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Author Topic:   How novel features evolve #2
Taq
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Message 335 of 402 (677057)
10-26-2012 2:48 PM
Reply to: Message 334 by mindspawn
10-26-2012 2:21 PM


Re: adding an extra functional gene
The lack of sequence divergence just means the genes are the same.
Yes. If they were not the result of duplication then they would have many differences in sequence. The lack of variation between the sequences is the evidence for a recent duplication.
Why do I say this? There is nothing stopping neutral mutations from accumulating in these genes. It is entirely possible to change the nucleotide sequence without change the protein sequence due to third base wobble (i.e. some amino acids are coded for by more than one codon). Therefore, if these genes had existed for quite some time as separate copies then they would have different a lot of different neutral mutations. They don't. Therefore, the evidence is strongly in favor of a recent duplication.

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 Message 334 by mindspawn, posted 10-26-2012 2:21 PM mindspawn has replied

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 338 of 402 (677097)
10-26-2012 5:58 PM
Reply to: Message 337 by mindspawn
10-26-2012 5:21 PM


Re: adding an extra functional gene
I believe its possible God created the original with two identical genes.
What evidence do you have that a supernatural deity created any species? Surely you demand as much evidence for creationism as you do for evolution, right?
I see nothing in your evidence that says the population without the duplicate came before the population with the duplicate, except your presumption that evolution is more logical than intelligent design.
It would appear that your beliefs you discussed above are preventing you from accepting the evidence that I have presented. I'm sorry, but "I believe . . " is not a valid reason for rejecting evidence.
If you can show me proof that the population without the duplicate was on earth first, you would have a point. Otherwise you are trying to prove a process of evolution based on the assumption that the duplicate evolved which is frankly illogical.
Why is it illogical?

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 Message 337 by mindspawn, posted 10-26-2012 5:21 PM mindspawn has replied

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 Message 341 by mindspawn, posted 10-26-2012 6:28 PM Taq has replied

  
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 359 of 402 (677379)
10-29-2012 1:13 PM
Reply to: Message 341 by mindspawn
10-26-2012 6:28 PM


Re: adding an extra functional gene
I haven't got evidence , except that the bible is a proven and accurate book, which is of topic for this thread.
You are contradicting yourself. If the Bible is proven and accurate then you should be able to provide the evidence that species were created by a supernatural deity. You should be able to evidence your claims independent of what the Bible says.
In a court of law, do we find people guilty because the District Attorney says so? Or does the DA have to provide evidence?
Neither have you got evidence for your evolutionary process because you are using the assumption of evolution to prove evolution.
Not at all. We are making predictions of what we should and should not see in the field of biology if evolution is true. For example, if the carboxylesterase gene went through a recent duplication then we should see a lack of divergence between the two genes. This is a testable prediction. It is a scientific prediction.
So what predictions does creationism/ID make, and why? How do we test for these mechanisms as it relates to the emergence of novel features?
To what extent are these neutral mutations truly neutral, when some so-called "junk-DNA" has recently been found to have a function.
They set the bar really low for what they consider "function". Using an analogy, they would consider the trash in your kitchen to be functional since it adds odor molecules to the air which changes the biochemistry of your kitchen. Using their definition of functional they would classify real junk as having function.
The fact of the matter is that there is a lot of junk DNA, and a lot of changes within genes that are selectively neutral (e.g. third base wobble and conservative changes to amino acids). As I cited earlier, there is a 40% difference between human and yeast cytochrome C and yet the human gene can replace the yeast gene without a change in fitness.

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 Message 341 by mindspawn, posted 10-26-2012 6:28 PM mindspawn has replied

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 360 of 402 (677385)
10-29-2012 1:25 PM
Reply to: Message 350 by mindspawn
10-29-2012 2:37 AM


Re: adding an extra functional gene
Theodoric, you are missing the point of this thread, where is the proof for essential evolutionary processes?
I have cited both the Luria-Delbruck fluctuation experiment and the Lederberg's plate replica experiment as examples of beneficial mutations arising through random mutation. These experiments looked at bacteriophage and antibiotic resistance, and it involved the modification of genes into new genes that changed the fitness of the organism.
Lenski's experiments demonstrating the evolution of citrate utilization involved DNA duplication and substitution mutations that resulted in a novel phenotype and a new gene.
I have also cited the evolution of dark fur in pocket mice that was due to substitution mutations in the MC1R gene. This novel phenotype was strongly beneficial in the darker lava fields.
So how many evidenced examples have we been given of this supposed designer doing anything? Zero.
At least I have a religious book to back up my beliefs, . . .
That's what they said when they put Galileo under house arrest.
You can't use evolution to prove evolution, that lacks science.
We can use testable hypotheses to test the theory. That is scientific.
even the lack in evolutionary circles to assume both ID and evolution are valid hypotheses and then to look at DNA sequences with both view equally in mind, is showing non-scientific bias.
Even ID supporters are incapable of creating testable hypotheses that can be used to test ID. The Discovery Institute is full of people who claim that ID is scientific, so where is the science? Why aren't they doing the research? I can only conclude that ID is not scientific but it is purely religious.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 361 of 402 (677387)
10-29-2012 1:28 PM
Reply to: Message 354 by Tangle
10-29-2012 4:24 AM


Re: adding an extra functional gene
Geneticists [not evolutionists, whatever they are] established that a large part of our DNA did not code for proteins. It was labelled 'junk' to differentiate it from the parts that did seem useful.
If memory serves, "junk" DNA was first used to describe processed pseudogenes, not non-coding DNA in general. In the case of processed pseudogenes, it is quite obvious that they do not possess function related to their DNA sequence given the accumulation of frame shift and other mutations that knockout protein production.

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 362 of 402 (677389)
10-29-2012 1:46 PM
Reply to: Message 356 by mindspawn
10-29-2012 9:31 AM


Re: adding an extra functional gene
yes PaulK I agree they shouldn't be quite as dogmatic, mutations are quite common. But I don't see any proof that they are common enough to assume every gene would reflect them.
Let's do the math then. According to the chimp genome paper there are 35 million substituions and 5 million indels that separate humans and chimps, or 40 million mutations total. If we assume that half occurred in each lineage that puts us at 20 million in the human lineage.
So what is the observed human mutation rate? According to this paper that directly compared parent's DNA to offspring's DNA, the mutation rate is 50 to 100 mutations per individual per generation. This allows us to estimate the number of mutations that have occured in the human population over the last 5 million years since the chimp and human lineages diverged.
The math is pretty straightfoward. With a mutation rate 50 per individual per generation, a generation time of 25 years, and a constant population of just 100,000 that gives us 200,000 generations with 50*100,000 mutations per generation for a total of 1x10^12 mutations, or 1 trillion mutations. In comparison, there are only 40 million mutations that separate humans and chimps, or just 0.004% of all the mutations that have occured in the human population over the last 5 million years using the most conservative of assumptions.
So what makes you think that the observed mutation rate is incapable of producing the differences we see between humans and other species?
The duplications can't be proven . . .
Do you accept that duplications do occur naturally?
To contribute as an explanation for how complex organisms exist today, the mutation would have to improve fitness, and add a gene with a function. To find proof of this is near impossible because its difficult to reproduce evolutionary time frames in the laboratory.
Actually, it is quite easy to prove. The DNA differences seen between humans and chimps is responsible for the morphological differences between humans and chimps. Perhaps you could highlight those DNA differences that you think evolution could not produce?

This message is a reply to:
 Message 356 by mindspawn, posted 10-29-2012 9:31 AM mindspawn has replied

Replies to this message:
 Message 368 by mindspawn, posted 10-30-2012 3:51 AM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 371 of 402 (677521)
10-30-2012 11:09 AM
Reply to: Message 368 by mindspawn
10-30-2012 3:51 AM


Re: adding an extra functional gene
regarding the chimp/human mutations, ID assumes they were created like that. ie God created extra base-pairs in certain genes of the ape, and extra base-pairs in certain genes of the human.
If ID were science it would actually demonstrate that this was the case instead of just assuming it.
The "evolving" from a common ancestor is a huge assumption . . .
No, it isn't. It is a CONCLUSION drawn from evidence. We have the transitional fossils. We have the shared genetic markers such as shared ERV's and shared pseudogenes. We have different Ka/Ks ratios for coding regions and pseudogenes which evidences selection and random mutations. It is NOT assumed.
Regarding 50 per individual per generation, are you specifically referring to changed base-pairs in offspring that were not visible in both parents?
Yes. It would appear that they filtered out the indels for that specific paper so, if I am reading the paper correctly, the 50 refers to base substitutions.

This message is a reply to:
 Message 368 by mindspawn, posted 10-30-2012 3:51 AM mindspawn has replied

Replies to this message:
 Message 380 by mindspawn, posted 10-31-2012 11:10 AM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 373 of 402 (677579)
10-30-2012 4:19 PM
Reply to: Message 365 by mindspawn
10-30-2012 3:01 AM


Re: adding an extra functional gene
Good advice about the posting, thanks. For now I will just stick to the two threads. regarding the bible's relevance to this thread, well the bible does say that certain biological life-forms were created ~6000 years ago, which eliminates the necessary timeframes for evolution.
That would only be the case if what the Bible claims is true. This means that you need to present evidence for these claims. Simply stating "Because the Bible says so" is not going to convince anyone.
As you accurately point out the bible does not declare new novel features impossible,
Who cares? What does the evidence say? That is the important question.
well this particular thread is your chance to prove that evolution and not devolution works. And I haven't seen the proof yet.
I think you have shown that you will not accept anything as proof. Your mind is made up, and that's the end of the discussion.
To state that certain observed genes or base pairs or other parts of the genome have evolved or mutated and work from that is in most cases merely assumption.
We have shown that it is not an assumption, but a conclusion drawn from evidence.
I know that evolution believes in both processes but its the increased complexity part of evolution that allows for life to go beyond simple bacteria. Without increased complexity there is no evolution, so its only this part of the process that I object to , and this is an essential part of the theory of evolution as an explanation for the appearance of modern life-forms.
Why do you object?

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 374 of 402 (677584)
10-30-2012 4:26 PM
Reply to: Message 367 by mindspawn
10-30-2012 3:26 AM


Re: adding an extra functional gene
If ID is true, the duplications were always there and the carboxylesterase genes will continue to stay as they are with rare occasional mutations in future.
Even if ID is true I don't see how the predictions follow from the premise. Certainly genes can still go through the process of duplication after the design process is over. We observe that DNA recombination occurs in nature without a designer present, so I don't see how a designed organism would be immune from such a naturally occuring process.
ID with a recent creation would predict:
1) ID predicts that there will be more extinctions than new species. (a reducing number of species over time).
We have another ID supporter, Genomicus, who argues just the opposite, that organisms are front loaded to produce increasing biodiversity over time.
) Genomes will show fixity with no increasing length of functional DNA except when damaging. (devolution)
This has already been falsified in that we have observed beneficial mutations that result in beneficial function.
3) Most so-called mutations will be found to have always been in the genome.
Comparisons of parents and offspring shows that this is not true.
4) Many ancient fossils will be found to also have signs of recent life (DNA survives, carbon dated, found in human habitats)
That has nothing to do with ID since ID can be OEC, but it is still not true. No one has found surviving DNA in very ancient fossils.
5) there will be an increasing number of modern animals found fossilized in ancient layers.
No one has ever found a mammal in Cambrian strata.
6) devolution will become the more observed process, the ability of disabled genes and deletions to contribute towards fitness.
How do less fit organisms outcompete more fit organisms within a population? Can you please explain this?

This message is a reply to:
 Message 367 by mindspawn, posted 10-30-2012 3:26 AM mindspawn has replied

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Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 383 of 402 (677639)
10-31-2012 11:38 AM
Reply to: Message 380 by mindspawn
10-31-2012 11:10 AM


Re: adding an extra functional gene
Now this is what I am REALLY interested, true observed evidence without any assumptions. Correct me if I'm wrong, this is a new field to me, but when there is genetic recombination in the next generation, the 50 mutations largely disappear due to the recombination process.
That's not quite accurate. Each mutation will occur on just one chromosome in any given pair. This means that each new mutation will have a 50/50 chance of being passed on since just half of one's chromsomes are used to create eggs and sperm. So, on average, 25 of the 50 mutations that a person is born with will be passed on to the next generation, along with a set of brand new mutations that is specific to them.
Natural selection can eliminate the more damaging mutations, but we both agree the population has to collect mutations every generation. Given that the human Y chromosome has 1.67% of all base pairs (50 million of 3 billion), and the Y chromosome develops mutations at 4.8 times the normal rate of point mutations, the human Y chromosome should be collecting about 4 or 5 mutations each generation. Current studies show that there are approximately 28650 SNPs (old point mutations) in certain human Y chromosomes, but this figure could be vastly OVER-estimated. This is certainly pointing towards a recent beginning of mutations in the Y chromosome, rather than millions of years. Based at the current rate of 4 or 5 per generation.
I would need to see the study you are citing. From first glance the numbers you are citing may be the variation within just the human population. This would be a collection of mutations that have occurred over just the last 50,000 years as measured by the coalescence time for the human Y-chromsome most recent common ancestor.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 385 of 402 (677645)
10-31-2012 12:17 PM
Reply to: Message 382 by mindspawn
10-31-2012 11:36 AM


Re: adding an extra functional gene
That article says how varied the estimates are for the human mutation rate.
Those estimates are based on the sequence differences between orthologous pseudogenes in chimps and humans using probabilities based on neutral drift. What those estimates are really modelling is the mutation rate needed to produce the observed amount of divergence over the last 5 to 7 million years. They use pseudogenes and neutral drift because DNA sequence under selection can diverge at unpredictable rates. However, neutral mutations accumulate at a much more predictable rate, and become fixed at a rate dependent on population size.
As it turns out, the actual observed mutation rate is not that far off from the estimated rate needed to produce the observed amount of divergence.
Through genetic re-combination the point mutation could be eliminated in the very next generation,
No it wouldn't.
2) It is consistent with the theory of creation that the duplicates were created like like,
Anything is consistent with magic. That's the problem. If the genes were different you would still claim that they were created that way. Creationism makes no predictions as to the divergence seen in duplicated genes.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 388 of 402 (677657)
10-31-2012 12:51 PM
Reply to: Message 386 by mindspawn
10-31-2012 12:41 PM


Re: Hopefull not too meta...
The phylogenetic tree is just an evolutionist assumption.
False. It is a CONCLUSION based on a comparison of morphology and DNA sequence. You seem to have a tough time differentiating between assumptions and conclusions. One is not the other.
reality of the fossil record just shows that certain organisms proliferated when conditions were suitable.
The reality of the fossil record is that species fall into a nested hierarchy as predicted by the theory of evolution. A nested hierarchy is simply inexplicable in a creationist model. There is absolutely no reason that a creator would be confined to a nested hierarchy. For example, there would be nothing stopping such a creator from producing a species with teats and feathers.
The reality is that the theory of evolution is able to make very precise and testable predictions, and those predictions continue to pass every test we put in front of them. On the other hand, creationism makes no testable predictions. Creationism can not even explain the most fundamental observation in biology, that life falls into a nested hierarchy.

This message is a reply to:
 Message 386 by mindspawn, posted 10-31-2012 12:41 PM mindspawn has replied

Replies to this message:
 Message 390 by mindspawn, posted 10-31-2012 1:28 PM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(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:
Just a moment...
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 replied

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