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Debate: Does evidence support neo-darwinian evolution

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Debate: Does evidence support neo-darwinian evolution
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SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Debate: Does evidence support neo-darwinian evolution

This is a formal debate between Squawk and Micah1116 on "Does evidence support neo-darwinian evolution?"

This debate was inspired by a previous debate between qball17 and Micah1116 which can be found in the archives here.

That debate ended prematurely and resulted in Squawks offer to debate here.

The rules are as follows:

1. The debate will last for a maximum of 15 posts per participant plus an optional final summary post.
2. Each post shall have a maximum of 3000 words including quotes
3. Each post shall follow within 1 week of the previous post, with one wild card per participant enabling a 2 week gap.
4. Normal forum rules apply.
5. Neither poster will be permitted to offer comment about this debate in any public area of this forum.

Posting in this thread is restricted to the participants, Squawk and Micah1116
The comments thread can be found here

Micah1116 was offered the choice and elected to post second. Squawk has 1 week from today to make his opening statement.

##note: I'll get another mod, maybe gnug, to look after the debate from here on out. Bit harsh if I do it.

##edit: Gnug215 has sorta agreed to mod this debate, will confirm shortly

#edit: So much for me not modding it...
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Tue Oct 19, 2010 9:58 pm
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

It's a few years since I decided some introspection was in order. I'd left religion behind me, but I had a suspicion that within the few pounds of gray matter that comprise my brain there were likely various assumptions and presumptions that couldn't stand up to critical scrutiny. I made the decision to examine my beliefs and thus began my interest in what might be termed philosophy or epistemology. No sacred beliefs, no cherished ideas, no notions that I'd cling to because I liked them.

What does this have to do with evolutionary theory? Nothing, and everything. My epistemology places no value on anything that cannot be formulated as a coherent idea and then put to some kind of test, be that direct or indirect. It has left no room for faith, faith being the refuge of the credulous, and instead insists on evidence. Evidence leads to conclusions, conclusions that may be revised in light of more evidence being alighted upon.

And so to evolution. I deem evolution to be the most robust, most evidentially supported and most critically examined theory that science has to offer. This debate seems to me, right from the outset, to be something of a tautology. Science is, essentially, the process of forming conclusions from evidence. Evolutionary theory is the product of the scientific method, of that methodology. Does the evidence support the conclusions that were derived from that evidence. Tautological? Perhaps. Circular, most definitely.

Let us be clear from the start what we mean here. We're talking about the modern Darwinian synthesis, and I'll define a few terms for use throughout this debate.

Evolution: Descent with inherited variation in a reproducing population
Species: A population throughout which gene transfer can occur.

The definition of species is somewhat arbitrary, required to enable a proper discussion of taxonomy or phylogeny. It's necessarily woolly in that we are trying to apply discreet classification to a continuous reality, but it will suffice for now.

And so this debate. I'll be frank, I have no idea where to pitch this since I can't see an area where evolutionary theory is weak and I find it hard to conceive how anyone can object to it on rational grounds.

It's simple reality denial to say that evolution itself doesn't take place. I've defined evolution above, any evolutionary biologist will recognise and agree that my definition encompasses evolution. We're talking here simply about the name given to an observed process. Hell, go count blue eyed and brown eyed people in the world, come back in 20 years and do it again, and if you find any variation you've observed evolution.

If my opponent does not acknowledge that evolution both does and is occurring, as defined above, then this debate is over before it begins and I'll move to end it on grounds of incompetence.

Presuming that it is agreed that the above is occurring, and quite frankly I don't see how it can be denied, then we must look at the debate title and decipher exactly what it means. I know the title is somewhat woolly, I was well aware of that when I wrote it, it pretty much had to be.

Speciation is obviously out too, since a single post on ring species will be sufficient to dispel any notion that neo-darwinian evolution cannot produce new species.

Diversity would seem to be the only avenue left, and thus I suspect we shall head into the realm of phylogeny, of nested hierarchies, branching processes and the like, and again I can't see an avenue for my opponent to travel with any hope of success.

If this is indeed the way the debate will go then we'll look at the various independent means of constructing a phylogeny. No doubt we'll cover such subjects as ERV's, chromosome fusion, gene fixation and the like, and at every turn my opponent is going to find masses of evidence that I suspect can only be fought with outright denial. I predict logical fallacies will pervade Micah's argument, but I may be surprised.

And so I return to my opening statements. My epistemology compels me to place any ideas I have up for scrutiny. I don't care which ideas stand up to scrutiny, whether it be my own or those held by someone else's. If mine are shown to be in error then I will adjust them accordingly or abandon them altogether.

And so we go on, in which direction I have no clue. One way or the other I will learn something, either through research for my own posts, or simply because I get beaten. Enjoy

Micha, the floor is yours.

##edit. I posted can rather than cannot, essentially arguing for the other side. Now corrected :D
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Tue Oct 19, 2010 11:36 pm
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

"It's simple reality denial to say that evolution itself doesn't take place. I've defined evolution above, any evolutionary biologist will recognise and agree that my definition encompasses evolution. We're talking here simply about the name given to an observed process. Hell, go count blue eyed and brown eyed people in the world, come back in 20 years and do it again, and if you find any variation you've observed evolution."

most humans already have the genes for different eye colors. Please explain how changing color of anything, can change the form and structure of an organism. Claiming that changes to color is evolution, is total nonsense.

"If this is indeed the way the debate will go then we'll look at the various independent means of constructing a phylogeny. No doubt we'll cover such subjects as ERV's, chromosome fusion, gene fixation and the like, and at every turn my opponent is going to find masses of evidence that I suspect can only be fought with outright denial. I predict logical fallacies will pervade Micah's argument, but I may be surprised."

I'm surpised that evolutionists still use these arguements. First I'll start with ERV's:

Evolutionists claim that many viral infections in earlier life forms have resulted in the DNA of those viruses being passed on ancestrally in later evolving organisms. One example of the failure of this claim is that the PtERV1 is found in the Rhesus Monkey, Olive Baboons, and African great apes, but not in humans! This makes it clear that ERVs are evidence of common design, not evolution, since had man and the great apes shared a common ancestor, the great apes would also share the PtERV with humans. 14 our of so far discovered 98,000 human ERVs are found in the same location in the chimpanze genome (.00014%). However, this means that 99.99986% are not found in the same location!

What are called "retroviruses" are trasposable elements of DNA, which means they are capable of jumping around the genome and performing various functions. Endogenous means "produced or synthesizes within an organism", and retrovirus means the sequences in question are claimed to be remnants of viral DNA acquired by infections in evolutionary ancestors. However, PTERV1 is such a sequence of DNA that exists in Old World monkeys and chimpanzes, which are claimed to be man's closest living relative, yet it doesn't exist in humans. It should if retroviruses were viral DNA and evidence of evolution.

The Human Genome Project has verified that what evolutionists once called "junk" and "retroviruses" are involved in controlling the sequence and level of gene expression during embryonic development by moving to and from the sites of gene control, are interdependant with other portions of the DNA, function as promoters by starting transcription at alternative starting points, enable different RNA transcripts to be formed from the same DNA sequence, aid the transcription of 1/5 of the entire human genome. The list of known specific functions for what are called retroviruses is now so extensive that time doesn't allow me to even mention them all.

The sequrences of DNA called retroviruses are at the very heart of the genomic design, morphological design, and biochemical functions of creatures, and have been discovered to be elements of intelligent design and powerful evidence of a common designer.

The Human Genome Project report states, "We report the existence of 51,197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1,743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5 untranslated regions."

It also states, "Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome."

The evolutionist is therefore stuck with believing that 23.60% of the human genome is comprised of viral DNA. How perposterous it is to believe that the instructions of the human genome could be comprised of so much viral DNA considering that humans are intercellular creatures of incomparably greater complexity. Evolutionism is quite obviously so irrational and so far from having basis in science, that evolutionists must rely on conclusions not unlike believing that the instructions to build a portable radio could comprize over 23% of the instructions to build a computer.

Regarding the "junk DNA" claim, Dr John Mattick, director of the Institute for Molecular Bioscience at the University of Queensland, who is an evolutionist by the way, has stated, "The failure to recognize the full implications of this - particularly the possibility that the intervening noncoding sequences may be transmitting parallel information ... may well go down as one of the biggest mistakes in the history of molecular biology." In fact, the Encode Project has determined that 93% of human DNA is transcribed into RNA!

Refering to Junk DNA and retroviruses, Molecular biologist Linda Walkup has stated, "The molecular taxonomists, who have been drawing up evolutionary histories ("phylogenies") for nearly every kind of life, are going to have to undo all their years of "junk DNA"-based historical reconstructions and wait for the full implications to emerge before they try again." 9

Clearly, what evolutionists once declared was junk DNA and what are claimed to be retroviruses are now known to be similar sequences of DNA in different species which provide similar or identical critical functions. But evolutionist don't like embaressment or giving up their claims. Despite the fact that the Human Genome Project has dicredited the evolutionist claims of Junk DNA and retroviruses as evidence of evolution, Science Daily still has on their web site an article published in 2005 which states, "Much of the rest of our genomes,often referred to as junk DNA,consists of retroelements ... Human endogenous retroviruses make up one class of these retroelements."

http://www.sciencedaily.com/releases/20 ... 174826.htm

YouTube user Donexodus2 states regarding retroviruses in his video titled, This is Why Every Scientist Accepts Evolution (which is far from true by the way), I quote, "phylogenetic trees can be constructed from them alone." He states also, "this is why every rational person must accept evolution." to which I ask, based upon what? Antiqueted asumptions based upon an evolution paradigm? Like all evolutionists, he's still promoting antiquated assumptions as if they were science. Creationists predicted that what was claimed to be "junk DNA" and "retroviruses" would be revealed as evidence of a common designer, have critical function, and be part of what seperates creatures from each other, and we were right, as the Human Genome Project has discovered. Those still using this claim are uninformed and an embaressment to evolutionists. The now discredited retrovirus claim is a fine example of how evolutionists adopt remarkable evidence of a common designer into their paradigm, stamp the word "evolution" on them, and think this turns thier false assumptions into science.
9 Williams, A., Astonishing DNA complexity demolishes neo-Darwinism, Journal of Creation 21(3):111--118, 2007; p. 113.

--------------------------------------------


Viruses have genomes of 2,000 to 200,000 base pairs


Activated Retroviruses
Sometimes the production of a protien goes wrong and abnormal protiens called Prions (proteinaceous infectious particles) are produced. These can trigger the sequences evolutionists call retroviruses to transcribe abnormal protiens, which then themselves become rogues and spread from cell to cell and cause disease. This doesn't demonstrate that what are called retroviruses are viral DNA, but merely that faulty protiens cause these supposed retroviruses to transcribe a faulty protien, which then causes disease. The transposable feature of these supposed retroviruses is one of the reasons evolutionists falsely assume they are viral DNA, when in fact they are a normal part of the function of DNA to share critical design elements between cells where they are needed.
http://www.huliq.com/33532/expression-o ... -infection

Now I'll address chromosome 2: The theory that Ken Miller puts forth about our chromosome 2 being the result of the fusion of two ape chromosomes is nothing but an assumption that does not pass the scientific method. I could go on for probably a page describing the faulty assumptions with this theory. Ken Miller says that apes could not lose two chromosomes because that would be fatal, so what must have happened is that a fusion occured. So they looked in our genome and our chromosome 2 looks to be fused, so that proves we are related to apes. Can you not see the assumption in this? Since apes have 48 and we have 46, and he believes that we are related to apes, the fusion was from an ape ancestor. Ken Miller states that the fused chromosome is unique to OUR LINEAGE, so that theory goes out the window. If the fusion occured in apes, why isn't there a population of apes with 46 chromosome? If it happened in the human population, why isn't there a population of humans with 48 chromosomes? And here's a thought, since losing chromosomes would be fatal, and we apparently evolved from an amoeba, which has 500 chromosomes, are you saying that hundreds of chromosomal fusions occured in all phylum of life? Where are these fusions? Chromosome 2 underwent an inversion not a fusion. Here are two articles for you to read.

http://www.detectingdesign.com/pseudogenes.html#Fusion

http://www.evolutionnews.org/2005/10/an ... 01067.html
Thu Oct 21, 2010 6:10 am
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

I'll start this post with a quick reminder that all sources must be cited, and indeed note that a failure to cite sources is actually grounds for ending a debate early. Also, a polite inquiry, are you actually nephilimfree? Call it mod privileges/op abuse, but I'm going to exempt my alighting of your plagiarism from my 3000 word allocation since it has nothing to do with the debate itself, but needs to be said and it saves someone else doing it.

http://newscows.com/?p=37275
Direct quotes:
Nephi at Newscows wrote:
"What are called "retroviruses" are trasposable elements of DNA. Endogenous means "produced or synthesizes within an organism"
"However, PTERV1 is such a sequence of DNA that exists in Old World monkeys and chimpanzes"

Copied without citation into your first post. Even if you are Nephi it would still be nice to see a citation.

Then I'll turn to this
http://go.pastie.org/pastes/802225/text
This would seem to be an email exchange between nephi and a user named linux7master who I've had a quick go at tracking down, but his account seems to be inactive on youtube. Once again we find direct quotes

Nephi? wrote:PtERV1 is found in the rhesus monkey, olive baboons, and African great apes, but not in humans!

And once again, a direct copy is found in Micha's first post, without citation, even including the exclamation mark!

I'll then refer you to this document
http://creation.com/large-scale-functio ... troviruses

And point out that your post seems to be, though not a copy paste, simply a regurgitation of that website. It certainly contains the same quotes from scientists, in the same order. At least that site had the decency to cite it's sources. Even more fortunately the paper in question "Retroviral promoters in the human genome", Conley, A.B., Piriyapongsa, J. and Jordan, I.K., Retroviral promoters in the human genome, Bioinformatics 24(14):1563-1567, 2008" is free to read, it can be found here. I'll return to that shortly.

Next I'll refer you to this quote. Guess where it comes from (I'll tell you in a minute)

? wrote:What evolutionists claim are retroviruses and junk DNA has been verified as elements of common design principles. The Human Genome Project has discredited these claims, but evolutionists refuse to let go of the claims. Ofcourse, they still promote the concept that phylogeny, germ layers, and homologous structures are evidence of evolution in text books, so why should we expect them to admit to something scientific?


And compare it with this

micha wrote:Clearly, what evolutionists once declared was junk DNA and what are claimed to be retroviruses are now known to be similar sequences of DNA in different species which provide similar or identical critical functions. But evolutionist don't like embaressment or giving up their claims. Despite the fact that the Human Genome Project has dicredited the evolutionist claims of Junk DNA and retroviruses as evidence of evolution


Similarities? I thought so too, indeed I found the first quote when googling the phrase "the Human Genome Project has discredited the evolutionist claims of Junk DNA and retroviruses as evidence of evolution". Try it, see what the first link is (quick hint, it's a video by nephilimfree, that first quote is nephi's video description).

OK, that concludes my little intro. Personally I'd say I already have adequate grounds to move for a termination of this debate right here and now for the easy win, but I won't do that. Too easy, too boring, and nobody learns anything. And so, my real post begins. 3000 words from now.


################################################


micha wrote:most humans already have the genes for different eye colors. Please explain how changing color of anything, can change the form and structure of an organism. Claiming that changes to color is evolution, is total nonsense.

Since I defined evolution to be "descent with inherited modification in a reproducing population", this is simply reality denial and I'll dismiss it without further comment. Should you wish to redefine evolution we can address it, but I consider this to be yet more grounds for an instant termination of the debate.

micha wrote:Evolutionists claim that many viral infections in earlier life forms have resulted in the DNA of those viruses being passed on ancestrally in later evolving organisms. One example of the failure of this claim is that the PtERV1 is found in the Rhesus Monkey, Olive Baboons, and African great apes, but not in humans! This makes it clear that ERVs are evidence of common design, not evolution, since had man and the great apes shared a common ancestor, the great apes would also share the PtERV1 with humans.


The debate title was "does evidence support neo-Darwinian evolution". You're obviously comfortable with retroviral insertion but you dispute that it can be used as evidence of speciation and common ancestry. It would seem logical that this debate will be steered towards a discussion on common ancestry, so at least now I know where we are headed. The example you picked is, fortunately for me, an excellent example of precisely why we can construct phylogenies using ERVs and is excellent for discussing common ancestry. Lets get to some science.

Two papers to present to flush your assertion down the toilet, the first in some detail, the second just an aside:
http://www.plosbiology.org/article/info ... io.0030110 (paper 1)
"Lineage-Specific Expansions of Retroviral Insertions within the Genomes of African Great Apes but Not Humans and Orangutans" Chris T. Yohn1#, Zhaoshi Jiang2#, Sean D. McGrath2, Karen E. Hayden1, Philipp Khaitovich3, Matthew E. Johnson1,2, Marla Y. Eichler2, John D. McPherson4, Shaying Zhao5, Svante Pääbo3, Evan E. Eichler

http://www.sciencemag.org/cgi/content/f ... /5832/1756 (Free registration required to read) (paper 2)
"Restriction of an Extinct Retrovirus by the Human TRIM5{alpha} Antiviral Protein" hari M. Kaiser,1,2 Harmit S. Malik,3 Michael Emerman
Science 22 June 2007:Vol. 316. no. 5832, pp. 1756 - 1758


From the first
Paper 1 wrote:In order to further resolve the evolutionary relationship of these endogenous retroviruses, we compared the sites of retroviral integration in the genomes of chimpanzee, gorilla, macaque, and baboon.... We then compared the locations (Figure 3; Table 2) between species to determine whether the sites were non-orthologous. Based on an analysis of 1,467 large-insert clones, we mapped 299 retroviral insertion sites among the four species (Figure 3; Table S2). A total of 275 of the insertion sites mapped unambiguously to non-orthologous locations (Table 2), indicating that the vast majority of elements were lineage-specific (i.e., they emerged after the divergence of gorilla/chimpanzee and macaque/baboon from their common ancestor).


The research looked for instances of retrovirus insertion in the genomes of four species of ape, then looked to see if they were orthologous (in the same place in the genome across species). They eliminated all but 24 as being non-orthologous. That leaves us with 24 potentially orthologous locations.

paper 1 wrote:Within the limits of this BAC-based end-sequencing mapping approach, 24 sites mapped to similar regions of the human reference genome (approximately 160 kb) and could not be definitively resolved as orthologous or non-orthologous (Table S3). We classified these as "ambiguous" overlap loci (Figure 3). If all 24 locations corresponded to insertions that were orthologous for each pair, this would correspond to a maximum of 12 orthologous loci. The number of non-orthologous loci was calculated as 275/287 (275 + 12) or 95.8%. This is almost certainly a lower-bound estimate owing to the limitation of our BAC-based mapping approach to refine the precise locations of the insertions.


There were 24 instances of the ERV that could not be established as being non-orthologous, giving 12 instances (between species) of possible orthology, and the authors note that this is likely a high estimate due to the limitations of the method applied. They then continue.

paper 1 wrote:We performed two analyses to determine whether these 12 shared map intervals might indeed be orthologous. First, we examined the distribution of shared sites between species (Table S3). We found that the distribution is inconsistent with the generally accepted phylogeny of catarrhine primates [5]. This is particularly relevant for the human/great ape lineage. For example, only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee.


A problem? Of course not, simply science making an honest observation. Lets see how it gets resolved.

paper 1 wrote:For the three intervals putatively shared between macaque and chimpanzee, we attempted to refine the precise position of the insertions by taking advantage of the available whole-genome shotgun sequences for these two genomes. For each of the three loci, we mapped the precise insertion site in the chimpanzee and then examined the corresponding site in macaque (http://www.ncbi.nlm.nih.gov). In one case, we were unable to refine the map interval owing to the presence of repetitive rich sequences within the interval. In two cases, we were able to refine the map location to single basepair resolution (Figures S4 and S5). Based on this analysis, we determined that the sites were not orthologous between chimpanzee and macaque. It is interesting to note that this level of refined mapping in chimpanzee revealed 4- to 5-bp AT-rich target site duplications in both cases. These findings are consistent with an exogenous retrovirus source since proviral integrations typically target AT-rich DNA ranging from 4 to 6 bp in length [24]. Although the status of the remaining overlapping sites is unknown, these data resolve four additional sites as independent insertion events and suggest that the remainder may similarly be non-orthologous. This apparent independent clustering of retroviral insertions at similar locations may be a consequence of preferential integration bias or the effect of selection pressure against gene regions, limiting the number of effective sites that are tolerated for fixation.


So, thats one location that couldn't be properly examined, two locations that were examined and shown not to be orthologous, and by extension they resolved a further 4 (of the 12) sites that are non-orthologous. The remaining sites were not examined, but as the authors note the conclusion without further evidence is that the sites are non-orthologous.

Where does this leave your assertions? Completely flushed, actually. You're best evidence (surely you produced your best evidence) that ERV's cannot be used to show common ancestry involved the presentation of an ERV that validates the very principles that underpin the construction of phylogenies based on ERV's. When a retrovirus enters and fixes in a population any subsequent analysis of daughter species will show instances of it to be orthologous.

Analysis of PtERV1 and it's evolution in the genomes of the species in which it is found give us a good approximation of when it was prevalent and show that we should expect it to be non homologous within the genome's of the apes. That is, indeed, what we find.

The insistence that this particular example invalidates ERV's as evidence of common ancestry demonstrates that you didn't understand the papers that discussed PtERV1, or alternatively, that you never bothered to read them and simply believed dishonest anti-evolution propaganda from elsewhere. Given that I have already highlighted your willingness to plagiarize other material without reference I'm inclined to believe the latter.

What we find here is exactly the opposite of your claim, we have clear evidence of exactly how ERV's show us common ancestry, and I suppose I should thank you for giving me the incentive to go and read some fascinating papers.

I did mention the evolution of the ERV's themselves, so a quick quote from the paper is required.
paper 1 wrote:Using neutral estimates of primate LTR divergence [8], we estimate that a contemporaneous infection occurred in these ancestral gorilla and chimpanzee lineages 3-4 million years ago (see Materials and Methods). LTR divergence among baboon and macaque was significantly less (0.051% and 0.058%, respectively; p < 0.007, one-tailed t test), corresponding to a much more recent origin (approximately 1.5 million years ago). These observations may be reconciled with differences in the phylogenetic tree topology if the Old World monkeys were infected by several diverged viruses while gorilla and chimpanzee were infected by a single closely related exogenous source


I'd make the recommendation that everyone goes and reads the first couple of paragraphs (if not all) of the discussion section of the paper.

One observation made in paper 1 was that it was not known (they hypothesized) why PtERV1 was not found in Humans. The second paper is referenced here simply because it serves to show further work on plausible hypothesis. In other words, that far from the question being ducked, it is being addressed and revised in real time.


Micha wrote:The Human Genome Project report states, "We report the existence of 51,197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1,743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5 untranslated regions."

It also states, "Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome."

The evolutionist is therefore stuck with believing that 23.60% of the human genome is comprised of viral DNA.


Very intesting. Wrong, but interesting. First I'll refer you to the opening paragraph of the paper, where we read
paper 3 wrote:Approximately 5% of the human genome sequence is derived from retroviruses (Lander et al., 2001).


Following that reference, we find the actual human genome reporthttp://www.nature.com/nature/journal/v409/n6822/full/409860a0.html/.
I'm not inclined to cite or quote much from it, I didn't even read it all, but I link to it here for completeness.


The honest person is confronted with empirical data and is therefore presented with an option. To accept that reality and attempt to explain it, or to use a logical fallacy known as the appeal to ignorance in order to propagate some faith based myth that this is not the case. The web page that you plagiarized for this information referenced this paper


paper 3 wrote:Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome.


The claim of 23.6% of the genome being comprised of viral DNA would seem to be an addition of those two figures which again shows a complete misunderstanding. Even the dumb ass website you're plagiarizing doesn't make that mistake. Go re-read it.

Micah wrote:Evolutionism is quite obviously so irrational and so far from having basis in science, that evolutionists must rely on conclusions not unlike believing that the instructions to build a portable radio could comprize over 23% of the instructions to build a computer.


Point 1. I have no clue what evolutionism is. I've no real problem with evolutionist, where an evolutionist is defined as a person who accepts evolutionary theory, but you'll have to define evolutionism for me. Best guess is that it's an attempt to equate evolutionary theory with a faith based position such as religion in order to devalue it, a position I always find amusing since it demonstrates that the person making the assertion already realizes that faith is a weak concept.

Point 2. A simple appeal to incredulity based on a figure you don't understand (the 23.6% figure), which I shall simply dismiss for reasons already explained.

Then the funnies

Micha wrote:Regarding the "junk DNA" claim, Dr John Mattick, director of the Institute for Molecular Bioscience at the University of Queensland, who is an evolutionist by the way, has stated, "The failure to recognize the full implications of this - particularly the possibility that the intervening noncoding sequences may be transmitting parallel information ... may well go down as one of the biggest mistakes in the history of molecular biology." In fact, the Encode Project has determined that 93% of human DNA is transcribed into RNA!


Aside from the fact that this is yet another quote without citation, why are you bringing up junk DNA? You wrote "regarding the Junk DNA claim". I didn't mention junk DNA, yet you wrote this as if I did. That would be a straw man of my position. If you had asked me about junk DNA or brought it up in context I'd be compelled to answer. You didn't though, you wrote this as if it were a response to something I said. I'll refer everyone, once again, to this and let them make their own minds up about why you wrote this. My own contention is that you are simply regurgitating websites that you don't understand.

Micha wrote:Refering to Junk DNA and retroviruses, Molecular biologist Linda Walkup has stated, "The molecular taxonomists, who have been drawing up evolutionary histories ("phylogenies") for nearly every kind of life, are going to have to undo all their years of "junk DNA"-based historical reconstructions and wait for the full implications to emerge before they try again."

Did you note the source for this comment? Did you spot where it was published, read the reference at all? I did: The Journal of creation. Is this intended to be humorous? I found it funny. If you're going to present evidence please actually give evidence rather than an opinion piece in a magazine or the deluded rant of someone taken in by religious waffle.

I'm confused by the reference to youtube user donexodus2. Why would I care what his opinion is? The reference gives me more inclination to suspect that you are Nephilimfree. I happen to like DonExodus' work, but reference it in a debate?

Micha wrote:Now I'll address chromosome 2: The theory that Ken Miller puts forth about our chromosome 2 being the result of the fusion of two ape chromosomes is nothing but an assumption that does not pass the scientific method. I could go on for probably a page describing the faulty assumptions with this theory.

A full page? Not a full page!!!

How about full scientific papers from the peer reviewed literature, including the original discovery of the fusion site?
http://www.sciencemag.org/cgi/reprint/215/4539/1525.pdf?ijkey=3605112d431d235f6a5b70dd0278983d28dbe8fe (original discovery in 1982)
http://genome.cshlp.org/content/12/11/1663.full
http://genome.cshlp.org/content/15/12/1746.full
http://www.pnas.org/content/88/20/9051.short

If you need more I'll go get them, but I'm not inclined to present them in full unless requested to do so due to space constraints. I will though, if the tide of bullshit doesn't stop.

Micha wrote:Ken Miller states that the fused chromosome is unique to OUR LINEAGE, so that theory goes out the window. If the fusion occured in apes, why isn't there a population of apes with 46 chromosome? If it happened in the human population, why isn't there a population of humans with 48 chromosomes?


The theory goes out of the window? Since the fusion took place after the split of humans from the other apes, any other ape population with 46 chromosomes would have had to have experienced an independent fusion event that went to fixation. It's trivial.

As for a population of humans with 48 chromosomes we're talking about a simple case of fixation. If 46 chromosomes were neither deleterious nor beneficial then the calculation is simply dependent on population size and rate of reproduction. If it was beneficial then the route to fixation would have been faster.

Micha wrote:we apparently evolved from an amoeba


No, we didn't. Colonial and multicellular life evolved from single celled organisms billions of years in the past. Amoeba generally refers to a genus of modern day single celled organisms.

As a final point for this post, why did you bring up creation and a designer. This debate is testing the notion that evidence supports evolutionary theory. Surely you haven't made the error of presuming that the null hypothesis is anything other than evolution is false? Are you intending to present a false dichotomy?

Booya :-D

##edit: Changed decent to descent, seemed like the decent thing to do.
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Thu Oct 21, 2010 5:19 pm
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

Firstly, I must address your claim that I'm copying information. I get loads of info from people, including the person you mentioned, nephilimfree, he is a youtube friend of mine. I've also got information I have saved on my computer that I use too. I personally just find info that I believe refutes evolutionists claims, I'm not trying to plagurize anything, and this tactic you are using, is an attempt to ignore the information provided, and switch the subject. And no, I'm not nephilimfree, LOL! I live in NC, not mississippi, you can even search my IP address if you must, but I'm using another computer because I'm out of town in WV, either way, I'm not NephilimFree.

The main problem with your claim that ERV's are evidence for common ancestry is that only 14 out of the 98,000 ERV's that we share are in the same place in the genome. Secondly, ERV's are now known to play a key role in morphological developement, it is not common sense to think that a virus could control the morphology of an organism. Basic probability would allow for 14 ERV's to be in the same genomic location.

Junk DNA, is on par with the arguement of ERV's, and I assumed you would mention it sooner or later. Current research has discredited the claims that Junk DNA is indeed junk.

Here, I will provide what I believe to be the best evidence for creation:http://creation.com/meta-information

Why didn't you mention anything about chromosome 2?

It would be nice if you would atleast try and refute the infiormation I provided you, your going after the creationist sources, rather than the actual information.
Last edited by Squawk on Fri Oct 22, 2010 4:33 pm, edited 1 time in total.
Reason: I took the liberty of merging the posts
Fri Oct 22, 2010 2:37 am
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

Mod Note (Surely someone else should be doing this...)

The structure of the debate is that one user posts, followed the other. Edits of text to correct spelling or to improve grammar are acceptable. Double posting is not.

####################################


Micha wrote:Firstly, I must address your claim that I'm copying information. I get loads of info from people, including the person you mentioned, nephilimfree, he is a youtube friend of mine. I've also got information I have saved on my computer that I use too. I personally just find info that I believe refutes evolutionists claims, I'm not trying to plagurize anything, and this tactic you are using, is an attempt to ignore the information provided, and switch the subject.

The highlighting of your sources of information was my acting in a capacity as a mod on the boards. Plagiarism is illegal.

I did not switch the subject, I tackled the claims that you made head on. You cited PtERV1 so I decided to deal with it in depth. Your claim was that it was a refutation of common ancestry since it was found in certain ape lineages but not others. I trust you have now revised that opinion in light of the evidence I presented. At the very least I trust you have now realized that Nephilimfree is not a valid source of information on the subject of ERV's.

Micha wrote:The main problem with your claim that ERV's are evidence for common ancestry is that only 14 out of the 98,000 ERV's that we share are in the same place in the genome.

CITATION!!! ERV's that we share with what? This is yet another snippet of information that, without further information, is useless. Do we share 14 ERV's with blue whales, or blue-green algae? There is simply no point in my presenting anything at this juncture since it would appear you are to do a version of the gish gallop. I show your ideas on PtERV1 to be in error, you jump to numbers of orthologous ERV's. I show that to be in error, and you'll jump to something else. Nail your objection to the wall, if I can dismantle it then you can accept defeat. A debate requires that we actually debate, not that you simply evade every point I make. Cite your source for ERV numbers and explain what they are.

Micha wrote:Secondly, ERV's are now known to play a key role in morphological developement, it is not common sense to think that a virus could control the morphology of an organism.

What you mean to say is that ERV's play a key role in transcription, they influence gene expression. This is an argument from incredulity (the not common sense thing), a logical fallacy. It's also a complete contradiction. In the first half of the sentence you tell me that ERV's play a key role in development, in the second half you tell me that a virus cannot control development. Which is it? Cognitive dissonance here that you need to resolve, how can I possibly defend a position if you can't even state it succinctly? Surely you're not arguing that an ERV is not the remains of a retrovirus, are you?

Micha wrote:Basic probability would allow for 14 ERV's to be in the same genomic location.

Please explain the calculation to me. There are approx 3 billion base pairs in the human genome so if infection is random (it's actually not quite random, I'll present a paper on that if you want) your maths are out by several orders of magnitude. Please show your working so that I can see how you arrive at your figures. Without more information I will, once again, be vulnerable to the gish gallop/goal post shift, a common creationist tactic since defending an actual position always means defeat.

Just to keep any interested readers occupied while you ponder this, I'd recommend this paper
http://www.pnas.org/content/96/18/10254.full
"Constructing primate phylogenies from ancient retrovirus sequences" 1. Welkin E. Johnson "  and 2. John M. Coffin "¡
PNAS August 31, 1999 vol. 96 no. 18 10254-10260

It's a little outdated (1999), but as far as I can tell was pretty much the first attempt at the constructing phylogenies based on ERV's. Pretty fascinating reading.

Just a brief taster

paper wrote:Retroviruses are unique among RNA viruses in their ability to integrate DNA copies of their genomes into the genome of the infected cell. On occasion, integration takes place in a germ-line cell, giving rise to an endogenous retrovirus (ERV), which can be inherited by the offspring of the infected host, and may eventually become fixed in the gene pool of the host population (1). The genomes of vertebrate species contain dozens to thousands of ERV sequences (2), some of which were acquired in evolutionarily recent times, whereas others derive from "ancient" times, as indicated by their identical site of integration in more than one species (1, 3, 4). Typically, ancient proviruses have sustained numerous point mutations, deletions, and insertions, rendering them incapable of expressing virus. No biologically active viruses have been associated with the ancient proviruses.


Just a side note, the references in the part I've bolded require a subscription to read, a subscription I don't have.

The paper continues with

Paper wrote:HERVs can be organized into at least a dozen distinct groups, which vary in size from one to thousands of members (1, 12). Cross-hybridization and PCR studies consistently reveal that most HERV families are also found in other primates, including apes and Old World monkeys (OWMs) (12-19). Many HERVs, including the ones used in this study, are the result of integration events that took place between 5 and 50 million years ago, as indicated by the distribution of specific proviruses at the same integration sites (or "loci") among related species. The evolution of primates has been the subject of intense study for well over a century, providing a well established phylogenetic consensus with which to compare and evaluate the performance of ERVs as phylogenetic markers.


The bolded part here is of much importance. Part of the strength of evolutionary theory is the multiple independent means by which we can arrive at a phylogeny. Comparative anatomy was the first, as used by Linnaeus well before Darwin's time, though he wasn't so much creating a phylogeny as categorizing life. The discovery of DNA was a massive breakthrough, comparing the genomes of organisms provides a much more robust reconstruction of evolutionary history.

ERV's could have either disagreed with that structure, or confirmed it. If they disagreed with it the onus would have been on science to explain why. I'm not going to dissect the results and conclusion here other than to provide a link to the various trees produced and presented in that paper http://www.pnas.org/content/96/18/10254 ... nsion.html

If there are any specific objections fire away.

micha wrote:Junk DNA, is on par with the arguement of ERV's, and I assumed you would mention it sooner or later. Current research has discredited the claims that Junk DNA is indeed junk.

You assumed I'd mention it? I'm not agreeing with your premise (that junk DNA does not exist), but could you tell me why this is an issue for evolutionary theory? If you have an objection I'll deal with it, but once again please be specific otherwise I'll suspect a goal post shift. Right now all you've said is "Junk DNA doesn't exist, so evolution is false". Tell me why it's false and I'll have something to argue with. Otherwise you might as well say "the moon is made of green cheese, therefore evolution is false". It has the same weight in this debate, zero, since it is a logical fallacy, a non-sequiter.

micha wrote:Here, I will provide what I believe to be the best evidence for creation:http://creation.com/meta-information


Dismissed out of hand as being a complete irrelevance for this debate which concerns evidence for evolution. As already stated, the null hypothesis regarding the evidence for evolution is that evolution does not occur. Myth based doctrine has no place in this discussion and any further attempts to take the discussion off topic will result in my request that the debate is terminated.

Micha wrote:Why didn't you mention anything about chromosome 2?


I did, I went and dug up four papers from the peer reviewed literature including papers dating to the time of the discovery of the fusion site. I further showed your claims about a human population with 48 chromosomes and Ken Millers claims going "out the window" to be a simple case of misunderstanding concerning the timing of the fusion and the nature of gene fixation.

I declined to go into depth primarily because your claims were trivially refuted, but also due to space constraints. If you have a particular objection to chromosome fusion provide an accurate citation and explain the issue then I'll be glad to address it.

Micha wrote:It would be nice if you would atleast try and refute the infiormation I provided you, your going after the creationist sources, rather than the actual information."


Did you even read my post?
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Fri Oct 22, 2010 3:08 pm
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

I'm at a hotel and can't quote your posts, but you asked for a citation to my claim that we only have 14 out of the 98,000 that we share with apes are in the same location. Evolutionists claim that ERV's are in the same location because they are common ancestors, why aren't all of them in the same location? You even admitted that ERV's have a critical role in gene expression, they aren't viruses, they were designed for a purpose.

Will you atleast attempt to refute meta information in DNA as being proof for design? I think the reason you are avoiding it, is because you know that it does indeed prove design. It's almost like a chicken and egg arguement.

I'm not seeing where you mentioned anything about chromosome 2, maybe I'm missing something??
Sun Oct 24, 2010 2:22 am
Gnug215ModeratorUser avatarPosts: 2542Joined: Sat Feb 21, 2009 10:31 pm

Post Re: Debate: Does evidence support neo-darwinian evolution

MOD NOTE!

micah1116 wrote:I'm at a hotel and can't quote your posts, but... [...]
I'm not seeing where you mentioned anything about chromosome 2, maybe I'm missing something??


Yes, you are missing something.

Here is an excerpt from Squawk's 3rd post, the one immediately after your first post:


Squawk wrote:
Micha wrote:Now I'll address chromosome 2: The theory that Ken Miller puts forth about our chromosome 2 being the result of the fusion of two ape chromosomes is nothing but an assumption that does not pass the scientific method. I could go on for probably a page describing the faulty assumptions with this theory.

A full page? Not a full page!!!

How about full scientific papers from the peer reviewed literature, including the original discovery of the fusion site?
http://www.sciencemag.org/cgi/reprint/215/4539/1525.pdf?ijkey=3605112d431d235f6a5b70dd0278983d28dbe8fe (original discovery in 1982)
http://genome.cshlp.org/content/12/11/1663.full
http://genome.cshlp.org/content/15/12/1746.full
http://www.pnas.org/content/88/20/9051.short

If you need more I'll go get them, but I'm not inclined to present them in full unless requested to do so due to space constraints. I will though, if the tide of bullshit doesn't stop.

Micha wrote:Ken Miller states that the fused chromosome is unique to OUR LINEAGE, so that theory goes out the window. If the fusion occured in apes, why isn't there a population of apes with 46 chromosome? If it happened in the human population, why isn't there a population of humans with 48 chromosomes?


The theory goes out of the window? Since the fusion took place after the split of humans from the other apes, any other ape population with 46 chromosomes would have had to have experienced an independent fusion event that went to fixation. It's trivial.

As for a population of humans with 48 chromosomes we're talking about a simple case of fixation. If 46 chromosomes were neither deleterious nor beneficial then the calculation is simply dependent on population size and rate of reproduction. If it was beneficial then the route to fixation would have been faster.

Micha wrote:we apparently evolved from an amoeba


No, we didn't. Colonial and multicellular life evolved from single celled organisms billions of years in the past. Amoeba generally refers to a genus of modern day single celled organisms.

As a final point for this post, why did you bring up creation and a designer. This debate is testing the notion that evidence supports evolutionary theory. Surely you haven't made the error of presuming that the null hypothesis is anything other than evolution is false? Are you intending to present a false dichotomy?

Booya :-D

##edit: Changed decent to descent, seemed like the decent thing to do.



Now, in your post immediately after this one, you wrote:

micah1116 wrote:Why didn't you mention anything about chromosome 2?



As a mod, I have to ask: did you read Squawk's entire post? Or is there a technical problem that truncated his post, somehow? Is the hotel thing interfering again?

If there are technical issues that prevent you from properly participating in this debate, I suggest we postpone it until such issues are resolved, if possible.

If you're simply not reading Squawk's post properly, then I see no reason to continue the debate.

Please acknowledge this mod note in a separate post on this thread that does not address the debate itself. Your response will not count towards the final post count (provided it does not address any of Squawk's post - to do so you will make a separate post).

Thank you.
- Gnug215

YouTube channel:
http://www.youtube.com/user/Gnug215


The horse is a ferocious predator.
Sun Oct 24, 2010 8:33 am
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

Thankyou for clarifying, now would you explain how they found the fusion site? I wouldn't even argue that there was a fusion, if you can indeed prove to me that there was a fusion, but it still assumes that we are related to apes.

Here's a quote taken from the 2nd link to provided:

"Two ancestral chromosomes fused head-to-head to form human chromosome 2 (Yunis and Prakash 1982). This gross karyotypic change probably contributed to the reproductive barrier between the early humans who carried this new structure and closely related hominids."

All the article discovers is that a fusion took place, they assume the ancestor in which the fusion occured were apes, since they have to support evolution at all costs. If you test the theory with the problems I addressed before, it fails, so now you have a problem. Why aren't there any apes with 46 chromosomes? A fusion would not turn an ape into a human, do you even know what information is contained in the chromosomes you are talking about?


"I did not switch the subject, I tackled the claims that you made head on. You cited PtERV1 so I decided to deal with it in depth. Your claim was that it was a refutation of common ancestry since it was found in certain ape lineages but not others. I trust you have now revised that opinion in light of the evidence I presented. At the very least I trust you have now realized that Nephilimfree is not a valid source of information on the subject of ERV's."

No, my claim was that it was found in apes, but not humans, that's the problem. Here's another example.

http://holysmoke.org/01-herv-k-provirus.pdf

Many examples like this, totally refute your claims that ERV's prove common ancestry. Straying from the ERV arguement a bit, the claim that our DNA is 99% similiar to chimps is a myth, and evolutionists are now admitting it:

http://www.arn.org/blogs/index.php/lite ... n_dna_comp

There are several things, you haven't addressed yet, you haven't addressed my meta information claim, nor the question of how shape and size can cause new structures to be formed. Size and shape can be changed, mainly when human intervention is involved, like with different breeds of dogs, but new structures will never evolve according to what we observe.

Your stuck in naturalism and are trying to find a natural explanation for something that couldn't possibly have one. For example, a human is created when two humans of the opposite sex reproduce and have a child, so this is a natural explanation as to how humans come to be, here's the problem. Science shows us that it takes two humans of the opposite sex to create a human, but this natural process can't explain wher the first two humans of the opposite sex came from. Humans can't be the explanation of how humans came into existence in the first place, and this is true of any reproducing organism on the planet.

How come organisms llke bees and flowers have symiotic relationships and have totally different morphologies and if I'm correct, lived in totally different time eras? Flowers can't reproduce without bees, and bees can't live without flowers since they have to have pollen to make honey, which is their food source. There are literally thousands of examples like this.

Evolution tries to explain why your physical body is here, even if evolution were true, it couldn't possibly explain why you are a consious being and exist. What natural process determined that you would begin to exist and become conscious at this period of time and in the physical body that you are in? Why not 500 years ago and another body?

If you would like, we can change the subject to something else if you'd like. I think that the people on this forum would be interested in seeing how the creationists and evolutionists view geology and dinosaurs, and where they think they fit in, care to discuss this?
Mon Oct 25, 2010 12:55 am
Gnug215ModeratorUser avatarPosts: 2542Joined: Sat Feb 21, 2009 10:31 pm

Post Re: Debate: Does evidence support neo-darwinian evolution

Mod note:

Micah1116... read this!

I'll copy from my above message:


"As a mod, I have to ask: did you read Squawk's entire post? Or is there a technical problem that truncated his post, somehow? Is the hotel thing interfering again?

If there are technical issues that prevent you from properly participating in this debate, I suggest we postpone it until such issues are resolved, if possible.

If you're simply not reading Squawk's post properly, then I see no reason to continue the debate.

Please acknowledge this mod note in a separate post on this thread that does not address the debate itself. Your response will not count towards the final post count (provided it does not address any of Squawk's post - to do so you will make a separate post).

Thank you. "


I can't believe you just missed a message asking you whether you actually read everything... with big green letters, even.
- Gnug215

YouTube channel:
http://www.youtube.com/user/Gnug215


The horse is a ferocious predator.
Mon Oct 25, 2010 6:55 am
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

Yes, I saw your post, that's why I said "thanks for clarifying". There's not a issue anymore that I'm aware of.
Mon Oct 25, 2010 6:33 pm
Gnug215ModeratorUser avatarPosts: 2542Joined: Sat Feb 21, 2009 10:31 pm

Post Re: Debate: Does evidence support neo-darwinian evolution

micah1116 wrote:Yes, I saw your post, that's why I said "thanks for clarifying". There's not a issue anymore that I'm aware of.


But Micah, I didn't clarify anything.I just re-posted part of Squawk's message - and I also asked if you saw his message in the first place, since you claimed he hadn't said anything about Chromosome 2. (And since you didn't mention my name, or quote my post, and then went on to address Squawk's points, I was assuming you were addressing him, not me.)

It's one thing to skip past some points - or wholly ignore half a post - of your opponent, but to claim he didn't say anything about it is beyond me. So I assumed that you either didn't read his post properly, or had technical difficulties.

I suggest you look over the terms of the debate again in Squawk's initial post, and be sure to read his posts properly. Furthermore, to the benefit of yourself and everyone reading the debate, I highly recommend you make use of the quote function.

Thanks.
- Gnug215

YouTube channel:
http://www.youtube.com/user/Gnug215


The horse is a ferocious predator.
Mon Oct 25, 2010 8:35 pm
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

Technically I'm 120 words or so over my limit with this post, but since Micha posted twice I'm going to allow myself the oversight rather than going through and editing to get it under 3000. If it's a major issue Micha then let me know and I'll take the time to sort it.

########

micah1116 wrote:Thankyou for clarifying, now would you explain how they found the fusion site? I wouldn't even argue that there was a fusion, if you can indeed prove to me that there was a fusion, but it still assumes that we are related to apes.


Chromosome fusion doesn't assume we are related to apes, it is evidence that we are related to the other apes. It was known that humans were "missing" a pair of chromosomes long ago. This meant one of a few things were true.
1. Humans didn't share a common ancestor with the other apes
2. The other apes all gained an extra pair of chromosomes after the human line split from the others (ie, the last split, with the chimps)
3. Two chromosomes fused at some point since the last split.

This is trivial to understand. We can eliminate number 2 using evolutionary theory (somewhat ironically). 100 years of evidence suggested that humans and chimps share a more recent common ancestor than either does with the various other ape species. Therefore the probability that the other apes acquired an extra pair of chromosomes can be considered eliminated, unless the already existing ape phylogeny is in error. This is due to the fact that humans would have had to split from the other apes before the other apes diverged to allow inheritance of the new chromosomes. Alternatively, we'd have to calculate the probability of chance allowing the arrising of identical chromosomes in independent lineages.

That leaves us with 1 and 3. Either humans and the other apes don't share a common ancestor, or two chromosomes fused after our lineage broke away.

So far so good? Now, lets look at what you found after reading my second link.

Micha wrote:All the article discovers is that a fusion took place

So, in the first sentence of your post you accept that a fusion happened. I have now explained to you the implications of this fusion event, and you have agreed that this is a geunine fusion.

You should now understand the power of this particular finding and you should now understand why this next bit, from your post, simply displayed your previous ignorance.

micha wrote:they assume the ancestor in which the fusion occured were apes, since they have to support evolution at all costs.

Not at all. If a fusion event couldn't be found then a drastic revision of our evolutionary history would have been considered. For starters a re-writing of our own phylogeny, and that for all of the other apes. Depending on findings this branch of evolutionary theory may have had to be abandoned. However, the fusion was found, you've just read a paper on it and agreed that the fusion took place. Now you know what it means.

Micha wrote: If you test the theory with the problems I addressed before, it fails, so now you have a problem. Why aren't there any apes with 46 chromosomes?

Already addressed above, then referened again when you suggested I hadn't addressed it, and then quoted at you by Gnug215 when you continued to insist I hadn't dealt with it. You've been given the answer to this three times already. The fusion occured after the human line diverged from the other apes. This is trivial, if you don't understand this you can't possibly have undestood half the information that you copied without citation, so I conclude that you don't even know your own side of this argument, let alone the real science, or you are being intentionally dishonest.

Micha wrote: A fusion would not turn an ape into a human

No shit. How is this in any way relevent? Just for reference, a fused chromosome wouldn't necessarily have any effect on phenotype (and almost certainly didn't in the human lineage).

Micha wrote:Do you even know what information is contained in the chromosomes you are talking about?

The complete works of Shakespeare? Why is this pertinent to the debate?

Micha wrote:No, my claim was that it was found in apes, but not humans, that's the problem.

So you don't read my posts? You didn't understand any of the papers I presented, the papers detailing that PtERV1 was inserted into the genomes of numerous ape lineages after they split from one another? You didn't understand that the non-orthologous location of the sites studied accross species nor the divergence experienced by the ERV's indicated insertion events in most ape lineages around 5 million years ago? You didn't understand or bother to read the paper I linked to that showed the work (ongoing) to understand why the humans and orangutans were apparently immune to this family of virii or were not exposed to it?

You started the discussion on ERV's with this

Micha wrote:I'm surpised that evolutionists still use these arguements. First I'll start with ERV's:


What we seem to have found here, and I've exposed it in detail, is that you have absolutely no clue about ERV's, and the reason you are suprised that "evolutionists" continue to use them is that you haven't the first notion of what they are, how powerful they are as evidence, how they can be used and you haven't even got the intellectual honesty to try to find out.

micha wrote:http://holysmoke.org/01-herv-k-provirus.pdf
Many examples like this, totally refute your claims that ERV's prove common ancestry.

Oh really. Did you read the paper? Understand it? Thought not.
The paper in question can be found at http://www.cell.com/current-biology/abstract/S0960-9822%2801%2900227-5 and can be read in full for free (click the pdf link on the right). I note that you preferred, once again, to link to a website that references work rather than to the work itself, but no matter. The paper you linked to appears to be a complete reproduction and it contains all relevent information for citation.

The paper itself is written in such a way that pretty much anyone with familiarity with gene fixation and alleles can understand, so I won't quote it as I did the last paper. Instead I'll give a quick explanation of the papers findings, and then quote a relevent and important section from the conclusion.

HERV-K is a retrovirus that is known to have been active for periods of several million years. There are numerous instances of orthologous insertions in the gorilla, human and chimp genomes plus numerous instances of non-orthologous instances in all three lineages. The non-orthologous insertions almost all come from insertions after speciation, with the orthologous insertions from before.

The exception, which this paper discusses, is the instance of HERV-K-CG1 that is orthologous in the gorilla and chimp genomes, but is not present in humans. A problem for evolutionary theory? Of course not, as the paper goes on to discuss.

The explanation is one of gene fixation. In the common ancestor of gorillas, chimps and humans there existed numerous polymorphic alleles (more than one version of a gene that had not yet gone to fixation, think eye colour in humans as a quick example). Consider two alleles present within the population. Allele1, the newly infected allele containing the ERV, and allele 2 which is the ancestral version. The gorillas split off and allele1 goes to fixation within the gorilla population, while the remaining population is still polymorphic. A second speciation event occurs, leading to to the separation of the human and chimp lineages, both of which are polymorphic. individuals in both populations can contain either allele1 or allele2. In the chimp lineage the allele1 goes to fixation, the same as that in gorillas, containing the ERV. In humans allele2 goes to fixation is the ancestral gene, the original gene that was infected with the retro-virus.

There are numerous requirements here, the most obvious being that the populations must be of sufficient size to permit the populations to remain polymorphic for a sufficient period of time (from before the gorilla separation to after the human/chimp separation). Micha told us earlier that the probability of random insertion events at orthologous locations was sufficient to explain 14 instances of shared ERV's (it's not, but he ignored it when I asked for his working so we don't know what his maths was). I'll now ask if he can provide the maths for gene fixation presuming the new allele is neither deleterious nor beneficial. I want this information because I suspect that he will simply argue that this solution is implausible, and I propose that he will do so without actually knowing the maths behind it. Therefore, I'm not going to provide it, I'm going to make him tell me or I'm going to dismiss his objection as spurious.

This is actually a great example of why you don't always get identical trees when developing phylogenies from individual genes and is one of the reasons why muliple genes are sampled and assesed to form trees, the most parsimonious of which is then said to be a best representation of evolutionary history. For anyone interested in an easy to read explanation of this idea I'd recommend Richard Dawkins The Selfish Gene.

I'll quote a little from the conclusion of the paper.

paper wrote:The precise details of the nature of the phylogenetic separation of humans from the African great apes has remained uncertain. Genetic studies indicated that humans and chimpanzees are the most closely related pair for much of the genome [1-4]. However, for some fraction of the genome, they are not [1, 3, 4]. Such data are consistent with a model in which alleles segregated differently among the three eventual lineages [1, 4, 19-21].


We see here that the purpose of this study was to better understand the instances where gorilla and chimp genomes are more similar than humans. Far from ignoring it or sweeping it under the carpet it is, as usual tackled head on. This isn't because science wants past findings to be accurate. Instead it is driven by an insatiable desire to understand.



paper wrote:However, at positions in the genome where allelism was maintained throughout theperiod of existence of the human-chimpanzee commonancestor, some of the same alleles that became fixed inthe gorilla lineage may also have been fixed in only oneof the human or chimpanzee lineages. The HERV-K-GC1 provirus provides a compelling piece of evidencefor such a model, as it is the clearest example to date of a specific locus within the genome where chimpanzees and gorillas are more closely related to each other than either is to humans.


Here we see the real conclusion of this paper. Not that ERV's don't show common ancestry or that humans and the other apes don't share a common ancestor. Rather, the paper alights and provides evidence for a particular model of speciation involving polmorphism. Micha, just in case you are interested you'll find links in the very paper that you linked to which provide information on how long alleles last in a population, you might wish to read them.

Micha, if you had bothered to read the paper on PtERV1 that I presented earlier you would already have had some familiarity with the idea I've just presented, though it wasn't spelled out. That paper presented a number of trees developed from genetic comparison, a number of which showed slight discrepencies. The final tree selected as a best approximation of actual evolutionary history is the most parsimonious tree from all the data accumulated.

I think we can consider your objection to ERV's (and indeed to genetic comparison) to have been well and truely destroyed, so I presume that as a good and honest Christian you won't be using them again.


Micha wrote: Straying from the ERV arguement a bit, the claim that our DNA is 99% similiar to chimps is a myth, and evolutionists are now admitting it:
http://www.arn.org/blogs/index.php/lite ... n_dna_comp


I can't properly address this claim as the article referenced requires a paid for subscription. It can be found at http://www.sciencemag.org/cgi/content/summary/316/5833/1836

However, we've just been dealing with a paper that discussed base pair substitution in the genomes of gorillas, chimps and humans for specific genes and found discrepencies on the order of 1.6 and 1.7%. Do you have a specific objection to make rather than simply quotes out of context on an ID related blog? If you could provide specific objections rather than just "1% was wrong therefore evolution false" I'll dissect your claims more thoroughly.

micha wrote:There are several things, you haven't addressed yet, you haven't addressed my meta information claim]

And I won't, since it's off topic and sets up a false dichotomy. The null hypothesis of evolution is not evolution, not some nebulous concept of a deity.


micha wrote: nor the question of how shape and size can cause new structures to be formed.

You never asked this question, so now I suggest that are you lying about the aspects of your posts that I have or haven't addressed in order to score debate points.

micha wrote: Size and shape can be changed, mainly when human intervention is involved, like with different breeds of dogs, but new structures will never evolve according to what we observe.

You've already been schooled on this subject by Proteus here

A few quck observations. First, human intervention has not (until very recently) added new genetic information but has simply acted to select strongly in favour of certain traits. Variety arises entirely by natural means. Your objection must simply be with natural selection, and so I ask you for an barrior that could prevent natural selection having effects similar in nature to artificial selection given sufficient time.

micha wrote:A human is created when two humans of the opposite sex reproduce and have a child, so this is a natural explanation as to how humans come to be, here's the problem. Science shows us that it takes two humans of the opposite sex to create a human, but this natural process can't explain wher the first two humans of the opposite sex came from. Humans can't be the explanation of how humans came into existence in the first place, and this is true of any reproducing organism on the planet.


Your example would hold true save for one, tiny detail. Evolution. Evolution explains the above perfectly, and since we are dealing with the evidence for evolution it can just be dismissed out of hand. And so, I have.

Micha wrote:How come organisms llke bees and flowers have symiotic relationships and have totally different morphologies and if I'm correct, lived in totally different time eras?

How can organisms that are symbiotic live in different eras? Symbiotic organsims must exist together or the relationship cannot be described as symbiotic. Perhaps you should restate this so I know what I need to dismantle.

Micha wrote: Flowers can't reproduce without bees, and bees can't live without flowers since they have to have pollen to make honey, which is their food source. There are literally thousands of examples like this.

Evidence of this? It just so happens that I researced bees and orchids a few months ago for a similar discussion with a Jehovas Witness who offered up a similar statement. Funny how people with a religious agenda continue to gravitate to the same false claims. I'll just quote part of my email to him rather than going over the same ground again

email wrote:
Lets start with this one, from
http://www3.interscience.wiley.com/jour ... 1&SRETRY=0
Specificity and mutual dependency of the orchid-euglossine bee interaction
June 2008

I quote from the abstract
"The orchid-male euglossine bee interaction does not appear to
represent a mutually obligatory relationship. The orchids may have
exploited a preexisting behavioural phenomenon of the bees, and
reciprocal evolutionary responses may not have occurred.

http://www.springerlink.com/content/u1768kxv45h16853/
Next to this paper, entitled
"Long term ecology euglossine orchid-bees in Panama" from 2004

Again quoting from the abstract
"Although specialized orchid preferences are implicated for species
that visit few or no local orchids but pollinate other species and
carry pollinaria in other areas, euglossine bees do not need orchids
to survive or reproduce."

Here's a third paper on the subject
http://www.esajournals.org/doi/abs/10.1 ... 2.0.CO%3B2
Paper Title: ORCHID BEES DON'T NEED ORCHIDS: EVIDENCE FROM THE
NATURALIZATION OF AN ORCHID BEE IN FLORIDA

Again, a quote from the abstract
"The bee's ability to live and become abundant in the absence of its
orchid mutualists suggests that the orchid bee-perfume orchid
mutualism may be facultative for the bees, even though it is
obligatory for the orchids. "

I've also found Darwins original book on the subject free to read
online. Should you be inclined to do so you can find it at
http://darwin-online.org.uk/content/fra ... &pageseq=1


And so your claim would seem, once again, to be a fabrication. Do you have a source for it?


Micha wrote:Evolution tries to explain why your physical body is here, even if evolution were true, it couldn't possibly explain why you are a consious being and exist.

First, I'd dispute that it can't do that, but on what grounds do you base your objection? I base my confidence in evolutionary theory on its track record of success, I'd guess your base your objection on myth and doctrine.



Micha wrote: What natural process determined that you would begin to exist and become conscious at this period of time and in the physical body that you are in? Why not 500 years ago and another body?


Lets go either with determinism or random chance (or an amalgamation of the two). No wishful thinking involved here.

MIcha wrote:If you would like, we can change the subject to something else if you'd like.

This is a debate, a debate which you are losing badly, so I'm not inclined to do so. This would seem to be something of a concession.

Micha wrote: I think that the people on this forum would be interested in seeing how the creationists and evolutionists view geology and dinosaurs, and where they think they fit in, care to discuss this?


Almost certainly true. You could bring up dino's in context I suppose, you could even bring up geology if we are to discuss the geological column in relation to evolutionary history with fossils found in order from oldest to youngest sediment. We could also discuss geology from the point of view of plate techtonics which fits in extremely well with the distribution of species. However, my guess is that you will bring up the usual creotionist canards of polonium halos or polystrate fossils and I'll just dismiss these out of hand as previously debunked and not pertinent to this debate, so the choice is yours.

Lets face it Micha, you've been owned.
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Tue Oct 26, 2010 2:21 pm
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

#edit: This post has been reformatted by Squawk in order to use correct forum formatting for quotes to make the post more readable. This has been done without seeking the permission of Micah. No content has been altered.

####################

Squawk wrote:This is trivial to understand. We can eliminate number 2 using evolutionary theory (somewhat ironically). 100 years of evidence suggested that humans and chimps share a more recent common ancestor than either does with the various other ape species. Therefore the probability that the other apes acquired an extra pair of chromosomes can be considered eliminated, unless the already existing ape phylogeny is in error. This is due to the fact that humans would have had to split from the other apes before the other apes diverged to allow inheritance of the new chromosomes. Alternatively, we'd have to calculate the probability of chance allowing the arrising of identical chromosomes in independent lineages.

That leaves us with 1 and 3. Either humans and the other apes don't share a common ancestor, or two chromosomes fused after our lineage broke away.

So far so good? Now, lets look at what you found after reading my second link.


If the fusion happened after the human lineage diverged from apes, like you just stated, then why aren't there humans with 48 chromosomes?

Again, you are assuming that we are related to apes. How would having a fused chromosome be evidence that we are related to apes, the only way that would be considered evidence is if that's what your looking for and what you already believe. Why wouldn't it be evidence that we are related to a dear mouse, or a gray fox? Ken Millers theory is a grand assumption, not science.

Squawk wrote:"Oh really. Did you read the paper? Understand it? Thought not.
The paper in question can be found at http://www.cell.com/current-biology/abs ... %2900227-5 and can be read in full for free (click the pdf link on the right). I note that you preferred, once again, to link to a website that references work rather than to the work itself, but no matter. The paper you linked to appears to be a complete reproduction and it contains all relevent information for citation.

The paper itself is written in such a way that pretty much anyone with familiarity with gene fixation and alleles can understand, so I won't quote it as I did the last paper. Instead I'll give a quick explanation of the papers findings, and then quote a relevent and important section from the conclusion.

HERV-K is a retrovirus that is known to have been active for periods of several million years. There are numerous instances of orthologous insertions in the gorilla, human and chimp genomes plus numerous instances of non-orthologous instances in all three lineages. The non-orthologous insertions almost all come from insertions after speciation, with the orthologous insertions from before.

The exception, which this paper discusses, is the instance of HERV-K-CG1 that is orthologous in the gorilla and chimp genomes, but is not present in humans. A problem for evolutionary theory? Of course not, as the paper goes on to discuss.

The explanation is one of gene fixation. In the common ancestor of gorillas, chimps and humans there existed numerous polymorphic alleles (more than one version of a gene that had not yet gone to fixation, think eye colour in humans as a quick example). Consider two alleles present within the population. Allele1, the newly infected allele containing the ERV, and allele 2 which is the ancestral version. The gorillas split off and allele1 goes to fixation within the gorilla population, while the remaining population is still polymorphic. A second speciation event occurs, leading to to the separation of the human and chimp lineages, both of which are polymorphic. individuals in both populations can contain either allele1 or allele2. In the chimp lineage the allele1 goes to fixation, the same as that in gorillas, containing the ERV. In humans allele2 goes to fixation is the ancestral gene, the original gene that was infected with the retro-virus.

There are numerous requirements here, the most obvious being that the populations must be of sufficient size to permit the populations to remain polymorphic for a sufficient period of time (from before the gorilla separation to after the human/chimp separation). Micha told us earlier that the probability of random insertion events at orthologous locations was sufficient to explain 14 instances of shared ERV's (it's not, but he ignored it when I asked for his working so we don't know what his maths was). I'll now ask if he can provide the maths for gene fixation presuming the new allele is neither deleterious nor beneficial. I want this information because I suspect that he will simply argue that this solution is implausible, and I propose that he will do so without actually knowing the maths behind it. Therefore, I'm not going to provide it, I'm going to make him tell me or I'm going to dismiss his objection as spurious.

This is actually a great example of why you don't always get identical trees when developing phylogenies from individual genes and is one of the reasons why muliple genes are sampled and assesed to form trees, the most parsimonious of which is then said to be a best representation of evolutionary history. For anyone interested in an easy to read explanation of this idea I'd recommend Richard Dawkins The Selfish Gene."


So if ERV's are found in the same location in the genome, it's evidence for evolution, yet if they don't exist at all, when they indeed should, you'll come up with with response of what you think happened.

Squawk] wrote:How can organisms that are symbiotic live in different eras? Symbiotic organsims must exist together or the relationship cannot be described as symbiotic. Perhaps you should restate this so I know what I need to dismantle.


That's my entire point, there are many cases where organisms have entirely different morphologies and according to evolutionists lived in totally different time periods.

Squawk wrote:"Evidence of this? It just so happens that I researced bees and orchids a few months ago for a similar discussion with a Jehovas Witness who offered up a similar statement. Funny how people with a religious agenda continue to gravitate to the same false claims. I'll just quote part of my email to him rather than going over the same ground again

email wrote:
Lets start with this one, from
http://www3.interscience.wiley.com/jour ... 1&SRETRY=0
Specificity and mutual dependency of the orchid-euglossine bee interaction
June 2008

I quote from the abstract
"The orchid-male euglossine bee interaction does not appear to
represent a mutually obligatory relationship. The orchids may have
exploited a preexisting behavioural phenomenon of the bees, and
reciprocal evolutionary responses may not have occurred.

http://www.springerlink.com/content/u1768kxv45h16853/
Next to this paper, entitled
"Long term ecology euglossine orchid-bees in Panama" from 2004

Again quoting from the abstract
"Although specialized orchid preferences are implicated for species
that visit few or no local orchids but pollinate other species and
carry pollinaria in other areas, euglossine bees do not need orchids
to survive or reproduce."

Here's a third paper on the subject
http://www.esajournals.org/doi/abs/10.1 ... 2.0.CO%3B2
Paper Title: ORCHID BEES DON'T NEED ORCHIDS: EVIDENCE FROM THE
NATURALIZATION OF AN ORCHID BEE IN FLORIDA

Again, a quote from the abstract
"The bee's ability to live and become abundant in the absence of its
orchid mutualists suggests that the orchid bee-perfume orchid
mutualism may be facultative for the bees, even though it is
obligatory for the orchids. "

I've also found Darwins original book on the subject free to read
online. Should you be inclined to do so you can find it at
http://darwin-online.org.uk/content/fra ... &pageseq=1"



According to what you said, the orchids need the bees to survive, but the bees may be able to survive without the orchards

Squawk wrote:"You've already been schooled on this subject by Proteus here

A few quck observations. First, human intervention has not (until very recently) added new genetic information but has simply acted to select strongly in favour of certain traits. Variety arises entirely by natural means. Your objection must simply be with natural selection, and so I ask you for an barrior that could prevent natural selection having effects similar in nature to artificial selection given sufficient time."


Show showing me charts of different organisms with totally different morphologies, is evidence for evolution? How can showing a chart based on how he believes it happend be considered science? I'll ask you, show me one OBSERVABLE evidence of an organism acquiring a new structure, not some chart, or idea you come up with in your head.

Squawk wrote:"Lets go either with determinism or random chance (or an amalgamation of the two). No wishful thinking involved here."


I think you got a headache trying to figure that one out.

Squawk wrote:"And I won't, since it's off topic and sets up a false dichotomy. The null hypothesis of evolution is not evolution, not some nebulous concept of a deity."


So dicsussing DNA is off topic? :lol: I fail to realize how you would think discussing the properties of DNA is off topic, the debate topic is whether or not the evidence supports neo darwinan evolution, and when we look at the properties of DNA, it's an obvious no.

Squawk wrote:"What we seem to have found here, and I've exposed it in detail, is that you have absolutely no clue about ERV's, and the reason you are suprised that "evolutionists" continue to use them is that you haven't the first notion of what they are, how powerful they are as evidence, how they can be used and you haven't even got the intellectual honesty to try to find out."


So please tell me how finding out that we share 14 out of our 98,000 ERV's with apes is evidence for evolution? Then when we find ERV's in apes but not humans, you'll come up with some fantastic story of what you think happened. Please tell me how this is science. And most evolutionists treat ERV's as if they are a type of disease that have no function, while we know they have a large scale function. Your coming up with a package of assumptions and conjecturing them as if they are fact, you haven't show any observable evidence of evolution, and I haven't asked this entire time, but will now. Just show me one example of an organism acquiring a new structure
Tue Oct 26, 2010 7:06 pm
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

I'm taking the liberty of reformatting Micha's post since it's such a horrid mashup of quotes that it's virtually impossible to read. Micha, if you wish the post be returned to it's original format let me know, I have saved copy. Clearly this post is in my capacity as a mod, not part of this debate.
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Tue Oct 26, 2010 9:46 pm
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

And so we go on. I had thought we might be making some headway, but the Gish gallop at full throttle has lots of momentum. And so once more unto the breech, dear friends.

Micha wrote:If the fusion happened after the human lineage diverged from apes, like you just stated, then why aren't there humans with 48 chromosomes?


Why did you quote that specific bit of my post, then write this? It's not relevant. The text that you should have quoted came directly after the bit that you actually have. Conclusion: You didn't understand what I wrote and so offered up a generic objection that you hoped I'd let slide.

Your objection isn't valid, of course.

Your complete failure to grasp fixation or polymorphism prevent you understanding why your objection isn't valid, but I'll give it anyway.
1. Why would there be? (Can you explain that to me? Hint, it could have happened).
2. When the chromosome fusion occurred and was not deleterious one of two things could occur. Either the fused chromosome would spread through the population and become fixed, or it would go extinct. It happens to have become fixed, but it could have gone the other way. Without a full understanding of the benefits conveyed by this fusion (likely zero at a guess) I can't put figures on probability for you, but it would be a similar calculation to the chance of any given gene variant arising and becoming fixed in the population.

Until you understand this you won't have a chance of understanding the significance of ERVs either, demonstrated perfectly by your continued spurious objections to ERVs as evidence of common ancestry.

Micha wrote:Again, you are assuming that we are related to apes.

No, I'm testing that idea, and I'm using the existence or otherwise of a fused chromosome to do so. It's an important distinction and again one that you need to grasp in order to see why you are wrong. Once again I note the fact that you quoted the wrong part of my post.

Micha wrote: How would having a fused chromosome be evidence that we are related to apes, the only way that would be considered evidence is if that's what your looking for and what you already believe.

Simple. When we note that humans are "missing" a chromosome when compared with the other apes we know that there has to be an explanation. If humans do share a common ancestor with the other apes then there must be a fusion, for the reasons I've stated previously. The fused chromosome was a prediction of evolutionary theory before it was discovered, it's subsequent discovery as expected is further contributory evidence. This really is simple stuff, erect and then test a hypothesis.

Micha wrote: Why wouldn't it be evidence that we are related to a dear mouse, or a gray fox?

You have to ask this question and expect to be taken seriously? The most recent common ancestor of all apes (including humans) is more closely related to any species of ape (by definition) than to any of the species you mentioned. Any event that occurred in the ape line after the most recent common ancestor of the apes can be used most efficiently to investigate relationships within the clade than those outside.

If we wish to assess our relationship with these other species we must first establish our relatedness with our most recent common ancestors before we look further afield. Well, not quite true, but it certainly helps as it gives a basis for comparison. So, we establish relatedness with the other apes before looking to the relationship between old and new world monkeys, primates, mammals etc. We can establish human relatedness to, say, a gray fox by comparing the genome of the gorilla with the gray fox.

I must once again ask if you even read my posts. I explained to you why a fused chromosome was a prediction of evolutionary theory and the significance of it's finding, so how can you continue to make such inane questions? Is it that you really didn't know the answer, or is it intentional dishonesty?


Micha wrote:
So if ERVs are found in the same location in the genome, it's evidence for evolution, yet if they don't exist at all, when they indeed should, you'll come up with with response of what you think happened.


No, that would be the way an uninformed person would state the position after reading and not comprehending.

The informed reader would first of all take the time to consider the intricacies of gene fixation. With this knowledge they would then look at retroviral infection and note a few things.

1. By random chance alone the probability of a virus infecting the same location in the genome of more than one species is so small as to be ignored (it has to infect then become fixed).
2. If two species share a given ERV (orthologous in both genomes) then they are diverged from the same parent species
3. If two species share an ERV but a third, which diverged from the same line at a later date, does not, then either that ERV has been erased or the ERV was polymorphous at the time of the previous speciation events.

In the absence of evidence of an erasure, 3 must be true. A few lines from now (which I will quote) you will refer to this as a "fantastic idea". So please, present the maths of gene fixation and tell me exactly where they breakdown to prevent this from occurring, or agree that you are using a logical fallacy, the argument from incredulity.


Micha wrote:That's my entire point, there are many cases where organisms have entirely different morphologies and according to evolutionists lived in totally different time periods.

Citation please, show me an example from an "evolutionist" in a peer reviewed paper, or concede that once again you have made shit up.


Micha wrote:
Squawk wrote:"You've already been schooled on this subject by Proteus here

A few quick observations. First, human intervention has not (until very recently) added new genetic information but has simply acted to select strongly in favour of certain traits. Variety arises entirely by natural means. Your objection must simply be with natural selection, and so I ask you for an barrier that could prevent natural selection having effects similar in nature to artificial selection given sufficient time."


Show showing me charts of different organisms with totally different morphologies, is evidence for evolution? How can showing a chart based on how he believes it happend be considered science? I'll ask you, show me one OBSERVABLE evidence of an organism acquiring a new structure, not some chart, or idea you come up with in your head.


Well, you didn't answer my question, but I'll answer yours. Cancerous tumors.

Micha wrote:
Squawk wrote:"Lets go either with determinism or random chance (or an amalgamation of the two). No wishful thinking involved here."


I think you got a headache trying to figure that one out.


You're right, I'm finding it so difficult to argue with a person who can't even format quotes in a post despite being given specific instructions on how to do it, who has shown a complete inability to read and needs to be told the same information 4 times at least before actually seeing it and who is so unfamiliar with the field he/she is trying to argue that he can't even ask coherent questions.


Micha wrote:
Squawk wrote:"And I won't, since it's off topic and sets up a false dichotomy. The null hypothesis of evolution is not evolution, not some nebulous concept of a deity."


So discussing DNA is off topic? :lol: I fail to realize how you would think discussing the properties of DNA is off topic, the debate topic is whether or not the evidence supports neo darwinan evolution, and when we look at the properties of DNA, it's an obvious no.

Ahh, the straw man, I wondered when we would encounter this. I did predict it would arise, as I predicted the false dichotomy would be presented. You did not pose a question about DNA. You posted an article that you claimed was evidence (proof) of creation. You referenced evidence for creation in the form of Meta-Information, but you didn't say a word about it, you just provided a link. Let me quote the interaction on this subject for you.

Micha wrote:Here, I will provide what I believe to be the best evidence for creation:http://creation.com/meta-information


I of course responded with outright dismissal, as would be expected in debate, since this debate concerns the evidence for evolution, or the lack of it. My response was

Squawk wrote:Dismissed out of hand as being a complete irrelevance for this debate which concerns evidence for evolution. As already stated, the null hypothesis regarding the evidence for evolution is that evolution does not occur. Myth based doctrine has no place in this discussion and any further attempts to take the discussion off topic will result in my request that the debate is terminated.


I told you why I wouldn't answer it and I even stated that it was grounds for terminating the debate. I stand by that, but I won't end the debate, too much fun.

You came back with

Micha wrote:Will you atleast attempt to refute meta information in DNA as being proof for design? I think the reason you are avoiding it, is because you know that it does indeed prove design. It's almost like a chicken and egg arguement.


Which I ignored for the reasons already given, and now you come up with this bullshit? Straw man much?
If you wish to discuss information in the genome I suggest you get a grounding in information theory so that you will understand the distinction between shannon information and kolmogorov information when I refer to them. Once you've done so go back and read that link (and the references) and laugh at your former ignorance on the subject. Those articles really are designed to mislead the credulous (take a long, hard, look in the mirror. That, right there, is the credulous).

However, the point from before still stands, this is not the time or place to discuss evidence for design (which pretty much boils down to logical fallacies), so I shall continue to dismiss it out of hand.


Micha wrote:So please tell me how finding out that we share 14 out of our 98,000 ERVs with apes is evidence for evolution?

Since I've asked you for a citation for this on at least 2 occasions already and you continue to neglect to do so I'm simply going to ignore it. For starters it can't be accurate since it would presume that humans share identical ERV counts with all other apes which is demonstrably wrong, a fact you should be aware of since it's mentioned in some of the papers you have failed to grasp properly already presented in this thread. Second, you should now be more than aware of why ERVs shared by separate lineages is evidence of common ancestry, I've covered it enough in recent posts, so this can only be willful ignorance.


Micha wrote:Then when we find ERV's in apes but not humans, you'll come up with some fantastic story of what you think happened.

No. I referenced this earlier. You even linked to a paper that provided the answer you're looking for. Now, if you have an objection to the conclusion of polymorphism that is not simply an argument from incredulity put it on the table. As it is, that's all you have and the forum is laughing at you.

Micha wrote:And most evolutionists treat ERV's as if they are a type of disease that have no function

Bollocks, citation please or dismissed as the utter garbage it is. I've already presented a paper in which we saw that ERV's were found to influence transcription in 22.4% of PET regions. I'm sure you remember it, that was the paper that you didn't understand, where you thought it said that 23.6% of the genome consisted of ERVs.

Micha wrote:Your coming up with a package of assumptions and conjecturing them as if they are fact, you haven't show any observable evidence of evolution, and I haven't asked this entire time, but will now. Just show me one example of an organism acquiring a new structure

Forgotten your own questions then, since you already asked for this. I answered, a few lines up. Cancer.

In your next post you'll goal post shift of course and tell me that cancer is deleterious, that it's not a beneficial mutation, that it can't spread through the population since it doesn't effect germ line cells. And do you know what my answer will be?

I'm going to laugh my head off, because it will have demonstrated perfectly that you don't even know enough about this subject to phrase such a simple question properly, and when I do provide an answer to the question you have asked you simply ignore the fact that I've provided a perfect answer and goal post shift.

Owned? It doesn't even begin to cover it.
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Wed Oct 27, 2010 12:29 pm
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

Why did you quote that specific bit of my post, then write this? It's not relevant. The text that you should have quoted came directly after the bit that you actually have. Conclusion: You didn't understand what I wrote and so offered up a generic objection that you hoped I'd let slide.

Your objection isn't valid, of course.

Your complete failure to grasp fixation or polymorphism prevent you understanding why your objection isn't valid, but I'll give it anyway.
1. Why would there be? (Can you explain that to me? Hint, it could have happened).
2. When the chromosome fusion occurred and was not deleterious one of two things could occur. Either the fused chromosome would spread through the population and become fixed, or it would go extinct. It happens to have become fixed, but it could have gone the other way. Without a full understanding of the benefits conveyed by this fusion (likely zero at a guess) I can't put figures on probability for you, but it would be a similar calculation to the chance of any given gene variant arising and becoming fixed in the population.

Until you understand this you won't have a chance of understanding the significance of ERVs either, demonstrated perfectly by your continued spurious objections to ERVs as evidence of common ancestry.


A fused chromosome could not possibly be fixed in the population. If an ape had a fused chromosome it would have to find another ape in the opposite sex with the same fused chromosome in order to reproduce. I'll simply ask you one more question about ERV's, in a short paragraph, tell me why ERV's are considered evidence for evolution.

Simple. When we note that humans are "missing" a chromosome when compared with the other apes we know that there has to be an explanation. If humans do share a common ancestor with the other apes then there must be a fusion, for the reasons I've stated previously. The fused chromosome was a prediction of evolutionary theory before it was discovered, it's subsequent discovery as expected is further contributory evidence. This really is simple stuff, erect and then test a hypothesis.


How do you know humans are missing a chromosome? Because you are assuming we are related to apes which have 48. Our chromosome 2 wasn't the result of a fusion, it was an inversion, and interestingly enough, chromosome 2 is the chromosome that is most often inverted.

http://www.springerlink.com/content/f52ll07605132272/

No, that would be the way an uninformed person would state the position after reading and not comprehending.

The informed reader would first of all take the time to consider the intricacies of gene fixation. With this knowledge they would then look at retroviral infection and note a few things.

1. By random chance alone the probability of a virus infecting the same location in the genome of more than one species is so small as to be ignored (it has to infect then become fixed).
2. If two species share a given ERV (orthologous in both genomes) then they are diverged from the same parent species
3. If two species share an ERV but a third, which diverged from the same line at a later date, does not, then either that ERV has been erased or the ERV was polymorphous at the time of the previous speciation events.

In the absence of evidence of an erasure, 3 must be true. A few lines from now (which I will quote) you will refer to this as a "fantastic idea". So please, present the maths of gene fixation and tell me exactly where they breakdown to prevent this from occurring, or agree that you are using a logical fallacy, the argument from incredulity.


Please explain to me how a virus would have a key role in the morphological development of an organism? That's an absurd idea. Again, the fact that we would find 14 out of our 98,000 ERV's in the same place in the genome with apes, is in no way evidence for common ancestry. How do you know that the ERV was erased? Your just assuming it was, your coming up with an excuse as to why many ERV's should be in the genome when they aren't. What is your evidence for number 3? Your just making grand assumptions, not science. What we observe is that 14 out of our 98,000 ERV's are shared with apes, and we observe that there are many ERV's that apes and other monkeys have, and we don't, which totally demolishes the claim that ERV's are evidence for common ancestry. This is what we observe.

"Well, you didn't answer my question, but I'll answer yours. Cancerous tumors."


Firstly, I'll answer your question. Natural selection doesn't create anything, as you should know, it simply selects. Artificial selection is the same thing, except humans select already existing features to be expressed, and the process of selection is sped up, lets see artificial selection produce a new structure. Now, I have to address the canerous tumors claim. You think that a cancerous tumor is a new structure? Is a cancerous tumor a permanent change passed down generation to generation? If a tumor is your best example of a new structure, then I truly admire your faith, while I don't admire your intelligence. And, I don't have to tell you that it isn't beneficial, like you said towards the end of your post. I could care less whether it's beneficial or not, I just want to see a new structure. And here's a description of how cancer tumors form.

"Cancer is an entity where cells proliferate beyond normal control, so they grow to too big a mass, and they behave erratically so they'll go to other parts of the body. It's basically cellular proliferation out of control." http://www.cancerstory.org/index.php/ca ... article/45

So please tell me what's new here? Your really making yourself look stupid here.



"Ahh, the straw man, I wondered when we would encounter this. I did predict it would arise, as I predicted the false dichotomy would be presented. You did not pose a question about DNA. You posted an article that you claimed was evidence (proof) of creation. You referenced evidence for creation in the form of Meta-Information, but you didn't say a word about it, you just provided a link. Let me quote the interaction on this subject for you."

Straw man? I'm talking about the properties of DNA, I think it really unfair for you to just be able to avoid questions that you don't like. Meta information, is proof of design, and totally refutes evolution. And your threatening to end the debate? :lol:
Wed Oct 27, 2010 7:03 pm
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

Micha wrote:A fused chromosome could not possibly be fixed in the population. If an ape had a fused chromosome it would have to find another ape in the opposite sex with the same fused chromosome in order to reproduce.


Strike 1
And time to take the piss a bit. I present, from 1940, a paper describing instances when chromosome re-arrangements result in viable offspring.
http://jhered.oxfordjournals.org/conten ... 37.extract
That's a paper from 70 years ago discussing viable offspring from the mating of individuals with differing chromosome counts. So err, you're 70 years wrong ;-) We can bring up more modern examples if you want.

Onwards!

Micha wrote:I'll simply ask you one more question about ERV's, in a short paragraph, tell me why ERV's are considered evidence for evolution.


A short paragraph? The pages and pages already presented don't suffice? Fine. Construction of phylogenies based on orthologous ERV's found within genomes of organisms previously thought to be related confirm the pattern of divergence previously established via independent means. ERVs supply independent corroborative evidence. Understood?

Micha wrote:How do you know humans are missing a chromosome? Because you are assuming we are related to apes which have 48.


Strike 2
I knew you were not reading my posts. Consider common ancestry to be a hypothesis, chromosome fusion was the test. If it's found, the hypothesis is supported. If it's not, it wasn't. Assumption could only be supplied retrospectively (and even then would be ok).

Micha wrote:How do you know humans are missing a chromosome? Because you are assuming we are related to apes which have 48. Our chromosome 2 wasn't the result of a fusion, it was an inversion, and interestingly enough, chromosome 2 is the chromosome that is most often inverted.

http://www.springerlink.com/content/f52ll07605132272/


Might I suggest you link to a paper that isn't discussing extant processes that occur in the genome when trying to debunk an event that took place in the deep past. Unless, that is, you plan on dissecting this paper for us and explaining its implications for chromosome fusion. I'm ready and waiting for you to teach me, so teach.Maybe you could explain what this paper shows to our enraptured audience and describe it's influence on evolutionary theory.

Still not capable of using quotes properly I note.

micha wrote:Please explain to me how a virus would have a key role in the morphological development of an organism?

By influencing transcription. You keep stating to me that there are approximately 100k ERVs in the genome (you still haven't cited anything to back this up mind), how do you propose they got there?

Micha wrote:That's an absurd idea.

The argument from incredulity, logical fallacies galore. What fun

Micha wrote:Again, the fact that we would find 14 out of our 98,000 ERV's in the same place in the genome with apes, is in no way evidence for common ancestry.

You do like repeating this "fact". Gonna cite it anytime soon? No? Then I'm going to keep ignoring it as a figment of your imagination. Realized that we share differing numbers of ERVs with different species of ape yet? No. Well, I haven't cited my sources for that either, it seems only fair ;-) I've asked for this citation what, 4 times altogether? Gonna provide it?

Micha wrote:How do you know that the ERV was erased? Your just assuming it was, your coming up with an excuse as to why many ERV's should be in the genome when they aren't.

Reading comprehension fail. Never said it was erased, said there was no evidence that it had been erased and therefore concluded that it hadn't gone to fixation in the first place. READ! There are straw men, and then there is simple stupidity. You could have gotten that information either from my post or from the paper I referenced, therefore I conclude that once again you are not reading my posts. Some debate...

Micha wrote:Firstly, I'll answer your question. Natural selection doesn't create anything, as you should know, it simply selects. Artificial selection is the same thing, except humans select already existing features to be expressed, and the process of selection is sped up


No shit Sherlock. Didn't I write exactly that? Lets take a peek

Squawk wrote:A few quick observations. First, human intervention has not (until very recently) added new genetic information but has simply acted to select strongly in favour of certain traits. Variety arises entirely by natural means. Your objection must simply be with natural selection, and so I ask you for an barrier that could prevent natural selection having effects similar in nature to artificial selection given sufficient time.

I did! Why are you telling me what I should know, when I've already demonstrated that I do know this. Trying to points score without basis? This some funky debate tactic? Or simply yet more examples of your lack of reading ability?


Micha wrote:lets see artificial selection produce a new structure.

So, having acknowledged that selection cannot do anything but select from the existing material you want it to do what it can't? Arguing against straw men of evolution? That's not something a creationist would do, is it?


Micha wrote:Now, I have to address the canerous tumors claim. You think that a cancerous tumor is a new structure? Is a cancerous tumor a permanent change passed down generation to generation?


Yay! I knew you wouldn't let me down. The goal post shift. Let me quote for you

Micha wrote:I'll ask you, show me one OBSERVABLE evidence of an organism acquiring a new structure, not some chart, or idea you come up with in your head.


That's exactly what I gave you. I gave you an observable instance of an organism acquiring a new structure. A cancerous tumour. Cancer is actually the product of quite a long serious of mutations, it's an example of an accumulation of lots of small changes, which is one of the reason I chose it. It answered your question perfectly, and served my purpose of both highlighting your inability to phrase a question properly whilst opening you up to the ridicule I'm now pouring your way. See, I even predicted exactly what you would do. Lets take a peek again, just for shits and giggles.

Squawk wrote:In your next post you'll goal post shift of course and tell me that cancer is deleterious, that it's not a beneficial mutation, that it can't spread through the population since it doesn't effect germ line cells. And do you know what my answer will be?

I'm going to laugh my head off, because it will have demonstrated perfectly that you don't even know enough about this subject to phrase such a simple question properly, and when I do provide an answer to the question you have asked you simply ignore the fact that I've provided a perfect answer and goal post shift.


Consider this to be me laughing my head off ;-)

You never mentioned heredity, you never mentioned fixation, and yet when I answer your question exactly as stated you claim I haven't done so. That, my friend, is dishonest. You better go repent or something.


Micha wrote:If a tumor is your best example of a new structure, then I truly admire your faith, while I don't admire your intelligence.

Ahh, the equivocation fallacy, you realize that faith is a weak concept, without merit, so you attempt to project it onto evidenced based positions in order to degrade them and lift your own petty doctrine out of the gutter. Not gonna fly, not while I'm here at least. I'll just keep exposing your general ignorance of scientific positions and you can keep goal post shifting so it's clear to all that your position is untenable. As for my intelligence, how's that lack of reading comprehension working out for you?

Micha wrote:And, I don't have to tell you that it isn't beneficial, like you said towards the end of your post. I could care less whether it's beneficial or not, I just want to see a new structure.

Bollocks, since I provided precisely that and you are now saying I didn't what you wanted and what you asked for are either at odds, or you're dishonest. Are you simply incompetent, or are you dishonest? Cognitive dissonance going on here.

Micha wrote: And here's a description of how cancer tumors form.

"Cancer is an entity where cells proliferate beyond normal control, so they grow to too big a mass, and they behave erratically so they'll go to other parts of the body. It's basically cellular proliferation out of control." http://www.cancerstory.org/index.php/ca ... article/45

So please tell me what's new here?

What do you propose any structure in the body, new or old, is made of if not cells replicating? Titanium? Are you a borg? If you want to discuss what cancer really is why don't you dissect a paper on a specific form of it. Tell you what, I'll get you started, go look at P53.

Micha wrote:Your really making yourself look stupid here.


;-)

Micha wrote:Straw man? I'm talking about the properties of DNA, I think it really unfair for you to just be able to avoid questions that you don't like. Meta information, is proof of design, and totally refutes evolution.

Stick to the subject at hand, evidence of design is not to be considered in this debate. If you wish to expand on a particular property of DNA then be my guest. I'm curious whether or not you're going to claim the Nobel prize with this metric of yours for establishing design.

MIcha wrote: And your threatening to end the debate? :lol:


The "debate" ended a long time ago. This is me taking the piss out of you for showing no ability to comprehend the basics of biology, for straw manning, for numerous logical fallacies, for a lack of reading comprehension and generally for not having the first clue what you are talking about.

There is nothing more frustrating than arguing with someone who know what they are talking about. True, init.
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Wed Oct 27, 2010 10:55 pm
micah1116Posts: 58Joined: Sat Aug 07, 2010 2:12 am Gender: Male

Post Re: Debate: Does evidence support neo-darwinian evolution

Strike 1
And time to take the piss a bit. I present, from 1940, a paper describing instances when chromosome re-arrangements result in viable offspring.
http://jhered.oxfordjournals.org/conten ... 37.extract
That's a paper from 70 years ago discussing viable offspring from the mating of individuals with differing chromosome counts. So err, you're 70 years wrong We can bring up more modern examples if you want.


The paper you provided talks about a Chromosome inversion, not fusion. A chromosome inversion doesn't effect the number of chromosomes.


A short paragraph? The pages and pages already presented don't suffice? Fine. Construction of phylogenies based on orthologous ERV's found within genomes of organisms previously thought to be related confirm the pattern of divergence previously established via independent means. ERVs supply independent corroborative evidence. Understood?


So your saying since we find the same ERV's in the same place in the genome, that's evidence for common ancestry, but when I showed you many examples of ERV's that are not even in the genome they should be, you claim gene fixation solves the problem. Do you have any evidence for this claim? Your just making assumptions. And don't you find it odd that these "viral infections" have a large scale function? Afterall the evolutionist claim is that ERV's are just viral infections that are passed down.

Might I suggest you link to a paper that isn't discussing extant processes that occur in the genome when trying to debunk an event that took place in the deep past. Unless, that is, you plan on dissecting this paper for us and explaining its implications for chromosome fusion. I'm ready and waiting for you to teach me, so teach.Maybe you could explain what this paper shows to our enraptured audience and describe it's influence on evolutionary theory.


That's a really bizarre statement. How do you know it took place in the deep past? I'm showing you event that occur in the real world, not long ago and far away. I find it interesting that chromosome 2 is the chromosome that is most often inverted.

By influencing transcription. You keep stating to me that there are approximately 100k ERVs in the genome (you still haven't cited anything to back this up mind), how do you propose they got there?


They are a design feature.

http://en.wikipedia.org/wiki/Endogenous ... troviruses

You do like repeating this "fact". Gonna cite it anytime soon? No? Then I'm going to keep ignoring it as a figment of your imagination. Realized that we share differing numbers of ERVs with different species of ape yet? No. Well, I haven't cited my sources for that either, it seems only fair I've asked for this citation what, 4 times altogether? Gonna provide it?


http://www.detectingdesign.com/pseudoge ... Endogenous

"In any case, of these tens of thousands of recognizable ERVs, only seven are currently known to infect both humans and chimps at identical locations within the separate genomes . Isn't it interesting that out of 30,000 ERVs only 7 of them are known to have inserted at the same site in humans and chimps?"

He has a source for this claim, but it no longer works, I will have to contact him and see if I can get another source for it. Actually, here's one from talkorigins.

"http://www.talkorigins.org/faqs/comdesc/section4.html#Sverdlov2000"

It states:" In humans, endogenous retroviruses occupy about 1% of the genome, in total constituting ~30,000 different retroviruses embedded in each person's genomic DNA (Sverdlov 2000). There are at least seven different known instances of common retrogene insertions between chimps and humans, and this number is sure to grow as both these organism's genomes are sequenced."


That's exactly what I gave you. I gave you an observable instance of an organism acquiring a new structure. A cancerous tumour. Cancer is actually the product of quite a long serious of mutations, it's an example of an accumulation of lots of small changes, which is one of the reason I chose it. It answered your question perfectly, and served my purpose of both highlighting your inability to phrase a question properly whilst opening you up to the ridicule I'm now pouring your way. See, I even predicted exactly what you would do. Lets take a peek again, just for shits and giggles.


A cancerous tumor isn't a new morphological structure. Do you really expect me to believe that fish evolved into amphibian tetrapods, because you can show me a cancerous tumor? How is a tumor moving anything to become another phylum of life? And I don't believe I mentioned this before, but DNA recombination would prevent permanent structural change from even occuring. The past 70 years of genetic experiments show us that even when mutations cause deformities, the organism reverts back to their wildtype within 1 to several generations. By the way, what do you propose the mechanism for permanent morphological change is?

And here's something interesting, that I'd like to share just for fun. Out of the estimated 200,000 proteins we have, apes don't have 80% of them, that's right, 80% are different.

http://www.sciencedirect.com/science?_o ... 893165a46f

And I'm sure your going to reply, just as proteus did, and say "but there's only a 1-2% difference". Question for you, what makes a protein unique? The arrangement of nucleotides, so they are indeed a different protein, and a 1-2% difference can be a massive difference.

Here's something interesting that just shows how genetic similarity can have little effect on morphological similarity. We actually share 7,000 genes with sea urchins:

http://news.nationalgeographic.com/news ... enome.html
Thu Oct 28, 2010 8:29 pm
SquawkModeratorUser avatarPosts: 2011Joined: Sun Feb 22, 2009 8:25 pm Gender: Tree

Post Re: Debate: Does evidence support neo-darwinian evolution

##Note: This post is, once again, slightly over the length limit. I only realised that a few hours after posting. Since it's a debate and major edits to the work would compromise the discussion I am leaving it as is for now. Micha, if that's an issue pm me and I'll chop it down (actually all I'll do is remove some of the quotes).

###

Micha wrote:
Squawk wrote:Strike 1
And time to take the piss a bit. I present, from 1940, a paper describing instances when chromosome re-arrangements result in viable offspring.
http://jhered.oxfordjournals.org/conten ... 37.extract
That's a paper from 70 years ago discussing viable offspring from the mating of individuals with differing chromosome counts. So err, you're 70 years wrong We can bring up more modern examples if you want.


The paper you provided talks about a Chromosome inversion, not fusion. A chromosome inversion doesn't effect the number of chromosomes.


The paper mentions inversions in a historical context (past studies). The paper is not about inversions, it is about translocations, a subset of which is fusion. I did make an error when I referred to fusion, the text before the link was accurate, the text after wasn't, it should have discussed re-arrangements/translocations (no idea what happened, link to wrong paper, can't remember). But no matter, the principle still stands.

The paper looked at translocations, at how sections from one chromosome can be moved to another chromosome without detriment to the organism, and how this can lead to viable offspring.

Lets dig into this subject properly and take a look at Robertsonian Translocations so we can see that, despite my laxity in providing a proper rebuttal, you're still dead wrong

Allow to me to present http://creation.com/changing-chromosome-numbers. Not a peer reviewed journal. It is, instead, a page from the website that you plagiarized in your first post in this debate, so presumably you think they have some kind of reliability as a source. Lets take a peak at what they have to say on the issue.

Creation ministries wrote:Although ROBs can be associated with problems, there are times where no adverse outcomes are observed. For example, they have been observed in Saanan goats with a normal phenotype and no reported fertility problems.3 There are crossbreeding studies with sheep carrying up to three different translocations that showed no significant effect on phenotype or fertility for any of the combinations.4 In fact, the normal chromosome number of domestic sheep (Ovis aries, 2n = 54) is inferred to be the result of three different translocations relative to domestic goats (Capra hircus, 2n = 60). The variation in chromosome number in the Bovidae family (including the tsoan5 and cattle6 monobaramins) appears to be mostly due to ROBs.

There are other types of chromosomal rearrangements that have contributed to the range of chromosome numbers in animals that are monobaraminic (known to be from the same created kind). Some of these rearrangements are quite unexpected. For example, the Indian muntjac (Muntiacus muntjak, 2n = 6 in females, 7 in males) has the x-chromosome fused with one of its autosomes. The y-chromosome is separate. The male will have one of this autosomal pair fused to an x, and the other without a fused sex chromosome and a separate y, giving it an extra chromosome compared to the female. It is interesting to note that viable hybrids have been formed between this species and Reeve's muntjac (Muntiacus reevesi, 2n = 46).7 Some species of antelope have a fused y-chromosome


That's your own past source of reference first discussing chromosome polymorphism and fertility, then noting numerous instances of individuals with different chromosome counts being able to breed and produce fertile offspring.

I confess I'm somewhat astounded to find myself referring to such a website in this context, but the irony was too much to ignore. Try putting "chromosomal polymorphism", "karyotype speciation" or "telomere fusion" into google scholar and enjoy reading.

Or alternatively, just go and look up one of the papers from that site. Lets take a peak at this one. I'll just quote from the abstract here, the full text pdf is available for anyone interested.

http://www.reproduction-online.org/cgi/ ... t/57/2/363
Cytogenetics and reproduction of sheep with multiple centric fusions (Robertsonian translocations)
Journal of Reproduction and Fertility (1979) 57 363-375
Bruere, A.N. and Ellis, P.M.,

Paper wrote:Summary. The significance of centric fusions (Robertsonian translocations) in domestic animals, with special reference to sheep, is reviewed. The mating is described of a further 856 ewes with either a normal chromosome number 2n = 54 or carrying one or more of the three different translocations (centric fusions) t1, t2 and t3 in various heterozygous and homozygous arrangements. Rams which were used in the matings were homozygous for one of the translocation chromosomes (2n = 52), double heterozygotes (2n = 52), triple heterozygotes (2n = 51) or were carriers of 4 translocation chromosomes (2n = 50) and 5 translocation chromosomes (2n = 49).

A remarkably even distribution of segregation products was recorded in the progeny of all combinations of translocation ewes x translocation rams in those groups in which sufficient animals were available for statistical analysis. Forty-eight chromosomally different groups of animals were mated. Further, the overall fertility of the translocation sheep, measured by conception rate to first service, lambing percentage and number of ewes which did not breed a lamb, was not significantly different from New Zealand national sheep breeding data. In some groups the poorer reproductive performance could be explained by the age structure of the flock and inbreeding depression, which probably affected the performance of some animals.

Sheep with progressively decreasing chromosome numbers, due to centric fusion, 2n = 50, 2n = 49 and 2n = 48, are reported. The 2n = 48 category represents a triple homozygous ewe and a triple homozygous ram and is the first report of the viable evolution of such domestic animals. Less than 1% of phenotypically abnormal lambs were recorded in a total of 1995 progeny born over 10 years. It is now considered that there is little or no evidence to suggest that centric fusions in a variety of combinations affect the total reproductive fitness of domestic sheep. It is suggested that future research should be more actively directed to understanding their genetic significance.


Now, thats not so much ruined your argument as set a big old nuclear bomb off under it. Still confused? I'll present that paper in full for you if you like.

Micha wrote:
Squawk wrote:A short paragraph? The pages and pages already presented don't suffice? Fine. Construction of phylogenies based on orthologous ERV's found within genomes of organisms previously thought to be related confirm the pattern of divergence previously established via independent means. ERVs supply independent corroborative evidence. Understood?


So your saying since we find the same ERV's in the same place in the genome, that's evidence for common ancestry, but when I showed you many examples of ERV's that are not even in the genome they should be, you claim gene fixation solves the problem.

Where did you show me "lots of ERV's that should be in the genome", but aren't? What constitutes lots? Should be in the genome of what, precisely? You highlighted a single instance of an ERV that is found at orthologous loci in the gorilla and chimp genomes but not present in the human genome, and I presented a paper that explained precisely why that particular instance of an ERV was a fantastic discovery for science, it provided a great research tool for scientists working on both gene fixation and speciation.

Gene fixation doesn't "solve the problem". There is no problem. There is just reality, and our understanding of it, enhanced by this particular finding. It would be great to find another just like it as it enhances our knowledge of gene fixation and speciation and allows us to make better use of such interesting ideas as the molecular clock (which I'll come to shortly).

1. Evolution happens, it's observable in real time (or nearly so, enough time for new generations). It's a consequence of inheritance with variation in a reproducing population (see my definition of evolution from early on).
2. Rates of evolution are well understood, in particular the rates at which mutations occur (and the reason there are exceptions).

This gives rise to a very useful feature that geneticists exploit when looking at relatedness (amongst other things).
The molecular clock.

http://www.genetics.org/cgi/content/abstract/135/2/599
Genetics, Vol 135, 599-607
Simple Methods for Testing the Molecular Evolutionary Clock Hypothesis
F. Tajima
Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411, Japan

I've linked to the paper above (though I'm not going to present it since it's a nats out of place here), since it deals with the conditions required for the molecular clock to be reliable. In particular it analyses various assumptions and either removes them from the calculation entirely or shows why they are acceptable. If you have an objection to use of the molecular clock we can look at it in more detail, as always.

The molecular clock allows us to determine how long ago two instances of similar genes would have been identical (ie, how long ago they diverged), by comparing the accumulated mutations in the two instances with what an amalgamation of the two. Ie, how much they have deviated from the norm. Such analysis permits us to determine how long has passed since two species (in which the gene is present, in a derived form) separated, or at least establish a rough estimate. Multiple genes are sampled in order to eliminate anomalies, anomalies that arise due to, for example, gene fixation.

So, we can look at the human genome, the chimp genome and the gorilla genome. We can establish how far diverged they are from each other at different locations in the genome. You don't just sample the whole genome, you sample small sections and compare them in each. In some instances the genomes of the chimp and gorilla are closer together than are those of the human and chimp, and in others the human and gorilla genomes are closer than either is to the chimp.

The "final" tree, as it were, is based on what might be called a group vote, its the most parsimonious tree when given all the available data.

The ERV that you're bleating on about, and that I explained at length, is a fantastic example of exactly why the human genome is not all closer to the chimp than either is to the gorilla. It's a perfect demonstration of real world processes, of the workings of gene fixation and mutation, or retroviral insertion into the genome.

I've battered this to death, in all honesty I can't think of what else to tell you. You can argue until the cows come home that 2+2 doesn't equal 4, but you'll be as wrong the next time as you were the last.


Micha wrote: Do you have any evidence for this claim?

Your just making assumptions. And don't you find it odd that these "viral infections" have a large scale function? Afterall the evolutionist claim is that ERV's are just viral infections that are passed down.


And life is a sexually transmitted disease with a 100% mortality rate. I can misrepresent stuff too, but it gets us no further. An ERV is simply the remnants of a retrovirus inserted into the genome at some past time. Whats the issue here? Who cares what I find "odd". I find quantum mechanics and relativity far more "odd", but I long ago abandoned the idea that common sense leads to truth. Common sense leads you to answers based on your cogent experiences, not to truth.

micha wrote:
Squawk wrote:Might I suggest you link to a paper that isn't discussing extant processes that occur in the genome when trying to debunk an event that took place in the deep past. Unless, that is, you plan on dissecting this paper for us and explaining its implications for chromosome fusion. I'm ready and waiting for you to teach me, so teach.Maybe you could explain what this paper shows to our enraptured audience and describe it's influence on evolutionary theory.


That's a really bizarre statement. How do you know it took place in the deep past? I'm showing you event that occur in the real world, not long ago and far away. I find it interesting that chromosome 2 is the chromosome that is most often inverted.


Once again I must ask, did you read my post? I noted that you presented a paper discussing extant processes. I asked you for a dissection of that paper and an explanation of its implication for chromosome fusion. Or rather, I stated that it was a funny thing to link to unless you provided such a dissection. Feel free to present it.

Tell me, why do you find it interesting that chromosome 2 is the most often inverted? What part of that interests you and is pertinent to this debate? That you even have to ask the question about my reference to "deep past" is telling, how long do you think it takes for a given genetic variant to go to fixation in a population?

Micha wrote:
Squawk wrote:By influencing transcription. You keep stating to me that there are approximately 100k ERVs in the genome (you still haven't cited anything to back this up mind), how do you propose they got there?


They are a design feature.

http://en.wikipedia.org/wiki/Endogenous ... troviruses


Dismissed as baseless assertion unless you can present a metric for assessing the "designedness" of a given structure. As I noted before, presentation of such a metric would win you a nobel prize. And just what do you expect to achieve with a link to wiki? After all that has already gone in this debate are you actually trying to tell me what a HERV is?

Micha wrote:
Squawk wrote:You do like repeating this "fact". Gonna cite it anytime soon? No? Then I'm going to keep ignoring it as a figment of your imagination. Realized that we share differing numbers of ERVs with different species of ape yet? No. Well, I haven't cited my sources for that either, it seems only fair I've asked for this citation what, 4 times altogether? Gonna provide it?


http://www.detectingdesign.com/pseudoge ... Endogenous

"In any case, of these tens of thousands of recognizable ERVs, only seven are currently known to infect both humans and chimps at identical locations within the separate genomes . Isn't it interesting that out of 30,000 ERVs only 7 of them are known to have inserted at the same site in humans and chimps?"

He has a source for this claim, but it no longer works, I will have to contact him and see if I can get another source for it. Actually, here's one from talkorigins.

"http://www.talkorigins.org/faqs/comdesc/section4.html#Sverdlov2000"

It states:" In humans, endogenous retroviruses occupy about 1% of the genome, in total constituting ~30,000 different retroviruses embedded in each person's genomic DNA (Sverdlov 2000). There are at least seven different known instances of common retrogene insertions between chimps and humans, and this number is sure to grow as both these organism's genomes are sequenced."


Nice citation... Two websites, one that no longer works, the other with figures nothing like those you presented and interestingly one that refutes most of your assertions before I even type anything. This tells me a lot about the validity of the points you raise before I even read them. But the points I've raised throughout still stand. Why don't you present the maths to show how many should be orthologous, by random chance (it's zero, though I suppose people do win the lottery every week). You could have talked about frequency of insertion in given regions, why certain regions are favoured, what frequencies are involved etc. But of course you didn't, despite my references to such points earlier. Go for it now if you want though.

Micha wrote:
Squawk wrote:That's exactly what I gave you. I gave you an observable instance of an organism acquiring a new structure. A cancerous tumour. Cancer is actually the product of quite a long serious of mutations, it's an example of an accumulation of lots of small changes, which is one of the reason I chose it. It answered your question perfectly, and served my purpose of both highlighting your inability to phrase a question properly whilst opening you up to the ridicule I'm now pouring your way. See, I even predicted exactly what you would do. Lets take a peek again, just for shits and giggles.


A cancerous tumor isn't a new morphological structure.

Provide a definition of a new morphological structure otherwise you will keep moving the goalposts. Make it unambiguous and concise please.

Micha wrote:Do you really expect me to believe that fish evolved into amphibian tetrapods, because you can show me a cancerous tumor?

Of course not, that would be a foolish thing to believe based on the evidence of cancer alone. I'd expect you to accept tetrapod evolution due to the evidence in support of it. What is it about tetrapod evolution that vexes you? Are there are "new" morphological structures, as you put it, between Acanthostega and Ichtyostega that that you have issues with? Just saying "tetrapod evolution is impossible" is a bit broad, no idea where to pitch, so can you nail down an objection please.

micha wrote:How is a tumor moving anything to become another phylum of life?

It isn't. Who said it was?

Micha wrote:And I don't believe I mentioned this before, but DNA recombination would prevent permanent structural change from even occurring. The past 70 years of genetic experiments show us that even when mutations cause deformities, the organism reverts back to their wildtype within 1 to several generations.


Citation please. I'll also note the contradiction, since i presume you would count a deformity as a change to morphology? Yes, no? What is artificial selection (which you are happy to accept I note) other than humans selecting deformities that they like? What is natural selection if not the environment doing the same? Therefor, how can the variation that we see in just the domestic dog arise if your wild type assertion is accurate? Sounds like you made this shit up, so I really do want that citation, not just a link but a dissection of the information contained in the link and an explanation of how it impacts evolution. In fact, sod all that, tell me how recombination is going to resolve the fused chromosomes from my link on sheep above.

Micha wrote:By the way, what do you propose the mechanism for permanent morphological change is?

Non-perfect replication and inheritance (AKA, evolution).

Micha wrote:And here's something interesting, that I'd like to share just for fun. Out of the estimated 200,000 proteins we have, apes don't have 80% of them, that's right, 80% are different.

http://www.sciencedirect.com/science?_o ... 893165a46f

And I'm sure your going to reply, just as proteus did, and say "but there's only a 1-2% difference". Question for you, what makes a protein unique? The arrangement of nucleotides, so they are indeed a different protein, and a 1-2% difference can be a massive difference.


Wait one second. Lets back this up a bit. What did you post just a couple of days ago?

Micha wrote:Straying from the ERV arguement a bit, the claim that our DNA is 99% similiar to chimps is a myth, and evolutionists are now admitting it:"


Is similar, isn't similar? Make your mind up.
First question, why is this a problem for evolution? Second question, why is this not expected? A 1% difference across the genome would require a base pair difference in, on average, every 100 base pair sequence. Proteins are coded for by specific nucleotide sequences (though certain different chains produce the same protein), genes which must be slightly different in humans and chimps (or the other apes), so a 1% difference would suggest that the majority of proteins would be different. Where is the issue for evolution here? If I'd had to guess I would have gone for a figure above 80%, with conservation only of genes that are fatal if mutated. That would be a guess, I couldn't answer (at least not without doing some research) the question of how many genes are immutable, but 20% seems plausible as a figure plucked out of the air. But that's just speculation on my part.

So I ask again, where is the issue for evolution here? What figure would you "expect" to be identical, and why?


Micha wrote:Here's something interesting that just shows how genetic similarity can have little effect on morphological similarity. We actually share 7,000 genes with sea urchins:

http://news.nationalgeographic.com/news ... enome.html

No argument from me. Interesting isn't it, though, that the more "similar" an organism is to another, in general, the closer are their genomes. Interesting to note that you don't have to diverge that far from a "standard" genome in order to generate the massive diversity of life on earth. Interesting indeed, that the variation observed in the genomes of all creatures is diverged in such a way that it could have diverged, in an appropriate amount of time, from a common ancestor, represented by a tree structure indicitive of a branching process.

I agree, what you linked to is interesting. Very interesting.
Pope Rat: "Exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus a reductive vision of a person and his destiny."

Squawk response: "O Rly?"
Tue Nov 02, 2010 2:14 pm
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