The fruit of evolution model ?

[juvenissun]

No, you haven't spelled it out. Please tell me specifically how I can determine the mutation rate just by comparing human and chimpanzee genomes, taking the time from paleontology, but not using the assumption of common descent. What calculation should I make, and why?

The mutation rate changes only slowly, as the biology of the organism changes significantly. If the generation time gets substantially longer, the mutation rate per generation goes up. Beyond that, it doesn't vary too much within mammals, say. DNA replication and repair mechanisms are pretty similar across a wide range of species.

We live longer than chimps. Does that mean our mutation rate is higher than that of chimps? And would chicken have a pretty low mutation rate in comparison?

Does the "generation time" of human change?

-----

OK, now is here a new question: why must you need the the assumption of common descent to calculate the mutation rate? How is that done? I have no idea on how to answer this question.

 

[juvenissun]

I started my summer field work. It is a long one, almost 8 weeks.
I will check this forum whenever the connection is possible.

 

[Papias]

Juvie-

Back around post 88, I had listed several examples from medicine, such as the evolutionary response to the SARS virus, the medical treatment of atavistic mutations, and the understanding of cranial anatomy. Real medical doctors point out that these and so many other medical benefits are a result of an evolutionary understanding. I gave you references to read. Your response was that because you don't understand medicine, the medical doctors must be wrong and you must be right. Your response to a detailed explanation of other benefits from Lucaspa was met with the same response.

In fact, in the link I gave to the United States National Academy of Sciences page, the podcast there (have you listened to it?) has the head of the United States Institutes of Medicine - representing thousands of doctors of all fields of medicine - confirming that evolution is fundamental to the field of medicine, and that it is the key to successful treatment.

I also mentioned benefits outside of medicine, such as the evolutionary generation of new kinds of agricultural crops, feeding literally millions of people - which you ignored.

I didn't mention yet the H1N1 virus, but it too is addressed based on evolutoin, and you can see from the tree of common ancestry below that it isn't just "looking at similarities" in hindsight - the evolution is followed as it happens.

http://mendel.bii.a-star.edu.sg/SEQUENCES/H1N1/Tree_all_NA_subtypes_nr90.jpg

Here is a brief list of some of the examples given of the direct benefits to humans of an understanding of evolution:

1. Atavistic gill pouch treatment and hundreds more similar conditions
2. the SARS virus response
3. Current evolution of the wheat plant to feed millions
4. 2,500 generated new kinds of agricultural crops, again feeding millions of people
5. the H1N1 virus response and tracking
6. the annual flu vaccine

Lucaspa, and others, what other examples have been given?

Lastly, Juvie, I gave a simple example to show how natural selection works. Basically, mutations that result in an organism having more successful descendants naturally increase in the gene pool over those that don't or are harmful. It's really quite simple and I question if you really fail to understand that. You didn't respond to my example, and I can copy and past it up here if you like.

I hope all of this helps, and that your busy summer is going well.

Papias

 

[philadiddle]

To those posting examples of how evolution is used in science:

If you really want to be convincing, I would suggest highlighting how it is "macroevolution", and not "microevolution" that makes evolution useful in the examples you gave. If I were to try to argue some of your examples I would start with "That just works because it uses microevolution."

Just an idea.

 

[Papias]

Well, we could do that, but note that the standard reality denialist response is to claim that all evolution is microevolution. In other words, any example given is simply claimed to be microevolution by going up the biological classification system until a common name can be used to group both creatures.

So, with the classification system being:
Domain
Phylum
Class
Order
Family
Genus
Species

Example: For #2 above, a creationist will simply go up to the Domain level, say "those viruses are still viruses, so it is just meaningless micro evolution", and ignore that example. For #1, the creationist can go up to the phylum level and say: "fish evolving into humans is just a vertebrate evoling into another vertebrate, so that's just microevolution." and so on.

It's sad to see.

Papias

 

[philadiddle]

Well, we could do that, but note that the standard reality denialist response is to claim that all evolution is microevolution. In other words, any example given is simply claimed to be microevolution by going up the biological classification system until a common name can be used to group both creatures.

So, with the classification system being:
Domain
Phylum
Class
Order
Family
Genus
Species

Example: For #2 above, a creationist will simply go up to the Domain level, say "those viruses are still viruses, so it is just meaningless micro evolution", and ignore that example. For #1, the creationist can go up to the phylum level and say: "fish evolving into humans is just a vertebrate evoling into another vertebrate, so that's just microevolution." and so on.

It's sad to see.

Papias

Yes, ad hoc responses will always ensue, and we all know that micro and macro evolution are the same thing. The problem is that the critics think there is a big difference. So highlighting examples that require common ancestors at the highest levels will always be the most effective (lol, it's as though I think you can effectively argue with a creationist).

 

[sfs]

We live longer than chimps. Does that mean our mutation rate is higher than that of chimps?

It's probably been a little higher until recently, since we had modestly longer generation times, although when that started to be the case is completely unknown. Under good conditions, chimpanzees typically live 50-60 years, while humans live 70-80 years. (Today the difference is probably larger, since men are fathering children later than they did 100,000 years ago; mutations rise with male age.) The human lineage probably had somewhat (10% at a guess) fewer generations than the chimpanzee lineage, with a somewhat larger number of mutations per generation. This is one among many uncertainties in the estimate.

And would chicken have a pretty low mutation rate in comparison?

Probably, although I haven't seen an estimate of it. It probably has a lower mutation rate per generation but a higher rate per year, since that's the typical pattern with varying generation times.

Does the "generation time" of human change?

Yes.

OK, now is here a new question: why must you need the the assumption of common descent to calculate the mutation rate? How is that done? I have no idea on how to answer this question.

Because we're calculating the mutation rate by counting genetic differences between humans and chimpanzees. That means we're assuming that all of the differences are the result of mutations over the last 6 million years or so. (Why else would we be doing this comparison?) But it only makes sense for all genetic differences between humans and chimpanzees to be the result of mutations if their genomes were identical 6 million years ago, which is equivalent to saying that they were the same species 6 million years ago.

 

[sfs]

Example: For #2 above, a creationist will simply go up to the Domain level, say "those viruses are still viruses, so it is just meaningless micro evolution", and ignore that example. For #1, the creationist can go up to the phylum level and say: "fish evolving into humans is just a vertebrate evoling into another vertebrate, so that's just microevolution." and so on.

Your latter possibility will never happen. In practice, creationists do not claim that fish evolving into mammals is just microevolution, and no creationist will ever claim that evolution of humans from non-humans is microevolution. The one central, unchangeable requirement (and motivation) for creationism is that humans did not evolve from non-humans. Which is why I tend to focus my examples on humans.

 

[The Lady Kate]

So, with the classification system being:
Domain
Phylum
Class
Order
Family
Genus
Species

When did they change it from "Kingdom" to "Domain"?

 

[gluadys]

When did they change it from "Kingdom" to "Domain"?

Actually, domain was added above kingdom, at least for eukaryotes. Archea, Bacteria and Eukarya are the domains. Within the Eukarya, there are Plant , Fungi and Animal Kingdoms. Protists are Eukarya too, but they are not a monophyletic group like the kingdoms.

 

[Papias]

Thanks Gluadys -

Yep, I forgot "Kingdom".

So the correct list is:

Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species


And yes, I've purposefully cut out subs, intras, supers and such.

Papias

 

[Pete Harcoff]

To those posting examples of how evolution is used in science:

If you really want to be convincing, I would suggest highlighting how it is "macroevolution", and not "microevolution" that makes evolution useful in the examples you gave. If I were to try to argue some of your examples I would start with "That just works because it uses microevolution."

Just an idea.

The example I gave earlier, the discovery of an HIV supressing protein via a gene in the chimp genome is based on common descent (or "macroevolution").

To post it again: The potential significance of adaptive evolution and dimerization in chimpanzee intercellular cell adhesion molecules and EVOLUTIONARY GENOMICS DISCOVERS AIDS SUPPRESSION PROTEIN

The key in this example is not the origin of the genes themselves--as juvenissun seemily tried to dismiss it on eariler--but rather the analysis that led to the discovery of the genes. Essentially the researchers hypothesized that chimps have genes which supress the SIV virus (chimp version of HIV) which probably evolved in the past due to a pandemic. But how do you find those specific genes?

The key is common descent. Rather than using a pairwise comparison--IOW, lining up the genomes side-by-side and just comparing similarities and differences--they used a phylogenetic tree based approach. For those who know a little bit about evolutionary theory, they'd know that phylogenetic trees are trees based on the evolutionary relationships between. This is important because it gives an underlying benchmark to quantify the relative differences between genomes. For example, if two species last shared an ancestor 5 million years ago, you'd expect that on average, they'd have less difference than two species that last shared a common ancenstor 10 million years ago. What this does is give you something to measure against.

From there, they were able to use Ka/Ks ratio analysis (i.e. to determine evidence of positive selection) and a couple tree-based approaches to determine the lineage in which selection took place:

So there it is. Actual application of common descent. It's completely utterly irrefutable evidence that evolutionary biology, including common descent, has practical value in applied biology. Anyone denying this is literally denying basic reality.

 

[juvenissun]

Say hello from Shanghai to everyone.

As the learning and working on geology take over me, There is simply no more room for biology/genetics in my mind. Thanks for the arguments. I am even struggling to keep my daily Bible reading in this fascinating environment.