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Author Topic:   "The Edge of Evolution" by Michael Behe
Kaichos Man
Member (Idle past 2831 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 61 of 149 (532073)
10-21-2009 7:48 AM
Reply to: Message 59 by Modulous
10-21-2009 7:01 AM


Re: Joe Thornton
19th Century and early 20th Century conceptions were good but weren't quite right.

Care to elaborate on where they weren't quite right?

I mean really - neutral mutations having an effect on a genome later down the line?

Which particular effect did you have in mind?

What are those researchers trying to do - make creationist's life difficult??

With a single shred of empirical evidence, the could make our lives impossible. So far, nothing- other than just-so stories, this-looks-like-that, speciation to equal or lesser levels of complexity, mutations that do nothing or damage and an embarrassingly contradictory fossil record.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 59 by Modulous, posted 10-21-2009 7:01 AM Modulous has responded

Replies to this message:
 Message 64 by Modulous, posted 10-21-2009 8:24 AM Kaichos Man has responded

  
Wounded King
Member (Idle past 2438 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 62 of 149 (532076)
10-21-2009 8:14 AM
Reply to: Message 60 by Kaichos Man
10-21-2009 7:34 AM


Re: Joe Thornton
Can you tell me more about these genetic features?

Yes, but they are mostly obvious things like synonymous mutations and functionally neutral SNPS, two things with a high level of overlap, but not neccessarily exactly the same. You might also consider some elements of what have been considered 'junk' DNA such as degenerate non-expressed pseudogenes.

Again, really interesting if you can verify it or provide a reference.

Um, the reference would be exactly Joe Thornton's research we are just discussing. The whole point of Thornton's research is that the adaptive evolution of a genome is carried out against the shifting background of the rest of the genome and much of this shifting is effectively neutral in terms of adaptation/fitness. That is why it is harder to construct a path backwards from a more derived protein to the ancestral protein, because you don't know what the permissive backgrounds for the differing steps were.

What's wrong with good 'ole junk DNA as a background?

Junk DNA along with everything else in the genome does constitute the genetic background in vivo, in vitro the background was in this case the rest of the protein coding region which remained unchanged and the genome of the Chinese Hamster Ovary cell in which the constructs were tested.

No the writer's intention here was to try and give evolution a much-needed helping hand with a few lucky neutral mutations.

One can easily argue that this is clearly demonstrated in almost any selection intensice experiment. If we grow up a clonal colony of bateria to identify mutations conferring resistance to some anitbacterial agent then all we are doing is trying to generate a wide panel of effectively neutral mutations which will become beneficial on introduction to the selective environment.

TTFN,

WK


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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 8.3


(1)
Message 63 of 149 (532082)
10-21-2009 8:23 AM
Reply to: Message 55 by Kaichos Man
10-20-2009 8:38 PM


Re: Needs more information
Having pronounced this to be clear evidence that Irreducible Complexity has been overcome and genetic information increased, he then deftly shoots himself in the foot by pointing out that the extreme rarity of the double-mutant suggests two simultaneous mutations.

I have the book in front of me. He says no such thing.


This message is a reply to:
 Message 55 by Kaichos Man, posted 10-20-2009 8:38 PM Kaichos Man has responded

Replies to this message:
 Message 66 by Kaichos Man, posted 10-21-2009 8:56 AM Dr Adequate has responded

  
Modulous
Member (Idle past 447 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 64 of 149 (532083)
10-21-2009 8:24 AM
Reply to: Message 61 by Kaichos Man
10-21-2009 7:48 AM


Re: Joe Thornton
Care to elaborate on where they weren't quite right?

Seriously? We could start at the beginning: Darwin didn't know about DNA or genes so his ideas about inheritance weren't quite right.

I mean really - neutral mutations having an effect on a genome later down the line?

Which particular effect did you have in mind?

I described it in the post that you initially replied to.

With a single shred of empirical evidence, the could make our lives impossible.

Then your lives are impossible because there is a mountain of evidence. Sorry.

So far, nothing- other than just-so stories, this-looks-like-that, speciation to equal or lesser levels of complexity, mutations that do nothing or damage and an embarrassingly contradictory fossil record.

Blah blah blah. I know the creationist position there is no need to repeat it. Do you have anything to say that's on topic?


This message is a reply to:
 Message 61 by Kaichos Man, posted 10-21-2009 7:48 AM Kaichos Man has responded

Replies to this message:
 Message 68 by Kaichos Man, posted 10-21-2009 9:04 AM Modulous has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 8.3


(1)
Message 65 of 149 (532084)
10-21-2009 8:25 AM
Reply to: Message 57 by Kaichos Man
10-20-2009 11:52 PM


Re: Joe Thornton
So now we have this new element. The current theory appears to be: "Random mutation, followed by the fortuitous assembly of necessarily complex genetic structures courtesy of some very convenient neutral mutations, followed by natural selection."

Hard to believe it's all the work of a process that has no purpose or target, isn't it?

In fact, it's impossible to believe.

That's probably why the passage that you have presented in quotes is not actually a quotation from anyone other than you.


This message is a reply to:
 Message 57 by Kaichos Man, posted 10-20-2009 11:52 PM Kaichos Man has responded

Replies to this message:
 Message 67 by Kaichos Man, posted 10-21-2009 8:57 AM Dr Adequate has responded

  
Kaichos Man
Member (Idle past 2831 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 66 of 149 (532089)
10-21-2009 8:56 AM
Reply to: Message 63 by Dr Adequate
10-21-2009 8:23 AM


Re: Needs more information
I have the book in front of me. He says no such thing.

“No, the rarity of citrate metabolism suggests that we are looking for something more like the ‘irreducible complexity’ of creationist propaganda. This might be a biochemical pathway in which the product of one chemical reaction feeds into a second chemical reaction, and neither can make any inroads at all without the other. This would require two mutations, call them A and B, to catalyze the two reactions.” (pg. 129)

Emphasis added.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 63 by Dr Adequate, posted 10-21-2009 8:23 AM Dr Adequate has responded

Replies to this message:
 Message 69 by Wounded King, posted 10-21-2009 9:23 AM Kaichos Man has not yet responded
 Message 71 by Dr Adequate, posted 10-21-2009 10:41 AM Kaichos Man has not yet responded

  
Kaichos Man
Member (Idle past 2831 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 67 of 149 (532090)
10-21-2009 8:57 AM
Reply to: Message 65 by Dr Adequate
10-21-2009 8:25 AM


Re: Joe Thornton
That's probably why the passage that you have presented in quotes is not actually a quotation from anyone other than you.

Did I suggest otherwise?


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 65 by Dr Adequate, posted 10-21-2009 8:25 AM Dr Adequate has responded

Replies to this message:
 Message 72 by Dr Adequate, posted 10-21-2009 10:48 AM Kaichos Man has not yet responded

  
Kaichos Man
Member (Idle past 2831 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 68 of 149 (532092)
10-21-2009 9:04 AM
Reply to: Message 64 by Modulous
10-21-2009 8:24 AM


Re: Joe Thornton
Seriously? We could start at the beginning: Darwin didn't know about DNA or genes so his ideas about inheritance weren't quite right.

And what about Random Mutation/Natural Selection?

Then your lives are impossible because there is a mountain of evidence. Sorry.

But it wouldn't be considered evidence in any other field of science, would it? Unrepeatable, unfalsifiable storytelling.


"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 64 by Modulous, posted 10-21-2009 8:24 AM Modulous has responded

Replies to this message:
 Message 70 by Modulous, posted 10-21-2009 9:39 AM Kaichos Man has responded
 Message 73 by Dr Adequate, posted 10-21-2009 10:59 AM Kaichos Man has not yet responded

  
Wounded King
Member (Idle past 2438 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 69 of 149 (532097)
10-21-2009 9:23 AM
Reply to: Message 66 by Kaichos Man
10-21-2009 8:56 AM


Re: Needs more information
I don't see how this is shooting himself in the foot. Unless your contention is that he failed to take into account the magical intervention of the intelligent designer during the experiment. The mutations clearly occured, they need not be simultaneous but the required maintenance of the earliest one in the absence of positive selection does make their joint ocurrence less likely, but obviously not impossible.

Indeed Lenski's research clearly show that these mutations were not simultaneous since one of the mutations had already occurred by ~20,000 generations but the Cit+ trait didn't evolve for a further 11,000 generations. It also isn't clear that the potentiating mutation was selectively neutral, simply that it doesn't provide any ability to metabolise citrate (Blount et al., 2008).

TTFN,

WK


This message is a reply to:
 Message 66 by Kaichos Man, posted 10-21-2009 8:56 AM Kaichos Man has not yet responded

  
Modulous
Member (Idle past 447 days)
Posts: 7789
From: Manchester, UK
Joined: 05-01-2005


(1)
Message 70 of 149 (532099)
10-21-2009 9:39 AM
Reply to: Message 68 by Kaichos Man
10-21-2009 9:04 AM


And what about Random Mutation/Natural Selection?

Haven't we already discussed that? RM/NS have a big role to play in adaptation, but they aren't presently thought to be the lone contributors to biological change - for example epigenetic and horizontal gene transfer have their role too.

But it wouldn't be considered evidence in any other field of science, would it? Unrepeatable, unfalsifiable storytelling.

I wasn't talking about natural history, Kaichos Man. All history is unrepeatable 'storytelling'. Though natural history and the Egyptian dynasties' history are falsifiable alike.

I'm talking about biological change and its mechanisms which are repeatable, falsifiable and aren't stories. That's probably your problem, you've confused natural history with the theory of evolution - it's a common error, but it's not really on topic here. What is on topic here is whether the proposed mechanisms are enough to account for the biological change proposed in natural history. Maybe they aren't and there are other mechanisms out there. But the argument put forward in this thread that attempts to prove that the mechanisms currently proposed are not enough is what is being debated - try to keep focus on that.

Edited by Modulous, : No reason given.


This message is a reply to:
 Message 68 by Kaichos Man, posted 10-21-2009 9:04 AM Kaichos Man has responded

Replies to this message:
 Message 85 by Kaichos Man, posted 10-23-2009 7:23 AM Modulous has responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 8.3


(1)
Message 71 of 149 (532108)
10-21-2009 10:41 AM
Reply to: Message 66 by Kaichos Man
10-21-2009 8:56 AM


Re: Needs more information
You notice how the passage you have quoted in no way supports your false and ridiculous claim?

This message is a reply to:
 Message 66 by Kaichos Man, posted 10-21-2009 8:56 AM Kaichos Man has not yet responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 8.3


(1)
Message 72 of 149 (532110)
10-21-2009 10:48 AM
Reply to: Message 67 by Kaichos Man
10-21-2009 8:57 AM


Re: Joe Thornton
Did I suggest otherwise?

You were indeed suggesting that you were presenting the opinions of others, rather than some crazy nonsense that you'd made up in your head.


This message is a reply to:
 Message 67 by Kaichos Man, posted 10-21-2009 8:57 AM Kaichos Man has not yet responded

  
Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 8.3


(1)
Message 73 of 149 (532115)
10-21-2009 10:59 AM
Reply to: Message 68 by Kaichos Man
10-21-2009 9:04 AM


Re: Joe Thornton
But it wouldn't be considered evidence in any other field of science, would it? Unrepeatable, unfalsifiable storytelling.

Perhaps you could keep your absurd falsehoods at least vaguely on topic. If you wish to be wrong about the scientific method instead (and I can see why you'd want to stop discussing genetics) then that would be a topic for another thread.


This message is a reply to:
 Message 68 by Kaichos Man, posted 10-21-2009 9:04 AM Kaichos Man has not yet responded

  
Colin
Junior Member (Idle past 3589 days)
Posts: 27
From: Adelaide, Australia.
Joined: 10-14-2009


Message 74 of 149 (532202)
10-21-2009 11:46 PM
Reply to: Message 54 by Modulous
10-20-2009 4:16 AM


Re: Meaning of the Calculations
Hi Modulus, although my numbers are only estimates, i believe they are reasonably grounded in reality, I will try to outline why.


This, however, is not necessarily the correct answer. You just happened to find two values for the unknowns that satisfy the even-odds requirement. There are many pairs of values that would satisfy this requirement and you have given no reason for picking those particular ones. When you have two unknowns in an equation - the correct method for solving the equation is not to find any two values that fit. I suppose you could find all possible numbers that fit in, but I suspect that set is infinitely large.

Absolutely, this equation has many solutions. Let me give an example to explain why i used this equation anyway. Say i want to build a performance car. I know that the equation f=ma will apply to the exercise, and that the equation itself is the first thing that grounds the exercise in reality, though i still have no specific values. I begin to plug in estimated values such as a value for desired acceleration, and estimated mass. I find that with these values, the force required is greater than any affordable production engine could supply, so i consider my chassis and materials, and shed some mass. I do similar adjustments until i believe i have some realistic values on which to base my car.


If you had picked a billion games you'd find that the number of ways to win would have to be something other than 100,000 in order to get approximately even odds. The real problem is that you actually have no idea whether 100,000 is remotely close to being realistic. You haven't a shred of evidence that suggests that it is true.

I left the value of possible beneficial mutations until last, because it is the hardest value to estimate. Your right, I do not know what this value is, I can only guestimate at best. When i plugged in my other two values, and was left with 100000, and I thought this sounded reasonably generous. To elaborate on why, in life we see many common features that seem to be produced, or at least retained among many species. If we take the basic structure of DNA for example, which if i remember rightly is common to all life on Earth (maybe 1 or 2 exceptions?). Could we conclude from this that developing a new biological language is either too difficult or not really beneficial, at least in the short term. Considering the number of creatures that have been produced through the millenia, we should be justified in saying that such a mutation, or group of mutations, should not really be considered one of the typically available mutations, even if it is technically possible. Other features such as the eye, which is shared among a great deal of organisms and may have evolved independently several times, we could say is both reasonably within the grasp of evolution and also provides a significant and lasting benefit. Therefore we could say that evolutionary pathways that lead to the development of the eye are among the typically available mutations. Just to remind you of the point i was making, evolution as a process seems to be picky, and gravitates toward the same type of features many times over, suggesting that although the available likely evolutionary pathways are numerous, they are maybe not as incredibly numerous as they are often made out to be. Also, in this discussion the burden of proof is on me, since i used the calculation. But it is worth noting that in general, any lack of knowledge about this number also applies to evolution, so that in insisting evolution to be true is to do so without actually knowing the probability of the events occurring.

My number for the probability of one such mutation occurring - Behe calls a single chloroquine type event a CCC, or Chloroquine Complexity Cluster. Some discussion has gone into the question of whether this was accurately calculated, which is why i reduced Behe's number by a factor of a thousand. To put it another way, Behe says it took a few years for the very first cases of chloroquine resistance to appear. My number allows for 200 cases of spontaneous resistance in the first year, followed by 200 every single year for the next fifty years. I think this is more than generous. On whether or not the chloroquine type resistance is typically necessary on evolutionary pathways. If we consider that this change slightly alters an already existing protein pump, and requires up to 12 changes in the protein sequence, surely we are not being unreasonable is assuming that this is not an incredibly big step to take if we consider, looking around us, what else evolution has accomplished.

Onto the number I used for population. This brings some perspective to the amount of change we might expect over the course of time. I find it hard to believe that man evolved from an ape like creature, without using a mutation as complex as malaria altering a protein pump. I think it is reasonable to expect many equally complex mutations would be required, in addition to some more complex and many less complex. Had i been completely unreasonable and chose 1, as my poulation, you could rightly ask me why i would expect any change at all in just 1 new creature.

To bring my wider argument into focus, I see an inconsistency in comparing the amount of change we see in rapidly reproducing smaller organisms, to the amount of change that is assumed to have happened in much larger, slowly reproducing organisms such as ourselves.

Edited by Colin, : No reason given.

Edited by Colin, : No reason given.


This message is a reply to:
 Message 54 by Modulous, posted 10-20-2009 4:16 AM Modulous has responded

Replies to this message:
 Message 75 by Dr Adequate, posted 10-22-2009 3:02 AM Colin has responded
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Dr Adequate
Member
Posts: 16107
Joined: 07-20-2006
Member Rating: 8.3


(1)
Message 75 of 149 (532210)
10-22-2009 3:02 AM
Reply to: Message 74 by Colin
10-21-2009 11:46 PM


Re: Meaning of the Calculations
I left the value of possible beneficial mutations until last, because it is the hardest value to estimate. Your right, I do not know what this value is, I can only guestimate at best.

Well then.

From the evidence before me, I think that large-scale evolution (such as archosaurs to birds) has in fact happened.

You wish to "guestimate" that despite all the evidence that such events have happened, nonetheless it can't have happened on genetic grounds. But you confess that you find this hard to estimate, and that you are merely "guestimating".

At this point I would suggest that so far my appeals to reality which suggest that such a thing has happened kind of outweigh your "guestimations" that it can't have happened.


This message is a reply to:
 Message 74 by Colin, posted 10-21-2009 11:46 PM Colin has responded

Replies to this message:
 Message 76 by Colin, posted 10-22-2009 4:31 AM Dr Adequate has responded

  
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