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Author Topic:   How novel features evolve #2
NoNukes
Inactive Member


(1)
Message 391 of 402 (677667)
10-31-2012 1:29 PM
Reply to: Message 389 by mindspawn
10-31-2012 1:08 PM


Re: adding an extra functional gene
So this Y chromosome of humans would be accumulating mutations from the beginning of the evolving of the Y chromosome.

So how does the current Y chromosome compare to those of our ancestors one million years ago or to that of a lizard? Are you saying that there does not appear to be the correct amount of variation as predicted by the theory of evolution when we look at those things?

I don't believe you've shown any such thing. We don't have the DNA for any pre-human, ancestors and I don't think you can make the argument that human Y chromosomes look too much like modern lizard DNA to justify evolutionary thoery.

At least it is the case that neither of the quotations from Wikipedia seem to touch on the issue you are raising.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison.

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


This message is a reply to:
 Message 389 by mindspawn, posted 10-31-2012 1:08 PM mindspawn has responded

Replies to this message:
 Message 393 by mindspawn, posted 10-31-2012 1:49 PM NoNukes has responded

  
PaulK
Member
Posts: 14513
Joined: 01-10-2003
Member Rating: 1.5


(1)
Message 392 of 402 (677670)
10-31-2012 1:47 PM
Reply to: Message 389 by mindspawn
10-31-2012 1:08 PM


Re: adding an extra functional gene
quote:

Now to apply this to evolution, you don't go back just to when man was seperately defined from the common ancestor with the ape. This common ancestor had the y-chromosome too. There is no mechanism that would have cleaned up the male Y chromosome just before the first human evolved.

Obviously you don't understand what is being measured here. From a study involving only human Y-chromosomes we can only see variations introduced to the chromosome since the "Y-chromosome Adam", since all human Y-chromosomes are descended from his. There's no need for any "cleaning up". The only way to detect mutations is to look for differences, and so long as you only look at the human Y-chromosome you can only detect differences that got into the genome since the Y-chromosome Adam. According to Wikipedia, that gives us 142,000 years on the best estimates. Or, as I have said, in your view about 5,000 years.

Oh, and by the way, transitional fossills are not just assumptions, they are real, physical objects. As Kurt Wise admitted, even if many other creationists would rather deny reality, rather than accept the truth.


This message is a reply to:
 Message 389 by mindspawn, posted 10-31-2012 1:08 PM mindspawn has not yet responded

    
mindspawn
Member (Idle past 614 days)
Posts: 1015
Joined: 10-22-2012


Message 393 of 402 (677673)
10-31-2012 1:49 PM
Reply to: Message 391 by NoNukes
10-31-2012 1:29 PM


Re: adding an extra functional gene
So how does the current Y chromosome compare to those of our ancestors one million years ago or to that of a lizard? Are you saying that there does not appear to be the correct amount of variation as predicted by the theory of evolution when we look at those things?

I don't believe you've shown any such thing. We don't have the DNA for any pre-human, ancestors and I don't think you can make the argument that human Y chromosomes look too much like modern lizard DNA to justify evolutionary thoery.

At least it is the case that neither of the quotations from Wikipedia seem to touch on the issue you are raising

Under the assumption of evolution the human Y chromosome isn't a recent development, but has been accumulating mutations for hundreds of millions of years. The alternative, that the common ancestor of mammals did not have a Y chromosome is a ridiculous thought. The current state of the Y chromosome is not reflecting enough mutations if evolutionary time frames are true.


This message is a reply to:
 Message 391 by NoNukes, posted 10-31-2012 1:29 PM NoNukes has responded

Replies to this message:
 Message 394 by NoNukes, posted 10-31-2012 2:31 PM mindspawn has responded
 Message 395 by New Cat's Eye, posted 10-31-2012 3:06 PM mindspawn has responded

  
NoNukes
Inactive Member


(1)
Message 394 of 402 (677675)
10-31-2012 2:31 PM
Reply to: Message 393 by mindspawn
10-31-2012 1:49 PM


Re: adding an extra functional gene
The current state of the Y chromosome is not reflecting enough mutations if evolutionary time frames are true.

I'll be more direct. What is your baseline for comparison? Show me a Y chromosome from hundreds of millions of years ago, and then let's talk about the differences.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison.

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


This message is a reply to:
 Message 393 by mindspawn, posted 10-31-2012 1:49 PM mindspawn has responded

Replies to this message:
 Message 398 by mindspawn, posted 11-01-2012 2:54 AM NoNukes has not yet responded

  
New Cat's Eye
Inactive Member


(1)
Message 395 of 402 (677682)
10-31-2012 3:06 PM
Reply to: Message 393 by mindspawn
10-31-2012 1:49 PM


Re: adding an extra functional gene
Under the assumption of evolution the human Y chromosome isn't a recent development, but has been accumulating mutations for hundreds of millions of years.

Hundreds of millions of years ago, it would not have been a human Y chromosome. Humans weren't alive that long ago.

The current state of the Y chromosome is not reflecting enough mutations if evolutionary time frames are true.

Sure it is. You can't say that it has to have evolved by X much, because the selective pressures could weed out many of the mutations. There is not a minimum amount of mutation that must happen over a given timeframe.

But by comparing it to ealier human Y chromosomes, we can see that it has too many mutations to have happend in the last <10,000 years. There is a maximum amount of mutation that can be said to have happened within a given timeframe.

By studying the human Y chromosome, we can see that the creation scenario is impossible and we can see that the evolutionary scenario is plausible.


This message is a reply to:
 Message 393 by mindspawn, posted 10-31-2012 1:49 PM mindspawn has responded

Replies to this message:
 Message 397 by mindspawn, posted 11-01-2012 2:31 AM New Cat's Eye has not yet responded

  
Taq
Member
Posts: 7594
Joined: 03-06-2009
Member Rating: 3.4


(2)
Message 396 of 402 (677685)
10-31-2012 3:42 PM
Reply to: Message 390 by mindspawn
10-31-2012 1:28 PM


Re: Hopefull not too meta...
When an anoxic ocean recedes you get trilobite fossils below, then wetlands fossils, then terrestrial fossils. The evolutionists conclusion: They evolved??

Radiometric dating would place them all from the same geologic period, so no they would not assume that they evolved from one to the other. We also have many examples of very recent anoxic lakes that sit above much older terrestrial sediments.

There's nothing in DNA sequences that point to evolution.

The entire scientific community disagrees with you, as does 60 years of research done on DNA. Sorry, but you are extremely wrong about this.

As just one example of thousands, there is this paper on endogenous retroviruses:

http://www.pnas.org/content/96/18/10254.full

In this paper they state:

"Given the size of vertebrate genomes (>1 × 10^9 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14)."

Guess what? We share thousands and thousands of retroviral integrations with other apes, including chimps. Common ancestry is proven way beyond a reasonable doubt.

You have tried with the aphid example, but that fits in perfectly with creation and a subsequent gene deletion within the last 6000 years.

Anything would fit perfectly with magical poofing. I could claim that leprechauns faked my fingerprints at a crime scene. My evidence? The prints at the crime scene exactly match my own prints which is completely consistent with leprechauns planting my prints. That is the type of logic you are using here.

We already have a natural mechanism that explains the data. We don't need magic to explain it.

there is no reason to assume the two genes would show any difference in mutation over 6000 years,

Why is there any reason to assume that they would have had exactly the same sequence when they were created?

So where's your proof that evolution is a better theory than creation when even your base mechanism for the appearance of new beneficial novel coding genes is just one theory that fits the reality?

Creationism is not a theory. No scientist is using creationism to explain anything as part of a scientific research program. Scientists ARE using evolution, and it works. That is why evolution is a better theory: it works.


This message is a reply to:
 Message 390 by mindspawn, posted 10-31-2012 1:28 PM mindspawn has responded

Replies to this message:
 Message 399 by mindspawn, posted 11-01-2012 3:03 AM Taq has not yet responded
 Message 400 by mindspawn, posted 11-01-2012 3:33 AM Taq has not yet responded

  
mindspawn
Member (Idle past 614 days)
Posts: 1015
Joined: 10-22-2012


Message 397 of 402 (677706)
11-01-2012 2:31 AM
Reply to: Message 395 by New Cat's Eye
10-31-2012 3:06 PM


Re: adding an extra functional gene
Hundreds of millions of years ago, it would not have been a human Y chromosome. Humans weren't alive that long ago.

Exactly! thats what the others don't seem to get, if you assume evolution, there was not a single "Adam" moment when the ape-thing became a human. The Y-chromosome would reflect a continuous accumulation of mutations from long before humans appeared if evolution is true. that's not just 100 000 years. The principle of the Y chromosome collecting mutations would apply from the moment the Y chromosome evolved into a seperate chromosome representing the male. If you look at biology and the way common animals breed, and project a most likely point in evolution's so-called phylogenetic tree of the human, this point of the existence of the Y-chromosome in the human ancestor is millions of years ago. The alternative, that there were no male and female x and y chromosomes in the biology of the human ancestor 200 million years ago, is an illogical escape route if you would like to take that escape route. The Y chromosome is thought to have evolved 200 million years ago, I will be interested to see if you now start doubting mainstream evolutionary thought.

Edited by mindspawn, : No reason given.


This message is a reply to:
 Message 395 by New Cat's Eye, posted 10-31-2012 3:06 PM New Cat's Eye has not yet responded

  
mindspawn
Member (Idle past 614 days)
Posts: 1015
Joined: 10-22-2012


Message 398 of 402 (677708)
11-01-2012 2:54 AM
Reply to: Message 394 by NoNukes
10-31-2012 2:31 PM


Re: adding an extra functional gene
I'll be more direct. What is your baseline for comparison? Show me a Y chromosome from hundreds of millions of years ago, and then let's talk about the differences.

I'm not sure what you think I'm comparing? If the Y-chromosome has been accumulating mutations since it started 200 million years ago, then it should have more mutations than its currently showing. Scientists have come up with this 200 million date, not me:
http://www.the-scientist.com/?articles.view/articleNo/32368/

The human X and Y chromosomes are thought to have originated from a matching pair of non-sex chromosomes, or autosomes, some 200 million years ago. And now, they are so different that they share just a tiny length of sequence. Indeed, “the human X has about 1,000 genes, and the Y only has about 50,” explained Doris Bachtrog of the University of California, Berkeley, who led the new study.

You do believe in evolution don't you? If so then the human did not suddenly appear, the human is a result of accumulated mutations, where are those?

Edited by mindspawn, : inserting link


This message is a reply to:
 Message 394 by NoNukes, posted 10-31-2012 2:31 PM NoNukes has not yet responded

  
mindspawn
Member (Idle past 614 days)
Posts: 1015
Joined: 10-22-2012


Message 399 of 402 (677709)
11-01-2012 3:03 AM
Reply to: Message 396 by Taq
10-31-2012 3:42 PM


Re: Hopefull not too meta...
Radiometric dating would place them all from the same geologic period, so no they would not assume that they evolved from one to the other. We also have many examples of very recent anoxic lakes that sit above much older terrestrial sediments.

Huh? If the ocean recedes, why would they all be dated simultaneous? Obviously the fish were in that area before the ocean receded and only then you find land fossils. You not being logical here. Radiometric dating and ocean receding would show the same sequence. To assume evolution instead of animals walking onto new landscapes that used to be seabeds, isn't the most logical conclusion at all. If nearly everywhere around the world you find trilobites first, but there are one or two places where you do not find trilobites first, this fits in with isolated terrestrial animals taking a walk after oceans receded.

and of course if ocean fossils were there first, then terrestrial, this proves the ocean came first. Evolved seems to be the most illogical projection of the fossil sequence.

The entire scientific community disagrees with you, as does 60 years of research done on DNA. Sorry, but you are extremely wrong about this.

As just one example of thousands, there is this paper on endogenous retroviruses:

http://www.pnas.org/content/96/18/10254.full

In this paper they state:

"Given the size of vertebrate genomes (>1 × 10^9 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14)."

Guess what? We share thousands and thousands of retroviral integrations with other apes, including chimps. Common ancestry is proven way beyond a reasonable doubt.

What is the rate of ERV insertion between two parents and a child? You gave me a mutaton rate of point mutations, have they proved that some of these inheritable ERV's are found in offspring but not in parents. They have proved this with point mutations as you so correctly pointed out, what about ERV's?

(my argument here is that ERV's could all have a precise function in the genome, and be created 6000 years ago, what evidence have you got they are insertions)

Creationism is not a theory. No scientist is using creationism to explain anything as part of a scientific research program. Scientists ARE using evolution, and it works. That is why evolution is a better theory: it works.

Darwin wrote a well-written book. Since then evolution has been prematurely accepted by science. but there is no more actual evidence for evolution than for creation. The ONLY evidence you have brought forward is the point mutation rate that points more towards creationist time frames than evolutionist time frames.

The assumption for the aphid so-called duplication event has no proof to back it up. It is no more logical than an aphid created with two identical genes that subsequently undergoes a gene deletion. The only reason to reject the creationist view on the aphid, is a biased propensity to believe in the miraculous process of evolution rather than the miraculous process of creation.

Edited by mindspawn, : No reason given.

Edited by mindspawn, : No reason given.


This message is a reply to:
 Message 396 by Taq, posted 10-31-2012 3:42 PM Taq has not yet responded

  
mindspawn
Member (Idle past 614 days)
Posts: 1015
Joined: 10-22-2012


Message 400 of 402 (677712)
11-01-2012 3:33 AM
Reply to: Message 396 by Taq
10-31-2012 3:42 PM


Re: Hopefull not too meta...
Why is there any reason to assume that they would have had exactly the same sequence when they were created?

this is the nature of design. Think of a car with four cylinders, four pistons, four flickers, two rear doors, two front doors, if the best design requires a duplication then it works. the results are there to see, the duplication had more hardiness under attack (pesticides) so I would say the duplication added strength to that area.


This message is a reply to:
 Message 396 by Taq, posted 10-31-2012 3:42 PM Taq has not yet responded

  
Tangle
Member
Posts: 6262
From: UK
Joined: 10-07-2011
Member Rating: 2.4


Message 401 of 402 (677719)
11-01-2012 6:44 AM


In summary, I'd say we've made some progress but not as much as I'd hoped.

Much of the recent debate has really been off-topic and if there's enough interest in mutation events in the human Y chromosome (which there seems to be), a new thread should be started.

We got somewhere with lizards and we got very close with mice. All that was missing with the mice was to be able to totally nail the gene(s) that had changed and rule out others.

The bacteria seems to me to be proof of novelty caused by mutation and selected for by the environment - all that could be discussed here was equivocation about the meaning of 'novel.'
(At the moment I'm happy 'novel' could include a feature that enables an organism to live or die depending whether the feature is present or absent - and a clearer meaning is hard to imagine or test.)

The bacteria though doesn't pass my own ambition to show mutation and selection in a beast big enough to be seen by the naked eye from a distance.

So close, but no banana.

My own reading around has produced very little that I can actually understand as the subject very quickly gets in detailed molecular genetics which is well above (or below ;-) my pay grade.

But it does seem strikingly clear that it is a very difficult question to answer because the more we learn, the more complicated it gets. There seems to be no simple tail to be told.

I'll leave with this, which, if anybody is interested, I'll use as a start to a follow-on topic How novel features evolve #3. But I'll need help understanding it!


The Evolution of Novelty in Conserved Gene Families

We argue that the partial data on genomic variation are already sufficient to indicate that no specific attribute of a given molecular structure can indicate a priori more potentials than others to contribute to novelty at a higher phenotypic level. Uncoupling and buffering of natural variation at various integration scales has been clearly demonstrated, implying that the number of molecular events that can be directly correlated with a phenotypic change at the organismal level is probably very low, and that they are the results of exceptional contingency and structural constraints [72]. The possibility to detect de novo such interesting changes in nonmodel organisms is thus also probably very low, and it decreases quickly with an increase of the phylogenetic distance. Additionally, one should not forget that to really understand the link between genetic variation and phenotypic diversity, it is necessary to be able to explain cases where a molecular change triggers novelty, and those where phenotypic traits are maintained in spite of molecular innovations in the genes that specify them.


http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3388334/

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

  
mindspawn
Member (Idle past 614 days)
Posts: 1015
Joined: 10-22-2012


Message 402 of 402 (678081)
11-05-2012 3:00 AM


I haven't participated in the full thread, but I've really enjoyed the discussions I've been involved in. I'm more interested in novel genes than novel features per se. I am really keen to see if there are any ways that additional coding genes with novel functions that actually benefit fitness can evolve. Unfortunately the aphid example was not convincing enough because of the possibility that this was a deleted gene and not an evolved gene.

There were interesting side issues that were raised concerning mutation rates and ERV's, but these side issues were still core to the debate regarding if we should observe any divergence in the two identical genes of the aphid. True science would look at the respective so-called mutations from the view of an impartial observer, to see if there is evidence of mutations, or if these genetic sequences have always been there. There is definitely evidence of some mutations, unfortunately for evolutionists the mutation rates point more towards creationist time frames than evolutionist time frames, some seemed to battle to grasp this point.


  
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