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[__ Science __ ] Evolution and Harmless Mutations

AndyBern

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peewee.jpg

(Something I posted on my blog not too long ago...)

About 30 years ago, I acquired a white cat named Peewee. As you can see, he looks like a normal cat, and for all intents and purposes, he was normal. But notice the little bend near the tip of the tail. This was a genetic defect inherited from his mother, for she had the same bend in her tail. If Peewee had ever fathered kittens, some or all of them would likely have had that same defect. But this was a completely harmless mutation. It had no effect on Peewee or his mother, and it would have had no effect on his offspring. It gave no advantage or disadvantage over other cats. I think this points to a serious problem with evolutionary theory.

Evolution, we are told, works by natural selection favoring animals with certain random genetic mutational changes. These random mutations happen fairly often, and over x number of generations, those organisms with advantageous mutations survive and increase, and those that don’t eventually die out. This is an over-simplified explanation of how evolution is supposed to work, but I think evolutionary theory itself has been over-simplified to make it sound plausible.

Mutations do occur, but the vast majority of them are either detrimental or innocuous. We would call them birth defects if we noticed them at all. In comparison, beneficial mutations rarely (if ever) happen. In other words, the number of birth defects far exceeds the number of improvements to a species. We can understand how natural selection can filter out harmful mutations. Some make the offspring infertile. Others make it much more difficult for the animal to survive in the wild. But what about mutations like a bent tail that have no influence on the survival of the species? How can natural selection filter them out? Or perhaps we should ask if they are filtered out at all.

If a beneficial mutation occurs in a dog, that dog must separate from the other dogs to form its own pack to maintain that mutation in a separate gene pool. Otherwise the mutation gets ‘lost’ in the original gene pool as the dog breeds with other dogs that don’t have that mutation. But there can’t be a separate gene pool at first because the dog with the beneficial mutation has no other dogs with the same mutation to mate with. It has to breed with other non-mutated dogs, and hence each puppy may or may not have the mutation. Eventually, however, if the beneficial mutation is to have a chance to take over, the pack must split: one pack containing primarily dogs with the mutation, and another those without, and the packs must forever remain separate from each other. If evolution is true, this must have occurred at least billions of times between the first living cell and the large number of unique and complex lifeforms present today. This seems a bit of a stretch to me, but it’s only the beginning of the problem.

Assuming this has occured billions of times (and I think this is a big assumption), what is there to prevent this same mechanism from acting on innocuous mutations as well? They should also eventually form separate gene pools, and probably much more often, because there are more innocuous mutations than advantageous ones. But why don’t we see very many innocuous mutations? The features of most of today’s lifeforms are useful and advantageous. Why is that? Take bent tails for example. We can see that they occur. But why aren’t most tails bent? If tails came about through a series of random mutations, why should they be symmetrical at all? Yet we recognize a straight tail as normal, and anything other than that as somehow a corruption of the norm, never as something that hasn’t quite fully evolved yet.

Why are fingernails on the ends of fingers and claws on the ends of paws and feet? These are most useful locations. If mutations are random, nails and claws could have appeared almost anywhere – on one’s back for example. In most places they would not give a survival advantage or disadvantage compared to those without nails. Those ‘back nail’ mutations would have continued in the gene pool. But there are no ‘back nails’, ‘elbow nails’, ‘nose nails’, etc. What are the chances that nails and claws appeared only once and in just the most useful location? What are the chances that each of our bodily features appeared exactly where needed? Consider how many species there are and the number of supposed mutations required to reach their current stage of evolution. We’re talking at least billions, if not trillions, of mutations, and almost all of those mutations are optimal for the survival of the species. What are the chances of that happening with very few, if any, innocuous mutations being passed on? The ratio of advantageous features to innocuous features is too high for evolution to account for.

Of course, according to evolutionary theory, nails and claws would not have appeared fully formed at first. Nail and claws are defined by thousands of DNA base-pairs. If evolution is true, it would have taken tens or hundreds of thousands of years for them to evolve. The first mutations may have just produced a rough patch on the skin, if they were visible at all. But that means the beginnings of nails and claws were just innocuous mutations. They were not useful as nails, claws, or anything at first. Those innocuous ‘pre-claws’ survived natural selection to evolve into fully formed nails and claws. Why don’t other innocuous mutations survive? How does blind evolution know if an innocuous mutation will eventually lead to advantageous mutations so it can be retained, while filtering out the other mutations?

Moreover, even though evolution supposedly filters out sub-optimal mutations over time, we see plenty of lifeforms that have disadvantages coexisting with others that have advantages. Multiple varieties of ants, for example, exist in the same habitat, and although many times one has an advantage over the others and they fight each other, they’re not being forced in the direction of extinction. Apart from environmental changes, their populations remain steady over the long term.

Evolution simplifies things too much so it can sound believable. It appears true on the surface, but if you seriously think about it and investigate it, you’ll find many holes impossible to fill. Many evolutionary scientists, some tops in their field, have also considered the difficulties and abandoned the theory. (The Origin Of Species Revisited by W.R. Bird identifies many of these ex-evolutionists.) The Bible, on the other hand, seems very implausible on the surface, but the more I study it, the more I see it matches reality. The Bible will stand up to close scrutiny much better than evolution.
 

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KevinK

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I'm not sure what you mean by needing separate gene pools. That may be somewhat true of recessive gene alleles, but should not matter for dominant alleles. And even with recessives, you don't need separate populations, just time and enough chance matings.
 

Barbarian

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Almost all mutations have little or no effect. You have a dozen or so that weren't in either of your parents. A few are harmful, and tend to be removed from the population. And a very few are useful, and tend to spread through the population.

Evolution, we are told, works by natural selection favoring animals with certain random genetic mutational changes. These random mutations happen fairly often, and over x number of generations, those organisms with advantageous mutations survive and increase, and those that don’t eventually die out. This is an over-simplified explanation of how evolution is supposed to work, but I think evolutionary theory itself has been over-simplified to make it sound plausible.
It's directly observed to work that way. It was a serious problem for evolutionary theory in Darwin's time. Scientists thought at the time, that heredity was in the blood, and it seemed that a new trait would be swamped out of existence in a population like a drop of red paint in a barrel of white paint. Only after Mendel's work was discovered, did they realize that heredity is like sorting beads, rather than like mixing paint, and the problem was solved.

In general, evolution never produces something entirely new; it always modifies something already there. Often, one structure, such as a walking leg, is reconfigured over time to a new function, such as flight, digging, or swimming. This seems to never have happened suddenly; there are always transitional forms showing a gradual change with the limb serving more than one function at least for a period of time. Would you like to discuss that further?

For example claws in amniotes (reptiles, birds, and mammals) are entirely different than "claws" found in other vertebrates like the Sea Robin (fish) and the clawed frog. Each of these is genetically and histologically different than claws of amniotes.

The earliest likely amniote, Casineria, had rudimentary claws. Since claws are modified keratinous structures that are histologically and genetically like scales, it's likely that this tetrapod had body scales which were modified at the digits to form crude grasping structures. Existing structure, reconfigured to a new use.

Why do some harmless mutations survive? Because there's no selective force to remove them. However, over a long period of time, such mutations tend to either become fixed (all individuals have them) or disappear. If you do the math, you'll find that for a finite population, random events will very likely result in extinction or fixation over a long period of time.

I've got some work in entomology, and ants are an interesting case. Where there are more than one species in an environment, they are either adapted to non-competitive ways of life, or one is replacing the other. The arrival of fire ants in the American South was a disaster for many native ant species, but over time, they seem to have adapted to the intruder, and some are coming back. Others may be doomed.

The issues are much more complex than you suppose that they are. The field in which this is studied, is called "population genetics." Would you like to learn about it?
 

Barbarian

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Either way you put it, evolution theory does have many holes...like swiss cheese.
The reason almost all biologists accept it today is threefold:

1. Directly observed to happen.
2. Huge number of predictions made by the theory have been validated in the years since it was proposed
3. Nothing else adequately explains the evidence.

There's still a lot to learn. In Darwin's time the big hole was "how do new traits persist?" He had no explaination for this.
Then genes were discovered, and it became clear.

And there was the question of time. It appeared that the Earth's cooling indicated at most, 10 million years or so, not enough time for evolution to work. Then radioactivity was discovered, and that explained things.

Then there was the question of how new traits appear, which was answered when the function of DNA was discovered.

There are still unresolved questions, such as the role of epigenetics, and the relative role of neutral mutations, as well as the relative effect of chance vs. strict selectionism.

Pretty much like the rest of science.
 

Jim Parker

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Evolution, we are told, works by natural selection favoring animals with certain random genetic mutational changes. These random mutations happen fairly often, and over x number of generations, those organisms with advantageous mutations survive and increase, and those that don’t eventually die out. This is an over-simplified explanation of how evolution is supposed to work, but I think evolutionary theory itself has been over-simplified to make it sound plausible.
There is a key factor which you may have missed here. The advantages provided by the mutation make it possible for the mutated form to out produce (have more offspring) those without the mutation.

So, I wonder how having a kink in his tail would help a cat have more offspring than the rest of the cats.....:thinking

I try to remind people that the theory of evolution is a theory: ie: people's best guess given the available, observable evidence.

Evolutionary theory had been used very successfully in creating mutations (GMOs). And every one of those successes is an example of Intelligent Design. (heh heh heh heh heh)
 

KevinK

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So, I wonder how having a kink in his tail would help a cat have more offspring than the rest of the cats.....:thinking
Well, in all fairness the OP said the bent tail was an inocuous mutation, and the question is why do we still see cats with bent tails if they confer no reproductive advantage. Barbarian explained that there's really no selection pressure to remove such a trait, and if they disappear it's just that they fade out.
 

chessman

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There are still unresolved questions, ... the relative effect of chance vs. strict selectionism.
Are they ‘unresolved questions’ or failed hypotheses???

1. Hypothesis; Random mutations acted upon by natural selection originated all ‘species’: Does current evolution theroy say that mutations occur by random chance or are they now adaptive mutations? Or both depending on the theorist? Or neither?

2. Hypothesis; DNA evolved from RNA: then why is the same DNA code found in all living cells the same, if it evolved from RNA? Shouldn’t we find large numbers of different DNA codes in living cells if it evolved? Or did the RNA get it just right the first try?

3. Hypothesis; species diverge through their children who ‘branch off’ from their parents, forming a verifiable “Tree of Life”. Why has there been no progress in validating one universal tree of evolutionary life based on genetics then (THE fundamental prediction/hypothesis of Darwin’s theroy)? It’s not ‘unresolved’ it’s been falsified.

4. Hypothesis; simple life forms mutate into more complex life forms through small steps in complexity growth. Each good mutation is carried on, each bad mutation dies out. Poof, things became more complex. Then why is the protein-coding which occurs in sea anemones as complex as that which occurs in humans? Why were trilobite eyes just as complex as human eyes? Etc.

And, the kicker, what do all our so closely related cousin species have to say about the evolution theory anyway? Shouldn’t we just ask our closest evolutionary cousin (possibly even one more ‘evolved’ than us) what they think about things?

5. Hypothesis; DNA segments that do not have functional advantages for a species (a bent cat’s tail for example) should mutate and thus diverge over time. The result being you should not find identical DNA segments in distant species that are non-functioning segments. Yet science proves exactly the opposite occurs. 100% Identical DNA segments can be found in both cat and fish DNA. These segments can be deleted and both ‘species’ survive.
 

KevinK

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1. Hypothesis; Random mutations acted upon by natural selection originated all ‘species’: Does current evolution theroy say that mutations occur by random chance or are they now adaptive mutations? Or both depending on the theorist? Or neither?
I know that you addressed Barbarian (who knows far more about biology than I do), but thought I could ask a question. As far as I know, the actual gene mutations occur randomly; whether they are adaptive or not depends on the natural selection process. If they confer viability, they are retained in the gene pool; if not they are selected out or become fixed or fade out completely. Evolution cannot "look ahead" and predict adaptiveness. So I'm not clear what your question means.
 

Luminous_Rose

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The reason almost all biologists accept it today is threefold:

1. Directly observed to happen.
2. Huge number of predictions made by the theory have been validated in the years since it was proposed
3. Nothing else adequately explains the evidence.

There's still a lot to learn. In Darwin's time the big hole was "how do new traits persist?" He had no explaination for this.
Then genes were discovered, and it became clear.

And there was the question of time. It appeared that the Earth's cooling indicated at most, 10 million years or so, not enough time for evolution to work. Then radioactivity was discovered, and that explained things.

Then there was the question of how new traits appear, which was answered when the function of DNA was discovered.

There are still unresolved questions, such as the role of epigenetics, and the relative role of neutral mutations, as well as the relative effect of chance vs. strict selectionism.

Pretty much like the rest of science.
I guess the sad part is that evolution can't be observed. At least not evolution that refers to a change in kinds. Some scientists fail to understand the difference between evolution and adaptation.

I suppose as people, we fear the unknown and must strive to understand it in order to explain it. No, some can't enjoy the feeling of awe to know that something looks amazing just because that is the way God designed it.
 

chessman

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As far as I know, the actual gene mutations occur randomly
That’s what was taught for many years and on into the 20th Century because that was one of the hypotheses presented by evolutionary theroy.

“Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions“​
Julian Huxley​
chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact.​
Jacques Monod​

The problem is, that hypothesis is a provably false hypothesis. Gene mutations do not occur puerly randomly. DNA adapts to the pressures of it’s environment (or it dies of course). Putting pressures of various kind on a population, it WILL mutate (or die). Just ask sheep.

Evolution cannot "look ahead" and predict adaptiveness.
Which is a different subject than random mutations.
But the Hypothesis; Evolution cannot "look ahead" and predict adaptiveness???

You sure? The very same DNA code which is capable of maintaining gene segments that is still in (and more to the point, was in) early sea anemones is also our DNA code, still here expressing many of the same proteins (and more) for us quite nicely. That’s pretty predictive IMO.

I predict that if you alter the environment of one population of yeast slightly to that of another population of yeast, it will adapt genetically to it’s new and directed environment. The code is capable of adapting to a directed environmental change.
 

KevinK

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That’s what was taught for many years and on into the 20th Century because that was one of the hypotheses presented by evolutionary theroy.

“Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions“​
Julian Huxley​
chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact.​
Jacques Monod​

The problem is, that hypothesis is a provably false hypothesis. Gene mutations do not occur puerly randomly. DNA adapts to the pressures of it’s environment (or it dies of course). Putting pressures of various kind on a population, it WILL mutate (or die). Just ask sheep.


Which is a different subject than random mutations.
But the Hypothesis; Evolution cannot "look ahead" and predict adaptiveness???

You sure? The very same DNA code which is capable of maintaining gene segments that is still in (and more to the point, was in) early sea anemones is also our DNA code, still here expressing many of the same proteins (and more) for us quite nicely. That’s pretty predictive IMO.

I predict that if you alter the environment of one population of yeast slightly to that of another population of yeast, it will adapt genetically to it’s new and directed environment. The code is capable of adapting to a directed environmental change.
Forgive me, I seem to still have trouble with what you're saying. Can you clear up the confusion between the randomness of mutations, and the positive selective pressure on adaptive phenotypes? Maybe that's the confusion, the difference between genotype and phenotype.

Selective pressure does not work directly on the genes (which is what you're saying?); it can only work on the physical expression of a specific gene (i.e. the phenotype). The mutation of the gene code does occur randomly; its retention in the gene pool comes about because its corresponding physical trait is advantageous. The system as a whole is adaptive, but it's not like the gene code is telling itself, "Hmm, we need to make our fangs bigger because the prey species in our new environment are all larger".
 

chessman

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Selective pressure does not work directly on the genes
Selective pressures (heat for one example) pressures the actual genes to mutate at a higher rate (i.e. mutation is not random). That’s what I’m reporting.

Again, random mutations WAS an evolutionary hypothesis that has now been proven to be wrong by experimental observations.

“Bacteria have several stress responses that provide ways in which mutation rates can be increased. These include the SOS response, the general stress response, the heat-shock response, and the stringent response, all of which impact the regulation of error-prone polymerases. Adaptive mutation appears to be process by which cells can respond to selective pressure specifically by producing mutations.”​

Experiments ⬆ have shown how cells (mind you living/breathing cells not phenotypes) accomplish their stress response (adaptive ‘mutation’). They use their duplicate gene segments to ‘test the waters’, so to speak. Again, quite amazing for such a distant life form and definitely NOT a random reaction.

The mutation of the gene code does occur randomly
Sorry, that’s never been an actual observation within the process of evolution. It was merely an assumption (a hypothesis) taught for decades as ‘fact’ (see Jacques Monod quote) yet now has been experimentally shown to be a false assumption. Not just by Ms. Foster’s work with bacteria either. But that’s enough to show mutations are not random. It may take a generation or two for the idea of ‘random mutation’ to work it’s way out of the texts books though.
 

Barbarian

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Are they ‘unresolved questions’ or failed hypotheses???
Unresolved questions. Failed hypotheses are proposed explanations that didn't turn out to be true.

1. Hypothesis; Random mutations acted upon by natural selection originated all ‘species’:
Nope. For example, the evolution of O. gigas (a species of primrose) was just a random polyploidy event, with no natural selection involved. Evolutionary theory does not hypothesize that all speciations are by natural selection.

Does current evolution theroy say that mutations occur by random chance
Delbruck got his Nobel for demonstrating that favorable mutations appear randomly, not as a result of natural selection. Natural selection only acts after mutations appear. You're confusing mutations with natural selection.

2. Hypothesis; DNA evolved from RNA
Not part of evolutionary theory. It's part of abiogenesis.

then why is the same DNA code found in all living cells the same, if it evolved from RNA?
It isn't the same in all living cells. Even in animal cells, the coding in mitochondria differs:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191813/

Shouldn’t we find large numbers of different DNA codes in living cells if it evolved?
Not if only one line survived. But as I said, it's not part of evolutionary theory.

3. Hypothesis; species diverge through their children who ‘branch off’ from their parents, forming a verifiable “Tree of Life”. Why has there been no progress in validating one universal tree of evolutionary life based on genetics then
Turns out it has. The original "tree of life" was prepared by Linnaeus, who didn't think species evolved. Genetic data confirms the tree of Linnaeus to a very high precision. And these DNA phylogenies can be checked, by looking at the DNA of organisms of known descent.
https://www.researchgate.net/profile/James_Brown43/publication/5485211/figure/fig1/AS:213426770059277@1427896315989/Neighbor-joining-phylogenetic-tree-of-the-Dicer-protein-family-Major-organism-groups.png[/quote]

It's been confirmed by other molecules as well. Would you like to learn more about it?

(THE fundamental prediction/hypothesis of Darwin’s theroy)?
Yep. Verified by molecular biology. Let me know if you'd like to get some more data on that.

4. Hypothesis; simple life forms mutate into more complex life forms through small steps in complexity growth. Each good mutation is carried on, each bad mutation dies out. Poof, things became more complex.
Nope. Sometimes, evolution makes things less complex. You've been misled about that. Often it does lead to higher complexity, but not always.

Then why is the protein-coding which occurs in sea anemones as complex as that which occurs in humans?
It's close, but not quite. Human histones play a greater role in gene expression than is found in sea anemones. But as you just learned, it's often that increased complexity evolves over time.

Why were trilobite eyes just as complex as human eyes?
They aren't. they lack an iris, a focusing mechanism, and so on.

And, the kicker, what do all our so closely related cousin species have to say about the evolution theory anyway?
That human evolution was mostly a matter of retention of neotonous traits. That our closest relatives are chimpanzees, with other great apes as the outgroup. That bipedal movement was a matter of repositioning certain muscle groups, lower back, hips, and knees.

5. Hypothesis; DNA segments that do not have functional advantages for a species (a bent cat’s tail for example) should mutate and thus diverge over time.
Things like vestigial or missing eyes in cave fish or naked mole rats. Things like vestigial tails in humans; the coccyx is the remnant of a tail, and some humans are now born without them. Yes, that has been repeatedly verified.

The result being you should not find identical DNA segments in distant species that are non-functioning segments.
Over time mutations tend to change things. It's likely, but of course, not absolutely necessary. And it turns out that much of our non-coding DNA has other functions, so it's not surprising that those segments remain constant even for distantly-related organisms. And of course, since there are only 4 codons, the likelihood of finding identical sections by chance is quite high.

100% Identical DNA segments can be found in both cat and fish DNA. These segments can be deleted and both ‘species’ survive.
Yep. Statistically almost inevitable, merely by chance.
 
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Barbarian

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How evolution can change mutation rates:

Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases. Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection. Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations. Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved. The findings have important implications for our understanding of evolution and the control of mutations.
https://www.nature.com/articles/nature10995
 

Barbarian

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Selective pressures (heat for one example) pressures the actual genes to mutate at a higher rate (i.e. mutation is not random). That’s what I’m reporting.
A lot of chemical and physical factors can change mutation rates. Ionizing radiation, colchicine, heat, and so on. But the mutations are still random.

Again, random mutations WAS an evolutionary hypothesis that has now been proven to be wrong by experimental observations.
Nope. You're confusing mutation rates with the mutations that appear. They are random, something Delbruck and Luria got their Nobel prizes for demonstrating.
 

Barbarian

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I guess the sad part is that evolution can't be observed.
Perhaps you don't know what "evolution" means. It's defined as a change in allele frequency in a population over time.

At least not evolution that refers to a change in kinds.
DNA shows that all life known on Earth is of a single kind. If you mean "species", that's been observed to evolve. If you mean "phylum", that takes longer. It's like denying that giant redwoods can grow to maturity from seeds, because no one has ever seen it happen. No one takes such arguments seriously.

Some scientists fail to understand the difference between evolution and adaptation.
"Adaptation" is of two kinds. The first is when your body responds to changes in the environment and adapts. For example, if you move to a high elevation, you will produce more red blood cells to compensate. That's not evolution. On the other hand Tibetans, over several thousand years, evolved alleles to live at very high elevations. That sort of adaptation is evolution.

Life at high altitudes forced ancient Tibetans to undergo the fastest evolution ever seen in humans, according to a new study.

The most rapid genetic change showed up in the EPAS1 gene, which helps regulate the body's response to a low-oxygen environment. One version, called an allele, of the EPAS1 gene changed in frequency from showing up in 9 percent of the Han Chinese to 87 percent of Tibetans.

Such genetic changes suggest Tibetan ancestors split off from the Han Chinese population about 2,750 years ago, researchers say. But only those most evolutionarily suited for life at high altitudes survived when they moved to the Tibetan Plateau.
https://www.livescience.com/6663-tibetans-underwent-fastest-evolution-humans.html


I suppose as people, we fear the unknown and must strive to understand it in order to explain it.
It's true. The less you know about evolution, the more likely you are to fear or deny it.

No, some can't enjoy the feeling of awe to know that something looks amazing just because that is the way God designed it.
It's much more amazing that God created living things with the ability to evolve new adaptations as needed. God is much greater and wiser than many people would like Him to be.
 

chessman

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Failed hypotheses are proposed explanations that didn't turn out to be true.
As is the case for five failed hypotheses I listed.
Evolutionary theory does not hypothesize that all speciations are by natural selection.
Yea, the theroy’s very definition of species keeps changing. Which is why I put it in scare quotes.

http://a.co/haZmkcz

Natural selection isn’t the issue with hypothesis 1 . Random (or not) mutations is the failed hypothesis.

[1]Do mutations arise randomly over time? Or [2]are they induced by unfavorable environments? By addressing these crucial evolutionary questions, Salvador Luria and Max Delbrück won a Nobel Prize and helped to start the field of bacterial genetics.
Their answer was [1]. Now the answer is [2]. Learn about it here (or not):
Adaptive mutation appears to be process by which cells can respond to selective pressure specifically by producing mutations.”https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729700/
And notice the work proves the cells themselves (not just the next generation) responded non-randomly to the pressures. They adapted.

You're confusing mutations with natural selection.
nope.


Not part of evolutionary theory. It's part of abiogenesis.
The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage.​

It isn't the same in all living cells. Even in animal cells, the coding in mitochondria differs:
The code is “universal”, thus allowing non-universal codon changes to propagate via offspring). Much like the HTML code which runs on both our devices. From the article:

They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria)​

Not if only one line survived.
So that’s your hypothesis? Only one of many different life codes survived? Have you any observational results of life which is different than the universal DNA code of life?

Hypothesis 4:

The key was to identify “a long series of gradations in complexity, each good for its possessor” which could lead to “any conceivable degree of perfection.” (Darwin, 165)​

It is commonly believed that complex organisms arose from simple ones. Yet analyses of genomes and of their transcribed genes in various organisms reveal that, as far as protein-coding genes are concerned, the repertoire of a sea anemone—a rather simple, evolutionarily basal animal—is almost as complex as that of a human. (Technau)
Technau, U. 2008. “Evolutionary biology: Small regulatory RNAs pitch in.” Nature 455:1184-1185.​
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They aren't. they lack an iris, a focusing mechanism, and so on.
Complex doesn’t mean they have an iris (or not). Plus, the point of the research was about the protein coding complexity needed to form eyes in such an early creature, not the eye similarity themselves. The same complexity in the code that formed their eyes forms our. We need irises, they don’t.


 

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