Re: Challenge for Darwinists - Protein Synthesis

z wrote:
On Sun, 30 Jul 2006 19:05:13 GMT, Wall Of Sleep <Sabotage@xxxxxxxx>
wrote:

wade wrote:
Wall Of Sleep wrote:
r norman wrote:
On Wed, 05 Apr 2006 18:57:55 GMT, Wall Of Sleep <Sabotage@xxxxxxxx>
wrote:


If you're satisfied with "we don't know and we may never know" then so
be it. IMO, there are other ideas out there worth considering which
offer more reasonable explanations.
You abbreviated rather excessively. What we have now is "we don't
know and we may never know, but we are really working on it and all
the hypotheses and tentative ideas that we now have according to known
mechanisms seem to be sufficient."

Your answer is "I know who did it but I am not telling you just who it
was and I don't even have to provide any evidence that that is what
happened or that there even is somebody out there who can do it."
That answer may work in the realm of religion. It is not acceptable
science.


No, my answer is "The complex machine we call 'protein synthesis'
functions like, and bears all the hallmarks of a designed system."
Please itemize "all the hallmarks of a designed system".

1. A proofreading, error checking system.

"Decoding the base sequence of DNA to make proteins is a complex process with built-in molecular checks and safeguards to ensure that the instructions are correctly read. The cell is also actively at work to preserve the accuracy of the DNA code and eliminate errors."

"It may come as a surprise to learn that there are several thousand errors induced in your DNA each day! No need to panic, however - some 20 different enzymes are at work continuously proofreading and eliminating these errors. The repair mechanisms all depend on the existence of two copies of the genetic information - one on each strand of the DNA."

And different organisms use different error checking mechanisms. Even
for organisms as close as mice and men, there are some interesting
differences in how the ends of our chromosomes are protected and
repaired.


So does this reinforce or refute the common descent argument?




2. A transcription system from one code to another.

"Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a template by the RNA polymerase to synthesize a messenger RNA (mRNA)."

"RNA retains faithfully all the information of the original DNA sequence, and the process of RNA synthesis is known as DNA transcription. It shares some common features with DNA replication itself, in that the first step is the opening up of the DNA double strand in the region to be copied. Then one of the two strands of DNA acts as a template for the synthesis of RNA."

RNA world.

Hand wave.



3. A message delivery system.

"This mRNA migrates from the nucleus to the cytoplasm."

"Many thousands of RNA copies can be run off from the same DNA segment during each cell generation. In the cells of higher organisms, many of these RNA molecules undergo major changes before leaving the nucleus to act as messenger molecules (mRNA) that direct the synthesis of proteins. "

While transport of RNA from the nucleus of eukaryotes is fascinating,
it is irrelevant as the LUCA did not have a nucleus.


It *is* relevant for those eukaryotes among us.


4. An editing system for eliminating non-coding sequences.

"During this step, mRNA goes through different types of maturation including one called splicing when the non-coding sequences are eliminated."

"There are several essential differences between DNA and RNA synthesis. For example, the RNA strand does not stay attached to the DNA. As soon as the copy is completed, the DNA double-stranded helix reforms and the RNA is released as a single strand. RNA molecules are also much shorter than DNA itself, representing only a minor fraction of the genome. The production of RNA from a single gene can be carefully controlled by the cell - this is achieved by gene regulatory proteins, and this regulation of gene copying is important in controlling the differentiation and development of cells in all complex multicellular organisms."

As above, complex multicellular organisms are irrelevant to the origen
of translation. The first introns are almost certainlly self-splicing
so are a nonissue.


Of course you realize that LUCA and the first introns are merely assertions of your hypothesis - correct?
Either way, the *development* of the present systems of protein synthesis must *all* be explained.


This editing is not a system for correcting mistakes.

No, it's an elimination of non-coding sequences.

> It's an
elaboration that allows for the creation of multiple proteins from a
single locus. The best guess now is that it is derived from cooption
of self-mobile genetic parasites.


Explain the connection.

5. A dedicated initiator.

"The ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the initiator tRNA."

Not an absolute requirement.


It is present in known systems today. Where did it come from?

In bacteria a reasonable percentage of
proteins start with CUG and use a standard leucine tRNA.

This just gives you more to explain. Explain the development of that system and the others as well.


6. A complex translation mechanism.

"The ribosome proceeds to the elongation phase of protein synthesis. During this stage, complexes, composed of an amino acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one, translated into polypeptidic sequences dictated by DNA and represented by mRNA."

"Translation of the mRNA molecules takes place in the cell cytoplasm at specific protein synthesizing stations called ribosomes. These particles are barely discernible in the electron microscope, and their fine structure is slowly being unraveled. Composed of RNA and proteins, ribosomes allow the message to be decoded and enable assembly of the building blocks of proteins (amino acids) in their correct sequences."

And by mass, ribosomes are mainly RNA. The catalytic center is RNA.
RNA world pops up.

And does what? Explain how this "RNA world" functioned.


"The mRNA tape is threaded through the ribosome like punch tape and the appropriate amino acids are added to the growing protein molecule. However, the mRNA do not directly recognize the amino acids that they specify, in the way that an enzyme recognizes a substrate. The process of translation employs adaptor molecules that recognize both an amino acid and a group of nucleotide bases. These adaptor molecules are a family of RNA molecules known as transfer RNAs (tRNAs), each of which is between 70 and 90 nucleotides in length and with a looped structure produced by folding of the tRNA single strand. This characteristic shape is essential to its functional role as an adaptor."

Hmmm, we have RNA as information (mRNA), RNA's as adaptors (tRNA),
RNA's as enzymes (ribosomes, Rnase P), as targeting agents (5S RNA).
I begin to suspect that the system may have started with RNA.


My car is held together with bolts, so is the plane I rode in the other day, hmm... those systems must have originated from bolts.(?)

Your challenge is to come up with a way to explain how these separate RNA components (supposedly) came together to form these highly sophisticated and extremely specialized systems.


7. A dedicated terminator.

"At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome."

Whee- a protein that mimicas a tRNA in shape and charge.

"Whee" is right. Explain it's origin.



http://www.accessexcellence.org/RC/VL/GG/protein_synthesis.html
http://www.accessexcellence.org/RC/AB/BC/Reading_Messages_in_Genes.html


These seven "hallmarks" appear regularly in designed systems of all kinds. Manufacturing systems which use blueprints and computer programs in the manufacturing process share many of these very features. Having worked in manufacturing plants for almost thirty years - with the last ten as an electrical technician, troubleshooting and maintaining complex machinery - I regularly encounter such systems and readily see their parallels.

I see your parrallel and raise you the counter. You see ribosomes as
little assembly lines that are perfect little assemblages of uber
machines.

i see them as evolutionary grab-bags that work as well just as well as
needed. And I can back that claim up.

Given your model, wouldn't you expect there to be some sort of quality
control at the level of translation? After all, why would a Designer
expend so much effort into making sure that replication was as good as
possibe, incorparate some level of error correction in transcription
(very new and fun data), incorporate the famous "double seive" for
tRNA charging, and then have absolutely no ability for error
correction at the ribosome.

That's right, there is none. Once you make a mistake at a ribosome
it's nonreversible. You've made a flawed product- the end result of
you whole chain.

So you have a designer that makes great blueprints but lousy products?


This is a dodge. Why does my chair creak? Why don't my speakers have better bass response? Why doesn't my car horn play "Iron Man"? One can second guess *any* design, it still doesn't make it a non-design. Or do only "perfect" (to your mind) designs qualify as "real" designs?




That is, after all, a rather simple and discrete claim you are making.

Is being error prone one of the hallmarks? Having redundant failsafe
systems?

In a world with literally millions of living systems vying for the same resources, the ability to fight and inhibit a multitude of factors would be a hallmark of a well designed system.

Nope, just one that is successful under current conditions.

Like the world we live in.



But don't just make them up if you can cite an engineering text
that lists hallmarks of a well designed system.

-- that or you could apologize for being flipant.

I'm not being flippant. I've cited some examples of the systems involved in protein synthesis. If you can realistically explain the natural progressions which resulted in the formation of all of these systems - fine. Please do so.

Frankly, I think the only reason one can't see these systems as designed is because one doesn't want to.


This is the best explanation out there and it requires no wild
speculations about how some random process could accidentally build up a
functioning machine.
I gave you some speculation but it was based on chemistry and
specifically the chemistry of peptide bond formation. It was also
based on the currently observed behavior of macromolecules.

You spoke in generalities. Please address the rise of the seven systems I cited.


Your seven systems are arbitrary and not well informed. The LUCA
would not have to deal with some of your "systems".


How do you even know there was a LUCA? How do you know it wasn't a BFL (Big Front Loader)?
But, besides all that, *ALL* these systems arose from somewhere and require an explanation. A wave of the hand won't do.



--

"The Darwinians have discovered nothing more than the mechanism which can produce varieties. That was all that Darwin could document and it is all that can be established today. There is absolutely nothing in NeoDarwinism that ever had anything to do with the subject and title of Darwin's book, a book I have come to describe as an opus minimus."
John A. Davison 06-16-2006 05:43 AM
http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=37&t=2&m=166

"What is the genetic mechanism that adds new genes to transform, say, a mycoplasma with 500 genes into a mammal with some 100,000 genes? ... The required mechanism must generate immense coded language structures. There is no hint in the laws of chemistry and physics of any natural process capable of such feats." John R. Baumgardner, Ph.D. Geophysics/Space Physics
http://globalflood.org/letters/baumgardner090497.html

.

Relevant Pages

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