Larry Moran: Vitamin C Pseudogene is Powerful Evidence

_{Cornelius Hunter

May 27, 2011

Intelligent Design}

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In his on-going criticism of Jonathan Wells’ new book, The Myth of Junk DNA, evolutionist Larry Moran now asserts that the much discussed vitamin C pseudogene is powerful evidence for evolution and common descent: Read more

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Elizabeth, you simply have no basis for your Theological argument: For instance, I provided several links, and can provide several more, that show the evidence from phylogenetics is not nearly as conducive to neo-Darwinian thought as you believe. But you ignore all that evidence and focus only on the studies that were construed to arrive at your desired conclusion. Do Molecular Clocks Run at All? A Critique of Molecular Systematics - Jeffrey H. Schwartz, Bruno Maresca Abstract: Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”.. For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central … http://www.mitpressjournals.org/doi/abs/10.1162/biot.2006.1.4.357 A Primer on the Tree of Life - Casey Luskin - 2009 Excerpt: The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified. http://www.discovery.org/a/10651 Pattern pluralism and the Tree of Life hypothesis - 2006 Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. http://www.pnas.org/content/104/7/2043.abstract A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.htmlbornagain77_{May 29, 2011
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bornagain77: I think it's very easy to think that people who have adopted a different position than the one you yourself think is "obvious" are being dishonest. One of the reasons I appreciate being here is the opportunity to find out why people who think otherwise from the way I do, do so. That's because I actually believe that most people are not, actually, fundamentally dishonest - most people try to carve out a worldview that makes sense to them. What you call "neo-Darwinism" makes sense to me, and, more importantly, in my view makes sense of the data. You may disagree with my view, but I think you are making a mistake if you think that people like me are being dishonest, and I think people like me are also making a mistake when they think people like you are being dishonest (and they do). I think the most productive approach, myself, is to try to find out why the "other side" thinks the way they do - remaining open, of course, always, to the possibility that they may have a good case! Or, at least, that they may have an important point, or of course that one may have completely misunderstood what they actually think. Science isn't science if it isn't open to rethinking its current models, but that works both ways. A good start, I think, is taking what the "other side" is saying in good faith, at least until there is clear evidence of dishonesty. Mere disagreement isn't that evidence :) Cheers LizzieElizabeth Liddle_{May 29, 2011
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Mung: yes, I actually agree - common descent is "assumed at the outset", and phylogenies are constructed based on that assumption. However, if it were an invalid assumption, then, I suggest, we would not see either consistent, or highly nested, phylogenies, and phylogenies constructed from different sets of data would not tend to map on to each other. This is what I meant when I said that it is the distribution of characters (e.g. the broken GULO gene, but also anatomical features) that supports common descent, because when those distributions are used to generate a phylogeny, the tend to produced trees that are both deeply nested and consistent across datasets. I would certainly argue (and ellazimm clearly knows much more about this than I do) that "distribution" is not simply "a fancy way of saying they are there or they aren’t", and I struggle to suppress a sense of irony that point being put forward by a pro-ID person! It is because observed characters of living things have a non-random distribution that we can infer that there is some kind of pattern to be inferred,and the pattern that is consistently inferred is a nested hierarchical structure - the structure of a family tree. Linnaeus spotted this, and subsequent data supports it. However, there are processes other than family trees that can produce nested hierarchical patterns, so even the inference (the valid inference, I would argue) of a nested hierarchy does not necessarily allow us to infer common descent. It could, for example, imply a certain kind of design process. But the inference of the pattern it seems to me to be extremely well-founded. And of course, I subscribe to the view that common descent is the most likely explanation for the pattern :) At least partly because it is supported by the spatial distribution of fossils in the geological column. And also of course by longitudinal studies of heritability. @bornagain77: Thank you for your diligent efforts to keep me right! As I said earlier, we really are going to have to agree to disagree on this. You wrote:
Let’s try one more time here Elizabeth,,, you state;
So would finding organisms with the characteristics of a clade with a node at 100 billion years ago(sic) in a stratum dating from 200 billion years ago(sic).,, ‘So disconfirmatory evidence is certainly possible.’
Let’s just see how ‘certainly possible’ this is for you??? How about a ‘precambrian rabbit’ 635 million years ago???
Yes, I think a fossilised "precambrian rabbit" 635 million years would present a major problem for the Theory of Evolution. However, as we don't have one, we don't actually have the problem :) And I confess I don't see anything in your excerpted links that persuades me otherwise. Cheers LizzieElizabeth Liddle_{May 29, 2011
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ellazimm, whether you like the shallowness of neo-Darwinism being made fun of or not, whether you find it offensive or not that I would make play of this shallowness that would be laughed out of any other rigorous scientific discipline, The plain fact of the matter is that, whether neo-Darwinists know it or not, it always comes down to deception being told (sold), in the name of science, by those committed to the neo-Darwinian framework just to protect their 'preferred' religion of atheistic materialism. In fact you yourself ellazimm have, instead of addressing the evidence honestly to see if it offers solid support for your neo-Darwinian conjectures, made Theological arguments in regards to varying chromosome/gene number (c-value enigma), and you do this whether you realize it or not. i.e. your argument boils down to, God would not have done it that way therefore neo-Darwinism must be true. As solid proof that this 'religion driving science' criticism is correct, it has recently come to light, in peer review, that the strongest arguments for neo-Darwinism, in Darwin's "Origin Of Species", are Theological, not scientific, in their basis; Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011 Excerpt: “Charles Darwin’s use of theology in the Origin of Species,” BJHS 2011, argues that Darwin used theology throughout his 1859 masterwork to argue for the truth of his theory of descent with modification by natural causes. Darwin’s theology was not merely negative, entertaining the assumptions of his creationist opponents as hypotheses simply to contradict those assumptions with evidence. Rather, Dilley argues, Darwin employed theology in a positive fashion, as support for his own position. “In the Origin,” Dilley writes, “Darwin used a specific theological view of God’s relationship to natural laws in order to argue for evolution and against special creation.” The Origin supplies abundant evidence of theology in action; as Dilley observes,, http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html further note: From Philosopher to Science Writer: The Dissemination of Evolutionary Thought – May 2011 Excerpt: The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical. http://darwins-god.blogspot.com/2011/05/from-philosopher-to-science-writer.html I think Michael Behe does an excellent job, in this following debate, of pointing out that denying the overwhelming evidence for design in biology makes the science of biology ‘irrational’. As well Dr. Behe makes it clear that materialistic evolutionists themselves, by their own admission in many cases, are promoting their very own religious viewpoint, Atheism, in public schools, and thus are in fact violating the establishment clause of the constitution: Should Intelligent Design Be Taught as Science? Michael Behe debates Stephen Barr - 2010 - video http://www.isi.org/lectures/flvplayer/lectureplayer.aspx?file=v000355_cicero_040710.mp4&dir=mp4/lectures Evolution Is Religion--Not Science by Henry Morris, Ph.D. Excerpt: Evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion—a full-fledged alternative to Christianity, with meaning and morality,,, Evolution is a religion. This was true of evolution in the beginning, and it is true of evolution still today. Darwinian atheist Michael Ruse - Prominent Philosopher http://www.icr.org/article/455/ This following video, at about the 6:45 minute mark, is very interesting, for in it you see ‘Darwinian Theology’ been played out to its fullest, and most absurd, extent. The Anthropic Principle – Fine Tuning Of The Universe – Michael Strauss PhD. http://www.metacafe.com/watch/4323661/ Some may say the example in the video of 'Darwinian Theology' being played out to its fullest extent is 'overkill' as to the point, but is not that 'extreme extent' what it all really boils down to??? i.e. in final analysis, Does neo-Darwinism not all boil down to the fact that man wants to become his own god, playing by his own rules, instead of giving glory and honor that belongs to almighty God alone? =====================bornagain77_{May 29, 2011
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Also, the number of chromosomes varies dramatically, sometimes even within a species!! From the Wikipedia entry on Karyotype: "A spectacular example of variability between closely related species is the muntjac, which was investigated by Kurt Benirschke and his colleague Doris Wurster. The diploid number of the Chinese muntjac, Muntiacus reevesi, was found to be 46, all telocentric. When they looked at the karyotype of the closely related Indian muntjac, Muntiacus muntjak, they were astonished to find it had female = 6, male = 7 chromosomes. "They simply could not believe what they saw... They kept quiet for two or three years because they thought something was wrong with their tissue culture... But when they obtained a couple more specimens they confirmed [their findings]" Hsu p73-4[14] The number of chromosomes in the karyotype between (relatively) unrelated species is hugely variable. The low record is held by the nematode Parascaris univalens, where the haploid n = 1; the high record would be somewhere amongst the ferns, with the Adder's Tongue Fern Ophioglossum ahead with an average of 1262 chromosomes. Top score for animals might be the shortnose sturgeon Acipenser brevirostrum at a mere 372 chromosomes. The existence of supernumerary or B chromosomes means that chromosome number can vary even within one interbreeding population; and aneuploids are another example, though in this case they would not be regarded as normal members of the population." An 'average' number of chromosomes? Sometimes I'm just glad to be alive to be able to see all this being discovered and studied.ellazimm_{May 29, 2011
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JGuy: "Why waste resources making more “junk” genes?" I think that is an issue of genomic studies: at what point is carrying around lots of genomic material become a liability in itself? It seems to be a high threshold though; humans have roughly 3.2 billion base pairs in their genome whereas Pieris japonica (Japanese-native, pale-petal) has roughly 150 billion base pairs. And Polychaos dubium ("Amoeba" dubia) might have as much as 670 billion base pairs. There's some dispute over that I guess. The variety within similar creatures is also staggering: Tetraodon nigroviridis (type of puffer fish) has 385 million base pairs in its genome while Protopterus aethiopicus (marbled lungfish) has 130 billion. Three orders of magnitude difference between two species of fish? Very weird but very interesting.ellazimm_{May 29, 2011
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Seems to me if it was a broken vitamin C gene from many common anscestors ago, that the "junk" would have been selected out. Why waste resources making more "junk" genes? Perhaps, evolution was too busy trying to figure out how to select the rare unselectable slightly beneficial mutations to notice. :PJGuy_{May 29, 2011
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BA77: Sorry for being short and sharp. I know you've thought about all this a lot and it frustrates you at times that what seems crystal clear to you is not to others.ellazimm_{May 29, 2011
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Supports of non-design common descent with modification are accused of being liars, part of a conspiracy to block real science and ignorant of evidence and the failings of their own theories. Makes me feel very welcome.
Think of it as Darwinism in action. You'll come up with something that allows you to cope, or you won't. Me, I've reached an agreement with BA77 that I would pretty much ignore his posts unless they were directed at something I had written. I feel your pain. honestly. If you recall, I even tried to stick up for you. Consider the death of the following thread: https://uncommondescent.com/intelligent-design/the-spirituality-of-physics/ I tried to warn you.Mung_{May 28, 2011
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I have nothing to add to what Lizzie had to say; I think she stated the case very well. And I think the debate is getting a bit . . . . unrestrained. I don't know how to respond to statements like: "Got to love this theory, it is strong evidence except when it is not strong evidence,,, frankly this theory is best thing since sliced bread for science,, no real pesky falsifiability criteria to deal with, like actually having to demonstrate that purely material, neo-Darwinian, processes can actually produce completely novel functional genes,,, NO Sir, that is beneath the dignity of neo-Darwinism,, Man all you got to do is wait for the evidence to come to you and make up whatever story you want, with as many big words as possible, collect your paycheck from the taxpayers, and laugh all the way to the bank." In fact, if that's the thanks Lizzie gets for spending lots of time answering your questions and trying to explain then should she even bother in the future? Supports of non-design common descent with modification are accused of being liars, part of a conspiracy to block real science and ignorant of evidence and the failings of their own theories. Makes me feel very welcome.ellazimm_{May 28, 2011
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Elizabeth Liddle @45:
Neither shared nor unshared genes indicate common descent or infirm common descent.
Nearing the truth. Common descent is assumed to be true. Therefore, it does not require confirmation or dis-confirmation. What is not assumed is the various phylogenies, iow, what a specific pattern of decent with modification looks like. Now I can accept that as science. Hypothetical phylogenies can be tested. Common descent can't, because it's assumed from the outset. As an interesting aside, phylogenies are inferred. There's got to be a connection there to ID and inference to the best explanation (iow, some phylogenies explain the evidence better than others). Personally, I would admit that shared characters are evidence for descent from a common ancestor and the lack of those shared characters mitigate against a common ancestor. I don't see what's so controversial about that. The alternative, as BA77 points out, is to make the theory look like it can't be tested and is therefore not scientific, as it is not subject to falsification.
That’s why I said that the distribution of the similarities and differences is what is important.
But isn't "distribution" just a fancy way of saying they are there or they aren't? ;) But really, do what extent to these phylogenies take into account what isn't present? So it's the similarities that matter, isn't it? Can we build a phylogeny based on stuff that's missing? Is it done very often? Grr... I don't wanbt o have to haul out my books on phylogenetics, lol. Is this covered in Sober's Evidence and Evolution? I have that handy.
If the broken gene was scattered haphazardly through the primate phylogeny, i.e. in paraphyletic groups it would bring the original phylogeny into question.
Would it really? I don't think it would. I think it just would not confirm the original phylogeny. I think it would only bring the original phylogeny into question if it suggested an alternative phylogeny.
On the other hand, non-shared genes aren’t as interesting from the point of view of establishing relatedness.
Is it reasonable to ask why not? Why is one set of data to be preferred over another? Is it because the first set conforms to the picture we want to establish as the consensus while the other doesn't? I'd really like to understand why the two aren't equally important. I hope you don't have to work tomorrow Lizzie! Overall you've been a great debate partner. Thanks. You too ellazimm, if you're lurking. I love bouncing ideas around. It's such an un-natural thing to do.Mung_{May 28, 2011
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Let's try one more time here Elizabeth,,, you state; So would finding organisms with the characteristics of a clade with a node at 100 billion years ago(sic) in a stratum dating from 200 billion years ago(sic).,, 'So disconfirmatory evidence is certainly possible.' Let's just see how 'certainly possible' this is for you??? How about a 'precambrian rabbit' 635 million years ago??? More Questions for Evolutionists - August 2010 Excerpt: First of all, we have 65% of the gene number of humans in little old sponges—an organism that appears as far back as 635 million years ago, about as old as you can get [except for bacteria]. This kind of demolishes Darwin’s argument about what he called the pre-Silurian (pre-Cambrian). 635 mya predates both the Cambrian AND the Edicarian, which comes before the Cambrian (i.e., the pre-Cambrian) IOW, out of nowhere, 18,000 animal genes. Darwinian gradualism is dealt a death blow here (unless you’re a ‘true believer”!). Here’s a quote: “It means there was an elaborate machinery in place that already had some function. What I want to know now is what were all these genes doing prior to the advent of sponge.” (Charles Marshall, director of the University of California Museum of Paleontology in Berkeley.) I want to know, too! https://uncommondescent.com/intelligent-design/more-questions-for-evolutionists/ ================= The new animal phylogeny: Reliability and implications: Excerpt: "The new molecular based phylogeny has several important implications. Foremost among them is the disappearance of "intermediate" taxa between sponges, cnidarians, ctenophores, and the last common ancestor of bilaterians or "Urbilateria."...A corollary is that we have a major gap in the stem leading to the Urbilataria. We have lost the hope, so common in older evolutionary reasoning, of reconstructing the morphology of the "coelomate ancestor" through a scenario involving successive grades of increasing complexity based on the anatomy of extant "primitive" lineages." From Proceedings of the National Academy of Sciences, USA, in 2000 - http://www.pnas.org/content/97/9/4453.full.pdf?ijkey=USJfrrxyih/gM A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.htmlbornagain77_{May 28, 2011
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Elizabeth you state: 'Neither shared nor unshared genes indicate common descent or infirm common descent.' But alas you had just argued for the whole thread that vitamin c gene was 'strong' evidence for common descent. Got to love this theory, it is strong evidence except when it is not strong evidence,,, frankly this theory is best thing since sliced bread for science,, no real pesky falsifiability criteria to deal with, like actually having to demonstrate that purely material, neo-Darwinian, processes can actually produce completely novel functional genes,,, NO Sir, that is beneath the dignity of neo-Darwinism,, Man all you got to do is wait for the evidence to come to you and make up whatever story you want, with as many big words as possible, collect your paycheck from the taxpayers, and laugh all the way to the bank.bornagain77_{May 28, 2011
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No, bornagain77, it doesn't predict "exactly opposite things", and I didn't say it did! Neither shared nor unshared genes indicate common descent or infirm common descent. It is the distribution of those genes that strongly suggest a specific phylogeny. In the case of the GULO gene, it supports a phylogeny in which the haplorrhini primates form a single clade, which is interesting, because independent data suggest the same, so we have independent data leading to the same conclusion. If they suggested different phylogenies, then that would be a real problem for the theory that haplorrhini primates share a more recent ancestor than all primates do. As for pond scum: what evolutionary theory predicts is that populations will move towards fitness peaks, then stay there. So the similarity of billion year old pond scum and modern scum again neither confirms nor infirms evolutionary theory but is perfectly consistent with it. What would seriously infirm common descent would be genetic phylogenies that were wildly at odds with phylogenies constructed from other characteristics. So would finding organisms with the characteristics of a clade with a node at 100 billion years ago in a stratum dating from 200 billion years ago. So disconfirmatory evidence is certainly possible.Elizabeth Liddle_{May 28, 2011
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Man you got to love a theory that predicts exactly opposite things and is still considered true without the bat of an eye! shared = common descent not shared = common descent Thanks for clearing that up Elizabeth. Man this evolutionary science stuff is a breeze, find billion year old pond scum that looks exactly like modern scum, no problem, make a story up and wa la, evolution predicts that, find completely unique genes not found in any other species, no problem, make another story up and wa la, evolution predicts that too.bornagain77_{May 28, 2011
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Ah, thanks. But I think I got that. That's why I said that the distribution of the similarities and differences is what is important. If, for example, phylogenetic analyses indicate that primates share a common ancestor, and haplorrhini primates share a more recent common ancestor, and the GULO gene is found to be broken in all haplorrhini primates, but not on others, then that is confirmatory evidence in support of the original phylogeny. If the broken gene was scattered haphazardly through the primate phylogeny, i.e. in paraphyletic grups it would bring the original phylogeny into question. On the other hand, non-shared genes aren't as interesting from the point of view of establishing relatedness. Obviously non-interbreeding populations (i.e. pairs of species) will have a substantial set of non-shared genes each. It doesn't tell you much more than that they are not the same species, which you already know (by definition). The don't mean "not common descent", they just mean "different lineage".Elizabeth Liddle_{May 28, 2011
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His point is that if the presence of some "gene," say the Vitamin C pseudogene, counts as evidence for common descent due to the fact that it is shared with other species, why does not the absence of genes (by his count at least 1000 such) not count as evidence against common descent with those same other species by virtue of the fact that they are not shared? It's really a simple question. The simplicity sort of gets lost in all the quotes and links. If shared = common descent then ought not shared mean not common descent? Or is there no disconfirming evidence against common descent?Mung_{May 28, 2011
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Well, what it argues for is a distinct lineage. But then we know we are a distinct lineage anyway! So I'm not getting your point. Clearly we differ from our closest primate relatives in a large number of ways, and those differences must be genetic (because clearly we inherit them!) But equally clearly we share a large number of features (including our inability to synthesize vitamin C) and that is reflected in the degree of genotypic similarity.Elizabeth Liddle_{May 28, 2011
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correction ; Moreover Elizabeth, why does the fact that we have found over 1000 completely genes within humans NOT count against common descent?bornagain77_{May 28, 2011
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Moreover Elizabeth, why does the fact that we have found over 1000 completely genes within humans count against common descent? Human Gene Count Tumbles Again – 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes.,,, Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. (The 1,177 ORFan genes in humans are completely unique to our lineage) http://www.sciencedaily.com/releases/2008/01/080113161406.htm In fact it turns out that the authors of the preceding ‘kick the ORFans out in the street’ paper actually did know that there was clear and unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore that strong evidence in favor of their preconceived evolutionary bias of forcing the genetic sequences of chimps and humans to be as similar as possible. That is EXACTLY how you ARE NOT suppose to practice science!!!: https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358547 Moreover new ORFan genes are found to be just as essential as older genes: Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New Genes in Drosophila Quickly Become Essential - 2010 https://wiki.brandeis.edu/twiki/pub/Bio/MolGenJCSchedule/ChenScience.pdf As well, a large percentage of completely unique ORFan genes are found in each new genome sequenced: ORFan Genes Challenge Common Descent - Paul Nelson - video with references http://www.vimeo.com/17135166 I would like to reiterate that evolutionists cannot even account for the origination of even one unique gene or protein, much less over one thousand completely unique ORFan genes: Could Chance Arrange the Code for (Just) One Gene? “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).” http://www.creationsafaris.com/epoi_c10.htm “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: – Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.” http://www.mendeley.com/research/estimating-the-prevalence-of-protein-sequences-adopting-functional-enzyme-folds/ Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681/ Poly-Functional Complexity equals Poly-Constrained Complexity http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ etc.. etc.. etc.. The whole point being Elizabeth, is that the evidence for over 1000 completely unique ORFan genes in humans was severely distorted simply because of the researchers preconceived bias that dictated what the evidence should look like. It is just such blatant and prejudiced, bias that IDists continually fight againstbornagain77_{May 28, 2011
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Elizabeth, while you ignore the fact that you have no rigorous basis to make your common decent argument in the first place, since you have not shown that evolution can even produce a gene in the first place, your evidence, which you refuse to question yourself, is not nearly as strong as you think it is, for example,,, 'It would seem from the evidence of a potential human pseudogene for L-gulono-?-lactone and the presence of the other enzymes necessary for synthesizing vitamin C that humans have lost the ability to make vitamin C. However, there is more to this story. There are only four exons for the gene encoding L-gulono-?-lactone in humans. Two-thirds of the homologous rat gene is completely missing. Most pseudogenes represent 90% of the entire functional gene. This DNA sequence, labeled as a pseudogene, might have an entirely different function than the rat gene. Stating that only the last enzyme is missing for the pathway to convert glucose to vitamin C might imply to the untrained individual that there is a biochemical pathway that leads to a dead end. Actually, the biochemical pathway that leads to the synthesis of vitamin C in rats also leads to the formation of five-carbon sugars in the pentose phosphate pathway present in virtually all animals (Linster and Van Schaftingen 2007). There are several metabolic intermediates in this pathway illustrating that these substances can be used as precursors for many compounds in the cell. In the pentose phosphate pathway, five-carbon sugars are made from glucose (a six-carbon sugar) to be used in the synthesis of DNA, RNA, and many energy producing substances such as ATP and NADPH (Garrett 1999). Animals that synthesize vitamin C can use both pathways illustrated in the simplified diagram below. Humans and the other animals "less fortunate" than rats only use the pentose phosphate pathway.' http://www.icr.org/article/adam-eve-vitamin-c-pseudogenes/bornagain77_{May 28, 2011
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What is evidence for common descent is not the broken GULO gene by itself, but a) its pattern of distribution (it tends to be found within members of a clade, established from other data and b) the patterns of mutations found in pseudo-genes tend to match within those clades, again established from other data.Elizabeth Liddle_{May 28, 2011
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Elizabeth; once again you simply do not have the evidence to back up your 'assumptions'!!! For all evidence we have shows loss of information for 'sub-speciation' events; In fact that is the main argument for ID, in that neo-Darwinists have absolutely ZERO concrete evidence for purely material, neo-Darwinian, processes creating ANY functional information WHATSOEVER. And yet you, in your very own post, have 'intelligently' produced more functional information than can reasonably be expected by the entire material processes of the universe over the ENTIRE history of the universe. This is no small matter Elizabeth, you can imagine this or that as what may have happened in the history of life, but the brute fact is that when the rubber meets the road and a thorough search is made for a credible 'consistent' source for functional information, neo-Darwinian processes fail miserably, whereas Intelligence fits the bill perfectly.bornagain77_{May 28, 2011
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you hold sequence similarity as evidence for common descent, yet ‘horrendously different’, similarity, as one researcher described the Y chromosome study, does not count against common descent. Elizabeth, it is completely disingenuous for you to view the evidence in such a biased manner.
I disagree. Common descent accommodates both. If both similarities and differences did not co-exist we'd not even be talking about common descent. Take the Vitamin C gene, for example. Say there were no Vitamin C pseudogenes. And all Mammals had this Vitamin C gene. That would be strong evidence of common descent. Say further that not all mammals had this vitamin C gene, that some do and some do not. This also is strong evidence for common descent. Say further, that we have another group of mammals that do not have this Vitamin C gene, but have something that looks remarkably similar. Call it a pseudogene. That too, is strong evidence for common descent. See?Mung_{May 28, 2011
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bornagain77, we really are going to have to agree to differ here, I think. We seem to share so few assumptions! For a start, you use the term "subspeciation" which I don't in fact recognise - as I said, ALL speciation starts as "sub-speciation", and must - because every species starts as the bifurcation of an existing single population which, if it is one that human beings know about, we have given a "species" name. Then, in brackets, you imply that this "sub-speciation" is, in brackets, equivalent to "loss of information". Again, I profoundly disagree. When a population, over time, divides into two non-interbreeding populations, each occupying a different occupational niche, I do not regard net information has having been "lost". For example, if a population that inhabits one island is divided by a geological catastrophe that splits it into two, the two halves of the original population may well, over time, evolve down different routes that result in the inability of individuals from each to breed with the other. And it may be that on one island, the environment is rockier than on the other, which is more like the original island. The rocky inhabitants may lose the "information" required to survive in a lush environment and instead "gain" information required to survie in a harsher environment (thicker skin, for instances, a different beak size). Both genotypes possess whatever "information" is required to build phenotypes that can survive in the local conditions. At any rate, be that as it may - that's my model! And I'd claim substantial evidential support for it. However, it's off topic for this OP, and in any case I wish you well. Thanks for sharing your thoughts with me :) Cheers Lizzie PS: to return to the OP, I do, of course, agree,that when the GULO gene was broken, information was lost as to how to synthesise vitamin C. The gene wasn't weeded out, however, probably because the population happened to have access to a vitamin-C diet (it's speculation of course, but primates today tend to inhabit environments where vitamin-C bearing food is abundant). So I'm not saying that useful information, once gained, can never be lost. It can, and deleterious mutations can spread through a population simply through drift.Elizabeth Liddle_{May 28, 2011
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Elizabeth, you simply don't have the evidence to back up your assertions!!! You state: 'I am simply making the argument that the evidence does support a “tree of life” in which a single “trunk”, over time, diversified both laterally (into many species) and longitudinally (changes over time).' Deepening Darwin's Dilemma - Jonathan Wells - The Cambrian Explosion - video http://www.metacafe.com/watch/4154263 Jonathan Wells - Cambrian Explosion - video http://www.cross.tv/55196 The unscientific hegemony of uniformitarianism - David Tyler - 2011 Excerpt: The summary of results for phyla is as follows. The pattern reinforces earlier research that concluded the Explosion is not an artefact of sampling. Much the same finding applies to the appearance of classes. http://www.arn.org/blogs/index.php/literature/2011/05/16/the_unscientific_hegemony_of_uniformitar Fossil Finds Show Cambrian Explosion Getting More Explosive - May 2010 Excerpt: Cephalopods, which include marine mollusks like squid, octopus, and cuttlefish, are now being reported in the Cambrian explosion fossils. http://www.evolutionnews.org/2010/05/fossil_finds_show_cambrian_exp.html The Cambrian Explosion Just Got More Explosive - August 2010 - audio http://intelligentdesign.podomatic.com/player/web/2010-08-11T10_49_02-07_00 If this abrupt appearance for all these completely different and unique phyla in the Cambrian was not bad enough for materialists, the fossil record shows there was actually more variety of phyla by the end of the Cambrian explosion than there are today due to extinction. Of Note: "Phyla are broad categories of classification. All fish, amphibians, reptiles, birds and mammals are in the same phylum. Squid, octopi, oysters, clams and snails are in another phylum. Lobsters, crayfish, insects, and millipedes are in still another." Ray Bohlin PhD “A simple way of putting it is that currently we have about 38 phyla of different groups of animals, but the total number of phyla discovered during the Cambrian explosion (including those in China, Canada, and elsewhere) adds up to over 50 phyla. (Actually the number 50 was first quoted as over 100 for a while, but then the consensus became 50-plus.) That means there are more phyla in the very, very beginning, where we found the first fossils, than exist now.” “Also, the animal explosion caught people's attention when the Chinese confirmed they found a genus now called Yunnanzoon that was present in the very beginning of the Cambrian explosion. This genus is considered a chordate, and the phylum Chordata includes fish, mammals and man. An evolutionist would say the ancestor of humans was present then. Looked at more objectively, you could say the most complex animal group, the chordates, were represented at the very beginning, and they did not go through a slow gradual evolution to become a chordate.” Dr. Paul Chien PhD., chairman of the biology department at the University of San Francisco http://www.discovery.org/scripts/viewDB/index.php?command=view&isFellow=true&id=52 etc.. etc.. Elizabeth, I can assure you with 100% certainty, the reality of how life appeared on earth, is far, far, different from what you have pictured in your imagination of gradualnessbornagain77_{May 28, 2011
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Elizabeth you state: 'But speciation (I’d submit that ALL speciation starts as “sub-speciation” just as even great forks in great trees started as a pair of bifurcating twigs),' Which is exactly what evolutionists must hold to since they can't pass this simple test: Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution. http://www.evolutionnews.org/2010/03/thank_goodness_the_ncse_is_wro.html ,, But Elizabeth, even we grant your baseless assertion that sub-speciation (loss of information) must precede primary speciation (gain in functional information, and we test for it, as Lenski has done, here is what we find: These following articles refute Richard E. Lenski's 'supposed evolution' of the citrate ability for the E-Coli bacteria after 20,000 generations of the E-Coli from his 'Long Term Evolution Experiment' (LTEE) which has been going on since 1988: Multiple Mutations Needed for E. Coli - Michael Behe Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell. http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ Michael Behe's Quarterly Review of Biology Paper Critiques Richard Lenski's E. Coli Evolution Experiments - December 2010 Excerpt: After reviewing the results of Lenski's research, Behe concludes that the observed adaptive mutations all entail either loss or modification--but not gain--of Functional Coding ElemenTs (FCTs) http://www.evolutionnews.org/2010/12/michael_behes_quarterly_review041221.html Lenski's e-coli - Analysis of Genetic Entropy Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment. http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria Lenski's work actually did do something useful in that it proved that 'convergent evolution' is impossible because it showed that evolution is 'historically contingent'. This following video and article make this point clear: Lenski's Citrate E-Coli - Disproof of Convergent Evolution - Fazale Rana - video (the disproof of convergence starts at the 2:45 minute mark of the video) http://www.metacafe.com/watch/4564682 The Long Term Evolution Experiment - Analysis Excerpt: The experiment just goes to show that even with historical contingency and extreme selection pressure, the probability of random mutations causing even a tiny evolutionary improvement in digestion is, in the words of the researchers who did the experiment, “extremely low.” Therefore, it can’t be the explanation for the origin and varieity of all the forms of life on Earth. http://www.scienceagainstevolution.org/v12i11f.htm The loss of 'convergent evolution', as a argument for molecular sequence similarity, is a major blow to neo-Darwinian story telling: Implications of Genetic Convergent Evolution for Common Descent - Casey Luskin - Sept. 2010 Excerpt: When building evolutionary trees, evolutionists assume that functional genetic similarity is the result of inheritance from a common ancestor. Except for when it isn't. And when the data doesn't fit their assumptions, evolutionists explain it away as the result of "convergence." Using this methodology, one can explain virtually any dataset. Is there a way to falsify common descent, even in the face of convergent genetic similarity? If convergent genetic evolution is common, how does one know if their tree is based upon homologous sequences or convergent ones? Critics like me see the logic underlying evolutionary trees to be methodologically inconsistent, unpersuasive, and ultimately arbitrary. http://www.evolutionnews.org/2010/09/implications_of_genetic_conver037841.html Origin of Hemoglobins: A Repeated Problem for Biological Evolution - 2010 Excerpt: When analyzed from an evolutionary perspective, it appears as if the hemoglobins originated independently in jawless vertebrates and jawed vertebrates.,,, This result fits awkwardly within the evolutionary framework. It also contradicts the results of the Long-term Experimental Evolution (LTEE; Lenski) study, which demonstrated that microevolutionary biochemical changes are historically contingent. http://www.reasons.org/origin-hemoglobins-repeated-problem-biological-evolutionbornagain77_{May 28, 2011
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Hi, bornagain77:
Elizabeth, you simply do not have the evidence to back your assertion for ‘vertical evolution’. Sub-speciation in fact explains the evidence much better than evolution since information is lost in the sub-speciation events, as well it agrees with the overall pattern we find in the fossil record; i.e. abrupt appearance and Disparity of major lifeforms precedes diversity of sub-species within the novel major lifeforms:
I'm not quite sure what you are calling "vertical evolution" but I assume you mean where one population changes over time without diverging, and you seemed to agree that this occurs in an oscillatory fashion in, for example, Galapagos finches, yes? So is your point that you think we do not have evidence for lower frequency changes? Again, let me make it clear that I am not making an anti-ID argument here - ID is perfectly compatible (as Mung rightly reminded me in another thread) with gradual evolutionary change over time (albeit enhanced or directed by Intelligent processes). But I would point to, for example, various transitional series in the fossil record in which incremental changes over time amount to large changes between the beginning and end of the series, as evidence for "vertical evolution" (in the broadest sense of "evolution". But speciation (I'd submit that ALL speciation starts as "sub-speciation" just as even great forks in great trees started as a pair of bifurcating twigs), is indeed a hugely important part of the picture, and is what explains contemporaneous diversity, as opposed to longitudinal diversity. So I won't attempt, here, to make the argument that such changes are a result of "Darwinian" processes, as opposed to "ID" processes (although I am persuaded that they are). I am simply making the argument that the evidence does support a "tree of life" in which a single "trunk", over time, diversified both laterally (into many species) and longitudinally (changes over time). That, it seems to me, is clearly what the data support, which is essentially the pattern formalised by Linnaeus, and is, indeed, what Darwin sought to explain. Behe, for example, disagrees with Darwin's explanation, but he and I assume many other IDists (Mung?) agree on the explanandum.Elizabeth Liddle_{May 28, 2011
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Elizabeth, as well, you hold sequence similarity as evidence for common descent, yet 'horrendously different', similarity, as one researcher described the Y chromosome study, does not count against common descent. Elizabeth, it is completely disingenuous for you to view the evidence in such a biased manner.bornagain77_{May 28, 2011
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Mung - it's powerful evidence for common descent. I don't see that it is particularly powerful evidence for evolution by means of replication with variance and natural selection.Elizabeth Liddle_{May 28, 2011
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