Tuesday, December 27, 2011

the epigenome and top-down causation

RoyalSociety | Genes store heritable information, but actual gene expression often depends on many so-called epigenetic factors, both physical and chemical, external to DNA. Epigenetic changes can be both reversible and heritable. The genome is associated with a physical object (DNA) with a specific location, whereas the epigenome is a global, systemic, entity. Furthermore, genomic information is tied to specific coded molecular sequences stored in DNA. Although epigenomic information can be associated with certain non-DNA molecular sequences, it is mostly not. Therefore, there does not seem to be a stored ‘epigenetic programme’ in the information-theoretic sense. Instead, epigenomic control is—to a large extent—an emergent self-organizing phenomenon, and the real-time operation of the epigenetic ‘project’ lies in the realm of nonlinear bifurcations, interlocking feedback loops, distributed networks, top-down causation and other concepts familiar from the complex systems theory. Lying at the heart of vital eukaryotic processes are chromatin structure, organization and dynamics. Epigenetics provides striking examples of how bottom-up genetic and top-down epigenetic causation intermingle. The fundamental question then arises of how causal efficacy should be attributed to biological information. A proposal is made to implement explicit downward causation by coupling information directly to the dynamics of chromatin, thus permitting the coevolution of dynamical laws and states, and opening up a new sector of dynamical systems theory that promises to display rich self-organizing and self-complexifying behaviour. Full Article.


Big Don said...

A federal judge just ruled that minorities are too dumb to figure out a ballot...


CNu said...

BD, the bare minimum requirement for your trolls is that they be on topic and at least as clever as what a petulant 7 year old could muster. This morning's effort didn't meet that standard.

Dale Asberry said...

Donnie -- fields of mint. Fields. Of. Mint.

The joy of RSS means that LDs comment can't be erased from my reality. Lol.

nanakwame said...

What a year in science, and how far it has been made pragmatical.  This is a nice article; it remind me of  discussion you had last year, with your BD.
http://www.livescience.com/17635-science-journal-retractions-2011.html ...The site also has the 11 Biggest Science Stories of 2011. One factor in this discussion is how the laws of quanta fits into biology. What is the Self? Since they are getting ready to feed the brains?

Every day is a journey, and the journey itself is home.  Matsuo Basho

Tom said...

"your BD"

: ) When you look at it that way, I can see why some people might want a BD.  Maybe he barks too much, and slobbers on people, but he's kind of endearing.

nanakwame said...

Yes we got pookies everywhere?  Ridding ourselves of kooky, junk, and prescribed worthless folks is a Utopian dream. Even in our machine/human phase as Syfy has written there was the kook and definitively  junk. I f_k with my man all the time, if you haven't notice, for I enjoy his mental abilities - that being Doc CNu. I am pretty sure BD is quite smart. Smarts is but a part of life, if our genomes is made of how much "junk"?

CNu said...

I think you've forgotten how violent the instinct/emotion of disgust is Nana.  My man Cobb wrote something very profound and true the other day http://cobb.typepad.com/cobb/2011/12/american-meritocracy-bunny-slopes-black-diamonds.html#comment-6a00d834515ae969e201675f4cc9bd970b Planes only exist to fetch those in the ruling class back and forth to their important face to face meetings.

Nuclear weapons and multi-lingual, polymath, genius-level psychopath field agents who can beat you to death on your best day with a rolled up magazine only exist to serve the interests of the ruling class which bred them up, much as someone bred up Mastiffs and Chihuahuas in their day....,

That ruling class is deeply and profoundly disgusted by the teeming and unprofitable mass, and, it has many, many times more than enough of the means along multiple lethality vectors to rid itself of the mass by which it is disgusted and which no longer turns a profit.

nanakwame said...

http://www.paw-rescue.org/PAW/PETTIPS/DogTip_PoopEating.php...there is so much that make us human disgusted, I never forget the emotion of disgust, in was on most of those nuns faces every year I was in Catholic Grammar School, especially when I was found to be on the top ten. Or a Soldier who rapes a Vietnamese girl with contempt just to get his rock off. IRLAND is your position in complicity with the ruling class or Necessity and Science, for quite of few of them going too? I will read Cobb, but he bores me at times. He seems superficial to me.  Could you imagine some one like Fred Hampton even saying BS like that - about the ruling Euro Ethnicity, who was the ruling class, the dangers faced, you jest. What I like is the person who made their drone to watch the police. I will be back. The danger is from the middle class, and always been re-read your Fascism in the West.

nanakwame said...

What the f_k is multicultural nationalism? This is a guise for nativism shared by Afro and Euro American whom 9o% don't know the real history of this nation.  Tell me CNu where does these notion of equality and meritocracy fit in the brilliant essay you place here from recent science discoveries?  I am surprised at you, you have a dangerous streak. "unprofitable mass" what is that even in Marx's term. AND the reason the Black Panthers failed is they latched on the BS the lumpen-proletariat was the vanguard, and they were middle class kids. What garbage. One problem America has is that it created its own expectation of "we are moving to a third world status" in my life that means small oligarch, kiss ass middle class, and huge poor/working population to do as please. The masses taught it was keeping brown folks out, including Afro-American.

We of the sinking middle class may sink without
further struggles into the working class where we belong, and probably when we
get there it will not be so dreadful as we feared, for, after all, we have
nothing to lose.”

George Orwell quotes (English Novelist and
Essayist, 1903-1950 

As for America, it is the ideal fruit of all your
youthful hopes and reforms. Everybody is fairly decent, respectable, domestic,
bourgeois, middle-class, and tiresome. There is absolutely nothing to revile
except that it's a bore.”

Brooks Adams quotes (American writer, 1838-1918)

nanakwame said...

The masses were taught it was keeping brown folks, and Chinks out, including Afro-American, meaning Afro-American believed that too. Now look at the South, who runs the small businesses.  

CNu said...

I am surprised at you, you have a dangerous streak. "unprofitable mass" what is that even in Marx's term.


I am in complete agreement with Hypertiger's prognosis. There should be no surprises here what.so.ever...,

Big Don said...

The Mother of all Lethality Vectors: --->  The first day the welfare checks don't come out...

Uglyblackjohn said...

Or Social Security Checks - take your pick.

Big Don said...

Actually, that would be an interesting comparison.  Big difference in the level of civility and immediate lethal violence.  Geezers much more likely to find socially acceptable resolution with stronger well-established family for support.  To put in perspective, would you be dodging thrown objects if Lawrence Welk(RIP) failed to show up for a rumored appearance at Mall Of America...??


CNu said...

That ruling class is deeply and profoundly disgusted by the teeming and
unprofitable mass, and, it has many, many times more than enough of the
means along multiple lethality vectors to rid itself of the mass by
which it is disgusted and which no longer turns a profit.

nanakwame said...

btw I forget: The interesting Juxtaposition - There is no good w/o bad 


CNu said...



CNu said...

NYC = http://2.bp.blogspot.com/_863XycFk6SE/ScW5tTrpOFI/AAAAAAAAAKg/cjy4ijl-uwA/s400/chen4.jpg

nanakwame said...


nanakwame said...

My friend your tendency to reductionist is not saying anything new to me. As point out by you we go from the bacteria to the lofty goal of 5th Dimension. But the literacy of the 21st Century is build on the genius of the late 1800's, when capitalism and socialism become religions. So I leave you this, for every day is a quanta day, where traditions ride...

Shigalyovism is a philosophy specific to the book and
particularly of the character Shigalyov. Very similar to barracks communism,
Shigalyovism demands that ninety percent of society be reduced to a condition
of inhuman slavery so the other actually useful ten percent of society is free
to make progress. Dostoyevsky advances this bizarre doctrine, not with the
intention of proposing a viable philosophy, but rather an inane one, that lends
weight to his portrayal of Shigalyov and his fellow conspirators as radical
"demons", themselves more caricatures than accurate reflections of
revolutionaries…“…my conclusion directly contradicts the original idea I start
from. Starting from unlimited freedom, I conclude with unlimited despotism. I
will add, however, that apart from my solution to the social formula, there is
no other.”…

Nihilism, embodied by Pyotr Verkhovensky, is an
extreme ideology that demands the destruction of the current social order. A
description of Verkhovensky's philosophy of political change is posited as
"the method of a hundred million heads," referring to the predicted
death toll…

Conservatism is embodied by the provincial governor
Andrei Antonovich Von Lembke, and is shown to be incapable of dealing with
subversive extremism. Indeed, the elites of the provincial community initially
find the radicals fashionable and charming, arranging at their request the
literary banquet from which the fiasco of the planned revolution begins….wiki ...

Man is fond of counting his troubles, but he does not count his joys. If he counted them up as he ought to, he would see that every lot has enough happiness provided for it. Fyodor Dostoevsky

Uglyblackjohn said...

Really? But their children are probably even worse-off than themselves.
Their children will be the ones throwing bricks at an even bigger and more focussed Occupy event.