DNA Dethroned - Inheritance is Protein-Based.

originally posted by: whereislogic
a reply to: soficrow

Explain what I don't understand ...

No thank you. I won't.

Read and inform yourself. Learn and think. Come back with intelligent, intelligible questions. Maybe I'll be around. Probably not. But if you manage to maintain your interest and follow an actual train of thought, you won't need anyone to hold your hand.

One of the hardest things for Eugenicists to accept is that there is almost never a single gene for this or that trait. We share more genes with other species than not. Truth is, species, and individual differences within species, arise mostly from gene-regulation, not our DNA. As outlined in the OP, gene-regulation is often an adaptive response to environmental change.

In this light, one of the mysteries of the origins of complex and multi-cellular organisms is now solved. Turns out single-celled amoeba called “Capsaspora owczarzaki” had the tools for going multicellular all along - and evolution is mostly about proteins regulating genes.

One-celled life possessed tools for going multicellular

Scaling up from one cell to many may have been a small step rather than a giant leap for early life on Earth. …

“Animals are regarded as this very special branch, as in, there had to be so many innovations to be an animal,” says David Booth, a biologist at the University of California, Berkeley who wasn’t part of the study. But this research shows “a lot of the machinery was there millions of years before animals evolved.”

...That parallels what’s seen in animals: Proteins in different organs within the same animal show similar modification differences.

The researchers also found changes in the molecules that control the protein modification process. ...

...the perceived chasm between a simple single-celled existence and a complex multicellular one might not have required a flying leap to cross. “This gap,” Sabidó says, “maybe isn’t such a gap.”

a reply to: soficrow

It is more accurate to say instead of "Inheritance is protein-based - it’s epigenetic, not genetic. " Inheritance can also be protein based. This new knowledge doesn't change the fact that genetic ( DNA) mutation is also a method of heritable trait transmission.

dupe

dupe

originally posted by: richapau
a reply to: soficrow
dupe

edit on 16/10/16 by soficrow because: (no reason given)

originally posted by: richapau
a reply to: soficrow
dupe

edit on 16/10/16 by soficrow because: (no reason given)

originally posted by: richapau
a reply to: soficrow

It is more accurate to say instead of "Inheritance is protein-based - it’s epigenetic, not genetic. " Inheritance can also be protein based. This new knowledge doesn't change the fact that genetic ( DNA) mutation is also a method of heritable trait transmission.

Uh huh. The more accurate phrase is "Protein-Based Inheritance." Oh well and mea culpa. ...Not sure how many DNA mutations are methods of heritable trait transmission on their own though - an extremely low percentage methinks.

Thanks for your post.




.......sorry about all the duplicates. Things not working right - and doing so very slowly.

a reply to: soficrow

I don't understand your reply. I'm also confused about what you think he doesn't understand and would also like to know. I feel like I'm informed in this area since I spent so much time on it in school, so I'm not sure what exactly we are supposed to be looking for from your point of view.

a reply to: raymundoko

Hmmm. For example, whereislogic insists that prions by definition can only cause disease, and dismisses outright all the research showing otherwise. Moreover he is disrepectful in the extreme.

posted by whereislogic

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): [/url]

I have neither the time nor inclination to feed such behaviour. Aside from the fact that he makes NO point worth addressing, and has asked NO question that’s intelligible in the context of this thread. I have zero respect for lazy contentious researchers, trolls and disinfo agents who think they're accomplished social engineers. But here ya go. Just this once.

Nature, 2009: The beneficial side of prions

The Scientist, 2014: The Bright Side of Prions

Associated with numerous neurological diseases, misfolded proteins may also play decisive roles in normal cellular functioning.

Stanford Medicine 2016: Prions can pass on beneficial traits, study finds

Researchers have found nearly 50 helpful prions in yeast and comparable proteins in humans, suggesting that this dreaded protein type can boost survival and plays a role in evolution.

originally posted by: soficrow
a reply to: raymundoko
For example, whereislogic insists that prions by definition can only cause disease,

Still stuck on your painting a straw man argument on me I see. Never said such a thing. And even already pointed that out the last time you tried to paint that straw man on me and attempted to make that the subject of discussion (using it as a red herring as well when arguing against it now). Raymundoko might wanna read the article in my signature to get some clues regarding your last 2 responses to me. Especially the line that starts with "You are one of the smart ones, you are not alone,..." and on the page before it the paragraphs that have "agitating the emotions, by exploiting insecurities, by capitalizing on the ambiguity of language, and by bending rules of logic." and "Often we can spot appeals to pride by looking for such key phrases as: “Any intelligent person knows that . . .” or, “A person with your education can’t help but see that . . .” A reverse appeal to pride plays on our fear of seeming stupid. Professionals in persuasion are well aware of that."

In the longterm, these tactics have an effect on people (the fans of those using the techniques described above, and fans or students of those, snowball-effect) and the way they talk to and look down on other people who ask them questions they'd rather not think about or discuss. Behaviour (including way of arguing or conversing) is copied and it spreads by contact. See my signature and my description to the left again for details how this spreads by contact.

Pride: Insight, Volume 2

Asking questions is not "insisting". I summed up my commentary to you quite well and which question or subject to focus on if you want to respond to anything I'm commenting on rather than paint straw men and fight those in order to discredit my commentary and distract from the question you don't want to think about or discuss (or other people to think about). It's not such a complicated subject or complicated set of questions to me at least. I did probably say too much about it than necessary for the questions that I summed up in my last comment to you. But that was me sharing the processes I was going through as I researched the subject and noticed some peculiar behaviour regarding the word "prion". And the background behind my question.

It's interesting you say you don't want to explain what you say I don't understand (apparently not even give a clue what exactly you are referring to other than...), yet you do try to continuously respond to the argument you tried to pretend you were quoting from me earlier:

“prions only cause disease”

The only one I can see constantly presenting that argument is you. You much prefer debating that argument than responding to what I have questons about (than why reply at all? Why say things like "You clearly do not understand the science at all". Not for my sake it seems. Just thinking out loud here):

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)?

Throughout my commentary I've given or alluded to some of my thoughts regarding these questions, but I think I missed yours other than 'because you clearly do not understand the science' (ooh, clearly, a synonym for absolutely/certainly/for a fact), which doesn't quite fit the subjects in my questions but I guess if you interpret it broadly that type of answer could fit many questions, for example a kid asking their parents:

"Why do I have to go to bed at 8 o'clock?"

"Why are human babies born from mommies?"

a reply to: whereislogic

Your posts are disjointed, all over the map, and peppered with accusatory rhetoric. It is extremely difficult to decipher your points (if you have any) and identify the non-rhetorical questions. (I tend to stop reading after the 2nd or 3rd accusation-insult.) However…

(soficrow said, “whereislogic insists that prions by definition can only cause disease”) Never said such a thing.

Your lengthy quote from the CDC’s Prion Biosafety Manual indicated you were trying to use it to prove prions could not be beneficial, and that you thought prions could only cause disease. I apologize if misunderstood your point. …What was it, exactly?


Just realized you perhaps are not being rhetorical here…

Why do they refer to proteins in their native conformation as prion proteins …?

Answered numerous times: a specific brain protein is named the “prion protein” (PrP); this is the protein infected by TSE’s. Much confusion arises because of that protein’s name.

In fact, the so-called “prion protein” PrP is NOT the only protein that can mis-fold and become infectious - virtually any protein can do so - and consequently, PrPSc is not the only prion. There are many other “prions,” aka “proteinaceous infectious particles,” or infectious mis-folded proteins.

But elsewhere others define prion proteins as misfolded proteins (i.e. not in their native conformation)?

See above, and note: The standard view is that any protein coded for by DNA has one “normal,” healthy conformation (shape); this is called the “native conformation.” Misfolded proteins, or prions, have a different shape, and are “not in their ‘native conformation’.”

You may not know that prions can be: “sporadic” (arise spontaneously when a “native” protein inside the body mis-folds during its formation in response to an environmental perturbation); “acquired” (via ingestion, contact, aerosol - eg., from contaminated food, water, soil, insects, air and etc.); or “inherited” (not necessarily genetically, i.e., not due to a change in the genetic code).

Point being that prions act on proteins coded for in DNA, but are themselves an independent evolutionary system capable of hijacking genes and gene products (proteins) for good or ill, or even with no effect.

Hope that helps. In future, if you want a response, stick to the point and ask questions clearly - don’t bury everything in rudeness and rhetoric. …I don’t have much time to spend here - can’t and won’t dig through a lot of insults and rubble.

a reply to: soficrow
Thank you for telling me things I already learned about it (from other sources including the articles linked to in this thread) and taking the time and effort.

So like I mentioned before (and as you seem to confirm somewhat; and as I've seen confirmed through other sources) a protein in its "native conformation" is not a prion (protein). It itself is not infectious and therefore the classification PrP(c) for example is incorrect (cause the "Pr" stands for "Prion", but it's not prion or a prion, it's not infectious). PrP(Sc) is the prion protein, the infectious one. The confusion you spoke of will continue with people talking about this subject if they don't differentiate properly. And if they switch between terminologies such as "in their native conformation, prion proteins..." to "native nonprion conformation", especially when the word "prion" initially was used to refer specifically to their "infectious" attribute by the one who coined the term "prion". But even without that last consideration it's contradictory use of language. Either proteins "in their native conformation" are prion proteins or they are nonprion proteins (hint: it's the latter), you shouldn't talk about them as if they're both if you want to avoid confusion. Now if someone wants to indicate their potential to become prion proteins, then they could just make that clear (in order to avoid confusion).

Especially those researching the infectious prions and what's causing them when things aren't working in the cell according to "its intended function" (again quoting from the video about folding that uses very appropiate language to describe what's going on regarding folding issues and when they are not a problem for organisms when they are part of a regulatory network involving the subjects of variation and adaptability; that contain a lot of on/off-switches also referred to as "active" and "inactive" states for proteins and "nonprion" and "prion" respectively when talking about at least some of the phenomena in yeast that share so many similarities with the prions in human diseases, except one significant difference).

Not to get too sidetracked or anything but just so you know I didn't accidentily switch "nonprion" and "prion" there at the end:

Third, for prion that are inactive forms of a normally active protein,...

Source: Prions of Fungi: Inherited Structures and Biological Roles

a reply to: whereislogic

Thank you for telling me things I already learned…

Your posts just obstruct productive discussion. But you learned that too, didn’t you?


Also - One establishes one’s definitions out front for purposes of discussion, which I did.

1st page, OP, 2nd paragraph:

“Specifically, prions, aka “intrinsically disordered proteins” that can “pass heritable traits from cell to cell by their structure instead of by DNA.” ”

Towards unravelling the mysteries. More news about the protein named "prion."

Two studies describe the function of PrPc, the 'good' alter ego of prions

Two new studies coordinated by SISSA reveal important details about the physiological function of the prion protein, the non-pathological form of the notorious prion, the degenerate protein responsible for several diseases including "mad cow disease." According to the new findings, the protein in its physiological form serves the important function of promoting the growth of neurites, the neural projections along which nerve impulses travel. The two studies ideally complement each other in that one, published in the Journal of Cell Science, provides a general overview and the other, published in the Journal of Biological Chemistry, focuses on a specific stage in the process, which it describes with unprecedented completeness and detail.

The prion protein has two diametrically opposed faces: sadly notorious for its "degenerate" form that causes severe and incurable neurodegenerative diseases such as "mad cow disease" in cattle and Creutzfeldt-Jakob syndrome in humans, in its physiological form the prion protein (PrPC) serves a vital function for the brain. Its positive action had, however, never been clarified until now. Two new studies, both coordinated by Giuseppe Legname, professor at the International School for Advanced Studies (SISSA) in Trieste, finally provide a detailed description of the biochemical processes through which this protein stimulates and guides the growth of neurites, the neural membrane projections (axons and dendrites) that are all important for the conduction of nerve signals.

Characterization of prion protein function by focal neurite stimulation

ABSTRACT

The cellular prion protein (PrPC), encoded by the PRNP gene, is a ubiquitous glycoprotein, which is highly expressed in the brain. This protein, mainly known for its role in neurodegenerative diseases, is involved in several physiological processes including neurite outgrowth. By using a novel focal stimulation technique, we explored the potential function of PrPC, in its soluble form, as a signaling molecule. Thus, soluble recombinant prion proteins (recPrP) encapsulated in micro-vesicles were released by photolysis near the hippocampal growth cones. Local stimulation of wild-type growth cones with full-length recPrP induced neurite outgrowth and rapid growth cone turning towards the source. This effect was shown to be concentration dependent. Notably, PrPC-knockout growth cones were insensitive to recPrP stimulation, but this property was rescued in PrP-knockout growth cones expressing GFP–PrP. Taken together, our findings indicate that recPrP functions as a signaling molecule, and that its homophilic interaction with membrane-anchored PrPC might promote neurite outgrowth and facilitate growth cone guidance.

a reply to: soficrow

I have been suggesting for some time that the conventional evolutionary paradigm (the Modern Evolutionery Synthesis) is too 'reductionist' to adequately describe biodiversity.

Horizontal gene transfer, epigenetics, prions, standard genetics/mutations (and probably more to be discovered) ALL play a part in heritability of traits making the MES a bare framework of only one of biodiverity's systems.

Also, prions are not really epigenetic in the true sense (a binary state DNA sequence set by non-genetic factors).

a reply to: chr0naut

Great post. Thanks.

But re: " prions are not really epigenetic in the true sense (a binary state DNA sequence set by non-genetic factors)." ...My understanding is that there are epigenetic prions. Although proteins with prion potential (pretty much all of them) are coded for in DNA, environmental factors and not RNA can trigger the prion folding conformations - which makes them epigenetic I would think.

???

originally posted by: soficrow
a reply to: chr0naut

Great post. Thanks.

But re: " prions are not really epigenetic in the true sense (a binary state DNA sequence set by non-genetic factors)." ...My understanding is that there are epigenetic prions. Although proteins with prion potential (pretty much all of them) are coded for in DNA, environmental factors and not RNA can trigger the prion folding conformations - which makes them epigenetic I would think.

???

In the case of a normal protein and a prion form, I would think that the RNA sequence for both would be exactly the same (they are the same protein) but that the folding director would be non-genetic, as it is in CJD and BSE diseases.

I suppose that there could be genetic sequences that direct folding direction but I have not heard of them. Perhaps a future discovery after more of the proteome is mapped?

originally posted by: chr0naut

originally posted by: soficrow
a reply to: chr0naut

Great post. Thanks.

But re: " prions are not really epigenetic in the true sense (a binary state DNA sequence set by non-genetic factors)." ...My understanding is that there are epigenetic prions. Although proteins with prion potential (pretty much all of them) are coded for in DNA, environmental factors and not RNA can trigger the prion folding conformations - which makes them epigenetic I would think.

???

In the case of a normal protein and a prion form, I would think that the RNA sequence for both would be exactly the same (they are the same protein) but that the folding director would be non-genetic, as it is in CJD and BSE diseases.

I suppose that there could be genetic sequences that direct folding direction but I have not heard of them. Perhaps a future discovery after more of the proteome is mapped?

A long-standing assumption was (is?) that there is only one "correct" protein conformation - although proteins can "mis-fold" in myriad ways. ...I think what makes prions epigenetic is that their folding is "controlled" epigenetically and definitely NOT genetic. They can be inherited sometimes, but the inheritance is NOT genetic either.