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.

[garjog]

[”A code is a basic construct of language.”

No.]

Sure it is. To communicate, rational beings, such as a human, needs to encode complex meaning into codes which can be transmitted from a source (an intelligence) to a receiver. That is how language works.

Biology looks just like it is formed by some kind of super language. If there is a code, and if encoding exists, there must be a source for the code.

From Wikipedia:
In communications, a code is a rule for converting a piece of information (for example, a letter, word, or phrase) into another form or representation, not necessarily of the same type. In communications and information processing, encoding is the process by which information from a source is converted into symbols to be communicated. Decoding is the reverse process, converting these code symbols back into information understandable by a receiver.

[valkyry1]

You expect me to seriously believe that there aren’t archaeologists out there who wouldn’t destroy any evidence like that if they found it? Not buying it

Exactly, they have been shown to fabricate evidence they find attractive, therefore they are equally capable of destroying or throwing away evidence they dislike.

Dating schemes come to mind for one thing.

[metmom]

Fabrications can be shown to be lies, like Piltdown Man and archaeoraptor. Only those destroying evidence will ever know about it. It’s much easier and safer.

[valkyry1]

Yes, or the reconstructions that end up being shown the results of an over active imagination driven by wishful thinking.

Skull 1470 and rampithecus comes to mind.

[valkyry1]

In the ‘real world’ there are only a very few genuine scientist's, all the rest are essentially groupies to varying degrees.

[IrishCatholic]

I usually only get about this far on these threads when I see the condescending crap like this posted. Try advocating an idea, not tearing down the opposition. The noodly appendage game is for punks and keyboard warriors only.

If you think you can share knowledge then do so. Put forward an idea and discuss it without being rude.

You do not have the answer. Science does not pretend to have the answer. So I don’t see how you got it.

Trying to make yourself look intelligent by tearing down someone else is pathetic.

You are insulting. Look at my tag line. You belong there.

[GovernmentIsTheProblem]

” If you think you can share knowledge then do so. Put forward an idea and discuss it without being rude.”

I did - I posted a few links to scientific explanations - but it was dismissed out of hand. Scroll on up the thread. :)

The FSM/flintstones came after I got the typical nyah nyah/plug ears response.

[metmom]

I did - I posted a few links to scientific explanations - but it was dismissed out of hand. Scroll on up the thread. :)

So where did you post links to scientific explanations? Scrolling upthread reveals cartoons and a couple links to wikipedia. You surely can't be referring to wiki links, can you? Seriously?

[GovernmentIsTheProblem]

“So where did you post links to scientific explanations? Scrolling upthread reveals cartoons and a couple links to wikipedia. You surely can’t be referring to wiki links, can you? Seriously?”

Yes - they are a good high level view of the topic.

If you’re interested in learning more, there’s lots of source material links.

I posted the links in response to the challenge that there could be no materialist explanations for abiogenesis.

The really funny thing is that theologians were, for a long time, the biggest proponents of the idea of “spontaneous generation,” such as the idea that worms came from rotting wheat. It took scientists like Pasteur to disprove that concept.

[metmom]

Wikipedia, the notoriously unreliable internet source that allows you to edit articles yourself and then use them to back yourself up on another forum on the internet?

If that’s being passed off as scientific, it’s no wonder there exists the sad state of affairs in public schools in science education and it’s no wonder the general populace doesn’t take *scientists* seriously. How can you when you can’t trust the information in the sources they post?

Some time ago on FR, wiki was used frequently by evos to back up their position until the editing issue came to light. Then, anyone who used it was criticized by the evos. You’re behind times.

Spontaneous generation was the latest in prevailing scientific thought of the day, just as alchemy was at one time. Louis Pasteur was a Christian and Franciscan. So much for theologians being the biggest proponent of spontaneous generation.

I also seem to recall, it was the scientists of the day who laughed at Simmelweis for simply asking doctors to wash their hands between autopsies and delivering babies and this as late as the early 1800’s.

Funny thing is, Jewish law had prescribed hygiene thousands of years before *modern* science had a clue about germs and disease transmission. The *theologians* had the *scientists* beat again.

[allmendream]

“It is not the genes that code for the specific proteins themselves, that induce either, which combination of acetylation, methylation, and phosphorylation, occurs in the octameric complex, now is it?” Blue Dragon

No, all the processes are regulated or accomplished by proteins coded for by genes, and the code used to code for these genes is the Universal Code of Molecular Genetics.

The chemical composition of the complex (phosphorylation of proteins, methylation of DNA, etc) is indeed accomplished by specific proteins coded for by DNA (using the universal code).

Go apparently GGG accomplished his goal to muddy the waters with all these “Codes upon Codes” and got a few people thinking he was talking about an actual code that ran parallel or orthogonal to the Universal Genetic Code. Sorry all those other control mechanisms are either ‘on/off’ or ‘preferentially subset A/preferentially subset B/preferentially subset B/etc’ (as is the case with histone modification which will target it to specific types of genes turning them off).

So there is no circumstance where the Universal Code is abandoned for usage of a different code when turning DNA into protein. If that is what your comments meant then it was completely and totally erroneous. There is often post-transcriptional modification, such that a single ‘gene’ can produce several different protein products, based upon how the message is spliced. But the message is still translated using the Universal Genetic Code.

[Aquinasfan]

I would say, the more we learn how “fine-tuned” life is, the more we should be looking for the possibility of a “fine-tuner.”

Random changes fine tune things. Don't you find that to be true in your everyday life? < /s>

[GovernmentIsTheProblem]

“Wikipedia, the notoriously unreliable internet source that allows you to edit articles yourself and then use them to back yourself up on another forum on the internet?”

I thought the article was decent. Anyone can read the edit history.

Anyway you dismiss the concept out of hand anyway, so damn the source too while you’re at it.

Google the term and read about it elsewhere if you like!

[CottShop]

[[In his book, The Edge of Evolution, Behe proposes that evolutionary change requiring two specific steps is impossible from the standpoint of probability, but there are observations in existing literature of two and three step adaptations. Behe’s probability assumptions are observably wrong.]]

You are talking about two entirely seperate topics here- adaptation does NOT produce NEW organs or parts that are not species specific- We’re talking about complex parts in the case of the ecoli ‘outboard’ motor locomotion aparatus. There is absolutely NO evidence that ecoli carried around the parts before a final natural assembly- An adaptation can only work on information already present -it can’t create NEW parts or NEW information. All of the examples I gave NEED ALL of the information present in order to function and indeed to keep the species alive. The Dover trial asked if Behe had done hte experiments BUT it did NOT require the opposing scientific view to produce any such evidence- it allowed them a hypothesis while demanding proof from Behe? Behe’s hypothesis is sound and hte other examples given are sound.

[CottShop]

[[This highlights two things about intelligent design. It is rather unrealistic to expect complex objects to evolve while you wait — the human time scale is too limited. However, in the geological time scale, thousands of years is too short a time to be distinguished in the fossil record.]]

What has this got to do with IC? As well, ‘tens of 1000’s of years is too short to establish a fossil record’? Since when? You do realize that the shifting evolution hypothesis is now talking about rapid evolutionary events now, right? Once again, they are changing their view to fit the evidences- there is now not just one explosion of species (the cambrian explosion) but now there is another (The PreCambrian explosion) in which fully formed fully functional species show up all at once in layers labelled as ‘early’ and ‘earlier’ (given dates of millions of years old- using of course faulty dating methods, and ‘visual cues’ to come up with those numbers)

[[Behe was also asked at Dover about the time required to produce a particular adaptation, and he started out giving an astronomical number of years. He was led through the calculations, using the numbers and assumptions he supplied, and the answer was several thousand years.]]

This brings up an im,portant ID point- IF it would take astronomical times to ‘create’ ‘adaptations’ (And I’m assuming by adaptation you are talking about NEW parts not specific to a species) then the fact that ALL the parts were present and assembled and fully fuinctional in ALL the examples of ecoli in the records, then it goes to show that the parts NEVER ‘evolved’ over long periods- there is no evidence that any of the parts were present in other areas of ecoli and that htey had other functions- to suggest they had, is pure speculation which evidently the Dover trial fully allowed the evos to do, but not the ID folks.

[BlueDragon]

When I said;

“It is not the genes that code for the specific proteins themselves, that induce either, which combination of acetylation, methylation, and phosphorylation, occurs in the octameric complex, now is it?”

Another way to say it could be;

A specific gene itself, wasn't directly influencing the histones, to turn itself "on" or "off".

Nor was it the the histones alone, that be the root cause of transcription on/off determination, be though as they may, a controlling mechanism of achieving this on/off determination.

You are arguing something else..? But no, not really since you say,

"The chemical composition of the complex (phosphorylation of proteins, methylation of DNA, etc) is indeed accomplished by specific proteins coded for by DNA (using the universal code)."

All right...I'm certainly not disagreeing with that...

This very thread is entitled;

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

Looks very much like a "code within a code", to me. Why does this bother you so much?
The histone 'code', it is assumed, isn't independently self generating or modulating (since it didn't create itself, all by "itself" in the first place!)...which would leave us looking for the actual root of determining influences elsewhere in the genome, now wouldn't it?

You argue "universal code".
Ok, fine.

I, and many others, still see coding within coding, regardless of how much it is proclaimed "there is only one [universal] code, there is only one code!"

[CottShop]

[[Google the term and read about it elsewhere if you like!
]]

I did and it’s obvious that evos are trying to insinuate thaT SIMPLE SELF ORGANIZATION CAN RESULT IN TRILLIONS AND TRILLIONS OF HIGHLY COMPLEX IRREDUCIBLY COMPLEX SYSTEMS THAT VIOLATE several laws and statidstics at every step of the way- it’s nothing but another misleading simplification of a biological system that is far far more complex than evos are willing to acknowledge apparently- it is like saying that because a kid can place blocks on top of each other, then that means they are capable of producing not only nutron boms but the equiptment and technology to produce them as well- without any instructions- Actually it’s worse than that- pointing out simple self organizing events and claiming complex and irredicuibly complex systems can violate biological dictates. The idea of self organization equating to specified complexities is almost as rediculous as claiming that because nature can produce simple negative entropies, then evolution ‘could have’ violated the second law at trillions and trillions of ever increasingly complex stages that ALL worked to negate entropy altogether. It just boggles the mind how someone could make such a silly, gigantic leap of faith like that

[GovernmentIsTheProblem]

“it’s nothing but another misleading simplification of a biological system that is far far more complex than evos are willing to acknowledge apparently”

That’s why scientists study the complexity to understand it, but creationists say, its too complex, to boogie man must have made it.

(sigh)

Everything you said is untrue but it’s not worth debating.

Have you ever even met an actual research scientist?

“It just boggles the mind how someone could make such a silly, gigantic leap of faith like that.”

Same to you. Now empirically demonstrate the existence of a designer. ;)

[Twinkie]

I just must get my piano evolved. Perhaps if it sits in the corner long enough, it will evolve into proper pitch.

[js1138]

What has this got to do with IC? As well, ‘tens of 1000’s of years is too short to establish a fossil record’? Since when?

Since the beginning of geology as a science. It is obviously possible for an individual fossil to form in years or decades, but that is not what is meant by the fossil record. Fossilization is rare. If it weren't you wouldn't be able to dig anywhere for all the bones you would find. The fossil record doesn't have the resolution to pick out changes that occur on the scale of thousands of years. As for the evolution of the flagellum, the definition of ID includes the assertion that there are complex objects in living things which cannot be simplified or have parts removed without losing all functionality. The Dover trial gave Behe and the others a chance to establish this under oath in a court of law. Instead, the opposite was established. There are numerous functional flagella that are simpler than E.coli, and there are functional sub-components of the E.coli flagellum found in other bacteria. Irreducible complexity simply doesn't hold up to scrutiny. Now you may wish to argue that the Discovery Institute blew it, and through sheer incompetence, undermined 20 years of work promoting their ideas. I won't argue with that. If I were on your side in this argument, I'd certainly wonder why people contribute money to an organization that has set the movement back legally and politically.