promotes your religion
THAT IS MISREPRESENTATION

AKA- FRAUD

repeating a lie doesn't make it any more true than the first time you said it
things don't work like that in science!

it doesn't work like that any more than calling yourself POPE because you've heard of the leaning tower of Pisa would work

Sep 14, 2015
Nucleic acids link the sun's biological energy to the de novo creation of RNA and to the de novo creation of olfactory receptor genes via nutrient-dependent amino acid substitutions in the context of the physiology of reproduction.

To start, there is no such thing as a specific "biological energy"...
There is just radiation energy, translated to heat (within our atmospheric envelope), causing diverse actions/reactions/combinations of the various elements collected on little sphere.
"Life" is simply a result of those diverse actions/reactions/combinations...
You seem to miss the chemistry that occurred prior to the "biology" that we now experience.
Guess that makes you "physics and chemistry" uninformed...
Thusly making you biologically uninformed"
Hmmmm...

JVK
Sep 14, 2015
The light-induced de novo creation of nucleic acids links the sun's biological energy to RNA-mediated protein biosynthesis and degradation during thermodynamic cycles linked to cell type differentiation in all individuals of all living genera via their physiology of reproduction and fixation of amino acid substitutions.

That fact can be placed into the context of an atoms to ecosystems model
http://74g2t4f911...tion.jpg

The model links the anti-entropic epigenetic effects of sun's biological energy to cell type differentiation in all living genera.

See also: http://www.thebes...terview/

Excerpt: "Recently, summarizing your book Science Set Free at a TED talk, you addressed the problem of dogmatic materialism in science, only to have your TED talk banned because of pressure from, ahem, dogmatic materialists."

JVK
Sep 14, 2015
You seem to miss the chemistry that occurred prior to the "biology" that we now experience. Guess that makes you "physics and chemistry" uninformed...
Thusly making you biologically uninformed"


You seem to be another biologically uninformed science idiot who has never examine my publication or presentation history.

See, for examaple, this 5.5 minute video representation of "Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)" http://youtu.be/DbH_Rj9U524

Sep 14, 2015
"Sheldrake questions conservation of energy; he calls it a "standard scientific dogma",[75]:337 says that perpetual motion devices and inedia should be investigated as possible phenomena,[75]:72–73 and has stated that "the evidence for energy conservation in living organisms is weak".[75]:83 He argues in favour of alternative medicine and psychic phenomena,"

"he stated that minds are not confined to brains and remarks that "liberating minds from confinement in heads is like being released from prison".[75]:229 He suggests that DNA is insufficient to explain inheritance, and that inheritance of form and behaviour is mediated through morphic resonance.[75]:157–186 He also promotes morphic resonance in broader fashion as an explanation for other phenomena such as memory"
https://en.wikipe...heldrake

@JVK

Your link:http://www.thebes...terview/ isn't surprising, you and Sheldrake are both pseudoscience cranks.

JVK
Sep 15, 2015
Is anyone who does not support the pseudoscientific nonsense of neo-Darwinian theory not a pseudoscience crank -- in your mind?

"Morphic resonance" is the basis for works that link olfaction to consciousness via examples in flies and octopuses

Sep 15, 2015
See, for examaple, this 5.5 minute video
[sic] youtube is NOT a peer reviewed scientific journal, let alone reputable for scientific evidence
this is like linking a snoopy cartoon to support proof of talking dogs
neo-Darwinian
we've already been thru this, moron- just because you found a new word that you think describes something doesn't mean it is accurate: this is like calling you a "serious scientist"... you are neither "serious" nor a "scientist", and that is proven because you fail to do ANY research (Conservation of Energy is a scientific LAW, moron https://en.wikipe...f_energy ), you can't interpret what is actually science (Lenski, Extavour, et al), you promote creationist religion (PSEUDOSCIENCE) and you have Dunning-Kruger

those things combined prove you are about as serious a scientist is Scooby-Doo is...
and almost as intelligent, too (although i hate to slight Scooby with comparison to you)

JVK
Sep 15, 2015
See also: "Guidelines for the Care and Welfare of Cephalopods in Research –A consensus based on an initiative by CephRes, FELASA and the Boyd Group"

http://lan.sagepu...abstract

Citations to Anna Di Cosmo's works include:

Cephalopods in neuroscience: Regulations, Research and the 3Rs. Invert Neurosci 2014; 14: 13–36.

Dose-dependent effects of the clinical anesthetic isoflurane on Octopus vulgaris: A contribution to cephalopod welfare. J Aquat Anim Health 2014; 26: 285–294.

Conservative nature of oestradiol signalling pathways in the brain lobes of Octopus vulgaris involved in reproduction, learning and motor coordination. J Neuroendocrinol 2012; 24: 275–284.

The sequencing of the octopus genome links the conserved molecular mechanisms of biophysically constrained nutrient-dependent RNA-mediated cell type differentiation from marine invertebrates to insects and all vertebrates via olfaction and pheromones.

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