The pronoun 'I' is becoming obsolete

August 19, 2015 by David Salisbury, Vanderbilt University
The pronoun ‘I’ is becoming obsolete
Tree of life created with bacterial cultures. Credit: Robert Brucker / Harvard University

Don't look now, but the pronoun "I" is becoming obsolete.

Recent microbiological research has shown that thinking of plants and animals, including humans, as autonomous individuals is a serious over-simplification.

A series of groundbreaking studies have revealed that what we have always thought of as individuals are actually "biomolecular networks" that consist of visible hosts plus millions of invisible that have a significant effect on how the host develops, the diseases it catches, how it behaves and possibly even its social interactions.

"It's a case of the whole being greater than the sum of its parts," said Seth Bordenstein, associate professor of biological sciences at Vanderbilt University, who has contributed to the body of scientific knowledge that is pointing to the conclusion that symbiotic microbes play a fundamental role in virtually all aspects of plant and animal biology, including the origin of new species.

In this case, the parts are the host and its genome plus the thousands of different species of bacteria living in or on the host, along with all their genomes, collectively known as the microbiome.

(The host is something like the tip of the iceberg while the bacteria are like the part of the iceberg that is underwater: Nine out of every 10 cells in plant and animal bodies are bacterial. But bacterial cells are so much smaller than host cells that they have generally gone unnoticed.)

Microbiologists have coined new terms for these collective entities – holobiont – and for their genomes – hologenome. "These terms are needed to define the assemblage of organisms that makes up the so-called individual," said Bordenstein.

In the article Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes published online Aug. 18 in the open access journal PLOS Biology, Bordenstein and his colleague Kevin Theis from the University of Michigan take the general concepts involved in this new paradigm and break them down into underlying principles that apply to the entire field of biology.

They make specific and refutable predictions based on these principles and call for other biologists to test them theoretically and experimentally.

"One of the basic expectations from this conceptual framework is that animal and plant experiments that do not account for what is happening at the microbiological level will be incomplete and, in some cases, will be misleading as well," said Bordenstein.

The first principle they advance is that holobionts and hologenomes are fundamental units of biological organization.

Another is that evolutionary forces such as natural selection and drift may act on the hologenome not just on the genome. So mutations in the microbiome that affect the fitness of a holobiont are just as important as mutations in the host's genome. However, they argue that this does not change the basic rules of evolution but simply upgrades the types of biological units that the rules may act upon.

Although it does not change the basic rules of evolution, holobionts do have a way to respond to environmental challenges that is not available to individual organisms: They can alter the composition of their bacterial communities. For example, if a holobiont is attacked by a pathogen that the host cannot defend against, another symbiont may fulfill the job by manufacturing a toxin that can kill the invader. In this light, the microbes are as much part of the holobiont immune system as the host immune genes themselves.

According to Bordenstein, these ideas are gaining acceptance in the microbiology community. At the American Society of Microbiology General Meeting in June, he convened the inaugural session on "Holobionts and Their Hologenomes" and ASM's flagship journal mBio plans to publish a special issue on the topic in the coming year. However, adoption of these ideas has been slower in other fields.

"Currently, the field of biology has reached an inflection point. The silos of microbiology, zoology and botany are breaking down and we hope that this framework will help further unify these fields," said Bordenstein.

Not only will this powerful holistic approach affect the basic but it also is likely to impact the practice of personalized medicine as well, Bordenstein said.

Take the missing heritability problem, for example. Although genome-wide studies have provided valuable insights into the genetic basis of a number of simple diseases, they have only found a small portion of the genetic causes of a number of more complex conditions such as autoimmune and metabolic diseases. These may in part be "missing" because the genetic factors that cause them are in the microbiome, he pointed out.

"Instead of being so 'germophobic,' we need to accept the fact that we live in and benefit from a microbial world. We are as much an environment for microbes as microbes are for us," said Bordenstein.

Explore further: Could bacterial hitchhikers influence formation of new host species?

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118 comments

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Steve 200mph Cruiz
4.6 / 5 (9) Aug 19, 2015
It's hard to define what an individual really is.
Not only are we partially bacterial communities, 10% of our DNA is ancient viral DNA, very few of the cells we are born with are still parts of us (we reconstitute ourselves from our environment), and our personalities are created from all the people we've met over our lives.
I think all of these things are important to realize if you want to live healthily.
antigoracle
2 / 5 (4) Aug 19, 2015
We are just dwellings that bacteria created to sustain them.
verkle
Aug 19, 2015
This comment has been removed by a moderator.
DeltaX
1 / 5 (1) Aug 19, 2015
Where do the bacteria come from. Does the Mother pass bacteria to the embryo? Does most of the bacteria come from the environment? If it's the latter does my son have a point in not cleaning is room?
NIPSZX
not rated yet Aug 19, 2015
Most of the bacteria that breeds with you throughout your life comes from your very first breath when you exit the womb.
cgsperling
2.3 / 5 (3) Aug 19, 2015
We are Groot.
Egleton
not rated yet Aug 20, 2015
Help! I'm trapped in the web of life.
ArnoldasT
1 / 5 (1) Aug 20, 2015
what if we truly evolved only as a space for microbes and by microbes, but later in evolution by unpredicted mechanism gained an ego and became self-centered.
Da Schneib
5 / 5 (2) Aug 20, 2015
Well, perhaps the microbiological definition of the pronoun "I" might be. Certainly the physiological and most certainly the mental/emotional/physical/intellectual entity "I" as human intelligences define it isn't.

While it is obviously necessary that someone blow the Second Trombone in the orchestra, it's equally obvious that they're not the most "important" piece, though there may be parts of the symphony you can only "get" if you have a Second Trombone. It's nice that the Second Trombone has some important parts. But the First Violin is a lot more likely to be famous. And that leaves alone the Conductor.
JVK
1 / 5 (6) Aug 20, 2015
http://dx.doi.org...8-134304 "Quorum sensing allows bacteria to synchronize the gene expression of the group, and thus act in unison."

Gene expression is nutrient-dependent and pheromone-controlled via the physiology of reproduction.

http://medicalxpr...une.html
"...scientists found that in three-quarters of the measurements, nonheritable influences—such as previous microbial or toxic exposures, vaccinations, diet and dental hygiene—trumped heritable ones when it came to accounting for differences within a pair of twins."

It is interesting to see these facts repackaged and presented as if serious scientists did not know how cell type differentiation occurs in the context of metabolic networks and genetic networks that link the epigenetic landscape to the physical landscape of DNA in every species on the planet via symbiosis -- until we cause the extinction of other species.
JVK
1 / 5 (6) Aug 20, 2015

See also: Beneficial microbes kill beneficial mutations http://rna-mediat...tations/

https://www.youtu...AqvOBusU

Environment, not genes, dictates human immune variation, research finds
http://medicalxpr...une.html
betterexists
1 / 5 (2) Aug 20, 2015
Beachgoers in West are full of MarineShit! You can see those germs when they are walking!
No Healthy deal there.
thingumbobesquire
1 / 5 (1) Aug 20, 2015
One wonders what compels such ridiculous and erroneous leaps of logic that lead to this headline? Soon we will start hearing "my microbiome made me do it."
betterexists
1 / 5 (2) Aug 20, 2015
So, When they sequence the genome, they should provide categories of DNA Present in the Sample under VARIOUS CATEGORIES! Snakes, Scorpions, Lizards in the Body, WoW!
JVK
1 / 5 (6) Aug 20, 2015
"my microbiome made me do it."

The distinctions are subtle between us and other animals. It appears that only a single amino acid substitutions in our cell types might someday lead to the understanding of how to prevent us from eating ourselves to death. It could be the Val158Met substitution, for example:

http://link.sprin...4-0895-5
Captain Stumpy
5 / 5 (6) Aug 20, 2015
See also: Beneficial microbes kill beneficial mutations http://rna-mediat...tations/
THIS IS A PSEUDOSCIENCE SITE LINK which promotes creationist/7th day adventist non-scientific religious tenets, not science

it is also a personally owned PHISHING site
spam and pseudoscience from jk, how original
JVK
1 / 5 (5) Aug 20, 2015
See also: https://www.quant...es-code/

People like SSgt Stumpy, who I thought was banned from participation here, don't like the fact that young earth creationists already addressed de novo creation of genes and virus-driven pathology.

See: http://www.icr.or...cle/8661 Viruses are perceived by cells to be a threat, which is why the innate immune system of all individuals in all genera tries to protect organized genomes. This suggests:

"...viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, "The most parsimonious answer is: the RNA viruses got their genes from their hosts."6

Evolutionary theorists refuse to consider the most parsimonious answer to life and death questions. Even if they believe in God, they attribute things to random events in attempts to keep their beliefs contained by the pseudoscientific nonsense of their theories.
Captain Stumpy
4.8 / 5 (6) Aug 20, 2015
who I thought was banned from participation here
i never thought you would be banned... you have protection from several people already
i do think you SHOULD be banned for continually violating the rules and publishing PHISHING links, SPAM, PSEUDOSCIENCE, and more, but that is something else entirely
don't like the fact that young earth creationists already addressed de novo creation of genes and virus-driven pathology
the ONLY thing young earth creationists have uncovered is how to make an IDIOT out of someone, because they're a RELIGION

it is NOT SCIENCE

where are the REPUTABLE PEER REVIEWED PUBLICATIONS ascribed to this finding?
where is the reputable science?
is it in SCIENCEMAG? or just in your bible and on your PSEUDOSCIENCE links?

like i said: YOU PROMOTE PSEUDOSCIENCE, not science
always have, always will
JVK
1 / 5 (5) Aug 20, 2015
Scientists Map 5,000 New Ocean Viruses
https://www.quant...viruses/

How Structure Arose in the Primordial Soup
http://www.scient...20150519

https://www.quant...of-life/

Excerpt: Each variant adapted to suit a different ecological niche. But Blair Hedges, a biologist at Temple University in Philadelphia, has proposed a provocative alternative: Adaptation had little to do with it. It was simply a matter of chance and time.

These articles lack continuity / scientific integrity. Ecological variation is linked to ecological adaptations, which are prevented by viruses and facilitated by the nutrient-dependent physiology of reproduction. That is what serious scientists have shown. It doesn't matter what biologically uniformed science idiots claim. Experimental evidence supports what serious scientists know.
Dr_ Rock
4.2 / 5 (10) Aug 21, 2015
"...viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, "The most parsimonious answer is: the RNA viruses got their genes from their hosts." Evolutionary theorists refuse to consider the most parsimonious answer to life and death questions. Even if they believe in God, they attribute things to random events in attempts to keep their beliefs contained by the pseudoscientific nonsense of their theories.


This answer is not the most parsimonious one but merely the one that fulfills the desire of the questioner, that life was designed. Peter Borger is violating his duty to commit to scientific integrity and to not abuse his PhD title for promoting pseudoscientific nonsense. The alleged paradox between the 50,000 years of time in which all the extant species have diverged from a common ancestor and the millions of years that separates different animal species can be ascribed to .....
Dr_ Rock
4.2 / 5 (10) Aug 21, 2015
[cont'd]
....saturation of the type of molecular clock that was used. The virus families diverged much longer ago than that, but the dating method used is only reliable back to 50,000 years bp. Any divergence older than that results in a saturated molecular clock. Borger is wilfully misrepresenting data. Anyone who contributes to the Journal of Creation should be stripped of his PhD title imho.
JVK
1 / 5 (5) Aug 21, 2015
Where did the virus families come from before they diverged?

That is what Borger addressed, and it is the question that you just ignored.
JVK
1 / 5 (5) Aug 21, 2015
See also:

http://cancerres..../16/3203
Excerpt: "This paradigm shift in cancer cell biology and mitochondrial genetics, concerning mitochondrial movement between cells to meet bioenergetic needs, not only adds another layer of plasticity to the armory of cancer cells to correct damaged mitochondria..."

The paradigm shift also attests to the likelihood that what theorists have claimed about viruses is pseudoscientific nonsense that has prevented progress towards prevention of cancer and reduced the likelihood of effective treatments.

Re: ....saturation of the type of molecular clock that was used.

Is electrostatic force considered when calibration of the molecular clock(s) is performed?
JAVS
3 / 5 (4) Aug 21, 2015
Although we have more bacteria than our own cells in the body, the actual biomass is quite small - less than ten percent by weight.
In the long process of evolution, no doubt bacterial genes have been transmitted to our own genome (long, unlikely circuitous route, but demonstrated in other species such as fish), and we've probably gotten genes from species we've consumed as well. Why are so many genes so similar or identical in pigs and humans?
As for viruses, they're no doubt remnants of proto-life (many with RNA genomes), and they've simply been along for the ride for the past few billions of years. They're wonderful carriers of genome fragments that help mix and match genomes between and among different species.
Dr_ Rock
4.2 / 5 (10) Aug 21, 2015
Where did the virus families come from before they diverged?
That is what Borger addressed, and it is the question that you just ignored.


Another cheap creationist trick. Implying somebody is wilfully ignoring questions to mask caveats in their knowledge. "Human endogenous retroviruses are believed to be the legacy of ancient germ cell infections by exogenous retroviruses, dating from 60 million years ago to the present." (Ryan, 2004). A more useful working hypothesis, backed up by sequencing data, than the wild suggestion of Borger that RNA viruses 'got their genes from their hosts'.
Dr_ Rock
4.2 / 5 (10) Aug 21, 2015
[cont'd]
Continuing in his article with: "In other words, mammalian viruses may not have existed at all before the Curse, but after mankind's sin may have been allowed to develop from DNA sequence already present in the now-fallen people and animals of the earth. Again, cutting-edge genome research confirms the Genesis account of origins."

Kindergarten stories do not contribute to scientific debate.
Dr_ Rock
4.1 / 5 (9) Aug 21, 2015
Re: ....saturation of the type of molecular clock that was used.

Is electrostatic force considered when calibration of the molecular clock(s) is performed?

Do you know what a molecular clock is and how it's being used? If not, I'd suggest you go ride your motorbike. You're wasting bandwidth.
JVK
1 / 5 (5) Aug 21, 2015
I know how important calibration is. If calibration of the molecular clock does not include any aspect of the Laws of Physics, which appear to include a "fifth force," your faith in pseudoscientific nonsense in the context of the fossil record exemplifies your religious belief in pseudoscientific nonsense.

https://en.wikipe...ar_clock "The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation. The molecular data used for such calculations are usually nucleotide sequences for DNA or amino acid sequences for proteins. It is sometimes called a gene clock or evolutionary clock."

Anyone who refers to it as an "evolutionary clock" is probably a theorist, not a serious scientist.
JVK
1 / 5 (5) Aug 21, 2015
http://www.newswi.../627856/ "I've always been interested in speciation and how species form, but this is a whole different mechanism, that light can influence speciation," Ellis says. "I thought it was just fabulous."

I think that comments like this are fabulous representations of what is currently known to creationists who are likely to calibrate their clocks in the context of the laws of physics, which link the speed of light on contact with water to biodiversity or the lack of biodiversity in bacteria that live in ocean sediments (i.e., where the sun don't shine).

Apparently, the bacteria have not set their clocks forward or backwards to fit with what some people know about "daylight savings time," which links the sun's biological energy to circadian rhythms via internal clocks that are calibrated by light -- except in organisms that REPORTEDLY show no sign of evolutionary changes during the past ~2 billion years.
JVK
1 / 5 (5) Aug 21, 2015
See also: http://www.the-sc...ewiring/ for comparison to http://phys.org/n...ars.html

Remember to set your molecular clock forward by 2 billion years to account for the time missing from current theories about evolution that did not consider the role of viruses. Then, try to use your "clock" and your intelligence to explain the re-evolution of the bacterial flagellum in 4 days. If your explanation to yourself of how both issues can be addressed by intelligent researchers makes sense, please join those who are Combating Evolution to Fight Disease http://www.scienc...88.short

If your explanation makes sense to you in the context of the pseudoscientific nonsense touted by evolutionary theorists, keep promoting illness and suffering. It's what biologically uninformed science idiots have always done. They are like mushrooms.
JVK
1 / 5 (5) Aug 21, 2015
Mushrooms grow in the dark in decaying biomass akin to fecal material. Both have unpleasant odors, like those associated with diseases and death. But perhaps that is just a correlation. It may not accurately represent what is known to serious scientists about the nutrient-dependent energy that all organisms must continue to acquire for RNA-mediated cell type differentiation and species diversity.

See also: http://medicalxpr...lth.html
Dr_ Rock
4.3 / 5 (12) Aug 21, 2015
I think that comments like this are fabulous representations of what is currently known to creationists who are likely to calibrate their clocks in the context of the laws of physics, which link the speed of light on contact with water to biodiversity or the lack of biodiversity in bacteria that live in ocean sediments (i.e., where the sun don't shine).

Word salads that mean shit. Who do you think you're talking to here at phys.org? And don't give us your track record again, 'cause we all know you're just a former technician who has demonstrated again and again to not comprehend basic biology concepts. Jumbling molecular clocks with circadian clocks.. What a laugh. Creationists definitely need calibration of their clocks... Come again, when did God create Earth?
Dr_ Rock
4.2 / 5 (10) Aug 21, 2015
Then, try to use your "clock" and your intelligence to explain the re-evolution of the bacterial flagellum in 4 days."


It is being explained in the article. Start by actually reading the articles you're referring to. That is, if you can understand the contents...
JVK
1 / 5 (5) Aug 21, 2015
It is being explained in the article.


That seems unlikely. Re-evolution occurred in a single species left to grow in a culture "over-the-weekend." Growth is nutrient-dependent and pheromone-controlled.

Who do you think you're talking to here at phys.org?


Anonymous fools.
Dr_ Rock
4.3 / 5 (11) Aug 21, 2015
http://www.scient...tionist/
"Time and again, science has shown that methodological naturalism can push back ignorance, finding increasingly detailed and informative answers to mysteries that once seemed impenetrable: the nature of light, the causes of disease, how the brain works. Evolution is doing the same with the riddle of how the living world took shape. Creationism, by any name, adds nothing of intellectual value to the effort."

JVK, a voice crying in the wilderness, surrounded by anonymous fools.
Bongstar420
5 / 5 (1) Aug 21, 2015
Just because I am half microbe doesn't change the meaning of I.

I am the output of a brain of certain configurations. That is all
JVK
1 / 5 (5) Aug 21, 2015
JVK, a voice crying in the wilderness...


Not really. Just ahead of my time. See:

An alternative splicing event amplifies evolutionary differences between vertebrates
http://www.scienc...abstract

Anonymous fools; still killing us all with their pseudoscientific nonsense, despite our 1996 review published in Hormones and Behavior. See: "From Fertilization to Adult Sexual Behavior" http://www.hawaii...ion.html

In our section on molecular epigenetics, we wrote:
"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans... That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes."
Da Schneib
5 / 5 (6) Aug 21, 2015
"...viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, "The most parsimonious answer is: the RNA viruses got their genes from their hosts." Evolutionary theorists refuse to consider the most parsimonious answer to life and death questions.
There's nothing non-evolutionary about supposing that viral DNA sequences were created by disruption of the original cells' DNA, though this has never been observed while modern technology was available to evaluate it.

It's not a matter of "refuse;" it's a matter of there not being evidence that this has ever happened, and there being many more effective questions to ask and answer before we get around to this one.

Epigenetics is a very young field, and exogenetics (if I may coin a term) is pretty much nonexistent at this time, not due to dismissal, but to lack of data and lack of talent to obtain it. Certainly, however, this is no proof of jebus.
Da Schneib
5 / 5 (5) Aug 21, 2015
Then, try to use your "clock" and your intelligence to explain the re-evolution of the bacterial flagellum in 4 days."


It is being explained in the article. Start by actually reading the articles you're referring to. That is, if you can understand the contents...
Don't get too frustrated. There are many here who understand you. Use the "ignore" button revealed by hovering at the lower right of disagreeable posts liberally. Personally I am enjoying your contributions.
JVK
1 / 5 (5) Aug 21, 2015
There's nothing non-evolutionary about supposing that viral DNA sequences were created by disruption of the original cells' DNA...


Viruses perturb protein folding, which is why they have consistently been linked to pathology during the past 30 years by all serious scientists. Pathology is non-evolutionary except when it is biophysically constrained by nutrient-dependent RNA-mediated protein folding chemistry.

Epigenetics is a very young field...


It is much older than the 4 days it took for the bacterial flagellum to "re-evolve" via its nutrient-dependent pheromone-controlled physiology of reproduction.

I mentioned our 1996 review, but see also: Beyond neo-Darwinism—an epigenetic approach to evolution (1979) http://www.scienc...79901917
Captain Stumpy
5 / 5 (5) Aug 21, 2015
@Dr_Rock:
if you have issues with reading the ScienceMag study (that the pseudoscience creationist jk linked: http://www.scienc...868.full ), please feel free to contact me at http://www.sciforums.com

my profile is Truck Captain Stumpy, and if you message me, i can likely get you a copy so that you can specifically address the creationist BS he touts above.
PEACE

the bacterial flagellum to "re-evolve"
@jk
this study was already discussed with you jk, and you were shown to be a liar and mistaken in your interpretations of what was going on then... just like you lied/misinterpreted just about every study who's author contacted us back, from Dr. Extavour to Lenski. still batting 100% fail rate concerning interpretations of other work i see...

shall i contact the authors again?

JVK
1 / 5 (5) Aug 21, 2015

...shall i contact the authors again?


Yes, ask them about ignoring the role of viruses in cell type differentiation while claiming that species evolved.

Then, ask them to explain how the flagellum re-evolved in 4 days.

Also, see PZ Myers claims now that the octopus genome has been sequenced. He is completely unaware of the obvious links from viruses in the ocean to nutrient-dependent pheromone-controlled RNA-mediated cell type differentiation in octopuses with organized genomes that link ecological variation to ecological adaptation via olfaction in marine invertebrates to insects, and all vertebrates (like the white-throated sparrows).

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)."
Captain Stumpy
5 / 5 (7) Aug 22, 2015
Yes, ask them about...
@jk
we went through this already...
you already know what they will say... the same thing that almost all the other authors say: they ignore pseudoscience creationists like you because you are talking out of your RELIGION, not about science... much like your proselytizing here

so quit posting PSEUDOSCIENCE (like all mutations perturb protein folding, except, of course, your special mutations in your model somehow, or your quote "I've learned enough about physics to link the speed of light on contact with water to the de novo creation of amino acids" despite there not being a Nobel on your desk....!!!!)

then maybe you can get someone to take you seriously

also:
your link does NOT go to a Myers anything, NOR does it open a study that can be validated, so your claims are worthless unless you can provide access to said study
JVK
1 / 5 (4) Aug 22, 2015
VALIDATE THIS!

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

"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..."
http://www.huffin...216.html

"...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."
http://www.huffin...450.html
JVK
1 / 5 (4) Aug 22, 2015
Re: "I've learned enough about physics to link the speed of light..."

See: What is Life?: The Intellectual Pertinence of Erwin Schrödinger
1ZyEVInuD4f6yAS3wYGoDw&usg=AFQjCNEyM8UKB2r-7t8WyxJNGUI2x6oiBw&sig2=pccVuIyPONpBxZlSKAnm6g&bvm=bv.80642063,d.aWw&cad=rja

Excerpt: "Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of 'negative entropy' the sunlight)"

Schrodinger linked quantum physics to quantum biology. Others need only recognize that all biomass on earth arose in the context of what was made possible by the creation of light and water. Light is the anti-entropic life force.
Captain Stumpy
5 / 5 (5) Aug 22, 2015
@jk
1- the huffington post is NOT a scientific journal, so it is no wonder that you are linking... much like your links to creationist sites or your own personal creationist pseudoscience site
2- just because you failed out of college and can't comprehend the lexicon of the Biological and Medical field, doesn't mean no one else can
3- the terms within a field (lexicon/nomenclature) are used for clear, concise communication: something which you demonstrate NO ABILITY of, above or elsewhere

Schrodinger linked...
you are NOT schrodinger, nor have you linked the speed of light to the de novo creation of ANYTHING

this is perfectly clear in the journals in that you've not been able to produce ANY kind of valid evidence other than conjecture, speculations and your insistence that you did it... those claims, like any other lie you post, can be dismissed out of hand due to lack of evidence and considered pseudoscience, much like most of your posts
Captain Stumpy
5 / 5 (5) Aug 22, 2015
@jk cont'd
See: What is Life?: The Intellectual Pertinence of Erwin Schrödinger
just how, exactly, is a book written by a Professor of Literature at Stanford University about Schrodinger supposed to be evidence of your claims?

You will have to be very specific, because your "quote" (worthless without a valid reference source to review) does not, in ANY way, show that you are correct, nor does it validate your claims of
I've learned enough about physics to link the speed of light on contact with water to the de novo creation of amino acids
so, again, your "validate this" claim is proven to be nothing more than distraction from actual science and personal delusional belief based upon your narcissistic Dunning Kruger.

you have FAILED to validate anything!

you are the most prolific trolling creationist pseudoscience avolyte on PO... at least you can comfort yourself in knowing you will never be banned because you've got protection high up
JVK
1 / 5 (4) Aug 22, 2015
I wrote:
Light is the anti-entropic life force.


SSgt Stumpy (USAF ret, E-5) wrote:
you have FAILED to validate anything!


Before becoming a mushroom-like creature that lives on degrading compost fed to him by evolutionary theorists, he may never have been exposed to the light of ecological adaptation. However, expecting me to validate the fact that the light comes from the sun takes me out of my area of expertise.

All I can do is cite the literature; I cannot prove that all of creation is light- and water-dependent.
Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism
http://dx.doi.org...hem.2202

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

http://dx.doi.org....0135405
"The effect of any amino acid substitution can vary greatly..."
JVK
1 / 5 (4) Aug 22, 2015
Free pdf of book
http://whatislife...Life.pdf

Excerpt: "Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of 'negative entropy' the sunlight)"

Schrodinger couldn't prove that, either.
Captain Stumpy
5 / 5 (5) Aug 22, 2015
I wrote: Light is the anti-entropic life force
And yet again, how does this, in any way, prove that you've
learned enough about physics to link the speed of light on contact with water to the de novo creation of amino acids
it doesn't. it is what is called a "claim" (AKA conjecture without evidence) and can be taken to mean that, because you have no evidence to prove your statement, meaning you cannot prove to have "link[ed] the speed of light on contact with water to the de novo creation of amino acids", then we can see, by your comments and posts above that you are:
1- lying
2- fraudulently claiming something that cannot be proven, thus
3- posting pseudoscience

where is your study that proves your claim?
Where is your validation of said studies?
where is ANYTHING akin to scientific evidence proving anything you are promoting?

creationists/you (JVK) are PSEUDOSCIENCE and RELIGIOUS fundamentalists, not scientists
Captain Stumpy
5 / 5 (4) Aug 22, 2015
SSgt Stumpy (USAF ret, E-5)
@jk
and again, this has already been addressed
it is telling that you cannot read well enough to actually produce even validation of this single claim, making you even more fraudulent and proving that you are not capable of comprehending even the basic communications between people.

this is, by far, one of the most telling and descriptive posts you've done, showing that not only are you incapable of providing scientific evidence for your claims, but that you can't even comprehend basic english, nor communicate without fraudulently making statements that are known lies and blatantly so

thanks for continuing to prove your credibility is equivalent to any other pseudoscience troll here
Captain Stumpy
5 / 5 (5) Aug 22, 2015
also note that
ecological adaptation
is a part of evolution, or hadn't you heard in your mushroom state?
http://www.biolog...aptation

https://en.wikipe...aptation

also note, nowhere did i ask you to
validate the fact that the light comes from the sun takes me out of my area of expertise
for starters, even in your "supposed" expertise, you cannot actually make sense
see your model and how it uses MUTATIONS to accomplish what you are denigrating as "perturbed protein folding"... IOW- you are anti-mutations, but publish a model that requires them

then you make a claim
I've learned enough about physics to link the speed of light on contact with water to the de novo creation of amino acids
and continue to discuss it but somehow you cannot even produce evidence or proof.... that is not asking to validate the source of sunlight, it is asking you to validate your CLAIM

care to try again?
machapungo
4.4 / 5 (7) Aug 22, 2015
WOW!!! What an argument between the forces of superstition and rational thought!!!!!

For what its worth: I stand with rational thought.
I like what Dr rock and Captain stumpy say. As a newbie to this thread, I don't know what JVK's
history is but if he supports religious BS, I stand with the forces against him. Hey JVK, are U a Jesus junkie?
JVK
1 / 5 (4) Aug 22, 2015
http://dx.doi.org....0135405

Excerpt: "The effect of any amino acid substitution can vary greatly depending on its location in the protein structure. Thus, site-specific amino acid substitutions that do not confer structural changes in the protein can affect protein function, such as the changes in binding sites. Some amino acid changes in mt subunits cause inefficiencies in the electron transfer chain system, contributing to the increase of reactive oxygen species (ROS) that can lead to the disruption of OXPHOS [3–5]. On the other hand, the amino acid substitutions can also improve or decrease aerobic capacity and be linked with life history traits and environmental adaptation [6–8]."

The sequencing of the octopus genome helps serious scientists to understand how the fixation of RNA-mediated amino acid substitutions in the context of the nutrient-dependent physiology of reproduction links ecological variation to ecological adaptation.
JVK
1 / 5 (5) Aug 22, 2015
Hey JVK, are U a Jesus junkie?


Thanks for asking.

I am a medical laboratory scientist who is certified with the American Society for Clinical Pathology (ASCP). My most recent published work is Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

I linked nutrient-dependent amino acid substitutions to cell type differentiation in all cell types of all individuals of all living genera and provided examples of how genomes are organized in the context of the physiology of reproduction. Viruses perturb protein folding, which is why they are consistently linked to pathology -- not to the evolution of any species.

The fact that young earth creationists reported this in the context of what is currently known about cell type differentiation before Eugene Koonin reported that the role of viruses had not been considered in the Modern Synthesis can be compared to religious belief in theories.
Steve 200mph Cruiz
5 / 5 (5) Aug 23, 2015
JVK isn't anything, he's just some dude who absolutely refuses to learn how the DNA machine works.

I explained amino acids and gave him a bio 101, but he just thought I was some dude arguing politics.
Just ignore him, he's not here to listen, just to talk and he doesn't have anything good to talk about it, but he thinks he's pretty awesome (naturally...)
Steve 200mph Cruiz
5 / 5 (5) Aug 23, 2015
Well he is a Jesus freak, but he won't admit it because he thinks that is how educated people judge others, but that's the reasoning of a simpleton.

Unfortunately for him as a Christian, I believe it is a sin to deny your faith, so either way he loses.
Can't do science and is ashamed of his saviour... poor JVK, cursed to hell over cell division.
JVK
1 / 5 (4) Aug 23, 2015
I explained amino acids...


This explains the role of nutrient-dependent RNA-mediated amino acid substitutions in cell type differentiation and links it from the sequencing of the octopus genome to the physiology of reproduction in all living genera.

Excerpt: "The effect of any amino acid substitution can vary greatly depending on its location in the protein structure. Thus, site-specific amino acid substitutions that do not confer structural changes in the protein can affect protein function, such as the changes in binding sites. Some amino acid changes in mt subunits cause inefficiencies in the electron transfer chain system, contributing to the increase of reactive oxygen species (ROS) that can lead to the disruption of OXPHOS [3–5]. On the other hand, the amino acid substitutions can also improve or decrease aerobic capacity and be linked with life history traits and environmental adaptation [6–8]."

Accumulated mutations prevent ecological adaptation.
Whydening Gyre
5 / 5 (6) Aug 23, 2015

I linked nutrient-dependent amino acid substitutions to cell type differentiation in all cell types of all individuals of all living genera and provided examples of how genomes are organized in the context of the physiology of reproduction. Viruses perturb protein folding, which is why they are consistently linked to pathology -- not to the evolution of any species.

JVK. You were an only child, weren't ya...

EVERYthing "perturbs" protein folding...
The evolution of "protein folding" is what DRIVES the evolution of any given species(via adaptation). Natural selection is a further weeding out of any species not adapting to an environment sufficiently.
IOW - if a particular protein fold wasn't beneficial to the survival of the larger, more complex species, natural selection removes it.
Quit trying to re-define established terminology to suit your own agenda.
Captain Stumpy
5 / 5 (5) Aug 23, 2015
I am a medical laboratory scientist ...Clinical Pathology
Translation: i am a lab tech
My most recent published work...
debunked by rational thought by a biology graduate: see - http://www.socioa...ew/24367
there is no room fro braggadocio and conjecture, especially religious motivated conjecture which is proven false already (see also: http://rspb.royal...full.pdf )
the problem with jvk is simple: Dunning-Kruger mixed with religious fundamentalism and a failure to comprehend the rigors of the scientific method
this hasn't stopped him from publishing "some" actual science, but like anyone else, he fails to comprehend that just because he is published, doesn't mean his proclamations here are legit, supported or even real
I also know some published here who claim gravity isn't real... IOW- PSEUDOSCIENCE, like jvk
Captain Stumpy
5 / 5 (5) Aug 23, 2015
PS- note of importance:
I linked nutrient-dependent amino acid substitutions to cell type differentiation in...
he is also NOT the first to try this approach, nor is he the first to make any of the "links" proposed

it all boils down to the EVIDENCE
kohl attempts to subjugate science with his religious beliefs (creationist/7th day advent) and then interpret science in the perspective he has, much like any conspiracy theorists (or addict, if you want to know the truth)
this allows jk to ignore the facts around him validated by science for the sake of his fundamentalist religious beliefs, demonstrated above
See also: http://www.ploson...tion=PDF

all in all, the biggest problem is his "interpretations" of science here: to date, there is a 100% failure rate in his "interpretations" of other studies as VALIDATED by the original authors that have responded

and that is fact
JVK
1 / 5 (4) Aug 23, 2015
the biggest problem is his "interpretations" of science


What interpretations?

DNA and RNA structure: nucleic acids as genetic material
Jan 2013 http://www.mlo-on...rial.php

See also:
Dec 2012 http://www.mlo-on...ples.php
March 2013 http://www.mlo-on...-rna.php
Feb 2013 http://www.mlo-on...ases.php
Captain Stumpy
5 / 5 (5) Aug 23, 2015
What interpretations?
shall i start quoting your "interpretations" of Lenski? Dr. Extavour? Dr. Whittaker?

How about your quotes from your "model" that are debunked by Jones?
Why haven't you fixed that yet?
What about addressing the study i linked above?
what about addressing your own mistakes above?
what about actually posting your "definition" of mutation?
why would you argue that definitions are not important, or your arguments that you don't use them, but then link this: http://www.mlo-on...ples.php ????

are you trying to undermine your own arguments right out of the gate?
JVK
1 / 5 (4) Aug 23, 2015
debunked by rational thought by a biology graduate: see - http://www.socioa...ew/24367


My review was integrated into what is known about octopuses.
http://www.scienc...14004006

Others linked marine invertebrates to insects and all vertebrates via my model. The octopus genome sequencing evidence links microbes to man via the conserved molecular epigenetics of cause and effect we detailed in a section on molecular epigenetics in this 1996 review:

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

Excerpt: "Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation in at least two species, Drosophila melanogaster and Caenorhabditis elegans...."

Mutations have always been linked from perturbed protein folding to pathology.
JVK
1 / 5 (4) Aug 23, 2015
...debunked by Jones?


Mutations have always been linked from perturbed protein folding to pathology. Only biologically uninformed science idiots like Jones still believe they can be linked to the evolution of increasing organismal complexity in organisms that must eat to reproduce.
Captain Stumpy
5 / 5 (5) Aug 23, 2015
My review was integrated into what is known about octopuses
so you say... and yet you cannot validate that unless you can find a free copy of said paper
you also said
I've learned enough about physics to link the speed of light on contact with water to the de novo creation of amino acids
Pull the other one!
NICE TRY
Mutations have always been linked from perturbed protein folding to pathology
no, they haven't
this is called "personal conjecture without evidence"
i can refute it with a single link that has SCIENTIFIC EVIDENCE that you are a liar: http://myxo.css.m...dex.html
Only biologically uninformed science idiots like Jones still believe they can be linked to the evolution of increasing organismal complexity
so you're again calling Lenski, Extavour, Whittaker and the bulk of all biological/medical scientists idiots?
and that doesn't scream narcissistic Dunning-Kruger pseudoscience poster to you?
NoStrings
1 / 5 (1) Aug 23, 2015
'I' think this article is just stating the obvious. Maybe that was a revelation to the authors, which begs for the question, didn't they read anything published in the last 50 years on philosophy and biological sciences? Besides that 'I' being surprised about their lack of touch, they are not surprising anyone.
JVK
1 / 5 (4) Aug 23, 2015
so you're again calling Lenski, Extavour, Whittaker and the bulk of all biological/medical scientists idiots?


"Bird odour predicts reproductive success" by Whittaker et al., links Horton et al., "Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes" via "Feedback loops link odor and pheromone signaling with reproduction" to ecological adaptations manifested in the context of nutrient-dependent chromosomal rearrangements that are RNA-mediated in all genera as evidenced by the sequencing of the octopus genome.

See also "Nutrient-dependent pheromone-controlled ecological adaptations: from atoms to ecosystems" http://figshare.c...s/994281

It has forced biologically uninformed science idiots to revise the Modern Synthesis.

See also: http://rspb.royal...20151019

You are exposing their ignorance.
Captain Stumpy
5 / 5 (4) Aug 23, 2015
...by Whittaker et al...
and again, when discussing SPECIFICALLY you, your work, and your comments here: http://phys.org/n...ols.html

I am familiar with James V. Kohl, as my own research focuses on chemical communication and behavior in birds... Thus attributing the quote to me and tying it to my research on birds and primates is bizarre, as these things are entirely unrelated.

The paragraph that he chose to quote is taken out of context ("Mutations are rare; getting two mutations is even rarer...."), as I believe you have already noticed. The very next paragraph begins "Evolution isn't about playing one hand of blackjack though, its about playing lots and lots of hands, over a very long period of time. On a long enough timescale, you will eventually see one of these rare chance events."
[edited for brevity and content

full quotes found on link above
to be continued
Captain Stumpy
5 / 5 (4) Aug 23, 2015
cont'd
I don't understand what the second quote "The re-evolution of the bacterial flagellum over the weekend..." is referring to. It is also clearly out of context and unrelated to anything else being discussed in this particular thread. I just did a Google search and found several other science articles where he has commented saying something similar, and seems to be referring to this article, in which Rich Lenksi comments on a paper in which flagellar motility returned to Pseudomonas after a gene was deleted: http://www.the-sc...ewiring/
That study is an interesting example of a beneficial mutation, as I understand it.
you read that?
BENEFICIAL MUTATION?

so, we can see that ACTUAL scientists comprehend what mutations are, that they can be beneficial, and that jk doesn't know WTF he is talking about

shall i continue again, jk?
we've seen you are lying (again) and denigrating great work & people
JVK
1 / 5 (4) Aug 23, 2015
I don't understand what the second quote "The re-evolution of the bacterial flagellum over the weekend..." is referring to.


I've been through that with SSgt Stumpy before. Danielle is like other researchers who cannot link biophysically constrained protein folding biochemistry from ecological variation to RNA-mediated nutrient-dependent ecological adaptation. She is too specialized, but admits it.

See for comparison: "Molecular biology would not have been possible if it were not for the use of a prokaryote, E. coli, which was used to generate much of the essential data that forms the backbone of the field today. The fact that the genetics of E.coli and the biological machinery that coordinates it differs substantially from eukaryotes has done nothing to invalidate the absolute need for having chosen a suitable model species for the investigation of fundamental processes." http://www.ncbi.n...12496741
JVK
1 / 5 (4) Aug 23, 2015
Panksepp's group (cited above) won the same award my group won the year before for publication of Human pheromones: integrating neuroendocrinology and ethology http://www.nel.ed...view.htm

The nutrient-dependent pheromone-controlled physiology of reproduction in E. coli links the "re-evolution" of the bacterial flagellum to the same molecular mechanisms of biophysically constrained RNA-mediated cell type differentiation in all living genera.

Danielle Whitaker claimed "I don't understand what the second quote "The re-evolution of the bacterial flagellum over the weekend..." is referring to. It is also clearly out of context..."

It is not outside the context of "Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind" http://www.ncbi.n...12496741 or Kohl (2001).

The molecular mechanisms are not outside the context of anything linked to behavior by serious scientists.
Captain Stumpy
5 / 5 (4) Aug 23, 2015
researchers who cannot link biophysically constrained protein folding biochemistry from ecological variation to RNA-mediated nutrient-dependent ecological adaptation. She is too specialized, but admits it
1- where is this ever mentioned?
2- what makes you think she doesn't understand biology or medicine well enough to define mutations given that she works and researches in this exact field still?
3- by all means, you post here what exactly she doesn't understand and then we can actually discuss that with her... better be specific, so that she can actually answer this time, since you were vague and non-committal last time, which prompted the QUOTE
I don't understand what the second quote
this was because you were NOT clear, concise, and you were VERY "out of context and unrelated to anything else being discussed"
but of course, EVERYONE can read that above
and in the thread too

you are still LYING and hoping no one will notice!?
really?
JVK
1 / 5 (4) Aug 23, 2015
Re: The molecular mechanisms are not outside the context of anything linked to behavior by serious scientists.

See what happens when evolutionary theorists ignore what is known to serious scientists and try to revise their ridiculous theories to make the theories fit their assumptions without mention that their assumptions were based on de Vries definition of "mutation."

RNA-mediated permanent symbioses http://rna-mediat...mbioses/

The permanent symbioses cannot be achieved via mutations that perturb protein folding, and there in only one type of mutation. That's why Masatoshi Nei made this ridiculous claim: "...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

Two years later and we see only biologically uninformed science idiots making such ridiculous claims.
JVK
1 / 5 (4) Aug 23, 2015
what makes you think she doesn't understand biology or medicine well enough to define mutations


No one who understands how biologically-based cause and effect is linked to the practice of medicine uses de Vries definition of mutation or anyone's definition of evolution. They use what is known about RNA-mediated cell type differentiation, or they help to cause suffering and kill people. Since it is their responsibility to do no harm, they cannot be biologically uninformed science idiots, although there will always be exceptions.

Most have joined responsible medical practitioners who are Combating Evolution to Fight Disease http://www.scienc...88.short

Why is Stumpy fighting on the other side? Which one of your loved ones will suffer and/or die due to his incessant contributions to the ignorance of the masses of biologically uninformed science idiots who are just like him?
Captain Stumpy
5 / 5 (4) Aug 23, 2015
http://rna-mediat...mbioses/
PHISHING PSEUDOSCIENCE CREATIONIST SITE that you personally own
quit using it like a science reference... if you can't find another link, then you are posting PSEUDOSCIENCE
as long as you use this link, i will remind people that you personally own the site and use it for PHISHING, SPAMMING, trolling and pushing CREATIONIST IDEALS, all clearly visible by going to the site
reported
No one who understands how biologically-based cause and effect is linked to the practice of medicine uses de Vries definition of mutation or anyone's definition of evolution
then i'll make sure that they all know you think they are idiots (actually, i can quote you on that already, but i can say that you are calling them inept, right? you say they don't know their own chosen profession, after all)
Captain Stumpy
5 / 5 (4) Aug 24, 2015
Why is Stumpy fighting on the other side?
Truck Captain Stumpy is fighting to spread scientific discourse and prove that pseudoscience is nothing more than lies wrapped up in religious like dogma and unproven
THIS is where you and i differ, jk... i am able to adjust my perspective given the evidence, so i follow the evidence that can be PROVEN and thus make decisions based upon scientific information... you... you try scare tactics like
Which one of your loved ones will suffer and/or die due to his incessant contributions to the ignorance of the masses of biologically uninformed science idiots
to try and browbeat people into fearfully siding with you
WHY?
because YOU HAVE NO EVIDENCE TO OFFER THAT IS NOT REFUTABLE AND PROVEN TO BE PSEUDOSCIENCE or RELIGIOUS DOGMA

you are a creationist who failed out of college and thinks he knows better than researchers in the field (Lenski, Extavour, Whittaker)

THEY prove you wrong whit EVIDENCE

what else you got?
Captain Stumpy
5 / 5 (4) Aug 24, 2015
want proof that you don't know science?
Term misuse causes inaccurate understandings of definitions
http://beacon-cen...is-hard/
we all know you can't comprehend terms... you continue to demonstrate this with "mutations" and "Evolution theory"
wait... there is more!
you claim
Mutations have always been linked from perturbed protein folding to pathology
and historically you've said
all mutations perturb protein folding
but when you see EVIDENCE like this: http://myxo.css.m...dex.html
especially the first 100K generations... you claim Lenski or researchers are idiots for proving beneficial mutations

So which is it?
is it your inability to comprehend the science or your delusional religion getting in the way because you've already made up your mind but can't find evidence?

feel free to expound

tell us all how creationists are going to save the world
Vietvet
4.3 / 5 (6) Aug 24, 2015
Combating Evolution to Fight Disease

"Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations. However, these domains are beginning to converge in laboratories addressing molecular mechanisms that explain how evolutionary processes work, and bring these processes to bear on medical problems such as cancer and infectious disease. Each discipline can be viewed as a missing link in the other's description of biology, and in medicine."
http://www.scienc...88.short

Molecular biologists collaborating with theorists to "explain how evolutionary processes work"

Another reading comprehension fail by JVK.
Captain Stumpy
5 / 5 (5) Aug 24, 2015
i gotta share this gem real quick...jk said
The permanent symbioses cannot be achieved via mutations that perturb protein folding, and there in only one type of mutation
thus jk states that no mutations are viable and all "mutations" perturb protein folding and cannot be used for evolution
now read this...
hey JK- remember when I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
therefore, by self admission, jk states that NOT ONLY is he a "biologically uninformed science idiot" but, BY DEFINITION, his model cannot, per his own restraints and requirements, assist or help with evolution! therefore it cannot replace the Theory of Evolution because it uses the SAME mechanisms!!

Also note: his claims are also directly refuted by Lenski... see his link above
JVK
1 / 5 (4) Aug 24, 2015
See also: http://www.scienc...40.short

Excerpt: "While the mechanism for how lncRNAs establish these domains is not fully understood, it is becoming increasingly clear that lncRNAs are important at all levels of nuclear organization—exploiting, driving, and maintaining nuclear compartmentalization."

It has also become increasingly clear that mutations are not linked to any level of nuclear organization because perturbed protein folding cannot be linked to nutrient-dependent RNA-mediated gene duplication and RNA-mediated amino acid substitutions that differentiate the cell types of all living genera that have organized genomes.

I provided a link to 24 different open access articles with my comments on abstract excerpts. Please address any one of the articles and try to link what you think they are claiming about evolution to any experimental evidence of biologically-based cause and effect that supports their claim.
JVK
1 / 5 (4) Aug 24, 2015
The permanent symbioses cannot be achieved via mutations that perturb protein folding, and there in only one type of mutation

thus jk states that no mutations are viable and all "mutations" perturb protein folding and cannot be used for evolution


I stated that: The permanent symbioses cannot be achieved via mutations that perturb protein folding, and there in only one type of mutation.

Here's an opportunity for someone to claim how permanent symbioses are achieved by mutations, and to support their claim with experimental evidence of biologically-based cause and effect at the same time they remember to address re-evolution of the bacterial flagellum in 4 days.

ichisan
1 / 5 (1) Aug 24, 2015
"A series of groundbreaking studies have revealed"

Yeah, right. PhysOrg is becoming more and more like a site for crackpot pseudoscientific crap.
Vietvet
4 / 5 (4) Aug 24, 2015

"Bird odour predicts reproductive success" by Whittaker et al., links Horton et al
., "Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes" via "Feedback loops link odor and pheromone signaling with reproduction" to ecological adaptations manifested in the context of nutrient-dependent chromosomal rearrangements that are RNA-mediated in all genera as evidenced by the sequencing of the octopus genome.

JVK is so stupid to start a comment with "Bird odour predicts reproductive success" and follows with a quote not found in that study, but is quoting himself.

Bird odour predicts reproductive success
http://www.indian...2013.pdf

anonymous_9001
5 / 5 (5) Aug 24, 2015
Here's an opportunity for someone to claim how permanent symbioses are achieved by mutations, and to support their claim with experimental evidence


Ask and ye shall receive:

http://journals.p....1001943

http://journals.p....1001942

Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont.
JVK
1 / 5 (4) Aug 24, 2015
Symbiosis Plasmids Bring Their Own Mutagen to the Wedding Party
http://journals.p....1001943

"Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance." http://www.nature...smids-28

They link nutrient-dependent antibiotic resistance to the pheromone-controlled physiology of reproduction in species from microbes to man via thermodynamic cycles of protein biosynthesis and degradation, which are perturbed by viruses. That's how viruses are linked to pathology in the context of an atoms to ecosystems model exemplified in the facts that were presented about the sequencing of the octopus genome.

HGTransfer exemplifies how the innate immune system links bacteria to plants. It enables organisms from microbes to man to ecologically adapt to the presence of viruses if RNA-mediated DNA repair is facilitated by nutrient availability.
EnricM
not rated yet Aug 24, 2015
One wonders what compels such ridiculous and erroneous leaps of logic that lead to this headline? Soon we will start hearing "my microbiome made me do it."


LOL.... just wait for a whole new line of Hologenomic Rejuvenating Face Cream from L'Oreal XD or Yakult with Holobiontic Active Ingredients
JVK
1 / 5 (4) Aug 24, 2015
As is typical of the biologically uninformed, Andrew Jones (aka anonymous_9001) has again taken what is known to serious scientists about RNA-mediated cell type differentiation in all genera, and placed it into the context of a ridiculous theory where virus-driven mutations cause evolution instead of genomic entropy.

He goes further into the realm inhabited by science idiots, however, to provide us with yet another example of how a biologically uninformed science idiot can provide a few citations as if they were sufficient to refute everything known to serious scientists about how viruses link entropic elasticity to genomic entropy and all pathology unless they are biophysically constrained by an anti-entropic force that links protein folding chemistry from RNA-mediated amino acid substitutions to the stability of organized genomes.
JVK
1 / 5 (4) Aug 24, 2015
JVK is so stupid to start a comment with "Bird odour predicts reproductive success" and follows with a quote not found in that study, but is quoting himself.


I included the titles of three different articles below, and Vietvet thought the titles "IN QUOTES" were something I quoted.

I wrote:

"Bird odour predicts reproductive success" by Whittaker et al., links Horton et al., "Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes" via "Feedback loops link odor and pheromone signaling with reproduction" to ecological adaptations manifested in the context of nutrient-dependent chromosomal rearrangements that are RNA-mediated in all genera as evidenced by the sequencing of the octopus genome.

sascoflame
1 / 5 (1) Aug 24, 2015
The problem of the "one of the many" is as old as reason. Are scientists that ignorant that they thought they just discovered it? The assertion that there are no individuals and everything is a collective is a political one. The response is, "Don't you see the influence that the group as on the individual?" Of course I do. But every group is made of individuals and without their contribution the group would come up with nothing. This goes further then language. It plays a part in exaggerating the abilities of animals and minimizing the ability of humans. Does any one really believe that a highly motivated memory expert couldn't beat any chimp at a memory test? Recently they came up with the idea that the chimp's hand is more highly evolved (bad concept) then a human's. His hand is only fit for beating someone to a pulp. Scientists are the most egotistical individuals in the world. The problem is they see the rest of humanity as a faceless collective.
JVK
1 / 5 (5) Aug 24, 2015
...they see the rest of humanity as a faceless collective.


Medical laboratory science involves diagnostic laboratory testing from A to Z. These professionals do everything from providing your cancer testing results, to predicting the correct antibiotic to prescribe, to typing the correct blood for surgery. MLS professionals provide answers to life-and-death decisions every day. In our program, about 40 percent to 50 percent of students who apply to our major already have a BS, or even an MS or PhD, in another major (such as microbiology, biology or biomedical studies), but they are either unable to find a job or they find out they can't work in a clinical laboratory without the degree and MLS certification." http://www.elsevi...es-lives

My MLS certification can be compared in the context of comments by Andrew Jones (aka anonymous_9001). He had a degree in biology. I have 40 years experience working as a generalist.
JVK
1 / 5 (5) Aug 24, 2015
What most people have done is to trust their life and the lives of their loved ones to neo-Darwinian theorists. Despite their academic credentials (e,g., BS, or even an MS or PhD, in another major (such as microbiology, biology or biomedical studies) -- many can't find a job and they can't work in a clinical laboratory without the degree AND MLS certification.

Biologically uninformed science idiots can criticize the works of serious scientists, however. For example, see: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model http://www.ncbi.n...4049134/

Note: Andrew Jones (aka anonymous_9001) had not yet hit his displayed peak of ignorance.

Now he claims permanent symbioses are achieved by mutations, and supports his claims with experimental evidence that obviously links the anti-entropic epigenetic effect of nutrient-energy to cell type differentiation via the RNA-mediated amino acid substitutions in my model.
gkam
1 / 5 (3) Aug 24, 2015
Like everything else, the "secret" is in the integration of systems and parts.
JVK
1 / 5 (5) Aug 24, 2015
Top-down causation: an integrating theme within and across the sciences? http://rsfs.royal...abstract

Why do theorists think they can start from anywhere and tell others their pseudoscientific nonsense can be compared to the works of serious scientists?
Captain Stumpy
5 / 5 (5) Aug 24, 2015
As is typical of the biologically uninformed
how typical that jvk is given physical evidence that refutes his blatant stupidity and attempts to denigrate educated people by simply offering creationist ideals and diatribe as somehow a substitute for validated, proven empirical evidence I have 40 years experience working as a generalist this is equivalent to claiming you are a better rifle shot than Carlos Hathcock because you've fired a variety of weapons that he hasn't... IOW- pretty stupid
Jones is EDUCATED in biology, has experience that you refused to get when you failed out of school, and knows data that you refused to learn because you promote creationist ideals...
SCIENCE WINS because of one simple thing: EVIDENCE

why haven't you been able to get that Nobel for all your claims here on PO?
again, one simple reason: EVIDENCE

why aren't you world renowned as the man who debunked evolution?
EVIDENCE

quit spamming with pseudoscience
Captain Stumpy
5 / 5 (5) Aug 24, 2015
Why do theorists think
why do you think that starting with a false premise (like creationism) and looking for ways to explain evidence falsely (because you've not educated yourself to comprehend the technical details or the lexicon) somehow makes you more informed or intelligent than the people working in the field?
What most people have done is to trust their life and the lives of their loved ones to neo-Darwinian theorists
you do realise that this LIE is still a LIE, right?
if you knew how to READ, you would not still be promoting this blatant lie as truth: https://en.wikipe...ynthesis

EPIC FAILURE... yet again....
only this time you've proven that you cannot comprehend even BASIC english and communication!

perhaps you can buy an interpreter with your scads of dough from scamming perfume manufacturers and setting up PSEUDOSCIENCE web-sites?

one more EPIC debunk:
http://myxo.css.m...dex.html
JVK
1 / 5 (5) Aug 24, 2015
"...cancer patients with TET2 mutations had low levels of 5-hmC in their genomic DNA.4 Huang and her colleagues also used the CMS probe to map the methylation landscape of hematopoietic stem cells and to identify epigenetic differences between healthy and leukemic cells.5" http://www.the-sc...enetics/

Nutrient-dependent epigenetic effects on histone modifications and DNA methylation play an important role in stabilizing cell type identity and in orchestrating many developmental processes. For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional olfactory receptor genes Blaschke et al.(2013).

Researchers recently rediscovered a nutrient-dependent epigenetic variant that links vitamin C to what is probably a glucose and glucose dehydrogenase-dependent base pair change.
anonymous_9001
5 / 5 (4) Aug 24, 2015
For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional olfactory receptor genes Blaschke et al.(2013).


For comparison, here's what the paper you cited actually says:

For example, vitamin C may also stimulate histone demethylases, as has been shown in induced pluripotent stem cell (iPS cell) generation


It says NOTHING about olfactory receptor gene creation anywhere in that paper.

The full text can be found here:

http://santoslab....0DNA.pdf
.
anonymous_9001
5 / 5 (3) Aug 24, 2015
Edit: double post
JVK
1 / 5 (5) Aug 24, 2015
Ecological niche construction is biophysically constrained by nutrient availability

The likelihood that hemoglobin variants are associated with other beneficial nutrient-dependent changes in microbiota populations in the gut can be considered in the context of how balanced nutrition, which includes access to endogenous vitamin C in human populations, supports efficient metabolism and ecological niche construction (McNulty, et al., 2011).

Nutrient-dependent epigenetic effects on histone modifications and DNA methylation play an important role in stabilizing cell type identity and in orchestrating many developmental processes. For example, vitamin C appears to stimulate histone demethylases, which appear to alter the de novo creation of functional olfactory receptor genes (Adipietro, Mainland, & Matsunami, 2012; Blaschke et al., 2013; Jazin & Cahill, 2010; Lyons et al., 2013; Tan, Zong, & Xie, 2013).

Has anyone linked mutations to the de novo creation of any genes?
JVK
1 / 5 (5) Aug 24, 2015
Ignorance displayed here comes from the nonsense taught to biologically uniformed science idiots who learned nothing about epigenetics.

What Is Epigenetics? (2010) http://www.scienc...11.short

From Fertilization to Adult Sexual Behavior (1996) http://www.hawaii...ion.html

Excerpt: "Molecular epigenetics. It is now understood that certain genes undergo a process called "genomic or parental imprinting." Early in embryonic development attached methyl groups become removed from most genes. Several days later, methyl groups are reattached in appropriate sites. Fascinatingly, some such genes reestablish methylation patterns based upon whether the chromosomal segment carrying the gene came from maternal or paternal chromosomes. These sexually dimorphic patterns are labeled genomic or parental imprinting, and these imprintings are inheritable but non-genetic modifications of specific genes..."
anonymous_9001
5 / 5 (4) Aug 24, 2015
Has anyone linked mutations to the de novo creation of any genes?


http://www.geneti...487.full

http://www.nature...184.html

Here we formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes4 generated by widespread translational activity in non-genic sequences. Testing this model at the genome scale...


http://www.scienc...abstract

http://journals.p....1002381

http://www.nytime...tml?_r=0

http://cshperspec...996.full
JVK
1 / 5 (4) Aug 24, 2015
Gene duplication is nutrient-dependent and RNA-mediated.
RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. http://www.ncbi.n.../2427930

That fact has been known for 30 years, and Greg Bear integrated it into at least three different books about virus-driven biodiversity.

We linked pheromone-controlled RNA-mediated gene duplication in yeasts to mammals in our 1996 Hormones and Behavior review, and Greg also included that fact in his 1999 and 2003 novels.

Science fiction often becomes science fact.

Are you a terrorist? http://thedailysh...reg-bear

Who do you think Greg is talking about when he claims that he must make the stories believable to people who are working in the lab? Who do you think the terrorists are -- if not you, Captain Stumpy, PZ Myers, and all the other evolutionary theorists who must be pretending to be biologically uninformed science idiots?
Captain Stumpy
5 / 5 (4) Aug 25, 2015
Science fiction often becomes science fact
this is true... HOWEVER... and you can also see this in the historical record... RELIGION tends to be flushed away into ever receding anonymity and obscurity WRT advancement and SCIENCE

so just because Sci-Fi often becomes fact doesn't mean that your religious creationist beliefs will one day become scientific fact. there must be some FACTS there for it to build upon, and when you intentionally refuse to see fact in order to continue to support your own religious belief, then you will always fail

THIS is the inevitable truth of religion
unless you can accept and live with the facts of SCIENCE (or even reality), then you will simply be a pocket of ever receding gaps of ignorance and you will be scorned for your intentional choice to refuse knowledge

Captain Stumpy
5 / 5 (4) Aug 25, 2015
Has anyone linked mutations to...
and we see again that you are not capable of actually comprehending the SCIENTIFIC ADVANCEMENT of your own field
Who do you think the terrorists are -- if not you, Captain Stumpy, PZ Myers, and all the other evolutionary theorists who must be pretending to be biologically uninformed science idiots?
so now anyone who doesn't believe your way and follow creationists dogma is a TERRORIST?
wow... now that is what i call appeal to fear!

what is next?
you going to call a jihad against science?
your actions and religion have killed more people than any other ANYTHING in the history of the planet, but you want to call US terrorists???!!?!
and this is specifically directed towards religious fanatics like you, jk! those who would refuse knowledge, FACTS and validated evidence for the sake of a blatant fallacy!

you are the reason people are "biologically uninformed science idiots" because you spread PSEUDOSCIENCE
JVK
1 / 5 (3) Aug 25, 2015
Greg Bear linked virus-driven genomic entropy to terrorist threats in:

"The Darwin Code: Intelligent Design without God" http://rna-mediat...eg-bear/ AND http://thedailysh...reg-bear

Young earth creationists linked the anti-entropic effects of the sun's biological energy from Schrodinger's claims in "What is life?" to everything currently known to serious scientists about how biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry controls the physiology of reproduction. http://www.icr.or...cle/8661

The truth about religious beliefs in ridiculous theories is that pseudoscientists accept the theories and live in ignorance at the same time serious scientists provide experimental evidence of biologically based facts to those who refuse to live in ignorance, whether or not they join terrorist groups.

Combating Evolution to Fight Disease http://www.scienc.../1088.sh
JVK
1 / 5 (4) Aug 25, 2015
Proto-genes and de novo gene birth http://www.nature...184.html


Here we formalize an evolutionary model according to which functional genes evolve de novo through transitory proto-genes4 generated by widespread translational activity in non-genic sequences. Testing this model at the genome scale...


Gene duplication is nutrient-dependent and RNA-mediated.

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon. http://www.ncbi.n.../2427930

Why would anyone attempt to formalize a ridiculous evolutionary model in 2012 when the biological facts about gene duplication were established in 1985?
rthrust
1 / 5 (1) Aug 25, 2015
One wonders what compels such ridiculous and erroneous leaps of logic that lead to this headline? Soon we will start hearing "my microbiome made me do it."


LOL.... just wait for a whole new line of Hologenomic Rejuvenating Face Cream from L'Oreal XD or Yakult with Holobiontic Active Ingredients


Already working on it!
Captain Stumpy
5 / 5 (3) Aug 25, 2015
Combating Evolution to Fight Disease
More PROOF that your reading and comprehension skills are biased and you like to LIE while promoting a false agenda (PSEUDOSCIENCE and RELIGION)
Molecular biology and evolutionary biology have been separate disciplines and scientific cultures: The former is mechanistic and focused on molecules; the latter is theoretical and focused on populations. However, these domains are beginning to converge in laboratories addressing molecular mechanisms that explain how evolutionary processes work, and bring these processes to bear on medical problems such as cancer and infectious disease. Each discipline can be viewed as a missing link in the other's description of biology, and in medicine
The SUMMARY from your own link refutes your claims with clear, concise language

http://www.scienc.../1088.sh

it is NOT a battle over who is right... it is TWO fields working TOGETHER for clear, concise VALID SCIENCE
Captain Stumpy
5 / 5 (3) Aug 25, 2015
http://rna-mediat...eg-bear/
PHISHING PSEUDOSCIENCE SITE WITH CREATIONIST DOGMA AND RELIGIOUS POSTS
this is a jvk owned site that WILL steal your data and open you up to hack, cyber attack or worse!
it is also pseudoscience and since it promotes creationist dogma with science it is considered NOT REPUTABLE
reported
The truth about religious beliefs in ridiculous theories is that pseudoscientists accept the theories and live in ignorance at the same time serious scientists provide experimental evidence
lets see"
TO DATE- you have provided ZERO evidence sporting creationist or religious ideals
whereas JONES, ANON, REAL et al have provided EMPIRICAL EVIDENCE that you do NOT comprehend biology or physiology

i've proven you to be a Fraud, Liar and creationist, as well as limited in your ability to comprehend basic communication
your "interpretations" of the evidence clearly show that you do NOT understand what is going on as well

EPIC FAIL
Captain Stumpy
5 / 5 (3) Aug 25, 2015
Combating Evolution to Fight Disease
@jk
besides not comprehending even the summary, as noted above
why not actually pull out specific comments from the link YOU provided demonstrating that Evolution Theory is false?

can you use that link YOU gave to prove there is a problem with the Theory?
even your link references e-coli and directly proves you wrong about mutations as well as provides references which ALSO prove you wrong about mutations!

the ONLY reason that you linked it is because you think people can't access it at Science Magazine

by all means, try to explain WHY you think the link somehow supports your conclusions about mutations or your creationist dogma about Evolution!

you linked it because of the TITLE... too bad you didn't understand what was actually written IN IT
EnsignFlandry
5 / 5 (2) Aug 31, 2015
Why do creationists use every scientific report, even bad ones, as an excuse to push their theological dogma? I suspect they have teams who browse sites such as this one looking for opportunities to preach.
EnsignFlandry
5 / 5 (1) Aug 31, 2015
We are just dwellings that bacteria created to sustain them.


I'm waiting for the first bacterium to produce a theory of quantum gravity, or just Newtonian gravity, or prove a mathematical theorem.
JVK
1 / 5 (2) Aug 31, 2015
http://www.the-sc...st122986

Excerpt: "p-coumaric acid is probably only part of the caste-determination story..."

The rest of the story has been detailed by others, like Ryszard Maleszka, who was interviewed for this article, which links what is known about the de novo creation of olfactory receptor genes from the light-induced de novo creation of nucleic acids to the RNA-directed DNA methylation and the conserved molecular mechanisms that differentiate all cell types of all individuals of all species.

Ryszard Maleszka once commented that he did not want to see any of this "creationist crap," which has since linked the differences between nutrient-dependent microRNAs and adhesion proteins from viral microRNAs to pathology, when nutrient-dependent RNA-mediated DNA repair can no longer effectively prevent the accumulation of damage that leads to genomic entropy.
EnricM
5 / 5 (2) Sep 01, 2015
[cont'd]
... only reliable back to 50,000 years bp. ..


I am amazed: The Creationists handling periods of 50K years? Isn't this a contradiction to the 6K years since creation?

JVK
1 / 5 (2) Sep 01, 2015
I am not amazed. Biologically uninformed science idiots continue to ignore every factual representation of biologically-based cause and effect and complain about creationists.

Trolls never move forward. They live where the sun doesn't shine with their heads up their behinds.

http://phys.org/n...firstCmt
Captain Stumpy
5 / 5 (1) Sep 01, 2015

Trolls never move forward. They live where the sun doesn't shine with their heads up their behinds.
the absolute most accurate descriptor of jvk and his PSEUDOSCIENCE i've seen to date!

and it is his own descriptor ... WOW!

you tell them exactly how you are and don't worry about your credibility, jk! (like you ever did, pushing creationist dogma and PSEUDOSCIENCE)
JVK
1 / 5 (1) Sep 01, 2015
This attests to the experience-dependent de novo creation of olfactory receptor genes via RNA-directed DNA methylation and fixation of amino acid substitutions that determine cell types in all cells of all individuals of all genera.

http://medicalxpr...ode.html

Pseudoscientists claim that de novo genes automagically arise and lead to the emergence of new species.

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