Rapid Emergence

DogmaHunter

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DogmaHunter

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Is than an example?

I don't understand your question.

Are you asking for an example?

Okay:
- the simpler seed that becomes a more complex tree.
- any chemical reaction that takes simple atoms or molecules and produces more complex compounds as output
- you started out as a single cell. I guess you agree that you have become more complex since then...


So we literally have billions of examples of "simple things" becoming "more complex" over time, without the need of any kind of supernatural intervention.
Instead, physical processes make this happen.
 
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Loudmouth

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OK, that's fine. We can try using those 3.

So, there is some DNA that all 3 share, yes? Let's call that strand A. Then there is DNA that chimps and humans share, but is excluded from gorillas, yes? Let's call that strand B. Finally, the gorilla, chimp, and human have additional DNA that is unique to that species, yes? Let's call those strands G, C, and H (for gorilla, chimp, and human respectively).

So, could we describe our 3 sample species as:
gorilla = AG
chimp = ABC
human = ABH
Does that work?

You would use the same strand for all comparisons, one from each species. What differs is the base sequence of those strands. So at any one position in those strands two species may or may not match. For example:

basics_18_1.jpg
 
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Resha Caner

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You would use the same strand for all comparisons, one from each species. What differs is the base sequence of those strands. So at any one position in those strands two species may or may not match. For example:

basics_18_1.jpg

OK, maybe "strand" was a poor choice of words. Maybe it would be better to use a more generic term such as "sets". Therefore, in your above example, position 34 (if I counted correctly) is common to all 3 species so it would go into one set. However at position 35, the chimp has a unique base, so it would go into a different set.

With that said, I wasn't thinking the sets would be created at the base level. After all, doesn't each organism have a unique sequence? I was thinking we were comparing species, not organisms. As such, it seems we would need to use a higher level comparison to create sets of similarities and differences.

(edit) FYI, I leave for vacation on Wednesday and I don't know what my Internet access will be like. I expected this thread was going to die before now, but if it continues, the discussion may have to wait until I get back.
 
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Loudmouth

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OK, maybe "strand" was a poor choice of words. Maybe it would be better to use a more generic term such as "sets". Therefore, in your above example, position 34 (if I counted correctly) is common to all 3 species so it would go into one set. However at position 35, the chimp has a unique base, so it would go into a different set.

Those are actually codons. It is actually helpful to categorize these differences with reference to codons since synonymous and non-synonymous mutations have different implications for the theory of evolution.

https://en.wikipedia.org/wiki/Synonymous_substitution

Also of note, only a tiny fraction (~2%) of the human genome is made up of codons. The vast majority is not translated into protein.

With that said, I wasn't thinking the sets would be created at the base level. After all, doesn't each organism have a unique sequence? I was thinking we were comparing species, not organisms. As such, it seems we would need to use a higher level comparison to create sets of similarities and differences.

If there is just one base difference in 3 billion bases, that would still be a unique genome.

(edit) FYI, I leave for vacation on Wednesday and I don't know what my Internet access will be like. I expected this thread was going to die before now, but if it continues, the discussion may have to wait until I get back.

I am more in the mode of helping you understand how genetics works. I will be glad to answer your questions at whatever pace they appear. Have a nice vacation!!
 
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Resha Caner

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Also of note, only a tiny fraction (~2%) of the human genome is made up of codons. The vast majority is not translated into protein.

If it's part of what makes a gorilla a gorilla (as biologists distinguish the species from chimps & humans), then let's include it. If not, let's exclude it.

Those are actually codons.

Each set of 3 bases - sure.

It is actually helpful to categorize these differences with reference to codons since synonymous and non-synonymous mutations have different implications for the theory of evolution.

It's more than just these 2 isn't it? There's quite a long list of mutation mechanisms, though it seems they can be grouped into 3 categories: substitution, gain, and loss.

So are there differences due to synonomous mutations of the genome of gorillas and chimps that are considered part of what distinguishes those 2 species?

If there is just one base difference in 3 billion bases, that would still be a unique genome.

Well, yes, but your tree doesn't show a branch for Koko. It shows a branch for gorillas, so I assume biologists have some way of identifying the population of gorillas as unique compared to the population of chimps. That's what I'm after. I was going to write it out this way:

U->AP---------->AG
U->AP->ABQ->ABC
U->AP->ABQ->ABH

In addition to the sets I noted earlier (A,B,G,C,H), I've added U (universal ancestor), P (vertex of the first branch), and Q (vertex of the second branch).
 
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Loudmouth

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If it's part of what makes a gorilla a gorilla (as biologists distinguish the species from chimps & humans), then let's include it. If not, let's exclude it.

Then we are probably looking at about 10% of each genome for the apes (including humans). There are still DNA binding motifs, histone binding regions, transcription factors, RNA genes, and other features that are not made up of codons, nor are they translated into proteins.

It's more than just these 2 isn't it? There's quite a long list of mutation mechanisms, though it seems they can be grouped into 3 categories: substitution, gain, and loss.

Those are different categories. Synonymous and non-synonymous refer to the amino acid sequence of the protein. If a mutation does not change the amino acid sequence, then it is a synonymous mutation (i.e. it means the same thing). Some substitutions will be synonymous mutations, and all indels (i.e. gains/losses) will be non-synonymous.

So are there differences due to synonomous mutations of the genome of gorillas and chimps that are considered part of what distinguishes those 2 species?

Depends on what you are talking about. If you are talking about purely DNA sequence, then any difference in the genome can be used. If you are talking about phenotypic differences, then probably not. Most scientists consider the vast majority of synonymous mutations to be incapable of changing the phenotype of the carrier.

Well, yes, but your tree doesn't show a branch for Koko.

If we had enough DNA data, there could be.

It shows a branch for gorillas, so I assume biologists have some way of identifying the population of gorillas as unique compared to the population of chimps.

Mutations found in one species but not in another are considered a way of identifying one population from another. These are most often differences that exist in a large percentage of the population.

That's what I'm after. I was going to write it out this way:

U->AP---------->AG
U->AP->ABQ->ABC
U->AP->ABQ->ABH

In addition to the sets I noted earlier (A,B,G,C,H), I've added U (universal ancestor), P (vertex of the first branch), and Q (vertex of the second branch).

Not sure where you have the branches, or if you have any branches at all. Also, I don't know what those letters are supposed to represent.
 
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Resha Caner

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Mutations found in one species but not in another are considered a way of identifying one population from another. These are most often differences that exist in a large percentage of the population.

I don't think I follow. I think of a mutation as a change in a sequence, which implies a change from some baseline. So where are you starting from? You pick Koko the gorilla and sequence her DNA. Then you pick some other organism and sequence its DNA. Do you decide this organism is a gorilla before or after you sequence its DNA?

Not sure where you have the branches, or if you have any branches at all. Also, I don't know what those letters are supposed to represent.

I was showing the 3 lines of descent for your tree: the populations of gorillas (line 1 = L1), chimps (line 2 = L2), and humans (line 3 = L3). At Generation 0 there is only one population, denoted as U:

L1: U
L2: U
L3: U

The arrow (->) indicates descent. So, we reach a point where the first divergence of populations occurs. The letter "A" represents what will remain common between these two lines and the letter "P" represents what will diverge between these two lines:

L1: U->AP
L2: U->AP
L3: U->AP

For line 1, "P" mutates into "G" (the gorilla). For the other branch, "P" mutates into "BQ", where "B" represents what will remain common and "Q" represents what will diverge:

L1: U->AP->AG
L2: U->AP->ABQ
L3: U->AP->ABQ

For line 2, "Q" mutates into "C" (the chimp). For line 3, "Q" mutates into "H" (the human):

L1: U->AP--------->AG
L2: U->AP->ABQ->ABC
L3: U->AP->ABQ->ABH

As to whether the letters represent the associated codons or something else will need your help to determine.
 
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Loudmouth

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I don't think I follow. I think of a mutation as a change in a sequence, which implies a change from some baseline.

That's correct. The baseline in this case is the common ancestor. Let's say we have this situation for all of the apes (including humans)

ATATTCTCATGCTTT Homo
ATATTCGCATGCTTT Pan
ATATTCGCATGATTT Gorilla
ATATGCGCATGCTTT Pongo


That red T in the human sequence would be the lineage specific mutation because the consensus sequence has a G in that position. The consensus sequence represents the common ancestor. The red A in the gorilla sequence is a gorilla specific mutation. The red G in the orangutan sequence is an orangutan specific mutation. See how that works? It is not as if one lineage branches off and stops evolving.
So where are you starting from? You pick Koko the gorilla and sequence her DNA. Then you pick some other organism and sequence its DNA. Do you decide this organism is a gorilla before or after you sequence its DNA?

We usually already know which individuals belong to which species.

I was showing the 3 lines of descent for your tree: the populations of gorillas (line 1 = L1), chimps (line 2 = L2), and humans (line 3 = L3). At Generation 0 there is only one population, denoted as U:

That would be three separate blades of grass, not a tree.
 
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Resha Caner

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That's correct. The baseline in this case is the common ancestor.

OK, but it seems you're saying you don't actually have physical DNA evidence for the common ancestor. You're just assuming the common DNA came from the common ancestor.

It is not as if one lineage branches off and stops evolving.

Sure. I didn't mean to imply it would. For example, my "G" code for the gorilla line is meant to imply whatever is unique about the gorilla, changing or not. So, "G" can change over time. The only part I was saying would remain constant is the "A" set, which was inherited by all 3 species from their common ancestor.


We usually already know which individuals belong to which species.

OK, that's a new wrinkle. So you're selecting populations based on their morphology. I knew that was the practice at one time, but I thought it was fading away in favor of DNA identification.

That would be three separate blades of grass, not a tree.

No. I guess you're still not understanding my symbols. I'm using it simply to overcome the limitations of CF - as a means for communicating with simple text. I would much rather draw it ... the picture in my head looks like a subway map. Anyway ...

Anywhere the same letter appears, it is meant to indicate identity. So, the U in L1, L2, and L3 is identical. In other words, at that time, there is only 1 line - 1 population - 1 species. At that point L1, L2, and L3 are indentical. The same is true of AP. So, from U to AP there is 1 line.

After AP it diverges into 2 lines (AG and ABQ). Then ABQ splits again into ABC and ABH so the tree finishes with 3 lines. Is that more clear or will I have to mail you a picture?
 
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SkyWriting

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I don't understand your question.

Are you asking for an example?

Okay:
- the simpler seed that becomes a more complex tree.
- any chemical reaction that takes simple atoms or molecules and produces more complex compounds as output
- you started out as a single cell. I guess you agree that you have become more complex since then...


So we literally have billions of examples of "simple things" becoming "more complex" over time, without the need of any kind of supernatural intervention.
Instead, physical processes make this happen.


Ok. But 1 and 3 are no more complex than the original design or pattern. When I was a single cell, the entire
amount of information or coding needed was in that cell. Not one cell in my body can repeat that task.
#2 has potential because I've forgotten much of my chemistry due to lack of use.

Can anyone give a chemical example of increased complexity?
 
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Resha Caner

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To help, I drew out the tree and placed the text representation next to it.
http://www.christianforums.com/media/tree.53111/

The original tree you posted is on the left. Per the variables as I defined them, I can see at least 2 ways to draw the tree. I show one alternative on the right.
 
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Loudmouth

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OK, but it seems you're saying you don't actually have physical DNA evidence for the common ancestor. You're just assuming the common DNA came from the common ancestor.

It's not so much an assumption as it is a conclusion from mountains of data. The fact that a comparison between species produces a strong phylogenetic signal is evidence that the shared DNA between those species came from a common ancestor.

If you want a term with less baggage, you could use the term "consensus sequence" which is the base that is found in the majority of species at a specific position.

Sure. I didn't mean to imply it would. For example, my "G" code for the gorilla line is meant to imply whatever is unique about the gorilla, changing or not. So, "G" can change over time. The only part I was saying would remain constant is the "A" set, which was inherited by all 3 species from their common ancestor.

Humans and chimps may not have inherited A because it could have changed between the time of the gorilla branching off and chimps branching off.

OK, that's a new wrinkle. So you're selecting populations based on their morphology. I knew that was the practice at one time, but I thought it was fading away in favor of DNA identification.

We are selecting them based on who they mate with. Once you have a large enough sequence database, you can identify by DNA.

No. I guess you're still not understanding my symbols. I'm using it simply to overcome the limitations of CF - as a means for communicating with simple text. I would much rather draw it ... the picture in my head looks like a subway map. Anyway ...

Anywhere the same letter appears, it is meant to indicate identity. So, the U in L1, L2, and L3 is identical. In other words, at that time, there is only 1 line - 1 population - 1 species. At that point L1, L2, and L3 are indentical. The same is true of AP. So, from U to AP there is 1 line.

After AP it diverges into 2 lines (AG and ABQ). Then ABQ splits again into ABC and ABH so the tree finishes with 3 lines. Is that more clear or will I have to mail you a picture?
Thanks for the diagram. What are the letters representing, and why did you choose those specific letters? Why isn't AP or ABP the common ancestor? Why does ABQ become AG?
 
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whois

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No. I guess you're still not understanding my symbols. I'm using it simply to overcome the limitations of CF - as a means for communicating with simple text. I would much rather draw it ... the picture in my head looks like a subway map. Anyway ...
how about drawing it in paint, then uploading it in a zip folder?
 
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DogmaHunter

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Ok. But 1 and 3 are no more complex than the original design or pattern. When I was a single cell, the entire
amount of information or coding needed was in that cell. Not one cell in my body can repeat that task.
#2 has potential because I've forgotten much of my chemistry due to lack of use.


If you are going to argue that the level of "chemical complexity" in a full grown animal or plant, composed of gazillions of interconnected cells, is the same as the "chemical complexity" of a single cell or seed....



Then I'm going to have to ask you to define what you mean by "complexity"....

Can anyone give a chemical example of increased complexity?

Any chemical reaction that takes simple atoms/molecules as input and produces a bigger molecule as output.
 
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Loudmouth

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When I was a single cell, the entire
amount of information or coding needed was in that cell.

When you define a single cell as being complex, you pretty much lost the argument.

Can anyone give a chemical example of increased complexity?

The Miller-Urey experiment is a fine example. They started with water, nitrogen, hydrogen, ammonium, and methane. These are all simple chemicals. What the experiment produced was amino acids and nucleotide bases which are very complex.

imagesCAV08ZBU.jpg
 
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Resha Caner

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If you want a term with less baggage, you could use the term "consensus sequence" which is the base that is found in the majority of species at a specific position.

Yeah, I like that term. It seems less theory-laden.

Humans and chimps may not have inherited A because it could have changed between the time of the gorilla branching off and chimps branching off.

Well, all 3 species supposedly inherited something from their ancestor didn't they? Whatever DNA they were supposed to have inherited, I'm calling it "A".

We are selecting them based on who they mate with.

OK.

Thanks for the diagram. What are the letters representing, and why did you choose those specific letters?

The letters represent what can possibly be inherited by a descendent. The letter choices are arbitrary. I just tried to choose some convenient ones like "G" for gorilla, "C" for chimp, and "H" for human.

Why isn't AP or ABP the common ancestor?

Well, those are the most recent ancestors. U is a distance ancestor. Then things change over time, and at the point of divergence the most recent ancestor is AP (or ABP).

Why does ABQ become AG?

Remember I noted 3 general groups of mutation processes: substitution, gain, and loss. So, the gorilla inherits A from its ancestors. B is lost (and/or substitution occurs). Q changes into G via substitution and/or gain.
 
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Loudmouth

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Well, all 3 species supposedly inherited something from their ancestor didn't they? Whatever DNA they were supposed to have inherited, I'm calling it "A".

That is always going to be a retroactive conclusion because the amount of DNA that you inherit from the common ancestor decreases with time. The amount of DNA that orangutans, gorillas, humans, and chimps inherited from their common ancestor is much less than what humans and chimps inherited from their common ancestor.

The letters represent what can possibly be inherited by a descendent.

Then all branches connected to a letter should also have that letter. Using the left tree from your hand drawn diagram (which was very helpful, btw), we will go from bottom to top, left to right. Above U you have AP. One tier above AP, left to right, you should have APB at that single node. At the top tier left to right, you should have APG, APBC, and APBH.

Well, those are the most recent ancestors. U is a distance ancestor. Then things change over time, and at the point of divergence the most recent ancestor is AP (or ABP).

Those changes are also inherited by those further along the branch. I think that is what you forgot to include.

Remember I noted 3 general groups of mutation processes: substitution, gain, and loss. So, the gorilla inherits A from its ancestors. B is lost. Q changes into G via substitution and/or gain.

The problem is that B is going to be millions of mutations, so I don't see how they could all be lost with such precision. I would only expect a very tiny minority of B to be lost to indels because they are much more likely to happen elsewhere in the genome.
 
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Resha Caner

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That is always going to be a retroactive conclusion because the amount of DNA that you inherit from the common ancestor decreases with time.

Sure. But it is what it is. Whatever came from that distant ancestor is "A".

The problem is that B is going to be millions of mutations, so I don't see how they could all be lost with such precision. I would only expect a very tiny minority of B to be lost to indels because they are much more likely to happen elsewhere in the genome.

First, I noted that in the case of the gorilla B could have either changed or been lost. And I could have made a mistake - I may need to add some additional variables. But, with that said, my understanding is that loss in primates may be quite high. See, for example: "Accelerated Rate of Gene Gain and Loss in Primates" by Hahn, Demuth, and Han.

Then all branches connected to a letter should also have that letter. Using the left tree from your hand drawn diagram (which was very helpful, btw), we will go from bottom to top, left to right. Above U you have AP. One tier above AP, left to right, you should have APB at that single node. At the top tier left to right, you should have APG, APBC, and APBH.[/quote]

As I said, I might have made a mistake, but I don't think your version is correct either. What would really help is if you could watch me draw the diagram.

how about drawing it in paint, then uploading it in a zip folder?

Yeah, maybe I'll try that. I think I'll have to show the diagram being built up in stages and with color. I'll see if I have time to do that before my plane leaves for vacation.
 
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