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  #271  
Old 06-28-2011, 04:50 PM
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Originally Posted by Jose Fly View Post
Again I find myself astounded that a self-avowed expert such as yourself is so surprisingly ignorant of so much relevant science.

PLoS Computational Biology: Protein Molecular Function Prediction by Bayesian Phylogenomics

And just in case that too is beyond your "expertise", here is a blog entry for laypeople that describes this research:

The Loom : What's A Gene For?
I wonder if you've read your own papers, can you quote something from them that actually proves your case? What does SIFTER's accuracy on gene prediction have to do with Micro-evolution being used to define Macro?
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  #272  
Old 06-28-2011, 04:59 PM
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What does SIFTER's accuracy on gene prediction have to do with Micro-evolution being used to define Macro?
First because they use the theory of evolution to predict results with astounding accuracy. This is from the article.

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Those who claim to have a legitimate alternative to evolution might want to try to match SIFTER. They could take the basic principles of whatever they advocate and use them to come up with a mathematical method for comparing genes. No stealing any SIFTER code allowed--this has to be original work that doesn't borrow from evolutionary theory
Second Micro-evolution IS Macro-evolution given enough time.
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  #273  
Old 06-28-2011, 05:01 PM
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In that same amount of time you could have quoted something from it that actually discusses specific details of the findings.
I did. That's what the whole "complete fossil record" and "showing the entire evolutionary history" stuff was about.

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In the same amount of time you could have explained.
But you're avoiding the issue. Why do I need to explain the fundamental difference between a parvovirus and an endogenous retrovirus to a world-renowned expert?

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My calculations are as such: If Parvoviruses are 100% guaranteed to be able to replicate similarly in animals of drastically different species, then there's a 95% chance (5% margin of erro) that ERVs since they are similar in structure, will also affect species similarly in the same locations.
Wow. That's absolutely amazing! When do you plan on writing that up and getting it published?

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I wonder if you've read your own papers
Absolutely. I've read the PLOS paper many, many times.

Quote:
can you quote something from them that actually proves your case?
Sure. When you were asked why biological research continues to produce useful results when it's based on "macroevolution", you responded with a challenge to show modern research that is based on "macroevolution". So I posted the PLOS paper that shows how when researchers plugged genome sequences from taxa as diverse as flies, worms, humans and such into a program that's based on phylogenetic relationships, they were able to predict gene function to a 96% degree of accuracy. Here is the relevant part of the paper:

"Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy....Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods...The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems."

So tell me O' wise expert...if "macroevolution" is bunk as you claim, how in the world do we explain these results?
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  #274  
Old 06-28-2011, 05:07 PM
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If they can interbreed, that means they are technically the same species.
No, it doesn't. As you go on to admit. Do you even have a point?

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The word "Species" as I've mentioned is a bit of a muddied issue since Camels and Llama can have fertile offspring. As it stands, there are numerous claims by "reputable sources" that they were the same species. It helps if you keep up to date.

Human-Neanderthal Hybrid?
Neanderthal Code | Neanderthals the Same Species? | National Geographic Channel
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  #275  
Old 06-28-2011, 05:53 PM
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No, it doesn't. As you go on to admit. Do you even have a point?
What do you mean "As you go on to admit", and why do you say "No it doesn't?"

So what makes them different species then in the face of all those links I posted.
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  #276  
Old 06-28-2011, 05:55 PM
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Originally Posted by Jose Fly View Post
I did. That's what the whole "complete fossil record" and "showing the entire evolutionary history" stuff was about.


But you're avoiding the issue. Why do I need to explain the fundamental difference between a parvovirus and an endogenous retrovirus to a world-renowned expert?


Wow. That's absolutely amazing! When do you plan on writing that up and getting it published?


Absolutely. I've read the PLOS paper many, many times.


Sure. When you were asked why biological research continues to produce useful results when it's based on "macroevolution", you responded with a challenge to show modern research that is based on "macroevolution". So I posted the PLOS paper that shows how when researchers plugged genome sequences from taxa as diverse as flies, worms, humans and such into a program that's based on phylogenetic relationships, they were able to predict gene function to a 96% degree of accuracy. Here is the relevant part of the paper:

"Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy....Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods...The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems."

So tell me O' wise expert...if "macroevolution" is bunk as you claim, how in the world do we explain these results?
There's not enough of a difference between ERVs and Parvoviruses to say that one can't be like the other regarding triggering exact or similar locations through the insertions. SIFTER is nice but I don't see what your answer has to do with proving Macroevolution, its good for Micro, but if you're trying to say it can predict radical gene changes that make a fruit fly turn into something else, nope.

If anything this is just even more proof to my statement that the word "Micro" and "Macro" evolution are muddied to assume that one can assume radical changes from gradual ones that go out of the initial "mold".
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  #277  
Old 06-28-2011, 05:57 PM
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First because they use the theory of evolution to predict results with astounding accuracy. This is from the article.



Second Micro-evolution IS Macro-evolution given enough time.
But that's not what SIFTER proves. SIFTER can predict Micro transitions, which I've brought up such as in the links about Epigenetics.

Macro-evolution is the SPECULATION of what will happen through such gene changes, but SIFTER cannot prove such. Neither can any transitional gene be found to prove such.

I understand that Macro-evolution is the THEORY of what will happen with enough Microevolution, but as you can see with all the gaps I presented, it doesn't fly.
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  #278  
Old 06-28-2011, 06:03 PM
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There's not enough of a difference between ERVs and Parvoviruses to say that one can't be like the other regarding triggering exact or similar locations through the insertions.
Really? Any empirical evidence to back that up?

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SIFTER is nice but I don't see what your answer has to do with proving Macroevolution, its good for Micro, but if you're trying to say it can predict radical gene changes that make a fruit fly turn into something else, nope.
You didn't read any of the material, did you? I suggest you go back and read the paper, the blog post, and my subsequent explanation.

And you're avoiding the virtually complete fossil record I provided you as well as telling me when you're going to publish your calculations on ERV insertion.
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  #279  
Old 06-28-2011, 06:06 PM
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Unexpected endogenous viruses
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/ Until very recently, retroviruses were the only known endogenous viruses. This honor has now been extended to other RNA viruses, and to circoviruses and parvoviruses, which possess single-stranded DNA genomes. Such integration events constitute a fossil record from which it is possible to determine the age of viruses.
I asked for proof of this "Virtually complete fossil record", where is it?
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  #280  
Old 06-28-2011, 06:09 PM
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I understand that Macro-evolution is the THEORY of what will happen with enough Microevolution, but as you can see with all the gaps I presented, it doesn't fly.
As you stated a "species" might be able to procreate with another species. It is beside the point. We are talking about enough changes to make species incompatible with each other which given enough changes will eventually diverge into whatever you want to call a different species.

Also there are not any gaps that need creationism to explain away. The gaps need evolution to explain and as all good theories do, will predict that any gaps filled will support evolution even further.

It does fly and every single fossil IS a transitional fossil. EVERY fossil we find supports evolution further. What missing link can we possibly find that shows anything but slow gradual change?
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