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Author Topic:   Exposing the evolution theory. Part 2
JonF
Member (Idle past 285 days)
Posts: 6174
Joined: 06-23-2003


Message 136 of 1104 (847523)
01-23-2019 3:17 PM
Reply to: Message 133 by WookieeB
01-23-2019 2:38 PM


Re: Thread Copied from Proposed New Topics Forum
That's pretty close to a good definition. A nested hierarchy is a group of sets in which all sets except the initial one are wholly contained within one of the sets. So no duplicate sets or sets that appear within more than one set (in a Venn diagram, no set boundary crossing any set boundary).
Nested hierarchies are extremely difficult to construct from any reasonably large set of real sets. They are very rare in nature, so when one appears it demands explanation.
Life forms a nested hierarchy based on shared derived characteristics. Unless you have a different explanation. "We can't explain the designer" is not an explanation.

This message is a reply to:
 Message 133 by WookieeB, posted 01-23-2019 2:38 PM WookieeB has not replied

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


Message 137 of 1104 (847525)
01-23-2019 3:19 PM
Reply to: Message 128 by Taq
01-23-2019 1:04 PM


Re: Thread Copied from Proposed New Topics Forum
Axe used the gene sequence from two modern species which are both derived sequences. Modern species don't evolve from other modern species. Modern species evolve from a common ancestor who lived in the past. Both of the genes that Axe used had accumulated mutations since common ancestry, and neither gene represented the ancestral sequence that both of them evolved from. Therefore, Axe didn't model evolution because he didn't mutate the ancestral sequence.
You are on the wrong experiment. Our discussion is not talking about what you seem to be talking about (which I suspect is a later paper Axe did with Ann Gauger which was dealing with a different subject)
There was no "ancestor protein" being looked for, discussed, or referenced. Though I would point out that NOBODY knows what an "ancestor" protein is, as nobody has discovered one yet. For the moment, it is a red herring.
There are other functions that proteins can have, DUH!!! You can't test for one single function out of possible millions and claim that a protein has no function, DUH!!!
Dude! That wasn't his experiment. Duh!
He wasn't looking for new functions in the experiment we're talking about. His experiment was to estimate how flexible an enzyme could be changed before breaking, but he was gauging that based on the already known, no-higher than the already low-level functionality of the enzyme he started with. Since you apparently are thinking of the wrong experiment I guess I cannot fault you for not knowing what the correct experiment was about.
Then Axe should have tested for functions other than beta-lactamase activity that could have served as an island, BUT HE DIDN'T!! He also didn't use the ancestral sequence that could have contained those islands, DUH!!
No he shouldn't have. It wasn't the experiment you seem to think it should have been. Duh!

This message is a reply to:
 Message 128 by Taq, posted 01-23-2019 1:04 PM Taq has replied

Replies to this message:
 Message 140 by Taq, posted 01-23-2019 3:37 PM WookieeB has replied

  
Taq
Member
Posts: 10198
Joined: 03-06-2009
Member Rating: 3.1


(2)
Message 138 of 1104 (847529)
01-23-2019 3:24 PM
Reply to: Message 133 by WookieeB
01-23-2019 2:38 PM


Re: Thread Copied from Proposed New Topics Forum
WookieeB writes:
Please define what a nested hierarchy is. I think we have different ideas of this.
To me, in it's simplest form, it is groups within groups. Or a defined set that contains other defined sub-sets.
Nested hierarchies are groups within groups, and each group is defined by shared derived features, also called synapomorphies. These are often called cladograms or phylogenies:
Notice how each branch is defined by a shared derived feature. You never did that for your Corvettes. You just showed a bunch of pictures of Corvettes. If you want to claim that human designs also produce phylogenies with the same statistically significant phylogenetic signal that biological species do, then you need to actually show it. You may also want to brush up on your computational phylogenetics:
Computational phylogenetics - Wikipedia
Afterall, you wouldn't make the claim that common design produces the same phylogenetic signal as evolution unless you had already done the work, right? RIGHT????

This message is a reply to:
 Message 133 by WookieeB, posted 01-23-2019 2:38 PM WookieeB has replied

Replies to this message:
 Message 143 by WookieeB, posted 01-23-2019 5:08 PM Taq has replied

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


Message 139 of 1104 (847534)
01-23-2019 3:32 PM
Reply to: Message 129 by PaulK
01-23-2019 1:10 PM


Re: Thread Copied from Proposed New Topics Forum
You seem to have missed the fact that Hunt specifically addresses isolation:
Reading comprehension is a problem for you, isnt it.
I have been saying since the beginning that Hunt isnt disputing "rarity" so much as he is disputing "isolation". So I didnt miss that fact but have been saying that from the start.
Hunt has a problem with the rarity numbers because he thinks they may be exaggerated for the various reasons he gave. Axe responded to his charges of 'exaggerated' just fine. If you don't like the analogy, that is your problem. You don't seem to have any problem with Hunt's analogy. I wonder why.
I note also that you omit the fact that the forward approach is associated with the very highest figures.
Hmm. I quote Hunt regarding the "foward" method comparison, then comment directly about his highest number of 10^10 i the following paragraph. Nope, don't seem to have omitted it at all.

This message is a reply to:
 Message 129 by PaulK, posted 01-23-2019 1:10 PM PaulK has replied

Replies to this message:
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Taq
Member
Posts: 10198
Joined: 03-06-2009
Member Rating: 3.1


Message 140 of 1104 (847539)
01-23-2019 3:37 PM
Reply to: Message 137 by WookieeB
01-23-2019 3:19 PM


Re: Thread Copied from Proposed New Topics Forum
WookieeB writes:
Though I would point out that NOBODY knows what an "ancestor" protein is, as nobody has discovered one yet. For the moment, it is a red herring.
Using a phylogeny based on evolutionary distance and known sequences from living species you can reconstruct the ancestral sequence.
He wasn't looking for new functions in the experiment we're talking about. His experiment was to estimate how flexible an enzyme could be changed before breaking, but he was gauging that based on the already known, no-higher than the already low-level functionality of the enzyme he started with.
If an enzyme has a new function, then it isn't broken. It still has function.

This message is a reply to:
 Message 137 by WookieeB, posted 01-23-2019 3:19 PM WookieeB has replied

Replies to this message:
 Message 146 by WookieeB, posted 01-23-2019 6:22 PM Taq has not replied

  
PaulK
Member
Posts: 17856
Joined: 01-10-2003
Member Rating: 3.8


Message 141 of 1104 (847553)
01-23-2019 3:57 PM
Reply to: Message 139 by WookieeB
01-23-2019 3:32 PM


Re: Thread Copied from Proposed New Topics Forum
quote:
Reading comprehension is a problem for you, isnt it.
On the contrary. You claimed that there is no evidence of a lack of isolation with respect to rarity - but Hunt actually cited such evidence - and I quoted it. So unless you are complaining that I correctly comprehended Hunt’s point the problem seems to be yours.
quote:
Hunt has a problem with the rarity numbers because he thinks they may be exaggerated for the various reasons he gave. Axe responded to his charges of 'exaggerated' just fine.
Obviously he did not.
quote:
If you don't like the analogy, that is your problem. You don't seem to have any problem with Hunt's analogy. I wonder why.
Axe gives no reason to think that his alleged analogy is valid and neither do you. Hunt, in contrast does not rely on argument by analogy and his illustrations do appear to be valid.
Again, the problem is clearly yours.
quote:
Hmm. I quote Hunt regarding the "foward" method comparison, then comment directly about his highest number of 10^10 i the following paragraph. Nope, don't seem to have omitted it at all.
Ok, I’ll give you that one. But the idea that if the highest extremes are likely exaggerated then the lowest extremes are likely correct is hardly a good argument, not when there are more than 50 orders of magnitude involved. The mere fact that Axe’s figure is at the lower extremes is reason to suspect it is too low. So you still missed the significance of the forward method only supplying the highest end - its likely. flaws do not taint figures produced by other methods at all.

This message is a reply to:
 Message 139 by WookieeB, posted 01-23-2019 3:32 PM WookieeB has not replied

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


Message 142 of 1104 (847560)
01-23-2019 4:42 PM
Reply to: Message 135 by PaulK
01-23-2019 3:14 PM


Re: Thread Copied from Proposed New Topics Forum
PaulK writes:
An analogy can’t demonstrate anything unless it accurately represents the problem. Hunt talks about the actual question and gives references. Axe talks about his supposed analogy without giving any references that provide empirical support.
You're either hyper-sensitive or using a double standard. Using a graph image as Hunt does and presenting the experiment in terms of search space, islands of function, and his hill diagram, are just as much an analogy of the experiment as what Axe is analogizing with respect to the use of a lower-level functioning enzyme.
You may call one "Hunt talks about the actual question and gives references" and then say that Axe is using "supposed analogy" and giving no references (he does give references in his response, and don't forget he has the references from his paper that are directly involved too). Sounds like special pleading to me.
I disagree. Moving in a random direction is more likely to retain function if at the centre of the distribution (only moving too far can lose function).
Funny, but the actual science doesn't support that. If you start at the center/top of distribution, you only have one way to go - down. And where are you placing your standard of function for a positive result? Anything less that the top will fail, perhaps? If so, you've already limited yourself to results that are practically perfection. If not the top as standard, how low will you go? What is a reasonable level that would not be trying to stack the deck? (This is all besides the point that starting at the top will lead to less positives because the top configuration is the least amenable to mutation. Axe purposely moved lower down the function hill to remove the natural handicap that the wild-type enzyme had in place. So Axe helped the evolutionary possibilities)
The further from the centre, the more likely a random move is to lose function.
Not necessarily. If you pick a starting point lower on the hill, as Axe did, and then allow for a random search, and to some extent depending on the terrain, you could equally end going up the hill as down. If you apply the same \[b\]standard\[b\] of what is acceptable function as you did for your 'choose the optimal starting point' (but not necessarily the same level), you actually allow for more positives than if you chose the other scenario (because going UP would always be positive).
That is what Axe's analogy was demonstrating.
Axe’s actual objection doesn’t seem to make sense either. Nobody is suggesting that using a low level of function as the criterion is a mistake. Hunt actually says that Axe looked for some measure of function - not equal function to the originally protein. In suggestion otherwise Axe is the one suggesting that he set the bar too high.
The part in BOLD is ok.
Hunt is not saying the bar is too low per se, but he is saying the bar is restricted to a narrow area (or small spikey hill as in his diagram) as to the tested enzyme variety Axe uses. Hunt seems to think the function area is restricted to the black box that Axe uses as a starting point. (It's not specified very well in the diagram Hunt uses, nor does he provide any numbers to identify a function level). But Axe is actually pointing out to the effect that the function area is at the very least from the level of the black box and all the way up from there. So even if Axe is being strict that no function exists below the supposed spot Hunt highlighted, Axe's area of function (by the same standard) is a lot more than if he had chosen the top point. But Axe isn't saying he set the bar too high.
Hunt actually objects that Axe chose a variant unusually sensitive to mutation - which would be more likely to lose function.
Yes, Hunt does say that in relation to it being a "temperature sensitive variant". But Hunt doesn't provide any references to that specifically and neither does Axe comment on the temperature side of things (outside of his paper). So I'm not sure how relevent this is, as the temperatures for testing would be consistent for the whole experiment. If this does have any bearing, I'd have to see some references to that effect. Otherwise, using that statement to apply to the whole of the criticism is a bit disingenuous.
Elsewhere, it is acknowledged that the tested enzyme is mutation-sensitive, but I'm not seeing how that is a problem. That again refers to the removal of the wild-type handicap that prevents mutations from being allowed.
Behe stated that irreducible complex structures could evolve. This supports the assertion that the idea that they cannot is an error.
Well Behe qualified how an IC system could evolve. So unless you are including that, I'm not sure where or who said it cannot.
I listed ways other than cooption that irreducible complexity structures could evolve.
And where did you do that? Is that supposed to be where you said: " 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...", cause that is a lot of unintelligible nothing.
Of course i’m not and if you had any understanding of my point you would know that. The point is that the search space is structured such that stepwise refinement starting from a good point - for something close enough, not necessarily the desired function - is a lot, lot better than random search,
I understand the concept of search space just fine. But I don't understand what you are saying here. I understand up to when you say "starting from a", but not past that. What is "a good point - for something close enough, not necessarily the desired function" supposed to mean?

This message is a reply to:
 Message 135 by PaulK, posted 01-23-2019 3:14 PM PaulK has replied

Replies to this message:
 Message 144 by PaulK, posted 01-23-2019 5:24 PM WookieeB has replied

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


Message 143 of 1104 (847563)
01-23-2019 5:08 PM
Reply to: Message 138 by Taq
01-23-2019 3:24 PM


Re: Thread Copied from Proposed New Topics Forum
Nested hierarchies are groups within groups, and each group is defined by shared derived features, also called synapomorphies. These are often called cladograms or phylogenies
Ahh, see, you are restricting your language now. Originally you said Corvettes cannot be in a nested hierarchy. But of course they can.
But if you are limiting your nested hierarchies (which not all NH's are) to "shared derived features" or "phylogenies", which are implying a biological evolutionary process, than of course Corvettes would not fit into that NH.
But nobody is claiming that they do!
I'll say more about cladograms later. But think hard now and tell me what the lines and linked lines represent in your diagram.
you wouldn't make the claim that common design produces the same phylogenetic signal as evolution unless you had already done the work, right? RIGHT????
Nope, I wouldnt. Because in your case a "phylogenetic signal" is assuming evolution, and of course Design would not produce the same signal.
But design could produce the same endpoints in your cladogram. Just the process would be different. That is my point.

This message is a reply to:
 Message 138 by Taq, posted 01-23-2019 3:24 PM Taq has replied

Replies to this message:
 Message 145 by Taq, posted 01-23-2019 5:54 PM WookieeB has not replied

  
PaulK
Member
Posts: 17856
Joined: 01-10-2003
Member Rating: 3.8


Message 144 of 1104 (847567)
01-23-2019 5:24 PM
Reply to: Message 142 by WookieeB
01-23-2019 4:42 PM


Re: Thread Copied from Proposed New Topics Forum
quote:
You're either hyper-sensitive or using a double standard. Using a graph image as Hunt does and presenting the experiment in terms of search space, islands of function, and his hill diagram, are just as much an analogy of the experiment as what Axe is analogizing with respect to the use of a lower-level functioning enzyme.
Your inability to answer my points hardly means that there is something wrong with me.
Hunt uses images to illustrate points which stand without the images. Axe’s demonstration is entirely based on the supposed analogy - but neither he nor you have offered any reason that suppose that the analogy is valid. No hyper-sensitivity, no double standard just plain sense.
quote:
You may call one "Hunt talks about the actual question and gives references" and then say that Axe is using "supposed analogy" and giving no references (he does give references in his response, and don't forget he has the references from his paper that are directly involved too). Sounds like special pleading to me.
I said that Axe doesn’t offer any references that give empirical support for his analogy - or his claims of isolation.
quote:
Funny, but the actual science doesn't support that. If you start at the center/top of distribution, you only have one way to go - down.
And another failure of reasoning on your part. We are not concerned with changes in the level of function, only whether the changed protein is in the part of sequence space where some level of function is found. And so by applying an irrelevant criterion you miss a simple and obvious point.
quote:
That is what Axe's analogy was demonstrating.
If you wan to claim that Axe made the same mistake as you, that is your problem. Hunt is (correctly) concerned with whether the new sequences have some measure of activity - not whether the level increased or decreased.
quote:
Hunt is not saying the bar is too low per se, but he is saying the bar is restricted to a narrow area (or small spikey hill as in his diagram) as to the tested enzyme variety Axe uses. Hunt seems to think the function area is restricted to the black box that Axe uses as a starting point
I think you have misunderstood Hunt’s point. In fact Hunt says the small spikey hill
In addition, Axe deliberately identified and chose for study a temperature sensitive variant. In altering the enzyme in this way, he molded a variant that would be exquisitely sensitive to mutation. In terms of our illustrations, Axe’s TEM-1 variant is a tiny hill with very steep sides, as shown in the following (Figure 3)
So, in fact it represents sensitivity to mutation.
quote:
Yes, Hunt does say that in relation to it being a "temperature sensitive variant". But Hunt doesn't provide any references to that specifically and neither does Axe comment on the temperature side of things (outside of his paper).
As quoted above Hunt claims that the temperature sensitivity makes the variant chosen by Axe more sensitive to mutation.
That sensitivity to mutation naturally makes it easier to lose function (that’s the point of it). That is why the hill is small and spikey.
Hunt does note that the enzyme chosen by Axe is inactive at the temperatures at which E Coli is usually grown but does not make a point of it.
quote:
Well Behe qualified how an IC system could evolve. So unless you are including that, I'm not sure where or who said it cannot.
William Dembski did - in one of his books where he was attempting to apply his Explanatory Filter to the evolution of a flagellum.
quote:
And where did you do that? Is that supposed to be where you said: " 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...", cause that is a lot of unintelligible nothing.
I’m sorry that you didn’t understand but those are ways in which irreducible complex systems could evolve.
quote:
I understand the concept of search space just fine. But I don't understand what you are saying here.
quote:
I understand up to when you say "starting from a", but not past that. What is "a good point - for something close enough, not necessarily the desired function" supposed to mean?
I mean that if your initial sequence either has some of the desired function or a similar function it helps a lot in finding a sequence that is good at the desired function.

This message is a reply to:
 Message 142 by WookieeB, posted 01-23-2019 4:42 PM WookieeB has replied

Replies to this message:
 Message 149 by WookieeB, posted 01-23-2019 7:35 PM PaulK has replied

  
Taq
Member
Posts: 10198
Joined: 03-06-2009
Member Rating: 3.1


Message 145 of 1104 (847570)
01-23-2019 5:54 PM
Reply to: Message 143 by WookieeB
01-23-2019 5:08 PM


Re: Thread Copied from Proposed New Topics Forum
WookieB writes:
Ahh, see, you are restricting your language now. Originally you said Corvettes cannot be in a nested hierarchy. But of course they can.
My language has been the same from start to finish, and I still have not seen you put Corvettes into a nested hierarchy as we do with species.
But if you are limiting your nested hierarchies (which not all NH's are) to "shared derived features" or "phylogenies", which are implying a biological evolutionary process, than of course Corvettes would not fit into that NH.
If life evolved then they should fall into a nested hierarchy based on shared derived features. That has been the argument for evolution since the mid-1800's. The fact that designed things do not fall into a nested hierarchy when organized by shared derived features demonstrates why this evidence points to evolution and not to intelligent design.
I'll say more about cladograms later. But think hard now and tell me what the lines and linked lines represent in your diagram.
The lines represent groups, and where they meet represents a group of shared derived features.
Because in your case a "phylogenetic signal" is assuming evolution, and of course Design would not produce the same signal.
Phylogenetic signal does not assume evolution. It is a measure of how well the distribution of characteristics matches a tree-like structure. If you randomly assign characteristics to a set of hypothetical species then it will return a low phylogenetic signal. It is a measurement, not an assumption.

This message is a reply to:
 Message 143 by WookieeB, posted 01-23-2019 5:08 PM WookieeB has not replied

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


Message 146 of 1104 (847572)
01-23-2019 6:22 PM
Reply to: Message 140 by Taq
01-23-2019 3:37 PM


Re: Thread Copied from Proposed New Topics Forum
Using a phylogeny based on evolutionary distance and known sequences from living species you can reconstruct the ancestral sequence.
And yet nobody has ever done this.
No, you cannot. This is all just theoretical.
There is not even enough understanding on building proteins to be able to do this even if it was possible.
Assuming somebody did, how in the world would you verify it is an "ancestral" protein?
If an enzyme has a new function, then it isn't broken. It still has function.
Gosh. You really don't understand how this works.
How, pray tell, would one identify a new function?
The enzyme Axe worked with had a function - to catalyze a chemical function (interact with/break down a substrate). If it cannot perform that function, the cells cannot grow. How did he determine there was function? He put his mutants on a substrate and checked to see if they could grow. Strength of function could be determined by a number of parameters, but growth time would be a decent indicator.
If the mutants couldn't fold properly, function is obviously gone and they dont grow.
So if the enzyme somehow gets a new function, that means it is not doing it's original function. It will not grow, it dies, because it needs its original function to survive. So new function wouldn't matter and nobody would know.
A modification of the original function, like it getting 'stronger' or 'weaker' is perfectly fine, as that is well within normal variability (NS doing it's thing) and is no objection with ID. This would correspond to the 'varying positives'.
And whether or not it could get a new function is somewhat a moot point, as Axe was not working on the entire sequence of the whole enzyme. He was focusing on a particular domain (main folding structure) of the enzyme, that structure accounting for about 150 AA's (The whole protein is larger). So his research was focused on one particular part of the enzyme, and that part is critical to the function.
To use my own analogy, it's like taking a car model (my beautiful Corvette) and modifying the wheels, You can make them bigger, smaller, vary toughness, perhaps even take away one wheel, and it will still drive (it's purpose). But at some point you modify wheels too much and the car doesn't drive anymore.

This message is a reply to:
 Message 140 by Taq, posted 01-23-2019 3:37 PM Taq has not replied

Replies to this message:
 Message 147 by JonF, posted 01-23-2019 6:40 PM WookieeB has not replied
 Message 150 by JonF, posted 01-23-2019 7:52 PM WookieeB has not replied

  
JonF
Member (Idle past 285 days)
Posts: 6174
Joined: 06-23-2003


(1)
Message 147 of 1104 (847574)
01-23-2019 6:40 PM
Reply to: Message 146 by WookieeB
01-23-2019 6:22 PM


Re: Thread Copied from Proposed New Topics Forum
And yet nobody has ever done this.
No, you cannot. This is all just theoretical.
LMGTFY - Let Me Google That For You
"Just theoretical" does not mean "useless" or "untested".

This message is a reply to:
 Message 146 by WookieeB, posted 01-23-2019 6:22 PM WookieeB has not replied

  
Tanypteryx
Inactive Member


Message 148 of 1104 (847577)
01-23-2019 7:07 PM
Reply to: Message 120 by WookieeB
01-22-2019 7:18 PM


Re: Thread Copied from Proposed New Topics Forum
But basically I was indicating that you have no reason to say there is ANY 'ancestors and descendants' involved.
Well excuse me for using words you don't like. I was simply trying to be clear that no ancestor and descendant relationships were implied, because some people jump to that conclusion.
Assuming you are correct, then what is the process by which proteins actually evolve that Axe's work has absolutely no bearing on whatsoever?
First, proteins evolve when there are mutations in the genes that produce them. So new proteins evolve from already existing ones. Each new protein does not have to go through a long involved process of starting from scratch.
Second, calculating the probability of something occurring, for example 1x10^77, does not mean that 1x10^77 attempts have to occur before you have a functional protein. The functional protein could be formed after 1 try, or 50, or 1000.
Evolution almost totally occurs by modifying existing features.
WookieeB writes:
Tanypteryx writes:
I do think it's interesting that the few ID articles that I've read are short on convincing evidence and seem to be "preaching to the choir" rather than competing with mainstream science publishing. They don't seem to be able to cut the mustard when it come to critical scientific review. It always comes down to "you have to believe in magic."
Rather than more 'I say:you say' banter, can you provide an example?
An example of preaching to the choir is the fact that all their papers are only published in the journal that only they read. If you mean an example of "you have to believe in magic", then the magic designer for which there is not a shred of evidence.
WookieeB writes:
Tanypteryx writes:
Funny, because that's not what I said. That looks like a paraphrased quotemine to me. Kind of an unquoted quotemine.
I haven't read Dawkins' books, but I suspect that he didn't say exactly...
Nobody claimed it was a quote. It's just a short description of what the idea of evolution is in Dawkin's book, which is a pretty common meaning for evolution in discussions like these. If you haven't read it, then I guess you wouldn't know either way.
So I was correct, Dawkins didn't say that and you added the weasel words yourself.
You certainly implied it was a quote when you accused me of calling Dawkins a creationist based on my reaction to that fake quote.
I have looked up some of his quotes.
WookieeB writes:
Tanypteryx writes:
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.
No mention of mutations or natural selection here, unless that is what you would include in "an iterative feedback response". This needs to be fleshed out in more detail, as it doesn't provide any information as to what you meant earlier by mentioning "the process by which proteins actually evolve or how biology actually works".
"Changes in the composition of hereditary traits" are mutations.
"an iterative feedback response to the different ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats" is natural selection.
But within this description, do you allow for the process to be directed, purposeful, and/or via an intelligence? The definition is rather agnostic there.
Of course not. There is no evidence of direction, purpose or a designing intelligence involved in biological processes. Until there is evidence why would we include it? We also do not all the other things there is no evidence for.
I've been neglecting work while procrastinating here, so need to get my ass in gear and get caught up.

What if Eleanor Roosevelt had wings? -- Monty Python
One important characteristic of a theory is that is has survived repeated attempts to falsify it. Contrary to your understanding, all available evidence confirms it. --Subbie
If evolution is shown to be false, it will be at the hands of things that are true, not made up. --percy
The reason that we have the scientific method is because common sense isn't reliable. -- Taq

This message is a reply to:
 Message 120 by WookieeB, posted 01-22-2019 7:18 PM WookieeB has replied

Replies to this message:
 Message 153 by WookieeB, posted 01-24-2019 1:47 PM Tanypteryx has replied

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


Message 149 of 1104 (847578)
01-23-2019 7:35 PM
Reply to: Message 144 by PaulK
01-23-2019 5:24 PM


Re: Thread Copied from Proposed New Topics Forum
Hunt uses images to illustrate points which stand without the images
LOL, are you for real? "Images" were an analogy that Hunt used to "illustrate points" that was also part of his analogy. Just because you don't want to characterize it that way doesn't make it so. And Hunt didn't provide references for his analogy.
Touche!
I said that Axe doesnt offer any references that give empirical support for his analogy - or his claims of isolation
And neither did Hunt use references for his analogy. Axe wasn't the one making claims of isolation. That was Hunt.
I think you have misunderstood Hunts point. In fact Hunt says the small spikey hill...
So, in fact it represents sensitivity to mutation.
Hunt says (no references) that Axe's enzyme was too sensitive to temperature. Here's a picture I made to visualize that. (No reference either).
So I guess to you, if a critic makes up some picture that he says demonstrates some unsubstantiated claim, it's gotta be so!
Im sorry that you didnt understand but those are ways in which irreducible complex systems could evolve.
For the moment I'm not trying to dispute whether IC systems can or cannot evolve. What I am saying is that your statements: "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..." doesnt make sense in an English sense. I cannot figure out what you are saying, not on a technical level or a pro/against IC sense, but what the hell does that mean in normal English. "Change in parts" of what? "Reliance on other parts not previously present" is a disjointed statement. I need you to expound a bit, give some context. I cannot figure out what you are saying. Just because you say it the same way all the time is not helping with the understanding part.
I mean that if your initial sequence either has some of the desired function or a similar function it helps a lot in finding a sequence that is good at the desired function.
Still a little confused with your language. What are you meaning by "desired function" vs "similar function" and how are those distinct from "good at desired function"?

This message is a reply to:
 Message 144 by PaulK, posted 01-23-2019 5:24 PM PaulK has replied

Replies to this message:
 Message 151 by PaulK, posted 01-24-2019 12:37 AM WookieeB has replied

  
JonF
Member (Idle past 285 days)
Posts: 6174
Joined: 06-23-2003


Message 150 of 1104 (847579)
01-23-2019 7:52 PM
Reply to: Message 146 by WookieeB
01-23-2019 6:22 PM


Re: Thread Copied from Proposed New Topics Forum
How, pray tell, would one identify a new function?
Mostly you wouldn't. But that's irrelevant.
Failing to detect a new function does not prove there is no new function, nor does it indicate that there is any particular probability of a new function. That's why Axe's work is bootless.
Edited by JonF, : No reason given.

This message is a reply to:
 Message 146 by WookieeB, posted 01-23-2019 6:22 PM WookieeB has not replied

  
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