Intelligent Reasoning

Promoting, advancing and defending Intelligent Design via data, logic and Intelligent Reasoning and exposing the alleged theory of evolution as the nonsense it is. I also educate evotards about ID and the alleged theory of evolution one tard at a time and sometimes in groups

Sunday, February 17, 2008

Intelligent Design In Biology Textbooks Continued

Thanks to the anti-IDists who suggested that I read (mainstream) biology textbooks to find the data that supports their position, I have instead found that Intelligent Design in biology runs deep.

Recently, I wrote about proteins and the transcription/ translation process required for protein synthesis within a living cell- Intelligent Design in Biology Textbooks.

What that demonstrates is that it takes far more than some imperfectly self-replicating molecules to constitute a living organism.

Those molecules must also be able to somehow produce the required chemical products for self-preservation and replication. This alone should give one pause when considering the materialistic view of the origins of living organism.

Couple that with how this is done and any scenario requiring reducibility to matter, energy & time, is itself reduced to a fairy-tale, full of imaginary narratives and fanciful stories.

To further cement the design inference biology textbooks tell us of alternative gene splicing, (molecular) chaperones and transit peptides (also called signal peptides, signal sequence

Alternative gene splicing refers to the process in which mRNA is edited before it leaves the nucleus to rendezvous with the ribosome.

Genes are littered with sequences called exons and introns. Introns (almost) always get cut out from the mRNA sequence. The remaining exons can be left to form as they are or any number may be cut out thus changing the configuration of the mRNA product.

This is how one gene can code for multiple products. Which is why the “gene count” for any one organism may not be an accurate depiction of the number of proteins and other molecules coded for by the parent DNA. It also defies an explanation reducible to matter, energy & time. (nor reducible to parsley, sage, rosemary & thyme)

Splicing and editing are signs of design.

Chaperones- as one article has it:
Molecular chaperones have an essential role in the regulation of protein conformation states -- the process during which transient or stable interactions with client proteins affects their conformation and activity. Chaperones capture unfolded polypeptides, stabilize intermediates, and prevent misfolded species from accumulating in stressed cells.-- Roles of Molecular Chaperones


Another tells us:
It has recently become clear that protein folding in the cellular environment is not a spontaneous, energy-independent process akin to that observed when chemically denatured purified polypeptides are refolded in vitro. Rather, in vivo protein folding strongly relies on accessory proteins known as molecular chaperones and foldases.--Molecular Chaperones and Foldases (bold added)


IOW it has become clear that protein folding is not reducible to matter, energy & time.

That article goes on to say:
Molecular chaperones are a class of proteins that have been highly conserved in all kingdoms of life and identified in most organisms and cellular compartments examined to date. They are defined as proteins that help other polypeptides reach a proper conformation or cellular location without becoming part of the final structure.

Transit (signal) peptides, (N or C)-terminal extensions- these are interesting little starting sequences and tails that direct the protein to its proper destination. And if there is a membrane in the way it holds the key that allows the protein through.

Once at the destination this sequence gets cut off and is not part of the mature protein.

9 Comments:

  • At 11:27 AM, Blogger Hermagoras said…

    Joe you're wrong when you write that "it has become clear that protein folding is not reducible to mater [sic], energy & time." Look again at the quote you use to support this:

    It has recently become clear that protein folding in the cellular environment is not a spontaneous, energy-independent process akin to that observed when chemically denatured purified polypeptides are refolded in vitro. Rather, in vivo protein folding strongly relies on accessory proteins known as molecular chaperones and foldases.

    "not a spontaneous, energy-independent process" means that it is contingent and energy dependent. It also "relies on accessory proteins." The passage is simply saying that protein folding doesn't happen on its own, or without external energy. That doesn't mean that it's not reducible to material forces.

     
  • At 11:50 AM, Blogger Joe G said…

    Thanks for picking on a typo- what a loser.

    But anyways- I am not wrong and here's why:

    you say:
    "not a spontaneous, energy-independent process" means that it is contingent and energy dependent.

    But the NEXT sentence in the article says:

    Rather, in vivo protein folding strongly relies on accessory proteins known as molecular chaperones and foldases.

    IOW it is contingent on the programming encoded into the genome. The coding that produces those chaperones. The same coding that produces the proteins and all the processes I described.

    The same coding that is as reducible to matter, energy & time as any computer software program is.

    Any time you want to provide the scientific data which shows that what I posted in the OP is reducible to matter, energy & time, I will welcome it.

     
  • At 12:00 PM, Blogger Hermagoras said…

    But Joe, that's your spin on what they're saying, not what they're saying. Consider this:

    It has recently become clear that the size of the stomach of Hermagoras is not a spontaneous, energy-independent process. Rather, Hermagoras's girth strongly relies on accessory foodstuffs known as sandwiches and snacks.

    (You see, I'm kind of heavy. You know that and think it's hilarious. Always the kidder, you.) Now, if I said that my girth is contingent on the coding -- including the protein coding -- in the sandwich, that would in a sense be right. But my weight is still reducible to material forces.

     
  • At 9:08 AM, Blogger Joe G said…

    But Joe, that's your spin on what they're saying, not what they're saying.

    "They" don't have to say the obvious.

    "They" do not have any evidence that chaperones arose via matter, energy & time.

    That goes against all intuition- that bind material processes can produce a protein that will in turn help other proteins form into some spatial configuration.


    As Dr Behe explained in on Page 203,4, in Darwin’s Black Box:

    "Might there be some as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would work. [b]Further, it would go against all human experience, like postulating that a natural process might explain computers."

     
  • At 9:09 AM, Blogger Joe G said…

    Any time you want to provide the scientific data which shows that what I posted in the OP is reducible to matter, energy & time, I will welcome it.

     
  • At 2:21 PM, Blogger CJYman said…

    Joe G:
    "Any time you want to provide the scientific data which shows that what I posted in the OP is reducible to matter, energy & time, I will welcome it."


    Here is something from an introduction to biology and from a published article, which shows that life is not reducible to merely matter energy and time. In fact it includes information (akin to programming) to control that energy and is not reducible to the laws of physics and chemistry.



    “In the face of the universal tendency for order to be lost, the complex organization of the living organism can be maintained only if work – involving the expenditure of energy – is performed to conserve the order. The organism is constantly adjusting, repairing, replacing, and this requires energy. But the preservation of the complex, improbable organization of the living creature needs more than energy for the work. It calls for information or instructions on how the energy should be expended to maintain the improbable organization. The idea of information necessary for the maintenance and, as we shall see, creation of living systems is of great utility in approaching the biological problems of reproduction.”

    George Gaylord Simpson and William S. Beck, Life: An Introduction to Biology, 2nd ed. (London: Routledge and Kegan, 1965), 145.


    ...AND ...




    “A shaping of boundaries may he said to go beyond a mere fixing of boundaries and establishes a ‘controlling principle.’ It achieves control of the boundaries by imprinting a significant pattern on the boundaries of the system. Or, to use information language, we may say that it puts the system under the control of a non-physical-chemical principle by a profoundly informative intervention.”

    --Michael Polanyi, “Life Transcending Physics and Chemistry,” Chemical & Engineering News (21 August 1967): 64.

     
  • At 4:41 PM, Blogger Joe G said…

    sweet...

     
  • At 10:18 AM, Blogger Joe G said…

    And not only do we see molecular chaparones, we also see chaperonins- Chaperonins "are large multi-subunit proteins with ring structures and act by enclosing unfolded proteins and preventing their nonspecific aggregation during assembly."

    As I said- Intelligent Design in biology runs deep.

     
  • At 10:28 AM, Blogger Joe G said…

    The followimg is a good article on chaperonins:

    Chaperonins as protein-folding machines

    "The requirement of such accessory proteins for folding
    was somewhat surprising because it is well accepted that
    the amino acid sequence of a polypeptide is the primary
    determinant of, and contains complete information for, its
    final folded conformation7.
    Thus, many denatured polypeptides
    are able to regain their native folded structure
    with 100% efficiency in vitro, upon removal of the denaturant.
    The cellular milieu is, however, distinguished
    from the in vitro environment in terms of molecular
    crowding8. The total macromolecular concentration
    (mainly protein, RNA and DNA) in the cell is at least
    300 g/l9, with the result that 20–30% of the cellular volume
    is occupied by these macromolecules. Due to an excluded
    volume effect, the reaction rates and equilibria of many
    macromolecular reactions in the cell are expected to be
    considerably different in vitro, where reactions are usually
    studied at low concentrations of reactants. In particular,
    intermolecular association constants are expected to be
    greatly increased in the cell. Another aspect of in vivo
    folding that is different is that the folding information in
    terms of the amino acid sequence does not become available
    all at once, because protein biosynthesis is vectorial,
    i.e. from the N-terminus to the C-terminus of the polypeptide.
    As a consequence, the nascent polypeptide chains
    being synthesized on the ribosomes are in danger of misfolding
    in the absence of complete folding information,
    as well as in danger of aggregating because of the proximity
    of other nascent polypeptides being synthesized on
    the large poly-ribosomal assemblies10.

    It is the presence of molecular chaperones that maintains
    a high fidelity of protein-folding reactions in vivo,
    in spite of the potential hazards outlined above.
    (bold added)

     

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