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Author Topic:   Exposing the evolution theory. Part 2
WookieeB
Member
Posts: 100
Joined: 01-18-2019


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


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

How does it accumulate mutations?

That is why evolution works better than a random search.

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

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

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

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

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

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

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

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

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

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

  
WookieeB
Member
Posts: 100
Joined: 01-18-2019


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


PaulK writes:

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


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

Which leads to....

PaulK writes:

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

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

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

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

PaulK writes:

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

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

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

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

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

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

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

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

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

Edited by WookieeB, : No reason given.


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

Replies to this message:
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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 213 of 294 (848233)
02-01-2019 6:54 PM
Reply to: Message 210 by PaulK
02-01-2019 4:43 PM


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

success = improved fitness. We're saying the same thing.

And the probability of variants in sequence appearing is the probability of a mutation occurring which I am sure you can look up.

Ya, so what. Mutations happen. NS in a search cannot affect the rate, location, or type of mutation that occurs. It can only just view the mutation and do something AFTER a beneficial mutation occurs (assuming there is a beneficial mutation to be had - not a at a local peak or flat plateau).

And depending on the landscape, the rate of mutation can limit what NS can do.

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

If not, you tell me what a random search is looking for. It has to have a target, all searches do.

A random search simply picks points in search space at random

....and then does what? I think you misunderstand what a random search is. It is not just picking some random point and moving there. That is a random move. That is NOT a search! A random search has a target like any search does.

And what a random search is searching for in our context is "fitness" also. Same as your hill-climbing search. So what does a random search do when it finds fitness, it moves to that point and starts exploring, at random, again.

A hill climbing search explores points around the a location in search space until it finds a “higher” point, whereupon it moves to that point and starts exploring around there.

How does it "explore"? It looks in a random manner around it, just like in a random search.

Random search is same as your hill-climbing search.

So I gave an explanation of a hill climbing algorithm that is clearly distinct from random search

Ya, and it's incorrect because you are not characterizing a random search properly.

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

Mutating = perturbing. It's all random. So logically you must mean then that hill climbing is randomly changing the gene, which equates to a random search.

The search process is more than that,

You cannot justify that. NS cannot affect the 'perturbation in any way. It has no influence. It can only move after it has evaluated a random change to see whether it is a successful hit or not.

A random search does the same thing.

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

No! That is not what a random search is. What you just said is like morphing the landscape, then picking a random direction and moving that way. But in search, the landscape is static. The point you are starting form is the current state of things. A different point in the landscape is a different state of things, like a change to nucleotide(s) (mutation). A random search will look at a random point other than where it is, see whether it fits the search criteria, and either move or not move based on that criteria.

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

Same difference. Random Search

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

I do agree that Darwinian processes can explain some things in biology. But it cannot explain everything. Things categorized as microevolution - sure. But for the origins of life and macroevolution, which includes new proteins and body plans, IC structures, and all the new information that is required for them - Darwinism is not up to the task.

And at least that is starting to be acknowledged by some the scientific community.


This message is a reply to:
 Message 210 by PaulK, posted 02-01-2019 4:43 PM PaulK has responded

Replies to this message:
 Message 217 by AZPaul3, posted 02-01-2019 7:41 PM WookieeB has responded
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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 216 of 294 (848238)
02-01-2019 7:26 PM
Reply to: Message 211 by AZPaul3
02-01-2019 5:17 PM


AZPaul3 writes:

NS has no choice. It isn’t a thinking being with free will. It is process that will take place.


Yes, in general I agree with you in this section. But we've been talking in terms of search. In a search, other points around a starting point are considered against a 'target' criteria. In the search context we are considering, NS has to evaluate a point presented to it. And what point(s) are presented to NS for evaluation is determined by the mutation process that you described. NS 'evaluates' the point based on the target criteria, which we have been generally referring to as "improved fitness" (or a "successful variant" that you quoted me on). NS then 'selects" the first target hit as presented to it. This evaluation and selection roughly equates to what you referred to later as "the "reproductive differential".

A lot of the resultant mutations do nothing. A lot of them aren’t so good. Some, though, make it easier to live, love and propagate. Those are the ones that lead to the reproductive differential that is Natural Selection by definition.

But it is important to understand generally the ratio of deleterious to neutral to beneficial mutations. By far, the majority seem to be deleterious. And it seems that beneficial is extremely rare. This fits with our intuition on things. When making random changes to a working system, it is much easier to break or blunt things than to improve them.

The malaria resistance case is an good example. When a selective pressure was put on the malaria parasite, it showed a beneficial result (resistance) at a rate of 10^20. That number is based on empirical results, not probabilities of mutating the proteins. But when it was identified that at minimum, 2 specific point mutations (and possibly a third neutral one) were needed to confer some resistance, matching up the combinatorial options of the mutations with the 10^20 figure is not unreasonable. But in essence, what occurred was a breaking of a regulatory piece in the protein that allowed the protein to survive.

When you then take the population of the malaria parasite in the relevant time and compare that to populations and time for eukaryote life forms (especially vertebrates), you run into resource limits that suggest similar beneficial mutation options would not be likely.

Edited by WookieeB, : No reason given.

Edited by WookieeB, : No reason given.


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 Message 211 by AZPaul3, posted 02-01-2019 5:17 PM AZPaul3 has responded

Replies to this message:
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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 221 of 294 (848399)
02-04-2019 11:36 AM
Reply to: Message 217 by AZPaul3
02-01-2019 7:41 PM


AZPaul3 writes:

WookieeB writes:

And depending on the landscape, the rate of mutation can limit what NS can do.

Which is kind of odd since NS doesn't actually do anything. It is a measure of difference in reproductive rates.

Context!? Guess you don't know what that is. And your further comments suggest you have no concept of what 'search' is.

OK, then.....
Depending on the landscape, the rate of mutation can limit what differences in the reproductive rate can be.

By the way, if Natural Selection cannot do anything, why is the word "Selection" used at all?

Yes, I am familiar with this source and while some of the non-biologists had some interesting off-center proposals, as far as acknowledging your brand of nonsense ... no ... not even close. You did look at it first before you posted, yes?

Never said they acknowledged ID. Doesn't matter. What does matter is that they are questioning Darwinian processes. Why? Cause all the numbers and experiments and data show that it cannot do the big things it is claimed that it does.

Edited by WookieeB, : No reason given.


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Replies to this message:
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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 222 of 294 (848407)
02-04-2019 12:15 PM
Reply to: Message 220 by PaulK
02-02-2019 3:43 PM


As I said before, the mutations are just the perturbations, it’s the overall movement through sequence space that matters, and Natural Selection is a major factor there.

No objection here. Random search behaves exactly the same. The real number possibilities is where the question comes in. If NS only allows moves up, what happens if no up perturbation is presented to it?

Evolution does not have a target as such. There is no end state, other than extinction - which evolution works against.

Don't try to change the frame of reference on me. We've been couching this subject in the terms of 'Search'. In a search, there is ALWAYS a target.

The descriptions are very similar, although that just means that random search isn’t so bad. At least that version of random search.

So...then your hill-climb is the same as a random search. You haven't distinguished a difference.

In a random search the next sequence tried could be anything. Mutations do NOT completely randomise the genome at every generation. But that is what you would need for it to be a random search.
....
I’m certainly not talking about morphing anything I’d consider the landscape. Evolution works on the whole genome, so selecting a random point in the space would be selecting a random point for the whole genome.

Those are your statements. If you are suggesting that a random search randomizes the entire genome, you are incorrect.

A random search just looks in a random direction from the current position. The closest point around it's current position corresponds to the simplest of changes, or a single point mutation. So that is no different than your 'evolution' search.

It certainly manages new proteins and IC structures. I see no reason why it can’t manage body plans

Interesting phrase - manage. What does that mean?
As for creating those things, evolution cannot account for them.
As for body plans, since it hasn't really been identified where the information for them resides, you cannot infer why evolution WOULD be able to manage them.

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 Message 220 by PaulK, posted 02-02-2019 3:43 PM PaulK has responded

Replies to this message:
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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 226 of 294 (848413)
02-04-2019 6:47 PM
Reply to: Message 224 by AZPaul3
02-04-2019 1:44 PM


Your context is that “search” denotes a target to be achieved. Biology doesn’t do that. Your context is just a clumsy attempt to ascribe attributes to NS that do not exist so you can argue against them. It is a strawman.

You can equivocate all you want on the terms. 'Search" is a common explanatory analogy used by scientists to explain how changes in your "reproductive differential" happens. All searches have a target. In this case, the target is fitness, which come about by mutations (or other causes of change to the genome), and if beneficial may lead to a fixation in the population and ultimately lead to your reproductive differential. Cry all you want, but search is a commonly used idea in the literature.

The number of mutations (rate over time) means little to nothing.
...
While a higher mutation rate can, and often does, present the processes with more opportunities,

So which is it? Nothing?.... A little?..... Often does?
Obviously mutation rate can have some effect. I never stated how significant. That would depend I suppose on the rate on one item vs the rate on another. It's not equal across the board.

On this planet that mutation space involves every molecule and every combination of molecules within a genome (which is every gene sequence available to a population, not an individual)

.... which is the landscape.

If 100 mutations per individual produces 2 within a population that slightly increase fertility this is the same as 5 mutations per individual producing the same 2 over the same population over the same time.

To some extent you are correct. Despite the change in positive-result rates, as long as the 2 fitness-increasing-fertility mutations appear, and assuming continued existence of the species, that's all you need.

But note your numbers for this positive event. Even if we assume (as your example does) that the fixation is 100% guaranteed to spread given the appearance of the 2 beneficial mutations, you're showing mutation rates of 10000% (1x10^2) and 500% (5x10^1). That is nowhere near reality. For bacteria, the mutation rate is around 1x10^-8, and probably an order of magnitude less for eukaryotes. So ya, with a mutation rate 10-100 billion times more than normal, you're virtually guaranteed to see your 2-mutations-to-increased-fertility appear with a very modest population.

But unfortunately for you, that is not realistic. Go to malaria resistance to chloroquine example. Despite how many varying paths that ultimately can lead to an increased-fertility situation, the odds still come out to 1x10^20 per individual for just needing a minimum of 2 specific point mutations occurring. Can you really expect the rest of life does better than those odds to accumulate what would have to be many, many mutations in concert?

The quality, if you will, not the quantity of mutation determines the change in reproduction rate.

Well, I would think it has to be both? If there are only 1 in 1 million rate of quality mutations out there in your mutation space (assuming 100% fixation), you'll probably progress if you have a million events. But what if you only have 10,000 events occurring. Then you probably wont have any progress. Realistic numbers are way worse than that.

First, because we are an intelligent species with abstract thought processes.We see NS as “selecting” ....

Wow! So we actually can have an abstract description of NS to describe its effects as 'selecting' something. Go figure.

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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 227 of 294 (848415)
02-04-2019 7:14 PM
Reply to: Message 225 by AZPaul3
02-04-2019 2:22 PM


"Darwinian processes" went by way of the DoDo long ago. Darwin is not the be-all/end-all of everything evolution
....
A lot has been added to the original "Darwinian" concept in the last 150+ years, but the core process remains

"Darwinian processes", "Darwinism", "Neo-Darwinism", "Neo-Darwinian Synthesis" and "The Modern Synthesis" - are all colloquial terms to refer to the basically the same thing.

Don't talk Darwin. Talk evolution. The latter is much more robust. Read and understand Ernst Mayr, Stephen J Gould, Lynn Margulis ...

I'm not sure why you're so flustered by the term. Mayr, Gould, Marguilis, and many other all used the term(s).

You didn't read any of the submissions. Either that or your understanding of what they discussed is very poor.

Really? Go check out the review articles that the Royal Society put out. First article from Muller is pretty clear on the doubts for efficacy of the Modern Synthesis.
https://royalsocietypublishing.org/...10.1098/rsfs.2017.0015
I'm in no way saying they are ready to take up the gauntlet of ID. Just pointing out that scientists are seeing the flaws in the traditional evolutionary view of M+NS.

This message is a reply to:
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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 230 of 294 (848482)
02-06-2019 3:04 PM
Reply to: Message 228 by AZPaul3
02-05-2019 4:16 PM


Show me.

Cite some literature treating NS as a "search"; "a common explanatory analogy used by scientists to explain how changes in your "reproductive differential" happens."


It's a very general idea.
https://www.pnas.org/...nt/early/2014/07/08/1410107111.short
http://science.sciencemag.org/content/261/5123/872
https://pdfs.semanticscholar.org/...8010e43d72b9dfb0d022.pdf
https://pdfs.semanticscholar.org/...f43aea73e3c8e8581e9d.pdf
https://medium.com/...-behind-genetic-algorithm-df75af08d5d6
https://www.pnas.org/...early/2016/08/04/1606195113.abstract

Explaining general ideas of genetic algorithms
https://www.doc.ic.ac.uk/...6/journal/vol1/hmw/article1.html

Read a book -
https://books.google.com/books?id=htJHI1UrL7IC&printsec=f...

Look at what a Genetic Algorithm is.
https://en.wikipedia.org/wiki/Genetic_algorithm

NS is an accounting mechanism. It doesn't care if the result is increased fitness, decreased fitness or extinction. All the above are possible results with NS dispassionately watching and recording every step.

So if NS doesn't do anything, why is it even mentioned with regards to evolution. How does it have anything to do with your "reproductive differential"? Why is it even named the way it is? "Natural Selection" as a term has nothing to do with accounting logs".

Do you doubt the mutation rate can be any/all of these?

Yes I do. That would violate the laws of logic (PNC). It either does have an effect or it doesn't. It cannot be both.

Been down this useless rabbit hole. Not going again.
Besides, I was giving an illustration not an actual case. I feel it was lost on you.

The numbers matter. I'm sorry if you cannot handle realistic numbers, or even your own. That's your problem.
The purpose of using an illustration is to relate it to things that are real or likely to be real. Your illustration wasn't. I pointed that out. I'm sorry that your fantasy situation wasn't logical, but that is not my problem.

Such reading comprehension. Re-read my sentence. I said quite the opposite.

LOL! Go re-read yourself! I asked how the word "selection", which by definition implies doing something, applies to the term 'Natural Selection" when you claim that 'Natural Selection' doesn't do anything. And you're response is that we can have abstract thoughts and say that NS is selecting mutations when it is actually doing no such thing and instead just keeping a ledger. Umm, ok. Still not logical, but if you say that the thing that evolutionary theory is hanging on is not doing anything, so be it. That's much more critical of the process (oh wait,,, non-process) than even I would say, but so be it.

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WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 232 of 294 (848486)
02-06-2019 5:55 PM
Reply to: Message 228 by AZPaul3
02-05-2019 4:16 PM


To a creationist, I can understand that sentiment. It allows you to wiggle around sowing confusion depending on circumstance.
This is a science thread. To alleviate confusion we use quite specific terms for quite specific items. Evolution ≠ Darwin-anything and hasn't since before you were born.
This is a science thread. We talk science here, not your favorite personal vernacular.

LOL!!! You're going to be the arbiter of what is a science term? You, who has problems with simple laws of logical thought? And then your example of an acceptable 'specific terms for quite specific items" is is "EVOLUTION"?????
LOL!!! No! Please stop!!! My sides are hurting!!!

Puhleazzzze! Darwinism is a common term used today. Even wikipedia acknowledges that.
Granted, it can be an ambiguous term at times. But equally so the term "evolution".

But even if we restrict it to the classic meaning (Darwin's time and forward till Mendelian genetics was used) it still encompasses the following:

--More individuals are produced each generation than can survive.
--Phenotypic variation exists among individuals and the variation is heritable.
--Those individuals with heritable traits better suited to the environment will survive.
--When reproductive isolation occurs new species will form.

So, then according to you, "evolution" has no relation to the above?

Again, you either did not read this entry or did not comprehend it adequately.
He is pushing his Extended Evolutionary Synthesis as an incorporation of the Modern Synthesis with a laundry list of innovative evolutionary mechanisms, not as some great paradigm shift away from the core paradigm of the Modern Synthesis.

(This section is a bit long, and deals with THIS article by Gerd Muller.)
I understood it just fine. I never inferred that they we're throwing out the Modern Sysnthesis whole hog. When I introduced the link, I even acknowledged "Darwinian processes can explain some things in biology". So please don't strawman my argument.

But I find it interesting, if "evolution" is so firmly established, why the need for changes? What you quoted from the article is fine, it just shows that the "theory of evolution" hasn't been able to keep up with modern data and needs refinement. I wish you had continued your quote. His very next sentences were:

quote:
Indeed, a growing number of challenges to the classical model of evolution have emerged over the past few years, such as from evolutionary developmental biology [16], epigenetics [17], physiology [18], genomics [19], ecology [20], plasticity research [21], population genetics [22], regulatory evolution [23], network approaches [14], novelty research [24], behavioural biology [12], microbiology [7] and systems biology [25], further supported by arguments from the cultural [26] and social sciences [27], as well as by philosophical treatments [28–31]. None of these contentions are unscientific, all rest firmly on evolutionary principles and all are backed by substantial empirical evidence.

And just to show that his view, of the standard evolutionary theory being in need of some serious changes (and just before he introduces his idea of the Extended Evolutionary Synthesis), is not some unique idea, he says:

quote:
A rising number of publications argue for a major revision or even a replacement of the standard theory of evolution [2–14], indicating that this cannot be dismissed as a minority view but rather is a widespread feeling among scientists and philosophers alike.

And what are some of the problems with the theory? [I'm editing it a bit for the sake of space] -

quote:
current evolutionary theory.....performs well with regard to the issues it concentrates on,.... If the explanation would stop here, no controversy would exist. But it has become habitual in evolutionary biology to take population genetics as the privileged type of explanation of all evolutionary phenomena, thereby negating the fact that, on the one hand, not all of its predictions can be confirmed under all circumstances, and, on the other hand, a wealth of evolutionary phenomena remains excluded. For instance, the theory largely avoids the question of how the complex organizations of organismal structure, physiology, development or behavior — whose variation it describes — actually arise in evolution

and...

quote:
The real issue is that genetic evolution alone has been found insufficient for an adequate causal explanation of all forms of phenotypic complexity, not only of something vaguely termed ‘macroevolution’. Hence, the micro–macro distinction only serves to obscure the important issues that emerge from the current challenges to the standard theory.

Did you not even read through his section 2? He talks about problems with a lot of the core MS ideas, like gradualism, adaptation, natural selection (which by the way he mentions does a lot more than just tally accounts), and how they're not standing up to more modern data and thinking.
...

Here are a few other highlights. 1) How "evolution" is a variable term (in a manner just like I say 'Darwinian processes' are) -

quote:
Evolutionary biology, as practised today, does not represent a single coherent approach but includes sets of different topics and research programmes.

... and then he goes on to list 4 examples.

2) How criticism of evolution is usually taken (like on these forums) -

quote:
Sometimes these challenges are met with dogmatic hostility, decrying any criticism of the traditional theoretical edifice as fatuous [32], but more often the defenders of the traditional conception argue that ‘all is well’ with current evolutionary theory, which they see as having ‘co-evolved’ together with the methodological and empirical advances that already receive their due in current evolutionary biology [33]. But the repeatedly emphasized fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them.

3) How the concept of what I've been calling "search" is related to evolutionary theory.

quote:
The formalized core of the MS theory was—and still is—population genetics [35], a mathematical account of gene frequency dynamics in populations of organisms. The empirical basis and key concern of the population genetic approach is the measurement of trait variability in populations, and its intended explananda are adaptive variation, speciation and calculations of fitness. The flurry of fitness landscapes based on ever more nuanced algorithms is indicative of this received approach.

Did you note words like "mathematical account" (that's numbers for you), "fitness landscapes", "algorithms".

Go read it again. Maybe you will then understand why he and a lot of other scientists are looking for a Third Way apart from the Modern Synthesis/Neo-Darwinism

Also, note his use of "pre- and post-Darwinian periods". That academic distinction is going to throw you, isn't it? The Darwinian period was the old stuff. He is giving a historical reference not a synonym.

No. It obviously threw you though. LOL.
The "pre-" stuff was before Darwin. Not Darwin's old stuff.
Darwin's "post-" stuff, uses Darwin as the starting point and includes any related ideas of his up to today.
Academically speaking. PRE means 'before', POST means after.

Edited by WookieeB, : No reason given.

Edited by WookieeB, : No reason given.

Edited by WookieeB, : No reason given.

Edited by WookieeB, : No reason given.


This message is a reply to:
 Message 228 by AZPaul3, posted 02-05-2019 4:16 PM AZPaul3 has responded

Replies to this message:
 Message 234 by AZPaul3, posted 02-07-2019 12:59 AM WookieeB has responded

  
WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 240 of 294 (848517)
02-08-2019 12:13 PM
Reply to: Message 233 by AZPaul3
02-06-2019 11:18 PM


Genetic algorithms? Is that your source of an evolutionary biologist using NS “searching” to determine how reproductive differential happens? ... I know this subject. I was a nerd of the Bill Joy generation and we schemed the programming of sentience. ...
You do some fancy mixing and matching between the tables...
Is that “searching” using NS? No. It is targeted. And there certainly is nothing natural about it.

So we see here a common tactic of evolution supporters on these forums. Make a general request - "Cite some literature treating NS as a "search";" When some literature is provided (not an exhaustive list by any measure), take just one of the multiple examples and focus on it. Focus how? By using an anecdotal example of someone doing something that is at best, just generally related but had a focus and hand in things other than biological systems. Then treat the results of this anecdotal example as directly relating to what the original topic was.

And then the coup de grace?......

Targeted Artificial Selection. Not Natural Selection.
I suspect there is a reason for you to insist that it is Natural Selection (or your understanding of what you think NS is). Like maybe, oh, I don’t know, so it can be seen to be as malleable on Earth as it is in Computer? Therefore god?
Sorry. Doesn’t work.

Ya, finally finish that strawman and set it on FIRE!!!

Sorry. Doesn’t work.
....

Now on to the NS definitions....

We really are an abstract-thinking species

Yes, already acknowledged and understood. I'm also referring to NS in such a manner, the commonly understood manner where.....
It is succeeding. It has been chosen. It is anointed. It is elevated beyond its peers. It is good. It is selected for.

Glad to see that NS actually does something, in the abstract way of thinking.

So we take a look at this spreadsheet and what do we see? We see differences in reproductive success. We see what has been successful at making babies and what hasn’t. What is succeeding at making babies, what is chosen, is anointed, is elevated beyond its peers, is good, is selected for.

Yes! It is doing something again. Hallelujah!
The whole process after the mutations occur, which includes the effect mutations have on the phenotype that leads to differential reproduction which leads to some versions becoming the dominant type (the being selected part).....that whole process in symbolic language is called NS.
NS isn't just the spreadsheet, which you have been implying. It's the whole enchilada.
Not anybody or anything but the interface of population to the natural environment is responsible for what reproductive differential we see, what phenotypes were selected and what weren’t. Natural Selection.

YES!!!! That "interface" is what I have been referring to, and what practically everyone else (including you outside of your need to restrict it to a spreadsheet) has been relating to when we say NS. In the symbolic language, in the abstract, in the analogous examples, in search algorithms - 'Natural Selection' selects!

What the hell else was Darwin going to call it!

I have no problem with what he called it or meant. You are the one with the semantic issues.

Serial thinking. What makes you (serially) think there can be only one mutation rate?

What an irrelevant statement. A mutation rate (other than zero) either has an effect or it doesn't. You seem to think it could be both at the same time.

This message is a reply to:
 Message 233 by AZPaul3, posted 02-06-2019 11:18 PM AZPaul3 has responded

Replies to this message:
 Message 243 by AZPaul3, posted 02-08-2019 6:39 PM WookieeB has responded

  
WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 242 of 294 (848524)
02-08-2019 1:09 PM
Reply to: Message 234 by AZPaul3
02-07-2019 12:59 AM


AZPaul3 writes:

specific terms for quite specific items
...
Just the one word says it all


You're words that apply to "Evolution".

And you don't see the discrepancy in those statements?

AZPaul3 writes:

Right. Wiki.

quote:
While the term Darwinism has remained in use amongst the public when referring to modern evolutionary theory, it has increasingly been argued by science writers such as Olivia Judson and Eugenie Scott that it is an inappropriate term for modern evolutionary theory. -- Wiki

Let me paraphrase. While the term Darwinism has remained in use amongst the ignorant and none-too-scientifically-inclined public when referring to modern evolutionary theory, it has increasingly been argued by science writers such as Olivia Judson and Eugenie Scott that it is a really stupid thing to do so we don’t do it in our science discussions especially with insistent creationists.


ROFLMAO! When AZPaul3 says "Let me paraphrase", you can take that to mean "Let me setup a strawman".

You don't check your references very well.
Olivia Judson's contribution was an opinion piece, and she never mentioned anything about the " ignorant and none-too-scientifically-inclined public". She merely asserted (without any evidence, after all it's just an opinion piece) that Darwinism...

quote:
suggests that Darwin was the beginning and the end, the alpha and omega, of evolutionary biology, and that the subject hasn’t changed much in the 149 years since the publication of the “Origin.”

And Eugenie Scott's beef with the term was that despite that "scientists and teachers use “Darwinism” as synonymous with evolutionary biology", she didn't like it because the term sometimes has ambiguous or bad connotations associated with it.

You make it too easy.

But if it really is a sore point for you, replace "evolution" with every instance I used "Darwinian processes" and I'll stand by it.

AZPaul3 writes:

And it all starts, involves and ends with making babies. All of it.


which I assume links to your "differential reproduction". And may I assume that your talk of "differential reproduction" is involved with "evolution"?

I would hope that is a safe bet, since your phrase above about "making babies" was in reference to the concepts of -

quote:
--More individuals are produced each generation than can survive.
--Phenotypic variation exists among individuals and the variation is heritable.
--Those individuals with heritable traits better suited to the environment will survive.
--When reproductive isolation occurs new species will form.

...which are the central ideas of Darwinism (yes, the classical, from Darwin himself - version).

But wait!!! I guess now those concepts do NOT have anything to do with evolution. Since....

AZPaul3 writes:

none of the “Darwin-anythings” are synonyms for the Theory of Evolution, the Modern Synthesis, AKA Evolution.

So, I guess you're saying that if those concepts, which would include differential reproduction and any concept of Natural Selection, are not part of "Evolution" (that term that is oh so specific and the only one authentically used by scientists),..... what exactly are you referring to when you say "Evolution"????

Really. If you want to equivocate on your terms, at least try to spread apart you're varying meanings by a few posts. Doing it all in the same post? You make it too easy.


This message is a reply to:
 Message 234 by AZPaul3, posted 02-07-2019 12:59 AM AZPaul3 has responded

Replies to this message:
 Message 244 by AZPaul3, posted 02-08-2019 7:33 PM WookieeB has not yet responded

  
WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 247 of 294 (848662)
02-12-2019 4:32 PM
Reply to: Message 243 by AZPaul3
02-08-2019 6:39 PM


Glad you liked it. Thank you.

I'm tired of asking you if you understand logic, cause you evidently do not. So my asking: "Do you realize that a strawman is a logical fallacy, and you're cheering your strawman means your argument lacks merit?"
So then...you using a strawman, which you just admitted to, is a logical fallacy, and that means your argument is without any logical merit.

Except as a convenient turn of phrase, the objection to your characterization of search algorithms as examples of natural selection stands.

Which cements that you still don't understand 'search'.
In a search process, there is always a target. But that target may have nothing to do with how things move in a search space. In the case of a random search, and in the case of PaulK's search, the target does not have anything to do with how the search is performed. So the location of where a search looks, the accounting of YOUR description of NS, is randomly determined.

So what is the target? It is that part of the accounting, or a very specific subset of your NS spreadsheet, that notes a movement 'up' the landscape. This all translates to a beneficial mutation occurring that leads to a more fit organism that is shown, accounted for, demonstrated, selected as..... "more babies".

So essentially, in all these evolutionary searches that are being discussed, we do recognize that there will be cases of less babies, same number of babies, and more babies (in comparison to each other category). The more babies is really the only one we are concerned with, the target, because that corresponds to a forward move of evolution.

We can get wrapped in pedantic uselessness at this point.

And yet you will proceed to do so over the next few paragraphs.

But I especially like these two sentences - together at that....

No objections to the term Natural Selection "selecting" phenotypes as a way of saying that, in the accounting, this phenotype grew "fitter" and had lots of babies.

Natural selection "selects" phenotypes. That's a good shorthand for deeper processes. Just understand that, in actuality, natural selection does no such thing.


So NS, in some manner, "selects". But in the same sentence, NS "does no such thing". Really??? LOL! Don't give this guy any more rope, please!

The spreadsheet analogy is still there and is the essential piece.....
Over time it shows us the movements within those numbers.

Thought you didn't like the numbers. You seem afraid of them.
The NS numbers is what I have been using. Why can't you face them?

Not "a" mutation rate. Several. You know there are other species on this planet, right?

One or several, doesn't matter. It's irrelevant. Any mutation rate has an effect. You seem to be fighting that, and other than just to philosophically disagree with me, I can't figure why.

We object to the "Darwin-anything" as some kind of synonym for The Theory of Evolution - The Modern Synthesis. No repudiation of Darwinian ideas/concepts.

We object to this in the same way we would object to calling General Relativity Neo-Newtonianism. Which you may actually do. I wouldn't put it past you to not see the issue.


Ah, but "Darwin-anything" IS used as a synonym for TOE, Modern-Synthesis. "Neo-Darwinism" is explicitly a term that corresponds to the modern theory. Even your hero Mayr advocated that term.

And do you really think you can say you don't like using any term like "Darwin-anything" and not be repudiating Darwin's related ideas? Are you serious?!? And you think I am the one being pedantic? And you think it is creationists that a quibbling over terms? Pot, meet kettle. LOL!

And as I said, since it is YOU that is hung up about the wording, replace every prior instance where I said "Darwinian process(es)" with "evolution" and I am fine with it.

As for Neo-Newtonianism being used in place of General Relativity, I would have no problem with that. If that was a common phrasing for the idea, why would I object?

Edited by WookieeB, : No reason given.

Edited by WookieeB, : No reason given.


This message is a reply to:
 Message 243 by AZPaul3, posted 02-08-2019 6:39 PM AZPaul3 has responded

Replies to this message:
 Message 248 by Minnemooseus, posted 02-13-2019 8:20 PM WookieeB has responded
 Message 249 by AZPaul3, posted 02-14-2019 7:10 AM WookieeB has not yet responded

  
WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 250 of 294 (848724)
02-14-2019 12:34 PM
Reply to: Message 248 by Minnemooseus
02-13-2019 8:20 PM


Re: Older never responded to message
Minnemooseus writes:

Care to respond to message 91


Sure, because you asked nicely.

As I see it, "intelligent design" is just another way of saying "theistic evolution"

No. They are not the same.

And apparently the "design" is God doing some genetic engineering (aka guiding evolution to some degree). Now, the question is, how does one tell the difference between a Godly genetic tweak and a non-Godly random mutation?

No. ID makes no attempt to identify the designer, it only infers there is a designing intelligence behind many of the features seen in nature. The designer could be the Christian God, a Hindu God, (in some contexts) a super-intelligent alien species, or any from a host of other potential intelligent entities (known or not) - but ID doesn't care. In other words, design is detectable by science, who the designer is is beyond science.

I would assume that the method of design would involve some genetic engineering. I'm not sure what you mean by "guided evolution", as that term is somewhat an oxymoron, though that may depend on how you define "evolution".

As I recall, Michael Behe (one of the big guns of "intelligent design") is a big believer in the bulk of mainstream biological evolutionary theory.

That is a bit of a vague statement, but IMO that would not be an accurate characterization. Behe in the past has indicated agreement in the idea of Common Descent, but he does not subscribe to M+NS as the sole mechanism.

He just thinks that God had his fingers in the operation in some subtle way.

That might be true, but the statement is potentially a red-herring.
I do know Behe is religious and does believe in God. But that is rather irrelevant for his ID position. In his ID writings, he doesn't try to identify the designer, he just infers there is one. So, as it would refer to ID, it might be more accurate to say 'he thinks that a designer had its fingers in the operation in some subtle* way'. * - "subtle" is a quantitative description that is as yet undefined, and it is not needed in the statement.

Design" is at best an undetected and probably undetectable detail in standard biological evolutionary theory.

No. Design would be detectable, or at least inferred from the data. Standard evolutionary theory would not be the mechanism for bringing about many of nature's features.

God, the genetic engineer (or something like that).

Maybe, or maybe not. It is irrelevant to ID

This message is a reply to:
 Message 248 by Minnemooseus, posted 02-13-2019 8:20 PM Minnemooseus has responded

Replies to this message:
 Message 251 by RAZD, posted 02-14-2019 5:20 PM WookieeB has responded
 Message 253 by Minnemooseus, posted 02-16-2019 3:15 AM WookieeB has responded

  
WookieeB
Member
Posts: 100
Joined: 01-18-2019


Message 254 of 294 (849033)
02-21-2019 3:17 PM
Reply to: Message 251 by RAZD
02-14-2019 5:20 PM


Re: Older never responded to message
RAZD writes:

Wookieeb writes:

Design would be detectable, or at least inferred from the data. Standard evolutionary theory would not be the mechanism for bringing about many of nature's features.


How do you know that?

If you are asking about how "Design would be detectable", it is a technique that is used in other scientific endeavors. Information theory has a big hand in it, but design detection is used in Archaeology, Forensics, Crytography, search endeavors like SETI, and in many historical sciences.

If you are asking about what Standard evolutionary theory can produce? It can produce some things very easily, but they are usually small changes that correspond to minor phenotypic traits, what is often referred to as micro-evolution. This is demonstrable, has an empirical justification, and ID doesnt dispute this kind of natural change.

There are other features though that would be extremely difficult, if not practically impossible, for it to produce. Things that would be considered irreducibly complex would rarely, if ever, be able to be formed. Things like new body plans and regulatory networks. Anything that require an measure of complex and specified information have never been demonstrated to be formed via a random process, but in all cases where we do have knowledge of the origins, it has always been by a mind, intelligence. M + NS are just not up to the task of producing such things.

Please see Is ID properly pursued? -- an old thread but still valid methinks.

Yes, an old thread. From the OP, I can say there are some parts that I agree with, but I also was finding some things that are badly mis-characterized. On the whole, unfortunately, since I was finding many of the axioms put forward are not true, it ends up being a flawed argument.

This message is a reply to:
 Message 251 by RAZD, posted 02-14-2019 5:20 PM RAZD has responded

Replies to this message:
 Message 259 by Tanypteryx, posted 02-22-2019 2:27 PM WookieeB has responded
 Message 267 by RAZD, posted 02-23-2019 7:19 AM WookieeB has responded

  
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