What does having 96% chimp dna mean to you?

pitabread · Dec 26, 2017

rjs330 said:
The difference is obvious. Common design fits scriptures creation. Evolution from a common ancestor does not.

Describing the difference with respect to a particular interpretation of a particular religious text isn't particularly useful. Especially since yours is hardly the only interpretation and many are able to reconcile the concept of biological evolution with the Christian scriptures.

What you need to do is describe the differences with respect to biology. Can you do that?

Just like common design fits well with the building of cities. You can easily look at a city and find common designs used to build tall, short, long or wide buildings. They do not all look alike but all contain similar features and architecture that is needed for them to stand and be functional even though they may have a myriad of differing purposes.

Have you ever been to a city?

I can't speak to where you live, but where I live I see all sorts of variety in my city that hardly points to "common design". Whether it's different construction techniques, materials, architectural designs, you name it, it speaks to changing building standards and construction processes over time and, get this, different designers.

Of all the things you could have picked as an analogy for "common design" buildings and architecture is probably one of the worst.

Noxot · Dec 27, 2017

pitabread said:
Pretty sure that made up fantasy objects like "self replicating cars" don't have scientific implications for anything.

Though maybe you could write the plot for the next Transformers movie...

give it a few years and there will be self replicating robots.

Noxot · Dec 27, 2017

bhsmte said:
Agree.

Typically, when well evidenced science threatens a tightly held faith belief, that evidence, will only be accepted, when it becomes too painful to keep the defense mechanisms churning and ignoring the same. Right now, it is too painful to acknowledge their faith belief is wrong, or at least needs to be adjusted, so those defense mechanisms are in overdrive.

and you too are human and go through such things. I want to see scientist test atheist. I am sure that atheist tend to think of themselves as rational and intelligent beings. yet your guys tribe can get pretty serious with jumping on someone who gives a pov that does not align with your own systems of thinking. so I would say you are not immune from the same brain functions that you share with everyone else. at what point does "show me a citation" become cognitive dissonance and a defensive reaction?

Neuromodulation of group prejudice and religious belief | Social Cognitive and Affective Neuroscience | Oxford Academic

mark kennedy · Dec 27, 2017

sfs said:
You've never explained why it should destroy the host. Healthy humans are known to have mutations up to 3 million base pairs long. So how could it be impossible?

You got to be putting me on.

xianghua · Dec 27, 2017

sfs said:
I said that transposon insertions shouldn't be scattered randomly throughout a phylogenetic tree. They're not, as the papers you cite themselves indicate.

they actually saying the opposite:

An ancient retrovirus-like element contains hot spots for SINE insertion. - PubMed - NCBI

"We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry."

or:

Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life | Systematic Biology | Oxford Academic

"Despite the reasons to expect RGCs to be perfect homoplasy-free characters, many different RGCs can exhibit homoplasy (Ray et al. 2006, Gibb et al. 2007)."

so we indeed find many cases that contradict the phylogenetic tree. in this case they "solve" the problem by convergent insertions.

sfs said:
Then your comment is off-topic. I'm talking about reality, not your latest imaginary scenario. On this planet, studying the human species that actually lives here, I was able to use common descent to correctly infer something about human biology. What would happen on your imaginary world with 10 million year old human populations is not relevant.

again: you just assume that human and chimp share a common descent. assuming something isnt evidence you know.

sfs said:
Still sorry -- I agreed to talk about science, not about another one of your imaginary worlds.

fine. do you agree that the similarity between chimp and human may point to a common designer rather then common descent?

xianghua · Dec 27, 2017

pitabread said:
If species on Earth really were the product of a designer creating them independently, I would expect to find a whole host of chimeric organisms like these. Yet, we don't.

you mean something like that?:

Sea Slug Steals Photosynthesis Genes From Algae

evolution is false now?

sfs · Dec 27, 2017

rjs330 said:
Exactly what kind of mutations were you looking at? No one here is arguing that mutations do not occur. Much like the moth that mutated it's coloring. I think we can all agree that stuff like that occurs. What we disagree with is the mutations being so strong that it creates a new creature eventually. Like the common ancestor eventually evolving into us. It's nonsense and unobservable and can't be shown to ever have occurred. In fact there is no evidence of any kind of change like that.

It doesn't matter what kind of mutations they were. The point is that the genetic differences between humans and chimpanzees are the result of accumulated mutations. in other words, our ancestors and the ancestors of chimps and gorillas were once identical.

Bugeyedcreepy · Dec 27, 2017

xianghua said:
i asked you a simple question about nested hierarchy to test this idea: are you saying that if common descent is false (and common design is true) we should find cases that violate the nested hierarchy? (like a rabbit with a jellyfish gene in this case). yes or no?

Yes.

xianghua said:
we also observe non-hierarchy. so this claim isnt completely true.

Where? The citations you provide don't say this.

xianghua said:
not realy. since the best explanation for the existence of a robot\spinning motor is design rather then a natural process (see my signature link). so accodring to Occam's Razor the design is still the best explanation. with or without hierarchy.

Except Occam's Razor would agree that the addition of a designer and reasons why a designer would be restricted to the exact same outcome that Common Descent would specifically require, means that Common Descent would be the logical choice, not Common Design with all the extra unfounded and unevidenced assumptions required.

xianghua said:
its only a belief rather then science. since we cant test it.

Your ignorance doesn't refute the science. Plenty of Scientists have, and still do test this.

[Staff edit].

sfs · Dec 27, 2017

mark kennedy said:
You got to be putting me on.

Putting you on about what? About the existence of 3 million base pair variants in humans? "The copy number variation (CNV) map of the human genome catalogues benign CNVs among presumably healthy individuals of various ethnicities. The current map includes microscopic and submicroscopic variants from 50 bp to 3 Mb." (From "A copy number variation map of the human genome", Nature Reviews Genetics 16, 172–183 (2015).)

sfs · Dec 27, 2017

xianghua said:
they actually saying the opposite:

No, this is what they're saying: "The presence of a retrotransposon at a single locus in multiple taxa remains an extremely powerful phylogenetic marker, but caution is required before concluding that the existence of a particular SINE at a particular locus in multiple individuals is indicative of common ancestry." "Extremely powerful phylogenetic marker" means the opposite of "randomly distributed throughout the tree".

xianghua said:
or:

Are Transposable Element Insertions Homoplasy Free?: An Examination Using the Avian Tree of Life | Systematic Biology | Oxford Academic

"Despite the reasons to expect RGCs to be perfect homoplasy-free characters, many different RGCs can exhibit homoplasy (Ray et al. 2006, Gibb et al. 2007)."

What they actually say: "TE insertions retain a strong phylogenetic signal and have substantial potential for phylogenetic analyses. They exhibit very little homoplasy (Fig. 2); the retention index (RI) of TE insertions on the Hackett et al. (2008) tree is 0.97, much greater than that of Hackett et al. (2008) sequence data on the same tree (RIintron = 0.52, RIcoding exons = 0.54, RIUTR = 0.58)."

xianghua said:
so we indeed find many cases that contradict the phylogenetic tree. in this case they "solve" the problem by convergent insertions.

Yeah, they solve it by pointing to a process that actually happens. Whereas you deal with the extremely strong phylogenetic signal from transposons by ignoring it.

xianghua said:
fine. do you agree that the similarity between chimp and human may point to a common designer rather then common descent?

No. A common designer provides no explanation for the patterns we actually see when comparing human and chimpanzee DNA. If you recall, the last time I showed you some of the patterns, you offered the solution that human and chimpanzee DNA was originally nearly identical. You never did explain why human DNA shows the same patterns when compared to orangutans or with monkeys.

FrumiousBandersnatch · Dec 27, 2017

Noxot said:
...at what point does "show me a citation" become cognitive dissonance and a defensive reaction?

Asking for a citation is asking for authoritative support for a claim; how does that relate to cognitive dissonance or defensive reaction?

Note that it's not uncommon for believers to ask for scriptural references when a scriptural claim is made.

Seems like reasonable standard practice.

mark kennedy · Dec 27, 2017

sfs said:
Putting you on about what? About the existence of 3 million base pair variants in humans? "The copy number variation (CNV) map of the human genome catalogues benign CNVs among presumably healthy individuals of various ethnicities. The current map includes microscopic and submicroscopic variants from 50 bp to 3 Mb." (From "A copy number variation map of the human genome", Nature Reviews Genetics 16, 172–183 (2015).)

That's variation and while I'm a little shocked, especially that it could include up to 100 genes. We are talking about inheritable changes permanently fixed, throughout our species. It's always puzzled me a bit that HAR1f while highly conserved over 300 million years appears in a unique human sequence. Mutations and variations are one thing, adaptive evolution is another thing and adaptive evolution from random mutations is another thing entirely. I'll try to track down the paper, kind of curious was a mutation 3 million base pairs long looks like in detail.

bhsmte · Dec 27, 2017

Noxot said:
and you too are human and go through such things. I want to see scientist test atheist. I am sure that atheist tend to think of themselves as rational and intelligent beings. yet your guys tribe can get pretty serious with jumping on someone who gives a pov that does not align with your own systems of thinking. so I would say you are not immune from the same brain functions that you share with everyone else. at what point does "show me a citation" become cognitive dissonance and a defensive reaction?

Neuromodulation of group prejudice and religious belief | Social Cognitive and Affective Neuroscience | Oxford Academic

True, everyone is prone to bias.

The point I was making was specific though and that is when certain personal faith beliefs, are contradicted by inconvenient facts.

bhsmte · Dec 27, 2017

Noxot said:
and you too are human and go through such things. I want to see scientist test atheist. I am sure that atheist tend to think of themselves as rational and intelligent beings. yet your guys tribe can get pretty serious with jumping on someone who gives a pov that does not align with your own systems of thinking. so I would say you are not immune from the same brain functions that you share with everyone else. at what point does "show me a citation" become cognitive dissonance and a defensive reaction?

Neuromodulation of group prejudice and religious belief | Social Cognitive and Affective Neuroscience | Oxford Academic

Asking for independent evidence to support someone's claim, is nowhere near cognitive dissonance. Cognitive dissonance, happens when independent evidence is presented and it contradicts someone's beliefs.

xianghua · Dec 27, 2017

sfs said:
No, this is what they're saying: "The presence of a retrotransposon at a single locus in multiple taxa remains an extremely powerful phylogenetic marker, but caution is required before concluding that the existence of a particular SINE at a particular locus in multiple individuals is indicative of common ancestry." "Extremely powerful phylogenetic marker" means the opposite of "randomly distributed throughout the tree".

they also said that: "Our results also suggest that TEs should not be viewed as perfect characters exempt from homoplasy. Instead, TE insertions present many of the same challenges for phylogenetic analyses as other types of data, such as nucleotide sequences."

i also gave you this example:

Mosaic retroposon insertion patterns in placental mammals

as the author admit:

"Thus, to date, even retroposon insertion patterns have not satisfactorily resolved the basal split of placental mammals."

so they arent "Extremely powerful phylogenetic marker" in this case.

and they 'solve" it by hybridization or incomplete lineage sorting. in other words: when the data doesnt fit with the theory we made up another theory. this isnt a scientific approach.

there is also this case:

Bats and horses get strangely chummy

“I think this will be a surprise for many scientists,” says Norihiro Okada at the Tokyo Institute of Technology, Japan. “No one expected this.”

"Okada and his colleagues looked at genetic mutations caused by retroposons, lengths of DNA that can copy themselves into RNA and then reverse-copy themselves back into DNA at a different location on a chromosome. Closely related species share more of these mutations than more distant relatives. The analysis by Okada’s team forces a rethink of the relationships of many mammalian orders, which are currently classified by morphological and nuclear DNA sequence data."

sfs said:
No. A common designer provides no explanation for the patterns we actually see when comparing human and chimpanzee DNA. If you recall, the last time I showed you some of the patterns, you offered the solution that human and chimpanzee DNA was originally nearly identical. You never did explain why human DNA shows the same patterns when compared to orangutans or with monkeys.

since their both genomes are already near identical i dont see any problem to claim they were even more similar in the past. more than that: scientists also assume that human and chimp split off about 6-7 my ago. so their assumption base on the molecular clock. the problem is that the molecular clock itself can be unreliable:

Turn back the molecular clock, say Argentina's plant fossils | Penn State University

"The researchers are not certain why there is strong directional bias in these molecular clock dates."
The inaccuracy of the molecular clocks in this study raises new doubts about the accuracy of clock dates for many other organisms, from animals to human pathogens."

sfs · Dec 27, 2017

mark kennedy said:
That's variation and while I'm a little shocked, especially that it could include up to 100 genes. We are talking about inheritable changes permanently fixed, throughout our species.

So if it is seen only in some humans, it doesn't count because it's variation, while if it's seen in all of them, that's a difference between humans and chimpanzees and couldn't possibly be the result of a mutation?

Face it: your argument depends on large CNVs always being highly deleterious, and I've just given you solid evidence that they aren't.

mark kennedy · Dec 27, 2017

sfs said:
So if it is seen only in some humans, it doesn't count because it's variation, while if it's seen in all of them, that's a difference between humans and chimpanzees and couldn't possibly be the result of a mutation?

Face it: your argument depends on large CNVs always being highly deleterious, and I've just given you solid evidence that they aren't.

That's never been my argument, my argument is that mutations are either neutral or when they have an effect strong enough for selection to act the overwhelming majority of the time they are deleterious. I was unaware of a mutation millions of base pairs involving up to a hundred genes were documented, but these, as far as I can tell, are neutral and certainly not permanently fixed. It's interesting Steve, that's what I've always appreciated about your posts, you sometimes throw out interesting information like that. Variation on this scale doesn't necessarily mean permanently fixed and I suspect is cyclical.

I see your point, I'm not that hard headed. They will be highly deleterious if they have any effect at all the vast majority of the time.

46AND2 · Dec 27, 2017

mark kennedy said:
That's never been my argument, my argument is that mutations are either neutral or when they have an effect strong enough for selection to act the overwhelming majority of the time they are deleterious. I was unaware a mutation millions of base pairs involving up to a hundred genes were documented, but these, as far as I can tell, are neutral and certainly not permanently fixed. It's interesting Steve, that's what I've always appreciated about your posts, you sometimes throw out interesting information like that. Variation on this scale doesn't necessarily mean permanently fixed and I suspect is cyclical.

I see your point, I'm not that hard headed. They will be highly deleterious if they have any effect at all the vast majority of the time.

Don't you think in smaller populations of organisms, variations like this could more easily become fixed?

mark kennedy · Dec 27, 2017

46AND2 said:
Don't you think in smaller populations of organisms, variations like this could more easily become fixed?

I don't know that they become fixed at all, this is the first I've seen of mutations on this scale. Still haven't seen the paper yet and considering if they are cumulative or cyclical. We can speculate I guess but it's been my experience, any mutation or adaptation being permanently fixed is a very big deal. Not to be taken lightly and certainly not to be assumed. That said in a smaller population there might be some kind of a founder effect but I've never really seen that on this scale. Even with my limited purview, that seems rare at best.

46AND2 · Dec 28, 2017

mark kennedy said:
I don't know that they become fixed at all, this is the first I've seen of mutations on this scale. Still haven't seen the paper yet and considering if they are cumulative or cyclical. We can speculate I guess but it's been my experience, any mutation or adaptation being permanently fixed is a very big deal. Not to be taken lightly and certainly not to be assumed. That said in a smaller population there might be some kind of a founder effect but I've never really seen that on this scale. Even with my limited purview, that seems rare at best.

Why would a fixed adaptation or mutation be a "very big deal?"

What does having 96% chimp dna mean to you?

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