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Author Topic:   Exposing the evolution theory. Part 2
WookieeB
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Posts: 82
Joined: 01-18-2019


Message 196 of 294 (847968)
01-29-2019 6:36 PM
Reply to: Message 194 by JonF
01-29-2019 6:02 PM


Re: Thread Copied from Proposed New Topics Forum
At this point it's painfully obvious that ' "designer" and everything the meaning of that word entails' and "normal design constraints" mean "acts just as I imagine a human designer would".
So your "prediction" boils down to "assuming the designer wouldn't put in junk DNA, I predict the designer wouldn't put in junk DNA".
Very impressive.

LOL! You're hillarious.

So I guess it makes sense to you that someone designing a semiotic translation system more efficient than anything man has produced to date would purposely add something that takes away the efficiency of that system for the sake of aesthetics?


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 Message 194 by JonF, posted 01-29-2019 6:02 PM JonF has responded

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JonF
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Posts: 5527
Joined: 06-23-2003
Member Rating: 2.9


Message 197 of 294 (847972)
01-29-2019 6:57 PM
Reply to: Message 196 by WookieeB
01-29-2019 6:36 PM


Re: Thread Copied from Proposed New Topics Forum
It makes sense to me that neither of us have any defensible clue about what your designer would choose. Life operates with junk DNA, therefore your designer put it in or put in the possibility of it developing.

As I wrote a few days ago, Slartibartfast designed fjords with krinkly edges because they have such a baroque feel. How do you know your designer doesn't just like the baroque feel of junk DNA and doesn't care about any other aspects of it? (Need a hint?)

Maybe you could figure out the answer this time.

ABE Don't claim that the notion of junk DNA is dying without evidence and an understanding of how ENCODE defined "function".

Edited by JonF, : No reason given.


This message is a reply to:
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PaulK
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Posts: 15440
Joined: 01-10-2003
Member Rating: 2.9


Message 198 of 294 (847984)
01-30-2019 12:21 AM
Reply to: Message 193 by WookieeB
01-29-2019 5:30 PM


Re: Hunt versus Axe
quote:

So is it irrelevant when just explaining a mechanism (regardless of where it is applied). OK.

So now that we have a mechanism, we can apply it to reality and see how well it works....


That is, of course, why Axe’s response to Hunt is so inadequate, on isolation. Hunt looks at reality, Axe simply invents an “analogy” without any comparison to reality.

quote:

No, not really.
Let's take malaria developing a resistance to chloroquine. At minimum, it requires at least two specific point mutations, possibly involving a third. Odds of the resistance developing has been calculated to occur on the rate of 10^20 based on empirical studies.

You do realises that that is the probability of a single - specific - mutation ? Hill climbing doesn’t help there. It isn’t even applicable.

quote:

If you extract these numbers out to eukaryote life, and consider the types of mutations needed (lot more than 2 point mutations) to account for the differences we see, Darwinian processes run into some walls as to what it could do.

Except that hill-climbing does help accumulate useful mutations. More, cases where one very specific mutation is absolutely needed are rare.

quote:

RNA or DNA matters very little. You would still need a translation system. RNA nucleotides do not form proteins directly. Also, where does the initial RNA information come from?

This is a change of subject, to one where very little is known for sure. I will point out that the translation of DNA to protein goes through RNA. Whether the original replicating RNA formed naturally or evolved from a simpler predecessor is unknown, but both are possible.


This message is a reply to:
 Message 193 by WookieeB, posted 01-29-2019 5:30 PM WookieeB has responded

Replies to this message:
 Message 199 by NosyNed, posted 01-30-2019 10:33 AM PaulK has responded
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NosyNed
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Posts: 8863
From: Canada
Joined: 04-04-2003
Member Rating: 4.6


Message 199 of 294 (847991)
01-30-2019 10:33 AM
Reply to: Message 198 by PaulK
01-30-2019 12:21 AM


Parasite Numbers
...10^20 based on empirical studies.

You might ask for a reference to those studies.

You might also note that a malaria victim may have 8 x 10^10 parasites in a liter of blood. Thus if there are a million victims the chance of this mutation arising becomes 1 in 10,000. After a generation it starts to become highly probable.

And as you have noted there are other mutations.


This message is a reply to:
 Message 198 by PaulK, posted 01-30-2019 12:21 AM PaulK has responded

Replies to this message:
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PaulK
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Posts: 15440
Joined: 01-10-2003
Member Rating: 2.9


Message 200 of 294 (847993)
01-30-2019 10:58 AM
Reply to: Message 199 by NosyNed
01-30-2019 10:33 AM


Re: Parasite Numbers
It’s better than you think, Ned.

Behe originally argued that two mutations were needed to get any resistance. When it turned out that only one was needed to get some resistance and the second improved it, the odds of evolution succeeding in getting both went way up. And that is because evolution is basically a hill-climbing search (to the extent it is a search).


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Faith
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Posts: 33290
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.2


Message 201 of 294 (847994)
01-30-2019 11:05 AM


Don't mind me, just a creationist on the sidelines thinking how utterly ridiculous all this is. Mutations don't forward evolution. They do something to the DNA that changes what it does of course, but usually it's something destructive. So a mutation eliminates some function of the DNA and the microbe is now resistant to antibiotics. Nothing to do with evolution. But carry on of course. Far be it from me to interfere with all this Science.

Replies to this message:
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Theodoric
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Posts: 6667
From: Northwest, WI, USA
Joined: 08-15-2005
Member Rating: 4.3


(1)
Message 202 of 294 (847999)
01-30-2019 12:44 PM
Reply to: Message 201 by Faith
01-30-2019 11:05 AM


Troll
Troll alert.

Facts don't lie or have an agenda. Facts are just facts

"God did it" is not an argument. It is an excuse for intellectual laziness.

If your viewpoint has merits and facts to back it up why would you have to lie?


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 Message 201 by Faith, posted 01-30-2019 11:05 AM Faith has not yet responded

    
AZPaul3
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Posts: 4640
From: Phoenix
Joined: 11-06-2006
Member Rating: 4.5


(3)
Message 203 of 294 (848001)
01-30-2019 1:19 PM
Reply to: Message 201 by Faith
01-30-2019 11:05 AM


Don't mind me ... Far be it from me to interfere with all this Science.

Excellent idea. They should proceed as you request.


Eschew obfuscation. Habituate elucidation.

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 Message 201 by Faith, posted 01-30-2019 11:05 AM Faith has not yet responded

  
WookieeB
Member
Posts: 82
Joined: 01-18-2019


Message 204 of 294 (848006)
01-30-2019 2:03 PM
Reply to: Message 198 by PaulK
01-30-2019 12:21 AM


Re: Hunt versus Axe
That is, of course, why Axe’s response to Hunt is so inadequate, on isolation. Hunt looks at reality, Axe simply invents an “analogy” without any comparison to reality.

You do realize that Hunt's 'look at reality' only applied to TEM-1 relating to DD-Peptidases. You certainly are not suggesting that all proteins are grouped together, not in isolation, are you? That despite many protein families having no homology to other families in sequence space? Axe's analogy was for proteins in general. You might be able to make a case for TEM-1 not being isolated from DD-peptidases, but that doesn't extend for TEM-1 to all other proteins, or other proteins to other proteins in general.

You do realises that that is the probability of a single - specific - mutation ? Hill climbing doesn’t help there. It isn’t even applicable.

Of course it applies. A mutation that involves (at minimum) 2-3 specific point mutations is the easiest path for malaria to take to survive against chloroquine. There may be other ways to do it, but that would involve more than the 2-3 mutations, which would ramp up the probability against it. In other words, your hill-climber may have multiple paths to climb up, but in this case the easiest path up is a 1x10^20 opportunity. There is nothing to suggest that other hill-climbs for other climbers are any easier.

Except that hill-climbing does help accumulate useful mutations. More, cases where one very specific mutation is absolutely needed are rare.

I agree completely. But accumulating doesn't matter. The question is how likely will it move up? If the upward-opportunity doesn't present itself, it has nothing to accumulate. That's the random nature of Darwinian processes. NS cannot encourage a directional move. It can only capitalize AFTER the move is made.
When you then consider eukaryote population sizes, time, and mutation rates, you will then find you run out of resources.

Cases where one very specific mutation is absolutely needed are rare. Yes. The inverse of that means that more that one specific mutation being needed is common. That makes the case much worse for Darwinian processes.

I will point out that the translation of DNA to protein goes through RNA. Whether the original replicating RNA formed naturally or evolved from a simpler predecessor is unknown, but both are possible.

But RNA to protein needs a translator as well - the ribosome (which happens to be made of proteins as well. Chicken and egg problem). RNA may have formed by your two options, or probably not at all (more probable), but even if I granted you that, you still have to account for all the rest that makes proteins.

Edited by WookieeB, : No reason given.


This message is a reply to:
 Message 198 by PaulK, posted 01-30-2019 12:21 AM PaulK has responded

Replies to this message:
 Message 206 by PaulK, posted 01-30-2019 2:45 PM WookieeB has responded

    
WookieeB
Member
Posts: 82
Joined: 01-18-2019


Message 205 of 294 (848013)
01-30-2019 2:44 PM
Reply to: Message 199 by NosyNed
01-30-2019 10:33 AM


Re: Parasite Numbers
NosyNed writes:

You might ask for a reference to those studies.


Sure thing.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC385418/

Interesting thing about this is that the 10^20 number is not determined from probability of the point mutations. It is derived by empirical observations of how often the resistance has been found to have arisen independently. The probability consideration for mutation rates just happens to agree with the number.

You might also note that a malaria victim may have 8 x 10^10 parasites in a liter of blood. Thus if there are a million victims the chance of this mutation arising becomes 1 in 10,000. After a generation it starts to become highly probable.

Yes indeed. Though I think for the study the estimate for # of malaria cells in a person was 1 trillion and the infected in the billion range.
Since the resistance has appeared less than 10 times, it fits in pretty well with the numbers.

And as you have noted there are other mutations.

More information on specifics of the mutations -
https://www.pnas.org/content/111/17/E1759.long

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PaulK
Member
Posts: 15440
Joined: 01-10-2003
Member Rating: 2.9


Message 206 of 294 (848014)
01-30-2019 2:45 PM
Reply to: Message 204 by WookieeB
01-30-2019 2:03 PM


Re: Hunt versus Axe
quote:

You do realize that Hunt's 'look at reality' only applied to TEM-1 relating to DD-Peptidases

I don’t because Hunt’s statement was not restricted to that and the rest of it is consistent with what I’ve seen in other sources. Axe didn’t dispute it either.

quote:

You certainly are not suggesting that all proteins are grouped together, not in isolation, are you?

I am not suggesting that there is one single group and I wouldn’t expect there to be. However I am sure that there is a lot of overlap.

Consider the existence of gene families

quote:

Of course it applies.

Not to a single mutation, as should be obvious. The advantage is in accumulating mutations.

quote:

A mutation that involves (at minimum) 2-3 specific point mutations is the easiest path for malaria to take to survive against chloroquine.

There is one (neutral) mutation that seems to be required, but there are several known routes to achieving resistance in combination with it. Summers et al (2014)

quote:

I agree completely. But accumulating doesn't matter.

It certainly does. That is why evolution works better than a random search.

quote:

The question is how likely will it move up? If the upward-opportunity doesn't present itself, it has nothing to accumulate. That's the random nature of Darwinian processes. NS cannot encourage a directional move. It can only capitalize AFTER the move is made.

The problem for you is that hill-climbing algorithms can and do work. So long as one of the perturbations (mutations in evolution) finds a higher point it can move on. There is no need for the perturbations to automatically find a higher point and it is not a problem if many do not.

quote:

Cases where one very specific mutation is absolutely needed are rare. Yes. The inverse of that means that more that one specific mutation being needed is common. That makes the case much worse for Darwinian processes.

That is a failure of logic on your part since the inverse includes the case where many mutations will do, and that makes it better for Darwinian processes.

quote:

But RNA to protein needs a translator as well - the ribosome (which happens to be made of proteins as well. Chicken and egg problem). RNA may have formed by your two options, or probably not at all (more probable), but even if I granted you that, you still have to account for all the rest that makes proteins.

No, I don’t. I can live with unknowns. So long as it is the case that we do not expect all proteins to be related your point is answered.


This message is a reply to:
 Message 204 by WookieeB, posted 01-30-2019 2:03 PM WookieeB has responded

Replies to this message:
 Message 207 by WookieeB, posted 01-31-2019 12:04 PM PaulK has responded

    
WookieeB
Member
Posts: 82
Joined: 01-18-2019


Message 207 of 294 (848069)
01-31-2019 12:04 PM
Reply to: Message 206 by PaulK
01-30-2019 2:45 PM


Re: Hunt versus Axe
Not to a single mutation, as should be obvious. The advantage is in accumulating mutations.

How does it accumulate mutations?

That is why evolution works better than a random search.

Please, can you explain what is being searched for in an 'evolutionary' search? And how is that different from a random search?

The problem for you is that hill-climbing algorithms can and do work. So long as one of the perturbations (mutations in evolution) finds a higher point it can move on. There is no need for the perturbations to automatically find a higher point and it is not a problem if many do not.

No, I have no problem with the hill-climbing algorithm. It's not an issue of whether it can move up. It is an issue of whether it will move up. If you have a 1 in 10 chance to move up (where all the other 9 chances is not moving up), then it will only move up 1 in 10 tries. Now, if you are only allowed 2 tries, it is more likely to miss than to move up. No hill is climbed unless you happen to hit that '1' successful option.

Cases where one very specific mutation is absolutely needed are rare.
...
That is a failure of logic on your part since the inverse includes the case where many mutations will do, and that makes it better for Darwinian processes.

Oh, so your hinging your statement on the "absolutely needed" part? You've got to be kidding me. Intuition, testing, and all experience indicates that mutating something is FAR, FAR more likely to break the thing being mutated than it is to help it. Even neutral changes would outnumber beneficial changes by a large factor. So mutations will heavily be tilted more to to break than to benefit.

If you assume there are mutations that can benefit an organism, they will logically be far more specific than all other types of mutations.

No, I don’t. I can live with unknowns. So long as it is the case that we do not expect all proteins to be related your point is answered.

What? Protein relation is irrelevant at this point. You have to explain how to get protein from RNA. There is a lot involved, including two separate code systems to create. You need to identify how RNA nucleotides form a digital code, how particular nucleotide sequences map to a particular amino acid, and then a system to marry the two together to form a protein chain. There are more critical pieces even than that, but just explain those 3. Any of three coming about by itself does nothing. You need all three together to function. There is a high level example of IC.

This message is a reply to:
 Message 206 by PaulK, posted 01-30-2019 2:45 PM PaulK has responded

Replies to this message:
 Message 208 by PaulK, posted 01-31-2019 12:30 PM WookieeB has responded

    
PaulK
Member
Posts: 15440
Joined: 01-10-2003
Member Rating: 2.9


Message 208 of 294 (848073)
01-31-2019 12:30 PM
Reply to: Message 207 by WookieeB
01-31-2019 12:04 PM


Re: Hunt versus Axe
quote:

How does it accumulate mutations?

That is what the movement in sequence space equates to. Or if you want details it’s natural selection keeping successful variants (in the simplified version).

quote:

Please, can you explain what is being searched for in an 'evolutionary' search? And how is that different from a random search?

“What is being searched for” is not closely related to the search algorithm. Evolution search’s for improvements in fitness - in the current environment. I’ve already explained how hill climbing differs from random search.

quote:

No, I have no problem with the hill-climbing algorithm. It's not an issue of whether it can move up. It is an issue of whether it will move up. If you have a 1 in 10 chance to move up (where all the other 9 chances is not moving up), then it will only move up 1 in 10 tries. Now, if you are only allowed 2 tries, it is more likely to miss than to move up. No hill is climbed unless you happen to hit that '1' successful option.

And that leads us to the point where you would need numbers to say anything useful. Numbers you don’t have,

quote:

Oh, so your hinging your statement on the "absolutely needed" part? You've got to be kidding me. Intuition, testing, and all experience indicates that mutating something is FAR, FAR more likely to break the thing being mutated than it is to help it. Even neutral changes would outnumber beneficial changes by a large factor. So mutations will heavily be tilted more to to break than to benefit.

No, I’m hinging my point on there typically being a number of mutations that would do rather than one particular one. Which is what I said in the first place.

quote:

What? Protein relation is irrelevant at this point.

No it is the point you are trying to divert from. If we don’t expect all proteins to be related then we should also expect there to be groups of related proteins that may well be isolated from other groups - at least so far as evolution is concerned.

I don’t need to explain the rest because THAT is irrelevant. We don’t know how it happened but by the evidence we have, it seems more likely that we somehow got from RNA life to proteins and DNA. And I don’t expect to know without a lot more research - if it is even knowable this late in the history of life. It is a complex problem and evidence is hard to come by.


This message is a reply to:
 Message 207 by WookieeB, posted 01-31-2019 12:04 PM WookieeB has responded

Replies to this message:
 Message 209 by WookieeB, posted 02-01-2019 3:57 PM PaulK has responded

    
WookieeB
Member
Posts: 82
Joined: 01-18-2019


Message 209 of 294 (848192)
02-01-2019 3:57 PM
Reply to: Message 208 by PaulK
01-31-2019 12:30 PM


PaulK writes:

That is what the movement in sequence space equates to. Or if you want details it’s natural selection keeping successful variants.


So NS keeps a successful variant. Why? We would have to assume whatever you are constituting is a "variant" improves fitness. But NS cannot act on anything until the variant appears. So what is the probability of a variant appearing? NS cannot affect that probability.

Which leads to....

PaulK writes:

“What is being searched for” is not closely related to the search algorithm.

Pardon??? Can you read that statement again and tell me you're serious?

Evolution search’s for improvements in fitness - in the current environment. I’ve already explained how hill climbing differs from random search.

No, you haven't explained the difference because I think you are confused over how a hill-climb actually searches.
The only comment you made in trying to differentiate them was -

PaulK writes:

No, evolution is more like a hill-climbing search. I.e. it perturbs a parameter and moves to that value if it is higher, then it perturbs again and so on. A random search simply chooses completely random points until it hits the target with no feedback at all.

I didn't really notice it before, but you are not using consistent terms here when comparing both. When you mention hill-climbing, you said it "perturbs a parameter". No, it doesn't. In the context of what you are describing (the search itself), NS cannot do anything to a parameter, it cannot 'make' (perturb, influence, nudge, etc) a higher point into being. All it can do is wait for a search to reveal a higher point (and not necessarily the highest point to be found) and the lock that one in if found.

The search process itself is RANDOM. The search process itself is mutations occurring. NS cannot affect what/where/how mutations occur. It is a wholly random process, thus the search itself is a RANDOM SEARCH. "A random search simply chooses completely random points until it hits the target" is true, which is what is going on with your hill search when it actually is searching. "...with no feedback at all." is a bit misleading, since a random search is looking for a target too (same as NS), and that is the feedback it gets.

And that leads us to the point where you would need numbers to say anything useful. Numbers you don’t have,

But in many cases we do have the numbers. Like the malaria resistance to chloroquine. Without making unsubstantiated assumptions (like isolation) we can get a pretty good idea of the chances of new protein formation based on presumed times between ancestors. With orphan genes, you pretty much throw the isolation argument out the window, and you can estimate with a lot of wiggle room the likelyhood of genes appearing de novo. When it comes down to it, Darwinian processes do not have enough time or resources to do what it is claimed to have done.

No, I’m hinging my point on there typically being a number of mutations that would do rather than one particular one. Which is what I said in the first place.

Nobody is questioning that there may be multiple mutations vs one, or that there are multiple routes up the hill. It's not about the number so much as it is about the rarity of beneficial mutations. Take the malaria example again. It's acknowledged there are various ways resistance can occur. But the best chances for resistance is 10^20. That could possibly be due to a number of routes, but that number is still your floor. There is nothing to suggest that the chances are better than that. If that number can be taken in any way as an example of how Darwinian processes work in general (and there is no reason why it cannot), then it doesn't look good for the Darwinian paradigm to explain much.

If we don’t expect all proteins to be related then we should also expect there to be groups of related proteins that may well be isolated from other groups - at least so far as evolution is concerned.

I agree. And if that is the case, it doesn't provide much confidence in evolution to explain much.

Edited by WookieeB, : No reason given.


This message is a reply to:
 Message 208 by PaulK, posted 01-31-2019 12:30 PM PaulK has responded

Replies to this message:
 Message 210 by PaulK, posted 02-01-2019 4:43 PM WookieeB has responded
 Message 211 by AZPaul3, posted 02-01-2019 5:17 PM WookieeB has responded

    
PaulK
Member
Posts: 15440
Joined: 01-10-2003
Member Rating: 2.9


Message 210 of 294 (848204)
02-01-2019 4:43 PM
Reply to: Message 209 by WookieeB
02-01-2019 3:57 PM


quote:

So NS keeps a successful variant. Why? We would have to assume whatever you are constituting is a "variant" improves fitness. But NS cannot act on anything until the variant appears. So what is the probability of a variant appearing? NS cannot affect that probability.

Since improvement in fitness is success (and performing a useful function or doing it better will often improve fitness) natural selection will automatically tend to keep successful variants.

And the probability of variants in sequence appearing is the probability of a mutation occurring which I am sure you can look up. (And in the long term evolution may have “tuned” that probability, so it may not be completely true that natural selection can’t affect it)

quote:

Pardon??? Can you read that statement again and tell me you're serious?

It’s true. After all you imagine a random search rather than a hill-climbing search for evolution but still searching for the same things.

quote:

No, you haven't explained the difference because I think you are confused over how a hill-climb actually searches.

Nope, I already have explained. But here it is again. A random search simply picks points in search space at random. A hill climbing search explores points around the a location in search space until it finds a “higher” point, whereupon it moves to that point and starts exploring around there.

quote:

I didn't really notice it before, but you are not using consistent terms here when comparing both. When you mention hill-climbing, you said it "perturbs a parameter". No, it doesn't. In the context of what you are describing (the search itself), NS cannot do anything to a parameter, it cannot 'make' (perturb, influence, nudge, etc) a higher point into being. All it can do is wait for a search to reveal a higher point (and not necessarily the highest point to be found) and the lock that one in if found.

So I gave an explanation of a hill climbing algorithm that is clearly distinct from random search. And you can’t see how that relates to evolution since I used general terminology and you can’t see how it relates to evolution. Even though it is pretty simple. The fact that you keep wrongly equating evolution to Natural Selection isn’t helping you either.

To put it simply mutation varies the sequence of a gene - that is perturbing a parameter.

quote:

The search process itself is RANDOM.

No. The perturbations are random. The search process is more than that,

quote:

The search process itself is mutations occurring. NS cannot affect what/where/how mutations occur. It is a wholly random process, thus the search itself is a RANDOM SEARCH

In a random search the next sequence tried could be anything. Mutations do NOT completely randomise the genome at every generation. But that is what you would need for it to be a random search.

quote:

"A random search simply chooses completely random points until it hits the target" is true, which is what is going on with your hill search when it actually is searching. "...with no feedback at all." is a bit misleading, since a random search is looking for a target too (same as NS), and that is the feedback it gets.

The random search does not use feedback in any way to help it choose the next point. A hill-climbing search does, as I have explained.

quote:

If that number can be taken in any way as an example of how Darwinian processes work in general (and there is no reason why it cannot), then it doesn't look good for the Darwinian paradigm to explain much.

I think you need more than one example to justify using it as a general probability.

quote:

I agree. And if that is the case, it doesn't provide much confidence in evolution to explain much

Nor does it dent the confidence in evolution explaining a great deal of what is observed in biology. Evolution has always required some initial state which it cannot explain - and the earliest life has left so little evidence that any explanations involving it will tend to be highly speculative at best. So really the point doesn’t change a thing.


This message is a reply to:
 Message 209 by WookieeB, posted 02-01-2019 3:57 PM WookieeB has responded

Replies to this message:
 Message 213 by WookieeB, posted 02-01-2019 6:54 PM PaulK has responded

    
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