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Author Topic:   Genetic Redundancy and Natural Selection
BobTHJ
Member (Idle past 3078 days)
Posts: 119
Joined: 06-02-2010


Message 31 of 37 (565408)
06-16-2010 4:22 PM
Reply to: Message 21 by Dr Jack
06-15-2010 5:38 PM


quote:
That "quote" does not appear anywhere in the letter (mis-cited, btw, it's Gibson, T.J. and Spring, J.), the nearest is this:

quote:
However, in the KH and SRC cases, many, perhaps almost all, point mutations that damage the protein product also cause a deleterious phenotype. So the genetic redundancy cannot easily decay away through the accumulation of point mutations.
Being charitable we can forgive the paraphrasing to "in the redundant gene family of SRC-like protein" as perhaps meant as a clarifying alteration, although noting that it's bad form to alter a quotation without pointing out where you've altered it.

The section "and kill the organism" however is simply not found anywhere in the letter.


If this is a case of mis-quoting (and it appears it is) then Borger should have been more careful to notate his modification to the quote.

quote:
Most astonishing however, in it's dishonesty, is Borger's following line:

quote:
If the SRC genes are really so potently harmful that point mutations induce cancer, how could this extended gene family come into existence through gene duplication and diversify through mutations in the first place?
This is dishonest (or incompetent) in two ways, firstly he ignores a key part of the quoted line "many, perhaps almost all point mutations that damage the protein". I draw your attention to how that is a distinct subgroup both of point mutation, and of non-synonymous point mutations. Borger is dishonestly (or incompetently) acting as though this is not the case. Secondly, and more damningly, the question he poses is answered in the source he cites. The whole thrust of Gibson and Spring's argument is that the redundant gene family arose not by gene duplication but by polyploidy! So why does Borger not address this point?


It is doubtful Borger is trying to mislead. Based on the context it is clear Borger is speaking about non-synonymous mutations. And what makes you think that Gibson, T.J. and Spring, J are referring to a subset of non-synonymous mutations? All non-synonymous mutations "damage" the protein (though in many cases for non-SRC genes this still results in a valid phenotype). Maybe I'm wrong though - I can't read the article myself so perhaps they specify this more clearly.

I'm not sure why you think Borger should address a polyploidy origin. It seems a pretty weak hypothesis considering the SRC genes are located at different spots on different chromosomes. Again, I don't have access to the cited article - so maybe they explain this?

quote:
Also, for interested readers, I found a discussion in which Borger was thrashing out the ideas he later formed into this article, I haven't look in depth at it yet: it's here if anyone wants to trawl through it.

Thanks - I'm reading through it and finding it interesting. I'm a bit disappointed by Borger's arrogant and wild claims at the start - but it seems he shapes up a bit once you get a little further into the conversation.

Edited by BobTHJ, : a bunch of typographical goofs


This message is a reply to:
 Message 21 by Dr Jack, posted 06-15-2010 5:38 PM Dr Jack has responded

Replies to this message:
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BobTHJ
Member (Idle past 3078 days)
Posts: 119
Joined: 06-02-2010


Message 32 of 37 (565410)
06-16-2010 4:30 PM
Reply to: Message 25 by Coyote
06-15-2010 10:07 PM


Re: YEC model
quote:
Fortunately that model is incorrect.

Because you said so it must be true?

quote:
And incidentally I regard the notion that humans are inherently flawed and evil as the most pernicious notion that has ever been concocted in a shaman's diseased mind.

I'm sorry you disagree. I find the notion that humans are wise and good enough to divorce themselves from their Creator to be arrogant, unhealthy, and foolish.


This message is a reply to:
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BobTHJ
Member (Idle past 3078 days)
Posts: 119
Joined: 06-02-2010


Message 33 of 37 (565414)
06-16-2010 4:38 PM
Reply to: Message 26 by Coragyps
06-15-2010 10:11 PM


quote:
So fast-replicating critters like houseflies and Staphlococcus that also tend to get the short end of the stick on most health-care plans are at the brink of extinction now, ridden with cancer and ever-shorter lifespans? I hadn't noticed that trend, Bob - do you have any documentation of it?

I'm not sure how you got from my statement regarding a degenerating genome to this. Care to explain? What does fast replication have to do with my statement?

And no - I don't have evidence - but I'm sure somewhere someone is keeping statistics on this stuff. This is a prediction for the baranome hypothesis - and it can likely be proven true or false to some degree of accuracy within the next 50 years or so (though environmental agents such as carcinogens as well as medical efforts to prevent disease do rather complicate the recordkeeping).


This message is a reply to:
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Replies to this message:
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Dr Adequate
Member
Posts: 16087
Joined: 07-20-2006
Member Rating: 10.0


Message 34 of 37 (565460)
06-16-2010 11:33 PM
Reply to: Message 30 by BobTHJ
06-16-2010 3:49 PM


Try reading what I wrote again. Note the words "...at the cellular level."

I did note them. This is why I quoted them, when I wrote:

On the cellular level, we do not see:

(a) Massive complexes of laboratories to design organisms on a world-wide scale about 6000 years ago.

(b) Significant infrastructure for world travel about 6000 years ago.

(c) A major genetic bottleneck affecting all species about 6000 years ago.

Your logic is flawed. I could see you arguing this line of reasoning if you could demonstrate piece by piece the reversal of a process without the destruction of the functionary (still not sure I'd agree - but at least you'd have a logical argument). However, you are suggesting that since a single piece of a system can be removed and the system will still function then it must not be irreducibly complex - this argument has no merit.

This argument is true by definition of "irreducible complexity".

According to Michael Behe, who coined the phrase, an irreducibly complex system is:

A single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. --- Michael Behe, Darwins Black Box

I'm not sure whether the SRC genes fit the first clause of that definition, but according to your own post they do not fit the second clause, since it is possible to knock out entire SRC genes and still be left with a functioning system.


This message is a reply to:
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Dr Adequate
Member
Posts: 16087
Joined: 07-20-2006
Member Rating: 10.0


Message 35 of 37 (565467)
06-17-2010 12:47 AM
Reply to: Message 33 by BobTHJ
06-16-2010 4:38 PM


And no - I don't have evidence - but I'm sure somewhere someone is keeping statistics on this stuff.

People are indeed keeping records --- they're called "scientists". They can watch organisms becoming better adapted to their environments. If they are bacteria, we can even directly compare their fitness against that of their ancestors by putting them into direct competition, since it is possible to freeze samples of the ancestral generations.

What we do not see is the sort of genetic degeneration that is the stuff of creationist fantasy.

This is a prediction for the baranome hypothesis - and it can likely be proven true or false to some degree of accuracy within the next 50 years or so (though environmental agents such as carcinogens as well as medical efforts to prevent disease do rather complicate the recordkeeping).

Perhaps instead of looking at one of the few species (humans) for which you have an excuse for increased or stable phenotypic fitness, you should be looking at species for which you have no such excuse, such as bacteria.

You could, for example, look up the Lenski experiment.

So consider your hypothesis falsified.


This message is a reply to:
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Dr Jack
Member (Idle past 186 days)
Posts: 3507
From: Leicester, England
Joined: 07-14-2003


Message 36 of 37 (565477)
06-17-2010 4:37 AM
Reply to: Message 31 by BobTHJ
06-16-2010 4:22 PM


I'm not sure why you think Borger should address a polyploidy origin. It seems a pretty weak hypothesis considering the SRC genes are located at different spots on different chromosomes. Again, I don't have access to the cited article - so maybe they explain this?

I dunno, because the source he's citing gives it as their explanation. It's pretty bizarre to think a source is perfectly good on one point, while ignoring their explanation for the very thing you're looking at.


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 Message 31 by BobTHJ, posted 06-16-2010 4:22 PM BobTHJ has not yet responded

  
Percy
Member
Posts: 18313
From: New Hampshire
Joined: 12-23-2000
Member Rating: 3.2


Message 37 of 37 (565574)
06-18-2010 6:48 AM
Reply to: Message 18 by BobTHJ
06-15-2010 2:36 PM


Hi Bob,

You repeated Borger's claim that single non-synonymous point mutations in the SRC gene family are fatal because they cause cancer. I requested support for this statement, but I also provided a response just "for the sake of discussion."

So you addressed that response but provided no evidence for Borger's claim about the SRC gene being so sensitive to mutations, and WK had this to say in Message 17:

As Percy says, it is very hard to find anything that actually backs up this statement. Certainly we do know about mutations that produce constitutively active forms of SRC especially, since it has massive historical importance in our understanding of cancer and oncogenes, but to turn that into a blanket statement about many more mutations in all of the SRC family genes extends well beyond where the evidence takes us.

In other words, the available evidence does not support Borger's claim.

quote:
If the model for design is the way humans design, then in a YEC scenario we should see evidence of massive complexes of laboratories...etc...

Funny you should mention that - because that is exactly what we see at the cellular level. Intensely complex machinery working in synchronization, operating from a set of coded instructions that code multiple tasks simultaneously, and a self-regulating self-repairing, redundant system to carry it all out. The complexity far exceeds the limits of mechanics or computer science.

Gee, you completely dodged the question, what a surprise!

So again, if life was designed, where are the 6000 year-old remains of the necessary massive infrastructure, not only for design, but also for production and world-wide distribution. Where is the 4350 year-old genetic bottleneck?

You mean, other than the irreducible complexity I eluded to above? Nope that's it. See what you want to see.

The originator of the idea of irreducible complexity is Michael Behe of Lehigh University, and neither he nor anyone else has published or even submitted a scientific paper on the topic. Instead he publishes books in the popular press for creationists. There's no scientific support for the idea.

It should be apparent to you by now that every time you've referenced a scientific paper cited by Wile or Borger or AIG or ICR that it doesn't support their antievolutionary claims. How could they since the papers are all produced by the community of scientists who accept evolution based on the available evidence? Do you really believe that scientific papers containing meaningful evidence against evolution are buried in old issues of scientific journals? Scientific evidence calling evolution into question would find space on the front page of the New York Times, likely in the right most column and above the fold. The people and groups from whom you're drawing your "evidence" are not speaking to the community of scientists, but to people like you who need hope that science is wrong where it differs with their Biblical interpretations.

The people you're discussing with are not anti-religion. Many of us are religious or at least spiritual. We're united primarily by the threat to science education presented by the creationist movement. If creationists didn't keep showing up at school board meetings or conducting national campaigns of "Teach the Controversy" and so forth then websites like this wouldn't exist. People like you would keep your religious beliefs in your churches and out of our classrooms and we would all go our merry way almost completely unaware of each other.

As others have already noted, you're arguing that some things we have good evidence for are completely misunderstood, misinterpreted, or even unknowable, while simultaneously arguing that other things we have no evidence for are likely true. I think if you restricted yourself to arguing only for those things for which you have evidence that the nature of your arguments would change.

Remember that your starting point is that the Bible is correct, not that people like Wile or Borger or organizations like ICR or AIG are correct, and they don't all believe the same things about what the Bible says. When you finally achieve a community of conservative Christian scientists all backing the same set of consistent hypotheses, in other words when there's a positive consensus around ideas instead of just the unity of a common cause against evolution, then you'll probably find it's because they're taking their lead from real world evidence instead of Biblical revelation. Real world evidence can't be ignored, and that's why real scientists are able to develop meaningful consensus, something that never happens in religion and whose diverse nature also characterizes the creationist movement.

In science consensus happens because we've studied some aspect of the real world in sufficient detail that the same implications are apparent to many people. In religion consensus only happens through intimidation (e.g., the Spanish Inquisition), and only on the surface. The pattern of religion throughout history is continuous evolution of beliefs concurrent with the creation of new sects. A consistent set of scientific ideas is not going to emerge from what is fundamentally a spiritual search for meaning.

--Percy


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