The illusion of evolution and how it works

[Rumraket]

Yes, yes, It would be 98% after you remove 97% of the DNA and ignore the insertions and deletions of bp.

:facepalm:

Citation for your claim.

Honestly, is this how it will be with you? Are you just going to ignore the vast majority of what I write and make unsubstantiated claims in every post?

97% of the three billion letters of the Human Genome is described as ‘junk DNA’; only 3% of our DNA appears to code for proteins

http://www.thehumangenome.co.uk/THE_HUMAN_GENOME/Junk_DNA.html

In 2014, now it's "People Use Just 8.2% of Their DNA, Study Finds"

The results are higher than previous estimates of 3 to 5 percent, and significantly lower than the 80 percent reported in 2012 by the Encyclopedia of DNA Elements Project (ENCODE), a public research project led by the U.S. National Human Genome Research Institute to study the role of the 3 billion total letters in human DNA
http://www.livescience.com/46986-human-genome-junk-dna.html
.

There are several errors in your reasoning here, but I can understand why you are confused. I see that your source makes several errors that you are now repeating, so I guess you can't really be faulted for it. But regardless, they are errors on the part the people who write these articles and they have simply not got the terms and the history behind them right.

1. Non protein coding DNA isn't throught to be and indeed never were thought to be junk-DNA, merely because it doesn't code for proteins. The case for junk-DNA was never about coding regions, it was about genome size variations (the C-value paradox) and purifying selection.

2. Non protein coding DNA (whether junk or not) isn't ignored in comparative genetics. Even bona-fide junk regions are useful in comparative genetics, because (AFAIK) neutrally evolving DNA is useful for molecular clock estimates, among other things. Recently it has also been discovered that some junk-regions are useful for detecting genetic homologous regions for ORFan protein coding genes between species (making them, in some sense, non-ORFans).

3. There is a serious conflict between the first and second quote you give (which I guess is what you try to exploit) because, strictly speaking it is true that only about 3% of our DNA codes for proteins, but there are an additional 5-7% that are clearly functional regulatory regions of various sorts (areas where transcription factors bind, origin of replication regions and so on). These are all non-coding regions but are functional and were always known to be functional, they were never dismissed as junk simply because they weren't translated into protein.

One of the first fully understood genetic operons (and now famous for that reason) is the Lac-Operon in bacteria. Right from the beginning it was understood that large portions of the Lac-Operon was non-coding but was still important for regulatory function.

It is a sad state of affairs that there is so much miscommunication on this subject and as such, you can't really be faulted for it. But you have been misinformed about the state of junk-DNA research, the history of the term and it's correct application. In turn, you have several misconceptions about the state and application of comparative genetics.

Also, your first statement is not actually supported by any of your references. Nobody ignores insertions and deletions in similarity estimates.

 

[he_who_is_nobody]

Yes, yes, It would be 98% after you remove 97% of the DNA and ignore the insertions and deletions of bp.

:facepalm:

Citation for your claim.

Honestly, is this how it will be with you? Are you just going to ignore the vast majority of what I write and make unsubstantiated claims in every post?

97% of the three billion letters of the Human Genome is described as ‘junk DNA’; only 3% of our DNA appears to code for proteins

http://www.thehumangenome.co.uk/THE_HUMAN_GENOME/Junk_DNA.html

In 2014, now it's "People Use Just 8.2% of Their DNA, Study Finds"

The results are higher than previous estimates of 3 to 5 percent, and significantly lower than the 80 percent reported in 2012 by the Encyclopedia of DNA Elements Project (ENCODE), a public research project led by the U.S. National Human Genome Research Institute to study the role of the 3 billion total letters in human DNA
http://www.livescience.com/46986-human-genome-junk-dna.html


.

I guess that answers my question (i.e. you will ignore the vast majority of what I am asking you). Since that is the case, what is the point in engaging with you?

Oh, and I will just repeat Rumraket in response to your citations:

Also, your first statement is not actually supported by any of your references. Nobody ignores insertions and deletions in similarity estimates.

 

[Rhed]

I guess that answers my question (i.e. you will ignore the vast majority of what I am asking you). Since that is the case, what is the point in engaging with you?

What question do you want me to answer? I thought I answered the "Y" question.

Oh, and I will just repeat Rumraket in response to your citations:

Also, your first statement is not actually supported by any of your references. Nobody ignores insertions and deletions in similarity estimates.

The 98% figure came from ignoring the insertions and deletions. Now we get a 95% figure including the INDEL.
http://sandwalk.blogspot.com/2012/01/whats-difference-between-human-and.html

I have a question though for you or anyone here. Is the 95% including the all of the "junk" DNA ? Or does the 95% only included in the 8.7% of non-coded functional DNA?

Here's a list of the functional (8.7%), junk, (65%) and the unknown (26.3%):
http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html

 

[he_who_is_nobody]

I guess that answers my question (i.e. you will ignore the vast majority of what I am asking you). Since that is the case, what is the point in engaging with you?

What question do you want me to answer? I thought I answered the "Y" question.

You did answer one question (after I repeated it three(?) times for you). Now you see everything with a question mark or where I explicitly ask for a citation? I would like those answered as well. This seems like something I should not have to point out to an honest person, only one acting obtuse.

 

[Rhed]

Forget about the 95% or the 8.9 functional DNA. And forget about the junk DNA:

http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312

http://www.nature.com/nature/videoarchive/encode_video/index.html?WT.ec_id=NATURE-20120906

http://news.sciencemag.org/2012/09/human-genome-much-more-just-genes

As part of ENCODE, 32 institutions did computer analyses, biochemical tests, and sequencing studies on 147 cell types—six fairly extensively—to find out what each of the genome's 3 billion bases does. About 80% of the genome is biochemically active, ENCODE's 442 researchers report today in Nature

So I guess the theory of evolution is dead now? Or are there more rescuing devices to add to the list?

 

[SpecialFrog]

Forget about the 95% or the 8.9 functional DNA. And forget about the junk DNA:

http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312

http://www.nature.com/nature/videoarchive/encode_video/index.html?WT.ec_id=NATURE-20120906

http://news.sciencemag.org/2012/09/human-genome-much-more-just-genes

As part of ENCODE, 32 institutions did computer analyses, biochemical tests, and sequencing studies on 147 cell types—six fairly extensively—to find out what each of the genome's 3 billion bases does. About 80% of the genome is biochemically active, ENCODE's 442 researchers report today in Nature

So I guess the theory of evolution is dead now? Or are there more rescuing devices to add to the list?

I suggest you read this: http://sandwalk.blogspot.ca/2014/05/what-did-encode-consortium-say-in-2012.html.

The 80% figure is wrong (and possibly not even what the ENCODE researchers claimed).

 

[Inferno]

Forget about the 95% or the 8.9 functional DNA. And forget about the junk DNA:

http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312

http://www.nature.com/nature/videoarchive/encode_video/index.html?WT.ec_id=NATURE-20120906

http://news.sciencemag.org/2012/09/human-genome-much-more-just-genes

As part of ENCODE, 32 institutions did computer analyses, biochemical tests, and sequencing studies on 147 cell types—six fairly extensively—to find out what each of the genome's 3 billion bases does. About 80% of the genome is biochemically active, ENCODE's 442 researchers report today in Nature

So I guess the theory of evolution is dead now? Or are there more rescuing devices to add to the list?

I suggest you read this: http://sandwalk.blogspot.ca/2014/05/what-did-encode-consortium-say-in-2012.html.

The 80% figure is wrong (and possibly not even what the ENCODE researchers claimed).

I'd rather you read my blog post on the subject. I'm happy to say it was cited by Ryan T. Gregory, a researcher on the topic of the c-value paradox, as a "good resource" on the topic.
Of course Larry Moran's post is better, but I think mine has a broader approach.

 

[SpecialFrog]

I'd rather you read my blog post on the subject. I'm happy to say it was cited by Ryan T. Gregory, a researcher on the topic of the c-value paradox, as a "good resource" on the topic.
Of course Larry Moran's post is better, but I think mine has a broader approach.

Fair enough. I've read a few things debunking ENCODE but I knew I could find some of Moran's posts more quickly.

 

[JRChadwick]

I guess that answers my question (i.e. you will ignore the vast majority of what I am asking you). Since that is the case, what is the point in engaging with you?

Yeah, that pretty much sums him up. Thanks for getting him to at least sort of acknowledge my response.

 

[Rhed]

[quote-"Rhed"]So I guess the theory of evolution is dead now? Or are there more rescuing devices to add to the list?[/quote]

I suggest you read this: http://sandwalk.blogspot.ca/2014/05/what-did-encode-consortium-say-in-2012.html.

The 80% figure is wrong (and possibly not even what the ENCODE researchers claimed).

Sorry, but I don't see anything except Larry Moran disagrees with ENCODE along with evolutionists. He say's it a misunderstanding, but that is it. He goes on to say that evolutionists never claimed junk DNA to be junk, but believes that our genome is mostly junk. :facepalm:

So to an evolutionists, science works like this: Assume mindless unguided evolution and conclude with mindless unguided evolution.
Anything beyond that is not science.

What am I missing here?

 

[Rhed]

Inferno - I'll read your post later and see what I come up with.

 

[Inferno]

What am I missing here?

Pretty much everything. Please read the blog post I made, it fairly comprehensively sums up the debate up until... oh, 1-2 years ago I think. If you have serious questions then, I'll be happy to answer them.

 

[SpecialFrog]

I suggest you read this: http://sandwalk.blogspot.ca/2014/05/what-did-encode-consortium-say-in-2012.html.

The 80% figure is wrong (and possibly not even what the ENCODE researchers claimed).

Sorry, but I don't see anything except Larry Moran disagrees with ENCODE along with evolutionists. He say's it a misunderstanding, but that is it.

No, he is quoting the ENCODE scientists who are now saying that the "80% functional" statement is a misrepresentation. At the very least, it is a claim that the scientists involved are backing away from because they know it is unsound.

When the people who allegedly made the claim won't even defend it anymore, on what basis do you assert that it is correct and the scientists who disagree with it are wrong?

 

[he_who_is_nobody]

Forget about the 95% or the 8.9 functional DNA. And forget about the junk DNA:

http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312

http://www.nature.com/nature/videoarchive/encode_video/index.html?WT.ec_id=NATURE-20120906

http://news.sciencemag.org/2012/09/human-genome-much-more-just-genes

As part of ENCODE, 32 institutions did computer analyses, biochemical tests, and sequencing studies on 147 cell types—six fairly extensively—to find out what each of the genome's 3 billion bases does. About 80% of the genome is biochemically active, ENCODE's 442 researchers report today in Nature

So I guess the theory of evolution is dead now? Or are there more rescuing devices to add to the list?

You have been at this for at least six years and you are just finding out about ENCODE? Furthermore, how does finding out that 80% of our genes having a function kill evolution? Your conclusion does not follow from your citation (even if it were correct). Thus far, your modus operandi has been to quote something, declare it disproves evolution, and disengage with us when we correct you on your mistakes (and ignoring the vast majority of what anyone has told you). Why come to a discussion forum if you are only here to preach.

 

[Rhed]

You have been at this for at least six years and you are just finding out about ENCODE? Furthermore, how does finding out that 80% of our genes having a function kill evolution? Your conclusion does not follow from your citation (even if it were correct). Thus far, your modus operandi has been to quote something, declare it disproves evolution, and disengage with us when we correct you on your mistakes (and ignoring the vast majority of what anyone has told you). Why come to a discussion forum if you are only here to preach.

I took off for the last 6 years. The facts of evolution have evolved this then. Apparently Darwinian evolution has lost and now Neutral Evolution has taken its place.

 

[tuxbox]

Apparently Darwinian evolution has lost and now Neutral Evolution has taken its place.

It's just evolution, not Darwinian Evolution. I'm not sure why some Creationist can't get that through their head?

 

[he_who_is_nobody]

You have been at this for at least six years and you are just finding out about ENCODE? Furthermore, how does finding out that 80% of our genes having a function kill evolution? Your conclusion does not follow from your citation (even if it were correct). Thus far, your modus operandi has been to quote something, declare it disproves evolution, and disengage with us when we correct you on your mistakes (and ignoring the vast majority of what anyone has told you). Why come to a discussion forum if you are only here to preach.

I took off for the last 6 years. The facts of evolution have evolved this then. Apparently Darwinian evolution has lost and now Neutral Evolution has taken its place.

:docpalm:

he_who_is_nobody[/url]"]You did answer one question (after I repeated it three(?) times for you). Now you see everything with a question mark or where I explicitly ask for a citation? I would like those answered as well. This seems like something I should not have to point out to an honest person, only one acting obtuse.

 

[Rumraket]

Forget about the 95% or the 8.9 functional DNA. And forget about the junk DNA:

http://www.nature.com/news/encode-the-human-encyclopaedia-1.11312

http://www.nature.com/nature/videoarchive/encode_video/index.html?WT.ec_id=NATURE-20120906

http://news.sciencemag.org/2012/09/human-genome-much-more-just-genes

As part of ENCODE, 32 institutions did computer analyses, biochemical tests, and sequencing studies on 147 cell types—six fairly extensively—to find out what each of the genome's 3 billion bases does. About 80% of the genome is biochemically active, ENCODE's 442 researchers report today in Nature

So I guess the theory of evolution is dead now? Or are there more rescuing devices to add to the list?

The 95% similarity, 8.9% functional DNA paper you referenced earlier is a later publication than the ENCODE consortium claims, in part serving as a rebuttal to them.

Try to look at the dates and the contents of the papers(the arguments and the evidence they use to get their numbers), instead of just picking out single sentences. You have to look at the context of the claims. If you read the ENCODE papers you see that they actually don't establish any new functions, and if you look at the rebuttal papers that you yourself cited you see they are, in fact, partly papers that serves as rebuttals.

Instead of just mindlessly linking numbers (80% vs 9%), you have to look at how these numbers are arrived at and form a conclusion from there, to see who has the superior argument and better evidence.

 

[Rumraket]

I guess that answers my question (i.e. you will ignore the vast majority of what I am asking you). Since that is the case, what is the point in engaging with you?

What question do you want me to answer? I thought I answered the "Y" question.

Oh, and I will just repeat Rumraket in response to your citations:

Also, your first statement is not actually supported by any of your references. Nobody ignores insertions and deletions in similarity estimates.

The 98% figure came from ignoring the insertions and deletions. Now we get a 95% figure including the INDEL.
http://sandwalk.blogspot.com/2012/01/whats-difference-between-human-and.html

No, they weren't ignored. The previous estimates were done using methods that simply could not detect some of these indels. It was not that they were ignored (so you are lying when you say this, as your own source explains):

This value of 1.5%, rounded up to 2%, gave rise to the widely quoted statement that humans and chimps are 98% identical. Britton (2002) challenged that number by pointing out that humans and chimp genomes differed by a large number of insertions and deletions (indels) that could not have been detected in hybridization studies. He claimed that there was an addition 3.4% of the genome that differed due to indels. That means the the real difference between humans and chimps is closer to 5% and we are only 95% identical!

See that part in red? That means there was a technological limitation at the time, nobody was deliberately trying to ignore anything. An estimate was produced on the basis of available data, and as data collection methods became better, so did the methods for estimating similarities become more robust with time.

Why don't you actually read the entirely of Larry Moran's blog posts?

I have a question though for you or anyone here. Is the 95% including the all of the "junk" DNA ? Or does the 95% only included in the 8.7% of non-coded functional DNA?

This question is also answered by Larry in the blog post you link first, at the bottom.

It includes Junk-DNA. In fact most (and I emphasize MOST, not ALL, as Larry also explains) of the differences between human and chimp are IN the junk-DNA, because the functional parts are under varying levels of purifying selection.

Why do you link material you don't read?

 

[Rumraket]

I suggest you read this: http://sandwalk.blogspot.ca/2014/05/what-did-encode-consortium-say-in-2012.html.

The 80% figure is wrong (and possibly not even what the ENCODE researchers claimed).

Sorry, but I don't see anything except Larry Moran disagrees with ENCODE along with evolutionists.

Well to be fair, L Moran has many posts on ENCODE and junk-DNA. He has a whole set of blog posts devoted to "what you need to know if you want to participate in the junk-DNA debate".

He say's it a misunderstanding, but that is it.

He says a lot more than that.

He goes on to say that evolutionists never claimed junk DNA to be junk

False, he never says this anywhere.

What he says is that nobody ever claimed non-coding DNA to be junk.

non-coding =/= junk

And nobody who knew what they were talking about ever believed different.

What am I missing here?

All of it, all over again. Read it with comprehension, follow the links. Read it to try to understand what they're saying and why they say it, instead of just assuming they say it because they "hate god" or some shit.