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originally posted by: whereislogic
originally posted by: ScepticScot
a reply to: cooperton
The eye is completely consistent with evolution.
www.newscientist.com...
I see the storyline involving "light-sensitive cells" hasn't changed. See the remarks made in response to this storyline from 9:18 - 12:49 below:
Coming back to something I shared on page 13:
originally posted by: whereislogic
...
“You must know,” I replied, “that to give this neat picture, evolutionists have to leave out many of the fossils. They pick only the ones that support their theory, and assume that these are connected to each other.”
“They only simplify it to avoid confusion,” the student said.
I replied: “To avoid confusion they conceal the evidence, and in simplifying they oversimplify to the point of falsification.”
Indeed, that is just what Simpson says, that ‘the oversimplification of the horse fossil record amounts to falsification.’ ...
Source: Do I Have to Believe Evolution? (Awake!—1974)
The same can be said about the oversimplification of the storyline regarding the evolution of the eye.
A key point below at 2:44:
originally posted by: Nexttimemaybe
Religion.
The stupidest thing to have ever been created by man.
originally posted by: iamthevirus
originally posted by: Nexttimemaybe
Religion.
The stupidest thing to have ever been created by man.
2nd line
originally posted by: ScepticScot
If the human eye was designed it certainly wasn't intelligently.
thehumanevolutionblog.com...
originally posted by: Nexttimemaybe
It appears evolution made dumb people who created multiple gods.
originally posted by: Xtrozero
a reply to: whereislogic
Do you find it odd that everything has a relationship with each other? The closer lifeforms are to each other the more there is a relationship like the chimp is to man.
...
The old statistic that we are about 99 percent or 98 percent similar to chimps pertains only to alignable protein-coding sequences. In fact the statistic first originated based upon similarity between humans and chimps in just one single gene! But many non-coding sequences are highly dissimilar, and there are sequences of the human and chimp genomes that are so different that they can’t be aligned for comparison. For example, there are some parts of our genome, such as the human y chromosome, that are radically different from the chimp genome.
... However, one criticism I’ve heard of all current estimates is that they are based upon versions of the chimp genome that used the human genome as a “scaffolding,” potentially making certain sections of the chimp genome more humanlike than they ought to be. This could also artificially inflate the degree of human-chimp similarity.
...
Is the case for common ancestry, based upon the degree of similarity, an objective or rigorous argument that’s capable of being falsified? For example, if a 1 percent genetic difference implies common ancestry, but then that statistic turns out to be wrong, then does a 4 percent genetic difference mean common ancestry is false? How about 7 percent or 10 percent genetic difference? 25 percent? At what point does the comparison cease to support common ancestry? Why does the percent genetic similarity even matter? It’s not clear that there is an objective standard for falsification here, any identifiable reason why a particular percentage of genetic similarity should be taken to indicate common ancestry.
Indeed, Dennis Venema even seems to acknowledge this point, writing in 2018:
No one is more interested in the “% genome identity” thing than folks trying to cast doubt on common ancestry. It’s just not a precise value that scientists are interested in, because it doesn’t answer interesting scientific questions in the way other values do… (emphasis added)
That’s quite a bold quote from Professor Venema when earlier he was seen emphasizing how humans are a mere genetic “hand-breadth” away from chimps, as part of a case for common ancestry. This is in keeping with numerous other evolution apologists over the years who have cited the “1%” statistic in favor of human-chimp common ancestry. They are the ones who invented and promoted this fallacious argument, and we are simply responding to it. Yet somehow us Darwin-skeptics get blamed for spreading a fallacious argument.
Perhaps Dr. Venema has changed his mind about the import of the statistic—which he is fully entitled to do. Whatever the case, we agree with his point here that the “% genome identity” provides no rigorous argument for common ancestry and does not answer very many interesting questions within this particular debate.
The case for human-chimp common ancestry is further significantly weakened once one realizes that there are other potential explanations for functional similarities: notably, design based upon a common blueprint.
...
originally posted by: whereislogic
That argument and accompanying claims in the link you shared was already responded to in the 2nd video you ignored
originally posted by: whereislogic
originally posted by: ScepticScot
If the human eye was designed it certainly wasn't intelligently.
thehumanevolutionblog.com...
That argument and accompanying claims in the link you shared was already responded to in the 2nd video you ignored, yet still responded to (at least my comment, not anything that is said in the video that shows that argument and the accompanying claims to be bogus). Starting at 3:45, right after the first key point I mentioned in my previous comment.
originally posted by: whereislogic
Where you see an evolutionary relationship I see similarities. But besides that, my analysis of the numbers given for a certain % similarity between 2 different genomes, such as that between chimps and humans, has led me to the conlusion that these numbers are not reliable, and based on cherry-picking what one chooses to compare and what to ignore and fiddling around with the data* until one gets approx. the desired number. And in the past, 90% was deemed enough to make the argument you made at the end there. An honest comparison would result in quite different numbers, and then suddenly, that argument you made at the end doesn't work anymore. Just as it doesn't work anymore if they went back to 90% for chimp-human DNA similarity (given the other claims now regarding other organisms being more than 90% similar).
originally posted by: Ohanka
a reply to: iamthevirus
The Earth is the center of the observable universe, because that is where we happen to be looking at the universe from.
If you were on a planet in a galaxy millions of lightyears away, that would be the center of the observable universe. The universe itself likely has no central point. Though that is an assumption and not something that is known.
originally posted by: Nexttimemaybe
originally posted by: iamthevirus
originally posted by: Nexttimemaybe
Religion.
The stupidest thing to have ever been created by man.
2nd line
It appears evolution made dumb people who created multiple gods.
They still argue about whose God is the real one.
We know the earth isn't a few thousand years old dont we.
How do you know the believers in ancient gods weren't right and people have been worshiping false gods ever since. No one knows if jesus was real and if he did exist he wasn't called jesus as that is a relatively modern name.
originally posted by: whereislogic
originally posted by: Nexttimemaybe
It appears evolution made dumb people who created multiple gods.
It's actually the people who worshipped multiple gods that made up evolutionary philosophies and myths to begin with:
The Pagan Religious Roots of Evolutionary Philosophies and Philosophical Naturalism (part 1 of 2)
Also quite a few pantheists (those who believe that everything is god, the universe is god, Mother Nature) and Gaia (Mother Earth) worshippers amongst those religious philosophers promoting evolutionary mythology.
originally posted by: whereislogic
... But besides that, my analysis of the numbers given for a certain % similarity between 2 different genomes, such as that between chimps and humans, has led me to the conlusion that these numbers are not reliable, and based on cherry-picking what one chooses to compare and what to ignore and fiddling around with the data* until one gets approx. the desired number. ...
originally posted by: Xtrozero
... There are more similarities between Chimps and humans than Orangutans and humans as example. ...
Abstract
... Results from this study not only negate the concept of the 98.5% DNA similarity myth, but highlight the extremely flawed and humanized nature of the panTro4 version of the chimpanzee genome and its predecessors that are widely used to support the human evolution paradigm.
Introduction
One of the chief problems with all versions of the chimpanzee genome prior to PanTro6, is that they were not constructed through the use of an accurate integrated physical-genetic map and its corresponding genomic resources in a systematic fashion like the human genome and other key model animal genomes (Tomkins 2011). Instead, short DNA sequences generated by the sequencing machinery (known as trace reads) largely produced through a whole genome shotgun approach were assembled onto the human genome using it as a reference scaffold (Mikkelsen et al. 2005; Prado-Martinez et al. 2013; Tomkins 2011). This was done not only out of convenience and a lack of available resources, but the dogmatic evolutionary presupposition that humans evolved from apes and shared a common ancestor with chimpanzees about 3 to 6 million years ago.
Another serious potential problem with earlier versions of the chimpanzee genome is the distinct possibility of human DNA contamination that would also contribute to the development of a more humanized assembly. ...
While the problem of human DNA contamination in the chimpanzee genome has never been addressed by the secular community, researchers have recently openly acknowledged sequence assembly problems stating, “the higher-quality human genome assemblies have often been used to guide the final stages of nonhuman genome projects, including the order and orientation of sequence contigs and, perhaps more importantly, the annotation of genes” and “This bias has effectively “humanized” other ape genome assemblies” (Kronenberg et al. 2018). Even with a more recent version of the chimpanzee genome (PanTro5) that used a hybrid approach of next generation sequencing technologies, including PacBio long reads, the resulting contiguous pieces of de novo assembled DNA sequence were still oriented and aligned onto the human genome as a reference (Kronenberg et al. 2018; Kuderna et al. 2017).
At the time of this publication, a new version of the chimpanzee genome has been announced (PanTro6) that was assembled completely de novo without the use of a human as a reference scaffold (Kronenberg et al. 2018). [whereislogic: Well, that's the claim at least; whether it can be appropiately referred to as "de novo" or the assembly of this version of the chimp genome being thought of as not having been influenced by using data from the human genome at all, is not always entirely clear. I've noticed in an article about genetic assembly techniques some well hidden techniques where the human genome still somehow affects the endresult being spit out by assemblers working on the chimp genome for example. With the way these were hidden and justified in that article, I would not be surprised that the author of this article, Tomkins, would overlook those subtle techniques to 'humanize' the assembly process and final endresult in such versions of the chimp genome as PanTro6.] According to correspondence with UCSC genome browser staff at the time of this report, “The panTro6 assembly has not yet been reviewed by our Quality Assurance team” and is not available for public download. [whereislogic: so no way to check for what I just mentioned. Anyway...] However, LASTZ alignments with the human genome have been performed and are available for download (hgdownload.cse.ucsc.edu...). LASTZ is a large-scale genome alignment tool that can efficiently align chromosomal or genomic sequences millions of nucleotides in length. [whereislogic: but it does so by fiddling around with the data to help with alignment and comparisons.]
Queen Mary University of London evolutionary geneticist, Richard Buggs, recently performed an analysis of the UCSC LASTZ results and reported, “The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%” (Buggs 2018). Not only do these LASTZ PanTro6 results fit well with a previous report by Tomkins (2016) in which it was determined that the chimpanzee genome could be no more than 85% similar to human, but these results also match closely with data described below in this present study.
Interestingly, Buggs also calculated the amount of sequence that was unalignable between human and chimpanzee stating, “4.06% had no alignment to the chimp assembly.” Assuming that the genome sizes between human and chimpanzee are similar [whereislogic: they aren't the same, but this is never really counted as a basic % difference to begin with, even though it should at least be counted as a difference somehow], when the non-alignable sequence data is combined with the alignment data (Buggs 2018), the current level of overall human-chimpanzee genome similarity can now be estimated at about 80%. [whereislogic: yeah, whatever, that's not the right number either, for the reasons I explained so far regarding the reliability of the PanTro6 version, my remark about 'fiddling' concerning alignment tools as well as my remark about genome sizes just now ( regarding the topic of alignment, there's more to be considered in the paragraph below where I bolded something at the end; the "gap extension parameters" are something to fiddle around with to make the genomes compared appear more similar, i.e. get a higher % number for your comparison). But whatever, these numbers are already nowhere close to your 99.6%. So these numbers also don't work for the orangutan-chimp-human argument I'm responding to in this comment. And PanTro6 does appear less humanized than earlier versions with which the higher % numbers for DNA similarity are associated as well as the argument you used concerning Orangutans.]
Despite the recent improvements with the PanTro5 and PanTro6 versions of the chimpanzee genomes, no objective reassessment of human chimpanzee genome similarity has been forthcoming from the secular research community outside of the recent internet post by Buggs (2018), which at the time of this report, has received no credible challenge or rebuttal.
In an attempt to get around the bias presented by the humanized chimpanzee genome assembly issue, in a previous study, I sampled 25,000 unassembled trace reads at random from each of the 101 Sanger-style trace read data sets that provided the foundation for the initial versions of the chimpanzee genome (Tomkins 2016). As a follow-up to this previous research, and in an attempt to use higher quality, less contaminated (with human DNA), and longer sequences, 18,000 publicly available de novo assembled contigs combining Sanger-style reads, Illumina short reads, and PacBio long reads were queried against the human genome using the BLASTN algorithm with gap extension.
...
Comparison to Human
The main finding of significance to the issue of alleged common ancestry between humans and chimpanzees is the fact that the average alignment identity was only 84% (table 1). Despite the gap extension parameters being quite liberal, the average mean alignment length was only 10,509 bases as a result of the algorithm hitting a gap that was too large for it to traverse. Thus, only about one-third of each chimpanzee contig on average could be aligned to the human genome as the best hit. These data obviously exclude the less alignable portions of the contigs as well as those regions that would be completely unalignable. Thus, the overall identity of the chimpanzee genome compared to human would actually be significantly lower than 84%.
Comparison to PanTro4
The PanTro4 assembly of the chimpanzee genome has been the version most commonly used in recent years to support an alleged common ancestry with human. However, both this author (Tomkins 2011, 2016) and more recently, authors of the new de novo assembled PanTro6 version of the chimpanzee genome have asserted that past versions of the chimpanzee genome have been “humanized” (Kronenberg et al. 2018). This is especially true for the PanTro4 version and its predecessors.
The main finding of significance to the issue of humanization of the chimpanzee genome is the fact that the average mean alignment identity of the de novo assembled chimpanzee contigs was only 91% when queried against the PanTro4 assembly, not 100% as would be expected if the chimpanzee genome was an accurate representation (table 1). In fact, some regions had alignment identities lower than 70% with a minimum as low as 66%. The alignments were so poor that the average mean alignment length of only 10,699 bases was not much better than that achieved using human as a target database. Thus, only about one-third of each chimpanzee contig on average could be aligned to the PanTro4 version of the chimpanzee genome as the best hit. These poor alignments indicate that the humanization of the chimpanzee genome was extremely severe and heavily biased towards an evolutionary outcome.
Comparison to PanTro5
...
originally posted by: whereislogic
... Assuming that the genome sizes between human and chimpanzee are similar [whereislogic: they aren't the same, but this is never really counted as a basic % difference to begin with, even though it should at least be counted as a difference somehow], ...
Most people would be surprised to know that, until recently, the human genome was not entirely sequenced where all the DNA letters it contains are deciphered. With the use of new DNA sequencing technologies, a complete version of the human genome has now been produced (except for the Y chromosome).1 The startling discovery surrounding this novel achievement is that the previously unsequenced regions were once thought to be mostly evolutionary junk, but are actually full of important genes and other DNA sequences required for life.
...
The main finding of significance to the issue of alleged common ancestry between humans and chimpanzees is the fact that the average alignment identity was only 84% (table 1). Despite the gap extension parameters being quite liberal, the average mean alignment length was only 10,509 bases as a result of the algorithm hitting a gap that was too large for it to traverse. Thus, only about one-third of each chimpanzee contig on average could be aligned to the human genome as the best hit. These data obviously exclude the less alignable portions of the contigs as well as those regions that would be completely unalignable. Thus, the overall identity of the chimpanzee genome compared to human would actually be significantly lower than 84%.