Central Dogma revisited
| October 26, 2009 | Posted by idnet.com.au under Intelligent Design |
This new paper by James Shapiro may be of interest . In it he elaborates on the central dogma of molecular biology. It has become very complex since the old “one gene one protein and all the rest is junk” days.
Here is the summary table.
Conventional expression of the Central Dogma of Molecule Biology:
(DNA ==>2X DNA) ==> RNA ==> Protein ==> Phenotype
Contemporary statements of molecular information transfer in cell:
1. DNA + 0 ==> 0
2. DNA + Protein + ncRNA ==> Chromatin
3. Chromatin + Protein + ncRNA ==> DNA replication, chromatin maintenance/reconstitution
4. Protein + RNA + lipids + small molecules ==> Signal transduction
5. Chromatin + Protein + signals ==> RNA (primary transcript)
6. RNA + Protein + ncRNA ==> RNA (processed transcript)
7. RNA + Protein + ncRNA ==> Protein (primary translation product)
8. Protein + nucleotides + Ac-CoA + SAM + sugars + lipids ==> Processed and decorated protein
9. DNA + Protein ==> new DNA sequence (mutator polymerases)
10. Signals + Chromatin + Protein ==> new DNA structure (stimulated DNA rearrangements; Table 1)
11. RNA + Protein + chromatin ==> new DNA structure (retrotransposition, retroduction, retrohoming)
12. Signals + chromatin + proteins + ncRNA + lipids ==> nuclear/nucleoid localization
SUMMARY:
DNA + Protein + ncRNA + signals + other molecules <==> Genome Structure & Phenotype
You may view the paper here
50 Responses to Central Dogma revisited
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This is weird, I’m a OEC and Your a YEC and I’m the one arguing for a more direct link of causation for God in the formation of a body (humans in particular)
Jeremiah 1:5
Before I formed you in the womb I knew you, before you were born I set you apart;
That scripture should give you some serious pause, since I know YECers take scripture much more literally than most other Christians. And it is hard not to notice that that statement is a direct statement by God of causation.
To outline how reality is constructed a little more clearly:
In conjunction with the mathematical necessity of an “Uncaused Cause” to explain the beginning of the universe, in philosophy it has been shown that,,,
“The ‘First Mover’ is necessary for change occurring at each moment.”
Michael Egnor – Aquinas’ First Way
http://www.evolutionnews.org/2......html#more
I find this centuries old philosophical argument, for the necessity of a “First Mover” accounting for change occurring at each moment, to be validated by quantum mechanics. This is since the possibility for the universe to be considered a “closed system” of cause and effect is removed with the refutation of the “hidden variable” argument. i.e. There must be a sufficient transcendent cause (God/First Mover) to explain the quantum wave collapse to the “uncertain” 3D effect for “each moment” of the universe.
Why, who makes much of a miracle? As to me, I know of nothing else but miracles, Whether I walk the streets of Manhattan,
Or dart my sight over the roofs of houses toward the sky,,,
Walt Whitman – Miracles
Moreover, the transcendent cause must be sufficient to explain the semi-unique effect of 3D centrality witnessed by each individual observer in the universe.
Quantum Mechanics – The Limited Role Of The Observer – Michael Strauss – video
http://www.youtube.com/watch?v=elg83xUZZBs
That the “mind” of a individual observer would play such an integral yet not complete “closed system role”, in the instantaneous quantum wave collapse of the universe to each individual observers “3D centrality”, gives us clear evidence that our “mind” is a unique entity. A unique entity with clearly a superior quality of existence when compared to the “uncertain 3D particles” of the universe.
Genesis 2:7
And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.
Of more importance though, the “effect”, of universal quantum wave collapse to each “central 3D observer”, gives us clear evidence of the extremely special importance that the “cause”, of the “Infinite Mind of God”, places on each of our own individual minds.
Psalm 139:17-18
How precious concerning me are your thoughts, O God! How vast is the sum of them!
Were I to count them, they would outnumber the grains of sand. When I awake, I am still with you.
Tragic, I totally agree with you on second Law concerns (the universe is winding down) and would thus hold that God has chosen in his infinite wisdom to strictly limit His direct intervention in nature, but as to the formation of individual human bodies themselves, I see no way around scripture, Especially for us to literally be considered gods, God Himself must have a some sort of direct hand in creating us, At the very least He must be “conducting the symphony” of our bodies formation though not actually playing any of the musical instruments Himself. follow?
John 10:34-36
Jesus answered them, “Has it not been written in your Law, ‘I said, you are gods’?
Acts 19:26
,,,, saying that gods made with (human) hands are no gods at all.
i.e. I see no way for the secondary causation of nature to be allowed absolute and complete control of a individual human’s creation in the womb.
Tragic You also stated:
“I suppose that you believe God could, if he so chose, cause a bird to grow in the egg of a lizard without causing a change in DNA.”
Well He might have to construct an entirely different universe, built on different physical laws to do it, so that the specific information present in the DNA would unfold in the proper physical manner that would produce a lizard, but yes I have no doubt God could do it.
The main point though tragic is that despite man’s best efforts to produce major morphological change through mutations studies, no such changes have EVER been observed, save for Venter’s work with bacteria in which the entire DNA sequence was transplanted, yet when this is tried in “higher organisms” the onto-epi-genetic information which resides outside the DNA quickly comes into play in body formation. Where is this information? Nobody really knows! It may all reside in the genome. I have no hard and fast empirics to nail it down (I don’t think anyone has any hard evidence as of yet according to Meyer) But since I know reality is constructed a lot more “God friendly: than most people imagine, I put my two cents in for the Theistic position concerning “ontogenetic” information since I saw it was pressing.
You know Ken Miller uses the quantum mechanics argument as well. Funny thing is, if God uses quantum mechanics to “hide” his divine intervention from science, he could affect pretty much everything without ever being detected. In other words, ID is pointless since God pretty much acts in a way that is undetectable. This is why Ken Miller uses that argument.
As for those Bible verses, well, I happen to believe that a human being’s self is more referring to our spirits than our bodies. That God breathes into us the breathe of life I do not doubt, but that is a spiritual thing, not a physical thing.
As for the morphological changes never being observed, this pretty much reinforces the YEC position that the Biblical kinds can vary within certain limits. Try to change an organism beyond those limits, and it loses viability. Since body plans are determined during development, any major change would result in a miscarriage. Most changes that can occur do so by breaking an existing mechanism. Break a big enough one and you will never see the result. To study this will require a more sophisticated method than breaking genes one by one and observing the results.
Well, I don’t know, or really care, what Ken Miller thinks from what little I’ve seen of his work, but for him to say God is “undetectable” in quantum mechanics is the height of denial of reality for quantum mechanics clearly shows that reality IS “supernatural”.
What blows most people away, when they first encounter quantum mechanics, is the quantum foundation of our “material reality” blatantly defies our concepts of time and space. Most people consider defying time and space to be a “miraculous & supernatural” event. I know I certainly do! This “miraculous & supernatural” foundation for our physical reality can easily be illuminated by the famous “double slit” experiment. (It should be noted the double slit experiment was originally devised, in 1801, by a Christian named Thomas Young). (It should also be noted that the most solid indestructible “things” in the atom are the unchanging transcendent universal constants which exercise overriding “non-chaotic” dominion of all quantum events.)
The Miraculous Foundation of Reality – Dr. Quantum – Double Slit & Entanglement – video
http://www.youtube.com/watch?v=vzQuU6FpYAk
As well, the actions observed in the double slit experiment are only possible if our reality has its actual basis in a “higher dimension”:
The Electron – The Supernatural Basis of Reality – video
http://www.youtube.com/watch?v=jv_YQl6XSMM
This may interest you as well:
Proverbs 8:26-27
While as yet He had not made the earth or the fields, or the primeval dust of the world. When He prepared the heavens, I was there, when He drew a circle on the face of the deep,
Euler’s Number – God Created Mathematics – video
http://www.youtube.com/watch?v=0IEb1gTRo74
This related website has the complete working out of the math of Pi and e in the Bible, in the Hebrew and Greek languages:
http://www.biblemaths.com/pag03_pie/
Michael Denton – Mathematical Truths Are Transcendent And Beautiful – video
http://www.youtube.com/watch?v=h3zcJfcdAyE
Mathematics is the language with which God has written the universe.
Galileo Galilei
Nakashima @ 26
The central dogma is:
(DNA ==>2X DNA) ==> RNA ==> Protein ==> Phenotype
That’s what I was referring to, what the OP refers to and what Shapiro is referring to. This has nothing to do with the variation/selection dogma.
You know BA, I appreciate all the information you post, but I often fail to see the relevance.
Well tragic I’m sorry I guess you aren’t interested, at least take a look at the Euler’s Number video, I’m pretty sure that will lift an eyebrow.
BA77:
Actually, one gets the impression that you even don’t care what ID proponents think. Spamming UD with your YEC rant really did not and will not help ID.
Tragic M:
Too true.
@osteonectin
Spamming? YEC rant? Are we reading the same posts?
Look, I haven’t seen you post much here, but I recognize BA77 as a long-time contributor to this site. In my mind, BA77 he has earned the right to express her/his sometimes quirky, but often insightful perspective without this sort of marginalization. With a wee bit of open-mindedness, you might actually learn something from one of her/his posts.
I find the above well-stated, well worth saying, and well worth repeating. The more we dig to the bottom of the “natural” the more “super-natural” the foundation starts to look.
The relevance lies in recognizing that there are plenty of unknowns yet to discover, so it might be too early to put all of our eggs in the DNA basket. I am reminded of the bum who looked for his lost coin beneath the street light even though he dropped it further down the sidewalk. Quantum mechanics involve murky, shadowy things. It is much more comfortable to search in the comparatively illuminated DNA, whether there is any real evidence you’ll find what you are looking for or not.
Moderators: Signal-to-noise ratio could well be too low for this as well as osteonectin’s post, so please feel free to delete both if you deem appropriate.
Tragic @ 30,
I own Steve Meyer’s book Signature In The Cell and I can tell you it is not out of politeness that he says the information needed to form the novelty in body plans might exist beyond DNA. Meyer of course agrees in the super complexity and specification that the digital DNA code displays- but more importantly he says there are new discoveries that point beyond DNA- that there are other perhaps unknown sources of information he deems “hierarchical information filing.” The point and idea is that DNA does not have enough of the right kinds of information within it to produce the specified patterns required for assembly at the higher levels. That is DNA guides a lot of things but it does not guide all of these things together for the bigger goal of assembling the overall body plan. I wish I had the book on hand I would quote it- but I have lent it out- like i do with all of my books- to help educate others and get the word out on these important topics.
This really gets at the most interesting question surrounding ID which is “how did the intelligent designer do it?”
Here is a clip I recommend
http://www.youtube.com/watch?v.....re=related
Basically not only in DNA, but in all of the things that we as human beings design we somehow have this “power” to “will” matter into doing what we want it to through our physical systems. IN other words we have a physical system that allows and helps us to facilitate our thoughts but the origin of our minds does not come from within our physical systems- and hence our power to enact that will upon nature – that is use our intelligence- does not originate from within the system either. So the mystery of how intelligence influences matter and reality is a fundamental mystery.
Even, and especially, at the atomic and subatomic level we have this mysterious complex world of physical constituent parts needed and required for living systems to exist. The origins of the structure and make up of physical reality, at levels as intricate as the subatomic, is hardly one that can be chalked up to natural selection and chance etc. and this is just telescoping down before we can ever get to the specified complexity in DNA and the cell.
Frost:
Well I certainly agree with that. But right now we are talking about body plans, not the mind/body problem. I own and have read Meyer’s book and I seem to remember him discussing that in the book, but I don’t remember any evidence for it. I could have missed it.
Look, the point is that when you have proteins doing almost everything in the cell, and we know that DNA codes for all proteins, then we know that the information for everything required for life is in the DNA. And I don’t think Meyer would dispute that. Now if you want to start talking about some “hierarchical” information that determines body plans, well why not start talking about car accidents helping to determine body plans and qualifying as “hierarchical information”? lol. I just don’t see that there’s really any justification for saying something like that at this point, especially when our knowledge about how the information in DNA works is so incomplete.
And I particularly don’t like the argument, “Well this organ is shaped like this in this animal but shaped like that in that animal, so God must have done it.” One of Meyer’s recurring themes is that his design argument is not an argument from ignorance nor is it a God-of-the-gaps argument. It’s an argument from what we do know, not what we don’t.
When I was a kid, everyone and their mom told me I was the spitting image of my dad. Seeing as how the only thing I ever got from my dad physically is a single sperm, why do you think I look like him? lol.
It seems to me that almost everything in a cell carries some sort of specific information that is used in one way or the other.
The trivial example is the nucleotid order of the DNA, however the various states of proteins themselves contain plenty of information about the stages of the processes they participate in which affect what other parts of the cell do. I could continue with the concentration of certain organic molecules, hormones, the pH etc.
Now to me a cell looks much like an multitasking computer, where the hard disk is the DNA, but the RAM and the registers of the processors are the actual states of the various structural, enzymatic and messenger molecules. The processes can directly or indirecty query the information on the hard disk sometimes even modify a few files on the hard disk, but also get plenty of data from the environment.
In this sense there is no hierarchy of the information in the cell, just different types of information performing different types of tasks.
Right, so the DNA as database analogy fits. Since proteins come from DNA, anything a protein does can be seen as ultimately a query to the DNA database.
Rupert Sheldrake’s theory of morphic resonance closely relates to this. He believes an inherited field phenomenon transmits the data of form and development from generation to generation, in addition to the information in the genes. He also links this to the mystery of the origin of inherited instinctual behavior (inherited beneficial “habits” which can mysteriously spread in a population). Darwinism has major problems in explaining this, as discussed in another thread. Interestingly, Sheldrake so outraged mainstream biologists the editor of Nature deemed his first book a prime candidate for burning. This sounds a little like the reaction to ID.
Mr Mishap,
I had sever connectivity problems yesterday, and it appears a response of mine has gone missing.
The ‘Phenotype” that the Central Dogma includes is the tie into the variation/selection cycle. The Central Dogma tells you what goes on at the level of the cell in its workings. Variation/selection tells you which cells get to work in time t1, based on time t0.
TragicMishap, You may appreciate this article that came out recently on science daily:
Tragic @ 41,
here is a clip talking about it a little more in depth-
The question is about “ontogenetic” information. And the point is that the coding information in DNA is understood to produce certain parts but how those parts are matched to each other to build the overall body plan is still a mystery and probably cannot reside in the DNA because the DNA does not code for the larger system but merely makes the parts which eventually unfold to build the larger body plan.
And my point that you referred to as the “mind matter interface” was regarding the “philosophical” realization that “if” the information in DNA cannot account for the total design of these super complex specified body plans and structures, then we must leave open the door to the possbility that the information may not reside within the systems at all but perhaps somewhere else. And really this is what Steve Meyer is saying about the origin of DNA in gernal- that the information we find there must come from somewhere else- and ultimately we cannot appeal to the system to explain it’s own origin simply due to what we obviously know about its super complexity and the high cost of resources needed to purchase it’s evolutionary origin.
So my point is that the fundamental question at the higher ontogentic levels as well as the micro protein levels is essentially the same mystery which is “where does the information come from that structures the material coding that facilitates the development of these systems?”
Obviously, it is certainly reasonable and important to continue research into how these systems operate and arise but the information problem seems, at least at current, to escape any material explanation of their origin- and this conclusion or thesis is one that needs to be heard.
Excuse me- the video I was referring to about the ontogentic information is here
http://www.youtube.com/watch?v.....re=related