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]

You feel safe moving the goalpost back to the origin of life.

[metmom]

There are a number of things we can't make happen on purpose. Hurricanes, volcanoes, earthquakes, plate tectonics.

I can't make your lotto number come up, but people do win lotto.

Yet. Some day, when we have enough knowledge and enough power, those things will be possible, just like splitting the atom. But you know where that will lead. It won't support the idea that stuff like that happens by accident.

[CottShop]

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

nope not at all, and I hope you are not arguing that ALL the parts did have other useful uses despite a complete lack of evidence that it ever did. I am arguing that ALL the parts were needed fully formed and ready for assembly by a designer at a point of creation- While you can accuse us of having faith in a Creator Causation, I as well can accuse you of having faith that, despite the complete lack of evidence to support it, ALL the parts of the motor MUST have had other useful functions PRIOR to final naturally caused assembly

[Alamo-Girl]

Thanks for the link!

[CottShop]

Those aren’t all goalpost IC examples- I do however feel safe claiming that ANY MACROEvolution is biologically impossible

[metmom]

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.

Realistically, would you expect human and dinosaur bones to be co-mingled if they lived at the same time? Sure, they decide to build their little village right in the midst of a clutch of dinosaurs. That makes sense. /s

[js1138]

And you can demonstrate that as a fact how?

Because the intelligent design hypothesis has been around for more than two hundred years without producing anything more than the assertion that some unnamed entity or entities did some unspecified thing or things somewhere at some unspecified time or times using unspecified means for unspecified reasons, resulting in a fossil record and genome structure that looks exactly like what we would expect if all living things are related by descent.

There is nothing in the history of intelligent design that indicates any curiosity about the nature of the design or the design process. It's all stamp collecting.

[js1138]

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.

One has to wonder why an organization that can spare 27 million dollars to build a museum could spare a few dollars for field research.

Besides, the discovery that strata can be reliably identified by their fossils was made by a businessman, not a scientist, and before Darwin was born.

[CottShop]

[[Because the intelligent design hypothesis has been around for more than two hundred years without producing anything more than the assertion that some unnamed entity or entities did some unspecified thing or things somewhere at some unspecified time or times using unspecified means for unspecified reasons, resulting in a fossil record and genome structure that looks exactly like what we would expect if all living things are related by descent]]

First off- that is not all ID has accomplished- secondly, you have just stated your preferred opinion about the fossil record- not a scientif fact- ID expects to find in the fossil record species that have MICROEvolved and to find descendents of KINDS and that is what we find in the record

[[There is nothing in the history of intelligent design that indicates any curiosity about the nature of the design or the design process.]]

Wow- That’s pure denial of the facts- The facts of ID speak for themselves and directly refute your claim- The whole premise of ID is to study the nature of design just as ANY forensic scientist would do, and a logically and entirely valid conclusion CAN be made that presents the plausibility of a designer and is just as valid as any archeologist who comes to the logical conclusion that when 10,000 intricately carved and molded urns with designs are uncovered that a designer made them and that it is logically impossible for nature to have randomly formed them through a mistake driven mechanism

[Coyoteman]

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.

You seem to know very little about science and scientists, and what they are finding.

How many bone discoveries hit the newspapers before they are investigated by scientists? Quite a few, actually. Look at the famous Manis mastodon site in Washington. The first thing archaeologists knew about that one was a picture in a newspaper. Happens all the time.

This makes a complete shambles of your claim that archaeologists are destroying the evidence. A huge number of archaeological sites are discovered by bulldozers during construction, and any dinosaur or other huge bones would be common knowledge statewide or nationwide within a day.

Ever think about what dinosaur bones would look like if they were truly about 4350 - 6000 years old? They would be all over the place! And huge! And all you would have to do to find them would be to go look in 4350 year old dirt! And that is as common as, well, dirt.

Realistically, would you expect human and dinosaur bones to be co-mingled if they lived at the same time? Sure, they decide to build their little village right in the midst of a clutch of dinosaurs. That makes sense. /s

Even for large dinosaurs, some parts would be easy to hack off and drag back to the residential bases or hunting sites. Look at the number of elk and other large animal bones in archaeological sites. But for very large animals, such as buffalo, mammoth and mastodon, the campsites move to the kill sites, and butchering is done in place. This leaves a lot of very obvious evidence behind.

Your problem is that you are arguing from an overriding disbelief in evolution and evolutionary sciences, and you are willing to take the silliest assumptions and the flimsiest data as accurate when they support your beliefs. And you are eager to discount solid, well-supported science because of your a priori beliefs.

The real world doesn't work that way. Nor does science.

[CottShop]

Contrary to your assertion that ID scientists are “God dun did-it” blinder bound scientists:

Contents [hide]
1 Empirical research - current
1.1 Biosteganography
1.2 Reverse engineering
1.3 Centrioles
1.4 ID-innovation detection - Commercial Applications
1.5 Evolvability
1.6 Haldane’s Dilemma
1.6.1 Mutagenesis
1.6.2 Morphogenesis
1.7 Privileged Planet research
1.7.1 Gonzalez’s lunar research proposals
1.8 Neuroscience
1.9 Protein evolution
1.10 ID Metrics
1.10.1 Ontogenetic depth and the ontogenetic network
1.10.2 Specified Complexity
1.11 Genetics
2 Conceptually related
2.1 Junk DNA
2.2 Empirical demonstrations of causal adequacy/causal specifity.
2.3 Design Receptivity, design input, and information receptivity
2.4 Protein folding
3 Empirical research - potential
3.1 Irreducible Complexity
3.2 General Purpose Programmable Systems
4 See also
5 External links
6 Searches
6.1 Centriole
6.2 Empirical ID Research

http://www.researchintelligentdesign.org/wiki/Empirical_ID_research

R e s e a r c h I D . o r g

http://www.researchintelligentdesign.org/wiki/Main_Page

Intelligent Design Research Lab Highlighted in New Scientist

http://www.evolutionnews.org/2006/12/intelligent_design_research_la.html

The International Society for Complexity, Information, and Design (ISCID)

http://www.iscid.org/

[CottShop]

one point I want to make here- ID is not a religious beleif- it is a scientific dissagreement with Darwinian Macroevolution hypothesis.

ID doesn’t strive to ‘prove God’ or to even show God or any entity, it simply detects Design just as any foresnic scientis would, and it proposes the idea that life is BETTER explained by the idea that an entity was the causation of IC and specifid complexity, and it strives to ALSO scientifically point out hte impossibilities of the old model of MACROEvolution. A complete atheist can and often do think that there is enough design and complexities in nature to warrent a more serious concideration to the fact that there might just be a designer behind the designs

ID studies patterns that give high probabilities of there being a designer- that’s all. The public’s view of ID is unfortunately skewed by both biased and negative press and by biased and negative posters such as a few on this forum

[allmendream]

Your dim recollection must have been very dim if you thought it was a contradiction of the Universal Code of Molecular Genetics. Nor do I refer to Dr. Rice et.al. as the end all be all of genetic research in regards to every aspect of gene expression. However what they study is GENE EXPRESSION, i.e. if a gene is on or off. The actual code is always the same within a living organism, and if you can find a contradictory example your Nobel prize awaits.

[js1138]

Researching the capabilities and theoretical limits of evolution, mutation, and selection from a design perspective.
Ralph Seelke, PhD
John C. Sanford, PhD
Michael Behe’s proposals of Irreducible Complexity (IC) state that biological structures which show IC cannot evolve from mutations and undirected biological processes. Dr. Behe claims that the bacterial flagellum is one such biological component that exhibits IC. In order test Behe’s proposal in the laboratory, scientists are using gene knock-out methods to form a type III system with a missing flagellar component and see if the bacteria, on their own, can assemble the TTS into a functional flagellum. If the flagellum is not irreducibly complex, bacteria should be able to develop one through mass breeding of the bacteria with the disabled flagellum.

That's very interesting. At the Dover trial Behe was asked if he or anyone in the design movement had actually performed this experiment, or any equivalent experiment, and his answer, under oath, was no.

On the other hand, experiments similar to this one, but less ambitious, have been performed, with positive results.

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.

I suspect that the knockout technique will be used more and more in research.

[js1138]

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 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.

[editor-surveyor]

"It will not help creationism one bit."

But then it isn't creationism that needs any help; its a perfect fit for the real world. Its evolutionism that is beyond lifesupport. Its failure to mesh with the abundant natural repudiation of its premises has left it in shambles.

[editor-surveyor]

“Someone wrote the code.”

Space aliens?
Sounds like a Kucinich theory.

The space alien part does anyway. If you head the other way at line one, it all makes perfect sense.

[editor-surveyor]

” I dismiss it because it is unconvincing, science-wise. “

Except in the lab and in nature, at various levels - from the molecular to the system.

Plenty of organization in nature, just none of it is self originated. Its that preponderance of patterns at the most basic level that makes a belly laugh out of 'naturalism.'

[BlueDragon]

"The actual code is always the same within a living organism, and if you can find a contradictory example your Nobel prize awaits."

If I could remember what thread it was that made mention of how proteins would vary, depending upon other genes being present, or not, I still wouldn't be up for the "prize", since it wasn't my research in the first place. But-- "contradictory examples" as you put it, have been brought out, not as per coding itself, but as to result.
That, I do remember. Just not exactly how, though if memory serves, it involves subtle enough differences in the proteins which result, to have escaped notice for a long while. Beyond transcription being simply turned "on" or "off".

But nevermind that for now,
getting back to this present article of discussion;
I found the webpage at the Rice lab to be very well put together. Good information, put together in a clear and concise manner.
Did you closely examine the illustrations and renderings? That part that ran down the right side of the page was almost as interesting as the ones to the left...
"The complexed histones are encircled by DNA, shown as light gray strands".

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?

That points to other portions of coding. Which demonstrates overlapping "code". Otherwise, how does the chemical composition of the complex vary, and conversly, is controlled through natural cell processes?

From the abstract;

Although the structure of the nucleosome core is known at near-atomic resolution, even the most fundamental information about the organization of nucleosomes in the fibre is controversial.

Are you still certain my comments [which you claimed were errroneous] are completely wrong?

It beginning to look here, like a case of differing definitions and word usage, at least in part.

Overall, there certainly does appear to be, code within code --- or to put it another way, overlapping code resulting in interactions that convey information.