Scientists create possible precursor to life

Scientists create possible precursor to life

How did life originate? And can scientists create life? These questions not only occupy the minds of scientists interested in the origin of life, but also researchers working with technology of the future. If we can create artificial living systems, we may not only understand the origin of life - we can also revolutionize the future of technology.

Protocells are the simplest, most primitive living systems, you can think of. The oldest ancestor of life on Earth was a protocell, and when we see, what it eventually managed to evolve into, we understand why science is so fascinated with protocells. If science can create an artificial protocell, we get a very basic ingredient for creating more advanced artificial life.

However, creating an artificial protocell is far from simple, and so far no one has managed to do that. One of the challenges is to create the information strings that can be inherited by cell offspring, including protocells. Such information strings are like modern DNA or RNA strings, and they are needed to control cell metabolism and provide the cell with instructions about how to divide.

Essential for life

If one daughter cell after a division has a slightly altered information (maybe it provides a slightly faster metabolism), they may be more fit to survive. Therefor it may be selected and an evolution has started.

Now researchers from the Center for Fundamental Living Technology (FLINT), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, describe in the journal Europhysics Letters, how they, in a virtual computer experiment, have discovered information strings with peculiar properties.

Professor and head of FLINT, Steen Rasmussen, says:

"Finding mechanisms to create information strings are essential for researchers working with artificial life."

Steen Rasmussen and his colleagues know they face two problems:

Firstly long molecular strings are decomposed in water. This means that long information strings "break" quickly in water and turn into many short strings. Thus it is very difficult to maintain a population of long strings over time.

Secondly, it is difficult to make these molecules replicate without the use of modern enzymes, whereas it is easier to make a so-called ligation. A ligation is to connect any combination of two shorter strings into a longer string, assisted by another matching longer string. Ligation is the mechanism used by the SDU-researchers.

"In our computer simulation - our virtual molecular laboratory – information strings began to replicate quickly and efficiently as expected. However, we were struck to see that the system quickly developed an equal number of short and long information strings and further that a strong pattern selection on the strings had occurred. We could see that only very specific information patterns on the strings were to be seen in the surviving strings. We were puzzled: How could such a coordinated selection of strings occur, when we knew that we had not programmed it. The explanation had to be found in the way the strings interacted with each other", explains Steen Rasmussen.

It is like society

According to Steen Rasmussen, a so-called self-organizing autocatalytic network was created in the virtual pot, into which he and his colleagues poured the ingredients for information strings.

An autocatalytic network is a network of molecules, which catalyze each other's production. Each molecule can be formed by at least one chemical reaction in the network, and each reaction can be catalyzed by at least one other molecule in the network. This process will create a network that exhibits a primitive form of metabolism and an information system that replicates itself from generation to generation.

"An autocatalytic network works like a community; each molecule is a citizen who interacts with other citizens and together they help create a society", explains Steen Rasmussen.

This autocatalytic set quickly evolved into a state where strings of all lengths existed in equal concentrations, which is not what is usually found. Further, the selected strings had strikingly similar patterns, which is also unusual.

"We might have discovered a process similar to the processes that initially sparked the first life. We of course don't know if life actually was created this way - but it could have been one of the steps. Perhaps a similar process created sufficiently high concentrations of longer information strings when the first protocell was created", explains Steen Rasmussen.

Basis for new technology

The mechanisms underlying the formation and selection of effective information strings are not only interesting for the researchers who are working to create protocells. They also have value to researchers working with tomorrow's technology, like they do at the FLINT Center.

"We seek ways to develop technology that's based on living and -like processes. If we succeed, we will have a world where technological devices can repair themselves, develop new properties and be re-used. For example a computer made of biological materials poses very different - and less environmentally stressful - requirements for production and disposal", says Steen Rasmussen.


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More information: Europhysics Letters, epljournal.edpsciences.org/art … l16388/epl16388.html
Journal information: Europhysics Letters (EPL)

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Oct 20, 2014
Another truly misleading article title - they didn't create anything but a model that demonstrates a virtual process starting with advanced computer equipment and sophisticated programming.. Nothing was done in a test tube or with real molecules. Science fiction movie makers create all kinds of virtual life all the time (on the screen) but that doesn't make it real or even plausible.

Oct 20, 2014
possess the ability to eat, grow, propagate, etc. etc or else it would die... happended [sic]
Uh verk, these things are included in the definition of life.

"1. the condition that distinguishes animals and plants from inorganic matter, including the capacity for growth, reproduction, functional activity, and continual change preceding death."
Such nonsense is of course mathematically impossible
How would you know? Youve demonstrated that you dont know math, and you dont know what life is. Making an empty statement and adding words like 'mathematically' do not increase its credibility.

Why do you insist on offering opinions on things you know nothing about? You only serve to further discredit the creationist cause. If that is even possible.

I can only imagine how disappointed you will be when scientists finally figure out how life arises spontaneously, and how to make it in the lab.

And they will you know. So prepare yourself.

Oct 20, 2014
... it would have to additionally magically and immediately possess the ability to eat, grow, propagate, etc. etc or else it would die ... Such nonsense is of course mathematically impossible.


Energy drives such reactions -- they form "in food". They are already "eating". If the reactions are also building a shell around themselves for instance by forming a protein shell of their waste, then they only need to be subdivided and the two shells will continue to grow.

Oct 20, 2014
@LariAnn & verkle

If this article interests you then i highly recommend Stuart Kauffman's "At Home in the Universe" which explores these concepts in much more detail. It's a thoroughly engaging eye opener...

The work described here is intriguing because the results exhibit strong emergent order from a randomly-self organizing "edge of chaos" system - a quintessentially 'lifelike' property in the quest to find the aforementioned protocells.

Oct 20, 2014
This is an example of how complexities can emerge from simple actions. Cellular automata are demonstrations of this self-organizing ability. We are the consequence.

Oct 20, 2014
@verkle
The usual drivel from the anti-science creationist. Maybe one day you'll actually understand the science and appreciate the timeframe and the complex journey that life took to evolve to the beauty and diversity we have today, but I doubt it.

Oct 20, 2014
Verkle, it could of very well lasted (and since we're talking, it very well could have), it's just chemistry, you're alive because of the chemistry of your surroundings, and you're a lotmore complicated than these things.

JVK
Oct 20, 2014
Arrival of the Fittest: Solving Evolution's Greatest Puzzle http://www.amazon..._title_0 contains the most up-to-date information on the likelihood that scientists will ever create the most primitive of living systems.

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

JVK
Oct 20, 2014
"...selection will act on variation in free energy consumption, often manifesting itself as high metabolic efficiency, reproduction rate and motility, etc. [12]."

http://rsif.royal...abstract

Including the ecological variables associated with biophysically-constrained adaptations limits speculation about the creation of life or the creation of a possible precursor to life.

Ask yourself this: Are evolutionary theorists 'nob ends'? http://perfumingt...ob-ends/

How can any serious scientist ignore the facts that link metabolism to life?

Oct 21, 2014
How can any serious scientist ignore the facts that link metabolism to life?
how can you ignore empirical evidence that is right in front of you that proves that you are wrong as well as undermines your argument and shows you have no idea what you are talking about?
which is proven in your inability to comprehend the definition of the word mutation as well as your continued failure to recognize Lenski's et al's work and it's meanings
remember.. 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
your own words prove you are stupid and choose to ignore empirical evidence, so quit spamming and trolling/baiting with your perfume sites and creationist viewpoint which has been debunked

JVK
Oct 21, 2014
Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli http://dx.doi.org....1001490

Idiot minions of biology teachers like PZ Myers include Captain Stumpy who monitors phys.org for opportunities to contribute pseudoscientific nonsense to discussions that might otherwise include intelligent participants.

Serious scientists know that Lenski's experiments exemplified one carbon metabolism, not evolution.

"...adaptive diversification has been documented in microbial evolution experiments [11],[12],[27]–[31] in which well-mixed populations of Escherichia coli bacteria founded with a single genotype repeatedly evolve two metabolically distinct phenotypes. When grown in well-mixed serial batch cultures in medium with glucose and acetate as carbon sources, E. coli cells preferentially metabolize glucose and excrete acetate until the glucose is depleted and then undergo a diauxic switch to acetate consumption [32]."

Oct 21, 2014
Idiot minions of biology teachers like PZ Myers include Captain Stumpy who monitors phys.org for opportunities to contribute pseudoscientific nonsense to discussions
pseudoscience is a claim, belief or practice which is falsely presented as scientific, but does not adhere to a valid scientific method, lacks supporting scientific evidence or plausibility, cannot be reliably tested, or otherwise lacks scientific status.

Pseudoscience is:
-promoting a model that causes mutations as a method for diversity while antagonistically arguing against mutations as a method for diversity

-saying mutations are never beneficial and then posting a model as a means for beneficial mutations

-ignoring the lexicon of a field out of blatant stupidity even when taught time and again the definitions of simple things like mutation or even scientific theory

-jk and his creationist belief wrapped in word salads of stupidity appealing to self-authority that doesn't exist

Oct 21, 2014
Serious scientists know that Lenski's experiments exemplified one carbon metabolism, not evolution
serious scientists also know that:
Because bacteria reproduce so quickly, we use them in experiments to test evolutionary hypotheses. For over 20 years and 45,000 bacterial generations, my students and I have maintained twelve populations of E. coli in small flasks of sugar water. We measure the process that Darwin discovered – adaptation by natural selection – by competing 'modern' bacteria against their ancestors, which we store frozen and then revive for the tests
[sic] Lenski
http://www.nsf.go...say1.jsp

REAL SCIENTISTS trump perfumers posing as diagnosticians illegally any day of the week, jk

IOW - push your creationist pseudoscience elsewhere
it is NOT even supposed to be posted here : https://sciencex....omments/
you trolling crackpot


JVK
Oct 21, 2014
Epigenetics Kohl (Jul. 2013) http://youtu.be/DbH_Rj9U524

Epigenetics Nova (Oct. 2013) https://www.youtu...cu7v9x1w

http://wakeup-wor...y-finds/
"...the core tenet of classical genetics is patently false, and by implication: what we do in this life — our diet, our mindset, our chemical exposures — can directly impact the DNA and health of future generations."

Oct 25, 2014
What a hilarious turnout of anti-scientist creationists, I count 4 (including the pheromone troll, naturally)! That science is solving how life emerged bothers them, obviously.

This is relevant modeling for the step from non-replicating protocells to replicating ones (and the title is correct due to that). They explore a new area of the phase space during that process, since earlier models got that achieving replicators is easier yet. The combination of these models is yet to be attempted by this team.

This is the same kind of modeling that is used for exploring supernovas or AGW before it could be seen in the signal. It is relevant without lab tests, and in some case you can't do it any other way - you can't make a supernova in the lab (even less a star), you can't speed up the time for evolution of replicating strings from nucleotides in a suitable reactor to be less than the predicted ~ 10 000 years (for RNA).

[tbctd]

Oct 25, 2014
[ctd] Such reactors are known to have existed in the Archean (alkaline hydrothermal vents) as well as the rough pathways up to nucleotides. It is the best pathway we know of, and it is consistent with phylogenetic evidence (homologous traits between those vents and modern cells).

That said, we can test the emergence in the lab eventually, taking snapshots, in the same way that we have tested supernova and AGW models in nature.

This is how life emerged, and there is no competing theory. Particularly, while astrobiology has advanced on the found pathway, creationism has retreated further (as it is all it can do in front of evidence). Emergence of life or emergence of the universe (inflation did cosmological creationism in) or existence of minds (LHC killed religious 'souls', the brain-body is a pure biochemical machine) are no longer amenable for a religious "gaps-for-magic" argument.

The result is that creationists can only troll with ineffectual lies.

Oct 25, 2014
Reflecting more, isn't it curious that the creationists troll a result that could be used to imply "support"? As I noted, they found emergence was a tad more difficult (though not impossible) than earlier research.

It is as if creationists never bother to actually _read_ the papers... =D

Oct 25, 2014
No one know how to create life.

JVK
Oct 25, 2014
No experimental evidence of biologically-based cause and effect suggests that one species evolves into another across eons. Instead, what's just been reported is how quickly changes can occur in morphological and behavioral phenotypes.

http://www.utexas...florida/ "This latest study is one of only a few well-documented examples of what evolutionary biologists call "character displacement..."

Character displacement is ecological speciation. It is called other things because evolutionary theorists have taught most people to believe in pseudoscientific nonsense despite clear results from serious scientists that link the epigenetic landscape to the physical landscape of DNA in organized genomes of species from microbes to man via conserved molecular mechanisms.

Molecular epigenetics (1996): http://www.hawaii...ion.html "Small intranuclear proteins..."

JVK
Oct 25, 2014
It is the best pathway we know of, and it is consistent with phylogenetic evidence


Only if you ignore everything currently known about the biophysically-constrained thermodynamcis of chemical bonds and protein folding required to support the molecular biology of conserved molecular mechanisms that link physics, chemistry, and systems biology to biodiversity manifested in organism-level thermoregulation (i.e., the nutrient-dependent pheromone-controlled physiology of reproduction in species with different morphological and behavioral phenotypes).

What the ignorant leave out of their claims is everything known by the intelligent who refused to believe in ridiculous theories. Obviously, there are more ignorant people than intelligent people, which is why accurate dissemination of biological facts is important to me, and denial of biological facts is important to people like Torbjorn_Larsson_OM

Oct 25, 2014
this is all bullshit god didn't do this intelligent aliens from centauri B did this . it's aliens i tell you . they seeded life. smart ass aliens.

JVK
Oct 26, 2014
http://www.ieu.uz...tic.html "Genetic and metabolic networks drive all biological processes. You can think of them as bridges between the organism and the individual molecules – proteins and genes – that form all living cells."

Metabolic and genetic networks are required. That makes it less likely that anything scientist create can correctly be called a possible precursor to life. They would need to simultaneously create interacting precursors. Each could lead to half the requirement for life -- either a genetic network, or a metabolic network. Both are biophysically constrained by entropy. Thus, the fine-tuning of the interactive network(s) suggests another layer of complexity.

Those who suggest life arose in a self-organized fine-tuned state may not be from this planet. If they are, they are not intelligent creatures. Intelligent creatures do not believe in the magic of mutations/natural selection or in the evolution of biodiversity.

Oct 26, 2014
What the ignorant leave out of their claims is everything known by the intelligent who refused to believe in ridiculous theories. Obviously, there are more ignorant people than intelligent people, which is why accurate dissemination of biological facts is important to me, and denial of biological facts is important to people like Torbjorn_Larsson_OM

I suppose that begs the question "how do you define ignorance". I already know your answer, so don't bother.

On the topic of clear communication: Word salad - remember? You are clearly lacking in the skill.

And a reminder. As others have pointed out, you do have a business interest selling perfumes that are claimed to be infused with human pheromones. Your expressed "nutrient dependent, pheromone controlled" view is hardly unbiased.

JVK
Oct 26, 2014
Fear memory formation can affect a different memory: fear conditioning affects the extinction, but not retrieval, of conditioned taste aversion (CTA) memory http://journal.fr...w43-2014 links everything currently known about how the epigenetic landscape is linked to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms of experience-dependent learning and memory at the cellular level of amino acid substitutions that differentiate cell types and morphological / behavioral phenotypes.

Of course my details of how odor-induced changes in receptor-mediated behaviors associated with human pheromones and the pheromones of other species support the conclusions in the above article. What makes anyone think that my conclusions are part of a marketing ploy? How can anyone be that ignorant (no def. required)?

JVK
Oct 26, 2014
Why don't others cite the extant literature on biological facts so that pseudoscientists cannot keep touting their nonsense without addressing it. What Ren82 just expressed is not an opinion and it was stated in : A universal trend of amino acid gain and loss in protein evolution http://www.nature...306.html

"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."

This statement has been echoed in the extant literature since we detailed RNA-mediated cell type differentiation in our 1996 review. Yet look at all the 5-star ratings for comparison to my one-star rating.

Oct 26, 2014
Intelligent creatures do not believe in the magic of mutations/natural selection or in the evolution of biodiversity.
if intelligent creatures do not believe in this, why have you specifically supported it with your own model of mutations and proof that evolution is the cause of biodiversity?
this means that you are saying that you, jk specifically, are NOT intelligent, because your own model creates MUTATIONS and is a supporting model proving The Theory of Evolution is as true now as it ever was
remember.. I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
so by your own words, you are either NOT INTELLIGENT or you are blatantly lying to gain popularity for your perfume
i think it is BOTH, considering you admitted you couldn't make it through college

Oct 26, 2014
What makes anyone think that my conclusions are part of a marketing ploy?
maybe because you say one thing like
Intelligent creatures do not believe in the magic of mutations/natural selection
while then turning around and promoting a model that causes mutations? 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
so you are either LYING or promoting pseudoscience for the sake of marketing!
Why don't others cite the extant literature on biological facts
here is some FACTS that prove you are a LIAR and don't know what you are talking about
http://myxo.css.m...dex.html
PROOF of beneficial mutations that makes you a liar

there is plenty more
regardless of how YOU "choose" to interpret the evidence
it makes you a liar


JVK
Oct 26, 2014
How likely is it that someone who comments here as Captain Stumpy knows anything about anything. For comparison, see any of the 80 citations to my award-winning published review with co-authors from Vienna:

Human pheromones: integrating neuroendocrinology and ethology
http://scholar.go...mp;hl=en

NOM
Oct 26, 2014
If you are so successful, why are you trolling here?

You are a phony Kohl.

Oct 26, 2014
How likely is it that someone who comments here as Captain Stumpy knows anything about anything
lets see... i have never lied
i have admitted when i make mistakes
i continually put up links supporting my comments, or even quotes, directly from the source, like the ones i use directly from you, jk
I have 2 4yr degree's and experience that far outstrips even yours
and i can learn still, by research and by reading, which obviously YOU cannot do, because you still argue over the word mutation and your own model causes mutations, making you the biggest idiot poster here on PO!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
those are YOUR words, jk, not mine
quoted from YOU!
your appeal to self-authority only underscores your idiocy and how you are an epic failure

Oct 26, 2014
For comparison, see any of the 80 citations
how do ANY of your own citations copare with the stupidity you blatantly published above in your posts?

like anti-mutation writings when you have published a model that supports mutations?

or like anti-mutation and anti-evolution rants when your own model supports evolution by causing mutations?

your own words refute you! not just my posts, YOUR OWN WORDS!

then there is the blatantly ignoring of empirical evidence like Lenski because it is against your religion and faith

that is why you are a TROLL and PSEUDOSCIENCE CRACKPOT

JVK
Oct 26, 2014
http://dx.doi.org...4-0895-5

The A or Met allele is associated with lower enzymatic activity (due to thermoinstability), and with exploratory behaviour. That links exploratory behavior from nutrient availability to thermodynamic cycles of protein biosynthesis and degradation required for organism-level thermoregulation at every level of ecological adaptation manifested in increasing organismal complexity in species from microbes to man.

If you are so successful, why are you trolling here?


I've told you before; this is where the ignorance is. I measure my success in the amount of pseudoscientific nonsense I can refute by providing evidence of biologically-based cause and effect that only anonymous fools continue to ignore.

80 citations to our 2001 review predict what will happen now that nearly 10,000 people have viewed my 2013 review. http://www.ncbi.n...24693353

NOM
Oct 27, 2014
this is where the ignorance is
Certainly is when you are here Kohl. I don't care how many people have read your rubbish, it's still rubbish.

NOM
Oct 27, 2014
I bet that PZ Myers doesn't need to brag that a few people have read one of his peer reviewed papers.

And Kohl, out of those 10,000: 1,000 would be search bots hits; 3,000 spam bots (half of which you pointed there from physorg); 3,000 lost people; 2,900 people who were very disappointed; and 100 idiots like you, It isn't that impressive a number.

Oct 27, 2014
Is methylation amd deamination responsible for all base substitutions in your model? A to T, A to C, etc.?

Oct 27, 2014
Mathematics is a useful science when you need to distinguish effectively philosophical and speculative theories of reality in which we live. In real world we have not evolution but process of accumulation of random errors in the DNA of each generation, leading to a drop in the quality of the DNA with time due to the loss of information. This process is called genetic entropy and leads to a lower capacity and the vitality of human race or any other species over time. Immune system and the complex cell defense mechanisms are responsible to fight mutations and restoring normal consistency and integrity of the DNA, but not always successful in 100% of cases. Larger mutations are removed from the natural selection thus population returns to the original gene pool. However, over time the quality of the gene pool is falling, because smaller mutations that are passed on to future generations. This means that our distant ancestors were more developed mentally and physically.

Oct 27, 2014
I've told you before; this is where the ignorance is
we've already established that... but if you leave, the ignorance will drop drastically
the amount of pseudoscientific nonsense I can refute
the problem with this is that you are producing the most pseudoscience and nonsense, especially when you blatantly ignore empirical data for the sake of your own faith based pronouncements
see all of your above posts against putation!
considering your model causes mutations, then any arguments you have against mutations is nothing more than your ignorance and stupidity playing forth publicly for everyone to see

every time you post anti-mutation drivel while touting your own model, you proclaim yourself to be a pseudoscience crackpot and incapable of learning the basics of your own field, which makes you blatantly stupid
especially when you lie about your supposed authority (claiming to be a diagnostician)

you are not a scientists, jk, just blatantly stupid

Oct 27, 2014
The disputes are won with reason and arguments, not with emotions. My view point is shared by many honest researchers biologists who care about scientific truth more than for his career and a warm place in some research institute. Science does not need parrots who uncritically absorb everything they are told at the university, often teach anti science and are not sure criterion for knowledge. Such people are suitable to maintain the imposed system and scientific dogma, but do not contribute to real science, which are needed minded people. When all start thinking alike then nobody thinks properly.

JVK
Oct 27, 2014
Bacteria ecologically adapt: http://www.scienc...5415.htm

Plants ecologically adapt via conserved molecular mechanisms
http://comments.s....1259923

Viruses ecologically adapt "Identification of two amino acid residues on Ebola virus glycoprotein 1 critical for cell entry" http://www.scienc...06001882

"If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based." (p 1014) http://jp.physoc....abstract

Experimental evidence of biologically-based cause and effect now incorporates the laws of physics, the chemistry of RNA-mediated protein folding, and the molecular biology of cell type differentiation via amino acid substitutions in species from microbes to man.

NOM
Oct 27, 2014
Kohl. The reason that physorg added the "ignore user" button. Hopefully now he will go away.

JVK
Oct 28, 2014
Is methylation amd deamination responsible for all base substitutions in your model? A to T, A to C, etc.?


Why do you ask? What do you think is responsible for ALL base pair flipping and substitutions? The reason I ask is because I think you have no idea of how the epigenetic landscape becomes the physical landscape of DNA in the organized genomes of species from microbes to man, and yet you wrote a review of my model that loaded the entirety of your ignorance onto me.

Others, see: http://www.ncbi.n...4049134/ Criticisms of the nutrient-dependent pheromone-controlled evolutionary model

"Based on his writings, both published and unpublished, 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."

This comes from a fool with no model of biologically-based cause and effect.

JVK
Oct 28, 2014
When all start thinking alike then nobody thinks properly.


The goal of most professors seems to be to teach their students to think like they think and to believe what they believe. That's why at least two generations of students have been taught to believe in pseudoscientific nonsense. And they have been taught so well to believe in ridiculous theories that they don't recognize biological facts when they are presented.

Their knee jerk response is to regurgitate what they've been taught to believe in as if it ever made any sense whatsoever in the context of physics, chemistry, and the conserved molecular biology of cause and effect in species from microbes to man.

you are not a scientists, jk, just blatantly stupid
--Captain Stumpy

I am a medical laboratory scientist (ASCP) with a publication history that spans nearly two decades. See also: http://perfumingthemind.com/

Oct 28, 2014
--Captain Stumpy

I am a medical laboratory scientist (ASCP) with a publication history that spans nearly two decades. See also: http://perfumingthemind.com/
@jk
no need to SPAM and TROLL with your perfume site
and you also have claimed to be a diagnostician with years experience as well, shall i dig up that little quote for you too?
you DO know that it means you were "diagnosing" without a license and therefore subject to legal action as well as to action from the board, right?

go urinate on someone else and try to convince them it is raining, it will not work with me

you've already demonstrated, repeatedly, that you have no working knowledge of the lexicon of your field
nor do you comprehend modern advances in the biological field, as proven by your comments against Lenski et al

self-reference and appeal to self authority are not helping you either, pseudoscience boy

your whole approach is faith based and therefore bound to failure!

Oct 28, 2014
Why do you ask? What do you think is responsible for ALL base pair flipping and substitutions?


Shall I take that as a "yes"?

JVK
Oct 28, 2014
You should take it as two questions that you cannot answer because you know nothing about how cell type differentiation occurs.


JVK
Oct 28, 2014
you've already demonstrated, repeatedly, that you have no working knowledge of the lexicon of your field


Human pheromones: integrating neuroendocrinology and ethology (cited 80 times)
http://www.nel.ed...view.htm
"Zdenek Klein Award for Human Ethology" (2001)
http://www.nel.ed...ward.htm

Comparative approaches in evolutionary psychology: molecular neuroscience meets the mind (cited 70 times)
http://www.ncbi.n...12496741
"Claims regarding evolved, uniquely human, psychological constructs should be constrained by the rigorous evidentiary standards that are routine in other sciences."
"Zdenek Klein Award for Human Ethology" (2002)

JVK
Oct 28, 2014
Self-Sustained Replication of an RNA Enzyme
http://www.scienc...abstract

"An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely. Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population. These replicating RNA enzymes can serve as an experimental model of a genetic system. Many such model systems could be constructed, allowing different selective outcomes to be related to the underlying properties of the genetic system."

JVK
Oct 28, 2014
Search Results for: RNA-mediated
Number of Results: 126

http://perfumingt...mit.y=20

RNA-mediated events are biophysically-constrained and link the chemistry of protein folding to amino acid substitutions that differentiate the cell type of all individuals in all genera.

We provided the first details of these RNA-mediated events in our 1996 Hormones and Behavior review. From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism..."

No biologically-based mechanism has ever been described that links evolutionary events to the diversity of morphological and behavioral phenotypes manifested in the context of ecological adaptation to the availability of food and pheromone-controlled reproduction.

Oct 28, 2014
You should take it as two questions that you cannot answer because you know nothing about how cell type differentiation occurs.


Differentiation is a developmental process by which stem cells and other undifferentiated cells become specialized and form different cells and tissues. This process does not involve base flipping or substitutions. It relies on induced changes in gene expression.

Either you think methylation is the cause of said flips and substitutions or you don't. Which is it?

Self-Sustained Replication of an RNA Enzyme
http://www.scienc...abstract


The basis of my undergraduate thesis, where I *modeled* abiogenesis of RNA based protocells using prebiotic chemistry and physics! How nice of you to acknowledge that.

JVK
Oct 28, 2014
The article here states: "The oldest ancestor of life on Earth was a protocell, and when we see, what it eventually managed to evolve into, we understand why science is so fascinated with protocells."

That is precisely the type of pseudoscientific nonsense that my model refutes. Protocells could not have 'evolved.' Nutrient-dependent replication of cell types is required -- as is their controlled reproduction. The availability of nutrients biophysically constrains cell type replication and the metabolism of nutrients to species-specific pheromones controls ecological speciation by linking the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man -- none of which evolved from any other species; all of which ecologically adapted.

What kind of idiot enters discussion on a topic like this without knowing anything about physics, chemistry, or molecular biology? That was a rhetorical question.

JVK
Oct 28, 2014
...stem cells and other undifferentiated cells become specialized and form different cells and tissues. This process does not involve base flipping or substitutions. It relies on induced changes in gene expression.


I stand in awe of the magical world of cell type differentiation that you live in.

1) become specialized
2) form different cells
3) induced changes in gene expression.

Prolegomenon to patterns in evolution http://www.scienc...14000380

" Patterns of Evolution
If we can have no entailing laws for the detailed evolution of the biosphere, can we use the ideas above to help look for patterns in evolution?"

RNA-mediated events link the nutrient-dependent induced changes in gene expression to pheromone-controlled biodiversity of cell types in species from microbes to man. The anonymous fool claims he: "*modeled* abiogenesis of RNA based protocells using prebiotic chemistry and physics!"

JVK
Oct 28, 2014
Anyone else who claims they have
*modeled* abiogenesis of RNA based protocells using prebiotic chemistry and physics!
should accept my invitation to compare their model to mine.

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

What the anonymous fool (aka Andrew Jones) did was criticize my model without offering his model for comparison. That makes it appear that he has no model, and has only the pseudoscientific nonsense he was taught to believe in to compare to my model. We can all understand why someone with only the pseudoscientific nonsense he integrated into his *model* would not want to compare it to any accurate representation of biologically-based cause and effect.

See for example: http://www.ncbi.n...4049134/

Oct 28, 2014
What kind of idiot enters discussion on a topic like this without knowing anything about physics, chemistry, or molecular biology?


My primary thesis advisor is an ecologist and my secondary is a biochemist/molecular biologist.

I stand in awe of the magical world of cell type differentiation that you live in.


Cellular differentiation is well defined and studied. Differentiation is what your cells go through when you go from a fertilized egg to a fully grown organism. All your cells have the same genetic material. The difference between your brain cells and your liver cells is due to expression differences, not base substitutions.

criticize my model without offering his model for comparison.


All you have to do is Google "evolutionary model" and you'll find TONS of them backed by experimental evidence and involving mutation and selection, such as-

http://mbe.oxford...abstract

Oct 28, 2014
Kohl. The reason that physorg added the "ignore user" button. Hopefully now he will go away.
They should include an automatic 1/5 for all posts the ignored poster makes. Save us the trouble.

JVK
Oct 28, 2014
Differentiation is what your cells go through when you go from a fertilized egg to a fully grown organism.


In "From fertilization to adult sexual behavior" we started with nutrient-dependent pheromone-controlled cell type differentiation in yeasts and linked it to mammals. Elekonich and Robinson linked hormone-organized and hormone-activated behaviors to insects via our model of RNA-mediated events, and Elekonich and Roberts linked hormone-organized and hormone-activated behaviors in the honeybee model organism to life history transitions.

Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults http://dx.doi.org...4-0895-5 links a single amino acid substitution to human behavioral development via the conserved molecular mechanisms that link honeybees to humans and all other biodiversity.

Request a tuition refund. Your thesis advisers taught you to believe in their pseudoscientific nonsense.

JVK
Oct 28, 2014
The difference between your brain cells and your liver cells is due to expression differences, not base substitutions.


In Kohl (2013) I linked one base pair change to an amino acid substitution and differentiation of cell types in the liver, mammary tissue, sweat glands, and hair of mice and a human population via nutrient-dependent pheromone-controlled ecological adaptations.

You made no mention of the fact that fish odor syndrome is the link from genetic networks to metabolic networks in mice and humans in your ridiculous comments on my review. Instead, you wrote "Allele changes are not epigenetic and I know of no mechanism that makes deterministic gene sequence changes prompted by epigenetic alterations."

You should have written about how mutations lead to the evolution of biodiversity, since others had already confirmed they do not. http://genomebiol...15/1/401 "the interactions between pre-mRNA and proteins fine-tune alternative splicing..."

JVK
Oct 28, 2014
1996 "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 [flies] and Caenorhabditis elegans [worms]..."

Alternative RNA Splicing in Evolution http://jonlieffmd...volution

"...alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes."

Oct 28, 2014
In Kohl (2013) I linked one base pair change to an amino acid substitution and differentiation of cell types in the liver, mammary tissue, sweat glands, and hair of mice and a human population via nutrient-dependent pheromone-controlled ecological adaptations.


Thanks for pointing out your misinterpretation. The base pair change you're referring to was not a change *during* development/differentiation, it was a change *affecting* it. It was a change in the germline that got passed on to subsequent generations, not a change that occurred in those tissues during the life of the organisms.

You should have written about how mutations lead to the evolution of biodiversity


There are many such examples, this being one of them-

http://www.scienc...2649.htm

Another one-

http://www.sott.n...-survive

JVK
Oct 29, 2014
"...a mutation in a single gene in development can lead to different consequences not only in jaw shape, but how this leads to different feeding strategies.


My focus is on details that link feeding (nutrient uptake) to genetic networks and metabolic networks, which control the physiology of reproduction and enable fixation of amino acid substitutions that stabilize the organized genome.

For contrast, you again offer the magic of mutations as an example of cause and effect. You may be even more ignorant than PZ Myers and your thesis advisers.

Conventional wisdom has it that for any given niche there should be a best species, the fittest, that will eventually dominate to exclude all others.


http://www.ncbi.n...24693353
"THIS MODEL DETAILS HOW CHEMICAL ECOLOGY DRIVES ADAPTIVE EVOLUTION VIA: (1) ecological niche construction, (2) social niche construction, (3) neurogenic niche construction, and (4) socio-cognitive niche construction."

JVK
Oct 29, 2014
The base pair change you're referring to was not a change *during* development/differentiation, it was a change *affecting* it.


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

The A or Met allele is associated with lower enzymatic activity (due to thermoinstability), and with exploratory behaviour during the development of behavior. It obviously links epigenetic effects on genetic networks and metabolic networks to the hormones that affect behavior.

The anonymous fool (aka Andrew Jones) seems to think that a base pair change can automagically affect something without the epigenetic effects of food odors and pheromones that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms.

JVK
Oct 29, 2014
The companion paper to the one the anonymous fool cited detailed the involvement of nutrient-dependent pheromone-controlled ecological adaptations that link the epigenetic landscape to the physical landscape of DNA in organized genomes of species from microbes ot man without the pseudoscientific nonsense of evolutionary theory.

"Progress towards understanding adaptive radiations at the mechanistic level is still limited with regard to the proximate molecular factors that both promote and constrain evolution. Here we focus on the craniofacial skeleton and show that expanded Wnt/β-catenin signalling early in ontogeny is associated with the evolution of phenotypic novelty and ecological opportunity in Lake Malawi cichlids."

http://www.nature...629.html

"...proximate molecular factors that both promote and constrain evolution." can be compared to Nei's 'constraint-breaking mutations'.

JVK
Oct 29, 2014
I reiterate: "...proximate molecular factors that both promote and constrain evolution." can be compared to Nei's 'constraint-breaking mutations'.

"...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

The anonymous fool did not compare Nei's model to my model. He simply tried to tell others that my model was a misrepresentation of biologically-based cause and effect because he was taught to believe in pseudoscientific nonsense. So were you. Why did you believe it?

"Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... No, it wasn't dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact."

Oct 29, 2014
For contrast, you again offer the magic of mutations as an example of cause and effect.


Actually, I offered you a model of mutation and selection. No magic needed.

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


That doesn't conflict with what I said. Again, a change in a gene that controls development is not the same as a change DURING development.

He simply tried to tell others that my model was a misrepresentation


See my citation to the model I posted before. That's beside the fact that I don't necessarily need to provide an alternative if all I'm doing is pointing out how yours is flawed. You draw false conclusions from other people's research, therefore your assumptions are wrong amd your model is wrong.

JVK
Oct 29, 2014
I don't necessarily need to provide an alternative if all I'm doing is pointing out how yours is flawed.


You took the entirety of what is currently known about the physics, chemistry, and molecular biology of ecological adaptations -- as detailed across nearly two decades of my published works -- and dismissed cross species examples in model organisms as if nutrient-dependent amino acid substitutions did not differentiate their cell types via pheromone-controlled reproduction.

You have continued to dismiss all other evidence that supports my model in its entirety and claim that mutations somehow lead to the evolution of biodiversity, based on what others have asserted.

I concluded: "Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."

You conclude:
I don't necessarily need to provide an alternative...


You're nothing more than an anonymous fool.

Oct 29, 2014
Human pheromones: integrating neuroendocrinology and ethology (cited 80 times)
@jk
-cannot figure out how his own model causes mutations - repeated more than 120 times on Phys.org site in multiple comment threads
-cannot comprehend why he is called an idiot/stupid when he argues against beneficial mutation while promoting a model that causes beneficila mutation - repeated more than 120 times on Phys.org site in multiple comment threads
- cannot remember that 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
-argue's a faith on a science site against the overwhelming evidence of evolution theory more than 120 times on PO, etc
- tried to get us to believe in his experience as a diagnostician after admitting to failin gout of college!

shall i go on, jk-TROLL?

Oct 29, 2014
That is precisely the type of pseudoscientific nonsense that my model refutes
@jk
no, it does not
your model actually helps PROVE beneficial mutation right along with Lenski and others, therefore your continued claims of pseudoscience to actual degree'd professional scientists working in the field who know what the heck is going on is nothing more than a toddler-style rant and temper tantrum

you've never been able to refute a single study with any empirical evidence

you simply keep re-linking your perfumes site with more pseudoscience and attempts to re-interpret reality based upon your faith, which is why you will always be a failure in the eyes of science and why you are crackpot-trolling here

your work may have done more had you not turned into the uber-troll lying about your experience while ignoring the rest of reality that proves your faith wrong

Kohl the TROLL

Oct 29, 2014
Nutrient-dependent/pheromone-controlled adaptive evolution: a model
this "model" is nothing more than supporting evidence for EVOLUTION THEORY proving that mutations can be beneficial
when you argue against mutations with
Intelligent creatures do not believe in the magic of mutations/natural selection
but you've already admitted your model makes mutations 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
then you simply support my calling you a PSEUDOSCIENCE TROLL and that you are stupid, ignoring evidence while promoting a FAITH and NOT SCIENCE

this is why you continually FAIL

you think prior work trumps your current dogmatic faith based posted diarrhea here at PO

it doesn't
you post against SCIENCE
means you post PSEUDOSCIENCE

kohl=TROLL

Oct 29, 2014
as if nutrient-dependent amino acid substitutions did not differentiate their cell types via pheromone-controlled reproduction.


Your problem is that you're mixing up so many different terms and concepts that are dissimilar.

Cell differentiation refers to the specialization of cells within an organism, i.e. stem cells to mature specialized tissues. It is not the result of DNA base substitutions, because all your cells have the same genome (although it can be the result of amino acid substitutions at the level of RNA editing), it is the result of differential expression and splicing. You have refered to differentiation in the context of Lenski's E. coli. Bacteria do not undergo differentiation. They are single celled. They don't have different cell types. Differentiation, by definition, is not what occurs when genotypes/phenotypes change over subsequent generations, which is what you seem to imply you think it means.

Oct 29, 2014
You took the entirety of what is currently known about the physics, chemistry, and molecular biology of ecological adaptations -- as detailed across nearly two decades of my published works
and here we see WHY he cannot come to grips with reality: narcissism

he is stuck on himself so he cannot see the reality of the world around him since it refutes his ideas and faith with empirical evidence

want to know WHY kohl=TROLL?
this simple paragraph from Anon explains it all!
Thanks for pointing out your misinterpretation. The base pair change you're referring to was not a change *during* development/differentiation, it was a change *affecting* it. It was a change in the germline that got passed on to subsequent generations, not a change that occurred in those tissues during the life of the organisms
jk thinks he has no faults, but forgot that he failed out of college & can't remember basic terminology (like the definition of mutation)

kohl=PSEUDOSCIENCE TROLL

Oct 29, 2014
Your problem is that you're mixing up so many different terms and concepts that are dissimilar.
@anonymous_9001
this is something that i have been pointing out to him for a long time
and the reason that you don't even need a degree in biology to see that his faith based ideals are pseudoscience and he is spouting off about BS

thanks for continuing to bring legitimate science to the comment section, Anon

I continually learn more and more as you refute this particular idiot, although it is repetitious in a lot of ways

keep up the GREAT work, Anon!

and a sincere thank you

I think Otto might be on to something as well...
maybe the site should be more concerned about negative feedback and delete users that consistently carry a 1 to 2 star rating for their continued pseudoscience posts?

it would help a lot and allow those who come here to learn science the ability to read legitimate posts and not have to wade through & research loads of BS

Oct 29, 2014
"I think Otto might be on to something as well...
maybe the site should be more concerned about negative feedback and delete users that consistently carry a 1 to 2 star rating for their continued pseudoscience posts?

it would help a lot and allow those who come here to learn science the ability to read legitimate posts and not have to wade through & research loads of BS"

@Captain Stumpy
That's a ten star comment.


JVK
Oct 30, 2014
Differentiation, by definition, is not what occurs when genotypes/phenotypes change over subsequent generations...


DEFINITIONs are used by idiots to make it appear that species evolve. Serious scientists know that ecological adaptation occurs via amino acid substitutions that stabilize the genome. Ecolological ADAPTATION is nutrient-dependent and pheromone-controlled via conserved molecular mechanisms of cell type differentiation that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.

http://www.scienc...5415.htm "...established that the amino acid glutamate was essential to nisin's transformation."

The transformation of the gene was nutrient-dependent and RNA-mediated via thermodynamic cycles of protein biosynthesis and degradation. It required an amino acid substitution that changed the cell type to one with a more functional protein structure.

JVK
Oct 30, 2014
"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... The anglophone tradition was taught. I was taught, and so were my contemporaries, and so were the younger scientists. Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... No, it wasn't dishonesty. I think it was wish fulfillment and social momentum. Assumptions, made but not verified, were taught as fact." http://www.huffin...211.html

Decades after the invention of a ridiculous theory, we have anonymous fools and idiot minions of biology teachers like PZ Myers who still tout it in discussions like this one. The ignorant discussants are also those who support even more ridiculous theories proposed by scientists who think they can create life.

Assumptions are made and facts are eliminated by definitions.

Oct 30, 2014
DEFINITIONs are used by idiots to make it appear that species evolve.


Definitions are used so that people in a discussion can understand each other. If you keep changing the definitions of words arbitrarily, nobody is going to have any clue what you're talking about.

If you have a problem with how a word is being used, explicitly and separately make your case and bring it up with the proper people instead of writing papers and having discussions before telling people "Oh yeah, by the way, I don't use those words like everyone else does. I changed the definition so we've been talking about completely different things this entire time. Oops"


JVK
Oct 30, 2014
"If you learnt evolutionary biology and genetics a decade or more ago you need to be aware that those debates have moved on very considerably, as has the experimental and field work on which they are based." (p 1014) http://jp.physoc....abstract

You were taught to believe in a ridiculous theory and have learned to frame biologically-based cause and effect in terms defined by the pseudoscientists who invented the theory by bastardizing Darwin's works.

It's time for you to move on or simply admit that you have no intention of ever becoming a serious scientist.

http://perfumingt...tiation/

Oct 30, 2014
A decade or more ago? Good thing I learned it within the last 6 years.

Again- If you have a problem with how a word is being used, explicitly and separately make your case and bring it up with the proper people instead of writing papers and having discussions before telling people "Oh yeah, by the way..."

You were taught to believe in a ridiculous theory


No, I was taught to properly interpret evidence. Almost everything you cite actually disagrees with you or has nothing to do with the point you're trying to make.

Oct 30, 2014
DEFINITIONs are used by idiots

definitions:
are used by people to communicate ideas as well as knowledge in the same manner repeatedly for the sake of clarity and concise discussion/transfer

they are used by humans so that people don't continually change the subject and ignore reality

they are used for CLARITY, not obfuscation

people who alter and change definitions from the accepted norm, and who blithely decide to disregard a lexicon in use by professionals, are doing it to intentionally hide something

it is a known trait of criminals, faith based delusional idiots and con men
(because they all use deception for profit)

it is also a common train of pseudoscience: http://math.ucr.e...pot.html
(deception for profit)

it is used by kohl for the exact same reasons
deception for profit

that is why he lied about being an experienced diagnostician

make up definitions as you go- word salad helps in court

Oct 31, 2014
the must try to force their ridiculous perspectives on others by defining terms like 'pheromones'
you are truly a moron
first you say
DEFINITIONs are used by idiots
but when there is an attempt to clarify anything or specify what the definition of a term is, you claim it is forcing ridiculous perspectives?

you do realise that this is why you failed out of college, right?
you cannot even accept that a dictionary/lexicon of important terminology is vital to communicating clear, concise information, which is why you tend towards irrelevant word salad type posts where you appeal to self authority

and you call anyone believing in evolution theory an idiot minion?
at least we are not making it up as we go and hoping no one notices the lack of comprehension skills or the failure to know important definitions in the field like you do!

JVK
Oct 31, 2014
you call anyone believing in evolution theory an idiot minion?


Of course, I do. Doesn't every intelligent person on this planet do the same thing?

"In truth, for all the undoubted charms of dogs, their breeding is nothing other than degeneration."
http://www.evolut...751.html

Epigenomics and the concept of degeneracy in biological systems http://bfg.oxford...abstract

Unpublished "The plumage polymorphism is linked to a chromosomal rearrangement... We then collected brains from those males and isolated RNA from two regions: the medial amygdala and the hypothalamus. We used RNA-sequencing to generate transcriptome data..."

Only idiots like PZ Myers and his idiot minions believe that mutations and natural selection lead to the evolution of biodiversity caused by RNA-directed DNA methylation that results in ecological adaptations.

JVK
Oct 31, 2014
I was taught to properly interpret evidence.


You were taught to believe that evidence automagically appears in the context of observable changes in morphological phenotypes by those Dobzhansky referred to as bird-watchers and butterfly collectors. They taught you to play the role of the anonymous fool and/or Andrew Jones and to ignore biophysical constraints on the chemistry of protein folding and conserved molecular mechanisms of biologically-based cause and effect exemplified in species from microbes to man.

"...the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists!" http://icb.oxford...citation

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

Oct 31, 2014
Did you actually read the paper that quote is from? That's a serious question, because Dobzhansky's message in that passage is the COMPLETE OPPOSITE of what you're implying it is:

The notion has gained some currency that the only worthwhile biology is molecular biology. All else is "bird watching" or "butterfly collecting." Bird watching and butterfly collecting are occupations manifestly unworthy of serious scientists! I have heard a man whose official title happens to be Professor of Zoology declare to an assembly of his colleagues that "a good man cannot teach zoology." A good man can teach, of course, only molecular biology.

Such pronunciamentos can be dismissed as merely ridiculous.


Lets not forget that Dobzhansky was also the one who said "nothing in biology makes sense except in the light of evolution", but it's far more convenient to cherry pick quotes from a man who spent his entire career studying mutation and natural selection.

JVK
Oct 31, 2014
Dobzhansky's message in that passage is the COMPLETE OPPOSITE...


Combating Evolution to Fight Disease http://www.scienc...88.short

"...Theodosius Dobzhansky famously noted that "nothing in biology makes sense except in the light of evolution," but perhaps, too, "nothing in evolution makes sense except in the light of biology." Although the latter might be an exaggeration, an important gap is being filled by molecular understanding of the genesis of variation that confers the ability to evolve."

The genesis of variation is nutrient-dependent via the link between genetic networks and metabolic networks. The link is RNA-directed DNA methylation and cell type differentiation via amino acid substitutions. Dobzhansky (1973) also states: "...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla."

Make sense of that!

JVK
Oct 31, 2014
"Individuals and species belong to ecological communities and ecosystems. An individual taken out of the system in which it normally occurs is incomplete and it may be inviable.
The hierarchy of levels of biological integration may be represented schematically as the following sequence: molecule, cellular organelle, cell, tissue, organ, individual, Mendelian population, species, community, ecosystem. " http://icb.oxford...citation

Evolutionary theorists ignore that sequence. I did not:

"..as the requirement to address levels of epigenetically effected biological organization and activation of sex differences in behavior via the gene, cell, tissue, organ, organ-system pathway became known (Naftolin, 1981), it also became clearer that mammalian pheromones linked sensory input directly to effects on hormones and their affects on sex differences in brain development and behavior..." http://www.ncbi.n...3960065/

Oct 31, 2014
"Scientists create possible precursor to life"
Blockbuster title! However, the operative words are "possible precursor" - NOT life.
Altho, this line of research might be interesting in regards to amine structures...

Oct 31, 2014
Dobzhansky (1973) also states: "...the so-called alpha chains of hemoglobin have identical sequences of amino acids in man and the chimpanzee, but they differ in a single amino acid (out of 141) in the gorilla."


This supports you in what way? The substitution was the result of a mutation in the gorilla ancestor.

Evolutionary theorists ignore that sequence.


How so? Evolution is studied at all levels, from molecular evolutionary biology all the way up to supra-organismal and ecological evolution.

http://en.wikiped..._ecology
http://link.sprin...al/10682
http://en.wikiped...volution
http://mbe.oxfordjournals.org/
http://molbio.pri...volution

Oct 31, 2014
Oxygen atmosphere prevent the synthesis of amino acids necessary for the synthesis of proteins. But lack of oxygen in atmosphere is even worse because of the UV light due to a lack of ozone. There are plenty of conflicting requirements for sintesis by chance in one place at the same time for necessary elements for life. It takes magic to the emergence of life in this ancient environment, but at that time the magicians were not evolved yet.

Oct 31, 2014
From Dobzhansky's article "Nothing in biology makes sense except in the light of evolution."-

As expected, some of these mutations are deleterious to their carriers, but others apparently are neutral or even favorable in certain environments. Some mutant hemoglobins have been found only in one person or in one family; others are discovered repeatedly among inhabitants of different parts of the world. I submit that all these remarkable findings make sense in the light of evolution: they are nonsense otherwise.

JVK
Oct 31, 2014
"...the interactions between pre-mRNA and proteins fine-tune alternative splicing in a manner that can gradually create new protein functionalities without the need to create additional genes and without affecting existing proteins [4-6]." http://genomebiol...15/1/401

However, the odor-induced de novo creation of olfactory receptor genes links nutrient-uptake to the creation of other new genes that enable the thermodynamic cycles of protein biosynthesis and degradation to contribute to organism-level thermoregulation via RNA-directed DNA methylation and RNA-mediated amino acid substitutions that stabilize the genome when they are fixed by the pheromone-controlled physiology of reproduction.

There are 1180 hemoglobin variants, but only biology teachers like PZ Myers and his idiot minions claim that the variants arise with ecological variation due to mutations, like the one theorists think led to the hemoglobin S variant (sickle cell).

JVK
Oct 31, 2014
http://genomebiol...ent/15/1 A summary of the special issue appears in the context of "RNA and dynamic nuclear organization" by Rinn and Guttman.

See my comment on the Science article at http://comments.s...comments

Excerpt: "The requirement for DNA to be found in organized genomes is biophysically constrained via the conserved molecular mechanisms of protein biosynthesis and degradation in species from microbes to man."

Protein biosynthesis is nutrient-dependent and the physiology of reproduction is controlled by the metabolism of nutrients to species-specific pheromones in species from microbes to man. Those facts tell you everything you will ever need to know about evolutionary theorists, which is that they refuse to accept the facts and continue to tout their pseudoscientific nonsense about mutations and the automagical evolution of increasing organismal complexity.

JVK
Oct 31, 2014
The substitution was the result of a mutation in the gorilla ancestor.


What kind of fool believes that?

See: Criticisms of the nutrient-dependent pheromone-controlled evolutionary model by Andrew Jones, aka anonymous_9001 http://www.ncbi.n...4049134/

See also: http://www.scienc...5415.htm

"Through a painstaking process of elimination, Manuel Ortega, a graduate student in van der Donk's lab, established that the amino acid glutamate was essential to nisin's transformation."

Journal article excerpt 1): "As expected, the NisB-R784A mutant resulted in the accumulation of glutamylated NisA intermediates..."

Journal article excerpt 2): "The interactions observed in the crystal structure provide an explanation of why mutations within the NisA FNLD sequence greatly decrease NisB
binding19,20."

JVK
Oct 31, 2014
Mutations perturb protein folding; they do not lead to amino acid substitutions. Similarly, frying a chicken's egg, which perturbs protein folding, does not enable a link From Fertilization to Adult Sexual Behavior
http://www.hawaii...ion.html

RNA-mediated amino acid substitutions link fertilization to adult behavior via nutrient-dependent cell type differentiation and the pheromone-controlled physiology of reproduction in species from microbes to man. They also link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via the conserved molecular mechanisms we detailed in our 1996 Hormones and Behavior review.

In his comments on my 2013 review, Andrew Jones (aka anonymous_9001) wrote: "James Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research."


JVK
Oct 31, 2014
The assumption that a mutation could lead to an amino acid substitution is not supported by any experimental evidence of biologically-based cause and effect. Biophysical constraints on the chemistry of protein folding must first be considered.

Masatoshi Nei
1) first removed geographical and ecological factors from any consideration and
2) subsequently removed physics when he claimed: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.

1) http://gbe.oxford...abstract
2) http://www.amazon...99661731

Citing others who eliminate or fail to address what is required when serious scientists discuss the physics, chemistry and molecular biology that epigenetically link ecological variation to ecological adaptations and ecological speciation is all you can do until you learn the difference between pseudoscience and science.

JVK
Oct 31, 2014
https://systemsbi...s-vitkup "Research in the Vitkup Lab focuses on three main topics: 1) the global probabilistic reconstruction and analysis of metabolic networks based on completely sequenced genomes, 2) the development of methods to identify new human disease genes and genetic disease modules using probabilistic functional networks, and 3) the development of methods to combine mechanistic and probabilistic approaches for the dynamic simulation of biological pathways."

See: Long-term phenotypic evolution of bacteria http://www.nature...827.html "...the ability to metabolize different nutrient sources, although clearly not the only important phenotype, always remains an essential determinant of their fitness and lifestyle."

The link between genetic networks and metabolic networks is not mutations because they perturb protein folding, which means they don't contribute to amino acid substitutions.

Oct 31, 2014
The assumption that a mutation could lead to an amino acid substitution is not supported


Um... thats precisely what missense mutations do.

JVK
Nov 01, 2014
Um... thats precisely what missense mutations do.


Isn't that simply another ridiculous assumption?

You seem to be assuming that missense mutations somehow lead to increasing organismal complexity via amino acid substitutions that differentiate the cell types of all individuals of all species.

If so, why haven't missense mutations been linked from amino acid substitutions in viruses to cell type differentiation and evolution of all the cell types of all tissues in all organs and all organ systems of humans?

In my model, the problem is that mutations perturb protein folding. If you assume that mutations are sometimes beneficial, do you think they are more beneficial to the mutation-driven evolution of Ebola viruses than to the mutation-driven evolution of humans?

Nov 01, 2014
Isn't that simply another ridiculous assumption?


No. I literally just provided you with a list analysing mutations and their effects. You can easily find a wide variety of studies examining mutations and their effects relating to natural selection and phenotype. Over the past however many months, I've provided a ton of such articles.

Nov 01, 2014
When a gene is damaged (mutated by chance), there is change in the amino acid composition of the protein, which is produced by this gene. In this situation, it can not fold properly and acquire its unique for its proper function three dimensional shape. This makes it incomplete or non-functional, and in many of the cases detrimental for the cell. Nobody relies on chance if he wants to do a job properly. Therefore, the cells have a built-in mechanism for the recombination of genes from both parents to provide biodiversity without any mutation, and later to activate or deactivate certain genes, when certain proteins in the organism is needed. But behind the fruitless search for evidence of evolution and promotion of this theory in society stands whole industry.

Nov 01, 2014
This makes it incomplete or non-functional


Not always. Studies identifying neutral and positive mutations disagree with you.

Nov 01, 2014
I have preference for mathematics rather than irresponsible speculation.For someone who does not know well the problems in this area, everything seems possible. But who has enough empirical experience, knows that is not true. How many percent are hypothetical positive mutations against harmful?

JVK
Nov 01, 2014
What we see here is the continuing saga of Andrew Jones' ignorance. No matter what logical approach is tried in attempts to link physics, chemistry, biology, math, etc., Jones claims "mutations."

He can cite published works that also claim "mutations" cause what they cannot because others who are equally ignorant have made those claims since the invention of neo-Darwinism (i.e., by definitions that excluded any facts about how cell type differentiation actually occurs).

Cell type differentiation occurs via seemingly futile cycles of nutrient-dependent protein biosynthesis and degradation that lead to the pheromone-controlled physiology of reproduction in species from microbes to man. The direct link from the epigenetic landscape to the physical landscape of DNA in organized genomes is clearly via RNA-directed DNA methylation and RNA-mediated amino acid substitutions.

But Jones and other anonymous fools/idiot minions were taught to believe in mutations.

Nov 01, 2014
you call anyone believing in evolution theory an idiot minion?

Of course, I do. Doesn't every intelligent person on this planet do the same thing?
no, only you and your creationist religious idiot friends do!
you still haven't figured out why you look like an idiot arguing against mutations while promoting a model that causes mutations!
that doesn't makes you intelligent at all, it makes you stupid (because you have been shown the error of your ways, and even admitted it in your own words)
shall i post them yet again?
You were taught to believe that evidence automagically appears
again with the word salad that means nothing?
i've a new name for this tripe and stupidity: "kohl-slaw"

the only fool here is the one that cannot comprehend the links he uses and still argues against mutation while promoting it with a model that causes mutations

IOW - jk's "kohl-slaw" of idiotic verbiage only proves he is the reigning fool ignoring empirical evidence on PO!

Nov 01, 2014
He can cite published works that also claim "mutations" cause what they cannot


The works you cite for that imply no such thing. I have provided you with countless examples of mutation and selection viewed at the molecular level.

light-induced amino acid substitution


Nothing indicates the amino acid substitution in that example was caused by light. By what mechanism would that even happen? Light in the visible range has no capacity to break bonds.That's beside the point that light is not a nutrient. Energy source, sure, but not a nutrient.

Nov 01, 2014
Mutations perturb protein folding
really?
YOUR OWN MODEL CAUSES MUTATIONS
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
So now we can see, with CONCLUSIVE empirical evidence in your own words, that your model CANNOT cause diversity or support evolution, because your own model causes mutations and therefore causes detrimental effects...
unless, of course, you don't know what the heck you are talking about
then the model actually supports evolution by providing a small part of the picture in certain circumstances...
you choose which idiot you are, kohl-slaw

Nov 01, 2014
The assumption that a mutation could lead to an amino acid substitution is not supported by any experimental evidence of biologically-based cause and effect. Biophysical constraints on the chemistry of protein folding must first be considered
this statement PROVES that you are not capable of logical thought
it also proves, in your own words, that you are pushing pseudoscience
if you state the above, but then admit your model causes mutations, then either you are a seriously stupid faith based troll or you are simply a blatantly lying spammer trying to sell perfume
you admitted this as much when you answered my questions: remember.. I asked
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking

so which one are you?

Nov 01, 2014
Citing others who eliminate or fail to address what is required when serious scientists discuss the physics... learn the difference between pseudoscience and science
this can be demonstrated here on this thread:
jk says
Mutations perturb protein folding
but also admits his model causes mutations 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
jk says
The assumption that a mutation could lead to an amino acid substitution is not supported by any experimental evidence
but forgets about Lenski proving him wrong: http://myxo.css.m...dex.html

jk IGNORES empirical evidence quoted from his own links and cites

the only one citing PSEUDOSCIENCE is jk with his "kohl-slaw" verbiage of nonsense

it rhymes to make it easy to remember
Kohl = TROLL

Nov 01, 2014
I have preference for mathematics rather than irresponsible speculation.
@viko_mx
and we have a preference for that which can be proven with empirical evidence
jk is fighting for a faith/religion
you fight for math
Lenski is proving you both wrong with a single experiment
on his site alone: http://myxo.css.m...dex.html there is demonstrations of beneficial mutations which completely negate your claims of
When a gene is damaged (mutated by chance), there is change in the amino acid composition of the protein, which is produced by this gene. In this situation, it can not fold properly and acquire its unique for its proper function three dimensional shape. This makes it incomplete or non-functional
not ALL mutations are harmful, nor are all beneficial

Lenski proved that jk's "kohl-slaw" is wrong as well

arguing math in the face of empirical evidence is like urinating on someone's head while they watch but then trying to say it is raining

you are trolling

Nov 01, 2014
But Jones and other anonymous fools/idiot minions were taught to believe in mutations
apparently the idiot jk forgot that he also believes in mutations because he is promoting a model that causes mutations, which makes him not only a fool/idiot minion, but a delusional one who cannot comprehend what reality is
Theorists who think mutations can lead to the evolution of biodiversity
are people like kohl, who continue to support mutations with a model that causes mutations
he even admitted this 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


So now jk ADMITS to being an idiot/fool minion and admits to promoting PSEUDOSCIENCE

why does he do it?
it help him sell perfume and promotes his faith/religion

Nov 01, 2014
@Captain Stumpy
Lensky only offers his interpretation of what happened. If you pay him to look for evidence of this nihilistic theory, there is no way not to "find" it.

"not ALL mutations are harmful, nor are all beneficial"

Give me the numbers. Mathematics separates reality from illusions. How many percentage are harmful and how hypothetical beneficial mutations. What does meam a useful mutation and what it represents. Explain what happens when a protein is unable to fold properly and to obtain its original 3D shape, and how this will improve the cell? I do not want generalities, but what happens step by step to allow the cell to obtain new functionality.

JVK
Nov 01, 2014
Explain what happens when a protein is unable to fold properly and to obtain its original 3D shape, and how this will improve the cell?


Thanks for making it perfectly clear why Lenski's experiments have no explanatory power. They are simply a continuation of what occurred many years ago.

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

http://www.huffin...211.html

JVK
Nov 01, 2014
Even without mathematical proof it should be obvious that

...whatever emerges from the bottom up still must work within the context of the living system. Darwinian evolutionary processes in living systems are therefore not only ruled from the bottom up but also by fundamental emerging organizational principles that are hierarchically built up and impose necessary constraints from the top down. These principles are the key for defining organic life.


http://rsfs.royal...abstract

For comparison, we have:
...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

If you think constraint-breaking mutations explain anything, see Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Nov 01, 2014
Give me the numbers...


There are a tons of examples of mutational and protein function analysis that show positive and neutral mutations.

http://homepage.u...rger.pdf

http://www.jacobs...1999.pdf

The screening (or selection) of genetic diversity created by random mutagenesis and/or recombination can rapidly generate desired functional changes (Chen and Arnold 1993; Stemmer 1994; Arnold 1998).


http://www.che.ca...hysJ.pdf

http://www.scienc...05005541

http://www.pnas.o...96.short

http://www.pnas.o...95.short

http://www.scienc...14000591

http://www.scienc...13002322

Nov 01, 2014
Lensky only offers his interpretation of what happened
@viko_mx
personal conjecture without evidence based upon a fallacious set of beliefs which are stagnating under your dogmatic institution called religion
Give me the numbers
read Anon's reply from 11/1 and note the links
you have stated elsewhere
I do not believe in the dogma of evolution, because there is no facts to catch
which proves that you will completely ignore all science when produced to you, whether math, empirical or otherwise, just as you have done so here already with me

I don't converse with stupid people who ignore evidence, i prove them wrong
you've been proven wrong with evidence
deal with it

please feel free to go troll elsewhere, as further troling here will simply be downvoted and reported as pseudoscience spamming/trolling/baiting
thanks

JVK
Nov 01, 2014
I do not want generalities, but what happens step by step to allow the cell to obtain new functionality.


The anonymous fool responds to that reasonable request:

There are a tons of examples of mutational and protein function analysis that show positive and neutral mutations.


It's as if he thinks examples reveal something that has not been revealed by experimental evidence of biophysically-constrained biologically plausible cause and effect, when what has been revealed is that mutations cannot lead to the evolution of biodiversity via perturbed protein folding.


Nov 01, 2014
what has been revealed is that mutations cannot lead to the evolution of biodiversity


I literally just gave you experimental evidence of that via my most recent links.

Nov 01, 2014
Do I really have to go through my links step by step because you don't know what the takeaway messages of them are?

1. This is precisely what viko_mx was asking for- a mathematically supported model of mutation and selection.
2. You should actually really like this one, Kohl. It's an in-depth analysis of the effect of mutations on enzyme activity and thermostability.
3. Mathematical model relating enzyme stability and function, mutation, and selection.
4. If you read just one, read this one please. This is actually precisely what you're looking for. It's direct evidence of mutation leading to unique and functional proteins.
5. Mutagenesis leading to improved enzyme function.
6. Single amino acid mutations resulting in increased stability and function
7. Merging molecular biophysics and population genetics.
8. Analysis of fitness effect of mutations based on population size.


JVK
Nov 01, 2014
"...single amino acid mutations can enhance properties such as catalytic activity or stability and that adaptation can often occur through pathways consisting of sequential beneficial mutations." http://www.pnas.o...95.short

This would be a good start if they described an evolutionary event that linked the amino acid to protein folding that increased stability in a genetic network and a metabolic network important to the physiology of reproduction.

No need to go through other links step by step unless you can link them from the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms and amino acid substitutions that differentiate cell types, which is what I did in my model of nutrient-dependent pheromone-controlled ecological speciation -- with examples, of course.

JVK
Nov 01, 2014
The concept of how ecological variation leads to ecological adaptations manifested in the adaptive amino-acid sequences that link amino acid substitutions to cell type differentiation in all cells of all individuals seems more appealing than an alternative in which mutations somehow lead to the evolution of biodiversity.

In the context of physics; the chemistry of protein folding, and molecular biology, the substitution of glycine for a chiral amino acid in GnRH leads to a more constrained conformation for receptor binding, which links a single amino acid substitution to functional ligand-receptor binding via effects on receptor structure.

Kochman (2012) put this into the perspective of mutations compared to ecological adaptations. http://www.cabdir...D2FA0114

JVK
Nov 01, 2014
Kochman (2012) "It should be stressed that the surprising total conservation of GnRH II's primary structure, from bony fish to man, appears to be a result of the excellent coordinated evolutionary selection of amino acids participating in binding, activation and configuration such that its structure cannot be improved by substitution with any natural amino acid at any position."

It is this "coordinated evolutionary selection of amino acids" that must be addressed by theorists who think that it could somehow arise in the context of mutations that could be linked to the evolution of biodiversity, which appears to be nutrient-dependent and controlled by the physiology of reproduction in species from microbes to man. Mammalian GnRH, for example, is very similar to the molecule that serves as the alpha-mating pheromone in yeasts at the advent of sexual reproduction. GnRH secretion is also the central aspect of my model.

Nov 02, 2014
It is this "coordinated evolutionary selection of amino acids" that must be addressed by theorists who think that it could somehow arise in the context of mutations


That's precisely what my recent citations addressed and demonstrated. They showed mutations producing novel genotypes and phenotypes, which are selected based on their stability and improved enzymatic action.

Nov 02, 2014
@anonymous_9001
"The screening (or selection) of genetic diversity created by random mutagenesis and/or >>>recombination<<<< can rapidly generate desired functional changes (Chen and Arnold 1993; Stemmer 1994; Arnold 1998)."

Key is recombination, which is built-in mechanism. There is no way mutation to induce changing in functionality through recombination. These mechanisms are complex and random changes do not help, only harm. Clear to a reasonable person is that if mutations were beneficial, the body would tolerate them and would not have sophisticated mechanisms to combat them. It is paradoxically that mutations are not useful even for them after by them have appeared complex mechanisms to fight with them. But some scientists hold stubbornly to pure chance rather than to initially embedded functionality and information. Because they want to be in the place of the Creator through their controversial science. The ego always creates follies.

Nov 02, 2014
kohl-slaw ...seems more appealing than an alternative in which mutations somehow lead to the evolution of biodiversity
considering that your own model causes mutations, this means that you are against your own model!
you know that, right?
mutations that could be linked to the evolution of biodiversity
If mutations can never be beneficial, why are you promoting them in your model?
Anon provides many links proving your kohl-slaw word salad wrong... which makes you stupid and pushing pseudoscience

There is no way mutation to induce changing in functionality
@viko-veggie matic brain
evidence proves you wrong and says you are ignoring reality for a faith
see Lenski et al: http://myxo.css.m...dex.html
that makes you stupid

JVK
Nov 02, 2014
2. You should actually really like this one, Kohl. It's an in-depth analysis of the effect of mutations on enzyme activity and thermostability.


Fortunately, viko_mx recognized the crux of the anonymous fool's citation to: "Exploring Nonnatural Evolutionary Pathways by Saturation Mutagenesis: Rapid Improvement of Protein Function " See also the other publications from this lab: http://www.che.ca...ions.htm

The built-in mechanism that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man is nutrient-dependent alternative splicings that facilitate protein biosynthesis and degradation associated with the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction.

The fact that Captain Stumpy now attacks the only other intelligent participant in this discussion also attests to his ignorance.

JVK
Nov 02, 2014
See also: http://medicalxpr...nal.html
""This experiment demonstrates how rapidly these remarkable bacterial proteins can evolve in response to new demands. But even more exciting is what they can do in neurons, as Viviana discovered," says Arnold."

The comment was linked from this article: http://phys.org/n...#inlRlv, which may help others to recognize the conservation of what is known about physics, chemistry, and molecular biology in the context of articles from all disciplines except those associated with social science/pseudoscience.

Eshel Ben-Jacobs works exemplify the same thing. Only pseudoscientists tout theories and expect others to believe in what they were taught to believe in. Serious scientists expect to find experimental evidence that supports their hypothesis, and when it doesn't they abandon the hypothesis. Pseudoscientists cling to their hypotheses, indefinately.

Nov 02, 2014
The fact that Captain Stumpy now attacks the only other intelligent participant in this discussion also attests to his ignorance
I have never attacked Anonymous 9001

do you want to see ignorance at its finest, kohl-slaw?
DEFINITIONs are used by idiots
or
how about someone saying this
Intelligent creatures do not believe in the magic of mutations/natural selection
but then while being asked a question
DOES your model make any changes to the nucleotide sequence of the genome of an organism, virus, or extrachromosomal genetic element?
This is a yes or no answer
(this is the DEFINITION of mutation) to which you answered
YES!
--Thanks for asking
so which is it, stupid?
are you for or against mutations?
you are saying you are against
but you are publishing models that create mutations and support evolution

and you call ME ignorant?
your kohl-slaw word salads are the height of blatant stupidity
nothing but "philosophical regurgitation" TM

Nov 02, 2014
Key is recombination, which is built-in mechanism. There is no way mutation to induce changing in functionality through recombination.


I mean this in all seriousness, viko. Based on the way you've worded some things, I take it English isn't your first language? The "and/or" in the excerpt you quoted is important.

The built-in mechanism ... is alternative splicing


No. viko was referring to DNA repair. Splicing has nothing to do with DNA repair and has no effect on DNA in any regard.

Serious scientists expect to find experimental evidence that supports their hypothesis


Like all the links I've provided recently?

JVK
Nov 02, 2014
I wrote: The built-in mechanism that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man is nutrient-dependent alternative splicings that facilitate protein biosynthesis and degradation associated with the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction.

Andrew Jones quoted only this:
The built-in mechanism ... is alternative splicing


This is a despicable tactic of theorists who are cornered, and they fight back with more misinformation. They have never been able to accurately represent the biophysically-constrained chemistry of nutrient-dependent protein folding that links nutrient uptake and metabolism to the pheromone-controlled physiology of reproduction as we did in our 1996 review in the section on molecular epigenetics.

http://www.hawaii...ion.html

JVK
Nov 02, 2014
The Dark Secrets of the Bird World http://waitbutwhy...40109045

Within the next two weeks, serious scientists will report that they used RNA-sequencing to generate transcriptome data for each region that they subsequently used used to identify the genes that vary in expression with both morphological and behavioral phenotypes in the bird species they study.

No experimental evidence of biologically-based cause and effect suggests that the morphs have mutated and evolved via natural selection. Similarly, no experimental evidence of biologically-based cause and effect suggests that dinosaur morphs mutated and evolved during millions of years of natural selection to become birds.

Thank God, only evolutionary theorists are ignorant enough to believe in such nonsense.

Nov 02, 2014
Andrew Jones quoted only this:


I did it merely for the sake of brevity. I didn't leave out any details that changed the meaning of it like you do all the time.

No experimental evidence of biologically-based cause and effect suggests that the morphs have mutated and evolved via natural selection.


Except for all the links I've posted recently, which you seem to be unable to refute.

They have never been able to accurately represent the biophysically-constrained chemistry of nutrient-dependent protein folding...


Link #2 does exactly that! Read it!

JVK
Nov 02, 2014
Splicing has nothing to do with DNA repair and has no effect on DNA in any regard.


Transcript-RNA-templated DNA recombination and repair.
http://www.ncbi.n...25186730

"...considering the abundance of RNA transcripts in cells, RNA may have a marked impact on genomic stability and plasticity."

Alternative RNA Splicing in Evolution http://jonlieffmd...volution

"...alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes."

The anonymous fool has not realized that his "Criticisms of the nutrient-dependent pheromone-controlled evolutionary model" was published as an example of the pseudoscientific nonsense touted by evolutionary theorists.
http://www.ncbi.n...24959329


JVK
Nov 02, 2014
Even better, from the news report on the article linked above:

"We need to understand in which situations cells would activate RNA-DNA recombination."

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

"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation..."

The impact of nutrient-dependent pheromone-controlled RNA-mediated sex differences in cell types would have predicted the overwhelming influence of RNA-mediated amino acid substitutions on genomic stability and plasticity if not for the pseudoscientific nonsense touted by evolutionary theorists.

What's worst is that the anonymous fool and others like him are too ignorant to realize what they don't know about biologically-based cause and effect, even when it is repeatedly pointed out to them.

Nov 02, 2014
Transcript-RNA-templated DNA recombination and repair.
http://www.ncbi.n...25186730


"Small intranuclear proteins also participate in generating alternative splicing techniques of pre-mRNA and, by this mechanism, contribute to sexual differentiation..."


Recombination and splicing are two separate things. They are not the same.

The anonymous fool has not realized that his "Criticisms of the nutrient-dependent pheromone-controlled evolutionary model" was published as an example of the pseudoscientific nonsense touted by evolutionary theorists.
http://www.ncbi.n...24959329


My critique was published as an example of what not to do? That's the delusion you're going with?

JVK
Nov 02, 2014
Loss of the imprinted snoRNA mbii-52 leads to increased 5htr2c pre-RNA editing and altered 5HT2CR-mediated behaviour. http://www.ncbi.n...19304781

Excerpt: These data illustrate, for the first time, the physiological consequences of altered RNA editing of 5htr2c linked to mbii-52 loss that may underlie specific aspects of the complex PWS phenotype and point to an important functional role for this imprinted snoRNA.

Splicing has nothing to do with DNA repair and has no effect on DNA in any regard.

Recombination and splicing are two separate things. They are not the same.


Everything is a different thing to anonymous fools until they learn how to link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via RNA-mediated amino acid substitutions that differentiate cell types.

Then some of them see an obvious pattern to everything involved in biodiversity.

JVK
Nov 02, 2014
My critique was published as an example of what not to do? That's the delusion you're going with?


You wrote: "James V. Kohl overextends his expertise in trying to overthrow established evolutionary theory."

The editor replied: "The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers."

He politely called you an idiot because your criticisms were based on pseudoscientific nonsense, not on the facts I included with substantiation in the citations to published works. You dismissed the examples of amino acid substitutions and cell type differentiation as if you could simply say "Nuh-uh" because that's what idiots like PZ Myers do when confronted with biological facts about cell type differentiation sans mutations.

Nov 02, 2014
http://en.wikiped...bination

In molecular biology and genetics, splicing is a modification of the nascent pre-messenger RNA (pre-mRNA) transcript in which introns are removed and exons are joined


No matter how much you imply and try to insist they do the same thing, they do not.

The editor replied: "The 2013 review article by James Vaughn Kohl published in Socioaffective Neuroscience & Psychology and criticized in the above Letter to the Editor was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers."


The review process for mine was just as valid as it was for yours. Either you're conceding that they were subject to the same scrutiny, in which case they realized their mistake in letting yours through after the fact when they had your misinterpretations pointed out explicitly or you're saying their review process is inconsistent. Which is it?

JVK
Nov 02, 2014
He denies that predation was the driving force, followed by a seemingly irrelevant statement and citation concerning the moths' migration. ...Kohl has attributed the melanism to a change in the moths' diet brought on by the pollution, despite the fact that this hypothesis has been contradicted by experimental and statistical evidence stemming from three separate studies (Prakash, 2006).


See:
The genetics of monarch butterfly migration and warning colouration http://www.nature...812.html

Excerpt: "Migratory and non-migratory haplotypes differed by... 15 amino acid substitutions.
A subsection of the gene showed particularly high diversity within D. plexippus, as well as divergence between D. plexippus and other species, centred on the single amino acid substitution with evidence of positive selection, R1573Q (Fig. 3d)."

I cited an article on moth pheromones that changed via a single amino acid.

JVK
Nov 02, 2014
Oppositional COMT Val158Met effects on resting state functional connectivity in adolescents and adults http://dx.doi.org...4-0895-5

The article links the amino acid substitution to differences in adolescent and adult human behaviors, which are also linked to genetic networks and metabolic networks.

That completes the series of links from microbes to man that show how nutrient-dependent RNA-directed DNA methylation and amino acid substitutions established cause and effect in the context of ecological variation and links to ecological adaptations during life history transitions.

The transitions are exemplified in the honeybee model organism of nutrient-dependent pheromone-controlled cell type differentiation, which links their morphological and behavioral phenotypes via nutrient-dependent gains and losses of functions associated with the de novo creation of olfactory receptor genes.

Nov 02, 2014
See:
The genetics of monarch butterfly migration and warning colouration http://www.nature...812.html


What does this have to do with selection by predation? That's what that part of my critique concerned. It's also funny how you cite things that are evidence for something you claim doesn't happen-

single amino acid substitution with evidence of positive selection, R1573Q (Fig. 3d)."


That's positive [natural] selection, if you weren't aware.

By the way, back when I asked you about how methylation leads to base substitutions, which result in amino acid substitutions, it was because methylation and deamination can only cause A to T changes. All the rest remain unexplained in your model. You don't offer a mechanism for them.

Nov 03, 2014
Your choice is to believe in every article published somewhere on the web. Should I trust articles written by unfamiliar people whose motives are not known to me? False trials for purposes other than scientific truth are enough? When you confirm several independent sources from different parts of the world, then you possibly comment such as idea. It Does not seem you want to understand the nature of the problem and the fundamental obstacles you can expect for occasional occurrence of life. Explain how it works the change or appearance of an organ or system in a species that requires simultaneous change in the circulatory, nervous, skeletal, endocrine systems, connective tissue and etc. This requires changes in many genes and their control mechanisms simultaneously, which are at different places in the DNA? And the addition of many new information in DNA.

Nov 03, 2014
Which ensure that the necessary small mutations in the desired direction will be reserved in future generations to change these organs or systems? Which ensures that even small mutations in the desired direction are not harmful, until complete change in the organ or system is done and is functioning properly? Because we know that dysfunctional organs causing problems in the organisms. Which ensures that harmful mutations, before conditionally beneficial mutations can develop new functionality, will not worsen the condition of the organisms in the population. At what speed is the desired mutations occur if we assume because the thought experiment compromise with our conscience and accept the idea that there may be beneficial mutations? Natural selection actually clears big mutations in the population because of lost of functionality due to fatal changes in critical genes or sinhronization mechanisms in DNA.

Nov 03, 2014
Small changes can be saved, but can be not, and that does not depend on efects of natural selection, but on the dominating random factors in the environment and the quality of DNA does not mather here.

JVK
Nov 03, 2014
All the rest remain unexplained in your model. You don't offer a mechanism for them.


Since 1996, I've helped detail the molecular mechanisms for cell type differentiation in every cell of every individual: Cell type differentiation is nutrient-dependent and RNA-directed via DNA methylation and RNA-mediated events that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man.

I provided across-species examples in my review http://www.ncbi.n...24693353

You complained: "Kohl then refers to an allele change that occurred in a population in China 30,000 years ago as 'probably … nutrient-dependent' without making reference to what nutrient caused the change or how." http://www.ncbi.n...4959329/

Any question about "what nutrient" can be compared to questions about "what mutation" caused cell type differentiation to occur in all cell types of all species.

JVK
Nov 03, 2014
JVK
single amino acid substitution with evidence of positive selection, R1573Q (Fig. 3d).


Andrew Jones (aka anonymous_9001)
That's positive [natural] selection, if you weren't aware.


I am aware that a nutrient-dependent RNA-mediated amino acid substitution led to 1) color change, 2) the ability to fly, and to 3) pheromone-controlled reproduction.

Even if three different nutrient-dependent amino acid substitutions were required, none can be attributed to a mutation, and fixation of the substitution(s) cannot be attributed to predation.

Attributing everything known about the physics, chemistry, and molecular biology of cell type differentiation in species from microbes to man is akin to linking the ecological adaptations manifested in the development of the human brain during life history transitions to the snake-centric theory of evolution.

http://news.scien...te-brain


JVK
Nov 03, 2014
What we've seen here is more pseudoscientific nonsense touted by Andrew Jones, despite clear indications from yet another serious scientist that Jones (aka anonymous_9001) is an idiot.

viko_mx is new to the discussion forums, and it is people like Jones who eliminate intelligent participants from discussion by their failure to provide any alternative explanation of how cell type differentiation occurs in the context of what is known about physics, chemistry, and molecular biology.

People like Jones will be the death of us all, since they cannot grasp the fact that amino acid substitutions differentiate changes in the Ebola viruses and other viruses via the conserved molecular mechanisms of cell type differentiation in species from microbes to man.

As if their contributions to human suffering in the context of mutated proteins they think are beneficial was not enough, they won't stop until they end the world as we now know it -- because they know nothing.

Nov 03, 2014
False trials for purposes other than scientific truth are enough?


You saying they're false is not evidence that they're false. If you can point out false assumptions, logic, or bad methodologies in the papers I've posted that would falsify them, go right ahead.

Explain how it works the change or appearance of an organ or system in a species that requires simultaneous change...


Irreducible complexity is a tired argument that's been discussed to hell and back. Do you have any examples of traits necessitating such a change or an intermediate not being functional or overly detrimental?

Cell type differentiation is nutrient-dependent and RNA-directed via DNA methylation and RNA-mediated events


While methylation is a mechanism (that can only explain A to T), "RNA-mediated events" is not; it is a category. What specific RNA-mediated events result in substitutions?


Nov 03, 2014
I am aware that a nutrient-dependent RNA-mediated amino acid substitution led to 1) color change


I cited 3 studies contradicting that by showing nutrient exposure having no effect on wing color.

failure to provide any alternative explanation of how cell type differentiation occurs in the context of what is known about physics, chemistry, and molecular biology


I gave you 8 links in this thread alone that took all of those into account.

As if their contributions to human suffering in the context of mutated proteins they think are beneficial was not enough


Again, I provided direct evidence of beneficial mutations in the aforementioned links.

JVK
Nov 03, 2014
I provided direct evidence of beneficial mutations...


You've provided direct evidence of your ignorance, foolishness, and willing to believe in a ridiculous theory that suggests beneficial mutations somehow lead to increased organismal complexity AND DISEASE via conserved molecular mechanisms or perhaps via breaking the Laws of Physics (e.g., constraint-breaking mutations). In any case, you are determined to remain an anonymous fool (aka known as Andrew Jones).

What specific RNA-mediated events result in substitutions?


Those that are nutrient-dependent and pheromone-controlled by conserved molecular mechanisms, which incorporate what is known about the Laws of Physics and the chemistry of protein folding in species from microbes to man.

For examples, see my review Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

Nov 03, 2014
No experimental evidence of biologically-based cause and effect suggests that the morphs have mutated
so you are now saying your model does not show cause and effect or suggest biodiversity then?
What's worst is that the anonymous fool and others like him are too ignorant to realize what they don't know about biologically-based cause and effect
you mean your model, which CAUSES MUTATIONS and simply reinforces the evolution theory? it even causes mutations!
I've helped detail the molecular mechanisms
which is by MUTATION! remember.. 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


Nov 03, 2014
People like Jones will be the death of us all, since they cannot grasp the fact that amino acid substitutions differentiate changes in the Ebola viruses and other viruses via the conserved molecular mechanisms of cell type differentiation in species from microbes to man
HOW can anyone be the "death" of anyone else by simply calling a mutation a mutation?
you yourself said your own model causes mutations
remember.. 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
now you are saying that someone else is wrong for saying the same thing

the only danger anyone on PO poses is your own kohl-slaw mixed up lies being promoted as science!
you yourself argue against the lexicon by making up definitions on a whim because you don't like them... but think this is logical?

Nov 03, 2014
@jk
when you post
your ignorance, foolishness, and willing to believe in a ridiculous theory that suggests beneficial mutations somehow lead to increased organismal complexity AND DISEASE via conserved molecular mechanisms or perhaps via breaking the Laws of Physics (e.g., constraint-breaking mutations)
but you support your own model

then you are proving beyond the shadow of a doubt that you are a complete moron, stupid (because you HAVE been taught where you are wrong), and illiterate, as well as posting PSEUDOSCIENCE

your model CAUSES MUTATIONS
you argue against mutations means you argue against YOUR OWN MODEL
you are an idiot

Nov 03, 2014
You've provided direct evidence of your ignorance, foolishness, and willing to believe in a ridiculous theory


Theory backed by evidence like this- http://www.scienc...05005541

Proteins with improved or novel function were isolated


Overall, high-error-rate mutagenesis libraries are enriched in improved sequences because they contain more unique, functional clones.


Evidence that mutation can lead to improved and novel function. This is direct refutation of your claims.

Those that are nutrient-dependent and pheromone-controlled


I'm looking for names here. If I were to ask you what makes ATP, you could answer ATP synthase, as that's the enzyme that performs that function. It is preceded by the electron transport chain. What system are you referring to when you say "RNA-mediated events"?

Nov 05, 2014

"...Proteins with improved or novel function were isolated disproportionately from these high-error-rate libraries, leading to claims that high mutation rates unlock regions of sequence space that are enriched in positively coupled mutations..."

This is your proof? Someone somewhere claimed something without explaining what exactly has in mind and according to what criteria make such conclusion. With this method, anyone can become a great discoverer in the scientific press? Mutations cause genetic or malignant diseases, when fall within the more important zones or genes in DNA, or gradual loss of functionality and information in gene pool of certain sepcies with each successive generation, when there are less significant mutations. Therefore, the protective mechanisms of cells and the immune system is constantly fighting with them.

Nov 05, 2014
But for maintaining biodiversity are created integrated mechanisms in DNA for recombination of genes and their alleles, and in an ideal environment without harmful factors causing a random mutations, this mechanism is working just fine. So enjoy the beauty and variety in nature. This is the handwriting of the Creator and an expression of his love.

JVK
Nov 07, 2014
What system are you referring to when you say "RNA-mediated events"?


The system that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via nutrient-dependent amino acid substitutions and the metabolism of nutrients to species-specific pheromones that control the physiology of reproduction in species from microbes to man. I detailed it in the publication that you reviewed. http://www.ncbi.n...24693353

What other system could I be referring to? There is only one way to link RNA-directed DNA methylation to amino acid substitutions and cell type differentiation in species from microbes to man.

If I were to ask you which mutation(s) are involved in cell type differentiation in all cells of all individuals of all species, could you provide any information to compare to my model?

Nov 08, 2014
I didn't ask for a vague scheme of the system. I asked for the name of the system and the specific pathways it utilizes.

JVK
Nov 09, 2014
Does anyone else not recognize the details about the GnRH neuronal system that links nutrient uptake to the pheromone-controlled physiology of reproduction in my model?

http://www.ncbi.n...24693353

Specific pathways: see footnote 5 from Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. http://www.ncbi.n...3960071/

"Noradrenergic, dopaminergic, serotoninergic, and opiotergic pathways; inhibitory neurotransmitters (e.g. gamma aminobutyric acid) and excitatory amino acids (e.g. glutamic and aspartic acids); and other brain peptides including pineal secretions (melatonin) and corticotrophin-releasing hormone, and the complex interactions among them are subtle but functional species-specific influences on the electrochemical transmission of neuronal signals that the hypothalamus translates to the chemical signal GnRH."

What vague scheme? What unspecified pathways?

Nov 09, 2014
That's not what I was talking about and you know it. What makes the changes "theorists" refer to as mutations in your model?

Nov 09, 2014
That's not what I was talking about and you know it. What makes the changes "theorists" refer to as mutations in your model?

@JVKOHL
you REALLY need to answer this

JVK
Nov 09, 2014
Excerpt: "Stories that make mutations responsible for adaptive evolution or that make operant conditioning associated with visual or auditory input responsible for adaptive evolution lack details of the molecular mechanisms or scientific support that links them to the de novo protein synthesis required for adaptive evolution."

I have not modeled the role of mutations, which is why I concluded:

"Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific 'fit'."

http://www.ncbi.n...3960065/

@Captain Stumpy
You really need to admit to the fact that you are a brain-damaged buffoon.

@Andrew Jones (aka anonymous_9001)
You do not need to admit that you are an anonymous fool. You have shown that by asking me the name of the system and about the specific pathways it utilizes, after I detailed the system and the specific pathways during the past 20 years.

Nov 09, 2014
You really need to admit to the fact that you are a brain-damaged buffoon.
I have already TOLD you that you are a brain damaged buffoon !
you just don't listen

and like all other pseudoscience crackpots out there... you also don't get to redefine a lexicon based upon your dislike of certain words or phrases, like the word MUTATION

your model causes them, which you've readily admitted to
you still argue against mutations

either you are insane
stupid
religious
ignoring reality (insane, really)
or ALL of the above!

and your "detailed pathways" simply says
MUTATION!
but you don't get it, do you

and you call yourself mensa?
they need to revoke your membership

Nov 09, 2014
want PROOF that jk is a liar? simple enough

he says above
I have not modeled the role of mutations

but 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

so what is the real story, mr Brain-damaged Buffoon with the kohl-slaw word salad which means nothing?

your own model causes mutations
you cause mutations
you promote your model as supplanting evolution
you work on nothing but this religious model
but you also argue against mutations

truth is- you are a liar looking to support yourself by pushing a religious based pseudoscience in order to promote your perfume

and every time you argue against mutations you PROVE my comment is true
thanks

JVK
Nov 09, 2014
Nutrient-dependent changes in nucleotide sequences link RNA-mediated events to cell type differentiation via amino acid substitutions.

Captain Stumpy and anonymous_9001 may be the only two idiots in the world who cannot distinguish the difference between mutations that perturb protein folding and amino acid substitutions that staiblize the organized genomes of species from microbes to man.

The idiots like the idea that mutations do the impossible and despise the fact that conserved molecular mechanisms link physics and chemistry to the molecular mechanisms of cause and effect.

If you also are an idiot, please add your comments about mutations to this thread so we can tell if any others remain.

Nov 09, 2014
I detailed the system and the specific pathways during the past 20 years.


If that's the case, you should be able to name and list them so that others may examine what they are and what they truly do independently to verify your claims.

JVK
Nov 09, 2014
Obviously, I did that, which is exactly what I told you (above).

"Noradrenergic, dopaminergic, serotoninergic, and opiotergic pathways; inhibitory neurotransmitters (e.g. gamma aminobutyric acid) and excitatory amino acids (e.g. glutamic and aspartic acids); and other brain peptides including pineal secretions (melatonin) and corticotrophin-releasing hormone, and the complex interactions among them are subtle but functional species-specific influences on the electrochemical transmission of neuronal signals that the hypothalamus translates to the chemical signal GnRH."

http://www.scienc...14004006 cites Kohl (2013)
"The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and olfactory organ could exert regulatory action on the OL via epigenetic effects of nutrients and pheromones on gene expression (Kohl, 2013; Elekonich and Robinson, 2000)."

JVK
Nov 09, 2014
See also: http://onlinelibr.../summary

"...the method allows intensive and extensive analyses of the effects of various factors, such as neurotransmitters, gonadal steroids, energy balance, and pheromones, on the GnRH pulse generator, and will thus increase our understanding of the central mechanisms that control reproduction."

The anonymous fool may be the only idiot who does not realize that others have been examining this model since I first presented it in 1992, and all biologically-based experimental evidence supports its extension across species via the conserved molecular mechanisms of nutrient-dependent pheromone-controlled ecological speciation.

In response to his criticisms of my model, the editor wrote: "The 2013 review article... was subjected to standard peer review and the revised version was accepted by me after it had been accepted by both reviewers." http://www.ncbi.n...4049134/

Nov 09, 2014
1. Those are not present in organisms without nervous systems, so that doesn't apply to all organisms.

2. Peptides, hormones, neurotransmitters, etc. can affect gene EXPRESSION, but they have no means of making changes to gene sequence, which is what I've been asking you about.

Nov 10, 2014
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

so when you say
Captain Stumpy and anonymous_9001 may be the only two idiots in the world who cannot distinguish the difference between mutations that perturb protein folding and amino acid substitutions ...
what kinds of idiot moron retard does that make you?
YOU are the moron who keeps spouting off about a model that causes mutations but then turns around and says mutations cannot be beneficial

tell us all...WHY can't you comprehend the lexicon of your field?
Why do you make up definitions to suit your faith?
why don't you use the definitions that biologists/geneticists use?
why weren't you smart enough to finish college?


Nov 10, 2014
http://www.scienc...14004006 cites Kohl (2013)
"The OL acting as control centre may be target organ for metabolic hormones such as leptin like and insulin like peptides, and 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)."


Reread what you just posted here-

"EPIGENETIC effects of nutrients and pheromones on gene EXPRESSION"

Nobody denies that nutrient levels and pheromones/other signalling molecules effect gene EXPRESSION, but you're claiming they cause deterministic changes in DNA base SEQUENCE without supporting it and giving a mechanism.

JVK
Nov 10, 2014
...you're claiming they cause deterministic changes in DNA base SEQUENCE without supporting it and giving a mechanism.


I've supported my claims with an established model of cell type differentiation across species that incorporates the conserved molecular mechanisms of nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions, which are the only obvious link between the epigenetic landscape and the physical landscape of DNA in organized genomes of species from microbes to man.

What do you claim is an alternative mechanism at the source of deterministic changes in DNA base SEQUENCE(s) linked to biodiversity?

Do you believe "...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

If not, tell us what other pseudoscientific nonsense you believe in.

Nov 10, 2014
RNA-mediated amino acid substitutions


Once again, you use this vague term without saying by what pathway or enzymatic mechanism it occurs. That's what mechanism means.

This should look familiar: ATP synthase catalyzes synthesis of ATP from ADP and Pi.

_________ catalyzes RNA-mediated amino acid substitutions.

JVK
Nov 10, 2014
I asked
What do you claim is an alternative mechanism at the source of deterministic changes in DNA base SEQUENCE(s) linked to biodiversity?


It is pointless to attempt explanation of pharmacogenomics in the context of evidence levels and personalized medicine that links genetic networks and metabolic networks via enzymes and RNA-mediated cell type differentiation to an anonymous fool, or to anyone else who believes in mutation-driven increasing organismal complexity.

It's like trying to teach a pig to sing, or trying to teach an evolutionary theorist anything at all.

Nov 10, 2014
What on Earth does pharmacogenomics have to do with this? This conversation is about your belief that nutrients and pheromones can make changes to the DNA sequence and your inability to tell anybody the pathways by which that supposedly occurs.

What do you claim is an alternative mechanism at the source of deterministic changes in DNA base SEQUENCE(s) linked to biodiversity?


I have provided you with plenty of studies showing the production of functional and even improved phenotypes through mutation.

http://www.scienc...05005541

JVK
Nov 10, 2014
A study of 10,000 patients linked genetic networks to metabolic networks via RNA-mediated events that link enzymes and amino acid substitutions to the ability to metabolize specific drugs -- and also to behavior via the Val158Met amino acid substitution. http://www.nature...29a.html

There was no evidence of beneficial mutations in the context of experienced-based personalized medicine, which links cell type differentiation in all cells of all individuals of all species from microbes to man via conserved molecular mechanisms.

You ask:
What on Earth does pharmacogenomics have to do with this?


In my 2012 review I wrote: "The gene, cell, tissue, organ, organ-system pathway is a neuroscientifically established link between sensory input and behavior. Marts and Resnick (2007) stress the importance of this pathway in the context of a systems biology approach to pharmacogenomics." http://www.ncbi.n...24693349

Nov 10, 2014
http://www.nature.com/clpt/journal/v95/n4/full/clpt2013229a.html


That was merely a genotyping study. Counting how many people have what genotype says nothing of how the genotypes came to be.

I asked you about the mechanism that makes new genotypes. That citation does nothing to answer that question. You keep obfuscating and getting more and more off topic.

JVK
Nov 10, 2014
You know nothing about cell type differentiation, but claim I'm obfuscating and will not offer an alternative explanation of study results like this:

Excerpt: "The CYP3A5*1 genotype codes for a functional CYP3A5 enzyme and is the most common allele among AAs, but not among EAs."

Without RNA-mediated amino acid substitutions that stabilize the DNA in organized genomes of species from microbes to man there would be no differences in alleles common among AAs, but not among EAs.

Nov 10, 2014
Excerpt: "The CYP3A5*1 genotype codes for a functional CYP3A5 enzyme and is the most common allele among AAs, but not among EAs."


One group most commonly has one allele and the other group doesn't. That's great, but it has nothing to do with the topic at hand. What is that excerpt supposed to reveal about the mechanism in your model that makes base changes? It's completely unrelated.

This is the closest thing I can find to what I want you to explain:

http://users.rcn....ing.html

It explains the processes and enzymes involved in RNA editing. I want you to explain the processes and enzymes involved in RNA-mediated DNA base substitutions. They give actual names of the processes involved rather than vague descriptions like you give, so one can look up those processes in greater detail. Under substitution editing, for example, they list the enzymes that perform the editing. That's what you have yet to do.

JVK
Nov 10, 2014
That's what you have yet to do.


What you have yet to do is provide an alternative that makes sense. What you have done is continue to claim that the physics, chemistry, and molecular epigenetics of cell type differentiation that I have detailed are unrelated.

I want you to explain the processes and enzymes involved in RNA-mediated DNA base substitutions.


I want you to explain why you believe in the pseudoscientific nonsense of evolutionary theories. If you can do that, I may tell you again about the thermodynamic cycles of protein biosynthesis and degradation that are nutrient-dependent and pheromone-controlled in species from microbes to man.

Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation)
http://youtu.be/DbH_Rj9U524

Nov 10, 2014
Can you not see the difference between what the last link I provided and your model?

One provides specific molecular examples complete with names and pathways and the other provides generalized, non-specific schemes. Guess which is which.

What you have done is continue to claim that the physics, chemistry, and molecular epigenetics of cell type differentiation that I have detailed are unrelated.


No, what I have done is claim that your citations are unrelated. I asked you to provide detailed mechanisms and you gave me a genotype count.

If you can do that, I may tell you again about the thermodynamic cycles of protein biosynthesis and degradation


Luckily, people like Konishi:

http://nar.oxford...587.long

and Guo et al.:

http://www.ncbi.n...1383578/

know far more about that than you do, so I'll look to them instead of someone that has trouble grasping basic logic and reading comprehension.


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