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Author Topic:   Is Earth old enough for DNA to evolve?
jar
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From: Texas!!
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Message 16 of 60 (668115)
07-17-2012 10:15 AM
Reply to: Message 13 by bcoop
07-17-2012 9:28 AM


Re: well said
We are mammals.

Evolution has not been directed towards greater complexity except at the very beginning when the only life was single celled and so the only possible direction was greater complexity.

How many base pairs are in a mouse genome?

Remember that the first humans inherited an already complex genome.


Anyone so limited that they can only spell a word one way is severely handicapped!

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New Cat's Eye
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Posts: 11244
From: near St. Louis
Joined: 01-27-2005
Member Rating: 1.9


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Message 17 of 60 (668119)
07-17-2012 10:59 AM
Reply to: Message 15 by bcoop
07-17-2012 9:37 AM


Re: Generation lengths bogus
Hi bcoop,

I'm afraid you haven't conceptualized the Theory of Evolution very well.

the end of the chain where we are now,

See? Don't think "chain"... think "bush".

how much time it would take for a mammal to develop an functioning vision system or something like that.

Vision systems were evolving way before mammalia... as were most of the "things like that". They devolop consequently so your question doesn't make sense.

“Has mathematical modeling been conducted of the amount of time it would take to generate the human genome”?

I don't think so. I think its way to complex and complicated to form a model based on things like mutation rates and generation times n'stuff like you tried to do in the OP (opening post).

But, given that life has been on the Earth for about 3 billion years old and that modern human emerged about 200 thousand years ago, we can figure that it took about 2.9998 billion years for humans to evolve.


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Taq
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Message 18 of 60 (668120)
07-17-2012 11:09 AM
Reply to: Message 9 by bcoop
07-17-2012 9:09 AM


Re: Not so fast
I appreciate your detailed reply. The attempt here was to really ask the question:
“Has mathematical modeling been conducted of the amount of time it would take to generate the human genome”?

For more recent human evolution, yes it has been done. Namely, scientists have modeled the evolution of the human genome since we split off from the chimp lineage. First, they compared human and chimp pseudogenes. These were chosen because mutations in pseudogenes tend to be neutral and neutral mutations accumulate at a more or less even pace. They then estimated the human mutation rate by measuring the occurence of deleterious mutations for known dominant Mendelian diseases like achondroplasia or hemophilia. What did they find?

quote:
Hum Mutat. 2003 Jan;21(1):12-27.

Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendelian diseases.

Kondrashov AS.
SourceNational Center for Biotechnology Information, NIH, Bethesda, Maryland 20892, USA.

Abstract
I estimate per nucleotide rates of spontaneous mutations of different kinds in humans directly from the data on per locus mutation rates and on sequences of de novo nonsense nucleotide substitutions, deletions, insertions, and complex events at eight loci causing autosomal dominant diseases and 12 loci causing X-linked diseases. The results are in good agreement with indirect estimates, obtained by comparison of orthologous human and chimpanzee pseudogenes. The average direct estimate of the combined rate of all mutations is 1.8x10(-8) per nucleotide per generation, and the coefficient of variation of this rate across the 20 loci is 0.53. Single nucleotide substitutions are approximately 25 times more common than all other mutations, deletions are approximately three times more common than insertions, complex mutations are very rare, and CpG context increases substitution rates by an order of magnitude. There is only a moderate tendency for loci with high per locus mutation rates to also have higher per nucleotide substitution rates, and per nucleotide rates of deletions and insertions are statistically independent on the per locus mutation rate. Rates of different kinds of mutations are strongly correlated across loci. Mutational hot spots with per nucleotide rates above 5x10(-7) make only a minor contribution to human mutation. In the next decade, direct measurements will produce a rather precise, quantitative description of human spontaneous mutation at the DNA level.
[emphasis mine]


So we find that the observed human mutation rate is in the same ballpark as the rate needed to produce the differences seen between chimps and humans. Other scientists have found lower rates, but it is again in the same ballpark.

As to the larger picture and genome length, you are talking about a very volatile system. Yes, insertions can be the insertion of a single base. You can also have whole genome duplications where the genome doubles in size in a single generation. This makes it difficult to model because of the great disparity in the number of bases in each event, and the rare case of whole genome duplications.

More importantly, it would appear that 2 whole genome duplications (a 4 fold increase in the size of the genome in 2 distinct events) were vital in the evolution of the vertebrate genome.

quote:
PLoS Biol. 2005 Oct;3(10):e314. Epub 2005 Sep 6.

Two rounds of whole genome duplication in the ancestral vertebrate.

Dehal P, Boore JL.

SourceEvolutionary Genomics Department, Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California, USA.
Abstract
The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish-tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.
emphasis mine


Does that help answer your questions?


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Panda
Member (Idle past 1094 days)
Posts: 2688
From: UK
Joined: 10-04-2010


Message 19 of 60 (668121)
07-17-2012 11:12 AM
Reply to: Message 12 by bcoop
07-17-2012 9:24 AM


Re: probably is a flaw
bcoop writes:

...if there are a million people reproducing any number of them may have a positive mutation all at the same point in time.


Yes.
And they could also all have different individual mutations.

bcoop writes:

a. 3 billion generations would take 60 billion years if each female reproduced at the age of 20.


Q: How many people are alive today?
A: ~7 billion.
To create those 7 billion people took more than 7 billion generations (in the sense you were referring to generations).

Q: How many children were born in the 200,000 years since homo sapiens evolved?
A: ~100 billion (current estimate).
This is 100 billion chances at mutations while homo sapiens have existed - and we are a comparatively slow breeding species.

Q: How many of our evolutionary cousins were born in the 2 billion years before homo sapiens evolved?

I am going to guess at much more than 100 billion.


CRYSTALS!!

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bcoop
Junior Member (Idle past 1645 days)
Posts: 27
From: Maine
Joined: 07-14-2012


Message 20 of 60 (668123)
07-17-2012 11:27 AM
Reply to: Message 18 by Taq
07-17-2012 11:09 AM


Re: Not so fast
Very much so - this is fascinating and I appreciate the time you took to write this. In another life I would probably have taken this on as a field of study.
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bcoop
Junior Member (Idle past 1645 days)
Posts: 27
From: Maine
Joined: 07-14-2012


Message 21 of 60 (668124)
07-17-2012 11:30 AM
Reply to: Message 17 by New Cat's Eye
07-17-2012 10:59 AM


Re: Generation lengths bogus
Thank you for this reply - I need to ponder what you mean by "bush" instead of "chain".
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New Cat's Eye
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Posts: 11244
From: near St. Louis
Joined: 01-27-2005
Member Rating: 1.9


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Message 22 of 60 (668126)
07-17-2012 11:44 AM
Reply to: Message 21 by bcoop
07-17-2012 11:30 AM


Re: Generation lengths bogus
t think of it like this:

Think of it more like this:

Or even more accurately:

You can click on those to expand them.

Edited by Adminnemooseus, : Made thumbnails bigger because the last two are huge when full sized.


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Wounded King
Member (Idle past 1476 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


(1)
Message 23 of 60 (668127)
07-17-2012 11:55 AM
Reply to: Message 21 by bcoop
07-17-2012 11:30 AM


Re: Generation lengths bogus
Principally he means that while humans are currently the latest point in an evolutionary sequence so is every other living thing on the planet. Humans are no more evolved than the yeast you compared them too. They have a larger genome and more organismal complexity but there is no chain of being from lowly yeast to pinnacle humans, instead they both constitute distant but contemporary tips of a ramifying series of diverging branch populations that goes back to a common ancestral population of some form billions of years ago.

Those more primitive ancestors may have resembled yeast or bacteria more in a lot of ways, but a modern yeast is not necessarily any more closely related to them than a modern human is. Indeed the chances are that most unicellular organisms are several thousand, millions or even billions of generations more distant from the hypothetical latest universal common ancestor (LUCA) than the larger multicellular organisms, especially complex metazoans like vertebrates.

TTFN,

WK


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bcoop
Junior Member (Idle past 1645 days)
Posts: 27
From: Maine
Joined: 07-14-2012


Message 24 of 60 (668129)
07-17-2012 12:02 PM
Reply to: Message 16 by jar
07-17-2012 10:15 AM


Re: well said
Much to think on here - thanks!
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bcoop
Junior Member (Idle past 1645 days)
Posts: 27
From: Maine
Joined: 07-14-2012


Message 25 of 60 (668130)
07-17-2012 12:06 PM
Reply to: Message 22 by New Cat's Eye
07-17-2012 11:44 AM


Re: Generation lengths bogus
The last illustration is quite informative. Lots to ponder here to - like how the bush is shrinking.
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bcoop
Junior Member (Idle past 1645 days)
Posts: 27
From: Maine
Joined: 07-14-2012


Message 26 of 60 (668131)
07-17-2012 12:07 PM
Reply to: Message 23 by Wounded King
07-17-2012 11:55 AM


Re: Generation lengths bogus
This is also helpful - lots to think on here too.
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New Cat's Eye
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Posts: 11244
From: near St. Louis
Joined: 01-27-2005
Member Rating: 1.9


Message 27 of 60 (668133)
07-17-2012 12:16 PM
Reply to: Message 25 by bcoop
07-17-2012 12:06 PM


Re: Generation lengths bogus
The bush isn't shrinking. Take a second look at the time lines on the bottom. It starts in the middle and extends outward in both directions. The stuff on the far left in in the same time period as the stuff on the far right.
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Coyote
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Message 28 of 60 (668136)
07-17-2012 1:47 PM
Reply to: Message 9 by bcoop
07-17-2012 9:09 AM


Mathematical modeling
“Has mathematical modeling been conducted of the amount of time it would take to generate the human genome”?

They are working on it, and the answers are not coming out very favorable to the creationists' hopes. Here is one example:

Making Genetic Networks Operate Robustly: Unintelligent Non-design Suffices, by Professor Garrett Odell (online lecture)

Abstract: Mathematical computer models of two ancient and famous genetic networks act early in embryos of many different species to determine the body plan. Models revealed these networks to be astonishingly robust, despite their 'unintelligent design.' This examines the use of mathematical models to shed light on how biological, pattern-forming gene networks operate and how thoughtless, haphazard, non-design produces networks whose robustness seems inspired, begging the question what else unintelligent non-design might be capable of.

http://www.youtube.com/watch?v=EsbKzFdW2bM


Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

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Tangle
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Message 29 of 60 (668139)
07-17-2012 4:08 PM
Reply to: Message 1 by bcoop
07-17-2012 4:15 AM


bcoop writes:

2.The human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes

I think you picked the wrong target with humans. I understand why you picked us - it,s because you think that humans are important and special, but actually, in evolutionary terms we're merely interesting ( to ourselves). If you want to make the argument you are making, why not pick a flower...

The slow-growing plant, which is native to the mountains of the Japanese island of Honshu but is also found in gardens in the UK, boasts more than 150 billion base pairs – the basic building block that links together to form DNA – in its genome. Humans have just three billion base pairs.

http://www.telegraph.co.uk/...w-growing-mountain-flower.html


Life, don't talk to me about life - Marvin the Paranoid Android

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Taq
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Posts: 6076
Joined: 03-06-2009
Member Rating: 3.6


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Message 30 of 60 (668144)
07-17-2012 5:47 PM
Reply to: Message 20 by bcoop
07-17-2012 11:27 AM


Re: Not so fast
Very much so - this is fascinating and I appreciate the time you took to write this. In another life I would probably have taken this on as a field of study.

It is a very exciting era in biology. I am sure that you have heard of Moore's law where he predicted that the number of transistors on integrated circuits would double every 2 years. History shows that Moore wasn't too far off.

The same thing is occuring in biology. Our ability to sequence DNA is doubling about every 2 years. Sequencing a bacterial genome used to be a multi-year project (at least it was when I got into science). Now it could be done in a day or two if push came to shove. The original NIH Human Genome Project took 10 years, and it was projected to take 15 years when it started in 1990. Now we can sequence a human genome in just 4 months with a handful of scientists, and that was 4 years ago. It no longer sounds like a crazy idea to sequence one genome out of every animal and plant genera, although such a task would be daunting.

However, this also means that we are awash in a sea of data that requires a ton of sifting and testing. On top of that, DNA sequence only gives us a tiny glimpse into a species. How and when that DNA is expressed, and what those DNA sequences do, are also very important questions.

30 years ago this field was moving ahead at a comparative glacial speed. Now it is hurling ahead at quite a clip. I agree with you, it is a fascinating field.

Edited by Taq, : No reason given.


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