Gorilla Genome

mark kennedy

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It's been a while since I have taken up the topic but the Gorilla Genome was finally sequenced in 2012. There are a couple of insights, one I expected but the other came as a big surprise.

Overall:

In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression.​

Brain Related:

Genes expressed in the brain or involved in its development have not typically been associated with positive selection in primates, but our results show that multiple great ape lineages show elevated dN/dS in brain-related genes when evaluated against a primate background.​

Insights into hominid evolution from the gorilla genome sequence (Nature, 08 March 2012)

Of course, Creationists are having some fun with this one:

Gorilla Genome Is Bad News for Evolution

I'll be back later to see how the discussion develops.

Grace and peace,
Mark
 

ChetSinger

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Hello Mark. I'm going to ask a question that's a little sideways. But I don't want to derail your thread so I'll shut up if you consider it not relevant.

But, given that the ENCODE project has discovered more than 4 million gene-control switches in the human genome, many in areas previously considered to be junk, is it still possible to attempt to measure percent similarity between species without taking these switches into consideration?

That is, it seems to me that conclusions based on gene-similarity comparisons should be put on the back burner until we can include switch-similarity comparisons.
 
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Oncedeceived

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It's been a while since I have taken up the topic but the Gorilla Genome was finally sequenced in 2012. There are a couple of insights, one I expected but the other came as a big surprise.

Overall:
In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression.​
Brain Related:
Genes expressed in the brain or involved in its development have not typically been associated with positive selection in primates, but our results show that multiple great ape lineages show elevated dN/dS in brain-related genes when evaluated against a primate background.​
Insights into hominid evolution from the gorilla genome sequence (Nature, 08 March 2012)

Of course, Creationists are having some fun with this one:

Gorilla Genome Is Bad News for Evolution

I'll be back later to see how the discussion develops.

Grace and peace,
Mark

Hi Mark,

Just curious, what do you mean by Creationists are having some fun with this one? Who are 'Creationists' in your assessment?
 
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Loudmouth

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It's been a while since I have taken up the topic but the Gorilla Genome was finally sequenced in 2012. There are a couple of insights, one I expected but the other came as a big surprise.

Overall:

In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression.​

70% of the chimp genome is more closely related to humans. I don't see why this is a problem since this is the type of thing we would expect from incomplete lineage sorting. Don't forget that we also share a common ancestor with gorillas.
 
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Loudmouth

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Hello Mark. I'm going to ask a question that's a little sideways. But I don't want to derail your thread so I'll shut up if you consider it not relevant.

But, given that the ENCODE project has discovered more than 4 million gene-control switches in the human genome, many in areas previously considered to be junk, is it still possible to attempt to measure percent similarity between species without taking these switches into consideration?

That is, it seems to me that conclusions based on gene-similarity comparisons should be put on the back burner until we can include switch-similarity comparisons.

The problem is that ENCODE used a definition of "functional" that includes junk DNA. They defined "functional" as "changes the biochemistry of the cell". The trash in your kitchen trash can changes the biochemstry of your kitench by releasing organic molecules into the air. Using their definition, real junk would be defined as functional. What they didn't do is determine if these "functional" sequences affect fitness in any meaningful way.

A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect.
On the immortality of television sets: "function" in the human geno... - PubMed - NCBI

To use an analogy, imagine that you bought a brand new TV and it stopped working after 2 months. You take it back to the place where you bought it and ask for a refund. The manager tells you that the TV is still functioning just fine. He points out that the back of the TV is able to gather dust which means that it still has a function.

This is the type of "function" that the ENCODE project argues for. They argue that since it does something, like gathering dust, that it is functional. The question they need to answer is how a sequence of DNA can never lose function no matter how many mutations it accumulates, and why there is no evidence for selection against deleterious mutations in that stretch of DNA.
 
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J0hnSm1th

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what do you mean by Creationists are having some fun with this one?
I expect its because the Ven diagrams one could draw in terms of shared genes between gorillas, chimps, and humans will not line up properly. Creationists would use this as an argument against common decent.
 
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mark kennedy

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Hello Mark. I'm going to ask a question that's a little sideways. But I don't want to derail your thread so I'll shut up if you consider it not relevant.

But, given that the ENCODE project has discovered more than 4 million gene-control switches in the human genome, many in areas previously considered to be junk, is it still possible to attempt to measure percent similarity between species without taking these switches into consideration?

That is, it seems to me that conclusions based on gene-similarity comparisons should be put on the back burner until we can include switch-similarity comparisons.

It's been a while and this is the first time I've heard this described as '"function" in the human genome according to the evolution-free gospel of ENCODE' (Genome Biol Evol. 2013). It sounds like something I remember seeing emerge a few years back. Basically there are sections of DNA, even gene deserts, where RNA strands can be transcribed and have some kind of functionality. Not everything has to be a protein coding gene, there are regulatory genes and a long list of other RNA based molecular mechanisms in the genome.

This link has a fairly interesting Nature video and podcast showcasing some of ENCODE's work:

Nature 489, 46–48 (06 September 2012)​

The latest publication I can find on them was in 2012:


It's always interesting to see these broad sweeps of the genomic landscape, the idea that only a small percentage of the genome was actually functional always seemed grossly absurd to me. I remember back in the 70s we were always being told that 80% of the human brain does nothing, something now known to be false. Since the unveiling of the Initial Sequence of the Human Genome in 2001 we have learned a great deal about alleles and how the genomic landscape can be mapped.

The ENCODE project seems limited simply based on it's scope but never underestimate the power of genetics. When the 2001 publication of the Human Genome appeared in Nature everyone else had to adjust to them, something very few scientific disciplines can say definitively.

At a glance the effort looks promising and it is certainly a refreshing change from the Darwinian mutation plus selection equals everything rhetoric.

Grace and peace,
Mark
 
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Loudmouth

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Basically there are sections of DNA, even gene deserts, where RNA strands can be transcribed and have some kind of functionality.

Functionality by what definition?

Is a broken TV set functional because it is able to attract dust? Is just doing something considered a function? If so, then 100% of the genome is functional since 100% of it is copied for each new cell.

Not everything has to be a protein coding gene, there are regulatory genes and a long list of other RNA based molecular mechanisms in the genome.

Is that how you are defining function? If so, did ENCODE show that all of these low copy RNA transcripts are significantly changing gene expression? From what I read, all they did was see if they were transcribed. They never tested whether or not each RNA transcript changed gene expression in any meaningful manner.

It's always interesting to see these broad sweeps of the genomic landscape, the idea that only a small percentage of the genome was actually functional always seemed grossly absurd to me.

Then how can a large percentage of the human genome accumulate mutations at a rate consistent with neutral drift if it does have function? Where is evidence for negative selection in these sections of DNA?

I remember back in the 70s we were always being told that 80% of the human brain does nothing,

Reference? Or is this yet another claim that you have made up?
 
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ChetSinger

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...It's always interesting to see these broad sweeps of the genomic landscape, the idea that only a small percentage of the genome was actually functional always seemed grossly absurd to me. I remember back in the 70s we were always being told that 80% of the human brain does nothing, something now known to be false. Since the unveiling of the Initial Sequence of the Human Genome in 2001 we have learned a great deal about alleles and how the genomic landscape can be mapped.
I remember the scientific reaction when the number of human genes was finally counted: people couldn't believe the number was so small. Intuition told them that the specifications for a human required far more data points than that. It's turning out that the data was just elsewhere, and in different forms.

I find Home | The Institute for Creation Research an interesting site to check up on periodically. There's a geneticist there who periodically posts about the amazing complexity being uncovered every year.

I also remember being told years ago that most of our brains did nothing. It's amusing, looking back on it.
 
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morse86

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Have any of you actually seen DNA? By DNA, I do not mean cell debris or artist renditions of it.

Remember Dolly the sheep? Later found to be a hoax.

The million dollar challenge:
Show me an ACTUAL picture of DNA (NOT a computer rendering, not an artist rendering, not cell debris). Go ahead.

To see what a hoax DNA is, look at these "computer renderings"....http://www.theatlantic.com/technology/archive/2012/11/what-dna-actually-looks-like/265713/
 
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mark kennedy

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I remember the scientific reaction when the number of human genes was finally counted: people couldn't believe the number was so small. Intuition told them that the specifications for a human required far more data points than that. It's turning out that the data was just elsewhere, and in different forms.

Actually the early estimates were some 30,000 protein coding genes, the number finally fell below 20,000. The functional part of the genome is considerably larger and an enormous of RNA molecular mechanisms that can be coding about anywhere. There are molecular mechanisms that are involved in adaptive evolution but Darwinians don't want to admit it because that would suggest divine providence.

I find Home | The Institute for Creation Research an interesting site to check up on periodically. There's a geneticist there who periodically posts about the amazing complexity being uncovered every year.

I used to go on AIG regularly and when I started these debates I absolutely loved Apologetics Press. I had always favored Paleontology but the genetics stuff is so compelling and there is so much material available genomics seemed the best way to go.

I also remember being told years ago that most of our brains did nothing. It's amusing, looking back on it.

I remember I thought that has to be nonsense and as it turned out it was. There for a while people were saying that we should only worry about protein coding genes, there was no need for whole genome sequences, now they know better.

Grace and peace,
Mark
 
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Loudmouth

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Actually the early estimates were some 30,000 protein coding genes, the number finally fell below 20,000. The functional part of the genome is considerably larger . . .

There is selectable function in 5-10% of the human genome compared to coding regions which make up 2% of the genome. That is larger, but not by a lot.

There are molecular mechanisms that are involved in adaptive evolution but Darwinians don't want to admit it because that would suggest divine providence.

Since when does DNA methylation and histone ubiquitination require divine providence?

There for a while people were saying that we should only worry about protein coding genes, there was no need for whole genome sequences, now they know better.

Who said that? References?
 
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Loudmouth

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Have any of you actually seen DNA? By DNA, I do not mean cell debris or artist renditions of it.

Are you doubting DNA's molecular structure? That it exists at all? What point are you trying to make?

dn22545-1_300.jpg


MJ+2013+chromosomes+xy+micro.jpg


dna.gif


Those are a few electronmicrographs, if that is what you want.

Remember Dolly the sheep? Later found to be a hoax.

Huh?
 
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Split Rock

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Have any of you actually seen DNA? By DNA, I do not mean cell debris or artist renditions of it.

Remember Dolly the sheep? Later found to be a hoax.

The million dollar challenge:
Show me an ACTUAL picture of DNA (NOT a computer rendering, not an artist rendering, not cell debris). Go ahead.

To see what a hoax DNA is, look at these "computer renderings"....What DNA Actually Looks Like ? The Atlantic
Sure, here you go (I've isolated the stuff myself many times):

http://www.unc.edu/depts/our/hhmi/hhmi-ft_learning_modules/2012/dnamodule/images/pellet.jpg

http://biology.clc.uc.edu/fankhause..._dna_images/06_add_0.5_mL_chelex_P2193019.JPG

http://biology.clc.uc.edu/fankhause...ion_jpg/09_spooling_DNA_Jennifer_P2060010.jpg

http://www.enasco.com/prod/images/products/31/AC134125l.jpg
 
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Loudmouth

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So, they are close. Can a human mate with a gorilla to produce offspring? Can a gorilla mate with a human to produce offspring?

No.

Your point is mute.

If two species can not mate in modern times, how does this disprove common ancestry? Look at horses and donkeys. For their offspring, all males are sterile and only one female out of 10,000 is fertile. They are already well on their way to not producing offspring. Why can't the same happen for humans and other apes?

Also, I don't think anyone has fully ruled out cross-fertility between humans and other apes, although the ethical reasons for not doing those experiments is obvious.
 
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Loudmouth

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If genetics is the 'brains' behind evolution, how did the genome evolve?

How the earliest genomes came to be is not known. However, to evidence common ancestry between gorillas and humans, you hardly need to go back to the beginning of life.
 
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JacksBratt

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If two species can not mate in modern times, how does this disprove common ancestry? Look at horses and donkeys. For their offspring, all males are sterile and only one female out of 10,000 is fertile. They are already well on their way to not producing offspring. Why can't the same happen for humans and other apes?

Also, I don't think anyone has fully ruled out cross-fertility between humans and other apes, although the ethical reasons for not doing those experiments is obvious.


Stalin tried it. It never worked.

Horses and Donkey's produce mules and Hinny's. In all these years we do not have a new species of mules, it is just a dead end. Such is the case. Humans and apes cannot even start the process. It's even more of a dead end.
 
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