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# Another IDology challenge -- complete with complaints of harsh treatments ...

Author Topic:   Another IDology challenge -- complete with complaints of harsh treatments ...
Chiroptera
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 Message 16 of 63 (861635) 08-24-2019 12:38 PM Reply to: Message 15 by Theodoric08-24-2019 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.
He is known for... books on topics including... and what he sees as the destructive influence of liberal academia on American society, expressed in his book America-Lite: How Imperial Academia Dismantled Our Culture (and Ushered in the Obamacrats).
Sound like overall he's quite a piece of work.

It says something about the qualities of our current president that the best argument anyone has made in his defense is that he didn't know what he was talking about. -- Paul Krugman

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RAZD
Member (Idle past 771 days)
Posts: 20714
From: the other end of the sidewalk
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 Message 17 of 63 (861636) 08-24-2019 1:19 PM Reply to: Message 15 by Theodoric08-24-2019 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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 This message is a reply to: Message 15 by Theodoric, posted 08-24-2019 12:10 PM Theodoric has not replied

WookieeB
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 Message 18 of 63 (861660) 08-25-2019 4:02 AM Reply to: Message 14 by RAZD08-24-2019 11:59 AM

Re: Correction, sort of ... filling in the blanks.
Off topic, but...
RAZD writes:
The problem is that we have observed new species developed by the standard evolutionary model,
Where?
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?
Secondly, can you be more specific about what "way" biology supposedly doesnt operate by?
mutations occur in a number of ways of many different length segments from whole gene copying to single inserts
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.
----
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"? Regardless, 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.
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?

 This message is a reply to: Message 14 by RAZD, posted 08-24-2019 11:59 AM RAZD has replied

 Replies to this message: Message 19 by RAZD, posted 08-25-2019 9:39 AM WookieeB has replied

RAZD
Member (Idle past 771 days)
Posts: 20714
From: the other end of the sidewalk
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 (1)
 Message 19 of 63 (861668) 08-25-2019 9:39 AM Reply to: Message 18 by WookieeB08-25-2019 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.
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?
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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 This message is a reply to: Message 18 by WookieeB, posted 08-25-2019 4:02 AM WookieeB has replied

 Replies to this message: Message 20 by AZPaul3, posted 08-25-2019 11:46 AM RAZD has replied Message 44 by WookieeB, posted 08-29-2019 1:18 PM RAZD has replied Message 45 by WookieeB, posted 08-29-2019 1:36 PM RAZD has replied Message 47 by WookieeB, posted 08-29-2019 2:32 PM RAZD has replied

AZPaul3
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 Message 20 of 63 (861669) 08-25-2019 11:46 AM Reply to: Message 19 by RAZD08-25-2019 9:39 AM

Re: more filling in the blanks.
Which population will thus have a higher rate of evolution?
In lower selective pressure environments populations grow larger with greater genetic diversity within the species.
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.
I question a rate of evolution.
Is an increase of genetic diversity within a population a higher rate of evolution? Is the number of speciation events the higher rate?
I know we love to say this but I don’t think evolution has a rate.

Eschew obfuscation. Habituate elucidation.

 This message is a reply to: Message 19 by RAZD, posted 08-25-2019 9:39 AM RAZD has replied

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dwise1
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 Message 21 of 63 (861705) 08-25-2019 3:41 PM Reply to: Message 20 by AZPaul308-25-2019 11:46 AM

Re: more filling in the blanks.
I know we love to say this but I don’t think evolution has a rate.
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.
If a power supply's voltage output remains constant, that does not mean that it's not performing voltage regulation.

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 Replies to this message: Message 22 by RAZD, posted 08-25-2019 4:47 PM dwise1 has replied Message 24 by AZPaul3, posted 08-25-2019 5:38 PM dwise1 has replied

RAZD
Member (Idle past 771 days)
Posts: 20714
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 Message 22 of 63 (861712) 08-25-2019 4:47 PM Reply to: Message 21 by dwise108-25-2019 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.
Enjoy

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dwise1
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 (1)
 Message 23 of 63 (861718) 08-25-2019 5:34 PM Reply to: Message 22 by RAZD08-25-2019 4:47 PM

Re: more filling in the blanks.
When the ecology is stable, in equilibrium, then selection is to maintain that median position because it is successful.
Indeed. Selection is still selection and selection still happens. All it takes to be able to see that is some basic knowledge of evolution and thinking through how it works.
The backlash I would get would mainly be from creationists who are so wrapped up in definitions and, since the word "change" appears in their definition of evolution, they think that if there's no change then evolution isn't still happening.

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AZPaul3
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 Message 24 of 63 (861720) 08-25-2019 5:38 PM Reply to: Message 21 by dwise108-25-2019 3:41 PM

Re: more filling in the blanks.
When you are at the set-point, then the exact same mechanism keeps you at that set-point.
Understanding that the set point is flexible ...
I like the analogy. I'm going to steal it. Thanx.

Eschew obfuscation. Habituate elucidation.

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dwise1
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 (2)
 Message 25 of 63 (861731) 08-25-2019 8:39 PM Reply to: Message 24 by AZPaul308-25-2019 5:38 PM

Re: more filling in the blanks.
I like the analogy. I'm going to steal it. Thanx.
You're welcome to it. I'll even give you some of the background to its development in case that gives you more to work with.
I read an article from Nature or a similar science journal from around 1980 which reported on a paleontology conference centering around punctuated equilibria and similar topics. One pattern presented would be of a large population ranging over a broad environment such that it didn't change much but it lasted a long time because it had enough diversity to weather through changes in their environment; compared to that are smaller populations changing a lot to become highly specialized to their particular niches, but short-lived because they could not survive changes in their environment.
A graphic that formed the imagery in my mind was one which showed that the "sudden" change in geological time was still gradual in generational. The portion of the graphic showing generational time was a series of bell curves each representing a generation and showing the center of the curve (representing the optimal organism) moving as the environment changed. That would translate into our use of the term "set-point" here and of your point that that set-point does move so the population needs to track that movement.
Another contribution was made by a PBS popularization of evolution from the early to mid-80's hosted by Christopher Reeve. Towards the end was my first exposure to Evolutionstechnik, using evolutionary processes in engineering (eg, genetic algorithms, it was a few years later that I first heard of GAs). The mind-bender for me was when he presented a model of a 3-D "evolutionary landscape" in which the environmental optimum was the top of a hill (a local optimum) and he described evolutionary change as being faster when the population is farther away from that optimal point and would slow down as it got closer.
That idea took me by surprise, so I worked through some Gedankenexperimenten (I'm kind of good at visualizing things). This is what I ended up with (which would work better with good visuals, so my apologies):
1. Start with a bell curve to represent the initial population. Establish an optimal point to the right of that curve.
2. The population reproduces and creates the next generation. This causes the bell curve to grow in amplitude and also to spread out to the left and to the right. This could or could not involve the removal of the previous generation; removal would make the new bell curve represent only the next generation.
3. Selection happens. The individuals closer to the optimal point would have a better chance of surviving (ie, have an easier "saving roll" to make if you're familiar with RPGs like D&D) and those further away would have a worse change (ie, a harder "saving roll" to make). This would result in a lopsided curve whose center would have shifted closer to the optimal point.
4. Goto Step 2 and rinse and repeat observing what happens to the population's distribution curve over the generations.
In my mind, I saw that population work its way to that optimal point and then center around it. And over subsequent generations as the population's curve might try to spread out, selection would eliminate the more extremely different individuals and thus keep the population centered at that point.
A further application would be to start with an optimally adapted population and then start moving the optimal point and observe the population's response to that. Again, we should observe the population shifting its own center to track its optimal point.
I think that you could set up an experiment involving two optimal points, one that the population starts off tracking and the other a near-by one. I would visualize part of the parent population splitting off and starting to track the new optimal point.
I've also thought of adapting this visual model to a simulation program for study.
Let us know what you're able to do with this, if anything.
Share and enjoy!

 This message is a reply to: Message 24 by AZPaul3, posted 08-25-2019 5:38 PM AZPaul3 has seen this message but not replied

RAZD
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 Message 26 of 63 (861746) 08-26-2019 10:20 AM Reply to: Message 20 by AZPaul308-25-2019 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 [msg=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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RebelAmericanZenDeist
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RAZD
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 Message 27 of 63 (861824) 08-27-2019 1:21 PM Reply to: Message 26 by RAZD08-26-2019 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:
$\color{white} r=\frac{{\rm ln} X_2 - {\rm ln} X_1}{\Delta t}$
where $\color{white} X_{1}$ and $\color{white} X_{2}$ are the initial and final values of the trait and $\color{white} \Delta t$ is the change in time in millions of years. An alternative form of this equation is:
$\color{white} r=\frac{{\rm ln} \frac{X_2}{X_1}}{\Delta t}$
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 ($\color{white} Ma^{-1}$).
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,$\color{white} sp = \sqrt{(sp)^2}$, where
$\color{white} (sp)^2 = [(n_1-1) (s_1)^2 + (n_2-1) (s_2)^2 ] / (n_1 + n_2 - 2)$, where $\color{white} s_1$ and $\color{white} s_2$ are the standard deviations of the samples of natural-logged measurements; and
3. the time interval between the samples, $\color{white} I = t_2 - t_1$, counted or estimated in generations.
The resulting rate in haldanes is:
$\color{white} H_{log I} = \frac{Z} {I} , ~ where ~~ Z = \frac{d} {sp}$
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).
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 This message is a reply to: Message 26 by RAZD, posted 08-26-2019 10:20 AM RAZD has seen this message but not replied

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AZPaul3
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 Message 28 of 63 (861830) 08-27-2019 4:14 PM Reply to: Message 27 by RAZD08-27-2019 1:21 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.
Initial and final values of a trait over some mm years
How long to double the size of a mouse
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.
A. whosits took 62 darwins from this phenotype to that.
B. thingies took 65 darwins from this phenotype to that.
Does this mean *evolution* was faster for the whosits than the thingies and does it really matter?
All it means is that more time elapsed from this arbitrarily chosen version of the whosits to that one, than it did for the two arbitrarily chosen versions of the thingies.
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.
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.
This changes the inputs to the processes but does not change or speed up those processes. Stress Response Mutations only give the processes more to work with initially than they would without that scheme. They add to the available allele pool they do not make the selection or distribution of alleles any faster.
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.
Evolution does not speed up or slow down in comparison between sets of phenotypes. Each phenotype takes however long it takes generation to generation and comparisons between phenotypes are useless since each evolves by its own unique circumstance.
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?
Edited by AZPaul3, : No reason given.

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Faith
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 Message 29 of 63 (861842) 08-27-2019 7:02 PM

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.
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.
Not only is there no "rate of evolution," there is no evolution as defined by the ToE.
abe: What you call speciation could never happen, which is a population with its own overall characteristics that clearly differentiate it from its parent population. (Of course it would have sufficiently diminished genetic diversity to make further evolution impossible, but anyway....
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.
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 (2)
 Message 30 of 63 (861846) 08-28-2019 12:31 AM Reply to: Message 29 by Faith08-27-2019 7:02 PM

quote:
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.
And nobody says that it does happen or expects it to happen, except in a (very) long-term absence of any selection (which also never happens). It is even less realistic than your constant decline in diversity.
In reality the processes of mutation and selection tend to a balance (depending on population size). As we should expect, given that there is an element of negative feedback to selection and mutation is constant.
quote:
Not only is there no "rate of evolution," there is no evolution as defined by the ToE.
Unfortunately for you you are not God, so reality is quite free to ignore your imaginings. And it does. Your refusal to consider any realistic scenario is only proof of your prejudice against evolution.
quote:
abe: What you call speciation could never happen, which is a population with its own overall characteristics that clearly differentiate it from its parent population. (Of course it would have sufficiently diminished genetic diversity to make further evolution impossible, but anyway....
If we are restricted to the scenarios you imagine. However neither we nor reality are so restricted.

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