DNA Dethroned - Inheritance is Protein-Based.

originally posted by: soficrow

That's the standard eugenics-genetic argument, but no. As you know, humans have only about 20,000 protein-coding genes. That number of genes cannot even begin to explain the individual variety evidenced by our planet's human population. But epigenetics does - and by definition, epigenetic mechanisms operate above the genetic code.

Right, but they combine into around 200,000 species of complex proteins. Each one of these coded proteins has around 16 known variants. Meaning, 16^20,000 possible combinations of basic proteins in an individual, or greater than 1 with 24,000 zeros after it. Now those are going to combine to make the functional species in a similar expansion of possibilities, so add many more zeros after that again. I'd say there is ample room for explaining individual variety with 20,000 genes.

originally posted by: AshFan
I want the Water bear Dsup protein prion please!

If you were to breed them in suitably sized tanks, concentrate the liquid, you would get powdered water-bears. With the right enzymes you could extract that gene and inject it directly. Maybe a modified virus could get it into your cells.

originally posted by: stormcell

originally posted by: AshFan
I want the Water bear Dsup protein prion please!

If you were to breed them in suitably sized tanks, concentrate the liquid, you would get powdered water-bears. With the right enzymes you could extract that gene and inject it directly. Maybe a modified virus could get it into your cells.

So get a super waterbear solution, add some sugar, have someone with herpes scrape in a few scabs, and shoot up.

I am SO going to be immortal!

originally posted by: OrdoAdChao
Warning: Wall of text ahead!

a reply to: theantediluvian
a reply to: soficrow

Thanks for the thread OP - really brain tickling.

I don't know a whole lot about how information is stored in proteins. But, I do understand a bit about, well, bits.

For the sake of clarity and not pedantics: A bit is the smallest unit of information and our notion of the bit has recently been applied to the realm of the atom, the smallest possible unit of matter and is 1 nm (nanometer) in size. Cool, right?

Again, not being pedantic. I am sure a lot of people understand this but for the sake of clarity: We like to put bits in groups of 8 and call that group a byte. When we want to have bytes represent meaningful information, we have to apply an encoding scheme, which in the case of classical computing (not quantum) is binary, 1 or 0, and placement of each bit and that bits state (1 or 0) in each byte can then be made to represent byte as a number (0-255), which then can be passed on to further encoding along with other bytes. Do enough of this fast enough and a lot at once and you have a computer (in a nutshell).

In a sense(and this is where I might be totally off base), an atom (smallest piece of matter) = a bit (smallest piece of information)

In the article above, each hole that the chlorine atom can "fall" into represents the state, and which side it exists on determines the state of the atom (1 or 0) in relation to it's position on the base material (copper) which totaled 1kB. The field that the atoms could "fall" into was 96 nm x 126 nm in size. But we can just focus on the the blocks of 8x8 bits, which can contain up to 64 bits of information, or 8 bytes. Their physical size in nm directly correlates to the amount of information that can be stored.

As per google, a prion is 10nm. So, my reasoning (which could be absolutely wrong) is that a prion can hold a little more than one of our bytes of information. That's not much. In fact its not enough to represent a single English character to a modern computer in unicode-16.

But, to a prion, that might be a whole lot of potential depending on how it encodes itself in order to manipulate a cell. As to memories, I really don't know, but I can speculate.

In my mind, a memory, such as an instinct to be wary of water, would be an insanely huge amount of classic, bit based information even when the "computer" (organism) is set up for that information. I say that because scientists have estimated that the human brain contains 2.5 petabytes of "storage potential" in the sense of binary data. But, the only reason we have so much storage potential is because of the massive network of connections that each potential bit (neuron) has and how much one bit (neuron) can change a vast array of them. Also, we are just starting to understand how the brain represents information in the form of anything meaningful to the organism. So, we don't know how our brain "encodes" in the sense of how we've designed computers. In other words, no Rosetta stone for our brain has been discovered/designed yet.

If the prion uses information like a neuron would, there could be a lot more potential to the prion than my measly 10 bits.
That said, I really haven't a clue on how proteins in general and prions in specific "handle" their information, I just have an understanding of how information is handled via computers in the bit form to represent meaningful things to us.

I hope this makes sense, I am just trying to apply the idea of information to the topic at hand. The OP is no small discovery, it adds to one of our great endeavors in science: finding the blueprints of life.

Thanks for reading and I hope this contributed something to discussion.

The way that DNA is read is that each of the four amino acids encode for positive charge, negative charge, neutral and magnetic field.

Some prions consist of over 145 amino acids so thats a large number of atomic bits. Maybe it's even possible to hide aome histone units in there as well.

www.atsu.edu...

meanwhile :: Back in 1982

this is what got me interested in the first place

www.youtube.com...
Blade Runner (1982) - 'Roy Batty meets Dr. Tyrell'


Biol Chem. 2016 Jan;397(1):1-21. doi: 10.1515/hsz-2015-0158.
Ancestral protein reconstruction: techniques and applications.
Merkl R, Sterner R.
www.ncbi.nlm.nih.gov...


and this Scene

quite goes along with this Thread..

just need to listen to it ( if you can )
Altered States - The Monologue
www.youtube.com...



Form of Human Energy , in our Minds 6 billion years of Atoms , 6 billion years of memory in our Minds
_Professer Edward Jessup

originally posted by: bigfatfurrytexan
Fantastic thread. Something to consider and think about, for sure.

Makes you wonder if space travel is even really possible for us while we are biological in nature. Would prionic diseases in response to various off earth environments cause insanity or death?

Or would evolution take the opportunity to explode again?

Thanks. Good questions. Don't know, but suspect so.

Definitely think we'd best learn a lot more before tinkering. Oops. Too late.

it is proteins, for instance, that are the targets of most drugs and other therapeutic agents.

a reply to: Wolfenz

GREAT post, links, quote. Thanks.

Saving links to view later, but Bladerunner is a fave.

originally posted by: skunkape23

originally posted by: DBCowboy
a reply to: soficrow

Is this something in tune with "racial memory"?

Not sure if 'racial memory' is the proper term to apply. It would appear possible that there could be such a thing as inherited memory.
Never had to teach a dog that a rattlesnake is to be avoided, for example.

Inherited memory. Good one. Also called molecular memory btw.

a reply to: PhotonEffect
a reply to: dr1234
a reply to: raymundoko
a reply to: CyberGarp

Background -> Present

Before the Human Genome Project was completed, the assumption was that each single gene coded for one single protein - estimates of the number of genes in the human genome ranged between 80,000 and 150,000. The actual number, about 20,000 genes, shocked the scientific establishment.

When the results came in from the Human Genome Project, it was quickly noted, “The old paradigm that one gene makes one protein is clearly in need of revision.”

Johns Hopkins University School of Medicine’s Victor A. McKusick observed, “It seems to be a matter of five or six proteins, on average, from one gene.” ” It’s not that the genes actually code for that many, but because protein production is tweaked and modified in the translation process. As McKusick said, “People who now claim that the number of human genes is much higher, may be looking at and counting separate messenger RNAs—the molecules that take information from genes and direct the production of proteins.” Which suggests that RNA ‘translation’ results in the majority of ‘additional’ proteins, not the basic DNA coding. …Which leads us to the epigenome and epigenetic mechanisms.

QUOTES' SOURCE, 2001

The flow of information from DNA to RNA to proteins is one of the fundamental principles of molecular biology - sometimes called the “central dogma.” DNA sends the code to RNA (transcription), then RNA directs protein production (translation).

Proteins are made by ribosomes [RNA], in the process of protein synthesis, also called translation. The instructions for protein synthesis - the code for the correct order and number of amino acids for each protein - is contained in the DNA (in the genes, on the chromosomes). In fact, this is a main function of the genetic material - to store the instructions that allow the cell to make proteins.

From the assumption that DNA and genetics was the be-all-and-end-all, epigenetics emerged as definitive and powerful.

What is the epigenome?

DNA modifications that do not change the DNA sequence can affect gene activity. Chemical compounds that are added to single genes can regulate their activity; these modifications are known as epigenetic changes. The epigenome comprises all of the chemical compounds that have been added to the entirety of one’s DNA (genome) as a way to regulate the activity (expression) of all the genes within the genome. The chemical compounds of the epigenome are not part of the DNA sequence, but are on or attached to DNA (“epi-“ means above in Greek). Epigenomic modifications remain as cells divide and in some cases can be inherited through the generations. Environmental influences, such as a person’s diet and exposure to pollutants, can also impact the epigenome.

At first, RNA appeared to be the only player in the epigenome.

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.

…As the list of RNA epigenetic marks continues to expand, researchers will gain a clearer picture of how diverse cellular processes are regulated. The extremely large repertoire of such modifications is expected to reveal various RNA marks analogous to the known DNA and histone epigenetic marks…

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.

Then, following the revelations that RNA plays a significant role in inheritance - without altering DNA and affecting the genetic code - prions emerged as a separate and distinct epigenetic mechanism. By 2016, the Genetic Literacy Project stated, “Epigenetic factors include entities called prions…”

Originally, prions were thought only to spread disease, but the evidence has been accumulating to show their beneficial side, and their role in adaptation and evolution.

2009: Can Prions Be Epigenetic Regulators In Humans?

Although prions are infectious agents with a bad reputation, research suggests that prions also play a role in epigenetic regulation. …

Prions are most simply defined as misfolded infectious proteins. …As with viral and bacterial pathogens, prions are capable of replication. However, they do so with no involvement of nucleic acids. Prions instead, convert native forms of their corresponding protein into more prions. Furthermore, prions come in different strains and even exhibit differential specie host preferences.

…Prions are classifiable as epigenetic regulators because they are able to modify gene expression through protein interactions, as opposed to first receiving “instructions” provided by nucleic acids.

…“There could be prions in humans that are not causing disease but have important effects on the cell or organism,”

2010: Prions Take Epigenetics to the Extreme

Yeah, we know that somewhere between the X-games and base-jumping light beer ads, the term “Extreme” got a little played out. But, in their Perspective piece in Science, Randal Halfmann and Susan Lindquist make the case that certain proteins with unique folding properties, called prions, deserve the “extreme” label.

Prions are proteins that are stably folded in a different way than their normal siblings. Through that unique conformation, the protein’s function may be changed or inactivated altogether. And because the prion conformation acts as a template to replicate itself onto other members of the same protein, its impact can be huge.

Although prions aren’t thought of as a traditional epigenetic mechanism, the authors from the Whitehead Institute argue that maybe we ought to rethink that position. If you consider epigenetics to mean “…all mechanisms for the inheritance of biological traits that do not involve alterations to the coding sequence of DNA”, then prions certainly fit the bill; they just get the job done by altering protein folding instead of transcription or translation. Because these changes are robust, self-replicating and heritable, prions can be considered both an epigenetic process, and a way for traits to be passed from the environment to an organism (think mad cow disease).

....cont'd next post

cont'd....

Epigenetics in the extreme: prions and the inheritance of environmentally acquired traits.

Prions are an unusual form of epigenetics: Their stable inheritance and complex phenotypes come about through protein folding rather than nucleic acid-associated changes. With intimate ties to protein homeostasis and a remarkable sensitivity to stress, prions are a robust mechanism that links environmental extremes with the acquisition and inheritance of new traits.

2013: Epigenetic dominance of prion conformers.

Although they share certain biological properties with nucleic acid based infectious agents, prions, the causative agents of invariably fatal, transmissible neurodegenerative disorders… propagate by conformational templating of host encoded proteins. Once thought to be unique to these diseases, this mechanism is now recognized as a ubiquitous means of information transfer in biological systems…

2016: Genetic Literacy Project: Other epigenetic factors include entities called prions…

Most exciting, prions are able to transmit traits even when the cell’s DNA is destroyed - the proteins transmit the traits.

2016: Prions can pass on beneficial traits

"In evolution there's a paradox," said Daniel Jarosz, PhD, assistant professor of chemical and systems biology and of developmental biology, who is lead author of the study. "We know that there are an extraordinary number of mechanisms that exist to protect the integrity of the genetic code and to assure that it's faithfully passed on to future generations. But we also know that evolutionary success requires adaptability. How can you reconcile that need with the fact that the raw material for that innovation is really limited?"

… The newly discovered prions …were strongly attracted to DNA molecules and they featured long, floppy "arms" able to fold in a wide variety of ways.

…They found the traits were transmitted even though the cell's DNA had been destroyed -- indicating that proteins were transmitting the traits instead.

2016: Revising the meaning of 'prion’

…most of the identified "molecular memories" help yeast cells adapt to varied stressful environments.

Unlike canonical prions, which are noted for creating specific structures, these proteins contained large sections that are intrinsically disordered, meaning that those domains lack a fixed three-dimensional architecture. In this way, they are related to human proteins that also have prion-like characteristics. According to Sohini Chakrabortee, lead author of the Cell paper, the physical flexibility of intrinsically disordered proteins could allow them to fulfill a variety of roles in a cell, from an enzyme to a chaperone protein like Hsp70. When the team examined the human cognates of the prion-proteins, the intrinsically disordered domains were conserved over hundreds of millions of years.

a reply to: soficrow

You took so much out of context you have no idea what you are talking about. Since you obviously missed the references section that Wiki article I will let you know there are 147 scientific citations. I will take those over your inability to understand basic science any day.

a reply to: raymundoko

Would you mind pointing out exactly what was taking out of context? Are you saying those wiki citations refute the idea that prions are only now starting to be considered an epigenetic factor? I'm sorry, but I'm not sure I'm following along with your gripe.

a reply to: raymundoko

What on earth do you keep going on about? Whatever it is, it's buried in broad generalities and ad hominem attacks.

I find science quite exciting - from proteomics to epigenomics to the latest in prion science. And whether you choose to recognize reality or not, the paradigms are shifting.

a reply to: PhotonEffect

Prions have been considered an epigenetic factor for quite some time. This isn't new. My wiki link has an entire section on Prions. This has been accepted science for DECADES.

Soficrow also does not understand that the article is saying they can use prions to OVERIDE genetic inheritences. The very paper (actual link Here) his blog uses says just that. They can manipulate inheritable traits via prions.

Your traits are inherited via your parents via DNA/genes. Prions have the ability to alter traits true, but his subject: DNA Dethroned - Inheritance is Protein-Based, is a lie. No such thing has happened except in his own mind. Soficrow brings this up every few months and thinks he knows better than actual scientists. He believes all traits are epigenetic and that DNA and Genes have nothing to do with anything. I usually ignore these threads but it's obvious people are getting sucked into the pseudoscience because soficrow weaves in just enough actual science with their personal opinions to trick people. Why? I am assuming because of This, a point they bring up often.

Inherited epigenetic memory

In genetics, genomic imprinting or other patterns of inheritance that are not determined by DNA sequence alone can form an epigenetic memory that is passed on to subsequent generations through meiosis. In contrast, somatic genetic memories are passed on by mitosis and limited to the individual, but are not passed on to the offspring. Both processes include similar epigenetic mechanisms, e.g. involving histones and methylation patterns.[7][8]

The motto of this site is deny ignorance, so here I am. The subject of this post is ridiculous hogwash. No scientist would agree with the poster. But hey, let's all believe arm chair researches with google and a tad bit of free time.

a reply to: soficrow

You obviously don't know what an ad hominem attack is...

a reply to: raymundoko

Thanks for clearing that up.
I'm not familiar with soficrow or his/her beliefs, or his/her previous threads but found the information in this one to be very interesting, despite the title. It's clear that heredity has a considerable genetic component however the expression of traits seems to be a bit more ambiguous as to the nature of its causes. The distribution of phenotypes has more to do with gene regulation and expression and it's not an exact science afaik mapping a phenotype to the underlying genotype. What is for certain is we don't have the whole picture, and much of what we still have to learn could impact our current understanding

a reply to: PhotonEffect

So we should be saying what you said, instead of "DNA Dethroned - Inheritance is Protein-Based", which is a scientifically unsound statement.

a reply to: raymundoko

Yup. You're all about ad hominem attacks.

ad hominem

1. appealing to one's prejudices, emotions, or special interests rather than to one's intellect or reason.
2. attacking an opponent's character rather than answering his argument.

a reply to: PhotonEffect
a reply to: raymundoko

raymundo - you are the one who does not understand the science and new research. Let me walk you through it.

originally posted by: raymundoko

Prions have been considered an epigenetic factor for quite some time. This isn't new. …This has been accepted science for DECADES.

No, this has NOT been “accepted science” for “decades.” Many still question the very existence of prions, never mind their role as an epigenetic mechanism. In fact, the so-called “Prion Controversy” continued to rage in North America long after Prusiner received a Nobel Prize for his prion work. From 2011:

2011: Prion Hypothesis: The end of the Controversy?

…only recently has this once heretical hypothesis been widely accepted by the scientific community.

… The arguments were junk science of course, just a publicity campaign apparently funded by the cattle industry and Big Pharma to protect themselves from liability claims and preserve profitability. But it was effective.

Soficrow also does not understand that the article is saying they can use prions to OVERIDE genetic inheritences.

I referenced several articles on the subject, not just one. And that’s NOT what the articles say. Take this one from phys.org:

Prions can pass on beneficial traits

The study… indicates that… protein-based inheritance is more widespread than previously believed, and could play a role in evolution.

In fact, I have been saying for years that epigenetic mechanisms can overide the genetic code - that DNA is like the hardware, while epigenetic mechanisms are like the software. So that’s MY line.

As for the phrase “protein-based inheritance,” I copied it:

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

A comprehensive analysis uncovered a set of yeast proteins promoting protein-based inheritance that shares many of the non-Mendelian properties of prions. Lacking any sequence or structural signatures of known prions, these proteins represent a new class of non-amyloid, protein-based epigenetic determinants that can control phenotype without impacting genotype.

Transient Expression of Intrinsically Disordered Proteins Fuels the Emergence of Adaptive Protein-based Heritable Traits

…Such protein-based inheritance was also common in wild yeast strains.

Prions in Saccharomyces and Podospora spp.: Protein-Based Inheritance

2012: Discovering Protein-based Inheritance through Yeast Genetics

…yeast has prions (infectious proteins), proteins that are the carriers of genetic information, and thus are acting as genes (1).

Investigating protein conformation-based inheritance

Your traits are inherited via your parents via DNA/genes.

DNA is like the hardware; epigenetic mechanisms are like the software; and prions are an epigenetic mechanism that broadly governs adaptive traits.

IDPs (intrinsically disordered proteins) can drive multiple mechanisms of protein-based inheritance, each of which broadly governs adaptive traits in nature.

Prions have the ability to alter traits true, but his subject: DNA Dethroned - Inheritance is Protein-Based, is a lie. No such thing has happened except in his own mind.

I combined different titles about the same subject. It’s called a title btw, not a subject, and yes, it was written to be a bit ssensational.

[exOctober 6, 2016: DNA dethroned?

Stanford Medicine

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

A comprehensive analysis uncovered a set of yeast proteins promoting protein-based inheritance that shares many of the non-Mendelian properties of prions. …

Soficrow brings this up every few months and thinks he knows better than actual scientists.

I quote the scientists and scientific journals, unlike you, who references wikipedia or nothing.

And I am not a “he.” A bit of a nerd maybe, but one with a vagina. My name is Sofi Crow. Get it? “Sofi.” Female.

He believes all traits are epigenetic and that DNA and Genes have nothing to do with anything.

I do not believe any such thing. You are not psychic. You are wrong.

The subject of this post is ridiculous hogwash. No scientist would agree with the poster. But hey, let's all believe arm chair researches with google and a tad bit of free time.

I report responsibly on new research. Speaking of hogwash, your preconceptions, assumptions and presumptions clearly make it difficult for you to process new information.

Or maybe this info threatens your portfolio?

edit on 11/10/16 by soficrow because: post truncated - not showing???

edit on 11/10/16 by soficrow because: POST TRUNCATED - posting by section

Trying again... cont'd a reply to: PhotonEffect
a reply to: raymundoko


No, this has NOT been “accepted science” for “decades.” Many still question the very existence of prions, never mind their role as an epigenetic mechanism. In fact, the so-called “Prion Controversy” continued to rage in North America long after Prusiner received a Nobel Prize for his prion work. From 2011:

2011: Prion Hypothesis: The end of the Controversy?

…only recently has this once heretical hypothesis been widely accepted by the scientific community.

… The arguments were junk science of course, just a publicity campaign apparently funded by the cattle industry and Big Pharma to protect themselves from liability claims and preserve profitability. But it was effective.