DNA Dethroned - Inheritance is Protein-Based.

originally posted by: whereislogic
Epigenetic information is still contained within the DNA genome of an organism.

Erm. No. Epigenetic information is contained in RNA.

The information to produce proteins is also still contained within the DNA genome.

Yes, DNA codes for proteins - but not for prions. Prions code for themselves, and are a separate and distinct system of inheritance.

The evidence shows that prions do not just overide DNA coding, but also regulate their own transcription, translation, and signaling networks - functions previously considered to be exclusive to DNA.

In this context, we can consider DNA (and RNA) to be the genetic “background,” and the prion-related “foreground” to be significantly defining.

…‘Proteinaceous infectious particles’, or prions, exist stably in different conformational states, at least one of which can self-propagate over long biological timescales (Prusiner, 1982; Shorter & Lindquist, 2005). This endows prions with properties that are usually associated with nucleic acid-based elements of inheritance.

…In their native conformations, many yeast prion proteins regulate transcription, translation, and signaling networks (Halfmann et al., 2010). As a consequence, the prion states of these proteins can create diverse new traits. These can be beneficial, detrimental, or inconsequential, depending on the particular prion, genetic background, and environmental context (Shorter & Lindquist, 2005; True & Lindquist, 2000).

DNA is not dethroned.

DNA is dethroned as the exclusive determinant of inheritance, and as the primary one for “traits.” It is abundantly clear that precious few “traits” are coded in our DNA.

Darwin is not a god, nor is he the be-all-and-end-all in our understanding of evolution. And incidentally, Darwin greatly respected LaMarck, who amassed significant evidence showing that environmental exposures resulted in heritable diseases and traits. Now there is more evidence, AND identified mechanisms. Get over it. Move forward.

The evolutionary motivated philosophy of junk-DNA and pseudogenes is (dethroned) though.

What is your point, exactly? And how does it relate to this thread, precisely?

a reply to: soficrow

You keep acting like it's new information that traits can be altered via environment...you keep acting like it's new information that prions are associated with this...What is your angle? The only reason someone would be so intentionally deceptive is if they had some kind of motivation to do so. Your bash of Darwin speaks volumns when Darwin was only a starting point. Many of his ideas have been throughly superseded but he got the ball rolling.

This is how pseudoscientists work. They weave truth with deception and then cry afoul that everyone has been blinded by the institution of a specific scientist that they can't see past their own nose.

DNA has not been dethroned, even in the way you think. DNA can be overwritten for adaptation to environment, and prions seem to be the driving factor. The articles you keep quoting over and over say exactly that. The prevailing thought is that if an epigenetic trait persists through generations long enough, it can permanently flip on or off a trait stored in the DNA. This is the direction evolutionists have been going in for decades and how they are attempting to create a dinosaur out of a chicken.

To clarify: TWO papers showing Protein-Based Inheritance came out on the same day (October 6, 2016), and were published in the same Journal (Cell):

Remembering the Past:
A New Form of Protein-Based Inheritance

Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

I apologize if my flipping back and forth between the two papers confused any readers.

a reply to: soficrow

Explain why you think epigenetic information is stored in RNA. I think what whereislogic is trying to say is that DNA has all possible variants for a species already contained within it. Genes turn markers on and off just like prions can. Genes appear to be permanent and persist through future generations. Epigenetic traits are corrected through future generations as long as the external stresses revert to normal. Do you mean the drivers of epignnetic traits are contained in RNA? As in RNA determines when something needs to override genes and DNA?

a reply to: raymundoko

Thank you for your courteous words and post raymundoko.

Explain why you think epigenetic information is stored in RNA.

For starters:

RNA-mediated epigenetic regulation of gene expression

Diverse classes of RNA, ranging from small to long non-coding RNAs, have emerged as key regulators of gene expression, genome stability and defence against foreign genetic elements. …These co-transcriptional silencing mechanisms form powerful RNA surveillance systems that detect and silence inappropriate transcription events, and provide a memory of these events via self-reinforcing epigenetic loops.

Nature Reviews Genetics 16, 71–84 (2015) doi:10.1038/nrg3863
Published online 02 January 2015

RNA Epigenetics

DNA isn’t the only decorated nucleic acid in the cell. Modifications to RNA molecules are much more common and are critical for regulating diverse biological processes.

…A variety of chemical modifications decorate the nucleic acids, increasing the alphabet of DNA to about a dozen known nucleotide variants. The alphabet of RNA is even more impressive, consisting of at least 140 alternative nucleotide forms. The different building blocks can affect the complementarity of the RNA molecules, alter their structure, and enable the binding of specific proteins that mediate various biochemical and cellular outcomes. …

The Scientist » January 2016 Issue

And from your wiki reference…

Epigenetics studies genetic effects not encoded in the DNA sequence of an organism, hence the prefix epi- (Greek: επί- over, outside of, around).[1][2] Such effects on cellular and physiological phenotypic traits may result from external or environmental factors that switch genes on and off and affect how cells express genes.[3][4] These alterations may or may not be heritable, although the use of the term epigenetic to describe processes that are heritable is controversial.[5]

Do you mean the drivers of epignnetic traits are contained in RNA? As in RNA determines when something needs to override genes and DNA?

Yes, sometimes. See above.

Genes turn markers on and off just like prions can.

Yes, although most would say prions turn markers on and off just like genes can. …It is quite astounding to show that prions regulate genetic expression independent of DNA and RNA.

Genes appear to be permanent and persist through future generations.

Yes, genes are permanent and persist “as is” unless-and-until they mutate and change.

Epigenetic traits are corrected through future generations as long as the external stresses revert to normal.

That has been the assumption, based on initial observations that epigenetic responses to environmental stress/change “reverted to normal” once the environment “returned to normal.” As a result, epigenetic responses and adaptations were considered impermanent. [And of course, is based on the questionable assumption that there actually is a "normal."]

HOWEVER, in situations where the environmental cause persists, the epigenetic response will continue too. As well, if the ‘cause’ and epigenetic response continue long enough, that persistence may cause genetic mutation, and change the DNA. In short, the epigenetic process can move from response and temporary adaptation to evolution, complete with changes to the genetic code contained in DNA.

ALSO NOTE: Prions function independently as epigenetic mechanisms, separate from DNA and RNA, as shown by the research highlighted in this thread.

As well, prions can persist in humans for hundreds of thousands of years, able to affect and modify genetic expression without changing the genetic code contained in our DNA. Truly astounding.

Most important, we need to change our view of prions as “disease-causing villains” to recognize and acknowledge their much larger positive role in our adaptation and evolution. Simply put, prions are the good guys.

So the take-home point is: Our DNA and genes do not often mutate and change because they don’t have to. Epigenetic mechanisms like prions and RNA run interference between us (the organism) and the environment (micro-internal and macro-external) - they are Rapid Early Response Systems - mechanisms that allows us to adapt without changing our genes and DNA.

It is all truly elegant.

The one circumstance that might overload the checks and balances in our various response-adaptation-evolutionary systems is if numerous factors in our micro- and macro-environments change all at once and/or quickly. Most likely, that would be dangerous from an evolutionary and survival standpoint.

I hope I have answered your questions. Thanks again.

a reply to: soficrow

I kind of feel like an asshole because I agree with you completely. I just took issue with the title.

originally posted by: raymundoko
a reply to: soficrow

I kind of feel like an asshole because I agree with you completely. I just took issue with the title.

HAHAHAHA

...It's REALLY hard to write good titles. Especially for science topics. Can't win - either put people to sleep before they start reading or draw heavy fire.



PS. You owe me a drink.

I got an ‘alert’ about the OP articles because I am researching heritable, ancient, and potentially conscious memory for a fictional piece. I started this thread to see how the info might tweak others’ imaginations.

Seven pages and 126 posts later, I find myself shifting gears, going back to thinking more about biotech’s impact on our planet’s biological foundations.

Biotech routinely mucks with proteins - for over half a century, Big Pharma has been targeting proteins with all-new man-made prion-like proteins (which we ingest to the tune of trillion$ of dollars per year) - GMO’s and GEO’s use synthetic proteins (potentially biologically active prions) - biorobotics and bioengineering in general do the same. And mis-folded proteins and prions are common by-products of all these industrial processes.

Overall, we are looking at virtually tons of nano-size industrially created synthetic proteins and man-made prions contaminating our environment. But we are only just beginning to understand their impact on health, disease, inheritance and evolution. No one has done a full biological systems analysis to evaluate the potential effects on life on our planet.

Remember, prions can:
* Mutate and evolve into new strains to cross “species barriers” (and kingdom and other “barriers” too), as well as
* Be transmitted in the air, not just in water, soil and food; and that
* Prions, aka protein-based inheritance, can persist for hundreds of thousands of years inside living organsims, not just in the environment.

So what might the biotech indistries mean for the evolution of life on our Earth, including our own? Where are we headed now? Any idea?

At all?




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a reply to: soficrow

It's what Biotechonomy's CEO, Juan Enriquez, has dubbed Homo-Evolutis
Check out his TED talk - it's pretty fascinating stuff.

Chairman and CEO of Biotechonomy, Enriquez says that humanity is on the verge of becoming a new and utterly unique species, which he dubs Homo Evolutis. What makes this species so unique is that it "takes direct and deliberate control over the evolution of the species." Calling it the "ultimate reboot," he points to the conflux of DNA manipulation and therapy, tissue generation, and robotics as making this great leap possible.

We are already in the midst of minor improvements to the human body and mind; Enriquez gave examples of growing new tissues for successful transplant, programmable cells, and augmenting our abilities through robotics. As this trend accelerates, more and more aspects of the human experience, of the human life, will be capable of scientific manipulation. While some improvement may come post-birth, our understanding of DNA and biology may lead to something much bigger.

a reply to: raymundoko
Perhaps you'll understand my comment better if you think about where RNA comes from...
In case you don't remember:

For those who object because the video above is actually describing DNA>RNA>protein transcription and translation, pay close attention to the animation below especially at 0:38 (note though that the biomolecular machines/protein complexes/enzymes involved in all the processes discussed below are badly depicted, unlike the detail shown in the video above which is zoomed in a bit more, and you may think now about where these biomolecular machines also referred to as protein complexes or enzymes came from; where the video above can help again if you don't remember where proteins come from before they are folded by the folding machine to become functional and start interlocking with other proteins to form functional protein complexes):

Just so you don't forget the importance of proper folding:

What may also help is understanding what prions actually are and what they do to an organism (in reality, not imagination/La La Land/fancy speculation/'in the eye of the beholder'-spin, using preferences or philosophical bias in how things are phrased):

The term "prion" is derived from proteinacious infectious particle and refers to the pathogen that causes transmissible spongiform encephalopathies (TSEs).

This small infectious particle is a disease-causing form of a protein called cellular prion protein (PrPc). PrPc is mainly found on the surface of cells in the central nervous system, but it is also located in other bodily tissues. Although the specific role of PrPc is not clear, studies suggest that this protein plays a protective role in cells and helps them respond to oxygen deficiency.

A prion is composed of abnormally folded protein that causes progressive neurodegenerative conditions, with two of the most notable being Bovine spongiform encephalopathy (BSE or mad cow disease) seen in cattle and livestock and Creutzfeldt-Jakob disease (CJD) seen in humans. These mis-folded proteins do not multiply in the host organism that they infect. Instead, they affect the brain structure by acting as a template, inducing proteins with normal folding to convert to the abnormal prion form.

These newly formed mis-folded proteins, in turn, act as further templates for the conversion of more normal proteins, leading to an exponential accumulation of prions in the tissue of the central nervous system. These abnormally folded proteins form plaques which are thought to cause "entanglement" of neurofibrils and interfere with synapse function. The nerve cells are eventually damaged and lost, which causes tiny vacuoles to form in the brain. These give the brain a sponge-like appearance under the microscope, hence the term spongiform disease arose.

This leads to brain damage and the symptoms of prion disease, which include impaired brain function; changes in personality, memory and behavior; intellectual decline and movement abnormalities, particularly ataxia. These symptoms usually develop during adulthood and worsen over time, eventually causing death within several years or even a few months.
Prion features

Prions are so small that they are even smaller than viruses and can only be seen through an electron microscope when they have aggregated and formed a cluster. Prions are also unique in that they do not contain nucleic acid, unlike bacteria, fungi, viruses and other pathogens. Prions are therefore resistant to procedures that destroy pathogens by breaking down nucleic acid. Furthermore, because these particles are an abnormal version of a normal protein that is already coded for in the body, they do not trigger a host immune response, as other pathogens do.

The normal prion protein is thought to be made up of flexible coils referred to as alpha helices, but in the abnormally folded form, these helices are stretched out into densely packed structures called beta sheets. Cellular enzymes referred to as proteases can break down the normal protein, but prion proteins are resistant to this and subsequently accumulate in the brain tissue as they replicate.

Prion-like behavior can also be seen in some types of fungi. These fungal prions have been studied extensively to provide clues as to how prions affect mammals, although fungal prions are not harmful to their host. [whereislogic: this is the time to think about my comment about "spin" and why little mention is made of this rather significant difference between so-called "fungal prions" (like in yeast) and other prions that cause serious diseases in the OP; personally I'm thinking about whether the terminology prions is appropiate for both phenomena seeing that their effects are already so different, suggesting something else is going on in yeast and other fungi, unless they can just handle it better because of their other attributes]

Prion discovery

In the late1960's, research showed that the agent that causes sheep TSE or scrapie was highly resistant to being deactivated by ultraviolet and ionizing radiation, therapies that would usually destroy any pathogens that contained nucleic acid. However, the nature of these particles was still unclear and scientists made various suggestions including proteins, membrane fragments, small DNA viruses and polysaccharides.

Some researchers decided that whatever the nature of the agent was, it did not depend on nucleic acid to reproduce. In 1982, Stanley B. Prusiner from the University of California in San Francisco, published an article in Science demonstrating purification of the scrapie causing agent and he described a protein. Prusiner wrote in the article: "because the novel properties of the scrapie agent distinguish it from viruses, plasmids, and viroids, a new term "prion" was proposed to denote a small proteinaceous infectious particle which is resistant to inactivation by most procedures that modify nucleic acids." Prusiner’s discovery led to him being awarded the Nobel Prize in 1997.
Sources

www.cdc.gov...
www.nhs.uk/.../Introduction.aspx
www.uclh.nhs.uk/.../PriondiseaseFAQ.aspx
ghr.nlm.nih.gov...
www.bseinfo.org...

Source: What is a Prion?: news-medical.net

This is what was quoted to me:

In their native conformations, many yeast prion proteins regulate transcription, translation, and signaling networks (Halfmann et al., 2010).

Well, I don't know all the details about so-called "yeast prion proteins"* but the prions (in mammals) discussed in the article above screw things up...if you wanna spin that and pretend you can refer to that as "regulate" (when conflating with the prions in mammals)...then I object. Of course that wasn't done in just the line above, but possibly implied by the one quoting that line seeing how it relates to the title of the thread.

*: again, I'm saying so-called cause I'm not sure if using the same terminology "prions" is appropiate in this case. It might well be, but that still doesn't justify the conflation game being played (see the term "Prion-like")

originally posted by: soficrow
a reply to: raymundoko
It is all truly elegant.

I agree (as I understand the word "elegant" to be referring to). But what definition for the word "elegant" did you refer to when sharing this conclusion that you've drawn from the evidence?
Here are some options:

1. tastefully fine or luxurious in dress, style, design, etc.:
elegant furnishings.
2.
gracefully refined and dignified, as in tastes, habits, or literary style:
an elegant young gentleman; an elegant prosodist.
3.
graceful in form or movement:
an elegant wave of the hand.
4.
appropriate to refined taste:
a man devoted to elegant pursuits.
5.
excellent; fine; superior:
an absolutely elegant wine.
6.
(of scientific, technical, or mathematical theories, solutions, etc.) gracefully concise and simple; admirably succinct.

Source: Elegant | Define Elegant at Dictionary.com:
Or perhaps a shorter list is easier to choose from:

: showing good taste : graceful and attractive

: simple and clever

Source: Elegant | Definition of Elegant by Merriam-Webster:

In my agreement I'm combining definition 6 with part of the Merriam-Webster definition. "of technical,..., solutions, etc.).gracefully concise...; admirably succinct" "and clever".

a reply to: whereislogic
I also wonder (to myself) if the term "native conformations" in that quotation is referring to what the source I used referred to as a "normal protein" (or "proteins with normal folding") as opposed to a "mis-folded" or "abnormally folded protein". Which would make the term "prion" even more inappropiate considering the definition for "prion" given by Prusiner: "a small proteinaceous infectious particle which is resistant to inactivation by most procedures that modify nucleic acids." (or at least dubious) Cause that is perhaps not the case with a normally and correctly* folded protein. (* = correctly in relation to "its intended function", see the video about folding for that terminology).

Also note the possible inappropiate use of the term "a protein called cellular prion protein (PrPc)" when talking about a protein that is actually properly* folded from what I can tell and the way it is phrased in the article I used. (* = see footnote for correctly) These proteins called PrPc actually don't seem to qualify under Prusiner's definition for "prion": "a small proteinaceous infectious particle which is resistant to inactivation by most procedures that modify nucleic acids."

Wouldn't it be a bit more reasonable to use the terminology "prions" only for the "misfolded proteins"? Unless you want to confuse and bedazzle with technical jargon for other motivations of course.

originally posted by: soficrow
DNA is dethroned as the exclusive determinant of inheritance, and as the primary one for “traits.”

This is an example of what I earlier referred to as 'in the eye of the beholder'-spin. When I said "DNA is not dethroned." I made no claims regarding DNA supposedly being the exclusive determinant of inheritance, and it doesn't need to be in order to sit on its figurative throne. Which is in the eye of the beholder kind of stuff anyway. A fancy title to draw attention to something that does not diminish DNA's role in inheritance or gene regulation, expression, etc.

Same trick with making comments about RNA regulating gene expression when that RNA comes from the DNA first. What a big deal that other things than just DNA are involved or can affect gene expression and inheritance (2 different but sometimes related subjects) as well. Stop the presses. Now DNA is dethroned...sure. Because of prions? Really, misfolded proteins that cause death? Not the other type that are inappropiately called prion proteins (the properly folded proteins produced from DNA and in that process using machines/protein complexes that were produced from DNA as well)?

originally posted by: soficrow
...aboriginal experiences with shape-shifting.

yay, shape-shifting...I knew I was trying to reason with the wrong type. Well, perhaps it will help someone else see what's going on, seeing that you are not the one actively and deliberately deceiving anyway (knowing better, as the ones who wrote the articles you and I were quoting from; my article also referred to a properly folded protein as a "prion protein" twice at least*).

*: most notably in this paragraph (at least what trick is being played), I've bolded the word that should not be in this paragraph, try to figure out why it should not be in there and why the authors put it in that exact location (but correcting themselves later in the paragraph, in essence giving contradictory information, I'll put that part in italics). So this is from the article I used:

The normal prion protein is thought to be made up of flexible coils referred to as alpha helices, but in the abnormally folded form, these helices are stretched out into densely packed structures called beta sheets. Cellular enzymes referred to as proteases can break down the normal protein, but prion proteins are resistant to this and subsequently accumulate in the brain tissue as they replicate.

See? The 2nd terminology is the correct one, the first is not (hence why you need to leave out "prion" cause they're not talking about a prion protein there, they're talking about what they later call "the normal protein" as opposed to "prion proteins"). It's a cunning game (with excuses ready why the confusing use of terminologies and language was overlooked or is OK, or why it's not a problem for their other claims from your articles that are heavily dependent on this conflation game and not having people think about it, notice it; certainly not have them think about whether or not it might be deliberate). Yes, I'm sticking with using "their other claims" even though we're talking about different philosophers from the same school of thought and philosophy (philosophical naturalism, not what Isaac Newton would refer to as "experimental philosophy" and others later referred to as "modern science").

a reply to: soficrow
From that article you quoted:

In addition to a “native” nonprion conformation...

En daar komt de aap uit de mouw (the cat's out of the bag).

"Native" is referring to "nonprion", it's not a prion protein when it's folded properly (has a native conformation). Then philosophers referring to themselves and eachother as scientists should not use the terminology "In their native conformations [meaning properly folded, nonprion conformation], many yeast prion proteins..."

See the conflation game being played? You can't call 'm prion proteins when they're in their native nonprion (properly folded) conformation, yet they still do so to play the 'sell your latest philosophy and myth-game' and make it sound clever and exciting while keeping people in the dark and confused about the subject and what is a prion and what isn't a prion.

'Percy...it's green.' (nonprion, properly folded, normal proteins produced from DNA that "regulate transcription, translation, and signaling networks"; among other things and DNA-products that are involved such as different types of RNA, with no need to exclude the possibility of future discovery of even more being involved or a need to use attention-drawing titles and 'in the eye of the beholder'-spin about DNA being dethroned when those discoveries are made)

Quoting from the article you quoted again:

...they occasionally fold into a prion conformation...These changes in conformation profoundly alter the functions of the proteins involved...

Of course don't give too many details HOW they alter that function to the point of death for the organism or things having gone seriously haywire in the cell. That would not be something we want the flock to think about as we're talking about certain other ideas/philosophies related to this subject of prion proteins.

originally posted by: PhotonEffect
a reply to: soficrow

It's what Biotechonomy's CEO, Juan Enriquez, has dubbed Homo-Evolutis
Check out his TED talk - it's pretty fascinating stuff.

Enriquez is a great speaker - gotta love salesmen! And it IS cool stuff. But basically, he is just trying to market the idea of transhumanism as “Homo-Evolutis” through his venture capital company Biotechonomy - whose revenue is $2.4 million (relatively insignificant in biotech, even though the bulk of his investments seem to be in energy, industry, agriculture and GMO’s).

Enriquez’ concepts rely on DNA manipulation.

Prion research helps explain why DNA manipulation cannot deliver on early promises to ‘cure’ disease and improve human capacities, and why transhumanist efforts have effectively stalled (except for mechanical-electronic cyborg-type enhancements).

Prions, in the broad sense of the term, represent factors that cannot be overlooked or ignored in life sciences and biotech - or dismissed.

Bloomberg's Overview of Biotechonomy

Biotechonomy is a life science venture capital firm specializing in start-up and early stage entrepreneurial companies. The firm typically invests in companies in genomics-based energy, industrial and agricultural opportunities; companies with technologies that accelerate drug discovery and development; and businesses capable of improving the diagnosis and treatment of disease sectors.

Cyborgs actually do exist; 1. about 10% of the current U.S. population are estimated to be cyborgs in the technical sense, including people with electronic pacemakers, artificial joints, drug implant systems, implanted corneal lenses, and artificial skin.

Also see: 7 real-life human cyborgs

a reply to: whereislogic
RE: Your link, www.cdc.gov/biosafety/publications/bmbl5/BMBL5_sect_VIII_h.pdf

Your “prions only cause disease” reference is from the CDC’s Biosafety Manual. Prion Biosafety is about safely handling (infectious) prions - hence prion diseases, not general prion research and other concepts.

As well, the only prions that are controlled and regulated by government infect a brain protein named the “prion protein” - so it’s not appropriate for the manual to address other prions or infectious mis-folded proteins.

In fact, any protein can mis-fold and potentially become infectious, not just the brain’s so-called “prion protein.” You’re right though, public attention -and funding appeals- are directed almost exclusively to disease-causing prions and mis-folded proteins.

Also true, there is a now-disappearing ‘convention’ not to acknowledge other prions as infectious - but that bit was more about “damage control” than scientific fact (and likely because there are just too many prions for the government to try to control and regulate them all).

Here is a quick overview of the changing 'reference points.'

2003: protein misfolding. At school it all sounded so simple — transcription turns DNA into RNA, and translation of RNA gives you protein. …
…A huge variety of previously unrelated diseases, such as prion diseases, diabetes and cancer, share the pathological feature of aggregated misfolded protein deposits. This suggests the exciting possibility that these 'protein-misfolding diseases' are linked by common principles…

Trends Biochemistry, 2006: Intriguing recent data suggest that other protein misfolding disorders might also be transmitted by a prion-like infectious process.

Nature, 2016: Prions

Prions are an infectious protein usually referring to the protein in mammals called prion (PrP), but the term prions or scrapie protein can be generically applied to any protein that exhibits the same properties of taking on a misfolded conformation (PrPsc form) and templating and propagating further misfolding that leads to its infectivity.

There is an already huge and growing body of research showing that prions do not just cause disease, but are beneficial, and play a significant role in adaptation and evolution. So there is MUCH more to the prion story. The prion research highlighted in the OP and in the numerous links provided there and throughout this thread give just a taste.

You quote a 2014 Oxford Journal article I referenced earlier in the thread, but seem to miss the point that prion proteins regulate their own transcription, translation, and signaling networks (Halfmann et al., 2010) - and as well, hijack DNA control of transcription, translation, and singling.

Here is your quote again, more in context:

Prions are proteins that convert between structurally and functionally distinct states, at least one of which is self-perpetuating. The prion fold templates the conversion of native protein, altering its structure and function, and thus serves as a protein-based element of inheritance.

…. Prions were originally identified as the cause of several rare neurodegenerative diseases in mammals, but the last decade has brought great progress in understanding their broad importance in biology and evolution. Most prion proteins regulate information flow in signaling networks, or otherwise affect gene expression. Consequently, switching into and out of prion states creates diverse new traits – heritable changes based on protein structure rather than nucleic acid.

…prions (have) properties that are usually associated with nucleic acid-based elements of inheritance. …

….Prion-based inheritance is highly orchestrated. …
many yeast prion proteins regulate transcription, translation, and signaling networks (Halfmann et al., 2010). As a consequence, the prion states of these proteins can create diverse new traits. These can be beneficial, detrimental, or inconsequential, depending on the particular prion, genetic background, and environmental context …

Needless to say, the past two years has moved prion research even further forward.

Hope this helps you to better understand prions, and the current state of prion research.



wd, format

originally posted by: soficrow
a reply to: whereislogic
Your “prions only cause disease” reference is from the CDC’s Biosafety Manual.

Why do you pretend I used your straw man argument that I haven't used yet (even though from what you've presented so far I have little reason to doubt that REAL prions only cause things to go haywire in the cell, regardless if you want to call it a disease)? I hope you didn't do that on purpose because you were dissapointed with me not actually saying or quoting "prions only cause disease".

And I actually also quoted:

In their native conformations, many yeast prion proteins regulate transcription, translation, and signaling networks (Halfmann et al., 2010).

I think I've explained enough about why you can't honestly call these "prion proteins", especially if you leave out the fact that you're talking about proteins "in their native conformations" (properly folded) like in your quotations of the same research paper now. That's even more deliberately deceptive (cause then the reader can't see the big clue that these aren't misfolded/prion proteins). All throughout the rest of the papers and articles there are clues that the term "prion proteins" is referring to the misfolded proteins as opposed to the properly folded version of the same protein, which is a normal protein, not a prion protein (no matter how people call it and get their stamp of approval from the clique that likes to refer to these editorial stamps as "peer review" or "peer reviewed"). I'm going to continue using "prion" as if to mean or refer to "misfolded" (as you just did in your comment; also by bolding a certain quotation, thank you), sorry, won't play the same conflation game as certain others.

Again, "native conformation" is referring to "nonprion" as admitted in one of my quotations earlier. It is deceptive to follow up the terminology "in their native conformations" with "prion proteins", cause you're basically talking then about nonprion prion proteins. And to leave it out alltogether and pretend you're talking about prion proteins when you're actually talking about nonprion proteins "in their native conformations", well, that's 1 step extra on the deliberate deception scale. If I wasn't aware of the other quotation I'd have no idea that they were actually talking about nonprion proteins there that "regulate transcription, translation, and signaling networks".

And seeing that they conflated "in their native conformations" with "prion proteins" in the other quotation means I can no longer trust the other quotations you used now (regarding honesty and accuracy), a sad situation. I'm assuming they are continuing that conflation game and still talking about nonprion proteins most of the times they're saying "prion proteins", especially in that quotation that almost sounds the same as my quotation above* and is from the same research paper. (*: actually, you quoted it first in your first response to me, thanks for the clue I needed)

To sum up the truth of the matter (cause I can imagine it getting confusing for those who have misplaced their trust):

nonprion = in their native conformations = properly folded = normally folded = normal protein (only 1 of these terms is mine, see my earlier footnote under "correctly" and "properly" regarding "its intended function" and the video about folding to understand the full meaning of and justification for using that term; which I consider to be quite appropiate to remind people what's important to understand here, I hope people will have another look at that when they read this)
prion = not in their native conformation = in their prion conformation = misfolded = abnormal protein (none of these terms are mine, all have been used in the articles discussed so far)

Both types of proteins seem to require machinery produced from DNA and (thus) DNA to come into existence from a state of individual amino acids (from what I can tell from the way things are described). What happens and their capabilities or effect after that is another subject that I won't expect to get straight answers about from those doing the research since we've already discussed part of that subject (I mean "other subject" compared to how these proteins of either type come into existence from a state of individual amino acids; a subject that is nicely tip-toed around, especially when defending or using phrases such as "DNA Dethroned").

a reply to: whereislogic

You clearly do not understand the science at all - and are mixing the issues all together without sense or reason.

Please read at least some of the references. Forget your basic biology textbooks though, the information is woefully incomplete and consequently, inaccurate with respect to prions.

a reply to: soficrow
Explain what I don't understand regarding something I've said. I'm eager to receive accurate honest information.

Focus on the quotation that combines "in their native conformations" with suggesting that they're talking about "prion proteins" (in their native conformation apparently).

Why do they refer to proteins in their native conformation as prion proteins (also remember the terminology I quoted earlier "native nonprion conformation")? But elsewhere others define prion proteins as misfolded proteins (i.e. not in their native conformation)?

Is it possible to get a straight answer from those doing the above for motives that I have alluded to (perhaps a bit too cryptically)?