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 are simply lying. Every phenomenon or process required for evolution is routinely observed and manipulated by experiment.

The only assumption being made is that phenomena and relationships observed under controlled conditions can be generalized to the world at large.

Exactly the assumption codified by Newton in his Principia.

[CottShop]

[[So where would baraminology systems suggest looking for intermediate fossils, and on what basis?]]

The same place Cladistic scientists would suggest looking for htem IF by itnermediary you of course mean the step-wise patterns found in discontinuity. The predictions for intermediaries is no different in Baraminology than in continuity models.

If we’re talking Transitionals of course, then Baraminology doesn’t predict them because they don’t exist :)

[[I know of no one fimaliar with bioinformatics, including skeptics like Behe, Dembski, and Hubert Yockey, who have any doubts about common descent]]

Their personal unsupported beleifs don’t concern me- I’m ONLY concerned with true objective science- not theoretical presuppositions unsupported by hte evidence.

[[What do you mean by unsupportable? It strikes me that a theory published in 1859 that accurately predicts molecular evidence being found in 2008 is a pretty robust theory.]]

That isn’t very robust- anyone could have predicted molecular evidence would be found, what we’re concerned here with however is the ‘interpretation’ of that evidence and what it means. It supports discontinuity, however, continuity proponents once again MUST rely on Presuppositions and assumtpions that have no support in the actual factual evidence.

[CottShop]

[[You are simply lying. Every phenomenon or process required for evolution is routinely observed and manipulated by experiment.]]

Lying? lol- no sir- you are lying- MICROEvolution is observed and tested- NOT MACROEvolution Infact testing has proven just the opposite- that MACROEvolution is biologically not possible. Again we go back to the NEW information and NEW organs systems etc. Genetic variation is nothign but MICROEvolution—We’re going in circles here- I stand by what I’ve said because quite frankly it relies on factual observable science and NOT on assumptions and unsupported pressupositions. MACROEvolution is STILL a theoretical Pressuposition and nothign more.

[CottShop]

[[You are simply lying. Every phenomenon or process required for evolution is routinely observed and manipulated by experiment.]]

Let me just expand my response to more fully address your accusation- Words matter JS- Every phenomena and process has NOT been observed- MACROEvolution requires NEW ifnormation laterally transfered between different KINDS so that one kind receives NEW non-species specific information This has NOT been observed in hte wild EXCEPT between the same KINDS only htrough lab generated gentic manipulation and under ideal conditions conducive to the manipulations can interspecies lateral gene transference occure AND, and this is important, AND, the species receiving the leteral infromation has several layers of built in protections preventing it from perverting it beyond species specific upper limits- AS WELL, the simple transference material does nothign to move the species beyond it’s own KIND, it simply becomes a host and correction mechanisms immediately kick in to begin correcting hte mistake.

[Coyoteman]

I stand by what I’ve said because quite frankly it relies on factual observable science and NOT on assumptions and unsupported pressupositions. MACROEvolution is STILL a theoretical Pressuposition and nothign more.

And once again you are wrong.

Macroevolution is species-level change. Everyone agrees with that.

And there are some living examples of that change. They are called ring species. And the really neat thing about ring species is that the transitional or intermediate forms are still living and can be readily examined!

Now I know you can't accept any of this--it goes against your religious belief, but don't try to con others into thinking you either know anything, or care, about science. Its dishonest.

Now, to ring species:

Ring species provide unusual and valuable situations in which we can observe two species and the intermediate forms connecting them. In a ring species:

• A ring of populations encircles an area of unsuitable habitat.
• At one location in the ring of populations, two distinct forms coexist without interbreeding, and hence are different species.
• Around the rest of the ring, the traits of one of these species change gradually, through intermediate populations, into the traits of the second species.

A ring species, therefore, is a ring of populations in which there is only one place where two distinct species meet. Ernst Mayr called ring species "the perfect demonstration of speciation" because they show a range of intermediate forms between two species. They allow us to use variation in space to infer how changes occurred over time. This approach is especially powerful when we can reconstruct the biogeographical history of a ring species, as has been done in two cases. Source

See also: Ring Species: Unusual Demonstrations of Speciation, by Darren E. Irwin, for a longer discussion of this topic.

[js1138]

You can use argumentum ad CAPSLOCK all you want, but you are misinformed. There is no one writing about information theory who doubts common descent. This includes ID advocates like Behe and Dembsky, and the guy who literally wrote the book on bioinformatics: Hubert Yockey.

[GodGunsGuts]

From the article:

“Histones are a group of highly evolutionarily conserved proteins that play a critical role in the proper packaging of DNA within the eukaryotic nucleus. DNA (~146 bp) along with the histones (two each of histones H2A, H2B, H3 and H4) form the fundamental repeating subunit of chromatin, known as the nucleosome (Figure 1). Since the human genome is composed of around three billion bases of DNA (3,000,000,000 bp), it is likely that there are tens of millions of nucleosomes within a single human nucleus. Because of their tight association with DNA, it has long been postulated that the histones directly participate in many different DNA-templated programs including transcription, replication, recombination and DNA repair. But there is a conundrum: if each tiny histone protein contains the same exact amino acid sequence as the other millions of histones in the nucleus, how could they possibly direct distinct and, sometimes, opposing nuclear processes (i.e. transcriptional activation versus inactivation)? One possible answer to this question has gained widespread acceptance within the last decade – the histone code.”

Again, Allmendream’s argument is not with us, but with his fellow evolutionary scientists. If Allmendream is saying that somehow the DNA/Universal Code directs the myriad of functions of millions and millions of histones all by its lonesome, then the burden is on Allmendream to show how the DNA/Universal Code accomplishes this incredible feat. Let me underscore this point. Just describing what happens won’t cut it. He needs to specify HOW the DNA/Universal Code directs the “distinct and, sometimes, opposing nuclear processes” of the histone proteins. That means, Allmendream needs to translate the specific portions of the Universal Code such that he can explain the specific actions and functions of histone proteins. If Allmendream cannot do this, then his insistence that there is only one code operating is pure conjecture. Do computers operate on single code? No, they operate on many codes (ie binary, windows, word, etc)...in other words computers have codes upon codes upon codes. And computers are no match for the sophistication of the nuclear processes of even a single cell.

[CottShop]

I only use Cps lock to streess the key words that are most pertinent to the discussion- don’t infere anythign else from them.

Again- I don’t care what their unsupported theoretical pressupositions are- again- I care only about facts- not assumptions on this issue. They could beleive we all came from icecream if they like- their facts are all I’m itnerested in.

[[Macroevolution is species-level change. Everyone agrees with that.]]

You are welcome to your opinion, but that is simply wrong- there is absolutely NO evidence for MACROevolution- none- only for MICROEvolution

[[And there are some living examples of that change. They are called ring species. And the really neat thing about ring species is that the transitional or intermediate forms are still living and can be readily examined!]]

No- I’m sorry- but htis is nothing more than the discontinuity in the KINDS and not a NEW species KIND.

[[Now I know you can’t accept any of this—it goes against your religious belief, but don’t try to con others into thinking you either know anything, or care, about science. Its dishonest.]]

Wow- getting petty now are we? I expected more from you- but alas- it’s a common evo arguing tactic- so I guess I should have seen that coming.

As for your ring species (Just slight MICROEvolutionary adaptations of information ALREADY present) this has been refutted quite thoroughly- here’s one link

http://www.answersingenesis.org/creation/v16/i1/bird.asp

Now, either we can dissagree while being civil, or I can ignore any further posts from you as all you’ve presented so far are examples of MICROEvolution and are tryign to intentionally confuse the two totally different terms of evoltuion. You’ve also demanded precision while engaging in obscurities and generalities yourself. I give you precise explanations so that thgere won’t be any confusion, yet you ignore the precision and insist on labelling one term, MACROEvolution as something it is not- it’s a distinct biological hypothesis that has absoltuely no support in the records or testings for over 150 years and billions and billions of dollars spent trying to show it. The fact is that it can’t be shown, and to counter this biological impossibility, folks repeatedly try to insinuate that hte more simple process of MICROEvolution is the same thing. While you are welcomed to your preferred beleive, don’t expect others to accept such a simplification of the much more complex process of MACROEvolution. Genetic variation is indeed fascinating and can produce some wild subspecies, but trying to pass off a ring species as a NEW KIND is simply dishonest. I’ll be bakc later, but I really don’t expect anythignbmore than the same insinuations to which I’ve already replied.

[CottShop]

I’m sorry- didn’t notice that it was Coyoteman trying to pass off Ring Species as NEW species- My response should be directed to him on that issue- not you.

[js1138]

Do computers operate on single code? No, they operate on many codes (ie binary, windows, word, etc)...in other words computers have codes upon codes upon codes.

Let's hear it from Mr. Computer Science.

Are you suggesting that the executables of programs like Word are distributed in some form other than binary machine code?

There are, of course, script languages, but CPUs do not read scripts except as a byproduct of executing a script interpreter.

[Coyoteman]

I’m sorry- didn’t notice that it was Coyoteman trying to pass off Ring Species as NEW species- My response should be directed to him on that issue- not you.

That's OK. We're used to your mistakes.

[js1138]

No, Coyote did not try to pass off anything. He used ring species as an example of observable speciation in progress, complete with intermediates.

[Doc Savage]

Thank you Dr. Dan for asking! I, the Hildebeast, otherwise known as Hitlery, will explain.

Excuse me for just a moment Dr. Dan, I'm starting to tear up and I want the reporters to be sure and get closeups for the nightly news! There, that's better! Now back to your question regarding Huma, I mean histone!

Excuse me again Dr. Dan, I can't help it. I just have this overwhelming urge to cry. I hope they can get a good shot of this for my ads in South Carolina. Ok, I'm better now. Now then, your question on humping, I mean histone.........blubbber,blubbber, blubbber!

[GodGunsGuts]

That doesn’t change the fact that you have codes layered on top of each other, each with a different purpose and function. Do you deny this? In fact, if DNA is anything close to the biological equivalent of binary, it may turn out to be the least sophisticated code of all.

[CottShop]

Yes he did- He insinuated that speciation- which is nothign more than MICROEvoltuiopnary changes is the all that is required for MACROEvolution, and that ios flat out wrong for hte reasons explained i nthe link I provided. Ring Species are nothign more than subspecies changed by MICROEvolutionary genetic mistakes- nothign more- Baraminology accounts for such speciation within the KINDS, Nothign biologically surprising about them as they follow genetic ‘rules’ as it were that fall well within the KINDS parameters.

[GodGunsGuts]

I have never seen any evidence for evolution whatsoever. The only thing that is verified by the available evidence is a starting point (ie cambrian explosion), then devolutionary specialization. Do you know of any examples of evolution from tracing a simple to a more complex one? I have honestly never heard of any evidence that demonstrates such a thing.

[js1138]

Define simple to more complex.

[Coyoteman]

Now, either we can dissagree while being civil, or I can ignore any further posts from you as all you’ve presented so far are examples of MICROEvolution and are tryign to intentionally confuse the two totally different terms of evoltuion. You’ve also demanded precision while engaging in obscurities and generalities yourself. I give you precise explanations so that thgere won’t be any confusion, yet you ignore the precision and insist on labelling one term, MACROEvolution as something it is not- it’s a distinct biological hypothesis that has absoltuely no support in the records or testings for over 150 years and billions and billions of dollars spent trying to show it. The fact is that it can’t be shown, and to counter this biological impossibility, folks repeatedly try to insinuate that hte more simple process of MICROEvolution is the same thing. While you are welcomed to your preferred beleive, don’t expect others to accept such a simplification of the much more complex process of MACROEvolution. Genetic variation is indeed fascinating and can produce some wild subspecies, but trying to pass off a ring species as a NEW KIND is simply dishonest. I’ll be bakc later, but I really don’t expect anythignbmore than the same insinuations to which I’ve already replied.

More obfuscation.

Kind is a biblical term, not a scientific one. Macroevolution is clearly defined as species-level change. Check it out! (Avoid the creationist sites though; they lie.)

Ring species deal with species, not kinds, or NEW KINDS (whatever they are). And as an additional benefit, ring species preserve all of those "transitionals" or "intermediates" that creationists claim could never exist. No wonder you don't like ring species!

And the link you provided to Answers in Genesis is worthless. They are an avowed anti-science, pro-creationist website. To write for them you must agree to their Statement of Faith. (For the lurkers, please take a look at this and ask yourselves if agreeing to this kind of a statement seems consistent with doing science. Most all of the large creationist organizations have such a statement required for membership. One even requires that that statement be renewed each year!)

Not surprisingly, given the Statement of Faith required for AiG membership, their article "refuting" ring species, which you linked to, deals with religion, not science. For example:

Many have been misled into thinking this is evidence for evolution and against biblical creation. However, some thought reveals otherwise. The key to understanding this is to consider the vast amounts of complex information in all living things, coding for functionally useful structures and processes.

Creation as described in the book of Genesis implies that virtually all the genetic information in today’s world was present in the beginning, contained in separate populations (the original created kinds).

This information would not be expected to increase, but could decrease with time—in other words, any genetic changes would be expected to be informationally downhill. Source

Get back to us when you have something that actually argues against ring species or any of the other well-established principles in science.

[CottShop]

there are none that don’t involve assumptions unsupported by the evidence. The problem is that those who support the cladistic taxonomy try to pass off speciation, or any change in genetic information as MACROEvolution, and biologically, it is not. Furthermore, pracvtically every case of speciation involves a loss of information or a suppression of information. Evos count enhancements of information that is already present as MACROEvolution, and again, this falls far short of hte necessary NEW ifnormation necessary fro true MACRO- However, KINDS remain KINDS no matter the amount of speciation- there is no evidence linking dissimilar kinds together- Transitionals are absent. Rarity of fossils is a lame excuse for the lack when we should be inundated with transitionals, just as Darwin himself lamented

[GodGunsGuts]

We have never observed, either in real life, or in the fossil record, any line leading from simple organisim to a more complex organism. For instance, there is no evolutionary line from fish to man (as evolutionists would have us to believe). Instead, what we find are organisms that appear quite suddenly in the fossil record, and the ones where we can trace them up to modern times devolve (in most cases only slightly) from their original kinds.