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Author Topic:   Exposing the evolution theory. Part 2
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 169 of 1104 (847688)
01-25-2019 11:57 AM
Reply to: Message 162 by Tanypteryx
01-24-2019 10:29 PM


Re: Thread Copied from Proposed New Topics Forum
Tanyteryx writes:
Nope, in 150+ years that people have been studying life and evolution no evidence of a guiding entity has been found. If someone finds evidence they need to report it....
Those questions were unanswerable without evidence so we left it to those who want to spend their time trying to find that evidence....
Oh, I realize that's what you want, I'm waiting for evidence of guided, intelligent, purposeful, immaterial processes, in other words magic...
Yep, I've heard of it, but once again you have no evidence of an intelligent guide...
Yeah, I get that. Present your evidence for your intelligent designer....
It's still about evidence. EVIDENCE!!! Get it?
Nope!
You were complaining about a definition i provided. You were complaining about descriptive words in that definition that you apparently didnt like, but admitted you agreed with.
Everything you quoted by me here was in response to your objections about a definition.
In this instance, we were not talking about evidence for evolution. This was a dispute over language.
So you're now changing the subject and putting forth responses that are irrelevant to my statements.
This is an informal fallacy - Ignoratio elenchi.
It's also referred to as the Chewbacca defense, which is really offensive to me if you couldn't tell by my username.

This message is a reply to:
 Message 162 by Tanypteryx, posted 01-24-2019 10:29 PM Tanypteryx has replied

Replies to this message:
 Message 170 by ringo, posted 01-25-2019 12:21 PM WookieeB has not replied
 Message 171 by Tanypteryx, posted 01-25-2019 1:05 PM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 172 of 1104 (847718)
01-25-2019 5:33 PM
Reply to: Message 157 by PaulK
01-24-2019 5:32 PM


Re: Hunt versus Axe
Does that satisfy you ?
Yes it does. But that quote is NOTHING like what you said. Your statement used English words, but it was rambling and incoherent. Glad you stepped up and produced something understandable. Now maybe we can proceed.
PaulK writes:
WookieeB writes:
"one or more of the parts making up a system" - I will assume you mean an IC system.
Since I am speaking of how a system can become IC, I obviously include systems that are not (yet) IC. Even without that consideration I see no good reason why you would assume that I meant only IC systems.
Well which is it? If you are not talking about an IC system, then what is the point? A non-IC system is irrelevant to our discussion. Plus, as you comment further, you ARE talking about an IC system, so I will continue to assume that is what you meant here.
BUT.... I'm getting a feeling you may not understand what IC is. Behe's quote is not talking about evolving an IC system, but he is describing what an IC system is...assuming it exists. For example, lets assume we have an IC system that is made of 100 parts. That 1 IC system has a function. The 100 parts have a 'sub-function', that when combined in their particular configuration, produce the function of the IC system (In Behe's quote that is the "that contribute to the basic function"). Now if you have 2 of the parts present, you do not have 2% of the IC function available. If you have 99 of the parts present, you do not have 99% of the IC function available. In both cases, you have 0% of the IC function availalble, and thus you have no IC system, nor an 'almost' IC system.
So if you truly are talking about how a system can become IC (evolving IC?), then realize that the concept of (yet) IC might be problematic.
PaulK writes:
WookieeB writes:
"may change" - OK. But I might need to you flesh out how they are supposed to change (trust me, it's important)
That is going to be specific to the sort of system you are looking at.
"You're killin me Smalls!"
Provide an example, or analogy please. In other words, pick a specific system (real or imagined) and describe "change".
...
Your next responses are OK and understood up until -
PaulK writes:
WookieeB writes:
"dependent on one or more other parts of the system" - OK. But the parts within an IC system are already dependent on one or more parts. So what is changing? Is it a change in how they depend on each other?
It is an additional dependency. After all I am describing how IC systems can evolve, remember ? The creation of dependencies between existing parts has rather obvious relevance to that
I have to assume that any "dependency", whether current or new, refers to the sub-function of any part in how it interacts with the sub-function of one or more other parts. So any existing 'dependency' is one part well-matched and interacting with other part(s). Adding an "additional dependency" I suppose could be allowed, but it would also have to be well-matched and interacting with another part(s) and could NOT interfere with the sub-function of any of the prior existing parts. That in itself would be highly unlikely to occur.
So that is all possible, but not probable. Adding another dependency just complicates what is already working, and NS would tend to weed that out unless it somehow improves function (not new function) of the IC system. But then, so what? It does nothing to explain how the IC system came about in the first place.
I'm trying to envision what you mean by a part getting an additional dependency. Say I have 4 parts (W,X,Y,Z) in order among many other parts (A, B, C, D,...) in an IC system. W interacts with one side of X. X's other side interacts with Y and Z. They are "dependent' on each other in this arrangement. So adding a new dependency would be like X matching it's function to yet another part: A, perhaps. It's counter-intuitive that such a new dependency would convey some advantage, but suppose it did. It cannot change the sub-function of any parts, otherwise the IC system breaks. It can enhance, or more likely degrade a sub-function, but only so long as the parent IC system still functions.
Beyond that, and also applied to the rest of your comments on IC, I'm not seeing the point.
we are talking about the significance of the 10^-77 figure. Specifically the point is that you can’t use it as the probability of evolving a new functional protein because evolution is not the same as random search.
What do you mean? Of course evolution is doing a random search. (Random search or blind search, however you want to describe it) Anything other than a blind search means you have information added to filter the search parameters. But evolution is unguided, purposeless, so it has no thought, no target, and cannot set filter information as to what it is searching for. Navigating the search space is done by mutations, which are random/blind. Natural selection is the selector, but it has no power over how it traverses search space.
That is why Hunt brought up the point about isolation. That objection doesn't dispute the 10^77 number in general, it just says that maybe all the positives are clusted together. If it turns out proteins are not isolated (which is supported by work since the 2004 paper we've been covering), then Hunt's point loses any punch. (And that is to a great extent what Axe's analogy was demonstrating. If no isolation, the search space is too big to realistically cover by evolution)

This message is a reply to:
 Message 157 by PaulK, posted 01-24-2019 5:32 PM PaulK has replied

Replies to this message:
 Message 175 by PaulK, posted 01-26-2019 2:30 AM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 173 of 1104 (847728)
01-25-2019 6:32 PM
Reply to: Message 171 by Tanypteryx
01-25-2019 1:05 PM


Re: Thread Copied from Proposed New Topics Forum
I still reject your definition. I've spent my life as a biological scientist and I have never heard another scientist use your definition.
Than I hope your science is better than your rhetoric.
So which scientist has used the definition: "The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in an iterative feedback response to the different ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats."
Is that the OFFICIAL definition? Is there an official one? Hmm, are definitions usually set in stone by exact wording?
If you want to discuss evolution with scientists you will find that most will reject descriptive words that have no other purpose than to ridicule the theory, because science does not include your imaginary fantasy bullshit.
Really?
So what do you specifically reject in the definition?:
Wookieeb writes:
the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms.
Doesn't matter how many words, what specific words, or who is composing it are unless the idea is wrong. What is wrong with the idea? How am I "redefining" it?
If you wanted to have an honest discussion you wouldn't have played your gotcha "oh that's the first time I've heard Dawkins called a creationist, gotcha". Then it turns out that Dawkins didn't say what you implied.
And again, never said or implied it was a quote. If you still think so, you need to look up the definition of DEFINITION.
Oh, and by the way. I got this from a little letter signed by 38 Nobel Laureates to the Kansas State Board of Education -
Logically derived from confirmable evidence, evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection.
Signed by -
Alexei A. Abrikosov Nobel Prize, Physics (2003)
Richard Axel Nobel Prize, Medicine (2004)
Gunter Blobel Nobel Prize, Medicine (1999)
Linda B. Buck Nobel Prize, Medicine (2004)
Aaron Ciechanover Nobel Prize, Chemistry (2004)
Mairead Conigan Maguire Nobel Prize, Peace (1976)
Robert F. Curl, Jr. Nobel Prize, Chemistry (1996)
John B. Fenn Nobel Prize, Chemistry (2002)
Clive W.J. Granger Nobel Prize, Economics (2003)
David J. Gross Nobel Prize, Physics (2004)
Leland H. Hartwell Nobel Prize, Medicine (2001)
Herbert A. Hauptman Nobel Prize, Chemistry (1985)
Dudley R. Herschbach Nobel Prize, Chemistry (1986)
Avram Hershko Nobel Prize, Chemistry (2004)
Roald Hoffmann Nobel Prize, Chemistry (198 1)
H. Robert Horvitz Nobel Prize, Medicine (2002)
Eric R. Kandel Nobel Prize, Medicine (2000)
Wolfgang Ketterle Nobel Prize, Physics (2001)
Aaron Klug Nobel Prize, Chemistry (1982)
Sir Harold Kroto Nobel Prize, Chemistry (1996)
Anthony J. Leggett Nobel Prize, Physics (2003)
Jean-Marie Lehn Nobel Prize, Chemistry (1987)
Ferid Murad Nobel Prize, Medicine (1998)
Erwin Neher Nobel Prize, Medicine (1991)
Sir Paul Nurse Nobel Prize, Medicine (2001)
Stanley B. Prusiner Nobel Prize, Medicine (1997)
Irwin Rose Nobel Prize, Chemistry (2004)
K. Barry Sharpless Nobel Prize, Chemistry (2001)
Horst L. St6rmer Nobel Prize, Physics (1998)
Gerardus ”t Hooft Nobel Prize, Physics (1999)
Daniel C. Tsui Nobel Prize, Physics (1998)
Harold E. Varmus Nobel Prize, Medicine (1989)
John E. Walker Nobel Prize, Chemistry (1997)
Carl E. Wieman Nobel Prize, Physics (2001)
Elie Wiesel Nobel Prize, Peace (1986)
Frank Wilczek Nobel Prize, Physics (2004)
Jody Williams Nobel Prize, Peace (1997)
Betty Williams Nobel Prize, Peace (1976)
So if scientists never use such descriptive words....then you need to look up the definition of SCIENTIST too.
Have fun!
P.S. - Your whole rail against me is an informal fallacy: argumentum ab auctoritate

This message is a reply to:
 Message 171 by Tanypteryx, posted 01-25-2019 1:05 PM Tanypteryx has replied

Replies to this message:
 Message 174 by Tanypteryx, posted 01-25-2019 7:28 PM WookieeB has not replied
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WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 179 of 1104 (847858)
01-28-2019 3:19 PM
Reply to: Message 175 by PaulK
01-26-2019 2:30 AM


Re: Hunt versus Axe
PaulK writes:
By which you mean that you were unfamiliar with Behe’s definition of IC - which I quoted - and therefore unable to follow an informal discussion of the subject.
I understand the Behe quote just fine. But well before you quoted Behe, you said the following:
PaulK writes:
I notice that you mention nothing about changes in parts (causing a reliance on other parts that was not previously present) or loss of parts...
THAT is the statement you we're basing your argument on. And THAT statement is what I was referring to as being incoherent.
Your attempted clarification of that statement was:
PaulK writes:
one or more of the parts making up a system may change such that their operation becomes dependent on one or more other parts of the system
.. to which was better, but I still had to break down into components to ascertain what you meant.
Your statement(s) are much different that what Behe said:
By irreducibly complex I mean 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.
And here is a complemetary defintion (to Behe's) of what IC is:
A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system’s basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.
so continuing....
You are, of course, completely wrong. Since the point of the discussion is how evolution can produce IC systems it would be pointless to start with a system that is already IC.
You're not making sense. Look again at your statement, the second one I was breaking down for understanding. The "system" in that context is an already complete, functioning system made up of 'parts'. We are talking about IC systems I thought. That is what Behe and the other definition are referring to. That is the subject of what you are talking about evolving, isnt it? IF we are not talking about what in the end is an IC system, what is the point?
This is an amusing piece of idiocy. Are you imagining that the terminology in the definition is only applicable to IC systems ? That only an IC system can have “parts” ? I can see no other reason for such foolishness.
You're not getting it. If we are talking about an IC system, then YES!!!, the terminology is only applicable to an IC system. It doesn't apply to a non-IC system. The terminology isn't just "have parts", it also relates to what those parts do.
Lets say you have an IC system, and you have a non-IC system. Yes, they both can have parts, but so what? That is not what the terminology is saying. How does the terminology differentiate those two systems???
For the non-IC system, you can remove a part, and the function of that system may remain. (Each and every part is not necessarily critical to function of the system as a whole)
For the IC system, if you remove a part, the system function fails. (Each part is critical to the function as a whole, so you cannot remove a part without breaking the system)
My points are about changing or removing parts. If you have a non-IC system with 100 parts it must - by the definition of IC - have at least one part that may be removed without ceasing to function. And if a part changes it still has the same number of parts.
OK, fine. But I thought we were trying to speak about IC systems, not non-IC systems. Your non-IC system with 100 parts is.... non-IC. Add a part, it is still non-IC. Take away a part, still non-IC. so what?
My example was about an IC system.
So ya, my system and your system are unrelated. Ummm, ok. So, lets talk about IC then.
Only to someone who fails to understand that a system becoming IC means that the system was not originally IC.
...
Since the parts are already functioning in a system they are already interacting with other parts. Also, they must be adequately “well-matched”. Of course if this is not true then a system with “ill-matched” parts could become IC just by becoming better matched.
No. You're not getting what IC means. *sigh*
Becoming an IC system is not a matter of a having a non-IC system and then adding/changing a part (unless you are talking about the creation of the whole IC system from scratch, but I don't think you are going there).
If a non-IC system is functioning, taking a part away, by definition, will not necessarily crash the function.
If a non-IC system is functioning, adding a part, may not crash the system, and if it doesn't crash the system, you still have a non-IC system, just one more part than normal. It is not IC.
Now take an IC system. If you take away a part, by definition, the function will crash.
Take an IC system, and add a part. That may not crash the system, but if it doesn't crash, you have an IC system (core) plus a part. Adding that part doesn't change the status of it being IC.
When you say "ill-matched", what does that mean? From the sound of it, though, 'ill-matched' would indicate the parts are not contributing as a whole to the system function. So you wouldn't have a functioning system.
Now a new dependency might be a consequence of improved function, but it is not necessary to have any benefit. Neutral changes can and do spread through drift.
Ok, but it seems like you are weaseling on definitions. If something is 'dependent', than it is not 'neutral'. That is a contradiction in terms.
An IC system could have something added or changed about it that is 'neutral', but that wouldn't change the relationship of the core parts as they relate to the function of the system as a whole, thus no 'dependency'.
If you have something as an example in mind, please share.
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.
...
Natural selection does provide guiding information. See above.
You're assuming a lot about the landscape of the search space. In your hill-analogy, the only way Darwinism works is if the landscape is a smooth, gradual sloping up the whole way. But you are not taking into account any peaks or valleys, the steepness of a slope, nor that function lives on islands in a vast ocean, which is more accurate a description of the topology.
The randomness relates to the mechanism of change - mutations. NS cannot guide those. NS can pick the best of whatever is provided to it, but that is not accounting for whether it is presented with an upward option.
What does NS do when it reaches a peak? It doesn't know that there is another, higher point in the vicinity. Unless you have very smooth transition from one to the other, NS gets stuck.
You mean that if it turns out that proteins are not isolated Axe’s point loses any punch.
And that they were not isolated was supported by work before 2004. One of the papers Hunt cited was published in 1996
But if proteins families/superfamilies are isolated even a little, then Axe's point is fine. And with more recent information, that does appear to be the case.
The citation in Hunt's paper only relates to the TEM-1 and DD-peptidases having some related structures. But that similarity doesn't extend to across all proteins. So unless you want to focus on a very narrow area, it doesn't help the broader point.

This message is a reply to:
 Message 175 by PaulK, posted 01-26-2019 2:30 AM PaulK has replied

Replies to this message:
 Message 181 by PaulK, posted 01-28-2019 3:57 PM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 180 of 1104 (847860)
01-28-2019 3:30 PM
Reply to: Message 176 by JonF
01-26-2019 9:02 AM


Re: Thread Copied from Proposed New Topics Forum
JonF writes:
So, no defense of your claims other than repeating your contradictory claims. Sad.
Analogy - I go to the pound and say I want a dog. The pound-guy asks: "What kind of dog do you want?"
I answer: "I don't care, just a dog."
Pound-guy says: "What do you mean? Don't you care if it is family friendly, good with the kids, or barks all night, or bites intruders, or pees on your leg, or has long-shedding hair, or is hairless, flat face, smooshed face...?"
I say, "Don't care, just as long as it's a dog. You know: wags tail, pants when tired, barks, chases cats."
Pound-guy asks: "Pure bred? Mutt? Old? Puppy?"
Me: "Not really. Just a dog."
Pound-guy leaves and comes back with a cat. I sigh.
Don't give me a cat JonF.

This message is a reply to:
 Message 176 by JonF, posted 01-26-2019 9:02 AM JonF has replied

Replies to this message:
 Message 182 by JonF, posted 01-28-2019 4:28 PM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 183 of 1104 (847875)
01-28-2019 6:21 PM
Reply to: Message 182 by JonF
01-28-2019 4:28 PM


Re: Thread Copied from Proposed New Topics Forum
This isn't rocket science. Those two claims are contradictory.
Then you have a problem with language.
Beyond being a "designer" and everything the meaning of that word entails, there is nothing else being said about....a designer.
If you won't let me even use the definition of a word that you yourself included, then there is no point in continuing.
The simplest definition I could think up on the spot for a designer: the activity of an intelligent mind to realize a functional goal.

This message is a reply to:
 Message 182 by JonF, posted 01-28-2019 4:28 PM JonF has replied

Replies to this message:
 Message 186 by JonF, posted 01-29-2019 9:12 AM WookieeB has not replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 184 of 1104 (847880)
01-28-2019 7:20 PM
Reply to: Message 181 by PaulK
01-28-2019 3:57 PM


Re: Hunt versus Axe
I didn’t say otherwise. My point is that you needed me to quote it.
No, I didnt need help to understand Behe. I needed help to understand you. Your words were not Behe's.
The terminology is applicable to systems in general. If it didn’t you couldn’t use the definition to see if a system was IC - you’d have to know if the system was IC before you could even think about it.
Ok, I understand now what you meant by "applicable". You're using in more of a manner of "to test by". I was taking that more as "confers the property to".
PaulK writes:
Wookieeb writes:
OK, fine. But I thought we were trying to speak about IC systems, not non-IC systems. Your non-IC system with 100 parts is.... non-IC. Add a part, it is still non-IC. Take away a part, still non-IC. so what?
Really ? If you take away all the non-essential parts you will have an IC system, certainly in the important sense that taking away any part will stop the system from functioning.
Yes, I get that. But this is the reverse of 'building' up an IC system. So how does building up an IC system work?
Subtracting - not adding - a part can make a system IC.
Umm, ok. But before you 'subtract' a part, the system is already IC + some part. So you haven't shown how to make IC yet.
Changing a part so that it or another part become essential to the system’s function can make a system IC. This is not difficult.
No. The part(s) are ALREADY essential to the system if it is IC. You cannot 'change' part(s) to become essential.
Because if you do happen to do that, than if you reverse what you just did, per the test in the Behe definition of IC, your system fails. And that means that before you added/changed part(s), you did not have had a functioning system, thus no system would have been built up to the point of: add part > IC. The only way this works is if all parts appear together, de novo.
Congratulations on understanding one of the essential points of my argument.
Aye. But again, this is not talking about building up an IC system. Your talking about breaking or building down to something that is already there.
I mean not-well-matched, of course. And if the parts of any functioning system are automatically well-matched then that part of the definition of IC is redundant.
Perhaps. But then again, it could be there to prevent someone trying to say "ill-matched" parts are functioning. The basic idea is the parts work with each other. Ill-matched implies the opposite of that.
......
With all this back and forth, please try to use a real example of something that is IC, or non-IC to IC if you think that works.
Behe has used a mousetrap as an example in the past, so use that if you want. But come up with your own if preferred.

This message is a reply to:
 Message 181 by PaulK, posted 01-28-2019 3:57 PM PaulK has replied

Replies to this message:
 Message 185 by PaulK, posted 01-29-2019 12:27 AM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 187 of 1104 (847911)
01-29-2019 1:27 PM
Reply to: Message 185 by PaulK
01-29-2019 12:27 AM


Re: Hunt versus Axe
But I was never talking about building a system. I was talking about how the system gets to be IC. That, after all, is the important issue.
You are making a very fine distinction here. You're implying that "building a system" is very different from ""how the system gets to be". But you haven't explained how a system gets to be IC or given an example.
Really ? The original system is not IC, the system without non-essential parts is IC. That looks like “making IC” (sic) to me.
Yes, really. As I explained before, if you have an IC system and you add a some part that is not essential to the function of the system, it does not become a non-IC system. It is just an IC system with an extra part. So yes, "the system without non-essential parts is IC". But the (system without non-essential parts) + non-essential part still has an IC core. Explaining how you get to an IC system via a Darwinian process is what you need to explain.
Making IC does not consist of taking a system that is pretty much already IC + a non-essential part, and removing that non-essential part.
Provide an example of an non-IC system, one where you take a part away and make IC.
Even if the second point is true it is certainly true that a part can change so that it needs one or more of the other parts,
I really don't know what you mean by this. If a system is already functioning, parts already "need" other part(s) to have the system function. I think you might be equivocating on what "need" or "essential" means in this hypothetical system you are referring to. How would you take a part that is already finely tuned to work with other parts, and then change it to necessarily work with other parts without affecting it's first task?
I never intended to - or need to - discuss how systems evolve
I thought you brought this up at the very beginning to talk about how to evolve IC.
The only point that matters is how systems get to be IC.
I agree. And how do you get IC systems? The only demonstrated way to get an IC system is via design!
That is the problem Behe posed. After all if there was a case that non-IC systems couldn’t evolve there wouldn’t be much point in singling out IC systems.
Perhaps, but you haven't really given an example of non-IC either. Other than a couple materials being in proximity to each other by happenstance, I'm having difficulty in even conceiving of a non-IC system that has something akin to "parts". Give an example of a system with parts that is non-IC.
Behe's point in highlighting IC is because life appears full of IC systems, and there is no plausible route to creating IC via Darwinian processes.

This message is a reply to:
 Message 185 by PaulK, posted 01-29-2019 12:27 AM PaulK has replied

Replies to this message:
 Message 188 by PaulK, posted 01-29-2019 1:49 PM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 189 of 1104 (847914)
01-29-2019 1:57 PM
Reply to: Message 181 by PaulK
01-28-2019 3:57 PM


Re: Hunt versus Axe
No, I’m not. Describing an algorithm says nothing about the search space.
But how well that algorithm can climb the hill does depend on the landscape.
If it isn’t presented with an upward option it stays where it is. And that’s pretty common.
Yes, but if you do not have much in the way of options to climb, and you are limited by time, then your climb ends up remaining static. When you can work out the probabilities, Darwinian mechanisms have a tremendous problem going anywhere.
In reality it isn’t so simple.
Yes, I know. You're hill climb is not as simple as you make it sound to be.
More likely by the time genes came along life was already using multiple proteins.
Isn't that a bit of an oxymoron? How would proteins exist apart from genes?
But I will add the fact that the functions overlap is certainly evidence against complete isolation, and certainly a problem for the assertion that rarity strongly implies isolation as Axe claimed in his response.
This may depend on what you mean by overlap, but I don't think this helps as much as you think it would. In the vast expanse of all protein function, there is little overlap to be found.

This message is a reply to:
 Message 181 by PaulK, posted 01-28-2019 3:57 PM PaulK has replied

Replies to this message:
 Message 190 by PaulK, posted 01-29-2019 2:11 PM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 191 of 1104 (847922)
01-29-2019 3:09 PM
Reply to: Message 188 by PaulK
01-29-2019 1:49 PM


Re: Hunt versus Axe
And I am explaining how a non-IC system can become IC.
No, your not really. Because whatever you have up till now been saying is non-IC is actually turning out to be IC with something irrelevant on top.....
A system with a non-essential part is not IC therefore it is a non-IC system.
No. You're not using the definition correctly. If that part is non-essential than it is not being used to contribute to the essential function (of the IC portion) and it doesn't qualify in the IC definition. I think you are getting hung up in the semantics now.
If you take a car (that has an IC core function: drive) and slap a sticker on it (part with a function: to look pretty, get noticed, etc), that sticker-part is not germaine to the IC part of the car. Adding that sticker doesn't now make the car non-IC. Neither does adding Christmas antlers to the roof of the car, nor a tune-playing horn. Those all might be "parts", but they are not contributing to the essential function of the car (driving) and thus don't qualify as any of the "parts" that the IC test would flag as a positive.
Look at my other definition for IC -
Wookieeb writes:
A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, nonarbitrarily individuated parts such that each part in the set is indispensable to maintaining the system’s basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system.
A "non-essential" part is not "indispensable to maintaining the systems basic function"
And then back to you needing to explain how an IC system is made? That is the central question. How could evolution do it? So far you only have already assumed some functioning system is already in place with some fluff, and remove the non-important fluff and voila! - an IC system. IC doesn't work that way. You need to explain how to get the stuff without the fluff.
Of course there is nothing wrong with changing functions, so long as it doesn’t break the system.
Umm, normally it would break a system. In any working system, a part is tuned to have a particular interaction with another part. (Remember Behe's "well-matched" criteria?) Changing a function would mean something that is doing function X is now doing function Y. If it no longer does X, then you broke the system. Typically, changing the function will negate the prior function. But, if you can give an example where changing a part function does NOT negate the prior function, please let me know.
I don't think things realistically work like you have described it, but let's assume it can....
And let me remind you that you were insisting that the parts don’t need to be “finely tuned”, just to work with each other.
"Fine tuned", "work with each other", "well-matched" - tere all the same to me. By tuned, I mean of all the possible configurations a part could take, it's form and effect have to conform with another part, whose form and effect also has to conform back, just to get the 'interaction' (sub-function) of the parts. That leaves a very narrow range of possibilities. Anything within that range is probabilistically very low, ie: "finely tuned".
it might change by becoming more finely tuned, or losing a non-essential part of its function, or gaining an additional function.
"finely tuned" - more to the center of the efficiency of it's function. Nothing changes as to how it applies to IC.
"losing a non-essential part of function" - irrelevant. It's non-essential.
"gaining an additional function" - dangerous (see above), but irrelevant as long as it's first function doesn't stop.
And I tell you again that it is only the feature of being IC that is of concern.
So, can you describe how this happens without assuming an IC core pre-exists?
Do you know when a scientist first suggest that evolution should be expected to produce IC systems ?
Can't say with confidence I know the "first". Without using the specific words (irreducible complexity), I do know that Darwin alluded to it when speaking about the eye, and Aristotle (or maybe it was Plato) made statements of a fashion describing it. Why is this important?
In other words you can’t conceive of a non-IC system.
No, I can. It's just that many examples are happenstance of proximity and/or rely on rarely random events. Even then, more than two or three parts, and I'm not getting much. The problem comes when ascertaining a system is in place, defining the function, without placing a dependency on whatever is constituting "parts"
No plausible route that Behe could think of. Sadly for him, the flaw was in his thinking.
And your plausible route is.....?
Behe’s definition of irreducible complexity was always intended to test a Darwinian explanation where some function is built up gradually over time, a direct evolutionary pathway. You haven't even begun to do that.

This message is a reply to:
 Message 188 by PaulK, posted 01-29-2019 1:49 PM PaulK has replied

Replies to this message:
 Message 192 by PaulK, posted 01-29-2019 4:18 PM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 193 of 1104 (847953)
01-29-2019 5:30 PM
Reply to: Message 190 by PaulK
01-29-2019 2:11 PM


Re: Hunt versus Axe
Indeed. But since I was only describing the basic algorithm I still wasn’t making any assumptions about the landscape.
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....
Now you are making assumptions.
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.
So when the malaria is forced to try hill-climbing, it has a very small opportunity in time and space to move up. That accounts for the fewer in 10 accounts of this event independently occurring, despite the huge number of opportunities presented to malaria. 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.
It’s quite possible that RNA-based life was using proteins before DNA-based life existed
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 message is a reply to:
 Message 190 by PaulK, posted 01-29-2019 2:11 PM PaulK has replied

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 Message 198 by PaulK, posted 01-30-2019 12:21 AM WookieeB has replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 195 of 1104 (847967)
01-29-2019 6:31 PM
Reply to: Message 192 by PaulK
01-29-2019 4:18 PM


Re: Hunt versus Axe
Which only means that they are non-IC systems.
Nope. You are equivocating on what a part is and what a system is.
If you think not, give an example.
Remember we are talking about part of the system, just one that is not essential. Which is necessary for the system to be non-IC.
So what would a part be that is not-essential to the system? Can you give an example?
You are still dodging. but fine, let's play your game. Say we have a 11-part "non-IC" system. Take 1 part away, and we have IC. Explain how the 10 remaining parts came to be an IC core.
And that is the way - by losing the “fluff”. No I do not have to start with an IC system. If I did you would immediately declare my argument a failure - or you would if you had the sense to realise it.
So you're only explanation of how to get IC is to have somebody plop down a pre-existing mechanism that also happens to have some extra fluff, then remove the fluff, and you've explained IC. Kinda like having somebody give you a wrapped present, then you remove the wrapping, find a shiny Apple device sitting there and declare: "See, I just invented an iPad."
Yup, that makes sense.
Not if the original function was still performed. Adding an extra function is fine, modifying the function in a way that keeps the essential elements of the original function is fine.
Which is fine and I already made provision for. Got an example?
Or can you tell me how it is possible to have a working non-IC system without a minimal subset of parts that would adequately perform the necessary functions of the system.
Yes, more along these lines. Just give an example of a working non-IC system.
I didn’t ask about mentions of irreducible complexity.....
It's getting really tiring that you always ask leading questions but never answer them yourself.
So, to answer your question succinctly: "Do you know when a scientist first suggest[ed] that evolution should be expected to produce IC systems ?"
Answer: No.
What of it?
Which means that you can’t imagine a non-IC system. Too bad.
Not what I said.
Can you?
The whole point is that it is the indirect paths. Don’t forget that evolution works without foresight. It doesn’t care about constructing systems, all that matters is what works now. One of the problems in Behe’s thinking was that he didn’t see that.
Flesh out what you mean by "indirect paths". I think I know where you are going, but would like you to explain it first.
Behe understood just fine that Darwinian processes dont work with foresight or plan.
And I suspect he also knew full well about what you mean by "indirect paths".

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WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 196 of 1104 (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?

This message is a reply to:
 Message 194 by JonF, posted 01-29-2019 6:02 PM JonF has replied

Replies to this message:
 Message 197 by JonF, posted 01-29-2019 6:57 PM WookieeB has not replied

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 204 of 1104 (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 replied

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

  
WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 205 of 1104 (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

This message is a reply to:
 Message 199 by NosyNed, posted 01-30-2019 10:33 AM NosyNed has not replied

  
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