Intelligent Design

Central Dogma revisited

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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

50 Replies to “Central Dogma revisited

  1. 1
    vpr says:

    What I’d like to know is where the blueprint or architecture is stored. Who or what directs the cell?

  2. 2
    bornagain77 says:

    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?

  3. 3
    ellazimm says:

    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.

  4. 4
    bornagain77 says:

    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).

  5. 5
    Arthur Hunt says:

    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.

  6. 6
    tragic mishap says:

    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.

  7. 7
    bornagain77 says:

    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/

  8. 8
    tragic mishap says:

    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.

  9. 9
    bornagain77 says:

    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!

  10. 10
    tragic mishap says:

    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.

  11. 11
    tragic mishap says:

    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.

  12. 12
    bornagain77 says:

    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)

  13. 13
    bornagain77 says:

    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.

  14. 14
    bornagain77 says:

    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/astonishin.....ity-update

  15. 15
    tragic mishap says:

    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.

  16. 16
    tragic mishap says:

    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?

  17. 17
    bornagain77 says:

    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.

  18. 18
    bornagain77 says:

    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.

  19. 19
    tragic mishap says:

    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?

  20. 20
    tragic mishap says:

    I’m sure there are many diseases tied to genetic defects which we do not know what those genes actually do.

  21. 21
    tragic mishap says:

    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.

  22. 22
    Frost122585 says:

    Tragic, it is impossible scientifically and theologically to understand “why” “bad” things happen in full. We have theological explanation that explain these things in part- regarding the spiritual struggle between good and evil and how human action and choice influences material processes- and we have scientific explanation of why say a person develops physically one way over another- but we all know from the reality, or non-reality, of material causation at the quantum physical level- that is at the most fundamental level, and because of the problem of universal causation- also known as universal regress- that materialism is self defeating.

    So asking a question that we cannot answer in fool is not the same as foiling a theory of transcendent design. As far as how design can square with the things you noted it is widely held that what the designer intends ideally- that is the “actual desired plan” includes a certain amount of freedom. So these examples of bad design are not really bad design but simply non-ideal design. The concept of ideal design exists because the designer has ideals or perhaps is ideal in nature. Scripture says man was made in a likeness but not as an exact equal to God’s ideals.

    I think this idea of transcendental design is basically a lot like what Plato was getting at with his metaphysics. That is the true reality is not one of matter that can be seen- that is the world as we experience it with the senses is like a shadow. True reality is that which actually exists independent and beyond our senses. Information is that which “forms” matter. The information comes from intelligence in all of our known experiences.

  23. 23
    Frost122585 says:

    tragic at @21,

    Yes God could do this but when he does perform improbable things like the deigns of say novel body plans etc- God does this within the “domain” of the empirical science. In other words say you example happened- if it did there would be a scientific “explanation” of how it happened. Now we may never understand it in full- but we would understand it enough to say this is probably what basically brought forth this event.

    For example take the Cambrain explosion. Say we discover independant evidend that there was some kind of cosmolgical influx of high energy during the beginning and time if its origin. THis would begin to explain, partly though physical explanation- how all of a sudden all these body plans, and complexity could emerge.

    So we are not claiming pure “magic.” ID is not about what we “cannot know” but about how we better understand what we do know. Even if we don’t or cannot understand it in full- does not mean we don’t keep trying but we need to be honest when Darwinian explanations of random mutation and chance do not cut it.

  24. 24
    tragic mishap says:

    Well I certainly believe God designed body plans. My hypothesis is he designed them in exactly the same way he designed other things in biology, by encoding information into DNA.

  25. 25
    bornagain77 says:

    Well that didn’t work: lets try again:

    Well tragic,
    The bad design argument is basically a “religious argument” as Cornelius Hunter has amply pointed out many times. A religious argument that can be debated endlessly as such, and really has no bearing on the empirics at hand. Namely that, despite extensive studies, mutations to DNA have NEVER shown an ability to significantly effect Body Plans on their own. Though to be fair to your “Genetic Reductionism” position a “all or nothing” ability is noted for DNA by Venter for individual bacteria cells:

    That the DNA would be found to be a “all or nothing” deal at this level should be very disconcerting to materialists, but as a Theist I am not bothered in the least. Yet as a Theist, I am curious to the overriding question of exactly what, or Who, is conducting the symphony of how these 50 plus trillion cells are orchestrated into the human body. I maintain that a fairly solid argument can be made, both scripturally and empirically, that at this level of overriding organization for cells, the symphony is conducted by God transcendently, i.e. we are “not made by visible hands” but by invisible hands.

    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 hands are no gods at all.

    As well to add more weight to my claim I would like to outline how reality is actually constructed:

    Leading quantum physicist Anton Zeilinger has followed in John Archibald Wheeler’s footsteps (1911-2008) by insisting reality, at its most foundational level, is “information”.

    Why the Quantum? It from Bit? A Participatory Universe?
    Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.” Anton Zeilinger – a leading expert in quantum teleportation:

    Psalm 19:1-2
    The heavens declare the glory of God; the skies proclaim the work of his hands. Day after day they pour forth speech; night after night they display knowledge.

    Plus, In what I consider an absolutely fascinating discovery; 4-dimensional (4D) space-time was created in the Big Bang and continues to “expand equally in all places” i.e. The universe is not expanding into anything outside of itself. Thus from a 3-dimensional (3D) perspective, any particular spot in the universe is to be considered just as “center of the universe” as any other particular spot in the universe is to be considered “center of the universe”.

    Where is the centre of the universe?:
    Excerpt: There is no centre of the universe! According to the standard theories of cosmology, the universe started with a “Big Bang” about 14 thousand million years ago and has been expanding ever since. Yet there is no centre to the expansion; it is the same everywhere. The Big Bang should not be visualized as an ordinary explosion. The universe is not expanding out from a centre into space; rather, the whole universe is expanding and it is doing so equally at all places, as far as we can tell.

    This centrality found for any 3D place in the universe is because the universe is a 4D expanding hypersphere, analogous in 3D to the surface of an expanding balloon. All points on the surface are moving away from each other, and every point is central, if that’s where you live.

    As well to add significant weight to this “centrality” the Cosmic Microwave Background Radiation (CMBR), left over from the creation of the universe, forms a sphere around us.

    Earth As The Center Of The Universe – image
    http://docs.google.com/Doc?doc.....QydzV2OGhz

    >Psalm 102:19
    The LORD looked down from His sanctuary on high, from heaven He viewed the earth,

    On top of this “4D expanding hypersphere geometry”, the primary reason the CMBR forms a sphere around the earth is because quantum wave collapse, to its “uncertain” 3D particle/state, is dependent on “observation” in quantum mechanics; i.e. 3D reality does not truly “materialize” until a observer is present (A. Aspect). Moreover, this wave collapse, to its “uncertain” 3D particle/state, is shown by experiment to be instantaneous, and is also shown to be without regard to distance. i.e. It is universal for each observer. As well, CMBR ultimately indicates that information about all points in the universe is actually available to each “central” observer, in any part of the 4D expanding universe, simultaneously. i.e. The CMBR will form a sphere around any observer in the universe, no matter where they are in the universe, because quantum waves will collapse instantaneously, and universally, to each and every individual observer in the 4D expanding universe.

    This following study solidly refutes the “hidden variable” argument that has been, persistently and dogmatically, used by materialists to try to get around the Theistic implications of this instantaneous “spooky action at a distance” found in quantum mechanics.

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.

    (of note: hidden variables were postulated to remove the need for “spooky” forces, as Einstein termed them—forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    I find it extremely interesting that quantum mechanics tells us that instantaneous quantum wave collapse to its “uncertain” 3-D state is centered on each individual observer in the universe, whereas, 4-D space-time cosmology tells us each 3-D point in the universe is central to the expansion of the universe. Why should the expansion of the universe, or the quantum wave collapse of the entire universe, even care that I exist?

    Proverbs 15:3
    The eyes of the LORD are in every place,,,

    This is obviously a very interesting congruence in science between the very large (relativity) and the very small (quantum mechanics). A congruence they seem to be having a extremely difficult time “unifying” mathematically (Einstein, Penrose). Yet, a unification which Jesus apparently seems to have joined together with His resurrection:

    The Center Of The Universe Is Life – video
    http://www.youtube.com/watch?v=do2KUiPEL5U

    The End Of Christianity – Finding a Good God in an Evil World – Pg.31 – William Dembski
    Excerpt: “In mathematics there are two ways to go to infinity. One is to grow large without measure. The other is to form a fraction in which the denominator goes to zero. The Cross is a path of humility in which the infinite God becomes finite and then contracts to zero, only to resurrect and thereby unite a finite humanity within a newfound infinity.” http://www.designinference.com.....of_xty.pdf

    Philippians 2: 5-11
    Let this mind be in you, which was also in Christ Jesus: Who, being in the form of God, thought it not robbery to be equal with God: But made himself of no reputation, and took upon him the form of a servant, and was made in the likeness of men: And being found in fashion as a man, he humbled himself, and became obedient unto death, even the death of the cross. Wherefore God also hath highly exalted him, and given him a name which is above every name: That at the name of Jesus every knee should bow, of things in heaven, and things in earth, and things under the earth; And that every tongue should confess that Jesus Christ is Lord, to the glory of God the Father.

    “Miracles do not happen in contradiction to nature, but only in contradiction to that which is known to us of nature.”
    St. Augustine

    Thus, much contrary to the mediocrity of earth, and of humans, brought about by the heliocentric discoveries of Galileo and Copernicus, the findings of modern science are very comforting to Theistic postulations in general, and even lends strong support of plausibility to the main tenet of Christianity which holds Jesus Christ is the only begotten Son of God.

    Matthew 28:18
    And Jesus came up and spoke to them, saying, “All authority has been given to Me in heaven and upon earth.”

    Of related interest, this following article is interesting for it draws attention to the fact that humans “just so happen” to be near the logarithmic center of the universe, between Planck’s length and the cosmic horizon of the cosmic background radiation (10^-33 cm and 10^28 cm respectively) .

    The View from the Centre of the Universe by Nancy Ellen Abrams and Joel R. Primack
    Excerpt: The size of a human being is near the centre of all possible sizes.

  26. 26
    Nakashima says:

    Mr Mishap,

    I haven’t read the Shapiro paper of the OP, but I agree with your observation that each of the objects in the relations/processes shown are physical objects, store information in a physical way, can vary in their fidelity at replicating the information stored. None of the onto- or epi- genetic discoveries therefore is going to push the “selection/variation cycle” as a paradigm off its position atop the explanatory heap.

  27. 27
    bornagain77 says:

    Nak, you are wrong in this observation:

    “can vary in their fidelity at replicating the information stored.”

    Optimality of information is what we consistently find in fitness tests, compensatory mutations not withstanding, and is the overriding rule from which evolution has failed, even one time, to extricate itself. i.e. Abel’s Null Hypothesis is valid for “parent kinds” as well as origin of life research.

    The only variance of fidelity observed stays well within the principle of Genetic Entropy!

    Thus the “selection/variation cycle” has not even crawled out of the bottom of the valley, much less sits on top of the heap of explanations.

  28. 28
    Nakashima says:

    Mr BA^77,

    Variance in fidelity just means there is a non-zero error rate. Are you saying that you think there is a non-zero error rate in epigenetic information transmission?

  29. 29
    bornagain77 says:

    Nak, I’m just keeping you firmly in check with your claims that evolution has even one morsel of substantiating empirical evidence. It all honesty with the actual evidence available, evolution has never even risen above the level of hypothesis! And not even to the level of a hypothesis that has a coherent foundation in physics proper.

  30. 30
    tragic mishap says:

    Well I’m sorry for implying the bad design argument. I did not of course complete it because I do not agree with it. I’m just wondering if you understand the implications of your belief. You still haven’t answered my other question about the lizard egg.

    I’m a YEC. That means I believe God finished, finished, his creation in six days. Since then it’s been winding down like a great big wind-up toy, functioning through residual energy given to it at the beginning by God. If you wish to believe that God is stepping in wherever we do not know any material cause, well that is a classic example of god-of-the-gaps. You could be right, but there’s no point in doing further science if you are. I really, really doubt if Meyer or any other ID theorist would agree with the view that God miraculously designs each and every organism in the womb. The design is there because it has been put in place from the beginning in the form of mechanisms which have the awesome ability to self-replicate. This is why the CD/CD player analogy fails. Neither of them have this ability, yet life does. Meyer leaves open the possibility of other sources of information besides DNA, I think, primarily out of politeness to his host. But someone who has spent so much time on DNA would know that DNA is certainly capable of holding the information required for an organism’s body plan. Which I might add, must not only be utilized during development, but also must be maintained throughout the life of the organism. Failure to maintain it often results in a little thing called cancer. But I’m glad we had this discussion. Sounds to me like oncogenes are a prime candidate for information on body plans.

  31. 31
    bornagain77 says:

    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.

  32. 32
    tragic mishap says:

    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.

  33. 33
    bornagain77 says:

    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

  34. 34
    tragic mishap says:

    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.

  35. 35
    tragic mishap says:

    You know BA, I appreciate all the information you post, but I often fail to see the relevance.

  36. 36
    bornagain77 says:

    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.

  37. 37
    osteonectin says:

    BA77:

    Well, I don’t know, or really care, what Ken Miller thinks

    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:

    You know BA, I appreciate all the information you post, but I often fail to see the relevance.

    Too true.

  38. 38
    Phinehas says:

    @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.

    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!

    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.

  39. 39
    Frost122585 says:

    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.

  40. 40
    Frost122585 says:

    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.

  41. 41
    tragic mishap says:

    Frost:

    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.

    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.

  42. 42
    tragic mishap says:

    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.

  43. 43
    Alex73 says:

    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.

  44. 44
    tragic mishap says:

    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.

  45. 45
    magnan says:

    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.

  46. 46
    Nakashima says:

    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.

  47. 47
    bornagain77 says:

    TragicMishap, You may appreciate this article that came out recently on science daily:

    ‘Moonlighting’ Molecules Discovered; Researchers Uncover New Kink In Gene Control:
    Excerpt: Since the completion of the human genome sequence, a question has baffled researchers studying gene control: How is it that humans, being far more complex than the lowly yeast, do not proportionally contain in our genome significantly more gene-control proteins? Now, a collaborative effort at the Johns Hopkins School of Medicine to examine protein-DNA interactions across the whole genome has uncovered more than 300 proteins that appear to control genes, a newly discovered function for all of these proteins previously known to play other roles in cells.,,,The results, which appear in the October 30 issue of Cell, provide a partial explanation for human complexity over yeast but also throw a curve ball in what we previously understood about protein functions.

    “Everyone knows that transcription factors bind to DNA and everyone knows that they bind in a sequence-specific manner,” says Heng Zhu, Ph.D., an assistant professor in pharmacology and molecular sciences and a member of the High Throughput Biology Center. “But you only find what you look for, so we looked beyond and discovered proteins that essentially moonlight as transcription factors.”

    The team suspects that many more proteins encoded by the human genome might also be moonlighting to control genes, which brings researchers to the paradox that less complex organisms, such as plants, appear to have more transcription factors than humans. “Maybe most of our genes are doing double, triple or quadruple the work,” says Zhu. “This may be a widespread phenomenon in humans and the key to how we can be so complex without significantly more genes than organisms like plants.”,,,
    http://www.sciencedaily.com/re.....125536.htm

  48. 48
    Frost122585 says:

    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.

  49. 49
    Frost122585 says:

    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.

  50. 50
    Frost122585 says:

    Excuse me- the video I was referring to about the ontogentic information is here

    http://www.youtube.com/watch?v.....re=related

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