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Author Topic:   Is Earth old enough for DNA to evolve?
Taq
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Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(2)
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?

This message is a reply to:
 Message 9 by bcoop, posted 07-17-2012 9:09 AM bcoop has replied

Replies to this message:
 Message 20 by bcoop, posted 07-17-2012 11:27 AM Taq has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(3)
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.

This message is a reply to:
 Message 20 by bcoop, posted 07-17-2012 11:27 AM bcoop has replied

Replies to this message:
 Message 35 by bcoop, posted 07-17-2012 8:46 PM Taq has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(2)
Message 49 of 60 (668247)
07-19-2012 12:04 AM
Reply to: Message 48 by bcoop
07-18-2012 9:53 PM


Re: So what have I learned?
2. The complexity is beyond what I had even imagined. This is part of the problem that the general public like myself have in accepting the science that is presented to us. Most are not in forums like this. What we hear is that the genome has three billion pieces of information and that most if it occurred through random mutations. We think "so it just randomly organized itself three billion times and here we are". It is hard to accept intuitively that the utter complexity of genetics just randomly occurred even with natural selection. The science community has struggled with communicating this — maybe there is a straight forward presentation of genetics and evolution that does a good job of explaining these things and I suspect someone may have a suggestion. Several of the posts here were impressively clear and comprehensive in just a paragraph or two.
Trust me when I say this. The disconnect between the general populace and the scientific community has been a major issue for decades, if not centuries. Sometimes it feels like the "Who's on first" act. I wish there was an easy fix, but I really don't think there is. As you are finding out, learning about what science has discovered requires a lot of effort on the part of the general populace. If you really want to understand what scientists are talking about you need a lot of background knowledge in the given field. Even more, you need a great deal of knowledge to know when someone is full of bullshit (pardon the language, but this is the nicest term I could come up with).
I have just erased 5 paragraphs dealing with extremely varied topics that wandered all over the place, so trust me when I say that I am quite passionate about what you have posted. Science communication is a very, very interesting topic, especially for someone who sits on the science side of the fence. How to make it work, why it isn't working, and why it probably won't work are all questions that I find extremely interesting. I think you are starting to get a glimpse of what I am talking about. My advice? Take a firm grasp of that increasing sense of curiosity bubbling in your gut and don't let go. Enjoy the ride!!

This message is a reply to:
 Message 48 by bcoop, posted 07-18-2012 9:53 PM bcoop has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 50 of 60 (668248)
07-19-2012 12:07 AM
Reply to: Message 44 by Minnemooseus
07-18-2012 4:08 AM


Re: About the age and life diversity diagram
The diagram is still pretty confusing.
I would suggest using a Google maps approach. Start with the big picture and allow users to zoom in on the areas they are interested in. For that purpose, I would strongly suggest Tree of Life Web Project.
Start here.

This message is a reply to:
 Message 44 by Minnemooseus, posted 07-18-2012 4:08 AM Minnemooseus has seen this message but not replied

  
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