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


Message 121 of 1104 (847454)
01-22-2019 9:28 PM
Reply to: Message 118 by JonF
01-22-2019 6:58 PM


Re: Thread Copied from Proposed New Topics Forum
D does not predict a nested hierarchy. But of course it can account for a nested hierarchy
Yes, that is correct. Your language is better here. 'Account for' is preferred to predict.
since it can account for anything
Well that is not true. I doubt anyone would claim design for a totally random process.
Which means it can't predict anything, especially the result of any experiment.
Not so. ID doesnt claim to be able to predict anything or everything. I suppose a prediction on an experiment depends on the experiment. But nothing was predicted regarding the outcome of Axe's experiment.
Take Junk DNA as another example. Darwinian evolution predicted that junk DNA would be prevalent, most of the content of DNA. ID predicted that though there could be some junk, most DNA would prove to be functional. An lo and behold, as more evidence mounts the ID position is proving to be the correct one.

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 Message 118 by JonF, posted 01-22-2019 6:58 PM JonF has replied

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


Message 126 of 1104 (847476)
01-23-2019 12:35 PM
Reply to: Message 122 by PaulK
01-23-2019 12:31 AM


Re: Thread Copied from Proposed New Topics Forum
Since we are explicitly disagreeing about rarity, since Hunt explicitly points out that other studies show much less rarity and since Hunt also argues that Axes methods would exaggerate the rarity it seems that it very much is the point.
You need to read more carefully. Rarity is not the thing in dispute. Hunt doesn't dispute Axe's numbers per se.
If one part, Hunt is complaining that the sample is too restrictive in function as to lead to those numbers, but Axe pointed out in his response (his Objection 3) to Hunt's posting that Hunt is looking at it backwards. Essentially, in the search space, Axe picked a functional spot lower on the hill. Hunt seems to think that is a problem and characterized that low spot as new spikey hill. But Axe pointed out in his response that Hunt (and Stephenson, Venema) objections are misplaced. Axe's low spot allows for function to be found at any other low spot along that hill as well as higher up the peak, which allows for a whole lot more positives than Hunt is accusing Axe of allowing. But according to Axe, even that more generous allowance of function still is a small island in a large sea.
Hunt's other objection was related to isolation (not rarity). HE thinks that functional sequences along the same domain might be closer together in the sea of possibilities. Axe didn't directly address this in his experiment, but there is no evidence of a lack of isolation with respect to rarity, so rarity should still (to some extent) factor into determining functional fold possibilities. (Axe's response on Objection 2)
With respect to Hunt pointing out other studies, he give a range between 10^10 - 10^63 (in the apples to apples comparison, Axe's figure was 10^64). So Axe's results were not much outside the range of other studies, and Hunt did not indicate Axe was exaggerating with regards to his number). But note Hunts last paragraph in that section 3 of his response:
The uncertainties in estimating the densities of functional sequences are very high. Obviously, we all would like to home in on a narrower range. This is complicated by the technical and theoretical shortcomings of the various approaches. The reverse approach is tied to a single family of sequences and functions and makes assumptions that may not be warranted (Section 2 here is an example). The forward approach may find too many things, some (many?) of which may have no biological relevance. Sorting these things out is a tough nut to crack experimentally.
Axe's approach was the "reverse" one. As to the assumptions Hunt is saying that are not warranted, those are the objections above that Axe dispelled in his response, which would make Axe's numbers OK (barring some other objection). But the as to the 'forward' method, the one that lead to a 10^10 result, Hunt admits that the numbers might be too high essentially being a false positive (the "have no biological relevance" remark). So at the very least, between that wide range, it leans more in the direction of Axe's numbers.

This message is a reply to:
 Message 122 by PaulK, posted 01-23-2019 12:31 AM PaulK has replied

Replies to this message:
 Message 129 by PaulK, posted 01-23-2019 1:10 PM WookieeB has replied

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


Message 131 of 1104 (847491)
01-23-2019 2:02 PM
Reply to: Message 122 by PaulK
01-23-2019 12:31 AM


Re: Thread Copied from Proposed New Topics Forum
PaulK writes:
Note that Axe is also defending the criticism of his method. Except that there is no demonstration.
...
I understand that I was correct. Axe attempted to defend against the criticism of his experiment - which would exaggerate the rarity - by using an alleged analogy that was nothing of the sort.
I'm beginning to think you have a problem with logical language.
Axe is defending against the criticism of his method by showing that the criticism is without merit. Essentially the criticism is wrong because the charge is backwards in thinking. And he used an analogy to demonstrate that.
Hunt in the first section in describing what Axe did properly indicated that Axe didnt use the wild-type enzyme specifically because it would be too resistant to mutations. In other words, the wild-type enzyme has built in protections that would prevent the likelyhood of any mutations. In order to even be able to do the experiment, Axe instead used a molded enzyme that was less blocked from mutations occurring, which also set the bar lower for functionality compared to the wild type.
Hunt (and others) seemingly think that this less that optimal functioning starting point is too restrictive, but as Axe pointed out they are missing the point. By using this modified enzyme to start with, Axe wasn't picking a fixed low point on the hill (as illustrated by Hunt) to restrict positives too, but instead he was picking a lower position on the hill as a starting point that would be much easier to move away from (via mutations) and anything at the same elevation or higher (in relation to the starting point) would be a positive.
I'm not sure if you just have a problem with Axe using an analogy to describe it. But if so, then why don't you also have a problem with Hunt (and others) using an analogy to criticize it. What else do you think all the talk and pictures of hills that Hunt uses are?
You certainly are confused, since you were asking how it was shown that irreducible complexity could evolve. 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 which would also be reasonable elements in any explanation.
It was you who originally said: "The idea that irreducible complexity cannot evolve is another common error". And then you said something about Behe not making that mistake. I then asked you how so? To which you responded that Behe did say "as much", which I take it the "as much" to be "irreducible complexity cannot evolve". So which is it?
And it's not clear what you are referring to as to parts changing, relians, or loss of parts. I could talk about IC all day, but you gotta be clear in what you are stating/asking before I comment further.
latched up his argument to deal with opindirect routes
Huh? Normal english please.
Do you mean "ratched up his argument" and "indirect routes"? If so, I still don't know what you are saying
Because you would have to assume a uniform distribution and we know that isn’t true. The odds of getting a functional protein from a minor modification of an existing functional protein are much higher than getting a functional protein by assembling a random sequence.
I don't think you understand his experiment. Axe wasn't purely assembling proteins from a wholly random sequence. He was remaining in the TEM-1 penicillinase family and modifying an enzyme in amino acid blocks (because single point mutations is prohibitive to research, as the space of results in count would be well beyond the number of atoms in the universe), and to an extent restricting where mutations would occur that would not automatically wreck the basic folding structure. The whole point was to break down what is a impossibly huge effort (getting a functional protein by assembling a random sequence) and breaking that problem down into a smaller chunk (TEM-1 family of protein folds) and then even narrowing it down smaller (his 10-block amino acid changes) to even approach an estimate that could be extracted out to something useful.
Perhaps you're not aware, but this isn't the only enzyme or protein that has been looked at. Axe chose this one because it was a small-moderate length protein (153 AAs) and his actions was further refining experiments done previously by himself and other scientists.
Your characterization of what he was doing is way off.
Then you don’t understand search. The structure of the search space is important. A search mechanism that is able to take advantage of that structure will do better than a random search.
And you don't comprehend what the size of the search space is? Searching the entire space is prohibitive by time and technology. If you are talking about the entire search space for proteins in general, you are out of your mind. Humans alone have 20,000+ proteins, and the average size is roughly 480 AAs. Axe was looking at one enzyme (not in Humans) that would be considered moderate to small in size, that is 153 AA's long. Just the possible combinations of AA's for a protein of that size are greater than 10^199. (Just to give an comparison, it is estimated there are about 10^80 atoms in the universe). Nobody can search that much space. You have to break it down into more manageable chunks, which is what Axe was trying to do.
Axe was limiting his search to the same domain of the TEM-1 penicillinase family, which even within those constraints the search space is prohibitive. And if proteins do evolve through small changes, limiting your results within a family is being generous to evolution because you are limiting your search space to an area that is likely where evolution works. You want to expand that further, go ahead. It will only handicap the case for evolution even more.
If you're so keen on search, how would you explore that space?

This message is a reply to:
 Message 122 by PaulK, posted 01-23-2019 12:31 AM PaulK has replied

Replies to this message:
 Message 135 by PaulK, posted 01-23-2019 3:14 PM WookieeB has replied

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


Message 132 of 1104 (847502)
01-23-2019 2:19 PM
Reply to: Message 124 by JonF
01-23-2019 9:42 AM


Re: Thread Copied from Proposed New Topics Forum
Why would nobody claim design for a totally random process? Your designer can't flip coins?
Because design is: to do or plan (something) with a specific purpose or intention in mind. Kinda opposite to random.
It is nice that you acknowledge that ID makes no predictions
I did no such thing. Which you even demonstrate with your next line....
But then you claimed ID predicted little or no junk DNA.
...
How is that derived without lots of assumptions about the designer's abilities and motives? Do you contend that your designer was constrained to produce life with little or no junk DNA? If so, how?
ID doesn't comment on the abilities and motives of a designer outside of the base definition (so at least an intelligence and capability to do something according to a purpose). ID acknowledges all demonstrated natural processes, including Natural Selection. Allowing for known natural processes to be available, one would not expect that there could never be something akin to 'junk' (no function) in DNA. But design principles would suggest that in a designed semiotic system, there would likely not be a majority or a significantly high amount of junk.

This message is a reply to:
 Message 124 by JonF, posted 01-23-2019 9:42 AM JonF has replied

Replies to this message:
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WookieeB
Member
Posts: 190
Joined: 01-18-2019


Message 133 of 1104 (847512)
01-23-2019 2:38 PM
Reply to: Message 127 by Taq
01-23-2019 12:48 PM


Re: Thread Copied from Proposed New Topics Forum
Cars, paintings, buildings, and other human designs have common designers. Those designs do not fall into a nested hierarchy. Obviously, it is you who doesn't understand what a nested hierarchy, nor do you understand intelligent design.
...
Then show how designed things fall into a nested hierarchy based on shared derived characteristics. I have yet to see an ID supporter do this.
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.
So for example, of all nested hierarchies, there would be a subset of hierarchies based on "shared derived characteristics". But that doesnt mean that all nested hierarchies are based on "shared derived characteristics"

This message is a reply to:
 Message 127 by Taq, posted 01-23-2019 12:48 PM Taq has replied

Replies to this message:
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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:
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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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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:
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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.

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


Message 153 of 1104 (847630)
01-24-2019 1:47 PM
Reply to: Message 148 by Tanypteryx
01-23-2019 7:07 PM


Re: Thread Copied from Proposed New Topics Forum
Jonf writes:
Just theoretical" does not mean "useless" or "untested".
And I didnt say that. Nobody has made an ancestral protein. Yes, it is theoretical, and I never said studying that is useless. But any attempts to say x is an ancestral protein is prolematic, because you have no way to verify that. It is theoretical in that it is just something somebody thinks may have been the case. But it is pointless to say: Do an experiment based on an ancient protein, because there is nothing currently x that can be verified is an ancient protein. It is like saying:"Let's run an experiment based on the existence of unicorns". You can do all kinds of tests on that assumption and learn something, but until you produce a unicorn actually existing it has no realistic application. It's all theoretical.
Tanypteryx writes:
I was simply trying to be clear that no ancestor and descendant relationships were implied, because some people jump to that conclusion.
Great! That's what i was saying too, and we are agreed. The picture of skulls implies NO ancestor and descendant relationships.
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.
Yes, fine. Nobody is saying that they ALL have to start from scratch. But a great many likely would, as there are no common strunctures between many of the major fold families. (Meaning tweaking one protein fold umpteen times is not likely to lead to a different fold with a vastly different fold structure)
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.
Yes, that is all true. But getting a functional protein fold to form could equally occur on try, (10^77)-1, (10^77)-50, or (10^77)-1000. You can in no way say that the target is more likely to be found on try 1, 50, 1000, than at the end of 10^77 events. The point is, with all attempts being equal, on average it will take 10^77 tries before you see one result you are looking for. It's a probability.
How many events do you think actually can occur on Earth within it's suggested time of existence? How many protein events would you suggest were occurring per day. Would 1 trillion be generous enough for you? That is 1x10^12. Multiply that by 365 to get the yearly rate and your up to 3.65x10^14. And if the earth is around 5 billion years old (5x10^9), you're up to 1.8x10^24. So you still need a trillion x trillion x trillion x trillion x 100,000 earths to get ONE protein.
And evolution needs this to happen many, many times. Tweak the # of events if you want, but keep it plausible. It's not going to help much.
(And I haven't even mentioned issues like the sequence has to use peptide bonds, or the chirality issue - which would push the probability beyond reason)
Evolution almost totally occurs by modifying existing features.
Yes. It modifies things fine. But it doesn't create anything new.
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.
And as already pointed out, not all ID papers are in that journal, like the Axe paper that has been a point of discussion. Your complaining about that journal is using the No True Scotsman fallacy. You can do better. Your point about magic is just a strawman.
And I note you still haven't provided an example. Just responding with fallacious statements.
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.
Nobody said that was a "quote" from Dawkins. It wasn't implied that it was a quote. It is a summarized definition of 'evolution' that comport with thoughts Dawkins put forward in his book (and the only reason it was labeled that way is because Dawkins is a popular and well known figure in the evolution vs design debate). Feel free to dispute that using evidence if you want. But that definition of evolution is not controversial.
"Changes in the composition of hereditary traits" are mutations.
"an iterative feedback response..." is natural selection.
...
Of course not. There is no evidence of direction, purpose or a designing intelligence involved in biological processes.
LOL, this is rich. I think you are arguing just for the sake of arguing.
How is what you just said any different from?...
wookieeb writes:
Evolution is...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.

This message is a reply to:
 Message 148 by Tanypteryx, posted 01-23-2019 7:07 PM Tanypteryx has replied

Replies to this message:
 Message 154 by JonF, posted 01-24-2019 2:21 PM WookieeB has replied
 Message 155 by Tanypteryx, posted 01-24-2019 2:50 PM WookieeB has replied

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


Message 156 of 1104 (847647)
01-24-2019 4:49 PM
Reply to: Message 151 by PaulK
01-24-2019 12:37 AM


Re: Thread Copied from Proposed New Topics Forum
Oh, weve reached the point where you resort to outright lying ?
Dear Lord! You apparently cannot see the obvious.
Hunts diagrams (figures 1-3 and probably 4 too) are pictures Hunt made up. They are not based on numbers or data from Axe's paper or anywhere else. They are merely images to help describe something he is talking about. They relate to his analogizing Axe's paper by describing it in terms of hills and topography in sequence space. So his description is an analogy, and the pictures that relate to the description is analogy too. Figures 1-3 had no references, and were the subject of what Axe responds to as his Objection 3.
Figure 4 is probably also just a representative image Hunt made up. The only question is whether it is from the paper he later references, but I doubt it.
Now I'm not saying Hunt's analogy is necessarily a bad one, but it is an analogy nonetheless.
Wrong again. Hunt said that functions werent isolated. And he produces a reference to support it Knox et al, 1996; Adediran et al., 2005.
I think your getting your objections mixed up.
The question of isolation is what Axe deals with in his labeled Objection 2, but it is Figure 4 (and added reference) in Hunt's response. The picture really isn't anything more than a visual aid again referencing his analogy he employed before. The reference is used to support that proteins are not necessarily isolated, but has little if any direct link with Hunt's picture.
Let us also note that you wouldnt be making these ridiculous accusations if you actually could show that Axes analogy was valid.
You haven't demonstrated that Axe's analogy was bad. All you have said is that since it was a 'word' analogy, and proteins are not words, then it is a bad analogy. Well, Hun't analogy is a 'hill' analogy, and proteins are not hills. So then by your standards Hunt's analogy and diagrams should be a bad analogy as well. If you don't think that, then double standard by you.
Axe's analogy stands fine on it's own. If you don't understand it, that is your problem.
The problem seems to be that Behes terminology is a problem for you. Hes the one that expressed IC in terms of parts
I have no problem with Behe's terminology. But you haven't exactly mentioned his terminology beyond saying "change of parts", "other parts", "loss of parts" without any logical connecting words or context that in any way refers to something Behe said. Behe has said a lot of stuff. Quote something for God's sake so we have some clue what you are referring to.
So, or rephrase, 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
I hate to do this, but I have to break this down into chunks and ask questions to ever start to get an idea what you mean. (Let me also state that Behe doesn't describe IC in the manner you are here)
Do you mean: "So, to rephrase..."?
"one or more of the parts making up a system" - I will assume you mean an IC system. If not, please correct me.
"may change" - OK. But I might need to you flesh out how they are supposed to change (trust me, it's important)
"such that their operation" - I am assuming you mean the function of the part.
"becomes" - this implies a new state of the part. As in a new function, yes?
"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? Can you really do that and retain the function of the part? If it has a new function, it isn't doing the original function, and thus the IC system fails.
So your either saying something about IC systems that we already know, or your suggesting something occurs that breaks the IC system. The question really lies in what you mean, specifically, by "may change". If you can relate this to something Behe (or any one else defining IC) actually says (quote preferred) that would help immensely. Or give an example (or analogy *hehe*) if possible.
The desired function is the function being searched for.
A similar function is a function similar to the desired function
Being good at the function refers to how well the sequence performs the function.
Lets try this again. For the last time I swear. After this I give up. Lets insert your definitions into your original statements.
"if your initial sequence either has some of the [function being searched for] or a [function similar to the desired function] it helps a lot in finding a sequence that is [how well the sequence performs the function]"
Ya. So? You're still not clear on what is being looked for in the search space, but if I had to guess I think you might be suggesting (like a lot of others) that we should be looking for new function (which I assume is what "similar to the desired function" is supposed to be. But how one would do that and is it feasible? And again.... in the case of Axe's experiment it wasn't what he was looking for, nor did he have a reason to.
.....
I'm done with discussing this particular Axe experiment. It is after all from 14 years ago, and a lot has been done since then in studying enzymes. You might be happy to know that even Axe, through other experiments of his own and other papers by other scientists (and no not all ID scientists) has refined his numbers down a bit to 10^74, or so it seemed the last I checked.
But even that is not much help for evolution.

This message is a reply to:
 Message 151 by PaulK, posted 01-24-2019 12:37 AM PaulK has replied

Replies to this message:
 Message 157 by PaulK, posted 01-24-2019 5:32 PM WookieeB has replied

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


Message 158 of 1104 (847651)
01-24-2019 6:16 PM
Reply to: Message 154 by JonF
01-24-2019 2:21 PM


Re: Thread Copied from Proposed New Topics Forum
False. Click the link in my message and you will be inundated in links where people report making ancestral proteins.
Think about it. The oldest DNA found is about 700,000 years ago. The oldest reported protein sequence obtained is from 80 mya, though whether this is true is heavily disputed. Why? Because DNA/Proteins cannot normally survive that long. I'm all for it if it is true, but my point is that actual, ANCIENT protein is not around.
None of the initial papers from your reference dump seem to have any link to actual, ANCIENT protein/DNA. So at first glance, 'ancestral protein' doesn't map to anything that has been demonstrated actually existed.
So where does your so-called Ancestral Proteins come from? I'll use one of the first from your provided link. First sentence: "Ancestral sequence reconstruction relies on phylogeny and statistics to infer the most likely amino acid SEQUENCE ALIGNMENT". Hmm, so evolutionary assumptions are built right in. I note the word "infer", and other words like "synthetic" and "artificial" when describing some of the things that scientists were making. I would also point out that all of this......is INTELLIGENT DESIGN in action!
So, if you want to say that making things based on assumptions (of the bigger topic in question) is any equivalency with what an ancestral protein is,.... Knock yourself out!
I take your lack of response to be an admission that ID makes no predictions about junk DNA.
No, I didn't answer because it was a stupid statement. Your treading into a theological question that I don't care to pursue.
All that ID claims is that the inferred best explanation for some features of the natural world is best explained by the actions of a mind/intelligence. It doesn't attempt to explain who or what that intelligence is, nor whatever motives that intelligence mayor may not have.
The only characteristic it would attempt to infer is qualities directly related to a design paradigm. Thus, if someone was designing a semiotic system, and it displayed the many checks and error-correction mechanisms that DNA has, then it would be very unlikely to be a system that generated or allowed a significant amount of junk (per the evolutionary explanation). It's just a matter of normal design constraints. Which leads to the conclusion that there would more likely be less junk rather than more junk in the system. That is not to say that the semiotic system would be perfect, but all the other functions involved with DNA suggest a highly tuned and functioning system. There is no rational reason to suggest that the signal system was full of junk.
Yet that is what (at first) many evolutionary scientists were saying. The thought initially was that since only a small percentage of DNA coded for proteins, and there was no 'apparent' function for the rest of it, then it was surmised that most of that extra stuff was junk. Back then ID, even before ENCODE and more recent knowledge, disputed that was likely the case.
Now that more data is available, it turns out the idea of Junk DNA is practically dead and most evolutionary scientists back away from the idea and would like to sweep their history under the rug.
I suppose an intelligence designing DNA could include junk if they really wanted to, but the point of it is lost to me and that would not really support any idea of good or decent design.
Edited by Adminnemooseus, : Fixed first quote box (had used "qc" instead of "qs").

This message is a reply to:
 Message 154 by JonF, posted 01-24-2019 2:21 PM JonF has replied

Replies to this message:
 Message 160 by JonF, posted 01-24-2019 9:49 PM WookieeB has not replied
 Message 176 by JonF, posted 01-26-2019 9:02 AM WookieeB has replied

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


(1)
Message 159 of 1104 (847653)
01-24-2019 6:43 PM
Reply to: Message 155 by Tanypteryx
01-24-2019 2:50 PM


Re: Thread Copied from Proposed New Topics Forum
The only people who want to include those weasel words (including unguided, unintelligent, purposeless, material processes) in definitions of evolution are creationists and cdesign proponentsists.
OMG, you are so dense! How can they be "weasel words" when you actually agree with them? Do you think questions on origins, even evolutionary ones, never has anyone questioning whether the process is unguided? It has a bearing on the qualification of the definition of evolution because those are topics that are frequently involved when discussing evolution in the manner that we are (whereas yellow paint, breakfast cereal, leprechauns.. are not). How can you even be interacting on a forum like this without realizing that?
Ever hear of theistic evolution? Such questions such as whether evolution is by an unguided, unintelligent, purposeless process is central to the subject.
Whether evolution is by an unguided, unintelligent, purely material processes is not a subject brought up in many scientific papers (unless it is central to the theme). So I wouldn't expect to see it there, and there's no objection to it not being there. But we're not on this forum just discussing some technical features of a paper. The central theme is Evolution vs Creation, and we're in the sub-topic of Intelligent Design. (Hey, I just realized, this forum is structured as a nested hierarchy). Discussions of scientific things is just some structure for the greater theme. How you can not think that the nature of evolution (being guided or unguided, etc) would not factor into the discussion going on here is boggling to me.
It's context. CONTEXT!!! Get it? If not, you should go talk with the other guy that is hung up on ID being all about 'cdesign proponentsists'. He doesn't get context either.

This message is a reply to:
 Message 155 by Tanypteryx, posted 01-24-2019 2:50 PM Tanypteryx has replied

Replies to this message:
 Message 162 by Tanypteryx, posted 01-24-2019 10:29 PM WookieeB has replied

  
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