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#41 gilbo12345

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Posted 03 December 2012 - 05:56 AM

Another point is that we actually have neanderthal genes and they are way different than human DNA. Posted Image The Green is human human differences, the red is human neanderthal differences, and the blue is human chimp differences. http://www.talkorigi...homs/mtDNA.html


Really....

At roughly 3.2 billion base pairs,[3] the Neanderthal genome is about the size of the modern human genome. According to preliminary sequences, 99.7% of the base pairs of the modern human and Neanderthal genomes are identical, compared to humans

Additionally, in 2010, the announcement of the discovery and analysis of Mitochondrial DNA (mtDNA) from the Denisova hominin in Siberia revealed that this specimen differs from that of modern humans by 385 bases (nucleotides) in the mtDNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases.

#42 aelyn

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Posted 03 December 2012 - 06:33 AM

Really.... At roughly 3.2 billion base pairs,[3] the Neanderthal genome is about the size of the modern human genome. According to preliminary sequences, 99.7% of the base pairs of the modern human and Neanderthal genomes are identical, compared to humans Additionally, in 2010, the announcement of the discovery and analysis of Mitochondrial DNA (mtDNA) from the Denisova hominin in Siberia revealed that this specimen differs from that of modern humans by 385 bases (nucleotides) in the mtDNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases.


Right, and the next sentence in that paragraph (from the Wikipedia page for the Neanderthal Genome Project) is : "In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs."

Interestingly the article those numbers come from is also linked to in the Wikipedia page, here it is :
http://www.nature.com/nature/journal/v464/n7290/full/nature08976.html
I hope everyone can access it, it's under a Creative Commons license so I assume so.

As it turns out in their comparison they used 54 human genomes and one genome from a modern human fossil from the Pleistocene; here is the graph they get on the pairwise comparisons between all those human, Denisovan and Neanderthal genomes :
http://www.nature.com/nature/journal/v464/n7290/fig_tab/nature08976_F2.html

I assume there are two maxima for "Human-Human comparisons" because one of them is the Pleistocene human genome. But for those who can't see the graph, here are the nucleotide differences they get for all those comparisons :

Modern human/Modern human : 0-70 for present-day humans, 70-105 for the Pleistocene human (with some overlap)
Modern human/Neanderthal : 180-220
Modern human/Denisovan : 370-400
Modern human/Chimpanzee : 1462 (not on the graph so I don't have the range)

Both Neanderthals and Denisovans are clearly distinct from modern humans in this comparison, and Denisovans are not only almost twice as different from us as Neanderthals are, they're less than a fourth more different from us than Chimpanzees are.

EDIT : Actually considering the number of comparisons involved in the two human/human maxima and the phylogenetic tree they also show it doesn't seem likely it represents that single Pleistocene human's genome; it might be a Central Africa/vs Eurasia thing instead. Either way that second maximum represents under half the differences one finds when comparing with Neanderthals.

#43 gilbo12345

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Posted 03 December 2012 - 12:01 PM

Right, and the next sentence in that paragraph (from the Wikipedia page for the Neanderthal Genome Project) is : "In contrast, the difference between chimpanzees and modern humans is approximately 1,462 mtDNA base pairs." Interestingly the article those numbers come from is also linked to in the Wikipedia page, here it is : http://www.nature.co...ature08976.html I hope everyone can access it, it's under a Creative Commons license so I assume so. As it turns out in their comparison they used 54 human genomes and one genome from a modern human fossil from the Pleistocene; here is the graph they get on the pairwise comparisons between all those human, Denisovan and Neanderthal genomes : http://www.nature.co...re08976_F2.html I assume there are two maxima for "Human-Human comparisons" because one of them is the Pleistocene human genome. But for those who can't see the graph, here are the nucleotide differences they get for all those comparisons : Modern human/Modern human : 0-70 for present-day humans, 70-105 for the Pleistocene human (with some overlap) Modern human/Neanderthal : 180-220 Modern human/Denisovan : 370-400 Modern human/Chimpanzee : 1462 (not on the graph so I don't have the range) Both Neanderthals and Denisovans are clearly distinct from modern humans in this comparison, and Denisovans are not only almost twice as different from us as Neanderthals are, they're less than a fourth more different from us than Chimpanzees are. EDIT : Actually considering the number of comparisons involved in the two human/human maxima and the phylogenetic tree they also show it doesn't seem likely it represents that single Pleistocene human's genome; it might be a Central Africa/vs Eurasia thing instead. Either way that second maximum represents under half the differences one finds when comparing with Neanderthals.


I was posting in relation to Neandertal not the chimpanze


It was claimed that Neandertal DNA is very much different to ours... if its deemed 99.7% the same then how can that be claimed as vastly different?

#44 aelyn

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Posted 03 December 2012 - 12:23 PM

I was posting in relation to Neandertal not the chimpanze It was claimed that Neandertal DNA is very much different to ours... if its deemed 99.7% the same then how can that be claimed as vastly different?

You're nitpicking about the word "vastly" ? Dan's point was that Neanderthals are clearly outside the range of human variability, which they are.

#45 MarkForbes

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Posted 03 December 2012 - 12:35 PM

That 0.3 % is probably the divergence you'd find among any race of the human species. Did they actually test fresh DNA or was this from some fossil?
And it's worthwhile to compare this to human - chimpanzee differences as well:
http://creation.com/chimp-y-chromosome
Where there any examination of the Y-chromosome?


#46 aelyn

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Posted 03 December 2012 - 12:54 PM

That 0.3 % is probably the divergence you'd find among any race of the human species.

"Probably" ? You mean you didn't look it up to check ? I guess not because in fact it isn't. The divergence among humans is closer to 0.01% IIRC.

Did they actually test fresh DNA or was this from some fossil? And it's worthwhile to compare this to human - chimpanzee differences as well: http://creation.com/chimp-y-chromosome Where there any examination of the Y-chromosome?

That's exactly what the study explained in Dan's link does, maybe you could have a look.

#47 MarkForbes

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Posted 03 December 2012 - 01:27 PM

There is quite some different results from studies on human genetic divergence. And I think the decay may also play into that; assuming that the Neanderthal DNA is old.

#48 aelyn

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Posted 03 December 2012 - 01:48 PM

There is quite some different results from studies on human genetic divergence. And I think the decay may also play into that; assuming that the Neanderthal DNA is old.

They take decay into account, you could find out how by reading the papers (the one I linked to is open access AFAICT) and come back and explain to us what was wrong with their methodology. And you could also give us some of those studies on human genetic divergence and the different results they find.

#49 herebedragons

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Posted 03 December 2012 - 07:04 PM

Gilbo ....

What do you think Biology is? Genetics is a subset of Biology, ecology is a subset of Biology etc etc etc..

Really.... Then why is it cited as a "theory" of Biology... You're in denial if you claim its of Biology but yet not a part of it.


OK, evolution is "part" of biology. But you are missing my point. Evolution relies on data from multiple disciplines, some of which are not "experimental sciences." If you say that biology is an experimental science and that ecology and paleontology, which are clearly not "experimental sciences" are subsets of biology, you are taking an inconsistent position.

Biology is an empirical science which is different from experimental. I still think you are confusing the two terms.

Theories are validated or invalidated by testing predictions. Data that validates or invalidates a theory can come from "observational sciences" such as ecology and paleontology.

I think the confusion is in how "experiment" is defined. When I think of experiment I think of a controlled experiment. But experiment can be more loosely defined to include empirical tests, what I have been referring to as observation. By observation I do not mean just looking at something, it can involve testing, measuring etc...

Would you consider it an experiment if you observed a thermometer as water froze and determined that water freezes at 0oC? The falsification of your observation would be that I could look at the same thermometer and observe the same reading (or different if you were wrong).

Would you describe what you think an experiment (that meets the qualification of the scientific method) entails?

HBD

#50 gilbo12345

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Posted 03 December 2012 - 07:11 PM

Gilbo .... [/font][/color] OK, evolution is "part" of biology. But you are missing my point. Evolution relies on data from multiple disciplines, some of which are not "experimental sciences." If you say that biology is an experimental science and that ecology and paleontology, which are clearly not "experimental sciences" are subsets of biology, you are taking an inconsistent position. Biology is an empirical science which is different from experimental. I still think you are confusing the two terms. Theories are validated or invalidated by testing predictions. Data that validates or invalidates a theory can come from "observational sciences" such as ecology and paleontology. I think the confusion is in how "experiment" is defined. When I think of experiment I think of a controlled experiment. But experiment can be more loosely defined to include empirical tests, what I have been referring to as observation. By observation I do not mean just looking at something, it can involve testing, measuring etc... Would you consider it an experiment if you observed a thermometer as water froze and determined that water freezes at 0oC? The falsification of your observation would be that I could look at the same thermometer and observe the same reading (or different if you were wrong). Would you describe what you think an experiment (that meets the qualification of the scientific method) entails? HBD


I can accept the testing of predictions as something that can assist in support of a hypothesis however keep in mind that the riskier the prediction the stronger it will be as evidence. (I believe there was a cool quote about this but I've forgotten it)

Additionally there is always the issue of falsifiability which is my main issue with evolution.

Also the predictions are required to be made BEFORE the evidence, not after something is discovered and then its shoehorned in with some form of ad hoc reasoning relating it to evolution. Since nothing was actually being tested rather its just an observation that is believed to fit.

#51 herebedragons

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Posted 03 December 2012 - 08:38 PM

I can accept the testing of predictions as something that can assist in support of a hypothesis

This doesn't quite clarify what you would consider to be an experiment. Does it need to be a controlled experiment? Does an observation experiment fit the criteria for use in the scientific method?

however keep in mind that the riskier the prediction the stronger it will be as evidence.

Do you mean this the other way around? I am thinking the bigger or riskier the prediction the more substantial evidence it will require to verify it.

Additionally there is always the issue of falsifiability which is my main issue with evolution.

Understand. Many say that evolution is falsifiable, and in theory it may be, but in practice it doesn't seem to be so. But on the other hand there is a growing body of support that suggest that the modern synthesis needs to be completely revamped (not scrapped completely, but new discoveries don't fit neatly into the current paradigm). So at least some evolutionary scientists see the modern synthesis as flawed.

Also the predictions are required to be made BEFORE the evidence, not after something is discovered and then its shoehorned in with some form of ad hoc reasoning relating it to evolution. Since nothing was actually being tested rather its just an observation that is believed to fit.


I too have issues with ad hoc explanations for evolutionary phenomenon. You have to understand though that the ToE is an enormous body of knowledge covering very complicated issues. There is no way you would expect such a theory to have it right the first time. Which is why it cracks me up when evolution opponents cite Darwin's errors in their criticism of the theory. How could he have gotten such a profound theory right on the first go. So the fact that it needs to be revised doesn't weaken its validity, in fact it strengthens it because it takes into account new data and new knowledge.

The place that the ToE is weak is in its mechanisms. The ToE is a very mechanistic theory. It requires mechanisms to explain phenomenon, otherwise it is a theory of special providence. But its not, it a naturalistic theory. The problem with parallel evolution, convergent evolution and those type explanations of phenomenon, is that the evolutionary mechanisms don't adequately predict those patterns. The problem is not with the fossil record or "lack of experimentation" it is not having adequate mechanisms to account for the patterns we observe. It is this,in part, that is driving some to suggest that the Toe needs revising.

HBD

#52 Salsa

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Posted 03 December 2012 - 11:54 PM

Do you mean this the other way around? I am thinking the bigger or riskier the prediction the more substantial evidence it will require to verify it.


I think that what Gilbo means is that the riskier the prediction, when confirmed, the stronger it will be as evidence.
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#53 MarkForbes

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Posted 04 December 2012 - 08:16 AM

They take decay into account, you could find out how by reading the papers (the one I linked to is open access AFAICT) and come back and explain to us what was wrong with their methodology. And you could also give us some of those studies on human genetic divergence and the different results they find.

The problem isn't there methodology, but on a general nature when information or facts are missing. You do not know for certain whether they were there, nor whether they even existed. So it's basically a comparison towards erased information or blank spaces.

As study of human genetic divergence, the following may be interesting:
http://www.scienceda...61123115741.htm

But then I think we are exploding this thread dealing with it in depth. So another thread should be used.

#54 aelyn

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Posted 04 December 2012 - 09:09 AM

The problem isn't there methodology, but on a general nature when information or facts are missing. You do not know for certain whether they were there, nor whether they even existed. So it's basically a comparison towards erased information or blank spaces.

No, the problem is you don't even know what their methodology is. You have decided in advance their conclusions are wrong so you're throwing out whatever objections come to your mind. If you were actually interested in answers you would read the study and make your objections based on what you read.

As study of human genetic divergence, the following may be interesting:
http://www.scienceda...61123115741.htm

But then I think we are exploding this thread dealing with it in depth. So another thread should be used.

Copy number variants are quite interesting, and nice evidence that genetic duplications happen and aren't necessarily harmful, but that article says nothing about human diversity compared to the diversity of other species. What it says is that when you account for CNVs humans are more genetically diverse than if you don't, but that's true of all species, and if the studies comparing human genomes to Neanderthals included differences in CNVs the % difference between the two species would be larger too.

#55 gilbo12345

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Posted 04 December 2012 - 11:51 AM

No, the problem is you don't even know what their methodology is. You have decided in advance their conclusions are wrong so you're throwing out whatever objections come to your mind. If you were actually interested in answers you would read the study and make your objections based on what you read. Copy number variants are quite interesting, and nice evidence that genetic duplications happen and aren't necessarily harmful, but that article says nothing about human diversity compared to the diversity of other species. What it says is that when you account for CNVs humans are more genetically diverse than if you don't, but that's true of all species, and if the studies comparing human genomes to Neanderthals included differences in CNVs the % difference between the two species would be larger too.


The entire methodology of equating DNA similarity is bunk, I found this flaw myself and when I mentioned it to my lecturer he admitted that its a problem, but didn't seem to care that it invalidated the method in terms of defining what the natural % of similarity is.... Simply put even if a method is flawed most evolutionists don't care, just as long as it fits evolution that is the only thing that matters.

Now what is this flaw I keep going on about. Well when DNA is assessed for similarities rather than look at the DNA itself it is modified before its assessed. Gaps are inserted in order to align the DNA samples to each other, thus increasing their relative % of similarity. For example

ATTACTCA

and

ATACTCGA

these two would be aligned like this

ATTACTC-A
A-TACTCGA

7 aligned

rather than naturally like this

ATTACTCA
ATACTCGA

3 aligned

Now why is this done? This is based on the assumption that evolution occured which therefore changed it over time. Meaning that use of DNA similarity as evidence of evolution is circular reasoning since one must assume evolution occured in order to justify the method used. However it gets worse than that.

If I had DNA a b c d e f and aligned DNA a with b c d and then aligned DNA a with d e f the places where the alignments are change. What this means is that the program is arbitrarily adding in gaps in order to increase the amount of similarity, if we swapped the DNA a's over then the similarity % would reduce dramatically (I've tested this with DNA from blast).

Therefore the entire method is a way of trying to increase the similarity that may not have been there, no-one can tell which alignment gaps should or shouldn't be added and the fact that they change means they are added relative to the DNA being aligned.


Yes there are gap penalties however considering that there would be very little similarity without gaps... (since one DNA base out of line can cause the entire sequence to be out of line) means that imposing a "penalty" would most often not be enough to balance it.
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#56 MarkForbes

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Posted 04 December 2012 - 12:01 PM

No, the problem is you don't even know what their methodology is. You have decided in advance their conclusions are wrong so you're throwing out whatever objections come to your mind. If you were actually interested in answers you would read the study and make your objections based on what you read.


For your information, it's not their methodology you are trying to discuss, but their method they used to do their research. So perhaps you should get your own comments and statements straight, before you try to lecture others. The issue that I am pointing to is however fundamental (loss of relevant obkjects of evidence). That's not something you get around by just using another method. Looking back it seems that you were the one that approached the thing a bit with "advanced conclusions".

Copy number variants are quite interesting, and nice evidence that genetic duplications happen and aren't necessarily harmful, but that article says nothing about human diversity compared to the diversity of other species. What it says is that when you account for CNVs humans are more genetically diverse than if you don't, but that's true of all species, and if the studies comparing human genomes to Neanderthals included differences in CNVs the % difference between the two species would be larger too.


Careful, while this maybe duplications, it may just be identical genetic coding as well. The study doesn't say anything about it being harmful or not. Right, the method of counting does have influence on the figures one can come up with. That one could come up with a bigger difference using it on the Neanderthal genome is possible, It could also show that Neanderthals are closer to some modern humans. You were only asking for human divergence. That's why I posted an article on that.

#57 aelyn

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Posted 04 December 2012 - 12:47 PM

The entire methodology of equating DNA similarity is bunk, I found this flaw myself and when I mentioned it to my lecturer he admitted that its a problem, but didn't seem to care that it invalidated the method in terms of defining what the natural % of similarity is.... Simply put even if a method is flawed most evolutionists don't care, just as long as it fits evolution that is the only thing that matters. Now what is this flaw I keep going on about. Well when DNA is assessed for similarities rather than look at the DNA itself it is modified before its assessed. Gaps are inserted in order to align the DNA samples to each other, thus increasing their relative % of similarity. For example ATTACTCA and ATACTCGA these two would be aligned like this ATTACTC-A A-TACTCGA 7 aligned rather than naturally like this ATTACTCA ATACTCGA 3 aligned Now why is this done? This is based on the assumption that evolution occured which therefore changed it over time. Meaning that use of DNA similarity as evidence of evolution is circular reasoning since one must assume evolution occured in order to justify the method used. However it gets worse than that. If I had DNA a b c d e f and aligned DNA a with b c d and then aligned DNA a with d e f the places where the alignments are change. What this means is that the program is arbitrarily adding in gaps in order to increase the amount of similarity, if we swapped the DNA a's over then the similarity % would reduce dramatically (I've tested this with DNA from blast). Therefore the entire method is a way of trying to increase the similarity that may not have been there, no-one can tell which alignment gaps should or shouldn't be added and the fact that they change means they are added relative to the DNA being aligned. Yes there are gap penalties however considering that there would be very little similarity without gaps... (since one DNA base out of line can cause the entire sequence to be out of line) means that imposing a "penalty" would most often not be enough to balance it.


This is all irrelevant when we're comparing the levels of similarity between groups - given the method is the same for the different groups then whatever general biases the method has will cancel out. If it makes things look more similar than they really are then it will make humans look overly similar to each other, but it will also make Neanderthals look more similar to humans than they really are, and vice-versa.
But comparing similar DNA sequences together is hardly strange - are these two sentences almost identical, or almost completely different :
Coloured inks are used in printers
Colored inks are used in printers

Comparing letter-by-letter starting at the beginning you'd see them as almost completely different but that misses the obvious fact they're almost completely identical. You don't compare sequences of anything by comparing the positions of each element, you compare them by looking at whether sub-sequences within both the sequences are more similar than random chance would predict.

Careful, while this maybe duplications, it may just be identical genetic coding as well. The study doesn't say anything about it being harmful or not. Right, the method of counting does have influence on the figures one can come up with. That one could come up with a bigger difference using it on the Neanderthal genome is possible, It could also show that Neanderthals are closer to some modern humans. You were only asking for human divergence. That's why I posted an article on that.

I have no idea what you mean by "identical genetic coding". That's what duplicates are, two identical (or near-identical) bits of code.

#58 dan4reason

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Posted 04 December 2012 - 02:08 PM

Really.... At roughly 3.2 billion base pairs,[3] the Neanderthal genome is about the size of the modern human genome. According to preliminary sequences, 99.7% of the base pairs of the modern human and Neanderthal genomes are identical, compared to humans Additionally, in 2010, the announcement of the discovery and analysis of Mitochondrial DNA (mtDNA) from the Denisova hominin in Siberia revealed that this specimen differs from that of modern humans by 385 bases (nucleotides) in the mtDNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases.


How do you know that the Denisova Hominin are homo sapiens? In fact they are thought to be another species of hominid. Distinct species can be highly genetically similar, and the point I was trying to make is that humans and neanderthals are genetically distinct although they are similar.

Humans and neanderthals are 99.7% the same. Humans and Denisova are 99.4% the same, and humans and chimps are 98.0% the same. Human and human similarity is 99.9%. So human-neanderthal variance is anything but normal.

#59 gilbo12345

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Posted 04 December 2012 - 02:55 PM

How do you know that the Denisova Hominin are homo sapiens? In fact they are thought to be another species of hominid. Distinct species can be highly genetically similar, and the point I was trying to make is that humans and neanderthals are genetically distinct although they are similar. Humans and neanderthals are 99.7% the same. Humans and Denisova are 99.4% the same, and humans and chimps are 98.0% the same. Human and human similarity is 99.9%. So human-neanderthal variance is anything but normal.


IF you read the quote you will discover that in the first half there is not need to look at what it says about Denisova Hominin. However the Denisove Hominin is beleived to be a different form of human. So if the difference between Neandertal is less than that of a different form (species?) of human then one can surmise that the Neandertal is also a different form (species) of human since it is more alike. This is what the current evidence suggests, hence why I don't like Talkorigins because it uses biased out-dated data (of which much of it is debunked by modern discoveries, like Tiktaalik...). Therefore its not a source to be trusted, cherry picking data and omitting data that doesn't fit is not being scientific.




":At roughly 3.2 billion base pairs,[3] the Neanderthal genome is about the size of the modern human genome. According to preliminary sequences, 99.7% of the base pairs of the modern human and Neanderthal genomes are identical, compared to humans Additionally, in 2010, the announcement of the discovery and analysis of Mitochondrial DNA (mtDNA) from the Denisova hominin in Siberia revealed that this specimen differs from that of modern humans by 385 bases (nucleotides) in the mtDNA strand out of approximately 16,500, whereas the difference between modern humans and Neanderthals is around 202 bases."

#60 usafjay1976

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Posted 05 December 2012 - 06:46 AM

Ok, back to the scientific method. Let's use the model from my first post again. Here it is below.

Posted Image


So with these comparisons, I ask the evolutionists posting to fill in the below to support their posts.

Ask question:

Research:

Hypothesis:

Test:

Analyze:


This should make it easier to support your claims so we can all see exactly what you are doing to come to your conclusions.




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