The Histone Code (genetic code not the only code?)

USC/Norris Comprehensive Cancer Center ^ | 2007 | Judd C. Rice, Ph.D.

[GodGunsGuts]

It is now clear that genetics won’t be able to answer all of our questions about human development and disease. These basic biological processes rely heavily on epigenetics – the ability to ‘fine-tune’ the expression of specific genes.

This regulation of gene expression is essential for defining cellular identity and the dysregulation of these processes results in a variety of human diseases. Therefore, understanding these mechanisms will not only enhance our basic knowledge but will also lead to the improved detection, therapy and prognoses of several human diseases.

...

The histone code hypothesis predicts that the post-translational modifications of histones, alone or in combination, function to direct specific and distinct DNA-templated programs.

[js1138]

RNA does not require a cell structure in order to replicate. Nor does it require “protiens.” Nor does it require a cell structure to change and evolve. See my previous posts.

Let’s ask a simple question. Is there anything in your view of science that would have predicted Spiegelman’s monster? Is there anything in your approach to science that would suggest attempting this line of research?

I ask this because my main objection to intelligent design is that it doesn’t lead to any interesting research. Hasn’t in two hundred years. Why should we look for natural causes if everything is caused by angels?

[js1138]

'Furthermore, “self-making” is not reducible to the laws of physics and chemistry. There is an unbridgeable abyss between the dirty, mass-action chemistry of the natural environment and the perfectly-pure, single-molecule precision of biochemistry.’

Sounds like money well spent. Does he have any stock offerings in perpetual motion machines?

[GodGunsGuts]

Read the article when it comes out for free on their website. The implications are nothing short of stunning IHO.

[js1138]

Yes, it would be stunning to see vitalism resurrected after all these years.

[RightWhale]

So where’d the code come from if nobody wrote it?

The metaphor is hopeless.

[CottShop]

True- pure standalone RNA doesn’t- but systems are not made up of standalone RNA only- they are vastly more ocmplex, and it is biologically impossible to produce these vastly more complex systems from simple standalone RNA’s to the advanced irreducibly somplex we have today through a completely random mistake driven system- information is needed, instructions are needed, and life, with it’s DNA+ repair instrucitons couldn’t come about naturally- simply taking a single instance of a simplified structure such as RNA and claiming it extends to all life is misleading

[[I ask this because my main objection to intelligent design is that it doesn’t lead to any interesting research. Hasn’t in two hundred years.]]

If you beleive that, then you obviously aren’t very informed on what ID studies. You evidently simply dismiss out of hand any htought of design needing a designer, and as such, you you deprive yourself of the very interesting studies done in ID thinking that all design can be explained naturally when there is no scientific evidence that it was. The designs in nature, the complexities in nature, more point toward a designer than they do naturalistic causes that defy statistical, mathematical and natural laws at every step of the literally trillions of steps needed to get to where we are today. You dismiss stright out of hand a more logical explanation and I guess prefere one that takes an incredible amount of faith and evidence ignoring to beleive in.

I’’ll look into Spiegals monster a bit more later

[[Why should we look for natural causes if everything is caused by angels?]]

Because natural causes follow natural laws and can explain things we need to know- but this in no way automatically rules out a Creative Designer, infact, the natural laws and the complexities that accompany naturalk laws and which defy natural causations point to a creative causation time and time again. There are things, systems, which do defy natural causations, and which naturalistic explanations come up short in answering.

[CottShop]

[[Sounds like money well spent. Does he have any stock offerings in perpetual motion machines?]]

No- but I’ll bet hte people who say “Design can’t be divinely caused and must be naturally caused, we just don’t know how yet... but one day we might’ (Despite more andm ore evidence coming in from ID research that thigns are much more irredicubly complex and constructed as a whole rather than piecemeal as Naturalism demands they be) do have stock in the PM machine

[allmendream]

Actually your statement is absolutely incorrect. Histone affinity is a function of methylation of DNA. Thus methylation of DNA leads to higher affinity for Histones making the gene in question, and being bound to Histones makes transcribing the gene into a message capable of being made into a protein more difficult, thus turning ‘off’ the gene.

The gene, when turned on, will still make the same protein, according the the Universal Genetic Code (AUG = Methionine, etc). This paper is saying that post translational (after it was made from RNA) modifications of histone proteins can lead to some sections of DNA being preferentially turned on or off.

The code is still the code. This is all about on or off. The gene still makes the same protein.

[allmendream]

My computer committed sepuku over the weekend, deciding that the dishonor of not being able to update the graphics card was too severe a shame to live with.

I usually only Lurk from Work (good screen-name there, prolly taken), but am posting from work to say I will not be around to correct obvious errors, keep differentiated transcription and translation, or reiterate that determination of if a gene is on/off is not a ‘code’ in the same sense that AUG = Methionine is a code.

Hope to be back in a couple weeks with a new faster computer. Until then persevere FReepers, and keep up the good work. We have a long row to hoe to getting our Republican Nominee into the White House; lets keep our eyes on the prize and our noses to the grindstone and elect Thompson/Hunter in 08’ (or whoever our eventual nominee is)!!!!

[js1138]

Because natural causes follow natural laws and can explain things we need to know- but this in no way automatically rules out a Creative Designer, infact, the natural laws and the complexities that accompany naturalk laws and which defy natural causations point to a creative causation time and time again. There are things, systems, which do defy natural causations, and which naturalistic explanations come up short in answering.

No one can argue that natural causes rule out designers, but I'd like to see an example of a phenomenon that "defies" natural explanation, as opposed to simply being unexplained.

Let's have a little review of science history: Prior to Newton, did the planets require angels to push them around? Prior to Einstein, were angels required to explain the orbit of Mercury? Prior to the Grand Unification, are angels required to explain quantum gravity?

Give me a specific example of an event postulated by the theory of intelligent design that was caused by a designer. When did it happen? What happened?

[BlueDragon]

I was referring to some other study or finding --- which I have only a dim recollection of.

I was NOT referring to the article linked to the beginning of this thread.

don't make the mistake that the information coveyed by the good Dr. Rice & Co., is all inclusive, in regards to each and every aspect of gene expression.

[js1138]

Despite more andm ore evidence coming in from ID research that thigns are much more irredicubly complex and constructed as a whole rather than piecemeal as Naturalism demands they be

Let's have an example of something that can't be produced by incremental steps.

[GodGunsGuts]

If true, then IC will be found to apply to all life, and Behe’s examples of the same would be but a few drops in an ocean of irreducible complexity.

[CottShop]

[[Let’s have an example of something that can’t be produced by incremental steps]]

Better yet- let’s have an example of how Ecoli flagellum did evolve incrementally- evidences and such- not unsupported hypothesis

[GodGunsGuts]

Hunter in ‘08!

[CottShop]

[[No one can argue that natural causes rule out designers, but I’d like to see an example of a phenomenon that “defies” natural explanation, as opposed to simply being unexplained.]]

Ah- but htey are not unexplained- you just don’t- won’t accept the explanation

[[Let’s have a little review of science history: Prior to Newton, did the planets require angels to push them around? Prior to Einstein, were angels required to explain the orbit of Mercury? Prior to the Grand Unification, are angels required to explain quantum gravity?]]

What relevence does anything ‘prior’ have to the conversation? eitehr, based on our present knowledge, thigns are designed or they are not- no credible scientist is going to state there is no design- the debate is over whether or not that design is able to occure natrually. So far, there is no evidence, despite much research to prove so, that nature is capable of producing irreducibly complex systems. Using logic, when design is discovered, one can come to a very reasonable and scientific conclusion, that a designer was the causation. To suggest everythign must have a nturalistic cause is a non objective form of science practice- nay- it’s a religious beleif itself.

[metmom]

If crystals need and intelligent designer to form, then RNA, which has a crystalline structure and stable crystalline forms, needs an intelligent designer.

True.

[js1138]

Are you arguing that no subcomponent of the flagellum can have a useful function?

[metmom]

I ask this because my main objection to intelligent design is that it doesn’t lead to any interesting research.

Perhaps you could ask Newton and his contemporaries that question. He believed in creation and it was certainly the motivation for him to decide that the universe was orderly and predictable and we could learn more about it by observing it.

I ask this because my main objection to intelligent design is that it doesn’t lead to any interesting research.

And you can demonstrate that as a fact how?

[CottShop]

examples of irreducible complexities include energy molecules like ATP and GTP

“In addition, a potential ATP candidate molecule would not be selected for by evolution until it was functional and life could not exist without ATP or a similar molecule that would have the same function. ATP is an example of a molecule that displays irreducible complexity which cannot be simplified and still function (Behe, 1996). ATP could have been created only as a unit to function immediately in life and the same is true of the other intricate energy molecules used in life such as GTP.

Although other energy molecules can be used for certain cell functions, none can even come close to satisfactorily replacing all the many functions of ATP. Over 100,000 other detailed molecules like ATP have also been designed to enable humans to live, and all the same problems related to their origin exist for them all. Many macromolecules that have greater detail than ATP exist, as do a few that are less highly organized, and in order for life to exist all of them must work together as a unit.

A crucial difference between prokaryotes and eukaryotes is the means they use to produce ATP. All life produces ATP by three basic chemical methods only: oxidative phosphorylation, photophosphorylation, and substrate-level phosphorylation (Lim, 1998, p. 149). In prokaryotes ATP is produced both in the cell wall and in the cytosol by glycolysis. In eukaryotes most ATP is produced in chloroplasts (for plants), or in mitochondria (for both plants and animals). No means of producing ATP exists that is intermediate between these four basic methods and no transitional forms have ever been found that bridge the gap between these four different forms of ATP production. The machinery required to manufacture ATP is so intricate that viruses are not able to make their own ATP. They require cells to manufacture it and viruses have no source of energy apart from cells.”

http://www.trueorigin.org/atp.asp

More: irreducible complexity is present in the clotting system for blood, the light-detecting system for cells in the retina of the eye, and the repair and transcription systems for DNA.

“Many people don’t realize that even the simplest cell is fantastically complex—even the simplest self-reproducing organism contains encyclopedic quantities of complex, specific information. Mycoplasma genitalium has the smallest known genome of any free-living organism, containing 482 genes comprising 580,000 base pairs[11] (compare 3 billion base pairs in humans, as Teaching about Evolution states on page 42). Of course, these genes are functional only in the presence of pre-existing translational and replicating machinery, a cell membrane, etc. But Mycoplasma can only survive by parasitizing other more complex organisms, which provide many of the nutrients it cannot manufacture for itself. So evolutionists must postulate a more complex first living organism with even more genes.”

http://www.trueorigin.org/design01.asp

Design and IC everywhere- Dismissing a designer in favour of a biologically impossible model or hypothesis is irresponsible science that is based on religious belief and not good sound objective scientific practice.