Wednesday, October 07, 2015

Nobel Prize for DNA repair

Tomas Lindahl, Paul Modrich, and Aziz Sancar shared the 2015 Nobel Prize in Chemistry for "for mechanistic studies of DNA repair" [Nobel Prize, Chemistry 2015].

Here's some of the press release.
In the early 1970s, scientists believed that DNA was an extremely stable molecule, but Tomas Lindahl demonstrated that DNA decays at a rate that ought to have made the development of life on Earth impossible. This insight led him to discover a molecular machinery, base excision repair, which constantly counteracts the collapse of our DNA.

Aziz Sancar has mapped nucleotide excision repair, the mechanism that cells use to repair UV damage to DNA. People born with defects in this repair system will develop skin cancer if they are exposed to sunlight. The cell also utilises nucleotide excision repair to correct defects caused by mutagenic substances, among other things.

Paul Modrich has demonstrated how the cell corrects errors that occur when DNA is replicated during cell division. This mechanism, mismatch repair, reduces the error frequency during DNA replication by about a thousandfold. Congenital defects in mismatch repair are known, for example, to cause a hereditary variant of colon cancer.
What about Phil Hanawalt?

Meanwhile, in other news: Discovery and Characterization of DNA Excision Repair Pathways: the Work of Philip Courtland Hanawalt ...
In 1963, Hanawalt and his first graduate student, David Pettijohn, observed an unusual density distribution of newly synthesized DNA during labeling with 5-bromouracil in UV-irradiated E. coli. These studies, along with the discovery of CPD excision by the Setlow and Paul Howard-Flanders groups, represented the co-discovery of nucleotide excision repair.
And Wikipedia [Philip Hanawalt] says,
Philip C. Hanawalt (born in Akron, Ohio in 1931) is an American biologist who discovered the process of repair replication of damaged DNA in 1963. He is also considered the co-discoverer of the ubiquitous process of DNA excision repair along with his mentor, Richard Setlow, and Paul Howard-Flanders. He holds the Dr. Morris Herzstein Professorship in the Department of Biology at Stanford University,[1] with a joint appointment in the Dermatology Department in Stanford University School of Medicine.
Here's what Hanawalt himself says about discovering DNA excision repair [The Awakening of DNA Repair at Yale] ...
Upon joining the faculty at Stanford University in late 1961 as Research Biophysicist and Lecturer, I returned to the problem of what UV did to DNA replication, now that we knew the principal photoproducts. I wanted to understand the behavior of replication forks upon encountering pyrimidine dimers, and I was hoping to catch a blocked replication fork at a dimer. Using density labeling with 5-bromouracil and radioactive labeling of newly-synthesized DNA, we were able to observe partially replicated DNA fragments in E. coli [13]. However, in samples from UV irradiated bacterial cultures, the density patterns of nascent DNA indicated that much of the observed synthesis was in very short stretches, too short to appreciably shift the density of the DNA fragments containing them [14]. I communicated these results to Setlow by phone and learned that he had just discovered that pyrimidine dimers in wild type cells, but not in Ruth Hill’s UV sensitive mutant, were released from the DNA into an acid soluble fraction. We speculated in discussion that my student, David Pettijohn, and I were detecting a patching step by which a process of repair replication might use the complementary DNA strand as template to fill the single-strand gaps remaining after the pyrimidine dimers had been removed. At about the same time, Paul Howard-Flanders in the Department of Therapeutic Radiology at Yale had isolated a number of UV-sensitive mutants from E. coli K12 strains, and he was able to show that these mutants were also deficient in removing pyrimidine dimers from their DNA. The seminal discovery of dimer excision was published by the Setlow and Howard-Flanders groups, as the first indication of an excision repair pathway [15,16]. Of course, the excision per se is not a repair event but only the first step, since it generates another lesion, the gap in one strand of the DNA. We carried out more controls, to then claim that we had discovered a non-conservative mode of repair replication, constituting the presumed patching step in the postulated excision-repair pathway [17]. I later showed that DNA containing the repair patches could undergo semiconservative replication with no remaining blockage [18].

Richard Boyce and Howard-Flanders at Yale also documented excision of lesions induced by mitomycin C in E. coli K12 strains, indicating some versatility of excision repair [19]. In a collaboration with Robert Haynes, I found a similar pattern of repair replication after nitrogen mustard exposure to that following UV, and we concluded that “it is not the precise nature of the base damage that is recognized, but rather some associated secondary structural alteration …” We speculated that “[s]uch a mechanism might even be able to detect accidental mispairing of bases after normal replication,” thus predicting the existence of a mismatch repair pathway [20]. Mismatch repair was reported by Wagner and Meselson a decade later [21] and yet another excision repair mode, termed base excision repair, was discovered by Tomas Lindahl [22].
One of Hanawalt's students was Jonathan Eisen [Tree of Life]. I'll be interested in hearing what he has to say about this Nobel Prize. It seems unfair to me.


70 comments :

  1. Hi is specifically brought up in the documents describing the field. But no one really understands the inner workings for biases of these committees.

    http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2015/advanced-chemistryprize2015.pdf

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  2. He would not be the first to be overlooked and he will not be the last. Case in point, Lise Meitner who should have shared the Nobel Prize with Otto Hahn for the discovery of nuclear fission as her input was required to explain the results of Hahn's experiments. Case in point Chien-Shiung Wu (Madame Wu) who performed the experiment confirming the theory of parity violation in weak interactions proposed by T. D. Lee and C. N. Yang, who shared the prize in physics.

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  3. We might also add that the prize is limited to at most 3. Therefore, in order to include Prof. Hanawalt, one of the other 3 would have to be left out. So the question is, was his contribution more important then that of the other 3?

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    1. Another question is whether the three new Nobel Laureates really did discover DNA repair in the 1970s as the text implies. The answer to that question is clearly and unequivocally "no."

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  4. By selecting Lindahl, Sancar and Modrich, the committee could be reasonably seen as rewarding mechanistic understanding of these DNA repair processes rather than 'discovery' of the existence of the processes. Each of these investigators reconstituted fully functional repair reactions in vitro from purified proteins and defined DNA substrates first using all bacterial proteins, and later using all human proteins. This is classic biochemistry at its best as seems appropriate for the chemistry prize. No disrespect to Hanawalt of course.

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    1. I'm sure that's the justification for not giving a Nobel Prize to the discoverers of DNA repair.

      Why did the citation say, "In the early 1970s, scientists believed that DNA was an extremely stable molecule ..." when DNA repair and DNA polymerase error rates had already been known for a number of years?

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    2. This statement references Lindahl's work specifically and could mean "chemically stable in the absence of exogenous damage" I suppose, in line with Lindahl's 1972 papers on DNA depurination and strand breakage at depurinated sites. Lindahl discusses these concepts in a 1993 review - http://www.nature.com/nature/journal/v362/n6422/pdf/362709a0.pdf

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    3. The statement by the Nobel Committee is BS. They did not discover DNA repair. They did do reductionistic biochemistry of it and did it well. But it is lame that the Nobel Committee would misrepresent the facts.

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  5. DNA repair, yet another design object lacking evolutionary explanation.

    repair assumes knowledge of defects, and knowledge of the procees to successfully repair damage.

    Only intelligence has this capabilility.

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    1. Yeah, and when a bone breaks and it seals, or you shave your eyebrows and they grow back to the same length, praise the lawd!

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    2. Steve,

      An intelligent designer would have designed a DNA replication system that needed no damage repair system.

      Delete
    3. what lame ass commentary from Dazzled. your body is nothing if not intelligent. Dazzled would have us believe a pink unicorn magically sealed up the broken bone.

      But Dazzled won't get into the mud about just what goes on when a bone is broken or skin is cut.

      F&^%K, if we knew just how the body could do the amazing things that it does, the entrepenuers would make out like bandits. Thats why biomimetics is such a hot field of study.

      So yeah Dazzle, nature is intelligent to the hilt. I don't give a shit if that means there's a skydaddy at the levers from dawn to dusk.

      What is clear is that the body is intelligent and it didn't win the lottery to get it.

      Evolution: that simplistic, pseudo-intellectual haunt of luddites ranting against theism.

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    4. well no Chris, only your cartoon caricature of what an intelligent designer should be like requires a perfect design.

      If the intelligent designer is omnipotent and understand how its creation will develop and what kind of design skills it will acquire, then it will tailor its own design principles to make it recognizable to the creation.

      A created being by its very nature could not understand perfect design. That would be like me talking to my dog and anticipating it to talk back to me in English.

      But in reality we talk down to our dogs in single syllables in order to get a wag of the tail.

      And so it is with the intelligent designer and its creation. It speaks to us in a language we can understand until hopefully one day the lights turn on and we can speak the intelligent designer's silent language.

      Now I know why so many folks hate silence and go out of their way to make lots of noise in their lives. It distracts from having to sit with and get to know themselves.

      Its unsettling to be sure but then thats what life's about.

      Knowing yourself.

      Later.


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    5. But who, what is the designer is a needless distraction.

      We dont have to say one single friggin' word about God, a designer.

      But we still look at the genome and say THAT, my friend was DESIGNED.

      Why, because well if it quacks like a duck.....you know the rest.

      Evolutionists: the flat-earthers of the 21st century!!!

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    6. Steve, a strange thing is happening here. 'Evolutionists' need to explain every twist and turn from the first.
      But when asking ID proponents to explain their first beginning, aka which designer we are talking about, all of a sudden it's a 'needless distraction' and 'We dont have to say one single friggin' word about God, a designer.'

      Ah, so it *is* a god then, this designer. But now, which one are we talking about? Zeus? Jupiter? Odin?
      Or is the latest trend in ID land, *a* designer, thus a shared collaboration? Back to the old days of polytheism? The Norse Gods would get my vote.

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    7. Ed,

      Predictably, Steve just moves the goalposts. Notice how his "explanation" of the designer could fit any set of observations whatsoever. Throw in some trolling insults and speudointellectual nonsense about how if we don't agree with him we don't 'know ourselves' as if he were dispensing a life lesson, and declare victory. It's always the same with the creationists.

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    8. steve slobbered:

      "well no Chris, only your cartoon caricature of what an intelligent designer should be like requires a perfect design."

      Well then, steve, what "should" an intelligent designer be like and how do you know?

      "If the intelligent designer is omnipotent and understand how its creation will develop and what kind of design skills it will acquire, then it will tailor its own design principles to make it recognizable to the creation."

      Huh?

      "A created being by its very nature could not understand perfect design. That would be like me talking to my dog and anticipating it to talk back to me in English."

      Did you create your dog? And you're saying that the 'omnipotent-intelligent-designer-creator-God' designed its creation to be imperfect because the beings it designed and created to be imperfect could not understand perfect design because the 'omnipotent-intelligent-designer-creator-God' designed and created the beings to be imperfect? By "beings", you do mean humans, don't you?

      "But in reality we talk down to our dogs in single syllables in order to get a wag of the tail."

      So, to the designer (i.e. 'God') humans are essentially dogs? There goes the claim that humans were 'specially created in God's image', unless 'God' is a dog.

      "And so it is with the intelligent designer and its creation."

      How do you know what or how "it is with the intelligent designer and its creation'?

      "It speaks to us in a language we can understand until hopefully one day the lights turn on and we can speak the intelligent designer's silent language."

      "It"? I keep hearing from you 'God' pushers that 'God' is a 'he', or 'she' to some people. And who is "we"? What language can "we" understand that "It" is allegedly speaking to "us"? Is "It" talking down to us in single syllables and is "It' doing so in order to get a wag of our tail? Hmm, the intelligent designer's silent language, eh? Is that the voices in your head that other people can't hear?

      "Now I know why so many folks hate silence and go out of their way to make lots of noise in their lives. It distracts from having to sit with and get to know themselves."

      Yep, lots of people hate silence and make lots of noise and don't know themselves but how does that pertain to alleged intelligent design by your imaginary sky daddy, oops, I mean your imaginary "It"?

      "Its unsettling to be sure but then thats what life's about.

      Knowing yourself."

      Oh wow. Awesome. Amazing. Stunning. Jaw droppingly profound. You should do worldwide speaking tours (using intelligently designed silent single syllable language of course) so that other people can benefit from your blessed knowledge and insight.

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    9. F&^%K, if we knew just how the body could do the amazing things that it does, the entrepenuers would make out like bandits.

      Are you really unaware of the pharmaceutical industry?

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    10. repair assumes knowledge of defects, and knowledge of the procees to successfully repair damage.

      Only intelligence has this capabilility.

      Only intelligence and that goop you shoot into tires for when they get punctures.

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    11. Sure Steve. And a volcanic eruption assumes knowledge of high pressure. Planetary orbits assume knowledge of gravitation. Only intelligence has those capabilities! Wow! ID indeed!

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    12. Predictably, when ChrisB thinks he knows what an intelligent designer 'should' be like, and someone tells him that..well no...thats not the case....he gets all bothered.



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    13. Predictably, Steve tries to project his inadequacies onto other people.

      I am not the one who makes claims about what an intelligent designer should be like. I never claimed design should be perfect. It just seems to me though, if it is intelligently designed, why not design a system that doesn't require a Rube Goldberg type repair system which itself is easily prone to fail if a part of it breaks and has limited efficiency to begin with. That doesn't sound intelligent at all. If a code designer of software designer turned in a piece of work like that, the person would be fired, and they wouldn't be referring to that person as intelligent on the way out the door.

      No, Steve, you are the one making fanciful claims about how the intelligent designer should be:

      "If the intelligent designer is omnipotent and understand how its creation will develop and what kind of design skills it will acquire, then it will tailor its own design principles to make it recognizable to the creation.

      A created being by its very nature could not understand perfect design. That would be like me talking to my dog and anticipating it to talk back to me in English.

      But in reality we talk down to our dogs in single syllables in order to get a wag of the tail.

      And so it is with the intelligent designer and its creation. It speaks to us in a language we can understand until hopefully one day the lights turn on and we can speak the intelligent designer's silent language."

      So the intelligent designer made all kinds of suboptimal, not so smart design so that our feeble minds would be able to discern that an intelligent designer made it all? That doesn't make much sense, Steve, but let's go with it:

      By what mechanism did you reveal these goals and motives of the designer?

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  6. I am expected about what will this bring to biotechnology industry in the next year. Hope that will be a good news. http://www.cd-genomics.com/blog/index.php/nobel-prize-for-chemistry-2015-dna-repair-is-the-high-light/

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    1. We've known about DNA repair for 50 years. What do you think the biotech industry is going to do next year?

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    2. Develop drugs that target DNA repair? (see also: PARP inhibitors) That being said new drugs have more of a 15-20 year timeframe than a "next year" type of timeframe

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  7. Undirected evolution cannot account for DNA repair. Evos just ignore that fact and prattle on about undirected evolution anyway.

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    1. Yeah, none of these repair mechanisms could have evolved, like the blood clotting cascade, as Professor Behe conclusively proved during the Dover tr...oh, wait.

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    2. UNDIRECTED evolution, you equivocating jerk. BTW Miller lied at Dover about the blood clotting cascade. Loser.

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    3. Joe G,

      Explain the difference between undirected evolution, and the evolution that judmarc was referring to.

      How did Miller lie about the clotting cascade?

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    4. Chris, the lamprey blood clotting cascade is a different version of the human blood clotting cascade. You cannot say that the lamprey cascade debunks the IC of the human cascade.

      That would be like saying that an android version of an app is an intermediate step to an iphone version of the same app. But we all know that the apps are simply the same design in different version to fit different hardware/operating systems.

      Thats where he lied. Like his simplistic notion that using a part of the mousetrap as a tie clip debunks IC. Well, no. Behe was we cant have a mousetrap without that part that so happens to moonlight as a tieclip. Its moonlighting on the sly has absolutely nothing to do with how the mousetrap has to function.

      Now if you can show me a functional mousetrap missing the spring, or one missing the board, or one missing the latch, or one missing the rivet that holds the latch to the board, well then someone might take him seriously.

      But then Miller knew that already. He had to fight the good fight to keep theism 'out in the cold'.

      That's how silly arguments get bumped up to prime time status.

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    5. judmarc,

      It not COULD DNA repair have evolved. The question is how probable is it that DNA repair evolved.

      Thats why evolution is relegated to answering the most esoteric aspects of biology.

      IT has absolutely nothing (nor could it) to say about the 98% of the heavy lifting that was done prior to evolution actually having a job to do.

      So go ahead and argue your heart out for that 2%.

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    6. That would be like saying that an android version of an app is an intermediate step to an iphone version of the same app

      Isn't it sort of ironic that both Android and iOs actually share a common ancestor since both are UNIX based, and iOS is based on on a UNIX version called...

      Darwin

      How many creationists would be throwing away their iPhones and iPads if they realized that their operating system is based on Darwin?

      LOL

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    7. steve preached: "The question is how probable is it that DNA repair evolved."

      Oh really? Why is that "the question"? Because you say so? Because you're trying to make it look as though you're posing a profound question that legitimately challenges science and reality? Will you show the method/experiment/math/evidence by which you've determined that the evolution of DNA repair is as improbable as you believe it is, and by which you've determined that DNA repair and everything else exists only because your chosen, so-called "God" designed, created, and directs it?

      Which so-called "God" have you chosen to believe in?

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    8. BTW Miller lied at Dover about the blood clotting cascade.

      Actually, the only people found to have lied at the Dover trial were two members of the Dover school board. The judge did find that they had lied under oath, but fortunately for them, failed to heed calls from the community to have them prosecuted for perjury.

      Regarding the blood clotting cascade and other topics related to irreducible complexity, Professor Behe did a good enough job blowing apart his own case on cross examination (which the judge has suggested ought to be taught in law schools as an example of how to cross examine) that there were very few pieces left for Ken Miller to pick up.

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    9. UNDIRECTED evolution, you equivocating jerk.

      When we say "evolution" out here in the real world, undirected evolution is what we're talking about. "Undirected" would just be redundant.

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    10. I demand equal time in schools for Farted Evolution. I have a probabilistic model for the creation of DNA by supranatural squirrels farting square circles into the genome.

      This is far superior to the theistic evolution models, after all they just claim it's extremely improbable, but my model with square circles makes it totally impossible for DNA to come about by natural processes!

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    11. It not COULD DNA repair have evolved. The question is how probable is it that DNA repair evolved.

      Near as I can make out from this typically coherency-challenged argument, what you are trying to say is that the question isn't whether it's possible DNA repair evolved, but how probable that would be.

      I think the world works in the opposite way. Let's take the course of the Mississippi River. How probable is it the river would take exactly that precise course? The chances are minuscule. Is it *possible* for the river to take that course? Sure, we see it did. So the fact that the way reality occurs is often quite improbable is not seen by anyone as a problem. (Or do you figure geology, water and gravity aren't enough, and God personally had to fine-tune the Mississippi shoreline?)

      So probability calculations for events that have already occurred in reality aren't terribly interesting, since the overwhelming number of them are wildly improbable. (Go ahead and try to calculate the odds that your parents, of all the people in the world at the time, met and married, and that on a particular date a single sperm out of millions fertilized one egg out of all those your mother carried, then trace that back through all the generations of people leading to you. You will find the probability that you exist is utterly microscopic.)

      However, if you are interested, go ahead and show the probability calculations for the evolution of DNA repair. When you do so, please try not to make the probability math error Dr. Behe always makes, in spite of being told over and over that he's wrong as a matter of sheer mathematics. (Hint: The error he makes is why there are lottery winners every couple of weeks, in spite of the odds against any individual winning the lottery being ~175 million to one.)

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    12. Steve,
      "Chris, the lamprey blood clotting cascade is a different version of the human blood clotting cascade. You cannot say that the lamprey cascade debunks the IC of the human cascade."

      Steve, either the clotting cascade cannot change without breaking, or it can. Pointing that out is not lying, it's just showing the weakness of Behe's IC premise, which is just an argument from personal incredulity. Your argument about different aps to fit different hardware is an adhoc rationalization to try and shoehorn empirical observations into your beliefs.

      IC claims certain systems cannot change without breaking. The clotting cascade shows that isn't true. Lampreys and cetaceans show that isn't true. You will need evidence to support your 'different aps for different hardware' hypothesis. Real scientific evidence like creationists demand of scientists for every last detail of the natural world. Get to work.

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    13. judmarc, the reason there are lottery winners is because there are a limited amount of numbers so the probabilities are known and because of this knowledge, the lottery makes a shitload of money.

      Thanks for unwittingly confirming that life is intelligent and knows how to beat the odds.

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    14. So lottery balls are intelligent and know how to beat the odds? Steve, you're such a laugh dude

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    15. ChrisB,

      No, IC systems say ALL the parts are needed at one time to make it work.

      Comparing lamprey and human clotting cascades shows your misunderstanding of IC.

      You need to be comparing ancestral lineages of lamprey clotting systems to current ones and show that ancestral lineages had a simpler clotting system than now.

      You would have to show that crucial parts required now were not required then because the lamprey used some other configuration that worked before it came up with the current configuration.

      Showing that the human clotting system is more complex than the lamprey's is not supporting evidence that the modern lamprey clotting system is more complex than the ancestral lamprey clotting system.

      That is the trick that was used to try and debunk Behe.

      Its the same kind of trick Matzke tried to pull on the flagellum. He tried to show that the T3SS was the precursor to the flagellum when we now know if was in fact a derivative of it.

      The simple fact is that it is easier to take out parts of a complex system and still make it run than trying to add parts to a simple system.

      Just ask a software engineer. My company's system is shit but if we want to have it improved it has to be scrapped and started from scratch. There was a limit to what it could do with its basic code.

      The only way for systems to complexify is if the target is known. There is no way around it.

      By the way, tinkering analogies wont take you where you want it to go. Tinkering is very limited. Just ask a carpenter. You can only take makeshift solutions so far.

      Then you have to ...you know....actually DESIGN something.

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    16. Dazz dazzles us with his tidbit soundbites.

      Now for his tap dance.

      wait for it.....

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    17. seriously Dazzle seriously,

      so lottery balls walk themselves into the lottery basket. Then the lottery basket churns all by itself.

      Then of course the lottery balls jump pop out on their own....

      and voila.....evolution in action people!

      Dazzle is sizzling now!

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    18. Steve:
      "No, IC systems say ALL the parts are needed at one time to make it work."

      So? Behe said this of blood clotting in humans, it was IC. But other mammals like whales miss parts of their blood clotting system compared to humans and whale blood does clot. Thus blood clotting works fine even if you don't have all bits and pieces.
      Behe had two options, commit perjury and lie human blood clotting was still IC, even with all the scientific evidence shown to him regarding the whales. Or admit he hadn't read the whale blood clotting papers. He settled for option 2 and got his cross examination added to history books how to destroy credibility of a witness.

      It wasn't a trick, dear Steve, no matter how much you hope it was.
      This was a clear case of evidence (whale blood clotting) vs wishful thinking (IC).

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    19. judmarc, the reason there are lottery winners is because there are a limited amount of numbers

      so lottery balls walk themselves into the lottery basket. Then the lottery basket churns all by itself.

      Then of course the lottery balls jump pop out on their own....

      No wonder you believe Dr. Behe knows what he's talking about. OK, so it's useless talking to you about math, because you couldn't pass a middle school probability math exam. But just one thing about your belief that people picking up the lottery balls (which *do* pop out on their own, it works via air pressure - you've obviously never watched the lottery either, though you feel qualified to comment on what you've never seen anyway) has some effect on the odds: Go ahead and flip a coin and concentrate *really* hard on making it come up heads 100% of the time. Let me know when you succeed in showing that "adding intelligence" to the process alters the outcome. ["Why do you think we call them IDiots" indeed.]

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    20. Steve of course doesn't get it. He thinks that because the lottery is designed, he wins. He's incapable of noticing that the lottery is designed to be random and that's why it's a good analogy with random mutation.

      It's such a simple concept, yet creationists are always confused by this. It would be obvious to anyone with a handful of functional brain cells, but creationists are that special kind of stupid.

      There are plenty examples that could be used that don't involve human input. Take rain for example. What are the odds that rain drops hit a surface in the precise pattern the do at any given rainy day? Not two days are the patterns the same, so creatards must believe it never rains, it's all an invention of some evil Darwinist

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    21. Dazz, what a fanstastic admission!!!!!!!!!!!

      "The lottery was designed to be random"!!!

      Yes, you got it!!!!!!

      And it didn't dawn on you that is the same reason why organisms reproduce in excess???

      Excess reproduction guarantees success of the progeny, given unknown environmental impacts. The organism has no idea which ones will succeed. But it doesn't matter because an minimum will always succeed to carry on the line.

      Thats why successful progeny are not always the strongest, fastness, meanest. Its simply which ones finally pass the survival gauntlet.

      Geez, FINALLY you have made it. Sure, you had to outwit yourself in the process.

      But you are here nevertheless, and that's good enough.

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    22. See folks, how judmarc tries to misdirect. Watch how he takes parts of comments from two different posts to two different persons, and pastes them together.

      Not too clever there Judmarc.

      My comment still stands.

      The reason lotteries are successful is because the probabilities are known and favor the lottery company. Otherwise, they would go bankrupt in a heartbeat.

      Likewise, organisms reproduce in excess because it tilts the probabilities in the organisms favor. Otherwise, life would ground to a halt in a heartbeat.

      Please, don't make it more difficult than need be.

      Randomness is part of the design. It allow organisms to persist regardless of the environmental impact. Reproductive excess is the only reason natural selection works.

      And notice how each organism has a different rate of excess reproduction. Each tailormade to achieve reproductive success.

      Insects produce thousands to keep hundreds. Snakes produce hundreds to keep several. Rabbits produce several to keep a few. Humans used to have to do the same as rabbits. But now, (due of course to intelligence) can produce one to keep one (well, most of the time anyway).

      Design in action, people.






      "steve to judmarc (only part of the comment): judmarc, the reason there are lottery winners is because there are a limited amount of numbers"

      "steve to Dazz (only part of the comments):so lottery balls walk themselves into the lottery basket. Then the lottery basket churns all by itself.

      Then of course the lottery balls jump pop out on their own...."

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    23. Oh, and by the way, excess reproduction as another benefit.

      Each organism doesnt just guarantee its own survival through excess reproduction but also contributes to their neighbor's success by contributing to the food pot.

      Foresight and planning. At its best.

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    24. So says Steve the cannibal:

      "Each organism doesnt just guarantee its own survival through excess reproduction but also contributes to their neighbor's success by contributing to the food pot."

      Eating my dead neighbor didn't really come to mind when I went to her funeral.

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    25. Steve is coming to the kind of theistic evolution in which God design creation to look the way it would if it weren't designed. If God did a really good job of it, we'd never know! So this hypothesis can't be disproven.

      Of course, this renders the idea of God (or whatever other creator you choose) unnecessary. And it makes disbelieving this whole evolution and randomness thing a kind of sacrilege. I mean, if God went to so much trouble to set the world up with random changes, natural selection, etc., don't you think we should honor his efforts by believing the idea he's trying to demonstrate?

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    26. bwilson,

      "So this hypothesis can't be disproven."

      Creation myths that are untestable and cannot be falsified: that's intelligently designed religion.

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    27. Yes, it certainly is, Chris B. And by whom? :-)

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    28. Bwilson, random changes are built into the system. It is what ensures organisms survive no matter what the environment throws their way.

      It is a perfect system. Excess reproduction drives reproductive success through the mechanism of random variation.

      Why is it a perfect design? it has been going strong for 3 billion years. no changes to the design.

      Our biosphere is teaming with life.

      'nuff said.

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    29. Ed, i admire your attempt at humour.

      But isn't that the interesting exception to the rule. Only humanity is predator. All other organisms are both predator and prey.

      Yes, unfortunately humans get caught in shark teeth and bear claws and pitbull jaws, etc. etc. But I think you will clearly find that the motive is primarily defense and/or agressive instinct and not an empty stomach.

      So the point still stands.

      Excess reproduction is a designed object that works. Big time.

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    30. Steve,

      You're all over the place. On the one hand you accept all of evolution for the last 3 billion years, perhaps even more, with the caveat that, to you, the whole "system" was "designed" to evolve in the first place. On the other you think that evolutionary IC is something that has been really found in such things like the clotting cascade (which is unsustainable anyway). But the latter undermines your acceptance of the former.

      What are you thinking here? How could the cutting cascade be evolutionarily irreducibly complex if we share ancestries with such things as lamprey? Those things lack several of the components that our clotting cascade has. Do you see the contradiction you're engaging into? If everything has been evolving for billions of years, and if we share common ancestry with this and that, then, necessarily, those ancestral forms lacked some protein or another that in the cascade. So, maybe our own clotting cascade can't be without any component (that's not strictly true, but let's suppose so), but that was not necessarily true for forms ancestral to us (as living things today show, under some condition or another, component can be missing and clotting still works).

      So how are you thinking that evolutionarily IC things would exist if billions of years of evolution indeed happened? Do you think that the gods come from time to time because, what you describe as their "perfect" system, actually needs a lot of fixing?

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    31. Hi Steve, you wrote:
      "But isn't that the interesting exception to the rule. Only humanity is predator. All other organisms are both predator and prey."

      Steve, I don't agree. Lions, sharks, eagles are considered to be top of the food chain, and you rarely see these predators having a go at each other, unless extreme circumstances (no food) drives them.
      Humanity is predator and prey, thousands of people dying at the hands of other people every day. War, domestic violence, religious violence, violence because some one has a thing another one doesn't have aka robbery, sexual violence. A few tribes in secluded areas of the world until recently actually ate their fallen enemies. And yes, some mad serial killers also ate their victims.

      This type of behavior, killing fellow man, isn't really common in the (other) animal world. Au contrair, except the few times the new dominant male in a tribe of for example lions, kills of the off-spring of the former dominant male, killing within the species rarely occurs.

      Humanity seems to be 'special' I agree there, as it's one of the few species which actively hunts and kills it's own kind. And when one group of people slaughter another, typically a higher being is thanked for the support to the victors.

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    32. ChrisB, excess reproduction is not part of any creation myth I know of.

      Curious why you would inject creation myths into the discussion.

      Excess reproduction is an easy observation. It logically precedes the mechanism of random variation.

      And how is the above not testable? You can program Avida to adjust the amount of offspring for each virtual animal and see what combinations will lead to extinction.

      A hypothesis can be made that the requirement for a stable biosphere is that the higher up the food chain the lower the average rate of reproduction. If we flip that around and have a lower reproduction rate for insects and a higher reproduction rate for mammals, what will be the result. I predict a quick unraveling and demise of life on earth.

      So there is no reason the idea of different rates of reproduction depending on the position in the food chain as the driver of life's continuing success cannot be tested.

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    33. See folks, how judmarc tries to misdirect.

      Ah, so it's "misdirection" to point out that you know less probability math than an average grade schooler when you comment about the unlikelihood of evolution? The point is you don't have any idea about how to calculate likelihood, so your intuitions/opinions about the likelihood of evolution are completely worthless.

      There, was that simple enough for you, since you said there's no reason to make this more difficult than it needs to be?

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    34. Steve,

      Excess reproduction strategies (the spectrum of r to K selection) are explained by existing evolutionary and ecological theories. We studied computer models of population dynamics in my core ecology and evolutionary biology undergrad course 25-30 years ago. Your ID/creationists myths are unneeded and superfluous.

      If you want to provide evidence of intelligent design, your intelligent design theory will have to make a testable prediction unique to it (try to come up with something that doesn't look exactly like evolution) and then test that prediction. Good luck.

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  8. And Steve's 'Foresight and planning, at its best' accounts for the hundreds of thousands of species that have become extinct in the past?

    All those who's 'design' guaranteed their own survival through excess reproduction!

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    1. but wait a minute Tim Vowles, we are still here....and, and, the current biosphere is teaming with life.

      By last count, were are on the way to 7 billion people and counting.

      Sooooo.....saying millions of species have gone extinct shows how meaningless the 26 variations on the definition of species is.

      Now if a whole order of organims went excinct, it seems only then that life would probably unravel and disintegrate completely since all organisms are interdependent relying on the food chain.

      so the observation and conclusion still stands. Excess reproduction ensure the viability of life. It is what drives differential heritable traits.

      Natural selection is the outcome, not the driver.

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    2. Interesting. Anyway, natural selection is not a driver. Natural selection is not even a thing. t's just an anthropomorphic/metaphoric concept coined as a shorthand to describe that whatever has advantageous variations has a higher probability to survive and reproduce. Evolution is just the consequence of the way nature in general, and life in particular, work. So, sure, it has that probability we conceptualize as natural selection, but that's not the whole story.

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    3. Now if a whole order of organims went excinct, it seems only then that life would probably unravel and disintegrate completely since all organisms are interdependent relying on the food chain.

      Yeah, just like life on earth went completely extinct when the dinosaurs died out - oh, wait....

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    4. Steve's groundbreaking theory:

      Success ---> Design!
      Failure ---> Design!
      Randomness ---> Design!
      Design ---> yee hee
      yee hee ---> YHWH

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    5. Sorry Steve, I didn't wait for your goalposts to move.

      I didn't realise that when you said And notice how each organism has a different rate of excess reproduction. Each tailormade to achieve reproductive success. you really meant that all that reproduction resulted in different species, and that 'reproductive success' allowed for the extinction of that original organism.

      I guess that all these excessively reproduced offspring gave rise to all of the variety of teeming life we now have on earth.

      When do you think humans will start to reproduce different species?

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  9. judmarcTuesday, October 13, 2015 7:02:00 AM

    "It not COULD DNA repair have evolved. The question is how probable is it that DNA repair evolved."


    With 100 mutations per genome, the copying fidelity is 1- 1/30.000.000 = 1-0.00000003 = 0.99999997

    If copyig fidelity had to evolve gradually wat would happen with organisms having a CF of say 0.90 or 0.99?

    They would die because of genomic meltdown within <10 generations, resp. <25 generations.

    Genomes had to start with nearly perfect CF.

    There is no way out. Genomes were frontloaded.

    Frontloading is the new theory.




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    1. A typical small bacterial genome is 2,000,000 bp in size. The standard error rate of DNA/RNA polymerases without proofreading is 1 error per one million reactions. That means it could replicate a modern bacterial genome with an average of only two errors per generation.

      Once proofreading (not repair) arose the error rate dropped to one in 100 million so a DNA polymerase is more than capable of replicating the genome of modern organisms (small bacteria) without the absolute necessity of repair enzymes.

      It's reasonable to speculate that the earliest living cells had only 200 genes of average size 1000 bp for a total genome size of 200,000 bp. Even a DNA polymerase without proofreading could make error-free copies of such a genome. There's is no need for repair enzymes in such a system although in the long run they will be beneficial.

      IDiots need to stop and think before they open their mouths. It makes no sense to quote numbers based on the human genome which didn't exist until 3.5 billion years after life began on Earth.

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    2. Just wanted to point out Peer was actually quoting my quote of another IDiot, not quoting something I wrote.

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    3. So Peer, let's talk about even simpler math.

      Bacteria with tiny genomes carried "front loading" information for human genomes that are huge in comparison (but have no junk) where, exactly?

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