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Author Topic:   Another IDology challenge -- complete with complaints of harsh treatments ...
RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 1 of 63 (861547)
08-23-2019 9:52 AM


This has popped up on facebook, posted by some IDologist on "Daily Wire":

quote:
WATCH: Renowned Yale Prof Leaves Darwinism, Says Intelligent Design ‘Absolutely Serious’ Theory
"They will destroy you if you challenge it"

Renowned writer and Yale University professor David Gelernter has turned away from Charles Darwin's theory of evolution, arguing that it has too many holes and has aged out as a probable scientific theory.

The professor also argued that intelligent design is a serious theory that cannot be shooed away by anti-religious sentiment. Furthermore, he lamented the lack of "free speech" concerning theories outside of Darwinism, which has become a "religion" to many academics spanning the various scientific fields.

As highlighted by Rachel Alexander at The Stream, Gelernter outlined his rejection of Darwinian thought in an essay published in the Claremont Review of Books, aptly titled, "Giving up Darwin."

"Darwin's theory predicts that new life forms evolve gradually from old ones in a constantly branching, spreading tree of life," the professor says in the paper. "Those brave new Cambrian creatures must therefore have had Precambrian predecessors, similar but not quite as fancy and sophisticated. They could not have all blown out suddenly, like a bunch of geysers." He explains, "Each must have had a closely related predecessor, which must have had its own predecessors."

Among many other reasons, Gelernter also points to the near impossibility of creating a functional stable protein. "Immense is so big, and tiny is so small, that neo-Darwinian evolution is — so far — a dead loss. Try to mutate your way from 150 links of gibberish to a working, useful protein and you are guaranteed to fail. Try it with ten mutations, a thousand, a million — you fail. The odds bury you. It can't be done."

Though he doesn't personally subscribe to the theory of intelligent design, Gelernter said it is an "absolutely serious argument," noting that it is the "first, and obviously most intuitive [theory] that comes to mind," Alexander noted.


quote:
David Hillel Gelernter (born March 5, 1955)[1] is an American artist, writer, and professor of computer science at Yale University. He is a former national fellow at the American Enterprise Institute and senior fellow in Jewish thought at the Shalem Center, and sat on the National Endowment for the Arts. He publishes widely; his work has appeared in The Wall Street Journal, New York Post, Los Angeles Times, The Weekly Standard, Frankfurter Allgemeine Zeitung, and elsewhere. His paintings have been exhibited in New Haven and Manhattan.

Computer science is not biology (he even says he is not a biologist in the video), and math cannot change reality.

There are a number of PRATTS (points refuted a thousand times) in the video, and the monitor, Peter Robinson, has no apparent knowledge of biology either. Other participants are David Berlinski and Steven Meyer, both of the Discovery Institute.

Enjoy

Edited by Admin, : Reduce width of YouTube video.


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(2)
Message 3 of 63 (861570)
08-23-2019 11:39 AM
Reply to: Message 1 by RAZD
08-23-2019 9:52 AM


IDotic arguments
What upsets me is when IDologists make IDotic arguments.

Firsts the probability argument. They say it is a 1 in 1070 probability to assemble a protein molecule by molecule.

Let's cut that in half -- each half then has a 1 in 1035 probability to assemble by their argument. Now reassemble them: there is a 1 in 4 chance of making the "right" connection so that's:

(1 x 1035 + 1 x 1035) x 1/4 = 5 x 1034

repeat for each half segment and you get:

{(1 x 1017.5 + 1 x 1017.5) x 1/4} x 1/4 = 3.9528 x 1016

This is a significant reduction in the probability of actually assembling a protein, and quite obviously there are a large number of ways for molecules to assemble rather than one at a time, making the probability a meaningless argument.

Second Gelernter argues that it is impossible to make all the changes at the correct time during the development of a fetus to change a sheep into a horse ... in one generation. This is known as the hopeful monster concept and it is a strawman argument: evolution does not theorize speciation happening this way, and biologists would be quite surprised to see such an event. When arguing against evolution it behooves you to thoroughly understand evolution theory and processes, rather than use misinformation and misrepresentations.

Enjoy

Edited by Admin, : Remove spurious "^"

Edited by RAZD, : Note to admin: I add the "spurious ^" intentionally so that when the numbers are copied they don't look like 1035 or 1070.


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 6 of 63 (861592)
08-23-2019 1:14 PM
Reply to: Message 4 by AZPaul3
08-23-2019 12:14 PM


Re: IDotic arguments
Meanwhile they rake in money from their book sales to the gullible.

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 10 of 63 (861620)
08-23-2019 8:25 PM
Reply to: Message 8 by WookieeB
08-23-2019 6:23 PM


Re: IDotic arguments
What upsets me is when anti-IDologists make strawman arguments.

Curiously, I am happy to be corrected, but you have not really done that yet.

Please supply your supporting material. Especially if you have it in print. I found the video a real snooze-fest of PRATTS and misinformation, so I may have mixed some of it up. Videos are not the best conveyors of information, and I prefer print versions.

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 11 of 63 (861623)
08-23-2019 9:39 PM
Reply to: Message 8 by WookieeB
08-23-2019 6:23 PM


Correction, sort of ...
The 1 in 10^70* probability has nothing to do with assembling a protein. It is not relating to any molecule by molecule assembly issue. Go read Gelernter's article. Even in his layman's terms, he explains what the probability is referring to quite well.

Curiously I searched through the video to the part in question, and I was slightly incorrect. Starting at 12:25 is they are talking about assembling a protein, not molecule by molecule but with 1 of 20 amino acids adding them one by one, and the number they give is 1 in 1 x 10^77 (not 1 in 1 x 10^70). Gelernter at 13:20+ talks of building a string of beads one by one adding an emerald, a ruby and an opal ... using the DNA code to make the protein. So now we in essence have the probability of assembling the DNA with that code, and still in the molecule by molecule calculation mode, given the context of the discussion.

So I believe the critique I made of the improbability calculation is still valid.

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(3)
Message 14 of 63 (861632)
08-24-2019 11:59 AM
Reply to: Message 13 by WookieeB
08-24-2019 1:40 AM


Re: Correction, sort of ... filling in the blanks.
The impetus for the video was due to an essay by David Galernter in the Claremont Review of Books. Gelernter's essay is at: https://www.claremont.org/crb/article/giving-up-darwin/

Thanks for the link.

With regards to the probability argument, the primer to it starts under the heading "Mutations" where he talks about creating a protein from a modest-sized, 150 long amino acid chain.

Technically you should be providing quotes instead of just link references. I get tired of old PRATTs rehashed in emperor's new cloths, and misinformation.

Note this misinformation:

quote:
Demolishing a Worldview

... Yet there are many reasons to doubt whether he can answer the hard questions and explain the big picture—not the fine-tuning of existing species but the emergence of new ones. The origin of species is exactly what Darwin cannot explain.


The problem is that we have observed new species developed by the standard evolutionary model, so this statement is false.

And he goes religious ...

quote:
... But this view assumes a childishly primitive reading of Scripture. Anyone can see that there are two different creation stories in Genesis, one based on seven days, the other on the Garden of Eden. When the Bible gives us two different versions of one story, it stands to reason that the facts on which they disagree are without basic religious significance. The facts on which they agree are the ones that matter: God created the universe, and put man there for a reason. Darwin has nothing to say on these or any other key religious issues.

More misinformation:

quote:
... Darwin’s theory predicts that new life forms evolve gradually from old ones in a constantly branching, spreading tree of life. Those brave new Cambrian creatures must therefore have had Precambrian predecessors, similar but not quite as fancy and sophisticated. They could not have all blown out suddenly, like a bunch of geysers. Each must have had a closely related predecessor, which must have had its own predecessors: Darwinian evolution is gradual, step-by-step. ...

... but also that evolution would occur rapidly when there was a void in habitat that could be occupied; selection would be diminished and more varieties would survive and evolve. What that new habitat was, occurred when the ocean pH changed (due to oxygen being produced by algae iirc) and it became possible to make calcite shells. The Cambrian fossils are almost all shelled creatures, the pre-Cambrian fossils do not have shells. Having shells provides an obvious survival advantage, and those that had shells had an open habitat to inhabit: rapid evolution. Standard. Darwinian.

quote:
But those predecessors of the Cambrian creatures are missing. Darwin himself was disturbed by their absence from the fossil record. ...

Except they are no longer missing and more are being found every year. Way to keep up with the times.

Getting to your referred section:

quote:
Mutations

How to make proteins is our first question. Proteins are chains: linear sequences of atom-groups, each bonded to the next. A protein molecule is based on a chain of amino acids; 150 elements is a “modest-sized” chain; the average is 250. Each link is chosen, ordinarily, from one of 20 amino acids. A chain of amino acids is a polypeptide—“peptide” being the type of chemical bond that joins one amino acid to the next. But this chain is only the starting point: chemical forces among the links make parts of the chain twist themselves into helices; others straighten out, and then, sometimes, jackknife repeatedly, like a carpenter’s rule, into flat sheets. Then the whole assemblage folds itself up like a complex sheet of origami paper. And the actual 3-D shape of the resulting molecule is (as I have said) important.

Imagine a 150-element protein as a chain of 150 beads, each bead chosen from 20 varieties. But: only certain chains will work. Only certain bead combinations will form themselves into stable, useful, well-shaped proteins.

So how hard is it to build a useful, well-shaped protein? Can you throw a bunch of amino acids together and assume that you will get something good? Or must you choose each element of the chain with painstaking care? It happens to be very hard to choose the right beads.

Building a Better Protein

Now at last we are ready to take Darwin out for a test drive. Starting with 150 links of gibberish, what are the chances that we can mutate our way to a useful new shape of protein? We can ask basically the same question in a more manageable way: what are the chances that a random 150-link sequence will create such a protein? Nonsense sequences are essentially random. Mutations are random. Make random changes to a random sequence and you get another random sequence. So, close your eyes, make 150 random choices from your 20 bead boxes and string up your beads in the order in which you chose them. What are the odds that you will come up with a useful new protein?


One by one. As he further explicates on the video ...

The old improbable probability numbers game/s ...

quote:
The total count of possible 150-link chains, where each link is chosen separately from 20 amino acids, is 20^150. In other words, many. 20 roughly equals 10^195, and there are only 10^80 atoms in the universe.

What proportion of these many polypeptides are useful proteins? Douglas Axe did a series of experiments to estimate how many 150-long chains are capable of stable folds—of reaching the final step in the protein-creation process (the folding) and of holding their shapes long enough to be useful. ... He estimated that, of all 150-link amino acid sequences, 1 in 10^74 will be capable of folding into a stable protein. To say that your chances are 1 in 10^74 is no different, in practice, from saying that they are zero. It’s not surprising that your chances of hitting a stable protein that performs some useful function, and might therefore play a part in evolution, are even smaller. Axe puts them at 1 in 10^77.

In other words: immense is so big, and tiny is so small, that neo-Darwinian evolution is—so far—a dead loss. Try to mutate your way from 150 links of gibberish to a working, useful protein and you are guaranteed to fail. Try it with ten mutations, a thousand, a million—you fail. The odds bury you. It can’t be done.


And of course the problem with this argument (from incredulity after fabricating immense numbers -- a typical creationist/IDologist ploy) is that biology doesn't operate this way; mutations occur in a number of ways of many different length segments from whole gene copying to single inserts.

The numbers prove nothing, and never will, because the model is wrong.

One example of how biology actually works is polyploidy which results in new species in one generation. Mostly found in plants, though it does occur in animals.

Other more standard examples of speciation are also known. It seems that nature has no problem contradicting the mathematical model ...

Enjoy

Edited by RAZD, : added thread link


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 17 of 63 (861636)
08-24-2019 1:19 PM
Reply to: Message 15 by Theodoric
08-24-2019 12:10 PM


Re: Things I find funny
It is also quite telling where this article was published. Claremont Review of Books is the journal of the Claremont Institute a very radical right wing propaganda outfit.

I found the moderator to be the most believable in his ignorance ... but he sure threw a lot of softballs ...

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 19 of 63 (861668)
08-25-2019 9:39 AM
Reply to: Message 18 by WookieeB
08-25-2019 4:02 AM


more filling in the blanks.
Off topic, but...

... but it has bearing on the assumption of authority by the author making the claim. It speaks to the basis of his argument. Being founded on a falsehood, the argument is suspect.

RAZD writes:

The problem is that we have observed new species developed by the standard evolutionary model,

Where?

Several places. A quick google turned up these sites:

quote:
Evolution: Watching Speciation Occur | Observations

This process, known as Hybrid Speciation, has been documented a number of times in different plants. But plants aren't the only ones speciating through hybridization: Heliconius butterflies, too, have split in a similar way.

It doesn't take a mass of mutations accumulating over generations to create a different species - all it takes is some event that reproductively isolates one group of individuals from another. This can happen very rapidly, in cases like these of polyploidy. A single mutation can be enough. Or it can happen at a much, much slower pace. This is the speciation that evolution is known for - the gradual changes over time that separate species.


quote:
Observed Instances of Speciation

2.0 Species Definitions

2.2 The Biological Species Concept

Over the last few decades the theoretically preeminent species definition has been the biological species concept (BSC). This concept defines a species as a reproductive community.

5.0 Observed Instances of Speciation

The following are several examples of observations of speciation.

5.1 Speciations Involving Polyploidy, Hybridization or Hybridization Followed by Polyploidization.

5.1.1 Plants

5.1.2 Animals

5.2 Speciations in Plant Species not Involving Hybridization or Polyploidy

5.3 The Fruit Fly Literature

5.4 Housefly Speciation Experiments

5.5 Speciation Through Host Race Differentiation

5.6 Flour Beetles (Tribolium castaneum)

5.7 Speciation in a Lab Rat Worm, Nereis acuminata

5.8 Speciation Through Cytoplasmic Incompatability Resulting from the Presence of a Parasite or Symbiont

5.9 A Couple of Ambiguous Cases


You'll have to read the article to see the actual species involved, I omitted them to save space. Those who are truly interested will read the articles in their entirety, and those who aren't will ignore them.

On topic (the referred section) -

RAZD writes:

And of course the problem with this argument (from incredulity after fabricating immense numbers -- a typical creationist/IDologist ploy) is that biology doesn't operate this way;

First, what specifically are you saying is fabricated?

The probability numbers. See the old improbable probability problem. You can't calculate probabilities without knowing all the possibilities first. If you assume this, then obviously if your end result seems impossible when it has in fact occurred the error is in the assumed numbers.

I have two di -- a pair of dice -- what is the probability that I will throw/roll a seven in one try?

Secondly, can you be more specific about what "way" biology supposedly doesnt operate by?

The numbers used only refer to one specific type of mutation - a single replacement mutation. Biology operates on several different types of mutations, from single replacement to full gene duplication, many involving multiple segments inserted or deleted. This vastly increases the numbers of ways DNA is modified in the real world.

Ya. So? That there are myriad ways mutations can occur....is irrelevant. When evaluating the mathematics of evolution, that mutations do and will occur is inherent to the argument; it is built in and assumed.

I do not think you understand the argument.

When you only include one specific mutation in your calculations and ignore all the other "myriad ways mutations" occur you are obviously not counting all the possible mutations. It is hardly irrelevant but very germane to the issue of accuracy and appropriateness of the number fabrications. Note that most of the examples of observed speciation involve massive copying of DNA segments rather than single point mutations: it is rather obviously relevant.

I do not think you understand the critique of the argument.

Then perhaps off-topic again, I have to ask about this diddy?
but also that evolution would occur rapidly when there was a void in habitat that could be occupied; selection would be diminished and more varieties would survive and evolve.

What are you talking about? What is a "void in habitat"? ...

A void is an empty niche in the ecology. The ecology is composed of all species in a habitat in a quasi-balance of survival and reproductive abilities, not just in predator-prey arms races but also in like species competitions.

If one of the species can take advantage of a new habitat niche that is not currently occupied then it has more resources for survival and reproduction than previously, giving it an advantage. This offers more opportunity for speciation to occur as the selective pressure is lowered.

This is actually observed in the case of foraminifera:

quote:
EVOLUTION AT SEA
Complete Fossil Record from the Ocean Upholds Darwin's Gradualism Theories

Tony Arnold and Bill Parker compiled what may be the largest, most complete set of data on the evolutionary history of any group of organisms, marine or otherwise. The two scientists amassed something that their land-based colleagues only dreamed about: An intact fossil record with no missing links.

"It's all here--a virtually complete evolutionary record," says Arnold. "There are other good examples, but this is by far the best. We're seeing the whole picture of how this group of organisms has changed throughout most of its existence on Earth."

The organism that Arnold and Parker study is a single-celled, microscopic animal belonging to the Foraminiferida, an order of hard-shelled, planktonic marine protozoans. Often shortened to "forams," the name comes from the Latin word foramen, or "opening." The organisms can be likened to amoebas wearing shells, with perforations through which their protoplasm extends. The foram shell shapes range from plain to bizarre.

But it's the planktonic variety that chiefly interests Parker and Arnold. Unlike their oversized cousins, free-swimming forams are found almost everywhere in the oceans. Their fossilized skeletons, in fact, were among some of the first biological material recovered from deep ocean bottoms by scientists in the 1850s. For nearly a century, geologists have used the tiny fossils to help establish the age of sediments and to gain insight into prehistoric climates.

In 1980, Arnold successfully married computers with optical devices to create an efficient, precise way to analyze foram fossils. Before the technique was developed, the field was represented only by a few extraordinarily dedicated individuals who spent countless hours over microscopes, sorting and analyzing the sand-grain-sized shells virtually by hand.

The apparatus Arnold and Parker now use combines the latest in video technology with their specially programmed computer. Although it requires an operator, the system is the fastest, most reliable means of foram identification and classification available. It soon will become far more powerful if its developers succeed in linking it with a scanning electron microscope.

"There's a nifty passage in Darwin," says Arnold, "in which he descirbes the fossil record
By studying forams, Tony Arnold (front) and Bill Parker assembled many evolutionary sequences with virtually no missing links.
as a library with only a few books, and each book has only a few chapters. The chapters have only a few words, and the words are missing letters."

"Well, in this case, we've got a relatively complete library," says Arnold. "The 'books' are in excellent shape. You can see every page, every word."

As he speaks, Arnold shows a series of microphotographs, depicting the evolutionary change wrought on a single foram species. "This is the same organism, as it existed through 500,000 years," he says. "We've got hundreds of examples like this, complete life and evolutionary histories for dozens of species."

About 330 species of living and extinct planktonic forams have been classified so far. After thorough examinations of marine sediments collected from around the world, micropaleontologists now suspect these are just about all the free-floating forams that ever existed.

The resulting data base thus holds unprecedented power for evolutionary studies, says Arnold. Not only can he and Parker use it to describe how evolution has worked in a particular species, but they can use it as a standard for testing evolutionary theories, which are growing in number.

It may be in what the foram record suggests about how life copes with mass annihilation that eventually draws the most attention to the FSU paleontologists' work. The geologic record has been prominently scarred by a series of global cataclysims of unknown, yet hotly debated, origin. Each event, whether rapid or slow, wreaked wholesale carnage on Earth's ecology, wiping out countless species that had taken millions of years to produce. Biologists have always wondered how life bounces back after such sweeping devastation.

One of the last great extinctions occurred roughly 66 million years ago and, according to one popular theory, it resulted from Earth's receiving a direct hit from a large asteroid. Whatever the cause, the event proved to be the dinosaurs' coup de grace, and so wiped out a good portion of the marine life--including almost all species of planktonic forams.

Other scientists have theorized, but never been able to demonstrate, that in the absence of competition, an explosion of life takes place. The evolution of new species greatly accelerates, and a profusion of body shapes and sizes bursts across the horizon, filling up vacant spaces like weeds overtaking a pristine lawn. An array of new forms fans out into these limited niches, where crowding soon forces most of the new forms to spin out into oblivion similar to sparks from a bonfire.

The ancient record of foram evolution reveals that the story of recovery after extinction is indeed busy and colorful. "What we've found suggests that the rate of speciation increases dramatically in a biological vacuum," says Parker. "After the Cretaceous extinction, the few surviving foram species rapidly evolved into new species, and for the first time we're able to see just how this happens, and how fast."

As the available niches fill up with these new creatures, the speciation rates slow down, and the pressure from competition between species appears to bear down in earnest. The extinction rate then rises accordingly. This scenario, says Arnold, suggests that the speciation process is sensitive to how fully packed the biosphere is with other species, not the number of individuals. Ecologists, in referring to a given environment's ability to sustain life as its carrying capacity, generally mean the natural limit, in shear numbers, of individual organisms that any environment can support, as opposed to the number of different kinds of organisms or species. "This is an intriguing concept--a species carrying capacity, so to speak," says Arnold. "This implies that the speciation process is sensitive to how many spesies are already out there."


Foram mass death during the extinction event, followed by an "explosion" of new species to fill the void.

Similarly, the Cambrian "explosion" of new species types that first evolve protective shells occurred because the niche for species with protective shells was empty.

... Evolution doesn't care if there is a "void in habitat", it doesn't have any forward view, so it cannot occur any more rapidly to fill anything. It is unguided.

Wrong. The rate of evolution is "guided" by the selection pressure: low pressure, more variations survive and reproduce; high pressure, fewer variations survive and reproduce. In an ecology in equilibrium/stassis the rates of evolution for each species will stabilize around an equilibrium value, but is a disturbed ecology some rates will increase and some will decrease (leading ultimately to extinctions).

And wait, so diminishing selection allows more survival and evolving? How does that work, since the selection is the very thing that supposedly provides the surviving and evolving?

Let's start with this definition of evolution as a process:

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats.

Now consider these extremes:

  1. all offspring in a generation survive to reproduce (low selection pressure)
  2. only one offspring in a generation survives to reproduce(high selection pressure)

Case 1 will provide a large expanding population with many diverse variations, case 2 will provide only one variation -- which population will evolve more, generation after generation? Which population will thus have a higher rate of evolution?

Selection pressure is not static.

Enjoy

Edited by RAZD, : format


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 22 of 63 (861712)
08-25-2019 4:47 PM
Reply to: Message 21 by dwise1
08-25-2019 3:41 PM


Re: more filling in the blanks.
I've pointed this out before, but nobody will believe me:

I've pointed this out before, but nobody will believe me:


Evolution never stops. The same evolutionary processes are constantly at work, just with differing results. The processes that cause changes in the population in a new or changing environment are the same processes that keep a population from changing in an unchanging environment.

So even when there's no change, that's still evolution at work.


For those with a background in engineering or as a technician, it basically acts like a negative-feedback control loop. The further you are from the set-point (eg, a specified voltage, the optimal phenotype for that environment) the harder it will drive you back to that set-point. When you are at the set-point, then the exact same mechanism keeps you at that set-point.

When the ecology is stable, in equilibrium, then selection is to maintain that median position because it is successful.

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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 26 of 63 (861746)
08-26-2019 10:20 AM
Reply to: Message 20 by AZPaul3
08-25-2019 11:46 AM


Re: more filling in the blanks.
I had a reply ready yesterday, but it was a little muddled and I wasn't happy with it, and while I was fiddling with it I lost it. I hope this is better ... I incorporated some of DWise1's comments.

In higher selective pressure environments populations will grow more slowly but will speciate from the ancestor as they adapt to the selective pressures which, over time, lowers those pressures on the growing population.

This would be anagenesis as the high selective pressure creates a narrow opportunity for divergence.

We also know from some experiments that high stress can lead to more mutations as the immune system is suppressed and control systems over cell structure weakens.

So high selective pressure, increase in mutation rate, narrow selection of mutations for survival/reproductive fitness benefits, population changes -- bell curve narrows and moves to fit the ecology.

In lower selective pressure environments populations grow larger with greater genetic diversity within the species.

and spreads into more marginal environments as population growth increases competition for resources (selective pressure increases). The genetic diversity provides possible benefits to access those marginal habitats and this provides opportunities for cladogenesis, the division of the population into daughter species.

Low pressure, less stress, moderate mutation rate but more open selection, the bell curve spreads and covers more diverse ecologies.

The amount/number of mutations selected is higher than in the high selective pressure scenario because there is more opportunity for survival and reproduction.

I question a “rate of evolution”.

As noted in Message 19:

quote:
EVOLUTION AT SEA
Complete Fossil Record from the Ocean Upholds Darwin's Gradualism Theories

Other scientists have theorized, but never been able to demonstrate, that in the absence of competition, an explosion of life takes place. The evolution of new species greatly accelerates, and a profusion of body shapes and sizes bursts across the horizon, filling up vacant spaces like weeds overtaking a pristine lawn. ...

The ancient record of foram evolution reveals that the story of recovery after extinction is indeed busy and colorful. "What we've found suggests that the rate of speciation increases dramatically in a biological vacuum," says Parker. ...


An increased rate of speciation would be an increased rate of evolution in my opinion.

Is an increase of genetic diversity within a population a higher rate of evolution? Is the number of speciation events the higher rate?

One of the problems I've had with the genetic molecular clocks is the assumption of a constant rate of mutation and a constant rate of evolution. As yet I've seen no evidence of the and have no reason to accept this assumption. If we use this definition of evolution as a process:

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats.

Then the rate of evolution would be the rate at which these changes take place, the rate at which mutations are selected/incorporated into the population gene pool. This would be greater under low selection pressure than under high selection pressure.

In stasis conditions evolution still occurs but selection is to maintain the population, bell curve, in the current fitness level. The rate of evolution would be low -- neutral and minor variations would not be deselected -- and little visible change would be observed.

I know we love to say this but I don’t think evolution has a rate.

Respectfully disagree.

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 27 of 63 (861824)
08-27-2019 1:21 PM
Reply to: Message 26 by RAZD
08-26-2019 10:20 AM


Calculating a rate of evolution ... in darwins and haldanes
... If we use this definition of evolution as a process:

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats.

Then the rate of evolution would be the rate at which these changes take place, the rate at which mutations are selected/incorporated into the population gene pool. ...

So I've done a little more research on this:

quote:
The rate of evolution is a variable of considerable interest in evolutionary biology. It concerns the limits of adaptation to natural environments as well as the limits of artificial selection.

Interesting discussion of Evolvability, effects of koinophilia and issues of the Fossil record (including Punc-Eek) ... but they give no calculation of this variable. Disappointing. Should have a link to:

quote:
The darwin (d) is a unit of evolutionary change, defined by J.B.S. Haldane in 1949.[1] One darwin is defined to be an e-fold (about 2.718) change in a trait over one million years. Haldane named the unit after Charles Darwin.

Equation

The equation for calculating evolutionary change in darwins (r) is:

where and are the initial and final values of the trait and is the change in time in millions of years. An alternative form of this equation is:

Since the difference between two natural logarithms is a dimensionless ratio, the trait may be measured in any unit. Also for this reason the darwin is a specialist form of the inverse mega-annum ().

Application

The measure is most useful in palaeontology, where macroevolutionary changes in the dimensions of fossils can be compared. Where this is used it is an indirect measure as it relies on phenotypic rather than genotypic data. Several data points are required to overcome natural variation within a population. The darwin only measures the evolution of a particular trait rather than a lineage; different traits may evolve at different rates within a lineage. The evolution of traits can however be used to infer as a proxy the evolution of lineages.

Genetic information cannot be obtained from fossils, but modern (post-Haldane) techniques on extant organisms now rely on genetic data (q.v. phylogenetics).


Phillip D. Gingerich prefers to use haldanes:

quote:
Research on Rates of Evolution

Introduction

Evolution is a process that takes place from one generation to the next in living lineages of plants and animals. Evolutionary results are sometimes visible on the time scale of an individual generation, but we usually see and study these cumulatively on longer experimental, ecological/historical, and geological scales of time. Rates of evolution are important because they are a key indication of how the evolutionary process works -- rates quantify evolutionary change in relation to time.

How long does it take a mouse lineage to evolve to double its size? The answer depends, of course, on the rate -- how fast is evolution?

A rate in darwins is expressed in terms of factors of e (base of the natural logarithms) per million years, neither of which are intuitive units: e and millions of years are perfectly arbitrary in this context; the units do not appear in genetic models; there is an erroneous suggestion, or even implication, that evolution takes place on million-year time scales (see below); and rates in darwins cannot be compared for measurements that have different or unknown dimensionality (Gingerich, 1993).

It makes much more sense to follow a lesser known suggestion of Haldane and calculate rates of evolution in terms of proportional change divided by elapsed time, in a unit called the haldane (Gingerich, 1993). This calculation requires three quantities:

  1. the difference between means of two samples of natural-logged measurements, d = y2 − y1;

  2. the pooled standard deviation of the samples,, where

    , where and are the standard deviations of the samples of natural-logged measurements; and

  3. the time interval between the samples, , counted or estimated in generations.

The resulting rate in haldanes is:

Here the result is expressed in terms of phenotypic standard deviations per generation, and the subscripted log I is a reminder that the result is dependent on time scale (rates of most interest are H0 where I = 1 generation and log I = 0).

Quantification in haldanes requires knowledge about phenotypic variability but this is really necessary in any case in an evolutionary study because, as Haldane himself wrote, variation is the raw material of evolution. Standard deviations are components of selection intensity and response. A generational time scale, rather than millions of years, is the time scale on which evolution takes place. And finally, rates in haldanes are independent of the dimensions of the underlying measurements. These are all advantages of haldane rate units over darwins.


So we have two measurements of the rate of evolution in the literature. Both based on observed morphological changes.

Basing one on genetics could be more difficult as it is hard to tell when mutations get expressed in the phenotype. There is the rate of mutation, which I also think is variable, but then we need to know when mutations are expressed in a way that affects selection (survival, reproduction).

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 31 of 63 (861849)
08-28-2019 7:40 AM
Reply to: Message 28 by AZPaul3
08-27-2019 4:14 PM


Re: Calculating a rate of evolution ... in darwins and haldanes
This is where I have a problem.

In both of these treatments evolution is viewed like it is goal oriented.

That was Gingerich's problem with Haldane's darwin measurement, that and that it implied millions of years. Both are historic measurements of what occurred, because they are based on fossil evidence.

Whatever numbers, in darwins or in haldanes, one achieves are arbitrary and meaningless.

It took X million years for this A. whosits to grow a widget from # cm ## cm.
And it took Y million years for the B. thingies to double the size its whatever.

The haldane metric is based on generations and is dimensionless. Gingerich also notes that you can have different results for different traits in the populations.

Neither of these gives a rate to evolution but just a length of time to go from this version to that version. And this is not just semantics since it was not “evolution” that changed but the inputs to its processes that changed.

How would you define a rate of evolution?

My view. Evolution ran, not at any rate, but just ran day by day, generation by generation, for both lineages, but one took longer than the other for some various reasons dealing with chemistry, allele pool, environment, fecundity, luck, and circumstance.

So they did evolve at different rates, but the formula/s don't account for all the necessary inputs?

If we consider punk-eek, then it is fairly obvious that there are different rates of evolution/change involved.

quote:
Rate of Evolution
Fossil Record

The fossil record of an evolutionary progression typically consists of punctuated equilibrium, with species that suddenly appear, as if by macromutation, and ultimately disappear, in many cases close to a million years later, without any change in external appearance. This is compatible with evolution by smaller mutational steps because periods of a few tens of thousands of years can barely be distinguished in the fossil record: relatively rapid evolution will always appear as a sudden change in a sequence of fossils.[13][15][16] ...

Alternative explanations of the pattern of evolution observed in the fossil record. While apparently instantaneous change may look like macromutation, gradual evolution by natural selection could readily give the same effect, since 10,000 years barely registers in the fossil record.

Is this just semantics on my part? Is the "evolution" of the fruit fly "faster" than that of the elephant? Or does evolution just plod along dependant on the inputs?

Partly. If we look at evolution over a time period some species evolve faster because they go through more generations (why fruit flys and bacteria are used in experiments). But if we look at evolution from generation to generation the picture is not so clear.

Personally I think evaluating the rate of evolution gives us the ability to see how those inputs affect the process, to what degree each input has effect. And I think haldanes are better indicators of this, being based on generations rather than set amounts of time.

Enjoy


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RAZD
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Posts: 20714
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(1)
Message 32 of 63 (861851)
08-28-2019 8:09 AM
Reply to: Message 29 by Faith
08-27-2019 7:02 PM


Another input -- Faith-0-lution ....
Even if mutations galore increased the genetic diversity enormously in a population or gene/allele pool, even to the point that every trait is changed for every individual and every gene has so many alleles you can't identify them, what you'd have is a motley crew of individuals that differ wildly from one another in all those traits, some large, some small, some with purple fur, some with scales instead of fur, and every possible combination. Clearly it doesn't ever happen. But if it did some particular number of individuals would have to be selected in order to get a new breed or species, that is, for evolution of the population as a whole to occur. Which would have to happen to get a new species.

Nope. That is not how evolution works. btw you might be interested in koinophilia ...

quote:
Rate of Evolution
Overcoming koinophilia

If sexual creatures avoid mates with strange or unusual characteristics, in the process called koinophilia,[9][10][11][12] then mutations that affect the external appearance of their carriers will seldom be passed on to the next and subsequent generations. They will therefore seldom be tested by natural selection. Evolution is, therefore, effectively halted or slowed down considerably. The only mutations that can accumulate in a population are ones that have no noticeable effect on the outward appearance and functionality of their bearers (i.e., they are "silent" or "neutral mutations", which can be, and are, used to trace the relatedness and age of populations and species.[9][13])

This implies that evolution can only occur when mutant mates cannot be avoided, as a result of a severe scarcity of potential mates. This is most likely to occur in small, isolated communities. These occur most commonly on small islands, in remote valleys, lakes, river systems, or caves,[14] or during the aftermath of a mass extinction.[13] Under these circumstances, not only is the choice of mates severely restricted but population bottlenecks, founder effects, genetic drift and inbreeding cause rapid, random changes in the isolated population's genetic composition.[14] Furthermore, hybridization with a related species trapped in the same isolate might introduce additional genetic changes. If an isolated population such as this survives its genetic upheavals, and subsequently expands into an unoccupied niche, or into a niche in which it has an advantage over its competitors, a new species, or subspecies, will have come in being. In geological terms this will be an abrupt event. A resumption of avoiding mutant mates will, thereafter, result, once again, in evolutionary stagnation.


In a stable ecology where populations are at an equilibrium, selection will tend to favor the most average phenotypes, as they are the best fit for that stable equilibrium condition. It is only when that stable equilibrium is disturbed or the population expands into a new ecology that selection will shift towards varieties/mutations that provide benefits for the new conditions.

And selection eliminates. If you get an isolated new population of all these individuals with all their new characteristics that population will eventually blend those characteristics together until a particular phenotype emerges and it's got a look of its own: a new breed or species. That's what selection does. It will eventually blend tog3ether whatever proportions of traits are in the new set of individuals, their new collection of gene/allele frequencies, and eliminate others from the population. (Of course if mutations really did occur at such a rate as I describe it above you could never ever get a population with its own peculiar characteristics, never a breed let alone a pure breed, which already defeats the whole idea but anyway...) Unless you want to say that getting only a population made up of mutts is evolution, because that's all you'll ever get; you'll never get the specialized new phenotypes ordinarily recognized as a new species or breed, you know a whole population with the same characteristics, a whole population of trilobites that look alike, a whole population of raccoons with identical markings, a whole breed of greyhounds or chihuahuas or Great Danes, a whole population of little green men with antennae on their heads.

Again this is not how evolution works. It doesn't blend characteristics. It selects those that are more fit for survival or more attractive for reproduction.

Not only is there no "rate of evolution," there is no evolution as defined by the ToE.

Except that it has been defined and measured ... as defined by the (actual) ToE (and not Faith-0-lution).

Remember the Pelycodus chart ...

quote:
A Smooth Fossil Transition: Pelycodus, a primate


The numbers down the left hand side indicate the depth (in feet) at which each group of fossils was found. As is usual in geology, the diagram gives the data for the deepest (oldest) fossils at the bottom, and the upper (youngest) fossils at the top. The diagram covers about five million years.

The numbers across the bottom are a measure of body size. Each horizontal line shows the range of sizes that were found at that depth. The dark part of each line shows the average value, and the standard deviation around the average.


The slopes of those lines show the rates of evolution for each generation, and the divide at the top shows divergence with one group evolving more rapidly to smaller size.

What you call speciation could never happen, which is a population with its own overall characteristics that clearly differentiate it from its parent population. ...

Nope. What biological science defines as speciation has been observed to occur, so obviously you are wrong. Both in your definition of speciation (Faith-0-lution) and your denial of actual observed instances of speciation.

... (Of course it would have sufficiently diminished genetic diversity to make further evolution impossible, but anyway....

According to Faith-0-lution, but not according to reality.

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 36 of 63 (861876)
08-28-2019 1:55 PM
Reply to: Message 33 by Faith
08-28-2019 12:19 PM


Re: Another input -- Faith-0-lution ....
I rarely use the concept of selection as in natural selection, I think selection is what brings about new subspecies/breeds but that it's usually random. Faith O lution 101.

Wrong on three counts
(in one sentence ... WOW).

First, selection occurs with every generation:

Evolution is a two-step feedback response system that is repeated in each generation:

Like walking on first one foot and then the next. Selection can either be for new traits -- ones beneficial in non-equilibrium populations -- or for old traits: koinophilia in populations in equilibrium with their ecology and the ecology is stable.

quote:
Koinophilia is an evolutionary hypothesis proposing that during sexual selection, animals preferentially seek mates with a minimum of unusual or mutant features, including functionality, appearance and behavior.[1][2][3][4][5][6] Koinophilia intends to explain the clustering of sexual organisms into species and other issues described by Darwin's Dilemma.[3][4][5] The term derives from the Greek, koinos, "common", "that which is shared", and philia, "fondness".

Natural selection causes beneficial inherited features to become more common at the expense of their disadvantageous counterparts. The koinophilia hypothesis proposes that a sexually-reproducing animal would therefore be expected to avoid individuals with rare or unusual features, and to prefer to mate with individuals displaying a predominance of common or average features.[2][3] Mutants with strange, odd or peculiar features would be avoided because most mutations that manifest themselves as changes in appearance, functionality or behavior are disadvantageous.[7] Because it is impossible to judge whether a new mutation is beneficial (or might be advantageous in the unforeseeable future) or not, koinophilic animals avoid them all, at the cost of avoiding the very occasional potentially beneficial mutation.[8] Thus, koinophilia, although not infallible in its ability to distinguish fit from unfit mates, is a good strategy when choosing a mate. A koinophilic choice ensures that offspring are likely to inherit a suite of features and attributes that have served all the members of the species well in the past.[3]

The overwhelming impression of strict uniformity, involving all the external features of the adult members of a species, is illustrated by this herd of Springbok, Antidorcas marsupialis, in the Kalahari Desert. This homogeneity in appearance is typical, and virtually diagnostic, of almost all species,[25] and a great evolutionary mystery.[7][24] Darwin emphasized individual variation, which is unquestionably present in any herd such as this, but is extraordinarily difficult to discern, even after long-term familiarity with the herd. Each individual needs to be uniquely and prominently tagged to follow its life history and interactions with the other (tagged) members of the population.[26][27]
By Oggmus - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=39441411

Evolutionary process

The restraint koinophilia exerts on phenotypic change suggests that evolution can only occur if mutant mates cannot be avoided as a result of a severe scarcity of potential mates. This is most likely to occur in small restricted communities, such as on small islands, in remote valleys, lakes, river systems, caves,[9] or during periods of glaciation,[47] or following mass extinctions, when sudden bursts of evolution can be expected.[48] ...


This shows strong selection for maintaining the status quo.

Second, selection does not (on it's own) bring about "new subspecies/breeds" as other factors are involved, including mutations that provide the raw material for selection.

Third, selection is not random. Mutations are random, but selection is a response to ecological constraints: the ones who survive to breed are selected and the ones that do not survive to breed are deselected (see diagram at start of message).

And there's your favorite Pelycodus again, you do love that creature. And of course I have to answer the way I always do that they were merely buried in the Flood, so that I object to the idea that different sizes at different levels argues for evolution when it's just where they happened to end up. We get Great Danes at the same time we get chichuahuas from the same dog gene pool after all, various sizes are options in the genome of any creature that can be selected and isolated at any time in the present. And besides it may only be the creature at different ages too.

And this regurgitated comment still fails to explain the sorting by radiometric age, the sorting by sizes -- especially considering the split at the top and it still fails to explain a purported flood when the evidence does not show one.

Oh and one more thing. Of course selection itself doesn't blend characteristics, what I meant was that the new population of selected individuals with their many different characteristics would over time in reproductive isolation blend together into a phenotype that becomes characteristic of the population, as a new breed or subspecies. The selection merely isolates a particular collection of characteristics.

Which sounds like koinophilia again, rather standard evolutionary process for new populations, nothing radical of fanciful there. I would say "The selection merely consolidates a particular collection of characteristics (with better fitness for the new ecology)."

You might also be interested in Zygosity.

Enjoy


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RAZD
Member (Idle past 336 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 41 of 63 (861888)
08-28-2019 4:58 PM
Reply to: Message 37 by Faith
08-28-2019 2:16 PM


Re: Another input -- Faith-0-lution ....
Yes of course. I've made the point myself many times that the wildebeests of Africa are quite homogeneous in their huge numbers, the only clear variation being a separated/isolated herd called the "blue wildebeests." These are also homogenous as a herd, but this herd is characterized by smaller size, different shaped antlers and a bluish tinge to the hide, a result of the combination of some portion of the larger population's becoming reproductively isolated. The isolation would have lasted long enough to bring out this new set of characteristics from the new set of gene frequencies collectively possessed by the founding individuals.

Curiously I think you have these switched:

quote:
The black wildebeest or white-tailed gnu (Connochaetes gnou) is one of the two closely related wildebeest species. It is a member of the genus Connochaetes and family Bovidae. It was first described in 1780 by Eberhard August Wilhelm von Zimmermann. The black wildebeest is typically 170–220 cm (67–87 in) in head-and-body length, and the typical weight is 110–180 kg (240–400 lb). Males stand about 111–121 cm (44–48 in) at the shoulder, while the height of the females is 106–116 cm (42–46 in). The black wildebeest is characterised by its white, long, horse-like tail. It also has a dark brown to black coat and long, dark-coloured hair between its forelegs and under its belly.

The black wildebeest is currently included in the same genus as the blue wildebeest (Connochaetes taurinus). This has not always been the case, and at one time the latter was placed under a separate genus of its own, Gorgon.[7] The black wildebeest lineage seems to have diverged from the blue wildebeest in the mid- to late Pleistocene, and became a distinct species around a million years ago.[8] This evolution is quite recent on a geologic time scale.[9]


quote:
The blue wildebeest (Connochaetes taurinus), also called the common wildebeest, white-bearded wildebeest, or brindled gnu, is a large antelope and one of the two species of wildebeests. It is placed in the genus Connochaetes and family Bovidae, and has a close taxonomic relationship with the black wildebeest. The blue wildebeest is known to have five subspecies. This broad-shouldered antelope has a muscular, front-heavy appearance, with a distinctive, robust muzzle. Young blue wildebeest are born tawny brown, and begin to take on their adult colouration at the age of 2 months. The adults' hues range from a deep slate or bluish gray to light gray or even grayish brown. Both sexes possess a pair of large curved horns.[2]

Hybrids

The blue wildebeest is known to hybridise with the black wildebeest.[13] The differences in social behaviour and habitats have historically prevented interspecific hybridisation, but it may occur when both species are confined within the same area, and the offspring are usually fertile. A study of these hybrid animals at Spioenkop Dam Nature Reserve in South Africa revealed that many had congenital abnormalities relating to their teeth, horns, and the Wormian bones of the skull.[14] Another study reported an increase in the size of the hybrid as compared to either of its parents. In some hybrid animals, the auditory bullae are highly deformed, and in others, the radius and ulna are fused.[15]


So the black wildebeests were likely a 6th subspecies before they began evolving into a new species while isolated from the parent blue wildebeests parent population. Not the other way around as you have it.

The hybrids do show interbreeding is possible, with usually fertile but less fit results (as compared to horses and donkeys that generally have sterile hybrids). So technically they are not as far along as horses/donkeys in the process of complete reproductive isolation, but the "differences in social behaviour and habitats" are likely to keep them apart and continue the process. They are effectively different species for all intents and purposes.

Yes I know the ToE assumes a purposeful selection, I think that's very rare, that's all.

Not purposeful (ie not directed), it is a feedback result of the ecological opportunities and challenges: some survive to reproduce and others do not. Those that do pass on their genes, those that do not can't pass on their genes.

You don't need to keep arguing with me you know, we're only going to go around in the usual circles, I just like to interject my point of view from time to time so it's on the record. ...

And I'll keep pointing out your mistakes, misinformation and fantasies so that they are on record.

Enjoy

Edited by RAZD, : .


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