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Author Topic:   front loading: did evos get it backwards
randman 
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Posts: 6367
Joined: 05-26-2005


Message 31 of 164 (471381)
06-16-2008 1:25 PM
Reply to: Message 30 by Wounded King
06-16-2008 12:51 PM


Re: Types of genes?
I think you are not seeing the forest for the trees here. Take a step back and really consider the ND paradigm of morphology and genetic evolution roughly parralleling one another. We can argue about degrees of difference, but what we are seeing under any interpretation is a RADICAL departure from the predictions of NeoDarwinism.
You can't start out (latest common ancestor) with some master genome, nor can you start out with some massive or complex genome and fit the paradigm. ND predicts a gradual accumulation of genes and genetic complexity with random mutation and natural selection resulting in novel traits. Now, I know plenty of evos try to avoid this and say, well, evolution can occur via a loss of genes....sure, but the pattern predicted by ND means that you can't just get some massive, complex genome without new morphology.
What we are seeing is not NeoDarwinism.
Let me put it this way. There is one camp that predicted this and one or a few that did not. The front loaders predicted it. Evos based on their ideas (their theory) find it surprising, paradoxical, etc,....they predicted a simpler genome with a simpler organism morphologically. Now, evos can pretend all they want this is no big deal and I suppose evos have a theory so elastic they can fit any fact into it whatsoever, but if we want to be honest, there is the fact evos didn't expect this. It doesn't fit the ND paradigm.
Edited by randman, : No reason given.

This message is a reply to:
 Message 30 by Wounded King, posted 06-16-2008 12:51 PM Wounded King has replied

Replies to this message:
 Message 32 by Coyote, posted 06-16-2008 1:34 PM randman has replied
 Message 37 by Wounded King, posted 06-16-2008 6:13 PM randman has replied

  
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 32 of 164 (471383)
06-16-2008 1:34 PM
Reply to: Message 31 by randman
06-16-2008 1:25 PM


Re: Types of genes?
ND predicts a gradual accumulation of genes and genetic complexity with random mutation and natural selection resulting in novel traits. Now, I know plenty of evos try to avoid this and say, well, evolution can occur via a loss of genes....sure, but the pattern predicted by ND means that you can't just get some massive, complex genome without new morphology.
I pointed this out before, but you ignored my post.
How about changes in genes and gene expression instead of addition or loss of genes? As far as I know, the theory of evolution is based on change in the genome.

This message is a reply to:
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Message 33 of 164 (471384)
06-16-2008 1:37 PM


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randman 
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Message 34 of 164 (471391)
06-16-2008 2:20 PM
Reply to: Message 32 by Coyote
06-16-2008 1:34 PM


Re: Types of genes?
So the theory of evolution doesn't say anything about the evolution and origination of genes?

This message is a reply to:
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Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


Message 35 of 164 (471393)
06-16-2008 2:24 PM
Reply to: Message 34 by randman
06-16-2008 2:20 PM


So the theory of evolution doesn't say anything about the evolution and origination of genes?
Near as I can recall from my grad school days the theory of evolution dealt with change in the genome.
The fledgling field of abiogenesis dealt with origins.

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

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


Message 36 of 164 (471396)
06-16-2008 3:05 PM
Reply to: Message 35 by Coyote
06-16-2008 2:24 PM


Uh huh? So the theory of evolution doesn't explain how the genes evolve and novel genes are developed, eh?
All that bit about random mutation and natural seleection just doesn't apply to originating genes?
Edited by randman, : No reason given.

"Haeckel's much-criticized embryo drawings are .... evidence for evolution."
Richardson and Gerhard Keuck, 2002 paper

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


Message 37 of 164 (471413)
06-16-2008 6:13 PM
Reply to: Message 31 by randman
06-16-2008 1:25 PM


Do you disagree with parsimony as a principle?
We can argue about degrees of difference, but what we are seeing under any interpretation is a RADICAL departure from the predictions of NeoDarwinism.
Really? Care to provide any substantive argumentation about the comparative morphology of ancient single celled organisms and metazoa? Or even the comparative genetics? You haven't shown anything to substantiate this. The paper you presented in the OP certainly doesn't.
You can't start out (latest common ancestor) with some master genome, nor can you start out with some massive or complex genome and fit the paradigm.
No one other than perhaps creationists posits the starting point being an organism with a complex master genome. All we know is that there is research showing that some common ancestral lines, i.e. the metazoa in the case of A. millipora and the eukaryotes in the paper from the OP, are more complex than was previously estimated. As I pointed out in my post this is because we use a parsimony based model to estimate these things, obviously the assumption of parsimony will tend to underestimate the extent of a common ancestral genome more the fewer modern organisms are used to estimate the common ancestral genome.
Would you like to address this point and suggest how we could operate under any assumption other than parsimony?
But the fact that we are refined the data for these LCAs and expanding the estimated size of the LCA genomes involved does not equate to the sort of ludicrous front loading scenarios you posit.
Your case is certainly not helped by your equivocating between gene types and genes. As has been pointed out repeatedly gene types only refers to large overarching superfamilys and protein domains, each one of which can represent from one to a thousand or several thousand genes. Additionally the importance of gene regulation over gene complement is being more and more appreciated as we find out more about gene regulatory networks and especially since the discovery of further layers of regulation in the higher order structures of DNA and non-coding RNAs.
.they predicted a simpler genome with a simpler organism morphologically.
And there is not a shred of evidence contradicting this. You still don't seem to grasp that an estimated LCA genome more complex than a previous prediction is just that, it doesn't suddenly become more complex than all modern species just because you want it to. Can you tell us how the morphology of the putative LCA compared to that of primitive plants or metazoa? Beyond it sharing basal eukaryotic traits and some suggestions from the data in the OP I don't see that you would have anything to go on, and a lot of those proteins didn;t seem to have any morphological role at all, and why should they, single celled organisms tend to put their complexity into biochemistry more often than morphology. Similarly what do you think you can say about their genetic complexity, other than the latest estimates using a wider selection of organisms indicate a higher 'gene type' complement than previous estimates?
The most important issue to address is that of parsimony, it is the reason why we would expect to underestimate the diversity of an ancestral genome on the basis of only a few descendant lines. I'd rather you address that point than anything else in this post.
TTFN,
WK

This message is a reply to:
 Message 31 by randman, posted 06-16-2008 1:25 PM randman has replied

Replies to this message:
 Message 38 by randman, posted 06-16-2008 7:47 PM Wounded King has replied
 Message 41 by ICANT, posted 06-17-2008 12:00 PM Wounded King has replied

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


Message 38 of 164 (471423)
06-16-2008 7:47 PM
Reply to: Message 37 by Wounded King
06-16-2008 6:13 PM


Re: Do you disagree with parsimony as a principle?
I don't think the issue of parsimony is the crux of the matter unless you want to disagree with the paper's findings. The real issue as I have stated repeatedly is the NeoDarwinian hypothesis that random mutation produces genetic change that is then adapted via natural selection. This process envisions morphological and genetic evolution occuring roughly parellel so that the expectation is that simpler and more primitive organisms would have simpler genomes as well.
What we are finding, if you assume common descent in the first place, is that this hypothesis is wrong and doesn't match the facts.
But the fact that we are refined the data for these LCAs and expanding the estimated size of the LCA genomes involved does not equate to the sort of ludicrous front loading scenarios you posit.
Hmmmm...the fact is the front loaders predicted these findings and evos and ND predicted the opposite which is why they were "surprised" and found it "paradoxical" that the data did not match what they expected. You can call it ludicrous, but one model fit the facts, in this case, and the ND model did not.
You appear to want to move the goalposts and say:
it doesn't suddenly become more complex than all modern species just because you want it to.
Even if you want to say it's just as complex, the same holds true. We have a massive genome in the most primitive organisms of the latest common ancestors, evolution (assuming it occurred at all) via loss and recombination of genes instead of the slow accumulation of genes, just as the front loaders predicted and just as ND did not predict. ND is a gradualistic theory. It rests on small changes accumulating over time so that the genome should roughly parallel morphological evolution. The exact opposite is the case. The latest common ancestors of plants and animals and the latest common metazoan ancestor appear to have had genomes as complex or more complex than the following lineages. That's front loading whether you want to admit it or not.

This message is a reply to:
 Message 37 by Wounded King, posted 06-16-2008 6:13 PM Wounded King has replied

Replies to this message:
 Message 39 by Wounded King, posted 06-17-2008 5:40 AM randman has replied

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


Message 39 of 164 (471483)
06-17-2008 5:40 AM
Reply to: Message 38 by randman
06-16-2008 7:47 PM


You can't just handwave parsimony away.
I don't think the issue of parsimony is the crux of the matter unless you want to disagree with the paper's findings.
No matter what you think, parsimony is the issue. The OP paper's findings don't contradict parsimony in any way. The fact that after looking at a wider variety of organisms, by including Dictyosteliumn, they estimate a larger gene type complement for the LCA is a result of parsimony.
By parsimony we assume that identical or very high identity genetic features only arose once. If such a feature is shared by 2 species we assume it was present in their common ancestor. If we find 1 species out of a number which has a unique gene then we assume that the gene arose in that 1 species lineage rather than being lost in all of the others. Those are the fundamental principles of maximum parsimony, building phylogenies on the basis that they involved the least change neccessary.
Obviously then if you add another species into such a maximum parsimony phylogeny you cannot reduce the estimated gene complement of the LCA, since it is already as parsimonious as it can be. All adding a new species can do is increase the estimated genetic complement of the LCA, as in both the cases you have brought up, or leave the original estimated size as it is. I would suggest that given how few species most of the common LCA genomic estimates are based on, and the ever increasing number of sequenced genomes, we must expect to see increases in the size of the estimated LCA genomic complement.
Do you disagree with this analysis? If so why?
This process envisions morphological and genetic evolution occuring roughly parellel so that the expectation is that simpler and more primitive organisms would have simpler genomes as well.
What we are finding, if you assume common descent in the first place, is that this hypothesis is wrong and doesn't match the facts.
No it isn't, or if it is you haven't provided any research to suggest it is, certainly not either of the papers you have referenced here. If you think they do make this case then give us your reasoning don't just give us your conclusions.
Hmmmm...the fact is the front loaders predicted these findings and evos and ND predicted the opposite which is why they were "surprised" and found it "paradoxical" that the data did not match what they expected. You can call it ludicrous, but one model fit the facts, in this case, and the ND model did not.
Rubbish. There is no single front loader model, I have seen several suggested and they would make quite different predictions. If you have a particular favoured actual testable model then tell us what it is and what you think it predicts. Is it the supergenome type model? You think that the LCA for either all life or for the LCA of each created kind/baramin had all the genetic diversity represented in all its ancestors?
Simply saying 'Front loading' tells us nothing because there are several alternative 'Front loading' scenarios, i.e. John Davison's prescribed evolutionary hypothesis is a 'Front loading' hypothesis but doesn't require an ancestral supergenome. I have even seen people argue that simple de novo creation of an ancestral cell with the potential to evolve can be considered 'Front loading', see here.
Whatever the shortcomings of 'Front loading' as a specific term the other contention, that this contradicts neo-darwinian theory, is simply wrong. It suprecedes previous estimates of the LCA genomic complement for exactly the parsimony related reasons I described previously, it doesn't predict the opposite at all. If you have a reasoned argument why it does then make it, if you haven't then stop saying it does.
We have a massive genome in the most primitive organisms of the latest common ancestors,
Again you say something scientifically nonsensical. The latest common ancestors aren't the most primitive organisms. This is exactly what you did before, mixing up the concept of an earliest common ancestor, the most primitive organism, with that of the latest.
evolution (assuming it occurred at all) via loss and recombination of genes instead of the slow accumulation of genes
Bald assertion, none of your references support this, you have stretched hyperbole to the breaking point.
ND is a gradualistic theory. It rests on small changes accumulating over time so that the genome should roughly parallel morphological evolution.
I have made some arguments in the criticising neo-darwinism thread addressing this ...
Wounded King writes:
Yes, but there is not a 1 to 1 linear correspondence. Morphological evolution certainly depends on genetic evolution but there can be a large amount of genetic evolution independent of morphology per se, i.e. evolution of genes involved with cellular metabolism and biochemistry or even elements of the immune system.
It would be naive in the extreme to assume that just because an organism has a bigger genome it should be a bigger organism, or even necessarily a more complex one. Having said that it should be noted that in some cases of polyploidy, i.e. whole genome duplications, the resultant species are larger, the prime example being the frog Xenopus laevis.
The exact opposite is the case.
Nonsense, there are numerous examples of endoparastic organisms with reduced genomes, which would correspond to your genetic/morphological parallelism. There are also multitudinous examples of comparatively simple organisms with comparatively simple genomes. To go from the finding that LCAs may be more complex than expected to saying they are as complex or more complex than extant modern species is a leap from science into science fiction. Did A. milipora suddenly have an increased genome size just because it shared a gene with 'higher' metazoa? No.
The latest common ancestors of plants and animals and the latest common metazoan ancestor appear to have had genomes as complex or more complex than the following lineages
A completely unsupported assertion as you would realise if you understood parsimony. Show us the evidence and explain the reasoning which gives you LCAs with genomes as complex or more complex than all the following lineages. Don't just refer us off to some papers, because none of the papers you have referenced so far support your conclusion, if you still contend they do then make the blooming argument and demonstrate how they do.
That's front loading whether you want to admit it or not.
Maybe it is since there is no clear definition of what 'Front loading' is or what we should expect to see from it.
TTFN,
WK
Edited by Wounded King, : Some grammatical foibles

This message is a reply to:
 Message 38 by randman, posted 06-16-2008 7:47 PM randman has replied

Replies to this message:
 Message 50 by randman, posted 06-17-2008 2:05 PM Wounded King has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 40 of 164 (471487)
06-17-2008 6:37 AM


Randman is now so far off in his own little world that I have no idea what he's talking about.
Does anyone want to take a guess?

  
ICANT
Member
Posts: 6769
From: SSC
Joined: 03-12-2007
Member Rating: 1.5


Message 41 of 164 (471549)
06-17-2008 12:00 PM
Reply to: Message 37 by Wounded King
06-16-2008 6:13 PM


Re: Do you disagree with parsimony as a principle?
Hi WK,
Wounded King writes:
No one other than perhaps creationists posits the starting point being an organism with a complex master genome.
I must have missed something somewhere.
I believe in Creation.
I believe we have a common ancestor as every living thing on earth in the original creation was produced from the earth.
I just don't believe we got from there to here the way evolutionist believe we did.
God Bless,

"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."

This message is a reply to:
 Message 37 by Wounded King, posted 06-16-2008 6:13 PM Wounded King has replied

Replies to this message:
 Message 42 by Wounded King, posted 06-17-2008 12:09 PM ICANT has replied
 Message 43 by Brian, posted 06-17-2008 12:12 PM ICANT has replied

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


Message 42 of 164 (471550)
06-17-2008 12:09 PM
Reply to: Message 41 by ICANT
06-17-2008 12:00 PM


Re: Do you disagree with parsimony as a principle?
I didn't mean that statement to cover all creationists, since creationist beliefs are highly heterogeneous. People who argue from 'front loading' are predominantly creationists, there may be a few UFO cultists as well but mostly they are creationists.
Having said that ...
I believe we have a common ancestor as every living thing on earth in the original creation was produced from the earth.
... makes no sense at all to me are you saying that a planet itself is the common ancestor, are you being pointlessly metaphorical? Are you making the 'common creator' argument but mixing the words up to make it confusing and impenetrable?
TTFN,
WK

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Brian
Member (Idle past 4959 days)
Posts: 4659
From: Scotland
Joined: 10-22-2002


Message 43 of 164 (471551)
06-17-2008 12:12 PM
Reply to: Message 41 by ICANT
06-17-2008 12:00 PM


Re: Do you disagree with parsimony as a principle?
living thing on earth in the original creation was produced from the earth.
Apart from Eve?

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 Message 41 by ICANT, posted 06-17-2008 12:00 PM ICANT has replied

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ICANT
Member
Posts: 6769
From: SSC
Joined: 03-12-2007
Member Rating: 1.5


Message 44 of 164 (471555)
06-17-2008 12:23 PM
Reply to: Message 43 by Brian
06-17-2008 12:12 PM


Re: Do you disagree with parsimony as a principle?
Brian writes:
Apart from Eve?
Eve was produced from the original creation after the original creation.
God Bless,

"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."

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ICANT
Member
Posts: 6769
From: SSC
Joined: 03-12-2007
Member Rating: 1.5


Message 45 of 164 (471560)
06-17-2008 12:50 PM
Reply to: Message 42 by Wounded King
06-17-2008 12:09 PM


Re: Do you disagree with parsimony as a principle?
Hi WK,
Wounded King writes:
... makes no sense at all to me are you saying that a planet itself is the common ancestor
I am saying in my version of creation every living creature in the original creation was formed from the earth.
They were full grown creatures capable of reproduction.
That would mean we have a common place of origin.
The elements in the living creatures are contained in the earth.
Would that not make them related.
Isn't the evolution view that everything came from the first life form that spontaneously appeared giving everything a common ancestor.
The creatures formed this way took a very long time to reach the stage they are at today.
God Bless,

"John 5:39 (KJS) Search the scriptures; for in them ye think ye have eternal life: and they are they which testify of me."

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 Message 42 by Wounded King, posted 06-17-2008 12:09 PM Wounded King has not replied

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