Questions about nested Hierarchy

I am assuming that nested hierarchy is identifying the sequences in one creature that are duplicated in a “higher” one. For it to be “Nested” then, I would assume that all the sequences of the first creature are present in the second? If not how is it completely nested?
But, if the method of development is to adjust deform or mutate how can you identify which sequences are genuine and which ones have been deformed? If the complete sequences are all present then there has been no deformation
And,if you have not decoded DNA, how can you be certain that you have the right length of sequence? Or that all the sequences are of the same length? Where one sequence starts and another stops? And, of course, what any particular sequence represents in terms of structure or form?
How can you compare 2 sets of code if you cannot catagorise and decode either of them?

(This is not antagonistic. This is an attempt to understand. Feel free to laugh and mock, I am used to it)

Richard

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No. A nested hierarchy is groups within groups. For example, humans are nested within apes. Apes, monkeys, lemurs, and others are grouped within primates. Primates, cetaceans, bats, and others are grouped within mammals. This forms a tree-like structure. We find that both physical characteristics and sequences follow this tree like structure, the exact structure that we would expect from evolution.

We only have DNA sequences from living species and a few ancient species. We can construct a model of the common ancestral genome by aligning the sequences and finding the consensus. For example:

AATTTGTGGCCC
AATTCGTGGCCC
AATTTGTGGCCC
AATTTGTGGCCC

AATTTGTGGCCC--consensus

In the sequences above, there was only one base in one species that was different. Therefore, our common ancestral model would use the most common base at that position. This is a simplified description since we would also take the actual family tree into consideration as well.

Algorithms are used to determine the best alignment for two or more sets of sequences. The algorithms are able to accommodate for insertions and deletions of sequence, be it within the sequence or at the ends. For example:

I’m not sure what you mean by decode. Do you mean sequence, or something else?

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Nested hierarchy is evidence for continuity in evolution. It does not explain why change takes place and why change goes in certain directions and not others.

The nested hierarchy does tell us a lot about how changes occur. It tells us that changes are random with respect to fitness. If changes were a directed response to challenges then we would see the same adaptations in disparate groups which would do away with the nested hierarchy. For example, if feathers were a directed adaptive response to the need for flight then bats would have feathers, a clear violation of the nested hierarchy. The same would apply to separately created kinds where different design units could be mixed and matched in whatever pattern made sense for the environment.

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It would be good to have a comparison with products of design like cars to show how these have deviated from this nested hierarchy structure.

It may be useful to go over the basics of how genetic inheritance works.

image

Essentially, DNA is copied base by base. The double strand is pulled apart and a new complementary strand is created based on the single strand it is copying.

A few notes on the directionality of DNA and complementary base pairing.

image

You will notice labels that say 5’ and 3’. All copying and transcription occurs in the 5’ to 3’ direction. This means that copying goes in opposite directions once the two strands are separated. Genes can reside on either strand of DNA which means RNA transcription is occurring in different directions within the double stranded genome at any given moment.

Complementary bases are bases that stick to one another due to hydrogen bonding. A sticks to T and C sticks to G. When a DNA strand is copied the complementary bases are placed opposite of each other. For example:


Original DNA
5'--ATTTGGACCTTC--3'
3'--TAAACCTGGAAG--5'

Strands are separated

5'--ATTTGGACCTTC--3'


3'--TAAACCTGGAAG--5'


Strands are copied
5'--ATTTGGACCTTC--3'
3'--TAAACCTGGAAG--5'

5'--ATTTGGACCTTC--3'
3'--TAAACCTGGAAG--5'

Genetic inheritance works by copying DNA and giving a copy to the next generation. However, DNA is not always copied faithfully. For humans, there are about 50 to 100 mutations that occur during the copying process, and those are given to the next generation along with the rest of the copied genome.

DNA in the region of genes looks exactly like the diagrams above. There is nothing physically different about DNA in genes other than the sequence of the bases themselves.

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Playing cards might be a good example. We can treat each card as a species.

Creationists often argue that sharing features is what produces the nested hierarchy, and since each species or kind has a common creator it makes sense that life would fall into a nested hierarchy. We are saying that species could share features and still not fall into a nested hierarchy because a nested hierarchy is a specific pattern of shared features, and it is the pattern that matters, not simply sharing features. For a nested hierarchy, characteristics appear at a node and are found up the rest of the branch:

image

Is that the case with our playing cards which also share characteristics? Let’s see.

First, we have the commonality between all the cards. They are all rectangular, have the same dimensions, and have the same back. The first division is color. There is one branch with black and one with red. So far, so good. What is the next feature? We can divide the reds into hearts and diamonds and the blacks into spades and clubs. Again, so far so good. We still have a branching pattern. How do we further separate the cards so that we end up with single species on their own branch?

This is where we run into problems. The spades, clubs, diamonds, and hearts all have the same ranks (i.e. A, 2, 3, K, Q). This breaks the nested hierarchy of playing cards. We have the same adaptation appearing on separate branches without a node to connect them. Playing cards do not fall into a nested hierarchy even though they share features.

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I am sorry but that would involve abstraction and abstract thought does not appear to be part of the scientific mind. When I was at school, one of the ways to tell whether someone understood was for them to explain it in their own words. Here the modus operandae is to quote wholesale or just link to an authority.
It would appear that you do not need to understand the abstraction of a theory to believe it. Therefore it is very difficult to argue an abstract criticism because they have no idea what you are talking about as has been proved by my attempts to do so on this and another forum.
I actually did a potted evolution of the motor vehicle elsewhere but it was basically ignored, with no replies directly to it. Perhaps we should start a specific thread on abstract criticism of Evolution?

Richard

I see… so with cars something similar would be features where the car companies simply copied features from other designs independent of the previous changes they made to those designs from those of the other car companies. Those would be changes that are not nested. It’s not like animals can look at other animals and think that is a good idea so I will do that too.

And I think a look at examples of parallel evolution would be a good idea in such an explanation also. Apparently the octopus eye is considered an extra-ordinary example of this. Seems a good example for showing how the similarities don’t require the same genetics. Ah here is a paper on the subject.

Exactly. Intuitively, we would probably branch off vehicles by manufacturer, then type of vehicle (i.e. truck, car, SUV), then make, and then model. However, this produces some serious violations of a nested hierarchy, even though all these vehicles share parts. For example, you can find modern Ford Mustangs that have the same engine as a Ford Ranger, a pickup truck. At the same time, two Ford Mustangs will have two different engines. You can find a Chevy sedan and a Ford sedan that have the same tires. You can even find engines shared across manufacturers. There are numerous and obvious violations of a nested hierarchy among vehicles, even though they share parts.

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So the nest is the manufacturer? Not the similarity of parts? And when the engine is changed, how does this relate to evolutionary change? Or is it not comparable (IYO).
So far I am impressed with your abstraction.

Richard

The conclusion appears to be mixed results. In part the study shows that these where not so great an example of parallel evolution and more common ancestry is involved than we thought. But the genetic differences are far larger than the morphological differences.

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As I understand it parallel evolution is where two creatures have an organ with the same function but different design? (for want of a better term) The eye(s) being an obvious example.
So anything parallel denies nesting, yet I saw a nesting sequence that linked reptiles directly to mammals? Surely the metabolic systems are an example of parallel evolution? And here seems to be a “problem”: the nesting theory does not seem to take notice of other parts of the Evolution theory and vice-versa. The study has become so polarised that the proverbial left hand does not know what the right hand has affirmed.

Richard

The nest is the branching pattern of shared features.

Again, it is the PATTERN of shared features that matters here. Take a look at this tree:

image

See where lungs are on the tree? All of the species above lungs on that tree have lungs. The same for the other features. Playing cards and vehicles can’t be arranged in this type of tree where you can put features at one spot on the tree and have that feature in the rest of the branches above that point. Features in playing cards and vehicles are mixed and matched in a way that does not form a tree-like structure.

This isn’t just an abstraction. This is an objective pattern that can be measured.

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The nested hierarchy is about the actual design, not the function. For example, the bird and bat wings have the same function, but they have completely different designs.

Parallel does not deny nesting because the designs are only analogous, not homologous. Nesting occurs among homologous features, not analogous features.

Reptiles and mammals are linked by their common ancestor, so I’m not understanding the problem here.

How so?

What other parts?

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But it is a very simplistic model that does not seem to take all factors into consideration. So that the nest for a vertebrate (spine) starts much earlier? But the addition of legs cannot be successfully inserted because it crosses nests. And your position of feathers? Where do these reptiles that have feathers fit?

Richard

What other factors?

Yes. All of the species on that tree are within the Craniata clade. There are other branches of the vertebrate tree, namely Urochordata and Cephalochordata. You can read more about it here:

ToLWeb

Legs is the name of a function, not an anatomical feature. Insect legs are not homologous to tetrapod legs.

For the tree I showed you, there are no reptiles (as classically categorized) on the branch that has feathers.

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The details of the octopus vs human eye comparison is interesting.

80776-14f3_1o_rev1

So a good portion (69%) of the genes used to make the octopus eye are also used in the making of the human eye. BUT notice that far more genes are actually used in the making of the human eye so that commonality is only actually only 5% of what is actually used in the making of the human eye. To me this suggests that there are far more differences between human and octopus eye than might appear from just looking at the structure

Since this could just be about similarities of living organisms in general, a comparison is made between the similarities of genes used for making the eye and similarities of genes used in making something else (comparing genes used for making the octopus eye with those used for making human connective tissue). The result is that 4 times as many of the same genes are the making of the eye. This tells us that there is some common heritage between the octopus and human eye.

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Possible homologs to homeobox genes (aka Hox genes) are found in Porifera (sponges), so it isn’t surprising that to find similar sets of genes expressed in the descendants of that common ancestor. Another interesting tidbit is hox gene homologs in cnidarians:

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Or that they have the same building blocks.

Commonality does not necessarily mean inheritance. It might just be that there is a building system. But that would rather ruin Nesting Theory. So this suggestion (like many) will be shouted down as preposterous.

Richard

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