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Otangelo



Posts: 148
Joined: Oct. 2015

(Permalink) Posted: Nov. 15 2015,19:40   

Quote (OgreMkV @ Nov. 15 2015,18:38)

Quote (OgreMkV @ Nov. 15 2015,15:07)

It's trivial to show that many mutations are positive.


ah yah ? how so ? please explain.

Quote

Let me explain something to you. Meyer is a liar. If you think that Precambrian fossils don't exist then you are ignorant of reality. The only question becomes, "Are you willing to learn?"

I personally spent about 9 months digging into the issue you mention in response to writings by ID proponent Meyer. Do you know what I found? Not that he was wrong, but that he purposefully lied in his book about what science says on those subjects.

How do I know he lied? Because that is only possible explanation for having so many papers misrepresented to be the exact opposite of what they actually said.

Now, here's the question again. Are you willing to learn?

I can provide you with about 25,000 words and about 75 peer-reviewed research papers that show that there are plenty of Pre-cambrian fossils, that explains the origin of the body plans (which are pre-cambrian, the millions of intermediate forms that you think don't exist, and what evolution actually is.

Do you want them, will you read them, and will you admit that you are wrong afterwards?


I have read Meyer's book only partially. I know precambrian fossils exist. That is a non-issue. What does not exist, however, i repeat, are millions of intermediate fossils that should show a clear gradative increase of complexity in order to get to the cambrian fossils.

THESE DO NOT EXIST. Refute my claim, if you think i am wrong.

Example ? Show me the precursors of the Trilobite, and the trilobite eye.


Quote

Finally, I would like to point out that you are demanding information, very specific information, when you cannot respond in kind about intelligent design.

Tell us, in detail, what does ID predict about DNA repair enzymes? Why? What part of ID results in that prediction?

You tell us, in detail, where does information in the ID paradigm come from? What evidence do you have that such a source exists? (And, please say "the design". Because circular logic is so much fun to play with.)


Post-diction's, or adaptation of a theory, is common in science ==>> see the Big bang theory.

Truth being told, nobody really predicted DNA repair mechanisms.

The relevant question about them is : How are they best explained, through Design, or the ToE, or natural mechanisms ? ( since they had to emerge prior to life, since life depends on them, evolution is not even a viable option to explain their origin.

In my view, they are best explained through design.

I have a lengthy topic at my virtual library about the issue :

DNA repair mechanisms, designed with special care in order to provide integrity of DNA, and  essential for living organisms of all domains.


http://reasonandscience.heavenforum.org/t2043-d....ir#3475

Maintaining the genetic stability that an organism needs for its survival requires not only an extremely accurate mechanism for replicating DNA, but also mechanisms for repairing the many accidental lesions that occur continually in DNA.

DNA damage is an alteration in the chemical structure of DNA, such as a break in a strand of DNA, a base missing from the backbone of DNA, or a chemically changed base.  Naturally occurring DNA damages arise more than 60,000 times per day per mammalian cell.   DNA damage appears to be a fundamental problem for life. DNA damages are a major primary cause of cancer. DNA damages give rise to mutations and epimutations. The mutations, if not corrected,  would be propagated throughout subsequent cell generations. Such a high rate of random changes in the DNA sequence would have disastrous consequences for an organism

Different pathways for DNA repair exists, Nucleotide excision repair (NER),  Base excision repair (BER),  DNA mismatch repair (MMR),  Repair through alkyltransferase-like proteins (ATLs) amongst others.

Its evident that the repair mechanism is essential for the cell to survive. It could not have evolved after life arose, but must have come into existence before. The mechanism is highly complex and elaborated, as consequence, the design inference is justified and seems to be the best way to explain its existence.

Base excision repair (BER)  involves a category of enzymes  known as  DNA-N-glycosylases.

One example of DNA's  automatic error-correction utilities are enough to stagger the imagination.  There are dozens of repair mechanisms to shield our genetic code from damage; one of them was portrayed in Nature  in terms that should inspire awe.

From Nature's article :
Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA 11

How DNA repair proteins distinguish between the rare sites of damage and the vast expanse of normal DNA is poorly understood. Recognizing the mutagenic lesion 8-oxoguanine (oxoG) represents an especially formidable challenge, because this oxidized nucleobase differs by only two atoms from its normal counterpart, guanine (G).  The X-ray structure of the trapped complex features a target G nucleobase extruded from the DNA helix but denied insertion into the lesion recognition pocket of the enzyme. Free energy difference calculations show that both attractive and repulsive interactions have an important role in the preferential binding of oxoG compared with G to the active site. The structure reveals a remarkably effective gate-keeping strategy for lesion discrimination and suggests a mechanism for oxoG insertion into the hOGG1 active site.

Of the four bases in DNA (C, G, A, and T) cytosine or C is always supposed to pair with guanine, G, and adenine, A, is always supposed to pair with thymine, T.  The enzyme studied by Banerjee et al. in Nature is one of a host of molecular machines called BER glycosylases; this one is called human oxoG glycosylase repair enzyme (hOGG1), and it is specialized for finding a particular type of error: an oxidized G base (guanine).  Oxidation damage can be caused by exposure to ionizing radiation (like sunburn) or free radicals roaming around in the cell nucleus.  The normal G becomes oxoG, making it very slightly out of shape.  There might be one in a million of these on a DNA strand.  While it seems like a minor typo, it can actually cause the translation machinery to insert the wrong amino acid into a protein, with disastrous results, such as colorectal cancer.  12

The machine latches onto the DNA double helix and works its way down the strand, feeling every base on the way.  As it proceeds, it kinks the DNA strand into a sharp angle.  It is built to ignore the T and A bases, but whenever it feels a C, it knows there is supposed to be a G attached.  The machine has precision contact points for C and G.  When the C engages, the base paired to it is flipped up out of the helix into a slot inside the enzyme that is finely crafted to mate with a pure, clean G.  If all is well, it flips the G back into the DNA helix and moves on.  If the base is an oxoG, however, that base gets flipped into another slot further inside, where powerful forces yank the errant base out of the strand so that other machines can insert the correct one.

Now this is all wonderful stuff so far, but as with many things in living cells, the true wonder is in the details.  The thermodynamic energy differences between G and oxoG are extremely slight – oxoG contains only one extra atom of oxygen – and yet this machine is able to discriminate between them to high levels of accuracy.

The author, David, says in the Nature article :

Structural biology:  DNA search and rescue

DNA-repair enzymes amaze us with their ability to search through vast tracts of DNA to find subtle anomalies in the structure. The human repair enzyme 8-oxoguanine glycosylase (hOGG1) is particularly impressive in this regard because it efficiently removes 8-oxoguanine (oxoG), a damaged guanine (G) base containing an extra oxygen atom, and ignores undamaged bases.

Natural selection cannot act without accurate replication, yet the protein machinery for the level of accuracy required is itself built by the very genetic code it is designed to protect.  Thats a catch22 situation.  It would have been challenging enough to explain accurate transcription and translation alone by natural means, but as consequence of UV radiation, it  would have quickly been destroyed through accumulation of errors.  So accurate replication and proofreading are required for the origin of life. How on earth could proofreading enzymes emerge, especially with this degree of fidelity, when they depend on the very information that they are designed to protect?  Think about it....  This is one more prima facie example of chicken and egg situation. What is the alternative explanation to design ? Proofreading DNA by chance ?  And a complex suite of translation machinery without a designer?

I enjoy to learn about the wonder of these incredible mechanisms. If the apostle Paul could understand that creation demands a Creator as he wrote in Romans chapter one 18, how much more we today with all the revelations about cell biology and molecular machines?

Quote

So, the ball is in your court. If you are willing to learn, I will happily explain to you, in detail, where ID proponents have lied to you. Are you tough enough to handle it? And can you respond to the same level of detail about your own pet notions?


I am always keen to learn. It depends however, from who, and if i regard the information given as trust worthy, and the inferences drawn of the evidence compelling.

The same question goes to you. Are you willing to permit the evidence to lead wherever it is ? Even if it is towards the oposit direction that you wish ?

  
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