DNA errors are scanned electrically

[Elshamah]

DNA errors are scanned electrically

Location of DNA damage by charge exchanging repair enzymes: effects of cooperativity on location time

How DNA repair enzymes find the relatively rare sites of damage is not known in great detail. Recent experiments and molecular data suggest that individual repair enzymes do not work independently of each other, but interact with each other through charges exchanged along the DNA. A damaged site in the DNA hinders this exchange. The hypothesis is that the charge exchange quickly liberates the repair enzymes from error-free stretches of DNA. In this way, the sites of damage are located more quickly 2


New Scientists : Enzymes scan DNA using electric pulse

ENZYMES that repair DNA may check for mutations by sending electrons along sections of the strand, in much the same way that electricians test for faults in circuits. The mechanism might explain how enzymes locate problems in the genome fast enough to correct them.

Most genetic mutations are caused by free radicals scavenging electrons from DNA. This "oxidative damage" introduces errors such as base-pair mismatches when the strand replicates. If these errors build up they can be extremely harmful.

All organisms have enzymes that can repair the errors. They bind to DNA and are thought to move slowly along the strand, testing each base pair to see if there is a mismatch. But Jacqueline Barton of the California Institute of Technology in Pasadena is not convinced this is what happens. "That would take a lot of time," she says - too long to allow the genome to be comprehensively scanned. ... 3


This is a striking example of ingenious design inside the cell which points to a intelligent creator that made all living things.


2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1142343/
3) http://www.newscientist.com/article/mg18024171.200-enzymes-scan-dna-using-electric-pulse.html

 

[SpecialFrog]

This is a striking example of ingenious design inside the cell which points to a intelligent creator that made all living things.

Those articles are interesting though (seemingly) still speculative. Thanks for the link.

However, your conclusion is a complete non sequitur. How does it follow from those articles, even if their hypotheses end up being substantiated?

Also, I would suggest making it clearer when you are quoting rather than using your own words.

 

[Elshamah]

This is a striking example of ingenious design inside the cell which points to a intelligent creator that made all living things.

Those articles are interesting though (seemingly) still speculative. Thanks for the link.

However, your conclusion is a complete non sequitur. How does it follow from those articles, even if their hypotheses end up being substantiated?

Also, I would suggest making it clearer when you are quoting rather than using your own words.

the following paper is highly technical, but i think it gives further support to the hypothesis :

http://authors.library.caltech.edu/627/1/BOOpnas03.pdf

DNA-mediated charge transport for DNA repair

The [4Fe4S] cluster of these base excision repair enzymes,
containing a unique ligating peptide sequence, is thus well
designed for its function: robust in solution as [4Fe4S]2, stable
to oxidizing and reducing conditions of the cell, but, once buried
within DNA, activated to carry out redox chemistry.
A Role for DNA CT in DNA Repair. Importantly, our electrochemical
data indicate that DNA-mediated CT involving the [4Fe4S]
cluster of MutY is feasible. The primary lesson learned from our
many studies of DNA CT chemistry is that DNA CT is exquisitely
sensitive to perturbations in base pair structure . Indeed
we have shown DNA CT electrochemistry as a diagnostic tool for
mutations and lesions in DNA. Might DNA repair
proteins, MutY in particular, similarly exploit DNA CT to detect
mismatches and lesions in DNA?
Based on results of others, within the cell, MutY contains
a [4Fe4S]2 cluster . On binding DNA nonspecifically,
as our results indicate, MutY undergoes a shift in redox potential,
and the 32 couple becomes accessible, so that the
cluster may become oxidized and release an electron in a
DNA-mediated reaction. Upon oxidation, MutY could then
serve, through DNA-mediated CT, to reduce an alternate DNA
repair protein, perhaps another MutY, bound at a distant site
a along the duplex. The electrochemistry data indicate that such a
DNA-mediated process is possible. Moreover, association of two
MutY equivalents on the DNA template has been proposed
based on kinetic experiments . In the reduced form, the
DNA affinity of MutY should be diminished, facilitating dissociation
of the protein from its DNA site. We propose that this
process, as described, constitutes a scan of this region of the
genome. Significantly, the region must be well stacked and
contain no mismatches or lesions for CT to occur. Also shown
is association of MutY to a region containing a mismatch, where
the associated stacking perturbation would not permit DNAmediated
CT to occur. Here, the protein would remain associated
with the DNA, processively diffusing to the mismatch site
on a slower time scale. Data in support of this slower processive
mechanism for MutY (80) as well as descriptive models (81, 82)
have also been reported. The CT scanning mechanism does not
obviate these schemes. Instead, the DNA CT scanning strategy
confines the search to a manageable regime within the genome.
Furthermore, although the specificity ratio, 10–1,000, of these
repair proteins for their target site versus well-matched DNA is
too low to explain preferential recognition of mismatches within
the genome, this small level of specificity is sufficient for target
binding within the subset of mismatch-containing strands.

what is remarkable, is that the authors make a nice case for design : well
designed for its function:

 

[he_who_is_nobody]

Those articles are interesting though (seemingly) still speculative. Thanks for the link.

However, your conclusion is a complete non sequitur. How does it follow from those articles, even if their hypotheses end up being substantiated?

Also, I would suggest making it clearer when you are quoting rather than using your own words.

the following paper is highly technical, but i think it gives further support to the hypothesis :

http://authors.library.caltech.edu/627/1/BOOpnas03.pdf

DNA-mediated charge transport for DNA repair

[Snipped for space]

what is remarkable, is that the authors make a nice case for design : well
designed for its function:

:facepalm:

You have not actually read that paper, now have you. Nowhere in what you quoted above do the authors make a case for anything besides design by natural selection. It seems you just gleamed the sentence with "design" in it and thought you had a point. However, it appears you do not realize what evolution is and how it can create designs as well.

 

[Visaki]

If one says that something is well designed by an intelligent, purposeful agent, one also has to admit that tons of things are badly designed by that same agent and that a lot of things are specifically designed to cause pain, misery and death by that same agent. Even if one could show that a design by purposeful agent exists in nature it'd also show that the agent was about as smart as a boot. A rubber boot, not a leather one.

 

[Dragan Glas]

Greetings,

Welcome to LoR, Elshamah!

As HWIN notes, just because someone uses a turn of phrase - "well designed for its function" - does not mean that it's literally designed.

Kindest regards,

James

 

[Deleted member 619]

Molecule uses electromagnetic force for some of its chemical processes.

In other news, water is wet. Film at 11.

Tell me how this implies design again?

 

[SpecialFrog]

Those articles are interesting though (seemingly) still speculative. Thanks for the link.

However, your conclusion is a complete non sequitur. How does it follow from those articles, even if their hypotheses end up being substantiated?

Also, I would suggest making it clearer when you are quoting rather than using your own words.

the following paper is highly technical, but i think it gives further support to the hypothesis :

http://authors.library.caltech.edu/627/1/BOOpnas03.pdf

Note that the article's conclusion says, "Importantly, our electrochemical data indicate that DNA-mediated CT involving the [4Fe4S] cluster of MutY is feasible."

My bold.

So yes, still interesting but not anything like an established fact.

Even so, though they use the word "designed" at some point it is only a metaphor.

Do you agree that natural processes can give the appearance of "design"?

 

[Rumraket]

This is what I mean when I write he is baffled into halluscination-mode by technical jargon that is even remotely reminiscent of something you'd read related to computer science or engineering.

The key words that made him lose his mind here are "scanned electrically". Oh my god, that means there's a scanner! And scanners are designed! And.. and, ELECTRICALLY, it's an electronic scanner!

Oooh, Aaahhh! PRAISE THE LORD!

This is how he works.

You write something about biology and sprinkle it with some engineering or computer sounding technical jargon and metaphors, and Elsamah is collapsing on the floor with seizure induced halluscinations about divine designers and angels zapping organisms into existence fully formed.

 

[Elshamah]

You have not actually read that paper, now have you. Nowhere in what you quoted above do the authors make a case for anything besides design by natural selection. It seems you just gleamed the sentence with "design" in it and thought you had a point. However, it appears you do not realize what evolution is and how it can create designs as well.

It seems you are ignorant of the fact that the topic is not about evolution , but abiogenesis, and that evolution only starts to act upon replication, which depends on the machines in question.

 

[Elshamah]

If one says that something is well designed by an intelligent, purposeful agent, one also has to admit that tons of things are badly designed by that same agent and that a lot of things are specifically designed to cause pain, misery and death by that same agent. Even if one could show that a design by purposeful agent exists in nature it'd also show that the agent was about as smart as a boot. A rubber boot, not a leather one.

http://elshamah.heavenforum.org/t1302-does-bad-design-affect-the-argument-from-design?highlight=bad+design

Even suboptimal designs require a designer. The Newcomen steam engine was not nearly as efficient or practical as Watts’ steam engine, but no one in his right mind would suggest on that basis that Newcomen’s engine self-assembled by random chance. Second, some designs that may look suboptimal to us are actual optimal e.g. the panda’s thumb; the panda uses his “thumb” (actually a specialized bone in the wrist) for near continuous grasping of bamboo. If it had used an opposable thumb to do so, as proponents of naturalism suggest as a superior design, it would almost certainly suffer from permanent carpal tunnel syndrome. Third, what we see now is the world as marred by the curse upon sin. For all we know, people as created may have been able to synthesize every necessary vitamin, but some of those abilities may have subsequently been lost due to genetic corruption and drift.

 

[Elshamah]

Molecule uses electromagnetic force for some of its chemical processes.

In other news, water is wet. Film at 11.

Tell me how this implies design again?

Water is a amazing example of design

http://elshamah.heavenforum.org/t1532-the-wonders-of-water?highlight=water

 

[Elshamah]

This is what I mean when I write he is baffled into halluscination-mode by technical jargon that is even remotely reminiscent of something you'd read related to computer science or engineering.

The key words that made him lose his mind here are "scanned electrically". Oh my god, that means there's a scanner! And scanners are designed! And.. and, ELECTRICALLY, it's an electronic scanner!

Oooh, Aaahhh! PRAISE THE LORD!

This is how he works.

You write something about biology and sprinkle it with some engineering or computer sounding technical jargon and metaphors, and Elsamah is collapsing on the floor with seizure induced halluscinations about divine designers and angels zapping organisms into existence fully formed.

What came first, the dna repair mechanism, or dna itself ?

 

[he_who_is_nobody]

You have not actually read that paper, now have you. Nowhere in what you quoted above do the authors make a case for anything besides design by natural selection. It seems you just gleamed the sentence with "design" in it and thought you had a point. However, it appears you do not realize what evolution is and how it can create designs as well.

It seems you are ignorant of the fact that the topic is not about evolution , but abiogenesis, and that evolution only starts to act upon replication, which depends on the machines in question.

So, where exactly does your citation discussion abiogenesis? It appears to me they are discussing MutY and its fuction in DNA.

hackenslash[/url]"]Of particular interest is the way that all his citations ultimately link back to a forum (this 'elshamah' forum) with only one member, him.

http://elshamah.heavenforum.org/t1302-does-bad-design-affect-the-argument-from-design?highlight=bad+design

Even suboptimal designs require a designer. The Newcomen steam engine was not nearly as efficient or practical as Watts’ steam engine, but no one in his right mind would suggest on that basis that Newcomen’s engine self-assembled by random chance. Second, some designs that may look suboptimal to us are actual optimal e.g. the panda’s thumb; the panda uses his “thumb” (actually a specialized bone in the wrist) for near continuous grasping of bamboo. If it had used an opposable thumb to do so, as proponents of naturalism suggest as a superior design, it would almost certainly suffer from permanent carpal tunnel syndrome. Third, what we see now is the world as marred by the curse upon sin. For all we know, people as created may have been able to synthesize every necessary vitamin, but some of those abilities may have subsequently been lost due to genetic corruption and drift.

Nice prediction hackenslash. Now, I cannot wait to see this argumentum ad elbow-joint-of-the-lesser-spotted-weasel-frog you also predict is coming.

 

[Rumraket]

This is what I mean when I write he is baffled into halluscination-mode by technical jargon that is even remotely reminiscent of something you'd read related to computer science or engineering.

The key words that made him lose his mind here are "scanned electrically". Oh my god, that means there's a scanner! And scanners are designed! And.. and, ELECTRICALLY, it's an electronic scanner!

Oooh, Aaahhh! PRAISE THE LORD!

This is how he works.

You write something about biology and sprinkle it with some engineering or computer sounding technical jargon and metaphors, and Elsamah is collapsing on the floor with seizure induced halluscinations about divine designers and angels zapping organisms into existence fully formed.

What came first, the dna repair mechanism, or dna itself ?

Nobody knows.

 

[Rumraket]

Molecule uses electromagnetic force for some of its chemical processes.

In other news, water is wet. Film at 11.

Tell me how this implies design again?

Water is a amazing example of design

http://elshamah.heavenforum.org/t1532-the-wonders-of-water?highlight=water

No it isn't.

Any idiot can argue with blanket assertions. You are mindlessly asserting what you should be trying to prove. The fact that something works very well isn't evidence it was designed. You need to find another method of demonstrating design than "this works very well at this particular thing".

 

[Elshamah]

Nobody knows.

haha. :shock:

Ok. I will answer the question for you. Of course both had to come into existence at the same time, since 1. The repair machinery has no function without DNA. And 2. DNA would replicate and transcribe with such a high rate of mutations, that the organism would die quickly.

 

[SpecialFrog]

Ok. I will answer the question for you. Of course both had to come into existence at the same time, since 1. The repair machinery has no function without DNA. And 2. DNA would replicate and transcribe with such a high rate of mutations, that the organism would die quickly.

Citation needed for both assertions.

The enzymes involved in DNA repair could have evolved from an enzyme with a different purpose in pre-DNA life.

And certainly a multi-cellular organism may not be viable without repair mechanisms but single-celled organisms may not have this issue. I don't believe viruses have this kind of repair mechanism at all and they do okay.

 

[Dragan Glas]

Greetings,

One of the mutations could be a repair mechanism - thus that organism with the mechanism would propagate successfully.

Kindest regards,

James

 

[Elshamah]

Ok. I will answer the question for you. Of course both had to come into existence at the same time, since 1. The repair machinery has no function without DNA. And 2. DNA would replicate and transcribe with such a high rate of mutations, that the organism would die quickly.

Citation needed for both assertions.

The enzymes involved in DNA repair could have evolved from an enzyme with a different purpose in pre-DNA life.

the baseless assertions and fertile fantasy goes fast here.....it takes enzymes to make enzymes, and DNA.....

And certainly a multi-cellular organism may not be viable without repair mechanisms but single-celled organisms may not have this issue.

how do you possibly know ?

I don't believe viruses have this kind of repair mechanism at all and they do okay.

how can viruses survive without a host cell ?