Is neo-darwinism a scientific theory?
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02-12-2012, 10:49 PM
RE: Is neo-darwinism a scientific theory?
Evolution is a verifiable empirical phenomenon. The theory of evolution, or modern synthesis can and should be revised when faced by increasing challenges.

The misunderstanding of what is a phenomenon and what is the explanatory scientific theory constitutes the fallacy in your argument since the beggining.

Just because you want to use the putative insuficiencies of the evolution theory (it is still needed more data to revise a paradigm that possess thousands of peer review articles in its support) to say that evolution as a natural phenomenon is automatically refuted, does not make it true.

Another thing that you fail to understand is the dynamics of science. Paradigms are useful, because it provides a framework. Now, to change a paradigm you need more than a few articles. You need a very consistent case.

Science is self-regulated and very auto-critical, so don't you worry. In the case of you being a biologist, then you just gotta go to the lab and work on your hypothesis.

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03-12-2012, 09:01 AM (This post was last modified: 03-12-2012 09:13 AM by THEMAYAN.)
RE: Is neo-darwinism a scientific theory?
(02-12-2012 10:49 PM)tiagorod84 Wrote:  Evolution is a verifiable empirical phenomenon. The theory of evolution, or modern synthesis can and should be revised when faced by increasing challenges.

The misunderstanding of what is a phenomenon and what is the explanatory scientific theory constitutes the fallacy in your argument since the beggining.

Just because you want to use the putative insuficiencies of the evolution theory (it is still needed more data to revise a paradigm that possess thousands of peer review articles in its support) to say that evolution as a natural phenomenon is automatically refuted, does not make it true.

Another thing that you fail to understand is the dynamics of science. Paradigms are useful, because it provides a framework. Now, to change a paradigm you need more than a few articles. You need a very consistent case.

Science is self-regulated and very auto-critical, so don't you worry. In the case of you being a biologist, then you just gotta go to the lab and work on your hypothesis.
Maybe it is your response which is more fallacious than even you seem to realize. Its not enough to have thousands of peer review article that support neo Darwinsm. In fact you dont even need to read peer review to understand that a consensus supports the theory. What I'm more interested in is the amount of compelling evidence. There is not one case regarded as evidence that doe not have an alternative explanation. We now know that there are limitations to natural selection and random mutations.

We now know the gene centered view ala Dawkins selfish gene is flawed. We now know that many of the tenants as already mentioned including the junk DNA paradigm which was used for years as a poster child for bad design is also flawed, and in fact the term junk DNA itself was finally eulogized and laid to rest by ENCODE. For years we were told that this theory was validated when we discovered that the differential between human and chimp genome was only a 1% difference i.e. they were 99% the same, genomically speaking, but It seems this notion was misleading because it only dealt with a specific part of the genome referred to as SNP's single nucleotide polymorphism.

As ENCODE started to look further, the number dropped to 96% when we rightfully included indels/insertion and deletion events. We then started seeing more differences in copy number variations and align-able sequences etc. Now we know that the over all differential is closer to 30% with an overall similarity of 70%. I will include other studies below with the same counter data from what we have been told collectively speaking
Below are things your children will never be taught in any lessons program. I call this indoctrination not teaching. I believe that natural selection can explain a lot of things, but prokaryote to mammal is not even close to one of them.








Originally sourced from the 2005 draft

Human body

From Wikipedia, the free encyclopedia




The draft sequence of the common chimpanzee genome published in the summer 2005 showed the regions that are similar enough to be aligned with one another account for 2400 million of the human genome’s 3164.7 million bases[19] – that is, 75.8% of the genome. This 75.8% of the human genome is 1.23% different from the chimpanzee genome in single nucleotide polymorphisms[19] (changes of single DNA “letters” in the genome). Another type of difference, called indels (insertions/deletions) account for another ~3 % difference between the alignable sequences.[19] In addition, variation in copy number of large segments (> 20 kb) of similar DNA sequence provides a further 2.7% difference between the two species.[20] Hence the total similarity of the genomes could be as low as about 70%.











Chimpanzee?

10-10-2008 - Dr Richard Buggs - research geneticist at the University of Florida

...Therefore the total similarity of the genomes could be below 70%.

http://www.refdag.nl/artikel/1366432/Chimpanzee.html




Do Human and Chimpanzee DNA Indicate an Evolutionary Relationship?

Excerpt: the authors found that only 48.6% of the whole human genome matched chimpanzee nucleotide sequences. [Only 4.8% of the human Y chromosome could be matched to chimpanzee sequences.]











Chimps are not like humans - May 2004

Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that "83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect," Sakaki said.

http://cmbi.bjmu.edu.cn/news/0405/119.htm









Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:

The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. However, if one looks at proteins, which are mainly responsible for phenotypic differences, the picture is quite different, and about 80% of proteins are different between the two species. http://www.ncbi.nlm.nih.gov/pubmed/15716009


(Take note the above study did not even take into account non SNP factors yet still cited protein differentials)


(We share 99% homologous genes with mice but would anyone refer to them as our closet relative?)




the mouse genome
Nature 420, 509 (5 December 2002) | doi</abbr>:10.1038/420509a
"We share 99% of our genes with mice, and we even have the genes that... new human genes have been discovered while mining the mouse"



We now know that tonsils, appendix, plantaris muscles are useful and purposeful, so neo Darwinist simply change the definition of vestigial organism over the decades, and now say that they are still vestigial but they just developed use over time. They are now trying to do the same for the failed paradigme of junk DNA. This is why evolutionary theory concerning prokaryote to man evolution can never be falsified. No matter how much current counter evidence there is toward the theory, evolutionist will simply say, lets change the theory to follow the evidence, which is like the cart pulling the horse, and I know of no other theory that allows such leeway.
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03-12-2012, 09:20 AM
RE: Is neo-darwinism a scientific theory?
(02-12-2012 10:49 PM)tiagorod84 Wrote:  Evolution is a verifiable empirical phenomenon. The theory of evolution, or modern synthesis can and should be revised when faced by increasing challenges.

The misunderstanding of what is a phenomenon and what is the explanatory scientific theory constitutes the fallacy in your argument since the beggining.

Just because you want to use the putative insuficiencies of the evolution theory (it is still needed more data to revise a paradigm that possess thousands of peer review articles in its support) to say that evolution as a natural phenomenon is automatically refuted, does not make it true.

Another thing that you fail to understand is the dynamics of science. Paradigms are useful, because it provides a framework. Now, to change a paradigm you need more than a few articles. You need a very consistent case.

Science is self-regulated and very auto-critical, so don't you worry. In the case of you being a biologist, then you just gotta go to the lab and work on your hypothesis.
And keep in mind the subject is one of neo Darwinism as a theoretical frame work as taught and as defended at Dover trial in Pennsylvania. This is why Stuart Newman and others object to this ruling. As I said before, you can still believe in the principle of macro evolution, but without a sound theoretical framework, you are left with nothing but a handfull of educated guesses and many assumptions. In this case "the assumptions of the modern synthesis" which again is a valid scientific term.
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03-12-2012, 10:30 AM (This post was last modified: 03-12-2012 11:04 AM by tiagorod84.)
RE: Is neo-darwinism a scientific theory?
"We share 99% homologous genes with mice but would anyone refer to them as our closet relative?"

Are you f******* kidding me? You do know the difference between sequence similarities and percentege of homologous genes, don't you? You do know that phylogeny goes much beyond the comparison of total genome sequence similarities, don't you? You do know that the 98-99 % similiraties are related to the comparison of homologous genes, don't you? Have you ever tried to perform a BLASTn with human genes? Try it! I assure you, it will be fun!!!

"I believe that natural selection can explain a lot of things, but prokaryote to mammal is not even close to one of them."

What makes you so sure that natural selection does not explain the evolution from prokaryotes to mammals? You're for discussion and make absolute sentences like this... Please!

Another thing, you do know that the 'Extended synthesis' proponents are not IDers, don't you?

Please enlight me if I'm wrong, but I've found your arguments very... dishonest!

Now, why don't you put your cards on the table: You refuse to be a primate, don't you?

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03-12-2012, 11:03 AM (This post was last modified: 03-12-2012 11:26 AM by THEMAYAN.)
RE: Is neo-darwinism a scientific theory?
(03-12-2012 10:30 AM)tiagorod84 Wrote:  "We share 99% homologous genes with mice but would anyone refer to them as our closet relative?"

Are you f******* kidding me? You do know the difference between sequence similarities and percentege of homologous genes, don't you? You do know that phylogeny goes beyond the comparison of total similarities of genomes, don't you? You do know that the 98-99 % similiraties are related to the comparison of homologous genes, don't you? Have you ever tried to perform a BLASTn with human genes? Try it! I assure you, it will be fun!!!

Another thing, you do know that the 'Extended synthesis' are not IDers, don't you?

Please enlight me if I'm wrong, but I've found your arguments very... dishonest!

Now, why don't you put your cards on the table: You refuse to be a primate, don't you?
If by "sequence similarities" you mean SNP's, then yes, and I gave examples of both including indel's, and even included copy number variations and align-able sequences as well as protein sequences. These are all components that make up the genome. I was speaking of the overall differential and not just picking and choosing what jives, and ignoring what doesn't. Keep in mind, even excluding protein differentials, the the overall differential between human and chimp genome still came to 70% or possibly less.

I have said many times in previous post that I made a clear distinction between ID'ers and evo devo who are trying to extend the synthesis and who are also coming under fire for doing so. The fact that you even ask, leads me to believe that you didn't actually read my former post. As for phylogenetic tree building, it may be fun for some people, but that is not the issue.

If you think that there is a sound and or accurate tree that all scientist draw from, you are mistaken. When doing cross species analysis, phylogenetic trees are fraught with conflicting data and well known incongruities. If you have a problem with data cited, then please be specific. Tell me why you seem to refute this data, and what is your refutation based on? Again please point out what I have said that you think is so dishonest, and please do so in proper context. Please feel free to quote me all you like, again as long as you do it in context.










Taxon Influence Index: Assessing Taxon-Induced Incongruities in Phylogenetic Inference 2012




Discovery of jumping gene cluster tangles tree of life (2/14/2011)




Gene tree discordance, phylogenetic

inference and the multispecies

coalescent

James H. Degnan

1,2

and Noah A. Rosenberg







Split Tree: analyzing and visualizing evolutionary data

Daniel H. Huson
MOTIVATION: Real evolutionary data often contain a number of different and sometimes conflicting phylogenetic signals, and thus do not always clearly support a unique tree. To address this problem, Bandelt and Dress (Adv. Math., 92, 47-05, 1992) developed the method of split decomposition. For ideal data, this method gives rise to a tree, whereas less ideal data are represented by a tree-like network that may indicate evidence for different and conflicting phylogenies. RESULTS: SplitsTree is an interactive program, for analyzing and visualizing evolutionary data, that implements this approach. It also supports a number of distances transformations, the computation of parsimony splits, spectral analysis and bootstrapping.

(The method above was proposed ten years ago yet has still not solved the problems of conflicting data and incongruities)







Testing for Phylogenetic Conflict Among Molecular Data Sets in Tribe Triticeae (Graminea) Robert J Mason.







Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene

Anja Rautenberg1, Dmitry Filatov2, Bodil Svennblad3, Nahid Heidari1 and Bengt Oxelman1,4*







Gene and genome trees conflict at many levels
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03-12-2012, 11:13 AM
RE: Is neo-darwinism a scientific theory?
"You do know that phylogeny goes beyond the comparison of total similarities of genomes, don't you?"


How does this argument help your case? On one hand you seem to be upset because I provided examples of different genes in addition with with SNP's which in turn help make genes, and or the proteins that also help make these same genes, and I didn't even include differentials in amino acids which I could have easily done, and which are also a part of phylogenetics.
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03-12-2012, 12:00 PM
RE: Is neo-darwinism a scientific theory?
Your best argument is to point out incongruencies in phylogenetic trees?

The genes that are used to make phylogenetic trees are not picked because they jive as you say, they're used due to their evolution rate.

Do you know that, per example, if you used MHC genes for phylogeny, you could be classified as a chimpanze and another human, let's say... me, as a human? Do you know why? Take an educated guess...

This is why you have to use genes with some degree of conservation and an adequate evolution rate to the phylogenetic tree you want make! If you want to make a phylogenetic tree of vertebrates you'll have to use very conserved genes; whereas if you want to make a phylogenetic tree of primates you'll have to use genes with a higher evolution rate. But you cannot use genes like the MHC. As the great Snoop Dog would say 'Ya diiig?'

Gene deletions, insertions, duplications are vey common and may occur within species in just one generation. You can only account with these mutations if they're conserved, just like the merged chromosomes in the chimpanze/human evolution.

Of course it is difficult to agree on the genes used in phylogeny there's always a great debate about that. But going from this, to imply that phylogeny doesn't group our species with the rest of the primates, that's just dishonest! To say that the scientific community is purely arbitrary in what it comes to choose the genes that are used in phylogeny, that's not only dishonest, that's insulting!

Once again I ask you: what are your claims?

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03-12-2012, 12:05 PM
RE: Is neo-darwinism a scientific theory?
(03-12-2012 11:13 AM)THEMAYAN Wrote:  "You do know that phylogeny goes beyond the comparison of total similarities of genomes, don't you?"


How does this argument help your case? On one hand you seem to be upset because I provided examples of different genes in addition with with SNP's which in turn help make genes, and or the proteins that also help make these same genes, and I didn't even include differentials in amino acids which I could have easily done, and which are also a part of phylogenetics.
You do know that unless you mutate a residue important for protein function the differential amino acids don't mean s**t, don't you? Can you easily account of how those differences in amino acids alter protein function? That's why protein sequences are used in phylogeny with caution...

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03-12-2012, 12:16 PM
RE: Is neo-darwinism a scientific theory?
http://www.nature.com/nature/journal/vao...11128.html

A damn good read...

You refuse to be a primate, don't you?

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03-12-2012, 12:31 PM (This post was last modified: 03-12-2012 01:04 PM by THEMAYAN.)
RE: Is neo-darwinism a scientific theory?
(03-12-2012 12:00 PM)tiagorod84 Wrote:  Your best argument is to point out incongruencies in phylogenetic trees?

The genes that are used to make phylogenetic trees are not picked because they jive as you say, they're used due to their evolution rate.

Do you know that, per example, if you used MHC genes for phylogeny, you could be classified as a chimpanze and another human, let's say... me, as a human? Do you know why? Take an educated guess...

This is why you have to use genes with some degree of conservation and an adequate evolution rate to the phylogenetic tree you want make! If you want to make a phylogenetic tree of vertebrates you'll have to use very conserved genes; whereas if you want to make a phylogenetic tree of primates you'll have to use genes with a higher evolution rate. But you cannot use genes like the MHC. As the great Snoop Dog would say 'Ya diiig?'

Gene deletions, insertions, duplications are vey common and may occur within species in just one generation. You can only account with these mutations if they're conserved, just like the merged chromosomes in the chimpanze/human evolution.

Of course it is difficult to agree on the genes used in phylogeny there's always a great debate about that. But going from this, to imply that phylogeny doesn't group our species with the rest of the primates, that's just dishonest! To say that the scientific community is purely arbitrary in what it comes to choose the genes that are used in phylogeny, that's not only dishonest, that's insulting!

Once again I ask you: what are your claims?
Can you cite evidence for this response of yours concerning what genes you have to use or that you cant use including MHC Major histocompatibility complex[font=arial, sans-serif] which is technically a cell surface molecule although also referred to as MHC genes. and which are found in all vertebrates, [/font]and what does this have to do with the claim that I am dishonest? First of all I never even mentioned the word "phylogeny" until you brought it up. I spoke of the genetic differentials between only humans and chimps, and I am still waiting for you say what is dishonest? You are the one that is using words like the "scientific community" and secondly, not all scientist think a like.

There are many who have stacked the deck so to speak, and there are many who do not, and are not afraid to speak of the problems, instead of ignoring they exist. The data I cited was from the scientific community, and not all members of the scientific community are neo Darwinist, even if most accept prokaryote to man evolutionary theory, & even if neo Darwinism is what is taught in class. I asked you to quote me and you could not, and instead you are making things up that I never said.

You see your paradigme concerning genes that can or cant be used in phylogenetic tree building is based on nothing other than the notion that some must have a faster evolutionary rate, which is not based on any known molecular clock, but rather, on an assumption that it must have happened this way. Again another example of backwards logic, i.e. the horse following the cart. This is a classic case where one uses the lack of evidence as evidence. In this case, an incohesive phylogenetic tree. This is done all the time in evolutionary theory.
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