Missing link in the evolution of complex cells discovered

May 6, 2015
Hydrothermal vent field along the Arctic Mid-Ocean Ridge, close to where 'Loki' was found in marine sediments. The hydrothermal vent system was discovered by researchers from the Centre for Geobiology at University of Bergen (Norway). Credit: Centre for Geobiology (University of Bergen, Norway) by R.B. Pedersen

In a new study, published in Nature this week, a research team led from Uppsala University in Sweden presents the discovery of a new microbe that represents a missing link in the evolution of complex life. The study provides a new understanding of how, billions of years ago, the complex cell types that comprise plants, fungi, but also animals and humans, evolved from simple microbes.

Cells are the basic building blocks of all life on our planet. Yet, whereas the cells of bacteria and other microbes are small and simple, all visible life, including us humans, is generally made up of large and complex cell types. The origin of these complex cell types has long been a mystery to the scientific community, but now researchers from Uppsala University in Sweden have discovered a new group of microorganisms that represents a missing link in the evolutionary transition from simple to complex cells.

In the 1970s, the acclaimed biologist Carl Woese discovered a completely new group of microorganisms, the Archaea, and showed that these represented a separate branch in the Tree of Life—a finding that stunned the scientific community at the time. Despite that archaeal cells were simple and small like bacteria, researchers found that Archaea were more closely related to organisms with complex cell types, a group collectively known as ''. This observation has puzzled scientists for decades: How could the complex cell types from eukaryotes have emerged from the simple cells of Archaea?

In this weeks' edition of Nature, researchers from Uppsala University in Sweden, along with collaborators from the universities in Bergen (Norway) and Vienna (Austria) report the discovery of a new group of Archaea, the Lokiarchaeota (or 'Loki' for short), and identify it to be a missing link in the origin of eukaryotes.

"The puzzle of the origin of the eukaryotic cell is extremely complicated, as many pieces are still missing. We hoped that Loki would reveal a few more pieces of the puzzle, but when we obtained the first results, we couldn't believe our eyes. The data simply looked spectacular", says Thijs Ettema at the Department of Cell and Molecular Biology, Uppsala University, who lead the scientific team that carried out the study.

Hydrothermal vent field along the Arctic Mid-Ocean Ridge, close to where 'Loki' was found in marine sediments. The hydrothermal vent system was discovered by researchers from the Centre for Geobiology at University of Bergen (Norway). Credit: Centre for Geobiology (University of Bergen, Norway) by R.B. Pedersen.

"By studying its genome, we found that Loki represents an intermediate form in-between the simple cells of microbes, and the complex of eukaryotes", says Thijs Ettema.

When Loki was placed in the Tree of Life, this idea was confirmed.

"Loki formed a well-supported group with the eukaryotes in our analyses", says Lionel Guy, one of the senior scientists involved in the study from Uppsala University.

"In addition, we found that Loki shares many genes uniquely with eukaryotes, suggesting that cellular complexity emerged in an early stage in the evolution of eukaryotes", says Anja Spang, researcher at Department of Cell and Molecular Biology , Uppsala University, and one of the lead-authors of the study.

The name Lokiarchaeota is derived from the hostile environment close to where it was found, Loki's Castle, a hydrothermal vent system located on the Mid-Atlantic Ridge between Greenland and Norway at a depth of 2,352 meters.

"Hydrothermal vents are volcanic systems located at the ocean floor. The site where Loki is heavily influenced by volcanic activity, but actually quite low in temperature", says Steffen Jørgensen from the University of Bergen in Norway, who was involved in taking the samples where Loki was found.

"Extreme environments generally contain a lot of unknown microorganisms, which we refer to as microbial dark matter", says Jimmy Saw, researcher at Department of Cell and Molecular Biology, Uppsala University, and co-lead author of the paper.

By exploring microbial dark matter with new genomics techniques, Thijs Ettema and his team hope to find more clues about how complex cells evolved.

"In a way, we are just getting started. There is still a lot out there to discover, and I am convinced that we will be forced to revise our biology textbooks more often in the near future", says Thijs Ettema.

Explore further: Researchers shed light on ancient origin of life

More information: Nature, DOI: 10.1038/nature14447

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Steve 200mph Cruiz
5 / 5 (13) May 06, 2015
I'm always surprised how many of the important forks in the road of evolution are still on this planet, we just have to find them/recognize them
viko_mx
1.3 / 5 (15) May 07, 2015
The action of some atibiotics is to pierce holes in the cell membrane of bacterial cells and although they are located in an environment where there is all needed for their existent and reproduction, they lose stasis and die.
Evolutionists want to convince us that the reverse process is possible and from the components of a bacterium (its chamical ingredients), which for some inexplicable miracle have got in one place at the same time can emerge the bacterium by itself. And such claims they call science?!

Eikka
5 / 5 (13) May 07, 2015
although they are located in an environment where there is all needed for their existent and reproduction


But that's a false assumption. The necessary ingredients must be in the right concentrations to sustain the operation. The lipid membrane is keeping the chemicals together so they may react, instead of dispersing around randomly.

Evolutionists want to convince us that the reverse process is possible


Why wouldn't it be? Cell membranes evolve because of diminishing concentrations of chemicals necessary to sustain the operation of life, like a fish needs a bowl when you take it out of the lake.

Fish can't blow glass, but DNA can synthetize lipids, ergo when the need arises those bits of DNA that can blow themselves lipid shells, or otherwise find themselves encapsulated, survive while the rest just disperse and stop functioning, becoming food for the newly formed cells.
Eikka
5 / 5 (12) May 07, 2015
which for some inexplicable miracle have got in one place at the same time


The "miracle" you're talking about is called chemical synthesis, which happens in places where chemicals are trapped in between some form of chemical energy flow, like in alkaine hydrothermal vents.

Like in the Miller–Urey experiment, very simple chemicals consisting of nothing but carbon, nitrogen and hydrogen spontaneously combine into complex molecules because the addition of energy into the local system tends to increase complexity. When these molecules are prevented from moving around because they're trapped in some sort of silt or clay, you get high complexity in high concentration.

On the other way, basic amino-acids may have come from space, but they were most likely concentrated by tectonic activity similiar to how oil deposits form.
I Have Questions
4.4 / 5 (14) May 07, 2015
The action of some atibiotics is to pierce holes in the cell membrane of bacterial cells and although they are located in an environment where there is all needed for their existent and reproduction, they lose stasis and die.
Evolutionists want to convince us that the reverse process is possible and from the components of a bacterium (its chamical ingredients), which for some inexplicable miracle have got in one place at the same time can emerge the bacterium by itself. And such claims they call science?!


Thinking that the world is awash in conspiracy is a mental disorder called apophenia. Perhaps you should see the appropriate doctor, I bet he can give you some nice pills you could take each day to clear that right up.
viko_mx
1 / 5 (13) May 07, 2015
Once you feel that it is not a miracle the presence of DNA and the mechanisms for reading the DNA information, molecular machines for protein synthesis and their energy providers molecules and mitohondrial structures at the same place in the same time, why life can not be reproduced in the laboratory from the scratch? The information stored in DNA is the product of idea and intelect, not due to random changes. In nature can happen random chemical reactions, but their end product always have a low degree of complexity, which does not meet the needs of living organisms. The process of disintegration of complex molecules in action of outer environmental factors always dominates. As we know entropy is unidirectional and only intellect and use of energy and matter in controlled manner based on ideas and purpose can lower the entropy localy and increase the order and information in the system.
viko_mx
1 / 5 (11) May 07, 2015
The most simple living cell which can live in the external environment have 1,3 milion base pairs in it DNA. Probably you heard for iredusible complexity. Some structures or mechanisms in the living cells and orgaisms can not work if their all constituents are not in wright place and the chance accidentally occur there is zero. All fosils confirm complexity of life from the begining. The very definition of a living organism requires a high complexity and organization of its biological structures so that they can provide its basic functions. Stasis, protection from the external environment - controlled permeability of the membrane, metabolism, removal of waste products from metabolism, reproduction and mechanism for repairment of its genetic infromation. This basic functions must emerge at once to survive this organism. And the environment at the same time must provide all chemical thar are needed for its metabolism.

viko_mx
1.7 / 5 (12) May 07, 2015

"Thinking that the world is awash in conspiracy is a mental disorder called apophenia. Perhaps you should see the appropriate doctor, I bet he can give you some nice pills you could take each day to clear that right up."

To think that your fantasies are reality or to invent your own reality for personal convenience despite the facts of observations or experiments or personal experience, is manifestation of the ostrich syndrome.

Returners
1 / 5 (12) May 07, 2015
God made man from mud. Mud.

What he didn't tell yah is he made microbes from Mud too. hehehe.

You guys lose either way, atheists.
cassandrahelm
4.8 / 5 (18) May 07, 2015
We know that life exists. We know that life evolves. The fossil record proves that the first life was microbial. While it is not a huge surprise that for most of the time that life existed on Earth it was simple rather than complex, it is exciting to discover how it all started.

There is no time machine. Scientists have to take the clues we have and try to discover how, from a world billions of years in the past and different in chemistry from today's world, life began.

Answers are not about magic.
Answers are not based on false claims.

Answers are found through patient hard work and deduction. Claims are not stated because they sound good and are then proposed as fact. Everything has to be based on evidence and deductions have to be testable. Science is not 'based on faith'.
syndicate_51
1.8 / 5 (5) May 07, 2015
A long ways to go yet.
gkam
1 / 5 (4) May 07, 2015
Xenu made it this way.

Just ask Tom Cruise.

Torbjorn_Larsson_OM
5 / 5 (13) May 07, 2015
Basic biology passes yet another test, with a lead from my alma mater by the way, and since creationists can neither abide by its success or attack the finds, what do they do? They put up irrelevant questions of exotic biology, and add irrelevant experiments to test the theories. We can't make a star or a planet in the laboratory, yet we know how they how they work and how they emerged. Similarly no one can put in the 10 - 100 000 years it is estimated that it took life to emerge, yet we know how life works and how species emerge - and yes, roughly how life emerged.

Ironically it is creationists who propose 'miracles' of magic 'poofing', while we know from basic biology that its processes are gradual, changing populations into new populations. But they are blind to the content of their magic incantations. 'Miracles', 'mud', 'gods' - if you want to discuss them in relation to what is, prove them! Everything science does is testable.

[tbctd]
PeterKinnon
2.3 / 5 (3) May 07, 2015
The extent to which the results of such genome research provide good evidence is somewhat questionable.

That, of course, is not not to say it is not intriguing inasmuch it supports an incremental model rather than the singularity favored by Nick Lane and others.

But a much stronger clue to the transition from prokaryote to eukaryote has been found by Masashi Yamaguchi et al.

In this case the fortuitous discovery of an extant deep sea organism (Parakyron myogenensis), the morphology of which strongly suggests an intermediate.

Both eukaryosis and abiogenesis are issues explored in my latest book as part of a far broader evolutionary process that is traceable from the formation of the chemical elements in stars right through to its latest manifestation, the emergence of the Internet. "The Intricacy Generator: Pushing Chemistry and Geometry Uphill". is now available as 336 page illustrated paperback from Amazon, etc.
Torbjorn_Larsson_OM
5 / 5 (14) May 07, 2015
[ctd]

"All fosils confirm complexity of life from the begining."

False. Our oldest type of fossils, from the RNA world, is the preserved RNA (ATP, NAD, ribosome PTC), and they test well the predicted simplicity. The RNA world predicts the quaternary code of base pairs, where enzymatic efficiency (increased by increased number of base types) and replication efficiency (decreased by increased number of base types) are balanced. This was a frozen basis that later the protein triplet code could evolve from.

[tbctd]
Torbjorn_Larsson_OM
5 / 5 (12) May 07, 2015
[ctd]

"The very definition of a living organism requires ...".

False. There is no consensus definition of life, but for testing individuals the NASA definition of a metabolizing, evolving system is often used. Nothing in that definition describes what it requires, same as the definition of gravity ("a process where masses accelerate other masses") do not tell us what it requires. (Which is a curved space, as it turns out.)

A Hadean hydrothermal vent that builds hydrocarbons out of the CO2 atmosphere by catalysis, and hosts RNA enzymatic replicating strands by PCR in its inorganic pores would be such a living system, _by definition_. Very simple beginnings, yet it does all the functions you mention. That system had those, and many more, traits in common with modern cells. ["The Drive To Life on Wet and Icy Worlds", Russell et al, Astrobiology.]
Eikka
5 / 5 (9) May 07, 2015
why life can not be reproduced in the laboratory from the scratch?


Because we don't know how to do it.

We've synthetized life by copying existing DNA code, but we have no idea what exactly it does and how, so we can't do the same trick. DNA is like a computer program that modifies its own code when you run it - it's very difficult to just look at it and predict what it will do.

That isn't to say it can't be done. Just that it hasn't been done.
Torbjorn_Larsson_OM
5 / 5 (8) May 07, 2015
@Peter: I can't find any of your references. [I happened to vote in the wrong direction on your fringe self promotion, by the way. Sorry about that!]

@Eikka: My description would be that it is like a recipe, most of the result comes from the environment that it channels its evolutionary information from by way of selection. (In this sense each gene sees the other genes work as its environment.)

But we do know some pathways and testing have started. Since it took about 50 years to parse out viable pathways, it can take 50 years to test them.

But in no way of form will we put a whole biosphere in a lab and test it for 100 000 years, same as we didn't take millions of years to test stellar fusion! Since the 5 remaining pathway roadblocks (that I know of) fell during the last year, we also know that we will see success. (Providing we can test in sufficient detail to weed out all but one, or a few, scenarios - or at least to reach consensus.)
viko_mx
1.4 / 5 (10) May 07, 2015
@Eikka

I can guarantee that people will never learn how to create biological life. We do not have enought intelligence for the perpose. But even if we understand how function the simplest living organism, again we can not create it because is needed 3D matrix which can arrange every single atom in of this organism in 3D space to create it structure and chemical environment and to start its metabolism. This can be done only by the Creator who can control every single atom or elementary particle in the universe at his will. In the universe direction of organization is from the top to bottom. A higher being creates inferior being. The main principle is that to understand how one complex physical system function, you have to be more complicated than this system. It is paradoxical that the intellect of man in combination with highly wonderfully equipped laboratories are not able to achieve what the blind chance done according to evolution theoreticians.
Eikka
5 / 5 (14) May 08, 2015
I can guarantee that people will never learn how to create biological life.


That depends on your definition of "create".

If we let evolution work on a synthetic pre-biotic soup or a test tube full of nucleotides in the correct conditions and have something emerge that fills the definition of life, have we created it?

Of course we can't feasibly build "life" atom by atom like building a brick house. It's simply too complex.

This can be done only by the Creator who can control every single atom or elementary particle in the universe at his will.


This definition of "Creator" is indistinguishable on any logical, ontological, philosophical or practical level from "The universe".

You are arguing that the Creator is arbitrarily pulling all the strings all the time in a consistent manner so that life emerges and manages to exist, but that is simply indistinguishable from the laws of physics at work.
Eikka
5 / 5 (11) May 08, 2015
The main principle is that to understand how one complex physical system function, you have to be more complicated than this system


That's an incomplete view of the situation.

Complexity in itself doesn't mean anything but the dense accumulation of energy - information. Packing energy tighter and tighter results in it assuming complex states because simple chemical bonds are no longer sufficient to hold it all in.

Where you have the right stuff and add energy, it starts to move, live, think.

It is perfectly reasonable to have simplicity, diffuse energy, collect up together towards greater complexity. Even if the world was a one-time event from the ultimate energy density of the great big bang or the creation towards all things vanishing to space, still it is possible and plausible to have one planet basking in the energy flow from its sun develop life from simplicity to complexity because some energy is temporarily accumulating in one small place.
Eikka
5 / 5 (12) May 08, 2015
Creationism should be more properly called "The Great Dollhouse Theory", because when you argue that God does not equal the Universe, you're essentially saying that reality isn't actually what we can observe - that this is not actually how things work deep down, but that God is simply building little artifacts like wind-up toys that work only if someone outside sticks their hand in the box to turn the key, or grabs the doll by the waist and shakes it about and pretends that it talks.

But that really throws the crank in the gears of Christianity at least, because if we really are just wind-up toys and dolls for God, what point is there in any of the sin business? It's all just a show!

You pray in church and feel really guilty about your sins, and you chastise other people for committing sins, but that's just God holding you by the waist and shaking you about, pretending that you're talking instead of him.
Eikka
5 / 5 (13) May 08, 2015
So the funny conclusion is, that if the world is a creation - an artifact - and that life is likewise an artifact that simply wouldn't happen without God's constant interference, then you don't actually exist. Your body exists, all the atoms in it exist, it moves and talks and eats but the "soul" is missing entirely.

Well then you say God puts the soul in your body, but the soul is yet another artifact, another creation that doesn't work without God's will or constant meddling. If nothing works of itself without the need for God, then everything is simpy God playing sockpuppets with himself.

That means you are God.

viko_mx
1 / 5 (10) May 08, 2015
@Eikka
The complexity of a system is determined by the amount of information therein. Information can be recorded with the help of energy, but it is not equivalent to the energy and always is the product of intelligence, and is associated with his ideas for establishing order in the system. It represents instructions for establishing and maintaining order in a system.

You do not believe in a reasonable God who created the universe and everything in it on his will and with a certain idea and purpose, but in god of the lucky chance that so finely tuned physical laws without the idea and purpose and thisof this you call reasonable scientific approach. Paradoxically. The difference between your and my faith is God's law. I wonder why man create goods by always considering the their purpose in advance and the technology by which will use controlled energy and matter to achieve the goal.
viko_mx
1 / 5 (12) May 08, 2015
I do not pray in churches because for the christians it does not matter when and where you communicate with God. This is a personal act and you do not need intermediaries and specially places for pray. I do not believe in God because of the guilt of sin, but because of his love to us, which shines in the beauty and harmony in the nature and his concern obout us. He gave to us recipe for just and divelopment society. And because of God's truth that frees us from the shackles of sinners. I guess you can distinguish feelings fear and love. The fear enslaves people. The love frees people.
Eikka
5 / 5 (11) May 08, 2015
The complexity of a system is determined by the amount of information therein. Information can be recorded with the help of energy, but it is not equivalent to the energy


Information equals energy, because energy is the potential to change something. No change, no information.

It is paradoxical that the intellect of man in combination with highly wonderfully equipped laboratories are not able to achieve what the blind chance done according to evolution theoreticians.


There's nothing paradoxical about that. "Blind chance" is an incredibly powerful phenomenon.

Because of blind chance, the reality that we live in is essentially uncomputable all the way down to everything but the simplest molecules, so the only way to figure it out is to try things directly, and when you try things out directly you only have so many scientists to run so many experiments whereas nature is constantly trying out every possibility at the same time everywhere.

Eikka
5 / 5 (11) May 08, 2015
always is the product of intelligence


If information must always be the product of intelligence, then you're simply saying that the Universe must be intelligent of itself. It doesn't need a separate God to be the intelligent source.

And you've still to define "intelligence" in a meaningful way in the first place.

but in god of the lucky chance that so finely tuned physical laws without the idea and purpose and thisof this you call reasonable scientific approach.


None of the sort. The fine tuning argument begs the question that ours is the only universe or reality that exists, that the rules have always remained the same, and that they will always remain the same. It's like asking "why am I me?" without considering that you'd ask the same question if you were anyone else - in fact ignoring that other people exist.

If we don't constrict ourselves to thinking that we're absolutely unique, then the fine tuning problem vanishes and there is no paradox.
Eikka
5 / 5 (13) May 08, 2015
This is a personal act and you do not need intermediaries and specially places for pray. I do not believe in God because of the guilt of sin, but because of his love to us, which shines in the beauty and harmony in the nature and his concern obout us.


Which is all the more funny because when you consider what your Creator actually means, by your description of what it is, all that you're describing there is Narcissus looking at the pond without realizing it's his own image.

There's nothing wrong with that as long as it pleases you, but it's nevertheless damn funny.

He gave to us recipe for just and divelopment society. And because of God's truth that frees us from the shackles of sinners. I guess you can distinguish feelings fear and love. The fear enslaves people. The love frees people.


Now you're confusing the Bible for God. That's really the sin of idolatry, because you're holding the imagination of man as substitute for God and praising that instead.
Whydening Gyre
5 / 5 (12) May 08, 2015
Stasis, protection from the external environment - controlled permeability of the membrane, metabolism, removal of waste products from metabolism, reproduction and mechanism for repairment of its genetic infromation. This basic functions must emerge at once to survive this organism. And the environment at the same time must provide all chemical thar are needed for its metabolism.

Here you make the fundamental mistake of assuming organisms are not the result of inherent self organization in any entropic system. Entropy only APPEARS random in that we have not yet evolved the capacity to understand it.
Anyway, if a god created us, he was a poor designer, cuz organisms are constantly having to re-design themselves in order to adapt to "environment du jour".
And a lot of those organisms get wiped out in the process...
Eikka
5 / 5 (11) May 08, 2015
The problem of idolatry is as follows:

If man is not equal to God, then any thought or idea that man can hold isn't sufficient to capture God in its full reality, and therefore any belief a man holds about God is essentially a false belief.

To worship these false beliefs is to worship false gods. To say "God wants this and that" is to put words in God's mouth and induce false beliefs in others who take your word instead of God itself as the subject of their beliefs, and make them worship false gods as well.

The paradox of idolatry means that you can't believe in any god at all - you must deny any thought of God entirely to find out who he truly is, but then you can't find any because you've got no idea what you're looking for.

That is also what the ignostics mean when they point out that the question of God is meaningless because nobody can say what "God" refers to.
Eikka
5 / 5 (8) May 08, 2015
The only way to get out of the bind is to admit that you're God. If God is necessary for you to exist, then you can't really be anything else. All that you do, all that anyone does, is what God does.

But then if I'm God and you are also God, you are really I, then why do we hold different opinions?

Well, why does the child play that one doll is bad and the other one is good?
Eikka
5 / 5 (9) May 08, 2015
Also, to be exact we have to separate "information" and meaning. You can re-arrange the pieces on a chessboard without changing the amount of information in it.

If you arrange them into the letter E, an person would find meaning in it, but meaning isn't information. Meaning is subject to intelligence, and not a real thing, and intelligence doesn't operate on information but meaning that it makes up. To a person who doesn't read, the E is just another random arrangement without meaning.

You can put molecules into a cell, or just jumble them around, without adding or removing information. Of course you use energy to move the bits around because the previous configuration has to dissapear first, but the aggregate remains the same.

The jumbled mess and the cell are equally complex as long as they're equally dense, which is why when you keep adding energy into a soup of organic molecules and don't let it come out, it either boils over or starts to behave like life.

Whydening Gyre
5 / 5 (3) May 09, 2015
But then if I'm God and you are also God, you are really I, then why do we hold different opinions?

We are Bipolar or Schizophrenic?

gkam
5 / 5 (8) May 09, 2015
Are we in the image of god? Does god have a penis? Does he poop?
Whydening Gyre
5 / 5 (11) May 09, 2015
Are we in the image of god? Does god have a penis? Does he poop?

Not sure about either of those....
But I AM pretty sure god has a vagina...

And Ren.
The scriptures are not the word of god. They are merely documented interpretations of men who had deep thoughts on what they think a god might be like...
Whydening Gyre
5 / 5 (13) May 09, 2015
As you wish. Your cynicism and rebellion against your Creator and constant supporter only demonstrated the size of human stupidity, clings to corruptible. Like horse with blinders.

No cynicism and no rebellion. Simply an understanding that there is no intellect driving our universe other than the one we choose to accept. Free will, remember?
However, it is not free will if we are forced/coerced to choose to accept the thing that a god forbids.

The answers are before his eyes but he rejected them because do not like them. What a fortitude.

Not that I may not like them. It's that I am being told what I am to like and dislike.

You people think in unending circles that contradict with your other unending circles...
Eikka
5 / 5 (10) May 10, 2015
The creator do not need the universe to live.


That's just a meaningless statement.

First of all, we can assume you didn't mean literally "live", because that would imply some thing - a process that exists in a reality, therefore in a universe of some kind greater than the thing living in it.

It boils down to saying that nothing needs to exist for God to exist, but that's a contradiction because God is not nothing, and if God is something and the only thing that is - then everything is simply God: Universe is God, God is Universe.

And when such God creates the universe within its universe and all the souls and whatnot, we're back to The Great Dollhouse Theory.

You see, you cannot make statements about a God that is greater than the entire universe without running into contradictions - any thought of such God is a false belief, and any such God is a false god.

Eikka
5 / 5 (9) May 10, 2015
It's kinda like the thought of the supernatural.

We might be inclined to believe that there exist this reality beyond reality that is completely unexaminable and unprovable, yet we can make statements of it somehow.

Well, the question becomes what difference does it make?

If there is to be any "communication" between us and it, then there must be exchange of information - something that makes a difference in both, and therefore this beyond nature reality becomes examinable and provable, and therefore we can drop the "super" from its name - it's simply our reality.

If not, if it makes absolutely no difference to us, which implies we make no difference to it because observation is interaction, then for us it doesn't exist and neither do we to it.

If there's any God lurking there, who cares?
Eikka
5 / 5 (11) May 10, 2015
For save this vain effort, the Scripture that explain His character, explain the Creation of our reality and define the moral laws and principles that are the base for just and dеveloped society.


Then why did God see fit to send down thousands upon thousands of such scriptures which all contradict each other - and themselves - on some or all ethical, moral and practical points.

Why for example can you advocate a free democracy, or even a republic, when the Christian god is really a monarchist? Afterall, it's the Kingdom of God instead of the Republic of God.

Or is it that what you take out of the scripture as your instruction and guidance has subtly changed in the 500 years of recent history? If so, then which of you was actually correct in interpreting God's intentions? Was it King James, or Martin Luther, or perhaps Joseph Smith?

Or is it that all of them, you, operate under false notions of God and God's will and practice idolatry for this false God of yours

tmarksur
5 / 5 (13) May 10, 2015
"God is the only one real (...)" If you define god in this way, then god is contradictory. He does not exist. The only way you can define god and get away with it, is if you give the same definition as The Universe: god is everything that exists (then, we just use a different word for the same thing, and The Universe is not 'benevolent').

In any other way, god either does not exist or is completely irrelevant to anything.

It is funny that in a comment section of an article about a discovery of a missing link of evolution of life on earth these discussions happen. I'm not sure if religious people understand the millions of humans lives that have been lost because of their actions.

Every second you think or debate these things, people are dying somewhere, and we all spent our energy on irrelevant discussions such as this. If hell exists, and there is justice in this world, then religious people are ALL CERTAINLY going there. But there is not.
Torbjorn_Larsson_OM
5 / 5 (9) May 11, 2015
@Eikka: ""The main principle is that to understand how one complex physical system function, you have to be more complicated than this system"

That's an incomplete view of the situation."

Worse, cosmology and biology both reject the hypothesis. We are part of the system we explore, so obviously those systems are more complex.

We have proved creationist magic belief wrong, on their own terms.

Now sit back and watch how they take no notice, but continue to spout inanities that has nothing to do with reality. And they wonder why people leave their flocks in droves...
Torbjorn_Larsson_OM
5 / 5 (8) May 11, 2015
By the way, I found Kinnon's reference. It is Parakaryon myojinensis, explaining why it was hard to find. [ http://blog.oup.c...aryotes/ ]

The paper ends with that they need molecular phylogenies, as in this article's work, to say something conclusive. Kinnon's claim of "a much stronger clue" is hence rejected by his own reference.

I have also read the current paper, and its companion editorial review by two experts on the area. The paper has good results (even if the statistical basis support is moderate, not strong) in that the found eukaryote genes roots the eukaryote ones, meaning they have found a real ancestor. The editorial is lauding the whole work and especially its statistical chops, which I found so-so but the again I am not an expert here.

Bottom line: This looks good!
JVK
1 / 5 (7) May 11, 2015
Study finds protein 'cement' that stabilizes the crossroad of chromosomes
http://phys.org/n...mes.html

This nutrient-dependent link between metabolic networks and genetic networks is obviously the link between ecological variation, the physiology of reproduction, and fixation of the RNA-mediated amino acid substitutions that differentiate the cell types of all genera. Increasing organismal complexity arises via the conserved molecular mechanisms of the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding.

The de novo creation of light-induced amino acids is the link to amino acid substitutions that differentiate all cell types in all individuals of all genera.

News article excerpt:
Ettema and his team hope to find more clues about how complex cells evolved.


How can anyone without a clue expect to find more clues?
JVK
1 / 5 (9) May 11, 2015
http://phys.org/n...sor.html
Sodium ions are key regulators in cellular processes. The fluids in cells, whether it is water, blood plasma, or nutrients, are regulated by the sodium concentration in cells. If scientists could study sodium ions within a live cell, they would gain important insights into cellular processes including ways to reprogram these processes for biotechnological applications.


If sodium is the key regulator of nutrient-dependent intracellular processes, which must be stabilized in the organized genomes of all genera via the biophysically constrained fixation of RNA-mediated amino acid substitutions, what can be learned about cellular processes from statistical analyses?

For example, population geneticists have left evolutionary theorists without clues about how ecological variation leads to ecological adaptation.

The clueless think in terms of mutations and evolution.
Whydening Gyre
5 / 5 (5) May 11, 2015
If sodium is the key regulator of nutrient-dependent intracellular processes, which must be stabilized in the organized genomes of all genera via the biophysically constrained fixation of RNA-mediated amino acid substitutions, what can be learned about cellular processes from statistical analyses?

For example, population geneticists have left evolutionary theorists without clues about how ecological variation leads to ecological adaptation.

The clueless think in terms of mutations and evolution.

Ahhh... What's a Phys.org article on evolutionary processes with a sage (sarcasm intended) comment from Mr. Kohl...?
The adaption process is what leads to variation.
If you wouldn't mind, also - how does RNA "mediate" amine substitutions again?
just one of the clueless, here....
Whydening Gyre
5 / 5 (6) May 11, 2015
Тhe worship to creation is idolatry and God explicitly forbidden it because it is the cause of many troubles in society.

Shouldn't that be "worship OF creation"?
See? - Contradiction...

Uncle Ira
4.3 / 5 (6) May 11, 2015
If you wouldn't mind, also - how does RNA "mediate" amine substitutions again?
just one of the clueless, here....


If you get him to answer that question could you try to get me an answer to the one that has been bugging me for 12 or 11 months now? He won't answer for me when I ask.

I want to know how the first hydrogens in the universe had noses to smell the other hydrongens's energy. He said that is how the dependable smells nourished the hydrogen atoms energy before molecules came on the scene to make the RNA stuffs.

I am not kidding, he really did tell me that while he was calling me a science idiot.
Whydening Gyre
5 / 5 (6) May 11, 2015
I want to know how the first hydrogens in the universe had noses to smell the other hydrongens's energy. He said that is how the dependable smells nourished the hydrogen atoms energy before molecules came on the scene to make the RNA stuffs.

I am not kidding, he really did tell me that while he was calling me a science idiot.

The answer is actually quite simple. One H atom in the close proximity of another (or of any other element) creates a "charge differential", thereby altering the "spin" of both - if even by only an tiny amount.
"Smell" is a fractal approximation of any molecular groups reaction to the total charge or spins of any other molecular aggregate.
Take THAT, JVK...:-)
And thanks for makin' me think on that one, Ira...:-)

JVK
1 / 5 (7) May 11, 2015
Thanks Whydening Gyre. Please explain to the biologically uninformed science idiot, Uncle Ira, how quantum physics and quantum smell are linked from quantum biology to quantum consciousness in the following two articles.

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

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

Uncle Ira claims I don't answer his questions because he doesn't understand anything about biologically-based cause and effect. Perhaps someone else can start with light-induced changes in hydrogen atom energies that link the de novo creation of amino acids to the substitutions that differentiate all cell types in all individuals of all genera and explain why only theorists believe in the pseudosceintific nonsense about mutations and evolution.
JVK
1 / 5 (8) May 11, 2015
See also the discussion at https://www.faceb...nt_reply
Whydening Gyre
5 / 5 (6) May 12, 2015
Thanks Whydening Gyre. Please explain to the biologically uninformed science idiot, Uncle Ira, how quantum physics and quantum smell are linked from quantum biology to quantum consciousness in the following two articles.

I wasn't even talking biological...
And "quantum" is just a term that expresses digital representation (ie- frame reference) of an analog signal.
(call me "old school" on that one...)

mooster75
5 / 5 (6) May 12, 2015
Real scientists test their theories in the lab; JVK debates his on facebook. Hmmm.
JVK
1 / 5 (8) May 12, 2015
Whydening Gyre, and other biologically uniformed science idiots, who seem always to participate anonymously (like mooster75), also ignore my publication history and the support for my model in the content of the domain RNA-mediated.com

http://rna-mediated.com/ Here you will find information that links physics, chemistry, and molecular epigenetics via RNA-mediated events such as the de novo creation of olfactory receptor genes in order to encourage a public discussion of a paradigm shift.
Uncle Ira
4.3 / 5 (6) May 12, 2015
@ Whydening-Skippy. See what I mean? He still won't tell about the hydrogen atom noses but still thinks they smell stuffs before there is any genes or anything to do the smelling. Now he changes the subject to talk about shifting to paradise whatever the heck that is supposed to mean.

Oh yeah, I almost forget. @ JVK-Skippy. The new picture of you still looks sort of goofy. Not as goofy as the other one where you look like you are getting your toes tickled but it still looks pretty goofy. Maybe you should just try to get by without a picture so you don't scare the little kids.
JVK
1 / 5 (8) May 12, 2015
http://medicalxpr...mon.html

...the cancer cells appear to rely primarily on the metabolism of an amino acid called glutamine for their energy.


This links the anti-entropic epigenetic effect of nutrient energy from differences in hydrogen atom energies to virus-driven differences in DNA repair. The differences link viral microRNAs to entropic elasticity and nutrient-dependent microRNAs to the stability of organized genomes via RNA-directed DNA methylation and RNA-mediated amino acid substitutions.

Thermodynamic cycles of protein biosynthesis and degradation are perturbed by viral microRNAs, which is why models of cancer must start with links from atoms to ecosystems via the conserved molecular mechanisms of biophysically constrained RNA-mediated protein folding.

http://figshare.c...s/994281
viko_mx
1 / 5 (7) May 12, 2015
Worse, cosmology and biology both reject the hypothesis. We are part of the system we explore, so obviously those systems are more complex.

Every single organism is different physical system that is designed with certain puropse. Your summary is pointless because any system can be divided into separate subsystems and the universe with its existing physics laws does not make exception. Each physical system has hierarchy. Every living organism is a separate physical system whose structural and functional organization are very complex and their full research and understanding is not within the power of human intelligence that can not piece together the whole picture. The human brain and brain of many living organisms is the most complex physical system in their body and it determine their degree of complexity. How does the human brain operate can fully understand only superior than human intellect.
viko_mx
1 / 5 (7) May 12, 2015
By the way how the theory of evolution explain the emergence of the mamals? Furst simple question at first sight. How have emerged the complex process of photosynthesis from the begining which engage complex molecular structures?
JVK
1 / 5 (7) May 12, 2015
Re:
Each physical system has hierarchy.


All systems are biophysically constrained by the availability of nutrient energy that links RNA-mediated metabolic networks and genetic networks to the chemistry of protein folding.
Organisms adapt; none mutate and evolve into another species.

http://medicalxpr...ood.html
Whydening Gyre
5 / 5 (9) May 13, 2015
By the way how the theory of evolution explain the emergence of the mamals? Furst simple question at first sight. How have emerged the complex process of photosynthesis from the begining which engage complex molecular structures?

A simple google of "evolution of mammals" or "emergence of mammalia" brings a veritable deluge of sources to read from.
(Notice the "Flood" reference there...;-)
You, undoubtably, will not take them at their face value because they do not fit into your created world view of creation...
Whydening Gyre
5 / 5 (6) May 13, 2015
Here you will find information that links physics, chemistry, and molecular epigenetics via RNA-mediated events such as the de novo creation of olfactory receptor genes in order to encourage a public discussion of a paradigm shift.

So... Let me get this straight -
RNA mediation is responsible for the CREATION of olfactory genes where there were none before?!?
Whydening Gyre
5 / 5 (6) May 13, 2015
All systems are biophysically constrained by the availability of nutrient energy that links RNA-mediated metabolic networks and genetic networks to the chemistry of protein folding.
Organisms adapt; none mutate and evolve into another species.

And it is your contention that the incredible variety of speciation (from microbes to man) is NOT the result of adaptation? They were created "de novo" by what?
JVK
1 / 5 (6) May 13, 2015
It is not possible to address the incredible amount of ignorance that you are continuing to display here, which is why I provide links to my published and un-published works and to my domain RNA-mediated.com and FB pages RNA-mediated and PheromonesResearch

If you refuse to examine what is currently known about the biophysically constrained chemistry of protein folding and ecologically adapted cell type differentiation via nutrient-dependent RNA-mediated amino acid substitutions, you will never know anything about the de novo creation of anything.

RNA mediation is responsible for the CREATION of olfactory genes where there were none before?!?


Of course it is! Only biologically uninformed science idiots attribute their creation to mutations, or to the magic of evolution.

http://www.ibiolo...ion.html
https://www.youtu...youtu.be
anonymous_9001
5 / 5 (6) May 13, 2015
http://www.ibiology.org/ibiomagazine/edmond-fischer-discovering-phosphorylation.html


Of what relevance is this to amino acid substitutions (as the result of DNA base substitutions)? Phosphorylation as a means of protein regulation does not involve substituting amino acids and especially does not involve making genomic changes.
JVK
1 / 5 (6) May 13, 2015
Are you still trying to link mutations to the biophysically constrained chemistry of nutrient-dependent pheromone-controlled ecological adaptations?

If not, quit trying to tell me what does not occur and what is not involved. Tell us all how mutations lead to evolution via what is known about physics, chemistry, and molecular epigenetics.
Whydening Gyre
5 / 5 (5) May 13, 2015
Are you still trying to link mutations to the biophysically constrained chemistry of nutrient-dependent pheromone-controlled ecological adaptations?

If not, quit trying to tell me what does not occur and what is not involved. Tell us all how mutations lead to evolution via what is known about physics, chemistry, and molecular epigenetics.

Changes in nutrient intake lead to changes in folding (f**k pheromones at this point) which then lead to mutations - most pathogenic, some not. Evolution (natural selection) takes the ball from there...
JVK
1 / 5 (6) May 13, 2015
http://medicalxpr...lls.html

"We know DNA damage is the initial step," said Professor Lu. "With the novel femtomedicine approach we can go back to the very beginning to find out what causes DNA damage in the first place, then mutation, and then cancer."

What kind of biologically uninformed science idiot links DNA damage to mutations and cancer and evolution and natural selection?

That was a rhetorical question. Dobzhansky, for comparison, linked RNA-directed DNA methylation from RNA-mediated amino acid substitutions to cell type differences in primate species via what was known about the chemistry of protein folding in 1973.

"... 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" (p. 127).
http://www.jstor..../4444260
anonymous_9001
5 / 5 (6) May 13, 2015
quit trying to tell me what does not occur and what is not involved


The validity of your model is self explanatory when you base it off things that don't actually happen.

Phosphorylation does not make substitutions. This is indisputable.
JVK
1 / 5 (6) May 13, 2015
Dietary influences on mutagenesis—Where is this field going? http://onlinelibr...abstract

Phosphorylation as a means of protein regulation does not involve substituting amino acids...


Phosphorylation does not make substitutions.


You present a moving target by altering your claim about what phosphorylation does not do.

I will cite the work that links nutrient-dependent RNA-mediated amino acid substitutions and phosphorylation to the stability of organized genomes in species from microbes to man, if you cite the source of your ridiculous opinion. Please also state your opinion without changing it to allow the "wiggle room" you need to weasel your way out of another discussion.

You've made yet another ridiculous claim about what does not happen, but never explain how mutagenesis is linked to anything currently known about biologically-based cause and effect.
animah
5 / 5 (5) May 14, 2015
support for my model in the content of the domain RNA-mediated.com

Ooh your pretentious hypocrisy is priceless!

Domain Name: RNA-MEDIATED.COM
Registrar URL: http://www.godaddy.com
Registrant Name: James Kohl

http://who.godadd...ATED.COM
anonymous_9001
5 / 5 (5) May 14, 2015
You present a moving target by altering your claim about what phosphorylation does not do.


What?! I'm saying the exact same thing in those two quotes.
anonymous_9001
5 / 5 (5) May 14, 2015
The only difference is I was more specific in pointing out what phosphorylation actually does in the first one.
JVK
1 / 5 (6) May 14, 2015
You made no claim about what "phosphorylation actually does."

I wrote:

You've made yet another ridiculous claim about what does not happen, but never explain how mutagenesis is linked to anything currently known about biologically-based cause and effect.


How do mutations lead to evolution without fixation of the RNA-mediated amino acid substitutions that differentiate the cell types of all individuals of all genera?

In my model, fixation occurs via the biophysically constrained chemistry of nutrient-dependent protein biosynthesis and degradation that is perturbed by mutations.

Fixation links ecological variation to ecological adaptation via everything currently known about physics, chemistry, and the conserved molecular mechanisms of cell type differentiation -- unless you ignore the role of phosphorylation.

What's worse is when a biologically uninformed science idiot claims that phosphorylation does not do something.
viko_mx
1 / 5 (5) May 14, 2015
@Whydening Gyre

I see that you are not able to understand and explain how emerged functionality mother to wear child in her womb, breast feeding and sucking instinct in children simultaneously. What is the drive for this and how can happen by random changes in genetic information? This complex functionality requires hundreds of different genes and their management mechanisms in the DNA acting in strict order? How supporters of the theory of evolution can explain these wonders?
I suspect that because none of them has an idea how it happened, again there will be links to meaningless nonscientific articles which is in fact typical escape from responsibility.
The whole theory of evolution is as a collection of fairy tales for still naive immature people.
JVK
1 / 5 (6) May 14, 2015
...requires hundreds of different genes and their management mechanisms in the DNA acting in strict order?


Thanks viko_mx

The molecular mechanisms must also be managed during life history transitions that link the 3D structure of proteins to the fourth dimension of what theorists still see as a linear progression of random mutations.

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

How supporters of the theory of evolution can explain these wonders?


Thanks for asking: Here's one way: "...as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed "the blind watchmaker." To some extent, it just happens."
http://www.scient...plexity/
JVK
1.6 / 5 (7) May 14, 2015
See also: Beyond Genetic Evolution. A Conversation With Eva Jablonka.
https://evolution...ablonka/

It is a desperate attempt by DS Wilson and Jablonka to make it appear that epigenetics can be considered the "second dimension of evolution." They ignore everything known to serious scientists about how the epigenetic landscape is linked to the physical landscape of DNA in the organized genomes of species from microbes to man.

They cannot link what they want others to think is the "second dimension of evolution" to facts about how ecological variation leads to ecological adaptation via the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding.

Those facts link the fourth dimension of evo-devo to what is obviously the biological basis of nutrient-dependent cause and effect via RNA-mediated amino acid substitutions and protein folding.

There is no "evo" in "evo-devo."
anonymous_9001
5 / 5 (5) May 14, 2015
You made no claim about what "phosphorylation actually does."


Phosphorylation is a reversible modification that regulates protein activity. G proteins/kinases/phosphorylation cascades ring any bells? There aren't any substitutions involved in that process.

How do mutations lead to evolution without fixation


Blue eyes, for example- a mutation we've recently identified in the regulatory region of OCA2:

http://www.scienc...0343.htm

Blue eyes are obviously not fixed.

In my model, fixation occurs via ... protein biosynthesis and degradation


This is about as vague as vague gets. Fixation, being when all alleles are lost except for one in a population, can occur through strong selective processes, genetic drift, or bottleneck effects.

No, what's worse is when James Kohl stumbles across a word he's never seen before, starts using it all the time, and attaches functions to it that he's pulled out of thin air.

JVK
1 / 5 (6) May 14, 2015
Fixation of amino acid substitutions is controlled by the nutrient-dependent physiology of reproduction

stumbles across a word he's never seen before


Search Results for 'phosphorylation' http://rna-mediat...rylation

For example:
Removing natural selection; reshaping the horse; adjusting evolutionary theory
http://rna-mediat...-theory/
Excerpt: "Evidence that phosphorylation led to rapid diversification of biodiversity after the Biblical flood via fixation of amino acids substitutions in the DNA of organized genomes that differentiate the cell types of all individuals of all species via their pheromone-controlled physiology of reproduction requires that the claims of theorists be supported, or dismissed. Does anyone think that evolutionary theorists will support their claims about horses and human evolution that occurred during the past ~5000 years..."
JVK
1 / 5 (6) May 14, 2015
Epigenetic and transgenerational reprogramming of brain development http://dx.doi.org.../nrn3818
Excerpt: Recent studies have produced mechanistic insight both at the level of epigenetics, which examines changes in the expression of specific genes or loci that result from the addition of epigenetic marks, such as DNA methylation, or from changes in the levels of a given microRNA, and at the level of epigenomics, which examines genome-wide changes in gene expression that can be attributed to broad chromatin modifications. Such outcomes, which might be directed by a given histone modification (such as histone H3 lysine 4 (H3K4) acetylation) or by changes in the methylome, can influence large sets of genes that are involved in specific functions and that generate changes in developmental programming in response to an insult or a perturbation9.

The honeybee mode organism links RNA-mediated cell type differentiation in species from microbes to man in my model.
JVK
1 / 5 (6) May 14, 2015
Elekonch and Robinson (2000) linked our 1996 model of RNA-mediated cell type differentiation to hormone-organized and hormone-activated behavior in insects.

See also: Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees http://www.biomed...4/14/666 (co-authored by Robinson)

Conclusion: "Our identification of GO categories related to protein phosphorylation that were enriched for genes with methylated splice junctions is consistent with a similar finding in a recent study of species-specific alternative exons [45]. The authors present evidence that argues that alternative splicing is used to alter protein phosphorylation, which can alter protein stability, subcellular localization, activity, and other properties [45]. Further research is needed to determine the mechanism by which splice junction methylation and hydroxymethylation affect mRNA splicing."

What does Andrew Jones (aka anonymous_9001) do with these findings?
JVK
1 / 5 (6) May 14, 2015
Andrew Jones takes everything known to serious scientists about cell type differentiation in all genera and makes this claim about my model: Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...3960065/

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

It was not a mistake to publish Andrew Jones' criticisms. It was a deliberate attempt to exemplify the ignorance of biologically uninformed science idiots.

Note the editor's response to Jones.
"The 2013 review article... was subjected to standard peer peer review and the revised version was accepted by me after it had been accepted by both reviewers."
anonymous_9001
5 / 5 (5) May 14, 2015
Evidence that phosphorylation led to rapid diversification of biodiversity after the Biblical flood via fixation of amino acids substitutions in the DNA


This is just nonsense because that's not what phosphorylation does. Most commonly, it's used as an on/off switch for enzymatic activity. Phosphorylation does nothing to DNA.

Show me one piece of research demonstrating that phosphorylation is a mechanism by which DNA bases are substituted.
JVK
1 / 5 (6) May 14, 2015
Why does Andrew Jones (aka anonymous_9001) continue to attack my model and my credibility?

In our 1996 Hormones and Behavior review we wrote (in our section on molecular epigenetics): "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... That similar proteins perform functions in humans suggests the possibility that some human sex differences may arise from alternative splicings of otherwise identical genes." http://www.hawaii...ion.html

Phosphorylation is the link from alternative splicings and RNA-mediated amino acid substitutions to the stability of organized genomes, which means evolutionary theories about beneficial mutations and assumptions about how accumulated mutations cause one species to evolve into another must be dismissed.
JVK
1 / 5 (6) May 14, 2015
Jones wants me to show him "...one piece of research demonstrating that phosphorylation is a mechanism by which DNA bases are substituted."

What this shows everyone else is that he has no idea about how cell type differentiation occurs. His thesis explains why he has no clues about anything that has ever been linked to biologically based cause and effect.

http://www.scribd...s#scribd "... ribozymes have made an interesting niche for themselves in the field of abiogenesis. The evolution of a successful RNA polymerase ribozyme is a lofty goal. While its discovery would not be the be-all and end-all of abiogenesis research, it would represent an important stepping stone between prebiotic chemistry and life. The encapsulation of such a ribozyme is also an important step, as it would enable a system of heredity and evolution through natural selection."

cont.
JVK
1 / 5 (6) May 14, 2015
Jones thinks mutagenesis experiments can be meaningfully interpreted to show how abiogenesis links the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding to evolution through natural selection.

He is the most ignorant person with a degree in biology that I have ever encountered, and doesn't have enough common sense to quit commenting on accurate representations of biologically-based cause and effect, which extend across two decades since we published our 1996 review of RNA-mediated sex differences in cell types.

The fact that all cell type differentiation in all genera is RNA-mediated continues to escape the notice of anonymous fools, like Jones, and most evolutionary theorists who have never asked anyone to explain their ridiculous belief in pseudoscientific nonsense, or ask "Is there a model for that?"

See also: Feedback loops link odor and pheromone signaling with reproduction http://www.ncbi.n...16290036
anonymous_9001
5 / 5 (6) May 14, 2015
You are so mixed up on so many things it's hard to know where to even start.

Phosphorylation mediates spliceosome activity like it does with any other enzyme. Due to your atypical use of terms, it's hard to actually know what you're referring to. When you use splicing and AA substitution in the same sentence like that, are you saying that the substitutions are due to the splicing? The smallest introns ever found are between 30-50 bases in length. Splicing does not take out individual codons nor does it insert others (I'm sure you know substituting consists of exchanging one thing for another, not just removing, which is what splicing does).
Vietvet
4.4 / 5 (7) May 14, 2015
Speaking of models---

http://phys.org/n...firstCmt
Whydening Gyre
5 / 5 (7) May 14, 2015
@Whydening Gyre

I see that you are not able to understand and explain how emerged functionality mother to wear child in her womb, breast feeding and sucking instinct in children simultaneously. What is the drive for this and how can happen by random changes in genetic information? This complex functionality requires hundreds of different genes and their management mechanisms in the DNA acting in strict order? How supporters of the theory of evolution can explain these wonders?
The whole theory of evolution is as a collection of fairy tales for still naive immature people.

Viko,
The process of live birth has EVOLVED. See this article - http://news.natio...th-eggs/ .
The instinct of species survival is one of the drivers behind this process.
Please don't insult by labeling a logical, incremental series of OBSERVED events as fairy tales.
Whydening Gyre
5 / 5 (7) May 14, 2015
The whole theory of evolution is as a collection of fairy tales for still naive immature people.
Viko,
The process of live birth has EVOLVED. See this article - http://news.natio...th-eggs/ .
The instinct of species survival is one of the drivers behind this process.
Please don't insult by labeling a logical, incremental series of OBSERVED events as fairy tales.

To continue -
to say it was done by some greater being's sleight of hand is to believe in magic and ignores the whole of the world around us.
JVK
1 / 5 (6) May 14, 2015
I mentioned above that "Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees http://www.biomed.../14/666" was co-authored by Robinson)

Conclusion: "Our identification of GO categories related to protein phosphorylation that were enriched for genes with methylated splice junctions is consistent with a similar finding in a recent study of species-specific alternative exons [45]. The authors present evidence that argues that alternative splicing is used to alter protein phosphorylation, which can alter protein stability, subcellular localization, activity, and other properties [45]. Further research is needed to determine the mechanism by which splice junction methylation and hydroxymethylation affect mRNA splicing."

Now we have yet another publication that he has coauthored: http://phys.org/n...ity.html See my comments there.
JVK
1 / 5 (6) May 14, 2015
Due to your atypical use of terms, it's hard to actually know what you're referring to.


I cited this conclusion: "Our identification of GO categories related to protein phosphorylation that were enriched for genes with methylated splice junctions is consistent with a similar finding in a recent study of species-specific alternative exons [45]. The authors present evidence that argues that alternative splicing is used to alter protein phosphorylation, which can alter protein stability, subcellular localization, activity, and other properties [45]. Further research is needed to determine the mechanism by which splice junction methylation and hydroxymethylation affect mRNA splicing."

What are the atypical terms you think I am using? The terms I use are consistently used by serious scientists who know the difference between an amino acid substitution and a mutation and who are not afraid to use proper terms.
animah
5 / 5 (6) May 14, 2015
When someone says
biodiversity after the Biblical flood

then pontificates about
biologically-based cause and effect

You know it's time to hit the ignore button. Seriously guys, what's the point? Especially as James V. Kohl is a known spammer AND scammer.
JVK
1 / 5 (5) May 14, 2015
The point would be to prove Dobzahanky wrong, since he wrote: "...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" (p. 127). and in the same article he claimed to be a creationist.

Moving forward, see "Combating Evolution to Fight Disease" for a more recent reference to his 1973 comment on what we now know about the RNA-mediated molecular mechanisms of cell type differentiation. http://www.scienc...88.short

Alternatively, continue to remain ignorant and force others to fight against the ridiculous theories of biologically uninformed science idiots.
JVK
1 / 5 (5) May 14, 2015
Please don't insult by labeling a logical, incremental series of OBSERVED events as fairy tales.


Please don't insult the intelligence of serious scientists with ridiculous claims about OBSERVED EVENTS.

http://www.scienc...abstract
Conclusion: "...there are lineage-specific genetic changes associated with independent origins of eusociality in bees, and independent elaborations of eusociality in both bees and ants. This includes different sets of genes showing caste-biased expression across species (24–26) and, as we have shown, evolutionary modifications of TEs, gene methylation, and cis-regulatory patterns associated with the suite of life history traits that define eusociality. ... [It] ...may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks."

The increased complexity is nutrient-dependent and pheromone-controlled.
anonymous_9001
5 / 5 (4) May 14, 2015
Conclusion: "Our identification of GO categories...


Okay. Wonderful. That excerpt says nothing about substitutions and neither does the paper.

Here's what I'm talking about when I say atypical use:

Phosphorylation is the link from alternative splicings and RNA-mediated amino acid substitutions


Either reword this in a way that makes sense or admit it makes no sense. As it stands, this doesn't mean anything.

Let's drop all the squabbles for just one minute here. Can you take an honest and sincere criticism about your writing style? Any time you use "link", what you're doing is crippling your flow of information and logic by using that in favor of a more detailed explanation. You leave out what are likely important details when you do that.

The "Non-CG DNA..." paper and excerpt was fine for connecting phosphorylation and splicing, but then you tacked on substitutions to that when that citation didn't have any apparent link to them. Please be more specific.
JVK
1 / 5 (4) May 14, 2015
Any time you use "link", what you're doing is crippling your flow of information and logic by using that in favor of a more detailed explanation. You leave out what are likely important details when you do that.


"...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

Do you think there are any details missing from that representation? How about this one?

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

See also: Ignoring systems complexity (it's too complicated)
http://rna-mediat...licated/

The links are clear to serious scientists, but they are too complicated for biologically uninformed science idiots to grasp. Thus, we have a publication that claims it is okay to ignore the links between the olfactory and immune systems.
anonymous_9001
5 / 5 (4) May 14, 2015
Do you think there are any details missing from that representation?


Considering the fact that that's merely one sentence of an entire book...

Thus, we have a publication that claims it is okay to ignore the links between the olfactory and immune systems.


Another misinterpretation. They've done with the immune system what physics has done with planetary motion- boiled it down to a series of equations from which you can derive anything.

Just as an example:

http://en.wikiped...r_System
JVK
1 / 5 (4) May 14, 2015
Are you claiming it is okay to ignore the links between the olfactory and immune systems so long as you can use a series of equations from which you can derive anything to explain biologically-based cause and effect?

This is one of two concluding sentences from Mutation-driven evolution

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world."

Are you claiming it is acceptable to explain biodiversity with claims that it is caused by constraint-breaking mutations?

Are you claiming that PZ Myers is not a biologically uninformed science idiot?

http://freethough...-page-1/

anonymous_9001
5 / 5 (4) May 15, 2015
Are you claiming it is okay to ignore the links between the olfactory and immune systems


Is that what they've done? Why don't you ask them instead of making broad assumptions?

re you claiming it is acceptable to explain biodiversity with claims that it is caused by constraint-breaking mutations?


You're still acting as if "contraint-breaking" is some magical barrier. It's clear you don't understand what they mean when it's well explained in the rest of the book.
JVK
1 / 5 (3) May 15, 2015
Why don't you ask them...


It is perfectly clear that they have linked the olfactory and immune systems via the Nobel Prize winning work (1991) by Linda Buck and Richard Axel. We did that in our 1996 review.

Elekonich and Robinson (2000) linked our model to hormone-organized and hormone-activated behavior of insects without use of the term mutation. http://www.ncbi.n...10980296

It is now perfectly clear that nutrient-dependent RNA-directed DNA methylation silences genes via the biophysically constrained chemistry of RNA-mediated amino acid substitutions and protein folding. The substitutions are fixed in organized genomes via the physiology of reproduction in all genera.

In the context of everything known to serious scientists about biologically-based cause and effect that links the epigenetic landscape to the physical landscape of DNA during the life history transitions of all organisms, what does CONSTRAINT-BREAKING MUTATION mean?
JVK
1 / 5 (3) May 15, 2015
Any time you use "link", what you're doing is crippling your flow of information and logic by using that in favor of a more detailed explanation. You leave out what are likely important details when you do that.


Serious scientists have already linked the olfactory and immune systems of honeybees and humans via one RNA-mediated amino acid substitution, which is linked to life history transitions in human behavior.

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

In this study, the A or Met allele is linked to metabolism (e.g., lower enzymatic activity) due to the difference a single base pair change and single amino acid substitution makes in the context of thermodynamic cycles of protein biosynthesis and degradation. The substitution links the thermodynamic stability of the organized genome to differences in exploratory behavior.
JVK
1 / 5 (3) May 15, 2015
http://medicalxpr...ugs.html

Excerpt: "Ultimately what defines a parasite is that they require certain key nutrients from their host," he says. "So they have had to evolve ways to get around their own barriers, to gain access to these nutrients."

How does a constraint breaking mutation lead to the evolution of the ability of a parasite to gain access to nutrients? The claim that the ability "evolved" continues to kill millions of people, which is why serious scientists are "Combating Evolution to Fight Disease" http://www.scienc...88.short
viko_mx
1 / 5 (3) May 15, 2015
@Whydening Gyre

I do not want declarations. Give me explanation how it is pasible random changes to cause abrupt simultaniuos emerge of functionality mother to wear child in her womb supported by handreds specific genes, breast feeding and the sucking instinct and metabolism oriented to mammary food in newborn, which is only temporary? If you are not aware of how theory and evolution explains these issues, in what you believe anyway?
JVK
1 / 5 (3) May 15, 2015
Thanks again, viko_mx
Obviously, theory and evolution have no explanatory power. What you are asking a biologically uninformed science idiot to explain is how the balance of viral microRNAs and nutrient-dependent microRNAs link virus-driven entropic elasticity to the anti-entropic epigenetic effects of RNA-mediated amino acid substitutions in all genera via the conserved molecular mechanisms of biophysically constrained nutrient-dependent RNA-mediated protein folding chemistry.

The fact that biologically uninformed science idiots can't explain anything in terms that link random changes and the simultaneous emergence of morphological and behavioral phenotypes in species from microbes to man attests to their limited awareness of biological facts, which I have detailed in a series of published works since book publication in 1995.

Rather than admit that they are biologically uninformed science idiots, most theorists continue to tout the theories that are killing people.
barakn
4 / 5 (4) May 16, 2015
What you are asking a biologically uninformed science idiot to explain is ... -JVK

Nobody should ask you to explain anything.
ryggesogn2
not rated yet May 16, 2015
"A woman in Florida is being harassed by the government for simply going off the grid and refusing to use city power and water. They've threatened her with having a month to "plug in" or face the consequences."
http://joeforamer...f-grid/#
JVK
1 / 5 (2) May 16, 2015
Nobody should ask you to explain anything.


Agreed.

If they already can explain it, they should tell me their explanation and we can discuss how ridiculous their explanation is and compare it to facts that link the epigenetic landscape to the physical landscape of DNA in the organized genomes of all genera via the conserved molecular mechanisms of cell type differentiation that begin with the de novo creation of amino acids and membranes that enable photosynthesis.

See for instance: http://phys.org/n...tml#nRlv

Theorists seem to think that the de novo creation of light-induced amino acids can somehow be linked to the evolution of proteins that form membranes. They can't explain any aspect of what is required to link what is known about physics, chemistry, and molecular biology to the composition of the proteins that form the membrane, but they believe in "evolution" via mutations.
JVK
1 / 5 (2) May 16, 2015
Agreed. I'm not so evangelical about it, but what amazes me is how adamant most biologically uninformed science idiots can be when they proclaim their religious beliefs.

Life on Earth - Flow of Energy and Entropy http://www.digita...ife.html

Excerpt: The concept of negative entropy (first introduced by E. Schrodinger - ref [2]) or information (Shannon - ref [20]) and the ability of the Biosphere to effectively extract it from the Sun's radiation is very important for life on Earth. This concept was not included in the original work of Darwin [9,10], which explained the natural selection of species, but did not explain the origin and maintenance of Life on Earth.

See also this 5.5 minute-long video: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation) https://www.youtu...youtu.be
JVK
1 / 5 (2) May 16, 2015
http://phys.org/n...tml#nRlv
Fusion protein controls design of photosynthesis platform

This links the de novo CREATION of light-induced amino acid substitutions to the CREATION of the proteins and membrane required for photosynthesis. Is it the missing link from the CREATION of plants to animals or vice versa?

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

Excerpt: "This strong connection between structural biology and physics means that ultrafast light-harvesting functions are under genetic and evolutionary control. The great diversity of solutions to light harvesting in the cryptophyte algae, in particular the combination of different chromophores and significantly different structural combinations, are quite extraordinary."

Too extraordinary to arise from mutations.
JVK
1 / 5 (2) May 17, 2015
See for comparison: Jones' thesis at http://www.scribd...s#scribd

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

Based on everything known to serious scientists about the biophysically constrained RNA-mediated chemistry of nutrient-dependent protein biosynthesis and degradation, Andrew Jones appears to be a biologically uninformed science idiot.
JVK
1 / 5 (2) May 18, 2015
You're still acting as if "contraint-breaking" is some magical barrier. It's clear you don't understand what they mean when it's well explained in the rest of the book.


What is explained in the book? Mutation-Driven Evolution http://www.amazon...9661731, which concludes: "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world."

What happens when you tell a biologically uninformed science idiot like Andrew Jones (aka anonymous_9001) that proteins do not "evolve"?

See also: #03 Biochemistry Amino Acids Lecture for Kevin Ahern's BB 450/550
https://www.youtu...xqQol0UU
animah
5 / 5 (2) May 18, 2015
What happens when you tell (...) Andrew Jones (...) that proteins do not "evolve"?


You look like the young Earth creationist idiot you are. As usual, Mr James V Kohl.
JVK
1 / 5 (2) May 18, 2015
Thanks. I bet you say that to anyone who cites anything that challenges the pseudoscientific nonsense of neo-Darwisim.

006.Transcribing Memories: New Mechanisms of Activity-Regulated Gene Expression and Their Roles in Experience-Dependent Plasticity.
Minisymposium
Saturday, Oct 13, 2012, 1:30 PM - 4:00 PM
New Orleans Theater C
Activity-regulated gene transcription is essential for orchestrating the gene expression programs that drive experience-dependent plasticity of neural circuits. Recent studies have not only vastly expanded our understanding of the mechanisms that mediate activity-regulated transcription, but have also identified direct links between activity-dependent gene expression, synaptic plasticity and/or behavioral outputs. This minisymposium will highlight these exciting new developments.

What part of what has been known about the biological basis of RNA-mediated cell type differentiation for more than a decade led you to comment on my beliefs?
anonymous_9001
5 / 5 (2) May 18, 2015
What is explained in the book?


What Nei means by "biophysical constraint" and how those constraints are overcome.
JVK
1 / 5 (2) May 18, 2015
Thanks. When do biophysical constraints not constrain the chemistry of RNA-mediated protein folding via the fixation of amino acid substitutions in the cell types of organized genomes?

Is there a model for that?

Dobzhansky (1973) claimed "...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" (p. 127). http://www.jstor..../4444260

There's a model for that! Nutrient-dependent/pheromone-controlled adaptive evolution: a model http://www.ncbi.n...3960065/

You claimed "...Kohl presents an unsupported challenge to modern evolutionary theory and misrepresentations of established scientific terms and others' research. It was a mistake to let such a sloppy review through to be published."

What model of constraints that are overcome links cell type differentiation in all cells of all individuals of all genera?
JVK
1 / 5 (2) May 18, 2015
May 18, 2015
Evolution of MicroRNA Research Over the Past Decade
More than 20,000 microRNA-Focused Publications Were Assessed as a Means to Characterize the Field http://www.geneng...;a=false

Who thinks that any of the 20,000 microRNA-Focused Publications support the claims of evolutionary theorists or big bang cosmologists?

Who thinks the "Modern Synthesis" should be viewed for what it is?

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

Simply put, is anyone else here besides Ren82 and viko_mx not a biologically uninformed science idiot?
JVK
1 / 5 (2) May 18, 2015
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]." 'Oming in on RNA-protein interactions http://genomebiol...15/1/401

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

What kind of biologically uninformed science idiot dismisses 18 years of scientific progress and what is currently known about RNA-mediated cell type differentiation with the claim that Nei explains how biophysical constraints are overcome in his book Mutation-Driven Evolution? http://www.amazon...99661731
anonymous_9001
5 / 5 (2) May 18, 2015
Thanks. When do biophysical constraints not constrain the chemistry of RNA-mediated protein folding via the fixation of amino acid substitutions in the cell types of organized genomes?

Is there a model for that?


If you read his book, you'd know he has entire sections dedicated to discussing models. 5 seconds worth of searching turns up this:

http://www.ncbi.n...24882821

Brief summary of what Nei means when he talks about biophysical constraints:

When an organism has only one copy of a gene, it's not resistant to mutations within it. It's constrained to only certain changes because some could alter it too much and its resulting protein won't be functional. If the gene is copied, the copy isn't constrained and can undergo more mutations because there's a backup copy, so those mutations won't effect the organism.
JVK
1 / 5 (2) May 18, 2015
5 seconds worth of searching turns up this


His book was published in June 2013 -- on the same day as my review. You just cited an article from May 2014. You did not address 18 years of publications that detail what has been learned about cell type differentiation since the time of our 1996 review . You are not addressing re-evolution of the bacterial flagellum in 4 days or any other aspect of what is currently known to serious scientists about physics, chemistry, and molecular biology.

You are a biologically uninformed science idiot.

Mutations link virus-induced entropic elasticity to loss of function. Mutations are biophysically constrained by nutrient-dependent microRNAs that link the anti-entropic epigenetic effects of RNA-directed DNA methylation and RNA-mediated amino acid substitutions to cell type differentiation in species from microbes to man via their pheromone-controlled nutrient-dependent physiology of reproduction.

http://rna-mediated.com
JVK
1 / 5 (2) May 18, 2015
Re: "Missing link in the evolution of complex cells..."

The missing link is "common sense." Complex cells do not evolve. Cell type differentiation occurs in the context of viruses that perturb protein folding. Cells with the innate ability to limit the damage that viral microRNAs cause exemplify nutrient-dependent ecological adaptations that are manifested in morphological and behavioral phenotypes.

Phenotypes link nutrient-dependent microRNAs from RNA-directed DNA methylation to RNA-mediated amino acid substitutions that stabilize the organized genomes of all genera. Species that accumulate too many virus-induced mutations become extinct, they do not evolve into other species.

The biophysically constrained chemistry of RNA-mediated protein folding links the de novo creation of amino acids and amino acid substitutions to the formation of proteins that create the membrane that enables photosynthesis and nutrient-dependent biodiversity.

http://www.rnasociety.org/
anonymous_9001
5 / 5 (2) May 19, 2015
His book was published in June 2013 -- on the same day as my review. You just cited an article from May 2014.


Yeah, you have a weird obsession with dates as if they have intrinsic meaning. We know.

You did not address 18 years of publications that detail what has been learned about cell type differentiation since the time of our 1996 review


Probably because I'm discrediting what you've written and pointing out the flaws in said publications.

You are not addressing re-evolution of the bacterial flagellum in 4 days


Which refutes evolutionary theory how, exactly?

virus-induced entropic elasticity


Which means what? This is a term only you have ever used. Can you explain what entropic elasticity is on its own before you add descriptors to it that don't make any sense?

Mutations are biophysically constrained by nutrient-dependent microRNAs


Not even sure what you mean here, but that certainly isn't what miRNAs do.
animah
5 / 5 (2) May 19, 2015
that certainly isn't what miRNAs do.

anon_9001, I think the reality is that Kohl just substitutes hormones for pheromones everywhere.

To see what I mean, have a look at what I think is the closest non-crank equivalent to his "work":

http://www.resear...eceptors

The rest of his position is just young-Earth religious fundamentalism. Your part of the thread is quite interesting to follow though.
viko_mx
1 / 5 (3) May 19, 2015
Observational facts and scierntific truth can no be religious fundamentalism. Obviously you use words whose true meaning you do not understand.
JVK
1 / 5 (2) May 19, 2015
the closest non-crank equivalent to his "work":
-- cite's Harm's et al (2013)

Also see Harm's lab: http://harmslab.u...earch-2/
"The overarching goal of the Harms lab is to understand the relationship between the biophysical properties of proteins and their evolution."

If proteins, such as steroid receptors evolved via mutations, there would be no need for serious scientists who are Combating Evolution to Fight Disease http://www.scienc...088.full
"Molecular mechanisms that generate biological diversity are rewriting ideas about how evolution proceeds..."

There would be no reason for the RNA Society http://www.rnasociety.org/

No reason for my domain http://rna-mediated.com/

A google search for "RNA mediated" would not show that evolutionary theorists are biologically uninformed. https://www.googl...mediated

However, as everyone else knows, evolutionary theorists are biologically uninformed science idiots.
JVK
1 / 5 (2) May 19, 2015
you have a weird obsession with dates as if they have intrinsic meaning.


We detailed RNA-mediated cell type differentiation in our Hormones and Behavior review ~16 years before Nei published "Mutation-driven evolution" on the same day as my review: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

That is not "a weird obsession with dates." If anything, it's a justifiable obsession with manifestations of ignorance by evolutionary theorists who still appear to think that the bacterial flagellum re-evolved "over-the-weekend"

Can you explain what entropic elasticity is...
It establishes the need for DNA repair. Without the epigenetic effect of nutrient-dependent microRNAs, the entropy of organized genomes would lead to the extinction of life on earth. Entropy of organized genomes is like what would happen if a mutagenesis experiment had been performed on all genera.
JVK
1 / 5 (2) May 19, 2015
Re:
a mutagenesis experiment... on all genera.


See: Stress-induced mutagenesis and complex adaptation http://rspb.royal...abstract
Excerpt: "...during evolution in a stable environment, constitutive mutators become associated with poor genetic backgrounds due to increased accumulation of deleterious mutations; this was evidenced both in the laboratory [4] and in the clinic [5]."

The stability of the environment is nutrient-dependent and pheromone-controlled in species from microbes to man. See: Nutrient-dependent / Pheromone-controlled adaptive evolution: (a mammalian model of thermodynamics and organism-level thermoregulation) http://figshare.c..._/643393

... or see this 5.5 minute video representation of biologically based cause and effect:
https://www.youtu...youtu.be
JVK
1 / 5 (2) May 19, 2015
I'm discrediting what you've written and pointing out the flaws...


I disagree.

that certainly isn't what miRNAs do.


What do they do?

If nutrient-dependent microRNAs do not biophysically constrain mutations, how are mutations biophysically constrained until everything changes to fit Nei's textbook claim that "...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world." (p. 199) http://www.amazon...99661731

Something appears to be constraining mutations in the bacteria that did not evolve during the past ~2 billion years but not in the bacteria that re-evolved their flagella over-the-weekend.
http://phys.org/n...ars.html
http://www.the-sc...ewiring/

Why don't all species adapt to an ever-wider range of conditions?
anonymous_9001
5 / 5 (3) May 19, 2015
miRNAs bind to mRNAs and prevent their translation and trigger deadenylation.

If nutrient-dependent microRNAs do not biophysically constrain mutations, how are mutations biophysically constrained...


Paralogous genes, for example- Like I said before, if an organism has just one copy of an essential gene, mutations to that gene may likely be detrimental and result in death or decreased fitness. If, however, that gene is duplicated, the duplicate is free to mutate and take on another function because the original gene is still present.
JVK
1 / 5 (2) May 19, 2015
Please make yourself clear.

1) What molecular mechanisms enable the duplication of genes?
2) Are the molecular mechanisms biophysically constrained?
3) Is the chemistry of RNA-mediated protein folding involved in the biophysical constraint?
4) What is the role of nutrition in the mutation of duplicate genes that somehow lead to the evolution of one species from another?

Alternatively, why don't you simply admit that you are a biologically uninformed science idiot?

miRNAs bind to mRNAs and prevent their translation and trigger deadenylation.


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

Abstract excerpt: "This atoms to ecosystems model of ecological adaptations links nutrient-dependent epigenetic effects on base pairs and amino acid substitutions to pheromone-controlled..."
JVK
1 / 5 (2) May 19, 2015
See also:

Gene expression, immortality, and cancer http://rna-mediat...-cancer/

Abiogenesis is to cancer as mutations and theory are to accurate representations of how nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions are to health and longevity.

Abiogenesis is a ridiculous approach to disease by theorists who think that the differences between health and pathology have not been detailed in my model of RNA-mediated amino acid substitutions and cell type differentiation in all genera. Mutations lead to undifferentiated cell types. Amino acid substitutions ensure the stability of organized genomes.

See also: Combating Evolution to Fight Disease http://www.scienc...88.short
anonymous_9001
5 / 5 (3) May 19, 2015
1) What molecular mechanisms enable the duplication of genes?


"Generation of duplicate genes" on page 2:

http://www.umich...._292.pdf

"How do duplications arise?":

http://www.ncbi.n...C449868/

http://en.wikiped...lication

Common sources of gene duplications include ectopic homologous recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.[1]


http://journals.p....1003691
http://www.ncbi.n...3312306/
http://www.hindaw.../846421/

Here's an EXTREMELY comprehensive list of articles related to dupliations:

http://www.umich....view.pdf

2) Are the molecular mechanisms biophysically constrained?


Everything is governed by physics.
anonymous_9001
5 / 5 (3) May 19, 2015
3) Is the chemistry of RNA-mediated protein folding involved in the biophysical constraint?


Yep. That's precisely what the constraint is. Just like that example in the comments of one of the other articles you commented on about the WORD->WORE->etc., only certain mutations can be tolerated. Duplication relaxes this constraint which I explained above.

4) What is the role of nutrition in the mutation of duplicate genes that somehow lead to the evolution of one species from another?


That's a bit of an indirect link.

Here's an example of a gene that causes hybrid male sterility, a sign of speciation, that arose through duplication:

http://www.pnas.o...abstract
JVK
1 / 5 (2) May 19, 2015
Here's an example of a gene that causes hybrid male sterility, a sign of speciation, that arose through duplication:


Is there a model for that? Can it be placed into the context of Nei's conclusion?

"...genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world. In this view of evolution there is no need of considering teleological elements" (p. 199).

Abiogenesis revisited:
Abiogenesis (A) is to cancer (C) as mutations (M) and theory (T) are to accurate representations of how nutrient-dependent RNA-directed DNA methylation and RNA-mediated amino acid substitutions are to health (H) + longevity (L).

Simply put, anonymous fools, like Andrew Jones, tout pseudoscientific nonsense. There is only one way to get to health, longevity, and biodiversity.

It is not via mutations. They perturb protein folding.
JVK
1 / 5 (2) May 19, 2015
We published a review article about RNA-mediated cell type differentiation in 1996.

Lessons from the RNA World: humility and hubris http://rnajournal...482.full

Excerpt 1)
The research community I have lived in for the past 20 years, near the 3′ end of mRNAs, began as a small enclave of labs and now is a vibrant city full of them. The field has moved from outlines of how 3′ ends were formed to the biochemistry of all the components involved, and now includes mRNA regulation via 3′ UTRs, developmental controls, miRNAs, and networks of interacting mRNAs, non-coding RNAs and proteins.


Excerpt 2)
If ever we should embrace the diversity evolution has generated, it is now, with the powerful new methods like RNAi and CRISPR in hand.


Evolutionary theorists refuse to embrace the facts about RNA-mediated amino acid substitutions and cell type differentiation in all genera. They don't like new methods; they love ridiculous theories.
anonymous_9001
4.8 / 5 (4) May 19, 2015
Is there a model for that?


Drosophila is a model organism and is what they studied in that paper...

Can it be placed into the context of Nei's conclusion?


Well, the duplication caused the speciation and as species number increases, biodiversity increases.
JVK
1 / 5 (2) May 19, 2015
In the molecular epigenetics section of our 1996 Hormones and Behavior review, we linked RNA-mediated cell type differentiation across species from yeasts to drosophila, nematodes, and mammals.

Their nutrient-dependent pheromone-controlled physiology of reproduction was the link to biodiversity. Most people still seem to agree that species must reproduce before biodiversity can arise.

Your claim that duplication caused speciation and biodiversity seems to not include the metabolism of nutrients to species-specific pheromones that control the RNA-mediated cell type differentiation of all cell types in all individuals of all species from microbes to man via fixation of the amino acid substitutions that differentiate their cell types.

Is that where mutations enter the picture in the minds of biologically uninformed science idiots? If so, how do mutations lead to the stability of organized genomes in all genera?
animah
5 / 5 (2) May 20, 2015
how do mutations lead to the stability of organized genomes in all genera?


I can't pretend to know as much as anon but whether you agree with them or not, there are in fact a number of models for that tug of war between destructive and protective mutations.

If there wasn't, modern cancer research would be at a standstill.

See tumor suppression genes: Caretaker genes, gatekeeper genes and landscaper genes.

See also diploids and topics like haploinsufficiency.

And also endoreduplication.

These mechanisms are evidenced in tens of thousands of studies, often funded by large, results-oriented industry stakeholders who would have noticed if fundamental tenets of evolutionary biology didn't add up.

Your resistance against such overwhelming evidence is pathological. Maybe long-term toxicity in those porcine extracts you handle in your day job?
animah
5 / 5 (4) May 20, 2015
While we're at it: Your insistence on genomic stability is also unwarranted: It's quite obvious there can be no speciation without genomic instability. Here:

The molecular basis of speciation: http://www.ncbi.n...19147922

Plant speciation through chromosome instability and ploidy change: Cellular mechanisms, molecular factors and evolutionary relevance: http://www.scienc...14000103

And this, especially illuminating when pondering your silly ideas:

Mechanisms of Speciation: http://www.ncbi.n...3357519/
JVK
1 / 5 (2) May 20, 2015
...there are in fact a number of models for that tug of war between destructive and protective mutations.

If there wasn't, modern cancer research would be at a standstill.


Modern cancer research has been at a standstill for at least two decades with the exception of reports coming from groups that have linked epigenetic changes in the balance of viral microRNAs and nutrient-dependent microRNAs from RNA-directed DNA methylation to the RNA-mediated amino acid substitutions that differentiate the cell types of all cells in all individuals of all genera via the biophysically constrained chemistry of protein folding during thermodynamic cycles of protein biosynthesis and degradation.

For review take 5.5 minutes to watch https://www.youtu...youtu.be and <3 minutes to watch https://www.youtu...G_9EEeeA

You will then know more about genomic stability than most other biologically uninformed science idiots.
JVK
1 / 5 (2) May 20, 2015
"animah" cites http://www.ncbi.n...19147922

Excerpt: We contrast these 'rules' of speciation to 'mechanisms' of speciation representing primary causal factors ranging across various levels of organization-from genic to chromosomal to organismal.

See our section on molecular epigenetics in our 1996 Hormones and Behavior reveiw: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html

The mechanisms of speciation are nutrient-dependent and pheromone-controlled via RNA-mediated cell type differentiation in species from microbes to man. That fact has not changed, no matter how many others try to present it as their original idea. The idea was portrayed by Darwin in the context of his 'conditions of life.'

See also the comments by anonymous fools on chromosomal rearrangements http://freethough...s-place/
JVK
1 / 5 (2) May 20, 2015
the duplication caused the speciation and as species number increases, biodiversity increases.


It's all so simple in the minds of biologically uninformed science idiots. Isn't it?
anonymous_9001
5 / 5 (2) May 20, 2015

It's all so simple in the minds of biologically uninformed science idiots. Isn't it?


That's DIRECT observation in that study.
animah
5 / 5 (2) May 20, 2015
Modern cancer research has been at a standstill for at least two decades


Checkmate:

http://www.cancer...ombined/
(charts 1.2, 1.3 and 1.4 - historical cancer survivability)

http://www.cancer...er-drugs
(details of 9 new cancer drugs in 2014 alone)

http://www.forbes...-cancer/
(future directions - "It really is a revolution. This is going to open the door for all sorts of cell-based and gene therapy...")
JVK
1 / 5 (2) May 20, 2015
Gene expression, immortality, and cancer
http://rna-mediat...-cancer/
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Excerpt from the conclusion of: The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

Further work is necessary to elucidate which other transcription factors are interacting with GABP at the mutant TERT promoter in order to drive aberrant transcription.

My comment: They attempted to solve the funding problem that might otherwise cause an early end to their careers and the careers of future researcher who have been taught that:

…genomic conservation and constraint-breaking mutation is the ultimate source of all biological innovations and the enormous amount of biodiversity in this world.
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The only progress being made in cancer research is by those who understand the role of microRNAs in cell type differentiation. Most of them also are Combating Evolution to Fight Disease.

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