Central Dogma revisited

_{Mark

October 26, 2009

Intelligent Design}

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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

Comments

I'm sure there are many diseases tied to genetic defects which we do not know what those genes actually do.tragic mishap_{October 26, 2009
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So you are saying that God forms every person's body plan individually in the womb? What does this say about birth defects like a cleft palate, spina bifida, missing limbs, etc, etc?tragic mishap_{October 26, 2009
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Well Tragic, I have my own belief from where our body plans came from: Psalm 139:15 My frame was not hidden from You, When I was made in secret, And skillfully wrought in the depths of the earth; Jeremiah 1:5 Before I formed you in the womb I knew you, before you were born I set you apart; We could go into the quantum mechanical basis of reality, ,,, reality based to each individual consciousness, to further solidify this "postulation", but I'll let these scriptures stand for now, since you cannot refute my claims based on any DNA mutation studies.bornagain77_{October 26, 2009
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Well Tragic, I believe the information for the body plan resides transcendentally of any material basis: I have my on belief from where my body plan came from: Psalm 139:15 My frame was not hidden from You, When I was made in secret, And skillfully wrought in the depths of the earth; Jeremiah 1:5 Before I formed you in the womb I knew you, before you were born I set you apart; We could go into the quantum mechanical basis of reality, to each individual human consciousness, to further solidify this "postulation", but I'll let these scriptures stand for now.bornagain77_{October 26, 2009
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Yes Stephen Meyer said that it's entirely possible that "ontogenetic" information is not in the DNA, but he did not give another possibility. The fact is that an organism develops from a single cell with a single set of DNA. From there it grows into many cells, including different tissues and organs and it's specific body plan. Let's say you think the information is actually coming from the mother's body, well, where does the information in the mother's body come from?tragic mishap_{October 26, 2009
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Well, bornagain, tell me where the information is located, if not DNA. You don't know either. Until you show me some other possible information carrier, I think it's perfectly reasonable to believe DNA is where it's at.tragic mishap_{October 26, 2009
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Astonishing DNA complexity update Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes. http://creation.com/astonishing-dna-complexity-updatebornagain77_{October 26, 2009
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Encyclopedia Of DNA: New Findings Challenge Established Views On Human Genome:
The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another.
bornagain77_{October 26, 2009
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Tragic, You claim he is wrong? Fine tell me exactly where the body plans are encoded in the DNA! Mutational studies to DNA surely have not revealed any such "Genetic Reductionism" of Body Plans, HOX genes not withstanding. For you to claim that he is wrong with no empirical evidence to back you up is not the way to go in refuting his claim... In fact this inability to find the Body Plans in the DNA is what, I believe, is one of the driving forces behind the emerging field of epigenetics. (Stephen Meyer uses another word, I believe "ontogentic", in the video I listed)bornagain77_{October 26, 2009
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Look, the central dogma holds, regardless of all this stuff Shapiro is talking about. DNA still goes to RNA, still goes to protein. Every last one of those equations contains one or more of those three ingredients, and RNA and protein both ultimately come from DNA. Epigenetics is the study of inherited characteristics that do not change the sequence of DNA, but what are the epigenetic changes being discovered? Various modifications of DNA that do not change the sequence but modify it in other ways. Methylation and a few other chemical alterations of specific bases, the histone code (which depends on enzymatic alterations of histones, enzymes coded for by DNA) all depend upon DNA and change the way DNA is accessed. It serves no purpose to deny that DNA holds the information. It's entirely possible and I think quite likely that DNA holds the information for body plans. It's certainly capable of that. Arthur Jones compares the information on CDs to the information in DNA. Well, we know that DNA contains the information required to reproduce itself. That's already one difference between it and the info on a CD. We already know that DNA encodes the information required to build many structures in the cell that are far more complex than CD players. We know that DNA encodes the information for RNA polymerases, which transcribe DNA to RNA. We know DNA encodes all the information required for transcription. So we do know that Jones' analogy is wrong. He claims papers from the 1950s saying, "We already knew this was wrong in 1950". Well now we know he's wrong.tragic mishap_{October 26, 2009
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Um, I agree, but what does this have to do with the topic? The primary finding of the ENCODE project was that almost all DNA is being transcribed to RNA, not just genes.tragic mishap_{October 26, 2009
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Tragic, the paper that leads this thread, in particular, precludes a Darwinian scenario since it gives a fairly clear view of the extreme level of poly-functional complexity being dealt with in life,,,to illustrate I will repost what I just submitted on another post: The primary problem that poly-functional complexity presents for neo-Darwinism is this: To put it plainly, the finding of a severely poly-functional/polyconstrained genome by the ENCODE study has put the odds, of what was already astronomically impossible, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face when I say genomes are poly-constrained to random mutations by poly-functionality, I will use a puzzle: If we were to actually get a proper “beneficial mutation’ in a polyfunctional genome of say 500 interdependent genes, then instead of the infamous “Methinks it is like a weasel” single element of functional information that Darwinists pretend they are facing in any evolutionary search, with their falsified genetic reductionism scenario I might add, we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford. S A T O R A R E P O T E N E T O P E R A R O T A S Which is translated ; THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS. This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation. This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations. The puzzle I listed is only poly-functional to 4 elements/25 letters of interdependent complexity, the minimum genome is poly-constrained to approximately 500 elements (genes) at minimum approximation of polyfunctionality. For Darwinist to continue to believe in random mutations to generate the staggering level of complexity we find in life is absurd in the highest order!bornagain77_{October 26, 2009
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I'm not a Darwinist. I'm an intelligent design theorist. A Darwinian paradigm can use random variations in other forms of inheritance besides DNA. It was based on random variations long before the discovery of DNA. ID does not require denying that DNA contains all the information necessary for life, nor does Darwinism depend on that.tragic mishap_{October 26, 2009
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Tragic: "These equations show that DNA is the first axiom upon which all life processes are built." But apparently not the axiom from which overall architectural bodyplans themselves are built: Intelligent Design - The Anthropic Hypothesis: Excerpt: body plans are not even encoded in the DNA code in the first place. This inability of body plans to be reduced directly to the DNA code is clearly shown by Cortical Inheritance. Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video Part 1 http://www.youtube.com/watch?v=5JzQ8ingdNY Part 2 http://www.youtube.com/watch?v=o1bAX93zQ5o This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show "exceedingly rare" major morphological effects from mutations to the DNA code. Hopeful monsters,' transposons, and the Metazoan radiation: Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable "hopeful monsters" render these explanations untenable. Paleobiologists Douglas Erwin and James Valentine This includes the highly touted four-winged fruit fly mutations. ...Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection." - Jonathan Wells Darwin's Theory - Fruit Flies and Morphology - video http://www.youtube.com/watch?v=hZJTIwRY0bs If that wasn't enough, the Human Genome Project really put the last nail in the coffin for "Genetic Reductionism": DNA: The Alphabet of Life - David Klinghoffer Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell's building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn't there. Instead, "It is as if the 'idea' of the fly (or any other organism) must somehow permeate the genome that gives rise to it." Higher Levels Of Information In Life - Stephen Meyer - video http://www.youtube.com/watch?v=HavmzWVt8IU this is also of interest: Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005: The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species. Amazingly, this evidence is just brushed aside as insignificant by materialists since some of the proteins differ by only a few amino acids. Yet, since the "1-Dimensional" genetic code is shown to not even code for body plans in the first place, and the proteins are at least 3-Dimensional in their configuration, as the bodies of the chimps and humans are 3 dimensional, then this shows the 80% difference in proteins should at least carry more weight of consideration, over the genetic code, when considering molecular similarities of the 3-Dimensional body plans. http://lettherebelight-77.blogspot.com/bornagain77_{October 26, 2009
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I think a better analogy is that DNA is a database. Anything that happens in the cell is in one way or another, dependent upon accessing and using the information in that database. These equations show that DNA is the first axiom upon which all life processes are built.tragic mishap_{October 26, 2009
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What I’d like to know is where the blueprint or architecture is stored. Who or what directs the cell?
Hi vpr, Here is one explanation.Arthur Hunt_{October 26, 2009
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I think this quote nails it: Revisiting The Central Dogma (Of Evolution) In The 21st Century - James Shapiro - 2008 Excerpt: Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations or replication errors. This view has had to change with the realization that the maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules. Genetic change is almost always the result of cellular action on the genome (not replication errors).bornagain77_{October 26, 2009
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From what I've read it's a better analogy to think of DNA as more a recipe than a blueprint. A blueprint is a one-to-one representation of what the final structure will be whereas a recipe is not. Admittedly, DNA is a hugely complicated recipe! And the analogy doesn't quite work but it's better than blueprint. If DNA were a blueprint then identical twins would turn out to be identical and if you've ever been around a pair of identical twins you know that there are differences, sometimes very small and minor, but differences nonetheless.ellazimm_{October 26, 2009
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Thanks for the paper idnet, excellent information is in it, but it seems Shapiro seems to think information can be had on the cheap and magically self generate,,, Is that right? Am I reading him correctly?bornagain77_{October 26, 2009
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What I'd like to know is where the blueprint or architecture is stored. Who or what directs the cell?vpr_{October 26, 2009
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