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Author Topic:   front loading: did evos get it backwards
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 151 of 164 (473765)
07-02-2008 7:12 PM
Reply to: Message 150 by randman
07-02-2008 6:51 PM


Re: Shaking up the tree of life
It'd be nice if you just corrected her logic to start out with
Why didn't you? Surely ...
illustration of the fallacy of her argument on that point.
is better served by actually pointing out the fallacy than by asking a purportedly hypothetical question which you already know the answer to?
TTFN,
WK

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


Message 152 of 164 (473798)
07-02-2008 11:29 PM
Reply to: Message 148 by Wounded King
07-02-2008 6:32 PM


Re: Don't you want to discuss the actual OP topic then?
Don't just keep repeating the same claims, why not show us some specific instances where 'front loader's specifically predicted findings like this?
Er ... because he's not telling the truth?

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Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 153 of 164 (473830)
07-03-2008 7:30 AM
Reply to: Message 145 by randman
07-02-2008 2:49 PM


Re: Shaking up the tree of life
randman writes:
And no, NeoDarwinism doesn't explain reality that well, but maybe we should stick more closely with the OP here and focus on it.
If you were really interested in staying on-topic you wouldn't be continuing your habit of issuing off-topic broadsides in the form of misinformation that can't be ignored and demands correction. If you're really sincere about staying on-topic, then when I again point out that you appear to have falsification backwards and that nothing in your reply corrects this impression, you'll propose a new thread instead of replying in this one.
--Percy

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Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 154 of 164 (473922)
07-03-2008 5:56 PM
Reply to: Message 147 by randman
07-02-2008 3:16 PM


Re: Shaking up the tree of life
Hi, Randman.
randman writes:
The big point is the genome starts out big, not that mutations or additions of new genes (especially since genes that were lost might come back) can never be involved. It does include the idea though of substantial loss of genes as a pattern of variation, but not necessarily some absolute.
I stand corrected: "front-loading" apparently does not deny addition or accumulation of genes.
randman writes:
Having more types of genes is still very significant, but since you are introducing size of base-pairs, would you accept then that size is a standard which if violated, disproves ND?
No. The whole point of my diatribe on that data was to show that the human genome has experienced a lot more addition to its genome since its split with Dictyostelium than loss. That humans have lost some "types" of genes is insignificant next to the fact that total gene count has more than doubled and genomic mass has increased one hundredfold. The major trend defining the evolutionary separation between human and LCA is addition, not loss, which is more difficult for front-loading to explain than ToE.
Note that this parallels the fossil record: we have “lost” many “types” of organisms to extinction (e.g. anomalocaridids, lepidodendrales, calamites, trilobites, thylacines, dinosaurs, multituberculates, cycadioids, ammonites, arthropleurids, phorusrhacids, chalicotheres, ground sloths, mesonychids, Titanopterans, Paleodictyopterans, Protodonatans, etc.), but we still have a rich and diverse biosphere alive today that is made up from only the few lineages that have managed to survive.
randman writes:
One of the problems with this thread is the lack of any attempt by evos to admit these findings are "paradoxical" and explain why they were considered paradoxical. There doesn't seem to be a willingness to really address the OP head-on in that regard.
The problem, then, is that you have failed to show how these findings are paradoxical. ToE doesn’t require or predict any specific pattern of change mechanics at all. It doesn’t even require that complexity increase over time. It only requires that changes (of any sort: addition, alteration, loss, duplication, etc.) accumulate as natural selection weeds out the ones that had detrimental effects. Please note that “losses” can also “accumulate,” which is a point you’re seeming to miss somehow.
Another thing that you’ve completely missed is the difference between last common ancestor and earliest common ancestor, despite it having been explained to you. Because ToE doesn’t require a net gain or loss over an unspecified evolutionary interval, it does not predict how big a genome will be at any given time. Common descent would suggest a simple beginning, but ToE also doesn’t really depend on common descent, either: everything could have just as easily evolved from two independent ECAs if two primal organisms could arise and compete with each other, or seven, or four hundred and ninety-three.

Darwin loves you.

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Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 155 of 164 (473927)
07-03-2008 6:12 PM
Reply to: Message 144 by randman
07-02-2008 2:44 PM


Re: hmm....
randman writes:
deerbreh writes:
Yes, molecular DNA evidence can support common ancestry arguments. Absolutely. That is NOT the same as saying molecular DNA evidence could support your notion of "front loading", however.
So you agree that molecular data can make indications of what the theoritical last common ancestor's genome contained, right? That's what I cited in the OP, and yet you insist it can only be considered as evidence for Darwinism, not front-loading, regardless of what the data says.
Read more carefully, and you'll see that he actually said, "molecular DNA evidence can support common ancestry arguments," not "molecular DNA evidenc can support Neo-Darwinist arguments." Last I checked, "common ancestry" is neither support nor hindrance to either Neo-Darwinism or front-loading.
It would take an entirely different line of research to distinguish between front-loading and Neo-Darwinism. Front-loading, as described here, amounts only to a theory of origins (the only thing it really describes is how life started) and you should know by now that ToE doesn’t rely on any specific circumstance of origins to still function. However the organisms popped into existence, they still had to compete with one another for survival, and conditions in the world invariably will lead to changes in their genomes.

Darwin loves you.

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bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 156 of 164 (473939)
07-03-2008 7:41 PM
Reply to: Message 155 by Blue Jay
07-03-2008 6:12 PM


Front loading
Bluejay writes:
Front-loading, as described here, amounts only to a theory of origins (the only thing it really describes is how life started) and you should know by now that ToE doesn’t rely on any specific circumstance of origins to still function.
Yes, that's how I understood it as well. For some time I've been thinking that this sort of thing will be the future of I.D., and it will become an attack on the abiogenesis hypotheses rather than the theory of evolution. An I.D.er/blogger called Mike Gene seems to be the best known advocate of this kind of thing.
He is what his fellow I.D.er, randman, would call an "evo".

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


Message 157 of 164 (473967)
07-04-2008 4:11 AM
Reply to: Message 156 by bluegenes
07-03-2008 7:41 PM


Re: Front loading
The type of front loading described at Telic Thoughts is only one approach, and definitely one on the more theistic evolutionary end.
There are other front loading scenarios such as the supergenome, which seems to be the view Randman is talking about, in which specially created ancestral organisms have genetic complexity unnecessary for their own function but which allows the generation of further diversity and complexity in descendant lineages.
There is also a form of cryptic supergenome where the genome is in some way pre-programmed to give rise to further genetic complexity and novel genes from a comparatively genetically simple created ancestor. This is similar to JAD's Prescribed Evolutionary Hypothesis although JAD has also said things which suggest he may be closer to the non-cryptic supergenome but that activation of specific genes is brought about by pre-programmed genetic events at the chromosomal level.
As I said before, 'Front loading' is such a broad church that it could cover virtually anything so it is hard to know what specific predictions Randman thinks 'Front loading' makes.
TTFN,
WK

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Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 158 of 164 (473981)
07-04-2008 8:07 AM
Reply to: Message 147 by randman
07-02-2008 3:16 PM


Re: Shaking up the tree of life
Just for the record, I think it's tacky to reply to the same message twice, but it was unavoidable this time. I failed to notice this beforehand:
randman writes:
The big point is the genome starts out big, not that mutations or additions of new genes (especially since genes that were lost might come back) can never be involved. It does include the idea though of substantial loss of genes as a pattern of variation, but not necessarily some absolute.
I can't help but notice that, under your definition of "predict," the above explanation of front-loading seems to allow front-loading to "predict" everything that Neo-Darwinism "predicts."
So, I now request that you support the claim that Neo-Darwinism can be made to predict all observations while simultaneously showing that front-loading cannot. I'm granting you your definition and usage of the word "predict" for the sake of this challenge, even though it's inaccurate.
If you can't do that, your entire point in this thread is defeated.

Darwin loves you.

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bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 159 of 164 (473984)
07-04-2008 8:33 AM
Reply to: Message 157 by Wounded King
07-04-2008 4:11 AM


Re: Front loading
Wounded King writes:
As I said before, 'Front loading' is such a broad church that it could cover virtually anything so it is hard to know what specific predictions Randman thinks 'Front loading' makes.
I see. A broad church or, to put it another way, lots of different Gods of the gaps.
The reason I think that this kind of thing is becoming popular is because the Michael Behe "IC" idea has failed, which means that the more scientifically literate of the I.D. advocates need to shift their designer's field of operations further "backwards', if you see what I mean.
For example, it wouldn't be easy for an I.D.er to support Behe on the blood clotting thread I've just put up.
So, I think that lots of the cleverer creationists that we'll see arriving on EvC in the future will be front loaders.
Randman's hedging his bets, as usual, which is a smart thing to do when there's no evidence around for the designer, front-loader or otherwise.
(Smart?! That's a surprise compliment for you, randman. Don't blush.)

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


Message 160 of 164 (474028)
07-04-2008 3:52 PM
Reply to: Message 159 by bluegenes
07-04-2008 8:33 AM


Re: Front loading
The only fun we're going to get out of them with this "front-loading" stuff is if any scientist takes it up. So long as it's just randman lying about stuff, it won't make any difference.
But if some actual scientist could start talking front-loading bollocks, some freak like Behe, only with front-loading, then eventually the creationists would start parroting it, and then we could have so much fun.
I guess we can still mock randman for telling lies in the cause of a notion he doesn't even believe in himself, but shooting fish in a barrel is not really a sport.

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


Message 161 of 164 (474281)
07-07-2008 12:31 PM


PFAM domains
Looking back at the paper and Loomis' comment that 'cells which gave rise to plants and animals had more types of genes available to them than are presently found in either plants or animals'.
The paper certainly doesn't support this claim but neither does it necessarily contradict it. It depends on whether Loomis is referring to the whole animal domain or to individual animal species. If he is referring to the whole animal domain then the paper clearly shows he is wrong, the metazoa have more gene types available than the conserved PFAM domains suggest were present in the latest common ancestor(LCA) of metazoa, plants, fungi, and amoebozoa (see my previous more detailed analysis in Message 25).
If he means that no modern species has the same level of gene type diversity as the putative LCA then the paper does not allow us to determine if this is true or not. From the description in the supplementary materials of how they performed their analysis it doesn't sound as if all of the domain families in a set are conserved throughout that set. They say they ...
sorted them according to their presence or absence within 12 completely sequenced genomes to arrive at their distribution amongst the major organismal groups
It isn't clear that a domain considered unique to the metazoa is necessarily present in all of the metazoa. So of the 1560 eukaryote specific PFAM domains found in metazoa not every one must be found in each of the 4 metazoan genomes analysed. Therefore it is possible from the presented data that none of the metazoan genomes has more gene types than the putative LCA.
There is a way to explore this to some extent ourselves, using the PFAM database. The taxonomy based search, one of the options down the left hand side, allows you to produce a boolean expression as a query using a number of species names or higher taxa. For instance we can make a query 'Homo sapiens AND Arabidopsis thaliana AND Dictyostelium discoideum AND Neurospora crassa AND NOT Escherichia coli' which will give us a set of PFAM domains common to humans, the plant Arabidopsis, the slime mold Dictyostelium, and the fungi Neurospora but not found in the prokaryotic bacteria E.coli. This expression produces a list of 457 domains fitting these criteria, which is quite far below the 711 eukaryote specific domains the original paper identifies as common to plants/animals/amoebozoa/fungi.
The query 'Homo sapiens AND NOT Arabidopsis thaliana AND NOT Dictyostelium discoideum AND NOT Neurospora crassa AND NOT Escherichia coli' gives us what we might expect to be only metazoan domains of which there are 1069.
If we actually add another metazoan, in this case Drosophila, with the query 'Homo sapiens AND Drosophila melanogaster AND NOT Arabidopsis thaliana AND NOT Dictyostelium discoideum AND NOT Neurospora crassa AND NOT Escherichia coli', in this case we get 485 domains, quite close to the 502 metazoan specific domains in the original paper.
It might be possible to use more complex boolean expressions to better replicate the sets the paper uses, but I can't figure out how.
If we really wanted to try and replicate the papers methods we would need to extract the domain lists for each species individually and then apply the paper's criteria to find out how the domains are distributed amongst, for instance, the metazoan genomes.
So I am willing to accept that the LCA of plants/animals/amoebozoa/fungi may have had more 'gene types' than any currently extant species of plant or metazoan, but I haven't seen a scrap of evidence to substantiate this. The evidence certainly isn't in the paper the OP is referring to.
TTFN,
WK

  
Livingstone Morford
Junior Member (Idle past 4773 days)
Posts: 28
From: New Mexico
Joined: 12-13-2010


Message 162 of 164 (598251)
12-29-2010 6:35 PM
Reply to: Message 9 by New Cat's Eye
06-13-2008 3:44 PM


Re: Types of genes?
Maybe he meant isoforms? Just a thought.

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New Cat's Eye
Inactive Member


Message 163 of 164 (598328)
12-30-2010 11:09 AM
Reply to: Message 162 by Livingstone Morford
12-29-2010 6:35 PM


Re: Types of genes?
Nice thread necromancy...
But seriously, this was from 1.5 years ago. The guy I was respnding to is suspended. And, he explanined what he meant in Message 10.

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merrytess 
Suspended Member (Idle past 4658 days)
Posts: 3
From: *Newly registered users*
Joined: 05-20-2011


Message 164 of 164 (616335)
05-20-2011 9:19 PM


Bones: Great Show!!
It's okay, but you should explore less despicable areas of employment. --Admin
Edited by Admin, : No reason given.

  
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