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Author Topic:   Macroevolution: Its all around us...
EZscience
Member (Idle past 5154 days)
Posts: 961
From: A wheatfield in Kansas
Joined: 04-14-2005


Message 226 of 306 (218386)
06-21-2005 11:07 AM
Reply to: Message 223 by TimChase
06-21-2005 12:37 AM


Re: "Convergent DNA"
Very nicely explained. I regret I am just to swamped with work right now to read all your citations, but I hope to eventually.

This message is a reply to:
 Message 223 by TimChase, posted 06-21-2005 12:37 AM TimChase has replied

Replies to this message:
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TimChase
Inactive Member


Message 227 of 306 (218389)
06-21-2005 11:17 AM
Reply to: Message 224 by Wounded King
06-21-2005 4:42 AM


A Little on DNA's Spectral Density
Anyway, I thought that might be nice to include a few links on spectral density, particularly in relation to DNA. First, a brief intro to spectral density:
Generating noise with different power spectra laws
CAS - Error - 404 Document Not Found
You will notice that it is actually brownian motion which has a spectral density of two, and white noise which has a spectral density of zero. Sorry, I got that wrong in the first post on this topic -- I was going by memory with regard to something I hadn't touched in quite a while -- I will go back and correct.
However, there has been a bit of work on this subject related to DNA. The next link gives a fair number of sources extending from 1992 to 2005:
1/f (One-Over-F) Noise in DNA Sequences
NSLIJ-GENETICS -

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TimChase
Inactive Member


Message 228 of 306 (218394)
06-21-2005 11:35 AM
Reply to: Message 226 by EZscience
06-21-2005 11:07 AM


"Convergent DNA"/Retroviruses in Mammalian Evolution
Well, I do think there are other things going on today in the field of evolution which is are of a great deal more interest (at least to me) -- such as the role which retroviruses appear to play in mammalian evolution in general, and primate evolution in particular.
If this sounds like something that might be interest to others (I know you have already seen this), they might want to check out:
Message 193
Message 198
As for you, I understand that your work must keep you quite busy. Any time you are able to spare I will always consider an honor.
Take care, my friend.
This message has been edited by TimChase, 06-21-2005 12:02 PM

This message is a reply to:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 229 of 306 (218610)
06-22-2005 6:29 AM
Reply to: Message 225 by TimChase
06-21-2005 10:36 AM


Re: "Convergent DNA"
Well personally I did go to the original paper. That is what I was basing my statement, that they compared microsatellite regions from throughout the genome, on.
(Vowles and Amos, 2004) writes:
From the human genomic sequence, maximum sample size was set at 5,000 randomly selected loci for length classes (AC)2 to (AC)5. For longer microsatellites, of which fewer than 5,000 could be found, all sequences encountered were included.
So they looked at 5000 randomly selected short microsatellite regions and all the available longer microsatellites from throughout the genome.
The effect certainly is local in that a microsatellite predisposes nearby regions to certain mutations. Since many similar microsatellites are found throughout the genome they will predispose many sites throughout the genome to similar patterns of mutation. Similarly if such microsatellites are found in another species there is no reason to suppose they they will not also predipose the local DNA sequence to similar patterns of mutation.
So while the effect of the microsatellites is local the similarities are seen around microsatellites throughout the genome. So the 'convergent' sequences are not necessarily near to each other.
TTFN,
WK

This message is a reply to:
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TimChase
Inactive Member


Message 230 of 306 (218704)
06-22-2005 3:23 PM
Reply to: Message 229 by Wounded King
06-22-2005 6:29 AM


Re: "Convergent DNA"
My apologies -- I was kind of tied up on another list where things had gotten a bit heated.
However, I have had the chance to glance over the paper, and it is definitely something I would like to look at more closely later this week.
Thank you for finding the article and making it available!

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deerbreh
Member (Idle past 2893 days)
Posts: 882
Joined: 06-22-2005


Message 231 of 306 (218761)
06-22-2005 6:24 PM


Why get into micro/macro in the first place?
I don't claim to be an evolutionary biologist but I have had courses in evolution and I don't ever remember the terms microevolution or macroevolution being used. I think these terms are a creationist construct to explain away solid evidence for plain old evolution. The funny thing is, the serious Noah's Ark apologists have to invoke greatly speeded up evolutionary rates in order to get all of the animals on the ark (the whole "kinds" thing). And they would have you believe that getting a lion from a housecat is not macroevolution.

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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 232 of 306 (218770)
06-22-2005 6:34 PM
Reply to: Message 231 by deerbreh
06-22-2005 6:24 PM


I don't claim to be an evolutionary biologist but I have had courses in evolution and I don't ever remember the terms microevolution or macroevolution being used.
You would be right. It's creationist semantic trickery. It would be like saying that the numbers from 0-10 were "micronumbers" and that every number greater than that was a "macronumber", and saying that they were so fundamentally different you couldn't get one from the other.

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randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 233 of 306 (218778)
06-22-2005 7:06 PM
Reply to: Message 225 by TimChase
06-21-2005 10:36 AM


Re: "Convergent DNA"
Tim, I find your blather about misuse and misunderstanding applied towards me to be rather amusing, especially since it took you longer that it did me to find the relevant section.
But you did quote the exact same area as I had done on an earlier thread, eventually.
Maybe after awhile you will concede I was correct in my assessment of convergent tendencies within DNA.

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 Message 234 by pink sasquatch, posted 06-22-2005 9:49 PM randman has replied

pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 234 of 306 (218823)
06-22-2005 9:49 PM
Reply to: Message 233 by randman
06-22-2005 7:06 PM


convergence to ancestry leap
Maybe after awhile you will concede I was correct in my assessment of convergent tendencies within DNA.
Hi randman,
I am hopping in late here, so if you get a chance would you please specifically state your "assessment of convergent tendencies within DNA" so I can see where I stand on that assessment?
Thanks for citing the Vowles and Amos work - it is definitely interesting, and points out that the concept of "random mutation" is a simplified one. The molecular nature of some DNA sequences, particularly repetitive ones, make them more mutation prone than non-repetitive sequence. It appears that this bias extends to regions flanking certain types of repetitive sequence as well (or perhaps that repetitive sequence stabilizes certain flanking sequences thereby providing selection).
However, it seems to me (please correct me if I'm wrong) that you are asserting that: because convergent evolution is apparent in certain non-coding sequences, sequence similarities cannot be used to establish common ancestry.
That's an overreaching jump in logic - it may be that we simply cannot used those specific types of non-coding sequences in isolation as a way to determine the nature of common ancestry. However, we still have the entire non-repetitive genome to use to establish common ancestry, since there is no evidence for convergent evolution of such sequences. The study you cite doesn't have an impact on using pseudogene sequence to establish ancestry, for example.

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 Message 235 by randman, posted 06-22-2005 10:55 PM pink sasquatch has replied

randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 235 of 306 (218837)
06-22-2005 10:55 PM
Reply to: Message 234 by pink sasquatch
06-22-2005 9:49 PM


Re: convergence to ancestry leap
Sure...First off, genetics is still fairly young as a science, and we will probably know more in a few years.
Secondly, my "assessment" is pretty simple. There exists convergent tendencies in DNA. The degrees of which, types, etc,...are still somewhat undetermined by science. But regardless, it is incorrect to think of mutations are purely random.
Thirdly, we need a better understanding of both convergency in DNA and via environmental conditions to properly assess whether claiming evidence (similar traits) can be "only explained" via common ancestry is accurate. It is that an accurate assumption?
The best we can say is maybe. Affirming common ancestry based on shared traits is an unfounded leap, an assumption that is falsified to a degree by convergency in general.
that you are asserting that: because convergent evolution is apparent in certain non-coding sequences, sequence similarities cannot be used to establish common ancestry.
I am not stating that, but I am not stating the opposite either. I think the issue is unclear. Sequence similarities, it seems reasonable, can be explained by some sort of shared commonality.
Evolutionists pretty much assign all shared similarities as the product of common descent except where this seems impossible to them, and then they advocate convergent evolution.
I think there is an inherent problem there since it is assumed that our impressions of likelihood, based on incomplete evidence, backs up assigning similarities to common ancestry instead of convergent evolution.
Creationists offer other reasons for similarities such as common authorship.
My view, in general, is that there are a lot of problems with evolutionary theory and the best approach is to try to take a good look at each piece of evidence without assuming the Big Picture.
In that regard, I am willing to consider any number of commonalities as causes for similarities. Similar causes equal similar effects.
Some are:
common ancestry
convergent evolution (maybe)
common authorship via special creation
common design embedded in the universe manifesting in DNA convergency

This message is a reply to:
 Message 234 by pink sasquatch, posted 06-22-2005 9:49 PM pink sasquatch has replied

Replies to this message:
 Message 236 by pink sasquatch, posted 06-22-2005 11:57 PM randman has replied

pink sasquatch
Member (Idle past 6023 days)
Posts: 1567
Joined: 06-10-2004


Message 236 of 306 (218845)
06-22-2005 11:57 PM
Reply to: Message 235 by randman
06-22-2005 10:55 PM


Re: convergence to ancestry leap
we need a better understanding of both convergency in DNA and via environmental conditions to properly assess whether claiming evidence (similar traits) can be "only explained" via common ancestry is accurate. It is that an accurate assumption?
First - I don't think anyone is claiming that similar traits can only be explained by common ancestry.
Second - I feel there is a strong understanding of DNA sequence evolution. There is no evidence for convergent evolution of coding or pseudo-coding sequence. Take the popular GLO gene as an example (it is involved in vitamin C production). The gene is mutated so that it is non-functional in humans, chimps, fruit bats, and guinea pigs; thus these species must get vitamin C from their diet.
Humans and chimps have the exact same mutation in the GLO gene, while the guinea pigs and fruit bats have different, distinct mutations. The current theory is that there were three mutational events leading to the three 'broken' genes in the four species - and that the GLO gene was mutated in a common ancestor of humans and chimps, with both species inheriting the mutation.
Does convergent evolution make sense in this case? How would you test it?
It doesn't make sense to me that the arisal of identically not-quite-functional-genes would arise by convergent evolution in two species, especially since there are countless examples of similar cases throughout the genomes of chimps and humans.
To put it slightly differently, why would all of the sequences in the human and chimp genomes end up more closely convergently evolved than, say, the mouse genome? If sequences were converging to a particular sequence in multiple species, and you compared numerous sequences across those species, there should be no correlation to morphology - instead there should just be genetic "noise".
The best we can say is maybe.
If you haven't figured it out yet, science is tentative, so it is always the case that "the best we can say is maybe". Science proceeds via falsification - common ancestry has yet to be falsified by any data, and there is an unimaginably enormous amount of data that tests common ancestry.
Affirming common ancestry based on shared traits is an unfounded leap, an assumption that is falsified to a degree by convergency in general.
I don't disagree, but you have to be careful here in switching between shared traits and shared sequence. The truth of the matter is that shared traits and shared sequence produce matching "family trees", and importantly, the result is the same even when sequence that does not contribute to phenotypic traits is used.
Sequence similarities, it seems reasonable, can be explained by some sort of shared commonality.
But is it convergent evolution at the DNA level at all reasonable to explain this commonality? Is it reasonable that all shared genes across all species convergently evolved? (For example, that the Cytochrome C gene arose separately in every single species on the planet, from bacteria to badger?)
That seems like an amazingly far-fetched explanation to me... and combined with the other characteristics of sequences I describe above, I think we can logically cross "convergent evolution" and "common design embedded in the universe manifesting in DNA convergency" off the list as being solely responsible for the commonality.
And an interesting side note: What I think is really fantastic is that your "common design embedded in the universe manifesting in DNA convergency" is essentially a rewriting of Haeckel's "biogenetic law" at the genetic level instead of the phenotypic level. That is the same law that lead him to start fradulantly representing embryos in the diagrams whose use you so abhor. It is also a "law" that has been continually falsified since the 1870s.

This message is a reply to:
 Message 235 by randman, posted 06-22-2005 10:55 PM randman has replied

Replies to this message:
 Message 237 by randman, posted 06-23-2005 2:22 AM pink sasquatch has replied

randman 
Suspended Member (Idle past 4899 days)
Posts: 6367
Joined: 05-26-2005


Message 237 of 306 (218876)
06-23-2005 2:22 AM
Reply to: Message 236 by pink sasquatch
06-22-2005 11:57 PM


Re: convergence to ancestry leap
I think it's hard to deal with your post if you deny convergent DNA in light of the data.
There is no evidence for convergent evolution of coding or pseudo-coding sequence.
There is evidence of convergent DNA, and that's the point. Since your line of reasoning rests on that, there is not much else to say except you are just incorrect there.
To put it slightly differently, why would all of the sequences in the human and chimp genomes end up more closely convergently evolved than, say, the mouse genome?
That's exactly what you would expect if the 2 were created via special creation. The data fits special creation perfectly.
But let's don't debate that now.
Let's just say that the reason we see genetic similarities between morphologically similar species is due to the fact genes produce morphology.
As far as the non-coding genes, it is established and an area of intense study that non-coding DNA exhibits convergent tendencies, that there is a predisposition within the DNA.
It is not surprising then that similar sequences of DNA would exhibit a similar predisposition.
What would be interesting is to study DNA over a long perdiod of time within a species and see if the pattern od predisposition can be unveiled, and even more interesting if we knew what caused convergent DNA.
One last note, I am not like evolutionists. I don't argue a sole explanation, as you suggest I do. Please open your mind enough to realize that I listed several commonalities, not just one, that could theoritically produce common features and similarities.
it is evolutionists always trying to fit everything into one commonicality cause, not me.
This message has been edited by randman, 06-23-2005 02:24 AM

This message is a reply to:
 Message 236 by pink sasquatch, posted 06-22-2005 11:57 PM pink sasquatch has replied

Replies to this message:
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crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 238 of 306 (218897)
06-23-2005 7:03 AM
Reply to: Message 237 by randman
06-23-2005 2:22 AM


There is evidence of convergent DNA
I guess I don't understand, because I thought the evidence you presented was of convergence between multiple satellite regions across one single genome. How does that apply to, or substantiate, convergence between multiple individual unrelated genomes?

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 Message 239 by Wounded King, posted 06-23-2005 7:32 AM crashfrog has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 239 of 306 (218899)
06-23-2005 7:32 AM
Reply to: Message 238 by crashfrog
06-23-2005 7:03 AM


The principle is still sound. If specific sequences can predispose neighouring regions of sequence to specifc patterns of mutation throughout the human genome there is no reason to believe that similar sequences will not lead to similar patterns in other species.
Of course there is a possibility that some specific mechanism is in operation in the human genome and that these patterns would not occur in species lacking the neccessary elements of that mechanism. But in the absence of any such mechanism and assuming it is the composition of the sequence itself that is leading to the effect then there is no reason to doubt that they could lead to convergence in sequences across species.
TTFN,
WK

This message is a reply to:
 Message 238 by crashfrog, posted 06-23-2005 7:03 AM crashfrog has replied

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EZscience
Member (Idle past 5154 days)
Posts: 961
From: A wheatfield in Kansas
Joined: 04-14-2005


Message 240 of 306 (218951)
06-23-2005 11:41 AM


Relevance?
Can some one please explain or discuss the implications of this 'convergent DNA' to our current understanding of macroevolutionary processes, infered cladograms or phylogenies?

Replies to this message:
 Message 241 by Wounded King, posted 06-23-2005 12:00 PM EZscience has replied

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