Exposing the evolution theory. Part 2

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

"Darwinian processes", "Darwinism", "Neo-Darwinism", "Neo-Darwinian Synthesis" and "The Modern Synthesis" - are all colloquial terms to refer to the basically the same thing. I'm not sure why you're so flustered by the term. Mayr, Gould, Marguilis, and many other all used the term(s). 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.

We have a pink crow situation here. I've never seen one. I also haven't read every word ever written by every biologists so I cannot say you are wrong. However, I did spend a few years in Missouri and it rubs off on you so...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."The cite should be from an evolutionary biologist, of course, the more prominent the better, absent which your cite will be labeled as bogus. Your source should cite this inanity as well. 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. Do you doubt the mutation rate can be any/all of these? 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. Realistic numbers are way better when one considers their parallel nature rather then serial. (He said as he peered down the rabbit hole he said he wasn't going to look at.) Such reading comprehension. Re-read my sentence. I said quite the opposite. 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. Yes, they did. But only in referring to the old Darwinian paradigm, not the Modern Synthesis. 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.

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The theory of evolution is the fundamental conceptual framework of biology all scientific explanations of living phenomena must be consistent with. As it does not describe a universal law regarding a single natural phenomenon, such as gravity, but rather the principles of organismal change over time, based on the highly complex inputs and interactions of a multiplicity of different factors, evolutionary theory cannot be expected to remain static but is subject to change in the light of new empirical evidence. This is a normal process of scientific advancement and not a heretical undertaking as it is sometimes perceived to be. Explanations of organismal diversity have changed significantly during pre- and post-Darwinian periods, and it should not come as a surprise that fresh stimuli arise from the new methodologies and the expanded scope of modern biological research.

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Not flaws, WookieeB. Extensions, additions, advancements.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. Edited by AZPaul3, : No reason given.

Yip. That's what all creationists do. In my field they tend to wiggle around terms such as "Uniformatism", "The Geologic Column", etc. Creationists tend to tell untruths about those terms all the time.Edited by Pressie, : No reason given.

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.abstractExplaining general ideas of genetic algorithms
https://www.doc.ic.ac.uk/...6/journal/vol1/hmw/article1.htmlRead 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 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". 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. 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. 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.

The word "selection" is modified by the word "natural". The "selection" is a result of "natural" events. The slowest zebras are the ones that get eaten first. It is a "natural" coincidence that the fast-zebra genes are preserved.

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? (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:

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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.

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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:

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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.

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

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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

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and...

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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.

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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) -

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

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... and then he goes on to list 4 examples.2) How criticism of evolution is usually taken (like on these forums) -

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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.

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

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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.

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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 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.

Genetic algorithms? Is that your source of an evolutionary biologist using NS “searching” to determine how reproductive differential happens?Hey. No problem. I know this subject. I was a nerd of the Bill Joy generation and we schemed the programming of sentience. Genetic algorithms were seen even then as a necessary step in that direction. Good stuff.This is gonna be fun for me so I’m gonna get verbose. Or is it the other . For those who don’t know about genetic algorithms . The infamous “they” cross-code hundreds of modules each with a unique set of algorithms all purposely targeted, fine tuning it used to be called, toward a specific problem, like producing a list of stocks that will go up tomorrow.The algorithms are actually groups of tables that feed the decision engines. In the tables would be things like the specific stock's past prices, the market indexes, seasonal and cyclic sensitivities and about 100 other variables for each module and each module having varying values in its tables. Then, spanning as much of the “reasonable” variances in the data as you can, you create as many modules as you have the ram available for in your system. Hundreds. Thousands. Run each.You can maybe get Percy to do it. He knows this stuff. Besides, he doesn't have anything else to do these days.Check the results against tomorrow’s stock prices. The modules are rated by how close they came to the actual price. Those closest are saved off, the rest are discarded.Now the magic happens. You do some fancy mixing and matching between the tables of the saved modules and (keeping the original or parent modules, you really don’t want to make that mistake) create X-hundreds of new modules ready to be tested. You can even make provisions for replacing table values with random values in a highly limited way. You could get pretty wild with some of the mix algorithms. It's true. Nerds used to get wild sometimes.Rinse. Repeat. X000s of times. It’s the mixing and matching where the mutations take place and tomorrow’s stock price is the environment. You get generations of modules with some rather strong artificial selection.Enough fun. Back to work.Is that “searching” using NS?No. It is targeted. And there certainly is nothing natural about it.I can understand why you and your sources use the NS nomenclature. We sure did. Replicating as close as possible with what nature has already done, especially in technology, is powerful stuff. Today ram is cheap and multi-threading job blocks by the thousands is routine. The types of targets grow ever more complex, and useful. The old mixing modules are now quite complex (understatement). Evolution is a good guide.But it is not Natural Selection as the evolution of life on this planet has experienced. It is a targeted forced adaptation.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. Apparently, Darwin called it that just to personally piss you off.Listen. We really are an abstract-thinking species.There is this mechanism that causes differences in fecundity/fertility called genetic mutation. But it doesn’t operate in a vacuum. It works better or worse depending on the environment. If one of these mutations has a good effect then that new DNA/RNA complement will spread through the population faster or slower depending on other environment factors. That mutation is having a positive effect.It is succeeding. It has been chosen. It is anointed. It is elevated beyond its peers. It is good. It is selected for.See the symbolic language?But before we can know the mutation really is selected we have to do something. Mother Nature® has to get out her laptop, fire up Excel and plug in a bunch of numbers. Numbers of babies, actually. Your babies, of course, along with the rest of the family, neighborhood, village, nation, population, species, ecosystem, from this generation, the next generation (the second best Star Trek series), and the next one and do this over centuries, millennia, epochs.You see where this is going?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.The other thing we see in all this data, this ledger of copious baby-making numbers, is that the determinator of this differential was the natural environment. 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.What the hell else was Darwin going to call it!Hagen-Dazs Chocolate Ice Cream? Actually, I’m ok with that. Serial thinking. What makes you (serially) think there can be only one mutation rate? "Ok," he says as he tiptoes around the creationist rabbit hole.Edited by AZPaul3, : No reason given.

No. Not me. The community of evolutionary biologists does that for me. I learned effective delegation of tasks a long time ago. Yep. Evolution. Just the one word says it all.Besides, it's much easier to say than "The Theory of Evolution, the Modern Synthesis." And it's blessed by the overlords. Right. Wiki.

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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

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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. And it all starts, involves and ends with making babies. All of it. Oh it is firmly established. Strongly so. But it is science and “evolutionary theory cannot be expected to remain static but is subject to change in the light of new empirical evidence.”Not wrong and not complete either. Many on Dr. Mller’s laundry list are well on the way to being integrated into the Theory of Evolution like EvoDevo, epigenetics, genomics, microbiology, one he missed, proteomics. Some will never be incorporated until they get their science right like evolutionary psychology, behavioral biology . I mean . Jordan Peterson? Seriously?

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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.

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Well, you can leave out the philosophers since they are worthless as scientists but these fights have been going on for decades. Nothing new. Dr. Mller’s opinions are well stated, but they are not definitive. The community will decide what gets adopted/adapted and what will stay in the penalty box. This is science.You are trying to give the impression that Evolution is broken. It is not. It is, however, improving. Evolution is still and is ever more strongly “the fundamental conceptual framework of biology all scientific explanations of living phenomena must be consistent with.” And none of the “Darwin-anythings” are synonyms for the Theory of Evolution, the Modern Synthesis, AKA Evolution. Edited by AZPaul3, : cite oops

For those who understand anything about evolution, yes, the one word does say it all.For those who don't understand anything about evolution (outside of the X-Men and other sloppy sci-fi *), that one word doesn't really say much to them.For the creationists, the fact that there are actually many different meanings for that word affords them the opportunity to muddy that water to their hearts' content, sowing confusion everywhere they go.Creationists love to obfuscate the term, "evolution". Kent Hovind (inherited by his son, Eric) loves to pontificate on the seven or more "kinds of evolution" and I have seen many lesser creationists use the same argument.My own research finds that the term first appeared around 1610, more that two centuries before Darwin. The word itself means "turning outwards" and so came to signify the "unfolding" or development of some system over time. We can therefore speak of "stellar evolution" as the development of a star over time, something that has no relationship to biological evolution. We can talk of "cosmological evolution" in order to discuss how the universe has developed over time, which likewise has no relationship to biological evolution.Being a retired US Navy Chief Petty Officer, I am particularly fond of this particular definition. "Evolution" means to "turn out". Well, without any possible shadow of a doubt, the United States Navy depends entirely on evolution for all its daily activities. Without evolution, the US Navy could not possibly function.In the Navy, an evolution is when the crew or a portion of the crew "turns out" for any kind group activity. Since my Navy time was in the reserves, most of our evolutions were training evolutions, of which there were far greater than "many". So just what the fuck does a US Navy evolution have to do with Darwin?Always question a creationist's use of the term, "evolution". A creationist has a vested interest in misconstruing that term in any way possible.

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FOOTNOTE:
Unfortunately, a lot of the general public's "understanding" of science comes from science fiction and from popularized science. As a result, their "understanding" of science can be very distorted and just plain wrong.The issues of science popularization are many and a separate discussion. Refer to Wikipedia's article at https://en.wikipedia.org/wiki/Popular_science in preparation.What I'm interested in here is science fiction's distortion. On Star Trek: TNG, it irritated me every time some stable "alien element" with exotic properties would crop up. Basic chemistry, people! What makes an element a particular element is the number of protons in that atom's nucleus. Change the number of protons and it becomes a different element. We know all the elements up to and beyond 111 protons in the nucleus (I'm too lazy right now to research the latest number). So if some new "alien element" were to be found, its atomic number (and hence the number of protons in its nucleus) would be greater than 111. And long before a nucleus grows to such an enormous size, that nucleus becomes unstable such that it breaks apart to lower-atomic-number daughter elements -- basically, that's radioactivity. Furthermore, the higher the atomic number, the more unstable the element and the shorter time it can exist and the more energy it takes to create it. Therefore, science fiction's evocation of stable "alien elements" is complete BS.Unique compounds developed by alien civilizations would be an entirely different matter. Just don't go calling those compounds "elements".But the smoking gun of sci-fi is what Stan Lee said in an interview that was included in a three-part documentary, "The Never-Ending Battle", a history of super-hero comic books which used to be on NetFlix. In that interview, Stan Lee described himself as the least scientific person in existence -- basically, if a gamma ray were to come up and bite him, he couldn't recognize it. So then, the Incredible Hulk, created by gamma rays. Stan Lee said that he thought (quoted from memory), "Gamma rays. That sounds scientific. Yeah, let's use that!" The same with "cosmic rays" giving the Fantastic Four their powers.Basically, in writing your story you know the end-result you want and you want to make it sound "scientific", so you use whatever sounds right regardless of whether it makes any sense at all. If your audience's only access to science is what you write, then they have just gotten wrong ideas about science.

The Relativity of Wrong

Great essay. I am posting this on all my social media accounts. Nice take down of creationists, antivaxxers, flat earthers and climate change deniers.

Yip. Creationists like to play with words. Reams and reams of paper with some random word sosaties everywhere. On the other hand scientists flourish on data.Edited by Pressie, : No reason given.

Hey I think I know what sosaties are. Aren't they lamb kebobs? I have been to South Africa a couple times. Going again in the fall.

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?...... Ya, finally finish that strawman and set it on FIRE!!!Sorry. Doesn’t work.
....Now on to the NS definitions.... Yes, already acknowledged and understood. I'm also referring to NS in such a manner, the commonly understood manner where..... Glad to see that NS actually does something, in the abstract way of thinking. 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. 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! I have no problem with what he called it or meant. You are the one with the semantic issues. 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.