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Nested Hierarchy: Evidence for Evolution

Speedwell

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I'm all for investigating our world. I'm fine with science creating theories, even if I think it's wrong. I just think science has become to militant and elitist. It can't accept that maybe, somewhere along the line, maybe they got something wrong. Or could be explained in a different way. Every scientist, even the creationist ones, go to work with a biased mind.
Of course, scientific theories (including evoution) are only ever taken provisionally, pending the discovery of evidence which will falsify them. The history of science is littered with falsified theories--the Luminiferous Aether, the Phlogiston Theory of Heat, the Miasma theory of Disease, and so on. And once a theory is falsified, it stays falsified. Even if a subsequent theory fails, it won't bring the previous theory back to life. Biblical creationism, considered as a scientific eplanation of our origins is in that category. It is no longer viable, and debunking evolution won't bring it back.

Do you think if a scientist ever came forward and said, "Wow, this has led me to believe we were created by God!" that they would ever be taken seriously ever again?
Many reputable and well regarded scientists are theists and believe eactly that without any harm to their careers.. Biblical creationism is something else again.
 
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Jjmcubbin

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Animals are amazing. They come in many varieties, and can be classified in groupings that can easily be seen. One of the first thing a child learns is the difference between a bird and a fish and a snake. These categories are unmistakable. How is it that life is aligned in such distinct categories?

You may think that all things can be similarly characterized, but that is not true. For instance, Carl Linnaeus, after establishing the modern groupings in plants and animals in his 1735 book, Systema Naturae, set out to do the same thing for rocks. Everyone could see that the groupings for animals were correct. But the rocks? He could not seem to find anything that people would agree on. Oh, one could classify rocks by mineral content, or depth of the formation, or apparent process in making the rocks, or apparent age, but each grouping leads to a completely different arrangement. He could find no grouping that all could agree was the correct one.

He had not had this problem with animals. Everybody could see that snakes, sharks, birds and mammals were distinctly different groupings. And one could subdivide the mammals into primates, rodents, carivora (cats, bears, dogs, etc.), and other groups. All could see those subgroups were real. And one can readily learn to tell which of those groups each mammal belongs to. The carnivora could be further divided into groups like Canidae (dogs, wolves and foxes), Felidae (cats), and Ursidae (bears). And even young children can readily tell if an animal should be grouped in a cat family, a dog family, or a bear family. The cat family can be further subdivided into over 40 different species such as lions, tigers, and bobcats. And the major groups like birds and mammals can be grouped together with all other animals with backbones to form the vertebrates, and the vertebrates can be combined with sea squirts and lampreys to form the chordates, and the chordates can be combined with starfish to make the Deuterosmoes, which are distinct from the larger group of animals called the Protosomes (insects, worms, etc.).

An interesting tidbit here is that the Protoosomes all eat with the hole that forms first in the embryo, using the second hole that develops to expel waste. But the Deuterosomes (us vertebrates and our kin) have it backwards, eating with what most animals would call the anus and sending waste out the end that most animals would call the mouth. So we find a clear distinction here. One group universally treats the first hole that forms as the mouth, and the other universally uses that same hole for expelling waste. This is no trivial difference. And again one wonders why it is that all sharks, birds, humans, and starfish would use one end to eat with, while all worms and insects walk in a direction that we would consider backwards, and eat with what we would consider the wrong end.

If one can examine the details, it is easy to distinguish between eating with the front end or eating with the back end. It is easy to distinguish having a backbone and not having a backbone. The groups are unambiguous.

We see multiple layers of groupings. Chimpanzees, for instance are part of a line that branches off in 40 different places from lines that lead to other living things. Starting with a group that includes all life, we find that all plants go their own way to make their own group, then later all the Amoebozoans, then the fungi, and on up through to the Protosomes which branch off to eat with what us dignified folks would consider to be the wrong end, and others branch off later to be distinct from the chordates, and some of the chordates branch off later without being vertebrates, and some vertebrates branch off without being descendents of the first tetrapods, and some of the tetrapod descendents branch off without becoming mammals, etc. in 40 different layers of branching, before the chimpanzees branch off from humans and then finally the bonobos to form their own group. And each of the groups that branches off forms its own tree of branching life forms.

This is what we refer to as a nested hierarchy. It is not simply sorting by size or some other characteristic. It is groups within groups within groups, all the way down. See figure below.

treeoflife.jpg


See also diagram at 29+ Evidences for Macroevolution: Phylogenetics .

Try doing that with rocks. You can't. Try doing that with chemical elements. You can't. Try doing it with mountains, planets, lakes, or streams. You can't. And again, the question is why?

Try doing that with vehicles. You can't. I hear the objection already. Many here have claimed that you can. They will probably respond to this post with a picture showing perhaps cars, light trucks and heavy trucks arranged in what looks like a nested hierarchy. But the arrangement is a simple arrangement based basically on one category, hauling capacity. Which brings up an interesting question. What is the definition of the truck? Look it up. A truck is a vehicle that hauls a lot of cargo. A heavy truck is a vehicle that hauls more than a light truck. Ok, so if we arrange vehicles by cargo capacity, we find small cargo capacity (cars), medium cargo capacity (pickups), and high cargo capacity (heavy duty trucks). Sure, you will see features that, almost by definition, are needed in bigger and bigger vehicles and so tend to exist in larger vehicles as one goes along. All this does is sort on one variable, cargo capacity. Now lets add in all the variables in which vehicles vary: air conditioning, make and model, engine type, fuel, brand of spark plugs, type of brakes, type of sound system, etc. Now give me a breakdown, please, that groups vehicles in all these categories in a single nested classification system that is readily accepted by all. You may think a beat-up '57 Chevy pickup should be classified with an '18 Ford F-150, but others would say that is closer the the '57 Bel Air.

There are only a few things that can be grouped in a clear, objective, readily accepted nested hierarchy. These include languages and manuscripts of old books. They share the same trait. They are all reproduced with changes from some previous reproduction with changes. Reproductions of reproductions tend to keep the changes in the line of ancestry that led to that copy. Where you see a clear, unambiguous, objective nested hierarchy of many layers, that is strong evidence you are dealing with something that has been reproducing with changes.

And so it is that nested hierarchies are evidence that things have descended with change from a common source. For living things, that means evolution. See 29+ Evidences for Macroevolution: Part 1 .

I conclude that nested hierarchies are evidence for evolution.
You're the first person I've seen on this site to use actual biology as evidence. Hats off to you.
IMO, the best evidence for evolution is taxonomy. Because it is based on phylogenetics.
 
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doubtingmerle

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All you have to do is look at the reaction creationists get, even on Christian forums. We're all treated like idiots because how dare we question almighty science!
I don't think we should derail this thread with complaints about how you have been treated. If someone has wronged you, please deal with that elsewhere.

If we opened this thread up as a complaint thread for everyone to share all the unkind things people have said about someone elsewhere in this forum, believe me, I would have a lot of stories to tell. But this is not the place for that.

I will not treat you as an idiot, nor will I claim that science is almighty. However, should you disagree with the consensus view of science, I will want to understand why, and I might explain to you why your view has not been accepted in the scientific community.
 
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doubtingmerle

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1) the fact that we find many cases of non-nested hierarhcy in nature. for instance some electric organs suppose to evolve several times convergently. when scientists find such a case that doesnt fit with the nested hierarchy they just "solve" this problem by claiming that this trait evolved several times convergently:


Fishgraph.jpg


(image from How Evolution Gave Some Fish Their Electric Powers)
I've answered this when you brought it up on another thread. And we all know what you do here. You just ignore the responses, and post the same argument over and over again that have been answered before. I will respond one more time here for the benefit of those who are seeing it first on this thread, but I won't waste my time endlessly repeating things to you.

When we say things fall into nested hierarchies, we are not saying that every thing fits perfectly with nested groupings. There are many exceptions. There are many reasons for this. For one, we are dealing with random mutations, and cannot always predict what they will do. Where many mutations have occurred since a split, the "noise" of all the mutations drowns out the "signal" so that the groupings are not as clear as one might otherwise expect. There can be convergent evolution where two creatures find similar solutions. There are times when gene duplications cause proteins to change rapidly, and those creatures don't always show the protein frequencies we might otherwise expect. There can be limited data with errors in the readings, leaving us with some confusion on the pathways.

But as I explained before, we are going by many characteristics when we produce the trees of animal life. Animals could theoretically fall into many different groupings, but when large sets of animals are studied for multiple characteristics, they consistently show that we are dealing with nested groupings from evolutionary relationships. Calculations have been done to verify that the degree of agreement on the groupings are extremely unlikely to have happened by chance, but represent real evolutionary relationships. The studies verifying this are listed in the link from the OP.

Per the article you reference, the electrical pulses produced in these animals are similar to the pulses in muscular movement. Some animals have genes that disable certain muscles and use the resulting voltage to generate a shock. It is as if the animals try to move a muscle that does not exist, and it produces an electric current as a result. So one can imagine an ancestor with strong pulses when it moves muscles, perhaps even displaying some electrogenic properties. Its descendents spread out into different environments. Many found these pulses an unnecessary drain on valuable resources, and mutations let the process atrophy. Others found the pulses valuable, and exploited the ability to disable those muscles and thus produce a strong shock. The potential to go either way could have been in the genes, with different descendants selecting different paths.
 
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doubtingmerle

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It can't accept that maybe, somewhere along the line, maybe they got something wrong. Or could be explained in a different way.
That's odd, for I have found that science is open to the truth, and frequently self- corrects.

The nested hierarchy argument presented here is sound. Do you have any reason to think it wrong?
 
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doubtingmerle

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I understand the basics. I just disagree with them.
Actually what I called you on was stating that life is thought to have begun in the Cambrian explosion. That is not a matter of disagreeing with a basic of science that you understand. That is a matter of misstating what science says. And when that happens, then the solution is instruction of that person in the basics (and sometimes, if that fails, instructions in honesty.)
 
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doubtingmerle

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if there are "many exceptions" then we have many exmaple of non- hierarchy too.
No, I said it right the first time. There are many exceptions.

Nested hierarchy means that statistically, the coordination of traits is far closer to a given nested hierarchy than the results we would expect by chance. You ignore that. You were given the site that lists the studies that did that analysis. You ignore that.

Science is based on probabilities. How do we know things are true in science? Because we do experiments, and determinine that, statistically, the result was not likely to have been by chance. That is how all science works. So when I show you that statistically the results of nested hierarchy studies show overwhelmingly that the overall pattern is not one of chance, that is using the essence of the scientific method.

When dealing with things like uncontrolled mutations, it is not enough to find a few that do not fit a certain pattern. If the data shows an overwhelming consistent pattern that almost certainly is not of chance, then it is not enough to point out a few points that are troublesome. You must show that statistically, these new data override the previous study that shows the nested relationships should be seen as real.

The only reasonable way to produce a real nested hierarchy is descent with modification ( or a deceptive God)·
 
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Speedwell

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No, I said it right the first time. There are many exceptions.

Nested hierarchy means that statistically, the coordination of traits is far closer to a given nested hierarchy than the results we would expect by chance. You ignore that. You were given the site that lists the studies that did that analysis. You ignore that.

Science is based on probabilities. How do we know things are true in science? Because we do experiments, and determinine that, statistically, the result was not likely to have been by chance. That is how all science works. So when I show you that statistically the results of nested hierarchy studies show overwhelmingly that the overall pattern is not one of chance, that is using the essence of the scientific method.

When dealing with things like uncontrolled mutations, it is not enough to find a few that do not fit a certain pattern. If the data shows an overwhelming consistent pattern that almost certainly is not of chance, then it is not enough to point out a few points that are troublesome. You must show that statistically, these new data override the previous study that shows the nested relationships should be seen as real.

The only reasonable way to produce a real nested hierarchy is descent with modification ( or a deceptive God)·
Are we not facing the same difficulty here as elsewhere that there is a basic confusion between "proof" and "confirmation?" I don't mean just the difference in the definitions, but a fundamental misunderstanding about the difference between deductive logic and inductive logic. Xianghua attacks the theory of evolution as if it was a discourse of deductive logic, such that if he could break any link, find any fault anywhere, the whole structure must come crashing to the ground.
 
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doubtingmerle

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Are we not facing the same difficulty here as elsewhere that there is a basic confusion between "proof" and "confirmation?" I don't mean just the difference in the definitions, but a fundamental misunderstanding about the difference between deductive logic and inductive logic. Xianghua attacks the theory of evolution as if it was a discourse of deductive logic, such that if he could break any link, find any fault anywhere, the whole structure must come crashing to the ground.
Yes.

And it seems for the theory of evolution, he will not consider anything as adequate. For his own views, no confirmation is required. As long as he can make himself say "not good enough" to evolution with a straight face, that seems to be all he needs.
 
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PsychoSarah

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if there are "many exceptions" then we have many exmaple of non- hierarchy too.
-_- no, the "exceptions" are mostly cases of convergent evolution only confirmed after genetic sequencing or careful examination of the bones is done. You'd be amazed at how many organisms with scientific names haven't been dissected, and far fewer have had their genomes sequenced.

In my molecular biology lab, the students (myself included) are testing if the known gene sequences of various plants are SAMT genes based on sequence similarity to confirmed SAMT genes and by forcing bacteria to integrate the gene (sans introns) and having the bacteria express it. SAMT stands for salicylic acid methyltransferase. If you can't tell from the name, those proteins transfer a methyl group onto salicylic acid, which produces chemicals associated with fragrance from plants (especially flowering ones).
 
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USincognito

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An interesting tidbit here is that the Protoosomes all eat with the hole that forms first in the embryo, using the second hole that develops to expel waste. But the Deuterosomes (us vertebrates and our kin) have it backwards, eating with what most animals would call the anus and sending waste out the end that most animals would call the mouth.

Protostome and Deuterostome literally man "mouth first" and "mouth second". In protostomes the mouth forms first, and in deuterostomes the anus forms first, but I think it's incorrect to say that deuterostomes eat through their anuses.
 
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USincognito

a post by Alan Smithee
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There is no evidence for evolution. It's all a lie.

Uh huh...

How does nested hierarchy prove evolution?

There's no such thing as proof in science. Once we clear that up, we can discuss the evidence for evolution.

And what is this type of response? Where does it get you? Oh, right, NOWHERE.

"I know you are, but what am I" is not a clever a response as you guys think it is.
 
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USincognito

a post by Alan Smithee
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There is no appearance of evolution. It's all made up garbage.

Creationists are long on rhetoric, but short on details and facts. For instance, let's see how you respond to this.

1. Why do you humans and chimpanzees share 203,000 endogenous retroviral insertions? Also why, when we compare humans and chimps with gorillas, and then h/c/g with orangutans and then h/c/g/o with gibbons does the number of shared ERVs decrease?
2. Why do all haplorhine primates including humans share a broken GULO gene for vitamin C production? Why in other beings that have a broken GULO are different exons non-functional?
3. Why do cetaceans have a non-functioning Sonic Hedgehog/Hand2 gene pathway for hind limb development if they never hand hind limbs? Why did marine reptiles like Plesiosaurs, Pliosaurs, Mosasaurs and Ichthyosaurs all have hind limbs, but cetaceans do not?
4. Why do all therian mammals have broken vitellogenin genes for egg yolk sac development?

Evolution explains all of these things. Creationism nor ID does not.
 
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USincognito

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You can believe whatever you want too! Isn't this fun? I know you believe science, created by fallible people, is the 100% absolute truth, despite that fact that it changes constantly. That's okay. I mean, the only thing that "evolves" more than nature, according to your science, are the theories that are created to try and explain it.

More rhetoric. Any chance I'll be seeing any substance as I read more of this thread?

Isn't there evidence that life just suddenly and spectacularly appeared on earth? I think it's called the Cambrian explosion.

No, just no. Life first appears in the Archaean, at least 3.5 billion years ago. The Cambrian explosion happened over the course of 20-50 million years ago and was really more of a situation where hard bodied beings fossilized more easily.

Oh. Apparently we need to start at the basics.

The Cambrian Explosion was over a billion years after the origin of life.

Closer to three billion.
 
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USincognito

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I am Christian so I don't believe this, but if the argument were true then it would have to be admitted that since humans are also animals, it is obvious that some people groups are further up the evolutionary ladder than others. We really do have superior and inferior humans from an evolutionary standpoint. To deny this would be to deny the argument.

Not only are there no humans that are "further up the evolutionary ladder" than other humans, humans aren't "further up the evolutionary ladder" than any other living thing. Every bacteria, mushroom, cactus, scallop, spider, and human is equally evolved.
 
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USincognito

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You don't need to start at the basics. I used to be a staunch atheist and defender of evolution, until I realized how it's 100% mathematically impossible. I understand the basics. I just disagree with them.

And yet your posts are nothing bur frothing screeds against a straw/boogie man version of science and not one of them has addresses a single point of the OP. In light that, you'll forgive us if we're skeptical of you claims about being a "defender of evolution".

So, how about actually addressing the OP?

(Oh, and evolution isn't "mathematically impossible". As soon as someone makes that claim, we know they're not actually familiar with the subject.)
 
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DogmaHunter

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How does nested hierarchy prove evolution?

Because nested hierarchies is the inevitable consequence of a process like evolution, where slightly modified traits are past on to off spring.

This nested hierarchy in life = a family tree

It would tell me that an intelligent God put it in place to ensure life's survival.

Except that this structure doesn't contribute to survival at all.
Having inactive DNA to build teeth while you are a chicken, does not help you as a chicken survive. But in a world where you as a chicken, have evolved from ancestors that actually had teeth - it makes perfect sense to have inactive DNA to build teeth.

They are an evolutionary relic of its distant ancestors.
Life is full of those.

A "designer" would have no use or reason at all to include such structures.
In fact, it would be really inefficient and stupid, to do so.

There are numerous plants and animals that cannot survive or even exist without each other.

Which has nothing to do with the reality of nested hierarchies.
The presence of a nested hierarchy is not a requirement for such symbiosis
Again, the fact of nested hierarchy has no contribution to the survivability of anything.

You take one out of the equation and the other doesn't exist, and vice versa. But sure, they 'evolved'.

Again, this has nothing to do with nested hierarchies.
And evolution provides explanations for such interdependent relationships in an eco-system. This really is not an issue.
 
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DogmaHunter

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The hierarchy doesn't prove evolution in any shape, way, or form.

It confirms / supports it, as such hierarchy is a prediction of evolution theory.
As in: if the evolution process, then nested hierarchy.

It's an inevitable consequence of the evolutionary process. If it didn't factually exist in life, then evolution theory would have to be incorrect.

But it does exist.
Other then in context of evolution, there is no sensible reason at all for this pattern to exist.
 
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DogmaHunter

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I am Christian so I don't believe this, but if the argument were true then it would have to be admitted that since humans are also animals, it is obvious that some people groups are further up the evolutionary ladder than others. We really do have superior and inferior humans from an evolutionary standpoint. To deny this would be to deny the argument.

Evolution is not a ladder and there is no such thing as "more or less" evolved.

Whenever someone says such a thing, they expose that their grasp on the theory is rather lacking.
 
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