DNA Repair- A Vital Function
by BradfordThe capacity to remedy damage to DNA is a very important biological function. Mechanisms involved in the repair of DNA are found in all forms of life. How important is it? Is it neccessary to sustain life as we know it? My views are known at this site but am I alone in viewing DNA repair as a critically important function? Not if the views of many researchers are relevant. There are many papers touting the importance of DNA repair. Here are just some of the samples:
and this:
The damaging effect of UV radiation and X-rays on genetic materials was already recognized in the early part of the 20th century, and the realization that cells sometimes could correct genetic mutations after damage emerged in the 1930s. Nonetheless, says Stanford University geneticist Philip C. Hanawalt, one of the pioneers in the field of DNA repair, "For many years after the discovery of the double-helical DNA structure, we thought the genetic material must be incredibly well-protected and not subject to chemical alteration." But now, Hanawalt says, "We know that damage to DNA occurs all the time and that DNA repair is essential to maintain the genome."
and there is this:
and this:
January 16th, 2008 at 7:16 am
I note each of those studies concerns the necessity of DNA repair in highly derived organisms (mammals or humans), and primarily having to do with maintenance of the organism over time rather than reproduction. This doesn't support the claim that DNA repair was essential for genomic integrity in primordial organisms with much smaller genomes not in competition with their more derived cousins. Or even that DNA repair is essential for genomic integrity in extant organisms with small genomes.
Comment by Zachriel — January 16, 2008 @ 7:16 am
January 16th, 2008 at 7:32 am
We know that DNA repair is really important. But in the previous thread we were discussing whether sustained life is *in principle impossible* without it. And the answer is no. Agreed?
BTW, there is also RNA repair. Did you know that RNA polymerase has error correction capabilities? Check out this paper:
Poole AM, Logan DT. 2005. Modern mRNA proofreading and repair: clues that the last universal common ancestor possessed an RNA genome? Mol Biol Evol 22:1444"“1455.
[edit: the paper is for FREE]
Comment by Raevmo — January 16, 2008 @ 7:32 am
January 16th, 2008 at 7:46 am
Zachriel:
Yet those small genome organisms have these functions too.
Comment by Bradford — January 16, 2008 @ 7:46 am
January 16th, 2008 at 7:50 am
I thought we agreed it is a matter of testing. You're not backtracking to please the crowd are you?
One of the links I supplied in the other thread was to a blog entry at IS about RNA polymerase. We are aware of it. It helps keep the damage from even showing up on the radar screen.
Comment by Bradford — January 16, 2008 @ 7:50 am
January 16th, 2008 at 8:40 am
Ugh. This is getting tiring. As said before, nobody argues that DNA repair is not important in principle or that some form of DNA repair is not essential in current complex organisms.
What we argued against was that DNA repair or error correction IN PRINCIPLE is a necessary prerequisite for life. The reason WHY I bothered to challenge your assertion is simply so that people don't make the following argument to show that DNA error correction could not have evolved:
1) DNA is required to encode DNA repair proteins and the error correction machinery.
2) DNA repair proteins/error correction machinery are essential for the maintenance of a genome.
3) Take 1) and 2) together and you have an IC (and supposedly unevolvable) system.
To invalidate such an argument all one has to show is that there is no logical barrier to a stable genome without error correction. That has been done in the previous thread.
Comment by hrun — January 16, 2008 @ 8:40 am
January 16th, 2008 at 11:38 am
For those of you who are more well versed in these matters that I:
Is it generally accepted that the rate of deleterious mutations is higher than the rate of beneficial mutations?
If so, how does evolution proceed in the primordial world without repair mechanisms?
In their acceptance of naturalistic origens and evolution what are the assumptions that the critics make to explain the verifiable observation that deleterious mutations are more numberous than beneficial?
Comment by 0112358 — January 16, 2008 @ 11:38 am
January 16th, 2008 at 12:13 pm
These are actually two somewhat unrelated matters: the repair machinery can not distinguish between a beneficial and deleterious mutation. So the repair machinery does not aid in the problem that deleterious mutations are more common than beneficial ones.
Comment by hrun — January 16, 2008 @ 12:13 pm
January 16th, 2008 at 12:56 pm
Let's abstract a bit so we can visualize a plausible process without a lot of arithmetic.
We have a stable population of a thousand asexual organisms. They each replicate once. Of these, let's say ten have non-neutral mutations, one is beneficial, nine are detrimental. To maintain a stable population, the survivors are selected randomly (one clone is as good as another), except the beneficial mutant will always be selected, and the nine detrimental mutants will always be deselected.
Generation 0: 1000 clonesGeneration 1: 999 clones, 1 beneficial
Generation 2: 998 clones, 2 beneficial
Generation 3: 996 clones, 4 beneficial
Over time, the beneficial mutants will overtake the population.
Real cases can be far more complex. Benefit and detriment are closely tied to the environment. Benefit and detriment are often slight. The effect of selection can depend on whether a population is stable. And the race is not always to the swift, but time and chance happen to them all. In any case, there is no inherent problem with the question you pose.
As hrun points out, repair mechanisms don't affect the ratio of beneficial to detrimental mutations. But what they do affect is the ratio of mutants to clones.
Comment by Zachriel — January 16, 2008 @ 12:56 pm
January 16th, 2008 at 1:05 pm
Hrun:
Oh no you don't. This is not a medieval fiefdom where all you have to do is present a logical argument. This is the 21st century where empirical evaluations hold sway. You need something you do not find naturally in nature- an organism devoid of any sort of repair function. Then you need to test it for Bradford's Law. Information loss will exceed gains for the genome in question- (any time period).
Comment by Bradford — January 16, 2008 @ 1:05 pm
January 16th, 2008 at 1:05 pm
OK. But my point is that, if the rate of deleterious mutation is higher than the rate of beneficial mutation, any self replicating machine that slaps itself together out of the ooze has a very bleak future.
Comment by 0112358 — January 16, 2008 @ 1:05 pm
January 16th, 2008 at 1:06 pm
Mr Fibonacci:
I believe it is.
Strange question. Are you suggesting it can't?
Here's a simple model. Suppose there is a beneficial allele with relative viability 1, and loads of deleterious alleles with relative viability 1-s, s>0. The beneficial allele mutates with frequency u>0 into a deleterious allele, but the reverse mutation rate (from deleterious to beneficial) is much smaller, and we neglect it. The frequency of the beneficial allele then changes from one generation (frequency p) to the next (frequency p') according to
p' = (1-u)p/(p+(1-p)(1-s))
Then the equilibrium frequency (where p'=p) of the beneficial allele is
1-u/s
Therefore, as long as the mutation rate u is smaller than the selection differential s, the beneficial allele remains in the population at positive frequency, even if mutation is heavily biased towards deleterious alleles.
Comment by Raevmo — January 16, 2008 @ 1:06 pm
January 16th, 2008 at 1:15 pm
Bradford vs. Bradford:
Bradford, where is your proof that error correction is a prerequisite for life. Since this is clearly an argument of the type 'there are no black swans' you can not simply prove it by showing that certain forms of life are not possible without error correction. To support your assertion you need to LOGICALLY show that life is not possible without error correction.
And I refer you back to my previous assertion: Life is not possible in solar systems that do not contain exactly nine planets. Call it hrun's law if you wish. Wait, what? You say you don't have proof. Keep an open mind man. I'm certain that you are unable to point me to a solar system with less or more than nine planets that contains life.
(leaving aside the question of whether or not Pluto should be considered a planet)
Comment by hrun — January 16, 2008 @ 1:15 pm
January 16th, 2008 at 1:16 pm
0112358 Says:
Yes.
That's an open question. The lack of such mechanisms signifies that the number of mutations would skyrocket. A stable genome needs to retain genomic sequences that enable reproductive fitness.
Critics accurately point out that mutations that are fatal to an individual organism cause its demise and elimination from the gene pool. We see this occur and call it natural selection. NS works fine as long as the rate of reproduction is adaquate to replace the genomes of organisms removed by their death or inability to reproduce.
Comment by Bradford — January 16, 2008 @ 1:16 pm
January 16th, 2008 at 1:21 pm
hrun:
C'mon hrun there is enough evidence as to the essential nature of repair to form a suspicion and predictions based on that suspicion. The reason you have to shout "logically" is your discomfort with the implications of my being right. It's a paradigm destroyer. You can't logically show that reproduction equals demise. You demonstrate it.
Comment by Bradford — January 16, 2008 @ 1:21 pm
January 16th, 2008 at 1:25 pm
Again with that assertion. Can you point to a source of what the mutation rate is in absence of repair mechanisms?
So you DO realize that high mutation rates can be accommodated through a sufficiently large number of progeny?
Comment by hrun — January 16, 2008 @ 1:25 pm
January 16th, 2008 at 1:25 pm
It's a good, honest question.
Comment by Bradford — January 16, 2008 @ 1:25 pm
January 16th, 2008 at 1:27 pm
OK. I give up. You destroyed my battleship… aehh paradigm.
Comment by hrun — January 16, 2008 @ 1:27 pm
January 16th, 2008 at 1:27 pm
Yes. Do you bother to think about the fact that unfettered genomic degradation lowers the rate of reproduction while increasing the rate of death?
Comment by Bradford — January 16, 2008 @ 1:27 pm
January 16th, 2008 at 1:29 pm
Bradford:
And I answered it. Do you dispute my answer?
Comment by Raevmo — January 16, 2008 @ 1:29 pm
January 16th, 2008 at 1:34 pm
So Raevmo and Zachriel have given good explanations of how a stable self-replicating population can survive even with a higher rate of deleterious mutation than beneficial. Do we have an estimate of how many genes would have needed to come together in the first progenitor of that population so that it was self-replicating and stable enough to actually become a population?
Comment by 0112358 — January 16, 2008 @ 1:34 pm
January 16th, 2008 at 1:36 pm
I would note that selection dynamics are altered for populations deprived of repair functions.
Comment by Bradford — January 16, 2008 @ 1:36 pm
January 16th, 2008 at 1:37 pm
Bradford:
I'm beginning to suspect that you are willfully ignorant. As has been pointed out numerous times by now, it is not true that a lack of repair mechanisms necessarily implies "unfettered genomic degradation".
Comment by Raevmo — January 16, 2008 @ 1:37 pm
January 16th, 2008 at 1:39 pm
Bradford:
Can you please be a little more specific?
Comment by Raevmo — January 16, 2008 @ 1:39 pm
January 16th, 2008 at 1:44 pm
Another good question. There is not precision in the sense of being able to say that x genes is the demarcation line between a minimally functional cell and non-viability. Nevertheless we can get a sense of what functions are essential and the minimal number of genes associated with those functions. IOW we can get a rough idea. Any genes essential to the replication of an organism would of course be counted.
Comment by Bradford — January 16, 2008 @ 1:44 pm
January 16th, 2008 at 1:46 pm
Fibo:
In theory, just one. A self-replicating RNA molecule could be regarded as a single gene. But so far, no such molecule has been found. However:
according to this paper:
Poole 2006. Bioessays 28.
Comment by Raevmo — January 16, 2008 @ 1:46 pm
January 16th, 2008 at 1:48 pm
I've responded to your RNA world claims by pointing out the need for evidence of pathways to cells. You and others are not willfully ignorant about such matters. You are genuinely ignorant.
Comment by Bradford — January 16, 2008 @ 1:48 pm
January 16th, 2008 at 1:53 pm
Raevmo is entitled to his theories but there is delicious irony here. For one accused of insufficient evidence for my POV the demand for the same of the other side is eminently reasonable don't you think 0112358?
Comment by Bradford — January 16, 2008 @ 1:53 pm
January 16th, 2008 at 2:02 pm
Very!!
Comment by 0112358 — January 16, 2008 @ 2:02 pm
January 16th, 2008 at 2:31 pm
Bradford:
You're being a bit disingenuous. You haven't been accused of insufficient evidence, but of making fatal logical errors. A demand for evidence is quite reasonable, and in this spirit I have referred to a number of recent and relevant scientific papers. What is ironic is that you thrive on a lack of evidence, since your point of view (ID) relies entirely on ignorance about events in the remote past. Unfortunately for you, the gaps you're hiding in are getting smaller every day. Read the papers I referred to. If you don't have access, I can email them.
Comment by Raevmo — January 16, 2008 @ 2:31 pm
January 16th, 2008 at 2:44 pm
And you're being inaccurate.
Logic is based on what actually occurs in nature as opposed to your arguments as to what must have occurred.
Comment by Bradford — January 16, 2008 @ 2:44 pm
January 16th, 2008 at 2:51 pm
You claim a self-replicator appeared and replicated itself en route to a cell. Since I allegedly thrive on a lack of evidence describe in your own words how such a process took place and don't forget the evidence.
Comment by Bradford — January 16, 2008 @ 2:51 pm
January 16th, 2008 at 3:16 pm
Bradford:
No, you argued that something cannot occur: sustained life without error correction. But you have failed to provide a correct logical argument.
It's not a claim, it's a hypothesis. The little evidence there is so far has been summarized in the references I supplied, in words far more eloquent than I could muster.
And where can I find the overwhelming evidence that refutes this hypothesis and shows that a Designer did it? No need to describe it in your own words, just a few references to recent ID research will do.
Comment by Raevmo — January 16, 2008 @ 3:16 pm
January 16th, 2008 at 3:23 pm
Logic is based on what actually occurs in nature as opposed to your arguments as to what must have occurred.
No logical argument would be acceptable to you. But these matters are testable. An organism able to thrive in the absence of error correction would be all you need. Arguments would not be necessary.
Comment by Bradford — January 16, 2008 @ 3:23 pm
January 16th, 2008 at 4:54 pm
Recalling Mike Gene's "error-correction runs deep," I mentioned (in another topic) Hopfield's "kinetic proofreading" hypothesis. Bradford, in order for critics to show that your hypothesis (error-correction is a necessary prerequisite) is incorrect, they cannot assume such (error-correcting) features exist. So the one paper cited, which assumes the intrinsic error-correcting property of the genetic code ("least significant" or degenerate nits) does not constitute an argument against your idea"”It assumes your hypothesis!
No "RNA-World" hypothesis is a counterargument, Bradford, because the RNA-World hypothesis is grounded exclusively in the RNA-code which differs from the DNA-code only in the substitution of uracil for thymine"”accepting all the intrinsic error-controlling functions of the DNA-code"”and more!
The critics' argument appears to be that because I can conceive of something which does not exist it must be true. An "Intelligent Design" argument if I ever heard one!
Comment by Rock — January 16, 2008 @ 4:54 pm
January 16th, 2008 at 5:14 pm
So the problem for the critic seems to be that ID, is not valid because it can never actually prove the existence of a designer. No tests can be run that will implicitly implicate a designer. The IDist bases his beliefs on negative reasoning (i.e. such and such could never have happened thus life must have been designed).
How, exactly, does this differ from Naturalism which can never actually prove that all life spontaneously arose. The Naturalist has the same problem because no tests can be run that will implicitly implicate naturalistic causes. He may show a possible mechanism but this does not prove the point. The Naturalists also bases his belief on negative reasoning (i.e. There is no such thing as the supernatural therefore life must have arisen by chance.
In the area of science the distinction between us is not really that big.
In the area of philosophy the distinction is huge.
Can we at least agree that we all are philosophers?
Comment by 0112358 — January 16, 2008 @ 5:14 pm
January 16th, 2008 at 5:43 pm
Fibo:
In principle it's possible that life has been designed. But there's just no positive evidence that I'm aware of. You're right that IDists like Bradford typically use negative reasoning. Has Bradford ever proposed a mechanistic ID hypothesis? Nope. All he does is criticize (and poorly at that) the work of others, without doing any of the hard work himself. It's quite pathetic.
Science proposes testable hypotheses. It doesn't conclusively prove anything. At best, it can show that life can arise "spontaneously", but that doesn't prove that it actually did on earth. But why do you say that "chance" is the only alternative to the supernatural?
Comment by Raevmo — January 16, 2008 @ 5:43 pm
January 16th, 2008 at 6:53 pm
I am "quite insane."
Indeed, I reject the idea that science doesn't "prove" anything. I wonder if anyone else is as sick of this dumb-ass argument as I am.
Because science didn't prove your theory it means science doesn't prove any theory.
You teach science?
I don't think you do.
Comment by Rock — January 16, 2008 @ 6:53 pm
January 16th, 2008 at 6:56 pm
Raevmo:
I'm not sure that I said that, but in regard to origins I see no other alternatives. Life either originated by chance events or it was created or directed by some intelligence. To suppress the idea of a supernatural entity (i.e. God) someone might speculate that a natural extraterrestrial intelligence of some sort planted life on earth. This would leave open the question of the origins of the extraterrestrial intelligence. As I see it chance and the Supernatural are the only two alternatives. Do you see another?
Comment by 0112358 — January 16, 2008 @ 6:56 pm
January 16th, 2008 at 7:05 pm
Raevmo:
I'm looking at the same mechanisms you are in an attempt to find out if information gains would exceed losses. If they do not data favoring intelligent input is suggested.
This is sour grapes. Actuallly some of the work done is incredibly good and the researchers themselves are careful about what the data suggests. It is internet ideologues who misuse data (read that ribozymes) to further their own purposes.
Comment by Bradford — January 16, 2008 @ 7:05 pm
January 16th, 2008 at 7:07 pm
Raevmo, be civil or find something else to do.
Comment by Bradford — January 16, 2008 @ 7:07 pm
January 16th, 2008 at 7:16 pm
The word "prove" has more than one meaning which can lead to equivocation. Science doesn't offer up proofs such as those found in mathematics. Rather, scientific claims are supported or contradicted by the evidence. Even the most strongly supported scientific claims are considered tentative and subject to being revised or discarded in the light of new evidence.
The origin of life could have been a lucky accident, but most scientists in the field believe it was a consequence of not yet completely understood natural processes.
Comment by Zachriel — January 16, 2008 @ 7:16 pm
January 16th, 2008 at 7:20 pm
Fibo:
I guess it depends on what you mean by "chance". Maybe the evolution of life is inevitable given the laws of nature. I don't know. Do you?
Comment by Raevmo — January 16, 2008 @ 7:20 pm
January 16th, 2008 at 7:23 pm
Rock:
Thanks for pointing that out Rock. Critics have become unwitting advocates of front loading error correction at the initial step in a putative pathway to life.
It's as if they want the desired conclusion drawn without demonstrating causal details.
Comment by Bradford — January 16, 2008 @ 7:23 pm
January 16th, 2008 at 7:26 pm
Bradford:
Information gains? What do you mean exactly?
Comment by Raevmo — January 16, 2008 @ 7:26 pm
January 16th, 2008 at 7:36 pm
Zachriel:
Raevmo:
If life developed as a consequence of natural processes (or was inevitable given the laws of nature) isn't it still just chance unless those laws were set up by a supernatural intelligence?
Comment by 0112358 — January 16, 2008 @ 7:36 pm
January 16th, 2008 at 7:38 pm
Related to beneficial mutations. Here's a question needing an honest response from you. What type of experimental outcomes would convince you that sequences of functional codons degrade faster than they would be generated in correction deprived genomes?
Comment by Bradford — January 16, 2008 @ 7:38 pm
January 16th, 2008 at 7:49 pm
Bradford:
Wow. Sequences degrading faster than a process. Can you at least make sure that the units on both sides of the equation are the same? Basic science. Try again.
Comment by Raevmo — January 16, 2008 @ 7:49 pm
January 16th, 2008 at 7:56 pm
Fibo:
What do you think? What do you mean by "chance"
Comment by Raevmo — January 16, 2008 @ 7:56 pm
January 16th, 2008 at 10:17 pm
Chance has various meanings, but we don't consider how planets move in their orbits, or the ratio of hydrogen to oxygen in water molecules, or the close biological resemblance of children and parents, to be chance. If certain conditions inevitably lead to the beginnings of life, then we wouldn't consider that chance.
Comment by Zachriel — January 16, 2008 @ 10:17 pm
January 17th, 2008 at 12:07 am
Raevmo, to Bradford:
Raevmo,
Double wow. Bradford was embarrassed enough by your criticism to go back and edit the awkward wording in his comment. But he didn't stop there — he also edited your quote of his comment to remove the awkward wording. Talk about a sensitive ego.
The revised wording still doesn't make sense:
I think he's really trying to ask this:
What sort of experimental results would convince you that genomes lacking error correction degrade over time?
One answer: evidence that the mathematical model of mutational meltdown is massively mistaken.
Comment by valerie — January 17, 2008 @ 12:07 am
January 17th, 2008 at 2:16 am
Raevmo:
By chance I simply mean that which is not planned or directed. In this sense I would even consider the order we see in the universe. . .
to be chance unless they were planned or ordered that way. We know the mechanisms behind these phenomena so there is something there which causes them to be so. The question then becomes why are those mechanisms there in the first place. If one holds the view that the laws of physics are absolute, that they are just there, that they have always existed and that they were not planned or ordered by some intelligence one is left with the view that all of reality is pure chance in the sense that I am using it.
Once again we are all back to philosophy and not science. We are all rational people and are trying to make rational sense of our universe. It's just that some of us feel that it is more rational to accept the notion of design than not.
Comment by 0112358 — January 17, 2008 @ 2:16 am
January 17th, 2008 at 6:18 am
Again, passing through TT for curiosity-sake. I won't wade through the pile of comments in the thread, other than to note that Bradford is only partly correct, and also partly wrong.
Is DNA repair a vital function? No, of course not. Look what happens when you delete a gene required for DNA repair in cell culture - you get something rather like cancer cells. That is, they don't die, and they actually thrive to the point of killing the host if injected into a mouse or other organism - ergo, they're not necessary, vital, or fundamental to cellular life. DNA repair does, however, improve the reproductive viability of an organism (be it cellular or multicellular), and thus confers an advantage to organisms and their progeny.
*sorry if this was said already*
Comment by Dan — January 17, 2008 @ 6:18 am
January 17th, 2008 at 6:25 am
Dan, it is believed that malfunctions of DNA repair can sometimes lead to cancer but you are not suggesting that cancerous cells have lost the capacity to repair their DNA are you?
Comment by Bradford — January 17, 2008 @ 6:25 am
January 17th, 2008 at 6:56 am
Valerie:
Geez Louis. Sad, really. To his credit though, he left your comment in place.
That would be an answer. Does Bradford think the model (Eigen 1971, or simplified version in Maynard Smith & Szathmary's 1995 book) is flawed? If so, in what way?
Another answer would be if sufficiently small genomes without error correction and sufficiently low mutation rate (such that the model would predict no meltdown) would degenerate anyway. That would be fairly convincing. In practice it will be hard to realize such an experiment, since RNA polymerase seems to have "hard-wired" error correction (Poole & Logan 2005). In case of no meltdown, it could then be argued that error repair prevented the meltdown.
Comment by Raevmo — January 17, 2008 @ 6:56 am
January 17th, 2008 at 7:07 am
"but you are not suggesting that cancerous cells have lost the capacity to repair their DNA are you"
Defective DNA polymerase-delta proofreading causes cancer susceptibility in mice:
Now, that's just one DNA mismatch repair enzyme, and there are others. Thus, one cannot rule out a certain amount of redundancy. Yet, deletion of this gene clearly causes a non-lethal yet significant change in phenotype at the cellular level. Ergo, it is NOT a vital function for cellular viability.
Comment by Dan — January 17, 2008 @ 7:07 am
January 17th, 2008 at 8:37 am
When Halley said we would see a comet in a certain year in certain sector of the sky, he wasn't appealing to chance. Using the word "chance" in this context leads to nothing but confusion.
An interesting question, but not knowing the answer doesn't mean it has to be chance. Many patterns in nature have been determined to be due to underlying symmetries. Not knowing the mechanism of planetary motions doesn't mean they move by chance. Moreover, even if there were valid reasons to apply the term "chance" to the ultimate symmetries of the universe, we still wouldn't apply the term to Halley's carefully delimited prediction.
Compare to a valid use of the word I gave earlier. And the race is not always to the swift, but time and chance happen to them all.
You're conflating science and philosophy. You can't just sweep away valid scientific claims with a sweep of the hand. Everyone in the world could look up and see Halley's Comet return on Christmas Eve 1758.
Comment by Zachriel — January 17, 2008 @ 8:37 am
January 17th, 2008 at 9:48 am
chance, something that happens unpredictably without discernible human intention or observable cause.
Comment by Zachriel — January 17, 2008 @ 9:48 am
January 17th, 2008 at 11:14 am
Zachriel:
I don't believe I am sweeping away any valid scientific claims. I simply stated that:
We have only two choices. Either there is an intelligence behind the order we observe in the universe or there is not. If there is no intelligence behind the order we observe and measure, the fact that it exists and that "there is something rather than nothing" is purely coincidental.
Comment by 0112358 — January 17, 2008 @ 11:14 am
January 17th, 2008 at 11:36 am
It may not be a perfect dichotomy. Intelligence may be involved with the order we observe without being behind the order. Or intelligence may not be a valid description of cosmic forces of which we have little understanding. It's like saying an electron is either here or it isn't. Well, the dichotomy doesn't work because the definition of "here" is not valid on quantum scales. Even "existence" is nebulous on quantum scales. Matter apparently just fades in and out of existence!
Your conclusion assumes that somethingness can't be explained by other means. Our parochial notions of existence may not be incumbent on the universe.
"Coincidental" may be a better word choice than "chance". And you have limited its application to a domain. But you may as well say that God is a coincidence, or the existence of God is just a matter of chance.
Comment by Zachriel — January 17, 2008 @ 11:36 am
January 17th, 2008 at 12:30 pm
Zachriel:
Yes, but now we are back to philosophy. Either the laws of physics are All-in-All or the existence of God (the Designer) is All-in-All. One of them is the basis of all there is. To me the fact that there is something rather than nothing and that the universe is so finely tuned would favor a philosophy that accepts the existence of an eternal Designer rather than a philosophy that accepts only the eternal existence of physical laws that eventually lead to order.
Comment by 0112358 — January 17, 2008 @ 12:30 pm
January 17th, 2008 at 1:47 pm
This was your original position:
I'm not sure if you have modified your position, or are just avoiding its repetition in the same terms.
Then you compared ID and Naturalism, as if they were opposing sides of the same question.
Intelligent Design (as normally construed) claims that there is scientific evidence of telic causes in biology. This is a false claim.
You then added,
There is substantial scientific evidence in support of the Theory of Evolution, and no scientific evidence in support of Intelligent Design (as normally construed). That is not a minor distinction.
Comment by Zachriel — January 17, 2008 @ 1:47 pm
January 17th, 2008 at 2:48 pm
Zachriel,
Maybe it would be better put: We all do science in the same way but our philosophies inform the interpretation of our observations.
I agree with you that there is no scientific evidence for telic causes. But I would also contend that there is no scientific evidence of non-telic causes. Since we are both beyond the realm of science at this point I will repeat:
Whether or not there is substantial scientific evidence supporting the theory of evolution is inconsequential as far as I'm concerned. The fact that there is even anything that might have evolved is enough for me to accept the existence of an eternal Designer rather than the existence of eternal physical laws that coincidentally led to the order we now observe.
Comment by 0112358 — January 17, 2008 @ 2:48 pm
January 17th, 2008 at 3:01 pm
From the reference you supplied:
If glitches in DNA replication fidelity lead to an increased risk of cancer then indcations are that as genomes degrade there is an increased risk of lethality for the individual affected. My points relate to what occurs at the level of an organism. Although cancer cells survive the genetic changes even they eventually die when the indivdual does.
Comment by Bradford — January 17, 2008 @ 3:01 pm
January 17th, 2008 at 3:27 pm
"My points relate to what occurs at the level of an organism."
My mistake. I thought you were claiming that DNA mismatch repair was vital for life, not vital for multicellular life. In that case, yes, I think I would agree with you.
Comment by Dan — January 17, 2008 @ 3:27 pm
January 17th, 2008 at 5:52 pm
??? Are cancer cells considered an independent life form?
Comment by Joy — January 17, 2008 @ 5:52 pm
January 17th, 2008 at 7:32 pm
Fine-tuning is not a strong argument as the fine-tuning may depend on symmetries of which you are simply unaware.
Douglas Adams: Imagine a puddle waking up one morning and thinking, 'This is an interesting world I find myself in, an interesting hole I find myself in, fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!'
So you have a belief, which is fine, but no justification.
The origin of humanity inconsequential? I suppose for some it does seem that way when contemplating the vastness of the cosmos.
Comment by Zachriel — January 17, 2008 @ 7:32 pm
January 18th, 2008 at 2:29 am
Zachriel,
There is one or a combination of things going wrong in our discussion. I may be a poor communicator, we may be speaking two different languages or you may not be reading carefully.
I would certainly never say that the origin of humanity is inconsequential. On the contrary, the origin of humanity is very consequential, especially if it was forseen and planned by an intelligent being.
I believe my exact words were:
So you see, what is inconsequential is not humanity but the status of scientific evidence supporting the theory of evolution. This evidence, if it is indeed there, is inconsequential in regard to the question of why there is anything at all. This question is beyond the scope of science not only for the IDists but even for you.
What we all need to realize is that the question of origins comes down to philosophy and not science. For IDists, there is no hypothesis that can be made and tested that will beyond a shadow-of-doubt implicate a designer as the ultimate source of the physical universe. For naturalists, there is no hypothesis that can be made and tested that will beyond a shadow-of-doubt implicate an eternal set of physical laws as the ultimate source of the physical universe.
At best we can look at the order we observe in the physical world and use this to inform our philosophy. Science is only possible because there is order in the universe. Can we agree that there is order in the universe? If so which is the most rational philosophy to hold:
An eternal intelligence arranged it so
or
A non-intelligent eternal set of physical laws that coincidentally led to order arranged it so?
Comment by 0112358 — January 18, 2008 @ 2:29 am
January 18th, 2008 at 8:55 am
Joy,
"Are cancer cells considered an independent life form?"
No.
Are cancer cells a viable life form for any length of time? (or possess any degree of vitality?)
Yes.
Comment by Dan — January 18, 2008 @ 8:55 am
January 18th, 2008 at 10:51 am
What you said was, "Whether or not there is substantial scientific evidence supporting the theory of evolution is inconsequential as far as I'm concerned." As the Theory of Evolution explains the emergence of the human species from non-human species, then the Theory of Evolution speaks to the origin of humanity. At the very least, it speaks to what most would reasonably consider an important, even essential, aspect of human history.
What one considers to be of "consequence" is a matter of taste, I suppose. I pose no argument to that.
Yes, the question, why there is anything at all, is currently beyond what science can reliably answer.
The question why there is anything at all has resisted scientific explanation, and may always remain outside of what science can investigate. Philosophy has made some attempts, but there is no valid solution to that problem. (All proposed solutions require making one assumption or another.) However, the origin of the human species occurred in the last few million years.
You seem to be saying that everything that happened after the first moment of Creation is "inconsequential".
Comment by Zachriel — January 18, 2008 @ 10:51 am
January 18th, 2008 at 11:25 am
Dan:
Interesting. I'd never heard anyone describe a neuron or a muscle cell or a kidney cell or a heart cell as an independent single-celled organism. Thus I also never heard anyone describe a cancer cell as an independent single-celled organism. When did this designation become popular (it's been awhile since I took biology)? Have you some links to papers, textbooks or biologists' statements claiming each cell in our bodies are independent single-celled organisms? Thanks…
Comment by Joy — January 18, 2008 @ 11:25 am
January 18th, 2008 at 12:03 pm
Perhaps everything was created in a single moment. And that moment may be the only thing that matters to you, a moment you attribute to a Creator. And the universe is of a whole and everything that happened after that, from the condensation of matter to the evolution of the opposable thumb, are "inconsequential" details. Perhaps. Others may find these details to be very interesting and important to understanding other "inconsequential", but causally related details.
But words create categories. They divide the universe into parts. When we talk of the "origin of humanity", we don't mean the origin of the universe. Even the Bible treats the creation of Adam as separate from the creation of the dust from which he was formed.
If all you are concerned with is an unprovable claim of Divinity in the Creation of the universe, then peace be with you.
Comment by Zachriel — January 18, 2008 @ 12:03 pm
January 18th, 2008 at 12:07 pm
Joy,
"Thus I also never heard anyone describe a cancer cell as an independent single-celled organism."
No one has suggested such - not here, anyway. What part of "no, they're not independent," do you not understand?
Comment by Dan — January 18, 2008 @ 12:07 pm
January 18th, 2008 at 12:13 pm
Hey Dan, ease up a bit. I was confused too by what you were saying.
It sounded like you were saying in one sentence that they are not an independent life form, but then in the next ('any length of time' comment) it appeared as if you were claiming them to be independent.
Comment by Doug — January 18, 2008 @ 12:13 pm
January 18th, 2008 at 12:18 pm
Zachriel,
Or not.
Doncha just love "Materialism of the Gaps"
Comment by chunkdz — January 18, 2008 @ 12:18 pm
January 18th, 2008 at 12:42 pm
Doug and Joy,
"…it appeared as if you were claiming them to be independent."
No, I said "viable," and offered an alternative, "vital." Do you understand the difference between independent and viable or vital? Both refer to "being alive," and although I wouldn't characterize cancer cells as being capable of being alive independently, I would consider them to be alive, just as much as I would consider an amoeba to be alive.
Why is this distinction important? Again, I return to the apology I offered Bradford - that I thought he was referring to life, whereas he was referring to multicellular life. Can single cells (even cancer cells) be considered alive; do they require proofreading to remain alive; and if they are alive, do they thrive without proofreading? Yes, no, and no. They are alive, don't require proofreading to live, but yes they do thrive with it.
Still don't agree? Take the same paper I cited above. It also goes on to talk about complementary experiments in yeast (single-celled eukaryote), in which the proofreading-null yeast do remain alive. Other mutant proteins exist for yeast in which their functions, when deleted, the cells die very quickly (a lethal mutation). Proofreading clearly is not a function in this category, and thus, non-essential for life, viability, vitality, etc.
In short, viability and vitality (the capacity for life) are NOT synonymous with independence. (for more we can consider parasitic bacteria, and ask whether they can be considered alive)….
Comment by Dan — January 18, 2008 @ 12:42 pm
January 18th, 2008 at 12:57 pm
Try to read that again. I'm not the one making the existence claim.
Comment by Zachriel — January 18, 2008 @ 12:57 pm
January 18th, 2008 at 1:13 pm
Doug:
That wasn't the first or even primary confusion Dan lobbed into the discussion. He even emphasized his first erroneous assertion when he said:
Phenotype is "any observed quality of an organism. Usually described as genotype + environment -> phenotype. It is NOT used to describe the differential gene expression profiles of individual cells in a multicellular organism. It is NOT used to describe the results of damage to individual cells in a multicellular organism either. IOW, cancer is not a "phenotype" of an organism unless a cancer cell is an independent living organism.
I simply asked the begged question, because it introduces terminological confusion.
Comment by Joy — January 18, 2008 @ 1:13 pm
January 18th, 2008 at 1:26 pm
Joy:
Actually, biologists do routinely refer to the phenotype of individual cancer cells. My girlfriend studies cell lines consisting of cancer cells and she was so kind to confirm this. An ISI search with keywords "phenotype", "cell line" and "cancer" yields numerous abstracts that confirm this too.
Comment by Raevmo — January 18, 2008 @ 1:26 pm
January 18th, 2008 at 1:32 pm
Joy,
"Phenotype is "any observed quality of an organism. Usually described as genotype + environment -> phenotype. It is NOT used to describe the differential gene expression profiles of individual cells in a multicellular organism."
Sure it is. Ask any cell/molecular biologist who's conducted a cell culture experiment. Insert or knockdown any gene, and the cell's phenotype changes.
Phenotypes, genotypes, and life, do not exclusively belong to multicellular conglomerates.
Comment by Dan — January 18, 2008 @ 1:32 pm
January 18th, 2008 at 1:38 pm
Google Scholar: cancer phenotype and cellular phenotype.
(Oops! Others have already answered. Forgot to adjust for Jovian time.)
Comment by Zachriel — January 18, 2008 @ 1:38 pm
January 18th, 2008 at 2:10 pm
Cell cultures are basically a colony of clones artificially maintained outside of the originating organism's genotype/phenotype. I suppose a specialist would talk about their phenotype as shorthand for what these particular cloned cells 'are' in relation to expression of their individual genotype.
Yet these are not independent living organisms either. Tossing a sub-specialty's jargon into a general public discussion is confusing, and possibly deliberately deceptive per the way it was being used in an argument about what constitutes "life." Per whether or not DNA repair mechanisms are necessary to life. NOT whether an organism (or a cell) with a terminal acquired condition is "alive" for as long as it lasts before the condition kills it, thus qualifies as a counter-argument to the topic of whether or not DNA repair mechanisms are necessary to life.
The only way that objection works is if these individual cells are to be considered independent life forms. Hence, the confusion.
Comment by Joy — January 18, 2008 @ 2:10 pm
January 18th, 2008 at 2:44 pm
Zachriel:
You are correct. You are not the one making the existence claim (at least by what you write). I am the one doing that. But you are making an existence claim by your silence or refusal to anwer the questions:
Do you deny the existence of a non-intelligent set of physical laws that coincidentally led to order?
Or is this really your unspoken existence claim?
Comment by 0112358 — January 18, 2008 @ 2:44 pm
January 18th, 2008 at 3:05 pm
I appreciate your attempt to pare your argument down to its essentials (though we may be meandering off topic).
It appears so.
They are equivalent in terms of empirical evidence, and reasonably so in terms of parsimony. (Note that you created a false dichotomy.)
"Physical law" is just another name for the observed order.
Comment by Zachriel — January 18, 2008 @ 3:05 pm
January 18th, 2008 at 3:22 pm
Joy,
How do you define "alive" then? Cancer cells growing in culture process simple nutrients and live in environments (ableit very controlled environments), just as bacteria do in culture. What about other single cells, proliferating and processing simple nutrients in nature? Are they not alive?
As with anything alive, yes, take away their energy source and they die. Cells live off nutrients, animals on food, plants on sunlight. Take those away, and life dissipates.
So again, are individual cells not alive?
Comment by Dan — January 18, 2008 @ 3:22 pm
January 18th, 2008 at 3:48 pm
Dan to Joy:
What point are you making with respect to DNA repair?
Comment by Bradford — January 18, 2008 @ 3:48 pm
January 18th, 2008 at 3:59 pm
Zachriel,
I know. You are the one who invoked unknown "symmetries" as an alternative to teleology. In fact, invoking the unknown seems to be your calling card lately. Funny, that.
Comment by chunkdz — January 18, 2008 @ 3:59 pm
January 18th, 2008 at 4:46 pm
Zachriel,
I assure you that we are not meandering off topic. What we are discussing are the essentials of the whole teleologic/non-teleologic debate.
So you acknowledge that this belief:
An eternal intelligence {coincidentally} arranged it so
(I disagree with your addition of the word coincidentally here because intelligence by definition does not neccesitate coincidence).
and this belief:
A non-intelligent eternal set of physical laws that coincidentally {or perhaps inevitably} led to order arranged it so?
In acknowledging this are you not admitting that both teleologists and non-teleologists are both in the same position in regard to support for their respective philosophies?
(As far as the charge that I have made a false dichotomy - What other real options are there besides intelligent causes and non-intelligent causes?)
Comment by 0112358 — January 18, 2008 @ 4:46 pm