Intelligent Design

Evolution Professor: Orphans Not a Problem for Evolution

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In my previous post I discussed Joel Velasco’s claim, in his recent debate with Paul Nelson, that biological designs fall into a nested hierarchy. Velasco is by no means alone in making this bizarre claim. It is not controversial that it is not true, yet evolutionists routinely insist that, as Richard Dawkins once put it, genes across a range of species fall into a “perfect hierarchy, a perfect family tree.” If, like many, your first question is “what are they thinking?” then go to the [1:33:21] mark in the Nelson-Velasco debate where for the final few minutes of his response segment, Velasco sheds light on the closing of the evolutionary mind.  Read more

56 Replies to “Evolution Professor: Orphans Not a Problem for Evolution

  1. 1
    bornagain77 says:

    In the following video, Jeffrey Tomkins PhD. states that 7% of human genes are unique:

    The Myth of 98% Genetic Similarity between Humans and Chimps – Jeffrey Tomkins PhD. – video
    https://vimeo.com/95287522

  2. 2
    JoeCoder says:

    I’m still worried about whether Tomkins’s research is trustworthy, based on this comment by AceOfSpades25 on his recent GULO paper. Can anyone comment?

  3. 3
    bornagain77 says:

    JoeCoder, and your confidence that Darwinian research is trustworthy is based on what exactly? wd400’s testimony? ,,, Frankly, I’ve been lied to so many times by Darwinists I don’t trust anything they say anymore.,,, Watch the video, note his credentials and the rigid methodology of his research. Then judge for yourself if his conclusion is trustworthy. I find his research trustworthy.

    Also of note as to ORFans:

    From Jerry Coyne, More Table-Pounding, Hand-Waving – May 2012
    Excerpt: “More than 6 percent of genes found in humans simply aren’t found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps.”
    Jerry Coyne – ardent and ‘angry’ neo-Darwinist – professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics.
    http://www.evolutionnews.org/2.....60271.html

  4. 4
    JoeCoder says:

    BA77: I’m skeptical of everyone. At first I was more skeptical of creationists but in the last couple years that has reversed. However Tomkins has been criticized by other young earth creation biologists.

    I will be watching the video (I found the full version on youtube) and will do as you’ve said. But I would be much more confident if AceOfSpade25’s points could be addressed.

  5. 5
    OldArmy94 says:

    From the article:

    “In fact Velasco’s appeal here to “all that other evidence” (my paraphrase) is typical. Yes, you can raise minor issues around the edges that have not yet been resolved, but we’ve got this mountain of rock solid, compelling, overwhelming evidence proving evolution beyond any reasonable doubt.

    This is yet another form of theory protectionism. It shifts attention away from a theoretical failure, appealing to a mythical, non existent, list of proof texts. Aside from the problem that no such set of compelling evidence exists, it is irrelevant. The question in hand is how evidence X (in this case unique genes) bears on the theory, regardless of the other evidence.”>

    That reminds me of A Christmas Story when the family goes looking for their tree. The tree salesman points out how solid and great a tree is until he notices the needles on the ground; he tosses it aside and then exclaims the virtues of another tree. The Darwinian uses the same tact–one piece of evidence under fire? Never fear! Just move on to the next fable and keep the entire cycle moving.

  6. 6
    bornagain77 says:

    Joecoder, ‘YEC’ Todd Wood is in the same book as Dennis Venema with me. In fact Denis Venema cites Todd Wood! i.e. both practice Shoddy Science!:

    In Todd’s own words, evolution is solid science:

    Evolution is not a theory in crisis. It is not teetering on the verge of collapse. It has not failed as a scientific explanation. There is evidence for evolution, gobs and gobs of it. It is not just speculation or a faith choice or an assumption or a religion. It is a productive framework for lots of biological research, and it has amazing explanatory power. There is no conspiracy to hide the truth about the failure of evolution. There has really been no failure of evolution as a scientific theory. It works, and it works well.
    http://biologos.org/blog/a-tal.....sts-part-1

    Need I say more?

  7. 7
    bornagain77 says:

    As to Aceofspades, I don’t know his exact credentials but I do know he put forward a very simplistic view of our brain, (more complex than the internet), randomly evolving. A simplistic view which was beyond laughable

    “our increased intelligence may be simply down to a few duplications of a gene (SRGAP2)”
    http://www.uncommondescent.com.....ent-498499

    Now JoeCoder, I assume you are in programming, do you really think anyone who says such things is being genuine to the evidence? I certainly don’t!

  8. 8
    JLAfan2001 says:

    Joecoder:

    Don’t bother with BA77. He only believes in evidence that supports his worldview. He refuses to look at anything else that could be detrimental to his belief in a god. He lacks critical thinking skills so he just eats up whatever christian propoganda he can. It’s funny how he claims that he is not a YEC but is willing to believe their research without question. Why? Cause it’s supports belief in his jeebus.

    Todd Wood is quoted as saying:

    “I’ve begun to notice a strange undercurrent of folks proposing that I’m not really a young earth creationist. One especially amusing person suggested that I was stupid, possibly bipolar, or just a liar…
    Lest my creationist credentials be doubted, let me be blunt:
    I believe that God created everything that you see in six consecutive days around 6000 years ago.
    I believe that Adam and Eve were the very first humans and were directly created by God…(Entire text may be found here)

    Creationist students, listen to me very carefully: There is evidence for evolution, and evolution is an extremely successful scientific theory. That doesn’t make it ultimately true, and it doesn’t mean that there could not possibly be viable alternatives. It is my own faith choice to reject evolution, because I believe the Bible reveals true information about the history of the earth that is fundamentally incompatible with evolution. I am motivated to understand God’s creation from what I believe to be a biblical, creationist perspective. Evolution itself is not flawed or without evidence. Please don’t be duped into thinking that somehow evolution itself is a failure. Please don’t idolize your own ability to reason. Faith is enough. If God said it, that should settle it. Maybe that’s not enough for your scoffing professor or your non-Christian friends, but it should be enough for you. (Emphasis in the original)”

    If this isn’t living proof of how religion makes you stupid, I don’t know what is. It’s obvious he believes there is evidence for Darwinian evolution and that the evidence is sound but rejects it because the bible tells him to. Utterly and completey STUPID!!!!! All religion does it make one lie to one self.

  9. 9
    bornagain77 says:

    Actually JLAfan2001 I’m very open to the evidence. Care to cite one molecular machine evolving by Darwinian processes?

    Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.- Dr Behe in 1997

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

    And since you can’t even clear that ridiculously small evidential hurdle JLAfan, why in blue blazes DO YOU believe so adamantly that unguided processes created all life on earth? You simply don’t have the evidence to back up your nihilistic faith!

  10. 10
    Piotr says:

    #1, #2

    AceOfSpades25 demonstrates very clearly that Tomkins results are artifacts of appallingly sloppy data handling, made worse by plain dishonesty in presenting the analysis. It’s an exemplary, professional review — a piece of real science. Bornagain77, if you have to distrust somebody, take my advice and distrust Tomkins.

  11. 11
    bornagain77 says:

    Actually Piotr, anyone who has Moran’s blog listed at the top of his profile as you do is not to be trusted by an ‘IDiot’ like me either 🙂

    And, since I gather you think you are also the result of unguided processes, you are also invited to falsify Behe’s claim for just one molecular machine.

  12. 12
    JLAfan2001 says:

    BA77

    Like Todd Wood said “there are gobs and gobs of evidence for evolution”. You just have to look for it but you focus on the pieces that we havn’t figured out yet rather than looking at what has been discovered. You want every single thing figured out before you accept it. You’re afraid of accpeting it because of what it will mean to your religious beliefs.

    Piotr
    BA77 won’t take your advice because you are an atheist, at least I think you are. He only listens to the lie of religious people.

  13. 13
    JoeCoder says:

    I know all about Todd Wood. I’ve been reading his blog for a couple years now, took his Historic Adam class last fall, and have his baraminology book on my shelf. I have the same quote you shared featured on my own page on evolutionary perspectives which also includes evolutionists saying things every bit as damaging on evolution. You said “Need I say more?” about Todd Wood? Yes. On my own page I followed that quote with what he said in his dialog with Darrell Falk of BioLogos:

    I did my doctoral dissertation in that field [evolution], I’ve been to conferences; I’m a member of evolutionary societies. I’m steeped in deep. I mean deep in the evolution community so I know it intimately well. And there’s never been anything in there that’s struck me as totally utterly irreconcilable with my creationist understanding. To be sure there are challenges and difficulties that still need to be resolved. But it wasn’t an issue of “Oh my goodness I can’t explain this.” And I never ever doubted my faith.”

    I disagree with Wood’s first quote about mountains of evidence for evolution. And unlike JLAFan, I have a lot of respect for Wood. While everyone else puts foward knee-jerk reactions to whatever the other side says, he’s not afraid to take a critical eye to creation science. We need more people like him, and like Lynn Margulis who is famous for lines like “The critics, including the creationist critics, are right about their criticism” of evolutionary theory.

    And BA77: I was on the same thread you linked to on AceOfSpades25 right beside you correcting many other things he got wrong. But that has nothing to do with whether his analysis of GULO is right or wrong. But your criticism of his GULO alignments is at the bottom of Graham’s Heirarchy “attacks the characteristics or authority of the writerwithout addressing the substance of the argument”.

    I would love it if Tomkins were right about GULO after all. Maybe he is. But distracting from the real issue isn’t helping us.

  14. 14
    bornagain77 says:

    Funny that ‘gobs and gobs’ of evidence never includes a single molecular machine arising by unguided processes.

    Venter: Life Is Robotic Software – July 15, 2012
    Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter.
    http://crev.info/2012/07/life-is-robotic-software/

    How we could create life – The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell – Paul Davies – 11 December 2002
    Excerpt: Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level.
    http://www.theguardian.com/edu.....ucation.uk

  15. 15
    Piotr says:

    Have you read AOS’s review? Can you understand it? If you have, and you can, my sympathies don’t matter. But if you can’t follow AOS’s explanation or see through Tomkins’s flawed and unprofessional methodology, you simply lack the competence to distinguish good science from bad science, or from pseudoscience. If so, how can you know whether Behe’s arguments (or their refutations, or Behe’s responses) make sense?

    All right, it’s your choice. Just don’t say I didn’t warn you 😉

  16. 16
    bornagain77 says:

    Well believe what you want JoeCoder. Personally, from his simplistic dismissal of evidence for design, I don’t trust ACE’s analysis and question his integrity first and methodology second..

  17. 17
    bornagain77 says:

    Piotr, so do you have a refutation of Behe’s claim or not?

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro, molecular biologist, National Review, Sept. 16, 1996

    ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
    Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
    *Professor Emeritus of Biochemistry, Colorado State University, USA

    Michael Behe – No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
    http://www.metacafe.com/watch/5302950/

    Calling Nick Matzke’s literature bluff on molecular machines – DonaldM UD blogger – April 2013
    Excerpt: So now, 10 years later in 2006 Matzke and Pallen come along with this review article. The interesting thing about this article is that, despite all the hand waving claims about all these dozens if not hundreds of peer reviewed research studies showing how evolution built a flagellum, Matzke and Pallen didn’t have a single such reference in their bibliography. Nor did they reference any such study in the article. Rather, the article went into great lengths to explain how a researcher might go about conducting a study to show how evolution could have produced the system. Well, if all those articles and studies were already there, why not just point them all out? In shorty, the entire article was a tacit admission that Behe had been right all along.
    Fast forward to now and Andre’s question directed to Matzke. We’re now some 17 years after Behe’s book came out where he made that famous claim. And, no surprise, there still is not a single peer reviewed research study that provides the Darwinian explanation for a bacterial flagellum (or any of the other irreducibly complex biological systems Behe mentioned in the book). We’re almost 7 years after the Matzke & Pallen article. So where are all these research studies? There’s been ample time for someone to do something in this regard.
    Matzke will not answer the question because there is no answer he can give…no peer reviewed research study he can reference, other than the usual literature bluffing he’s done in the past.
    http://www.uncommondescent.com.....ent-453291

    More Irreducible Complexity Is Found in Flagellar Assembly – September 24, 2013
    Concluding Statement: Eleven years is a lot of time to refute the claims about flagellar assembly made in Unlocking the Mystery of Life, if they were vulnerable to falsification. Instead, higher resolution studies confirm them. Not only that, research into the precision assembly of flagella is provoking more investigation of the assembly of other molecular machines. It’s a measure of the robustness of a scientific theory when increasing data strengthen its tenets over time and motivate further research. Irreducible complexity lives! –
    http://www.evolutionnews.org/2.....77051.html

    Dr. Behe, in an inappropriately named lecture, gives a talk on Intelligent Design in this following video (Of note, the last half of the video, at the 2:22:25 hour and minute mark of the video, is a Q&A session that gets into some of the interesting technical details of his defense of Irreducible Complexity of the Blood Clotting cascade from some high level criticisms)

    Theistic Evolution – Michael Behe – video
    http://www.youtube.com/watch?v=r4dpVpS38Cc

    of related note to the fact that Darwinists have ZERO empirical evidence of Darwinian processes EVER producing a molecular machine, there are several examples that intelligence can do as such, here is one:

    (Man-Made) DNA nanorobot – video
    https://vimeo.com/36880067

  18. 18
    Piotr says:

    JLAfan2001

    In one of his posts AOS writes he isn’t an atheist. If he isn’t, I respect his professionalism all the same. He does his job well and doesn’t let wishful thinking cloud his mind.

    I don’t think it matterst to BA, which is why I normally ignore his lengthy cut-and-paste collages.

  19. 19
    bornagain77 says:

    Piotr, the reason you will not answer my request for a molecular machine that has been produced by unguided processes is because, like Matzke, there is no answer you can give for there are no examples to give.

    Ignore all you want, and believe what you want, the evidential elephant in the living room you are ignoring remains!

  20. 20
    JoeCoder says:

    @BA77: I’m not satisfied to dismiss all of what everyone says because they get something wrong. In Edge of Evolution (one of my favorite ID books), Behe was wrong about the number of HIV binding sites, Ian Musgrave corrected him (although got other things wrong and his tone was unbecoming of a professional scientist), and Behe accepted he made an error in a subsequent blog post. But I’m not about to dismiss all of Behe’s arguments because of that. EVERYONE gets things wrong sometimes. And some more than others.

    AceOfSpades put a lot more research into his GULO analysis than any of his other arguments, going so far as to checking the alignments himself. I looked at them too but neither of us are biologists. Tomkins argued that there wasn’t enough time for evolution to have produced that many mutations in GULO. If AceOfSpades is right, then Tomkins is taking single mutations that affect many nucleotides and counting them as indivisual mutations to inflate the numbers. Unlike Behe’s honest mistake of not knowing about the binding site, Tomkins should know better. So back to the topic of errors:

    1. Behe on HIV binding spot: honest mistakes
    2. AceOfSpades25’s points in that other thread: honest mistakes
    3. Tomkins on GULO mutations: deliberate?

    Because of what Wood and AceOfSpades have shared about Tomkins, I now question more of his research. If you want to fix that please address the problems directly so my mind can be changed. I would be very thankful if someone could do so.

  21. 21
    bornagain77 says:

    JoeCoder, once again, believe what you want and side with the Darwinists if you wish. My money rides with Tomkins. If you want specific answers as to what is wrong with AOS analysis, I suggest you write Tomkins himself with AOS’s analysis to get to the real meat. If he addresses forthrightly you should knbow very quickly who is right and who is wrong. You simply are not going to get the clear resolution you want to your question on a blog buzzing with Darwinian dogmatists

  22. 22
    JoeCoder says:

    I just asked AOS if I could share it with Tomkins, and he told me he plans to himself when he gets some time, and will then share with me how it goes. So we wait.

    I’m not “siding with the darwinists” 😛 Only exercising due diligence. Sometimes creationists are wrong, and sometimes they even overstate their claims and leave out important details that hurt their case. We do it less than the Darwinists but it still happens. Truth is my ultimate goal even if we have to sacrifice claims and lose battles along the way.

  23. 23
    Barb says:

    Don’t bother with BA77 JLAfan2001. He only believes in evidence that supports his worldview. He refuses to look at anything else that could be detrimental to his lack of belief in a god. He lacks critical thinking skills so he just eats up whatever Christian atheist propoganda he can. It’s funny how he claims that he is not a YEC an anti-theist but is willing to believe their research without question. Why? Cause it’s supports belief in his jeebus.atheistic worldview.
    Fixed that for, well, everyone.

  24. 24
    Barb says:

    If this isn’t living proof of how religion atheism makes you stupid, I don’t know what is. It’s obvious he believes there is evidence for Darwinian evolution creation and possibly the existence of God and that the evidence is sound but rejects it because the bible his nihilist worldview tells him to. Utterly and completely STUPID!!!!! All religion atheism does it make one lie to one self.

    Fixed it again.

  25. 25
    bornagain77 says:

    Barb, with such skills, you could probably bring the New York Times back from the brink of collapse and make it respectable once again 🙂

  26. 26
    Aceofspades25 says:

    > BA77

    As to Aceofspades, I don’t know his exact credentials but I do know he put forward a very simplistic view of our brain, (more complex than the internet), randomly evolving. A simplistic view which was beyond laughable

    “our increased intelligence may be simply down to a few duplications of a gene (SRGAP2)”

    Oh dear… Is an ad hominem the best response you have?

    You’ve changed the subject to attack my character instead of dealing with the critique that JoeCoder has pointed you to.

    If you read my comment you will notice that I have provided all of the data to support my critique. Rather that criticise me for something unrelated, I’d encourage you to read my critique and engage with that.

    In that instance Tomkins was plainly wrong.

    I’m not is a position to address his claim that that 7% of human genes are unique though.

    On a side not, how does he define unique? One could argue that 99% of our genes was unique if one was pedantic enough to define single nucleotide polymorphisms as a marker for uniqueness.

    Regarding the genes we have that other great apes don’t, I’ve noticed that with many of those, other great apes have the (nearly complete) precursors to what has become functional genes in humans – so this is hardly a good argument.

  27. 27
    bornagain77 says:

    Aceofspades25 it is not an ad hominem. You did indeed say that something that is more complex that the entire internet, routers, and computers, combined was…

    “our increased intelligence may be simply down to a few duplications of a gene (SRGAP2)”

    I merely pointed out that I had a lot of trouble believing anyone who has such a simplistic notion as to how our unimaginable complex brain came to be as to be genuine in regards to anything else he might say in biology.

    Since both issues deal with biology and not whether or not you are a compulsive liar, cheat on your wife or whatever, it is directly relevant to your trustworthiness in this area!

  28. 28
    Evolve says:

    Cornelius,

    You certainly have no clue about what you’re blurting out.
    What Velasco said in his debate with Paul Nelson is immaterial. Velasco may not have done his homework properly. He’s unaware of recent studies showing that ORFan genes arise from ancestral intergenic regions via the well-understood process of mutation. You can trace the evolutionary history of ORFan genes in a particular species to intergenic regions in its cousins:

    1. Emergence of a New Gene from an Intergenic Region (in Mouse)

    http://www.cell.com/current-bi.....?cc=y?cc=y

    2. Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

    http://www.sciencemag.org/cont.....9.abstract

    3. Female fly genomes also populated with de novo genes derived from ancestral sequences

    http://phys.org/news/2014-03-f.....-novo.html

    Carl Zimmer wrote a nice piece on this recently:

    http://www.nytimes.com/2014/04......html?_r=1

    New studies are also showing that ORFans emerge and get lost at a rapid rate:

    http://www.ncbi.nlm.nih.gov/pm.....MC3927632/

    In short, ORFans are no longer a mystery or a problem for evolutionary theory.
    Sorry, but now creationists like you can go after the next “big problem” in biology to find a foothold for your fictitious designer. ORFan genes are passe.

  29. 29
    Dr JDD says:

    There may well be gobs and gobs of evidence for evolution.

    Evidence is not proof. Evidence is subject to interpretation.

    Fossil record = evidence (if you exclude the Cambrian?).

    Molecular homology = evidence.

    Phenotypic homology = evidence.

    Being able to direct evolution = evidence.

    But yet as a scientist (and a Christian), I have yet to see anything that made me (like quoted above of Wood) question whether that evidence fits with the Biblical account or with creation. In fact to me it makes near perfect sense, and where it is not perfectly obvious as a fit, it does not cause a big enough challenge to make me question my beliefs.

    Fossil record = fits with creation (e.g. sudden appearance of complex organisms, no true intermediate forms showing useless structures evolving, etc). Top-down appearance in-line with designer giving info to allow diversification.

    Molecular/phenotypic homology – perfectly expected if a common designer no less than common descent. Molecular data not unexpected for a designer.

    Being able to direct evolution in the lab – perfectly explainable with the understanding that you are selecting for something different (not necessarily better) on information already present (i.e. not adding new sequence, etc). In fact, most (surely all) design advocates fully believe in evolution – micro-evolution (modification of exisiting information and either loss of information or selection or differential gene expression, etc).

    Then you have the difficult questions – where is the evidence for the multiverse? What about the fine-tuning problems? All perfectly explained in a transcendent creator God. What about abiogenesis? Not a difficulty as despite no idea or evidence OR proof of how it happened (the theories around offer no real and true evidence for this embarassingly poorly supported theory), it is unnecessary with a creator designer.

    So all those “things” can be touted as “evidence” for evolution – and they are forms of evidence but they are certainly not proof and one would do well to remember evidence can be attributed to more than one model.

    I should note that while these are simplistic pieces of evidence, I have personally gone through extensive amounts of more complicated evidence for evolution and still nothing fits as incompatible at all in light of a Judeo-Christian OOL view point. The way it appears to me is that there are harder things to explain with a naturalistic point of view. Further, most naturalists show their lack of understanding of the Judeo-Christian viewpoint when they claim things don’t look perfect or some designs are not great/don’t make sense/lost functionality (which actually is entirely what you would expect if you take a literal interpretation of Genesis with the curse on man and creation as a result of sin).

  30. 30
    bornagain77 says:

    the fruit flies are still fruit flies! Does this not speak more to the epigenetic information in fruit fly genomes, rearranging genetic information, more than it does to the different ORFan genes between chimps and humans.,,,

    How life changes itself: The Read–Write (RW) genome – James A. Shapiro – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs).
    http://www.sciencedirect.com/s.....4513000869

    Response to John Wise – October 2010
    Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

    And why does such a obvious, and crippling, objection as to the non-plasiticity of fruit fly morphology, despite radical genome rearrangement, have to be pointed out to you in the first place?.

    Evolve, here is your response in a nutshell:

    https://www.youtube.com/watch?v=rSjK2Oqrgic

  31. 31
    sebastians says:

    Seriously, what mental disorder is BA77 suffering from? Same as Byers?

  32. 32
    Piotr says:

    the fruit flies are still fruit flies!

    Still? There was a time when their distant ancestors were not fruit flies. There was even a time when the ancestor of the fruit flies was also our ancestor.

  33. 33
    Jehu says:

    Evolve,

    We have been hearing the same hand waving, “Orphans are not a problem for evolution,” for years around here. I remember Nick Matzke telling everybody there was no problem because the parents would be found. However, the NYT article you site admits it is a huge problem.

    “They looked like perfectly normal genes, except they were only found in one species,” said Anne-Ruxandra Carvunis, an evolutionary biologist at the University of California, San Diego. “There was no explanation for how a gene could be in one species and not in other ones.”

    In grand materialist tradition, they now admit the problem because they (wrongly) believe they have a solution.

    “It’s almost like Sherlock Holmes,” said Dr. Tautz, citing the detective’s famous dictum: “When you have eliminated the impossible, whatever remains, however improbable, must be the truth.”

    Yes, it actually says that. The so-called solution amounts to little more than an assumption of evolution, regardless of the mathmatical improbabilities, and regradless of how it flies in the face of every argument about gene evolution that materialists have let fly for the last 30 years.

    “It seems kind of nutty to people when they first hear of it.”

    It says that too, and here is the nuttiness:

    The scientists found 142 de novo genes that were present in some populations of flies but not in others, meaning that they must have evolved recently: They’ve had only enough time to spread across part of the species.

    Circular reason much? Undermine every BS argument about gradualism climbing Mt. Improbable much? Well hey, why not? It gets better:

    Far from being a fluke, these studies suggest that de novo genes are abundant. In fact, scientists are now wondering why these fast-evolving genes aren’t swelling the genomes of animals and plants.

    Ya, with all this super-fast evolution going on I am worried the mold in my refrigerator will evolve legs and run away with my left overs. Don’t worry though, a solution is offered

    Dr. Schlötterer and his colleagues found the answer in their study: Along each lineage, many de novo genes are also lost. In some cases, a mutation disables a new gene, so that cells can no longer read them. In other cases, a mutation deletes the entire stretch of DNA where the new gene sits.

    Wow! Fancy that! The entire stretch of DNA deleted. And it must of been there at one time because (circular reasoning alert) evolution is true! /sarc

    Sorry Evolve, you are going to have to do much much better than that.

  34. 34
    bornagain77 says:

    sebastians asks

    “Seriously, what mental disorder is BA77 suffering from?”

    Apparently not the same mental disorder that allows people to believe that their brain, which is more complex than all the computers and routers and Internet connections on Earth,,,

    “of all the things I’ve lost, I think I miss my mind the most” – Anonymous

    Human brain has more switches than all computers on Earth – November 2010
    Excerpt: They found that the brain’s complexity is beyond anything they’d imagined, almost to the point of being beyond belief, says Stephen Smith, a professor of molecular and cellular physiology and senior author of the paper describing the study: …One synapse, by itself, is more like a microprocessor–with both memory-storage and information-processing elements–than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth.
    http://news.cnet.com/8301-2708.....2-247.html

    ,,,was,,,

    “simply down to a few duplications of a gene”

    If sanity includes believing that a accumulation of random genetic accidents can build such unfathomed complexity, then I will gladly stick with the mentally disabled!

    As an aside to the accusation of me having ‘lost my mind’, why is it that I’m not the one denying that I have a ‘mind’ in the first place to lose?:

    The Confidence of Jerry Coyne – January 6, 2014
    then halfway through this peroration, we have as an aside the confession that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant: But more on that below.)
    http://douthat.blogs.nytimes.c.....&_r=0

    Both Feet Firmly Planted in Midair
    Excerpt: “Suppose we think of a man made of water in an infinitely extended and bottomless ocean of water.
    Desiring to get out of water, he makes a ladder of water.
    He sets this ladder upon the water and against the water and then attempts to climb out of the water.
    So hopeless and senseless a picture must be drawn of the natural man’s methodology based as it is upon the assumption that time or chance is ultimate. On his assumption his own rationality is a product of chance. On his assumption even the laws of logic which he employs are products of chance. The rationality and purpose that he may be searching for are still bound to be products of chance.
    —Cornelius Van Til, The Defense of the Faith (P&R, 1972), p. 102.
    http://thegospelcoalition.org/.....in-midair/

    The Atheist’s Guide to Intellectual Suicide – James N. Anderson PhD. – video
    https://vimeo.com/75897668

  35. 35
    Mung says:

    CH:

    True, evolutionists have remained steadfast in their certainty, but that says more about evolutionists than about the empirical science.

    heh

  36. 36
    Mung says:

    By raising this example of “very distantly related” species, Velasco trivializes the ORFan problem and misrepresents the science.

    True. Take fruit flies, for example.

  37. 37
    Jehu says:

    Consider this quote again from Anne-Ruxandra Carvunis, an evolutionary biologist at the University of California, San Diego regarding ORFans.

    “There was no explanation for how a gene could be in one species and not in other ones.”

    Yet Velasco is claiming it is not a problem? Liar.
    Oh and the so-called explanation?

    they must have evolved recently

    in other words, “evolutiondidit”

  38. 38
    sebastians says:

    It’s quite obvious that you are suffering from some kind of disorder. Like, what’s up with the “,,,”? Did you have some kind of seizure while writing or what?

    I’m amazed how everyone can put up with your endless off-topic copypasting, whilst conveniently ignoring the arguments put forward (you do this all the time). Just goes to show how religion, rather than truth, drives you.

  39. 39
    bornagain77 says:

    sebastians, although you accuse me of mental illness again (i.e ad hominem again), in terms of mental illness, atheists are shown to be more inclined towards mental illness than theists:

    The Heretic -Who is Thomas Nagel and why are so many of his fellow academics condemning him? Andrew Ferguson – March 25, 2013 Excerpt: A materialist who lived his life according to his professed convictions—understanding himself to have no moral agency at all, seeing his friends and enemies and family as genetically determined robots—wouldn’t just be a materialist: He’d be a psychopath. http://www.weeklystandard.com/.....tml?page=3

    To back the preceding observation up, There are actually studies that show that people who do not believe in a soul are a little bit more anti-social (psychopathic) than normal people who do believe in a soul:

    Anthony Jack, Why Don’t Psychopaths Believe in Dualism? – video
    http://www.youtube.com/watch?l.....zOk#t=862s

    as well, atheists are far more inclined to suicide,

    Of snakebites and suicide – February 18, 2014
    RESULTS: Religiously unaffiliated subjects had significantly more lifetime suicide attempts and more first-degree relatives who committed suicide than subjects who endorsed a religious affiliation.
    http://www.uncommondescent.com.....d-suicide/

    and more inclined to early death

    Atheism and health
    A meta-analysis of all studies, both published and unpublished, relating to religious involvement and longevity was carried out in 2000. Forty-two studies were included, involving some 126,000 subjects. Active religious involvement increased the chance of living longer by some 29%, and participation in public religious practices, such as church attendance, increased the chance of living longer by 43%.[4][5]
    http://www.conservapedia.com/Atheism_and_health

    and atheists are more inclined towards depression than Theists

    Are Religious People Happier Than Atheists? – 2000
    Excerpt: there does indeed appear to be a link between religion and happiness. Several studies have been done, but to give an example, one study found that the more frequently people attended religious events, the happier they were; 47% of people who attended several types a week reported that they were ‘very happy’, as opposed to 28% who attended less than monthly.
    In practical terms, religious people have the upper hand on atheists in several other areas. They drink and smoke less, are less likely to abuse drugs, and they stay married longer. After a stressful event like bereavement, unemployment, or illness, those who worship don’t take it as hard and recover faster. All of the above are likely to be beneficial to a person’s happiness. Additionally, religious people, as a result of their beliefs, have a greater sense of meaning, purpose and hope in their lives.
    http://generallythinking.com/a.....-atheists/

    As well, Christians respond better to psychiatric treatment than atheists do

    Christians respond better to psychiatric treatment than atheists: – July 21, 2013
    Excerpt: “Our work suggests that people with a moderate to high level of belief in a higher power do significantly better in short-term psychiatric treatment than those without, regardless of their religious affiliation. Belief was associated with not only improved psychological wellbeing, but decreases in depression and intention to self-harm,” explained Rosmarin.
    The study looked at 159 patients, recruited over a one-year period. Each participant was asked to gauge their belief in God as well as their expectations for treatment outcome and emotion regulation, each on a five-point scale. Levels of depression, well being, and self-harm were assessed at the beginning and end of their treatment program.
    http://www.uncommondescent.com.....are-crazy/

    Study Finds Religion Helps Us Gain Self-Control – January 2012
    Excerpt: Thinking about religion gives people more self-control on later, unrelated tasks; according to results from a series of recent Queen’s University study.
    “After unscrambling sentences containing religiously oriented words, participants in our studies exercised significantly more self-control,” says psychology graduate student and lead researcher on the study, Kevin Rounding.
    Study participants were given a sentence containing five words to unscramble. Some contained religious themes and others did not. After unscrambling the sentences, participants were asked to complete a number of tasks that required self-control – enduring discomfort, delaying gratification, exerting patience, and refraining from impulsive responses.
    Participants who had unscrambled the sentences containing religious themes had more self-control in completing their tasks.
    http://www.medicalnewstoday.co.....240724.php

    In fact, although atheists pride themselves on their rationality, (even though rationality cannot be grounded in an atheistic worldview), atheists are found to be more irrational than Christians:

    Look Who’s Irrational Now
    Excerpt: “What Americans Really Believe,” a comprehensive new study released by Baylor University yesterday, shows that traditional Christian religion greatly decreases belief in everything from the efficacy of palm readers to the usefulness of astrology. It also shows that the irreligious and the members of more liberal Protestant denominations, far from being resistant to superstition, tend to be much more likely to believe in the paranormal and in pseudoscience than evangelical Christians.
    http://online.wsj.com/article/.....54585.html

  40. 40
    bornagain77 says:

    As well sebastians, you claim to be driven by ‘truth’ not by religion, (I disagree), but anyways, exactly how is truth to be grounded in an atheistic worldview where everything is in flux?

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind.”
    Darwin to Graham, William – 3 July 1881

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter”.
    J. B. S. Haldane [“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.

    The following interview is sadly comical as a evolutionary psychologist realizes that neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth, not even for the truth that he is purporting to give in the interview, (which begs the question of how was he able to come to that particular truthful realization, in the first place, if neo-Darwinian evolution were actually true?);

    Evolutionary guru: Don’t believe everything you think – October 2011
    Interviewer: You could be deceiving yourself about that.(?)
    Evolutionary Psychologist: Absolutely.
    http://www.newscientist.com/ar.....think.html

    Plaantinga has formalized this argument,,,

    Evolutionary Argument Against Naturalism by Alvin Plantinga – video
    https://www.youtube.com/playlist?list=PL80CAECC36901BCEE

    Thus, If you really were driven by truth and ‘rationality’, and not by religion, then you would not be an atheist sebastians!

    Verses and Music:

    John 10:10
    The thief comes only to steal and kill and destroy; I have come that they may have life, and have it to the full.

    John 14:6
    Jesus answered, “I am the way and the truth and the life. No one comes to the Father except through me.

    Shatter Me Featuring Lzzy Hale – Lindsey Stirling
    https://www.youtube.com/watch?v=49tpIMDy9BE

  41. 41
    Piotr says:

    BA77,

    I’m impressed. Your debating tactics are so unique that we need a new term for the phenomenon — one that will commemorate you for posterity. I understand that the word “gallop” qualifies as politically incorrect on this blog (and you have out-gished Duane Gish anyway), so what about the Bornagain Broadside?

  42. 42
    bornagain77 says:

    Piotr, instead of labeling me, why don’t present some evidence to counter the negative consequences, and logical incoherency, of being an atheist that I have outlined?,,, And since, in reality, you can’t ever rationally defend such an irrational position in the first place, why do personally choose defend the atheistic position as if it were tenable? Do you think God will ‘go away’ if you lie to yourself and others long enough? I have news for you, God is not ever going to ‘go away’, but you, through such foolishness as to oppose almighty God, may be denied to the ability to be in God’s presence forever.

    “Einstein’s equation predicts that, as the astronaut reaches the singularity (of the black-hole), the tidal forces grow infinitely strong, and their chaotic oscillations become infinitely rapid. The astronaut dies and the atoms which his body is made become infinitely and chaotically distorted and mixed-and then, at the moment when everything becomes infinite (the tidal strengths, the oscillation frequencies, the distortions, and the mixing), spacetime ceases to exist.”
    Kip S. Thorne – “Black Holes and Time Warps: Einstein’s Outrageous Legacy” pg. 476

    i.e. Black Holes are found to be ‘timeless’ singularities of destruction and disorder rather than singularities of creation and order such as the extreme order we see at the creation event of the Big Bang. Needless to say, the implications of this ‘eternity of destruction’ should be fairly disturbing for those of us who are of the ‘spiritually minded’ persuasion!

    “There are only two kinds of people in the end: those who say to God, “Thy will be done,” and those to whom God says, in the end, “Thy will be done.” All that are in Hell, choose it. Without that self-choice there could be no Hell.”
    – C.S. Lewis, The Great Divorce

    Verse and Music:

    John 8:23-24
    But he continued, “You are from below; I am from above. You are of this world; I am not of this world. I told you that you would die in your sins; if you do not believe that I am he, you will indeed die in your sins.

    Mystery Of Grace-4HIM – music
    https://www.youtube.com/watch?v=qcNbzvFylmc

  43. 43
    Joe says:

    Yeah, Piotr’s debating tactics include bald declarations. For example:

    There was a time when their distant ancestors were not fruit flies.

    No evidence provided. And-

    There was even a time when the ancestor of the fruit flies was also our ancestor.

    And still no evidence. Amazing debating tactics, indeed.

  44. 44
    Jehu says:

    When the materialist reductionists themselves post articles that assert,

    “There was no explanation for how a gene could be in one species and not in other ones,”

    you know they have lost the debate.

    Even these scientists that posit a Darwinian explanation for ORFans call their explanations “improbable” and “kind of nutty.” Don’t be surprised that the posters here have resorted to ad hominem attacks.

    #isleepwellatnight

  45. 45
    Querius says:

    Piotr,

    Bornagain77’s posts, while sometimes long, actually contain some interesting material. But you need to be a little patient to read it, rather than just criticizing him.

    -Q

  46. 46
    Piotr says:

    Jehu:

    “There was no explanation…”

    Note the past tense. There was no explanation at the time when orphan genes were discovered.

  47. 47
    Piotr says:

    Querius,

    BA77’s posts are a rambling hodgepodge of miscellaneous quotations and links, kept together by duct tape and chewing gum (rather than ordinary logic), and typically discharged in one massive salvo; and since BA77 seems unable to fix his attention on the topic being discussed, those logorrhaeic discharges are of null interest to me. I herewith officially name his posting style the Bornagain Broadside ®, and leave it at it.

  48. 48
    bornagain77 says:

    king piotr proclaims:

    “I herewith officially name his posting style the Bornagain Broadside ®, and leave it at it.”

    which is just as well since, from as far as I can tell, he just basically ‘officially proclaims’ Darwinian evolution to be true, ignores all evidence to the contrary, and ‘leaves it at that’ as if his evidence free proclamations on the truth of a subject matter one iota in the grand scheme of things.

  49. 49
    sebastians says:

    Ignoring evidence? Ohhh.. the irony

  50. 50
    bornagain77 says:

    To elucidate why ORFan genes present such a conundrum for Darwinists, (and with the reward of a ‘rambling post’ irritating king piotr being too tempting to pass up), it is important to note that Darwinists have ZERO empirical evidence of a single gene and/or protein arising out of four decades of laboratory evolution experiments,,,

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.
    http://behe.uncommondescent.co.....evolution/

    As a point of interest out of the four decades of work was Lenski’s e-coli:

    Lenski’s Long-Term Evolution Experiment: 25 Years and Counting – Michael Behe – November 21, 2013
    Excerpt: Twenty-five years later the culture — a cumulative total of trillions of cells — has been going for an astounding 58,000 generations and counting. As the article points out, that’s equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski’s project the best, most detailed source of information on evolutionary processes available anywhere,,,
    ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, –
    http://www.evolutionnews.org/2.....79401.html

    Not a single gene or protein arose out of the equivalent of a million years of supposed human evolution! Moreover, one of the first ‘loss of function’ mutations that Lenski’s e-coli initiated was to ‘toss the flagellum overboard’ to conserve energy since the e-coli no longer had to move long distances to acquire food in Lenski’s ‘cozy’ lab setting!

    Moreover, when the ‘top five’ mutations from Lenski’s experiment were combined, they resulted in ‘negative epistasis’ instead of any increased functional complexity:

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    Even if we ditch the lab setting, and use the ‘whole world as our lab’, the evidence for Darwinian evolution still fails to materialize:

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    Excerpt: The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    Behe’s ‘Edge of Evolution’ is stated here:

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    – Michael Behe – The Edge of Evolution – page 146

    Behe’s work agrees with Axe’s work:

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://www.biologicinstitute.o.....nt-collide

    “Any transition of form is pure fantasy. There is no demonstration of it.”
    Doug Axe – co-author of Science & Human Origins – video
    http://www.youtube.com/watch?v=XxMmLakH2LQ

  51. 51
    bornagain77 says:

    And please bear in mind, that was just the probability of a existing protein transitioning to carry out a new function. The probability of a new ORFan protein arising to perform a new function is even more improbable than that:

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    Stephen Meyer Critiques Richard Dawkins’s “Mount Improbable” – video
    https://www.youtube.com/watch?v=7rgainpMXa8

    And that is just trying to get a minimum single function for a protein. In reality both genes and proteins are shown to be multifunctional in their duties which only exasperates the problem exponentially for Darwinists:

    Human genes are multitaskers:
    Abstract: Genome-wide surveys of gene expression in 15 different tissues and cell lines have revealed that up to 94% of human genes generate more than one (protein) product.
    http://www.nature.com/news/200......1199.html

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013
    Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”
    http://darwins-god.blogspot.co.....rs-of.html
    http://www.fasebj.org/content/23/7/2022.full

    Researchers Uncover New Kink In Gene Control: – Oct. 2009
    Excerpt: a collaborative effort,, has uncovered more than 300 proteins that appear to control genes, a newly discovered function for all of these proteins previously known to play other roles in cells.,,,The team suspects that many more proteins encoded by the human genome might also be moonlighting to control genes,,,
    http://www.sciencedaily.com/re.....125536.htm

    “Is it really credible that random processes could have constructed a reality, the smallest element of which—a functional protein or gene— is complex beyond our own creative capacities, a reality which is the very antithesis of chance, which excels in every sense anything produced by the intelligence of man?”
    ~ Michael Denton

    And that is not even touching on the biophotonic communication and quantum computation capacity inherent in genes and proteins.

    Thus, as Jehu pointed out in post 33, Darwinists never actually demonstrate that a protein/gene can arise by Darwinian processes, Darwinists just assume that every new gene/protein that is found must have arisen by Darwinian processes (because the alternative is unthinkable for them). But as far as the real evidence goes, Darwinists are shown to be living in a pipe dream. i.e. It is delusional to think Darwinian processes will ever be up to the task of explaining where these exquisite genes and proteins came from.,,,

    Basically, the following is the reality of the Darwinian argument in a nutshell:

    Darwinism Not Proved Impossible Therefore Its True – Plantinga – video
    http://www.metacafe.com/watch/10285716/

    Dumb and Dumber ‘There’s a Chance’ – video
    https://www.youtube.com/watch?v=KX5jNnDMfxA

    Music and Verse:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God.
    The same was in the beginning with God.
    All things were made by Him, and without Him was not anything made that was made.
    In Him was life, and that life was the Light of men.

    Evanescence – The Other Side (Lyric Video)
    http://www.vevo.com/watch/evan.....tantsearch

  52. 52
    bornagain77 says:

    And please bear in mind, that was just the probability of a existing protein transitioning to carry out a new function. The probability of a new ORFan protein arising to perform a new function is even more improbable than that:

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”
    http://bio-complexity.org/ojs/.....O-C.2010.1

    Stephen Meyer Critiques Richard Dawkins’s “Mount Improbable” – video
    https://www.youtube.com/watch?v=7rgainpMXa8

    And that is just trying to get a minimum single function for a protein. In reality both genes and proteins are shown to be multifunctional in their duties which only exasperates the problem exponentially for Darwinists:

    Human genes are multitaskers:
    Abstract: Genome-wide surveys of gene expression in 15 different tissues and cell lines have revealed that up to 94% of human genes generate more than one (protein) product.
    http://www.nature.com/news/200......1199.html

    The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video
    http://www.metacafe.com/watch/8593991/

    Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013
    Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”
    http://darwins-god.blogspot.co.....rs-of.html

    Researchers Uncover New Kink In Gene Control: – Oct. 2009
    Excerpt: a collaborative effort,, has uncovered more than 300 proteins that appear to control genes, a newly discovered function for all of these proteins previously known to play other roles in cells.,,,The team suspects that many more proteins encoded by the human genome might also be moonlighting to control genes,,,
    http://www.sciencedaily.com/re.....125536.htm

    “Is it really credible that random processes could have constructed a reality, the smallest element of which—a functional protein or gene— is complex beyond our own creative capacities, a reality which is the very antithesis of chance, which excels in every sense anything produced by the intelligence of man?”
    ~ Michael Denton

    And that is not even touching on the biophotonic communication and quantum computation capacity inherent in genes and proteins.

    Thus, as Jehu pointed out in post 33, Darwinists never actually demonstrate that a protein/gene can arise by Darwinian processes, Darwinists just assume that every new gene/protein that is found must have arisen by Darwinian processes (because the alternative is unthinkable for them). But as far as the real evidence goes, Darwinists are shown to be living in a pipe dream. i.e. It is delusional to think Darwinian processes will ever be up to the task of explaining where these exquisite genes and proteins came from.,,,

    Basically, the following is the reality of the Darwinian argument in a nutshell:

    Darwinism Not Proved Impossible Therefore Its True – Plantinga – video
    http://www.metacafe.com/watch/10285716/

    Dumb and Dumber ‘There’s a Chance’ – video
    https://www.youtube.com/watch?v=KX5jNnDMfxA

    Music and Verse:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God.
    The same was in the beginning with God.
    All things were made by Him, and without Him was not anything made that was made.
    In Him was life, and that life was the Light of men.

    Evanescence – The Other Side (Lyric Video)
    http://www.vevo.com/watch/evan.....tantsearch

  53. 53
    Querius says:

    bornagain77,

    Since the LD 50/30 of bacteria is much higher than that of humans, it would seem that with a proportionally adjusted level of environmental ionizing radiation, one could simulate millions of years of human evolution using bacteria (E.coli comes to mind). This might seem to make an ideal laboratory for testing evolutionary drift, and other theories (instead of waiting 20 years and 44,000 generations).

    Interestingly, the E.coli bacteria subjected to an extreme test “evolved” radioresistance in just 20 generations through an unknown “repair” mechanism.

    http://www.news.wisc.edu/22641

    (One wonders whether the resistance evolved or was there all along in small numbers of the bacteria.)

    Would you know of any published experiments that have tried to simulate evolution through moderately higher doses followed by genetic sequencing?

    -Q

  54. 54
    bornagain77 says:

    Querius, in regards to the fascinating paper you cited:

    In the lab, scientists coax E. coli to resist radiation damage – March 17, 2014
    Excerpt: ,,, John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. “We blasted the cultures until 99 percent of the bacteria were dead. Then we’d grow up the survivors and blast them again. We did that twenty times,” explains Cox.
    The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human.
    http://www.news.wisc.edu/22641

    Here is Deinococcus radiodurans

    Extreme Genome Repair – 2009
    Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,,
    http://www.ncbi.nlm.nih.gov/pm.....MC3319128/

    The World’s Toughest Bacterium – 2002
    Excerpt: “When subjected to high levels of radiation, the Deinococcus genome is reduced to fragments,” (…) “RecA proteins may play role in finding overlapping fragments and splicing them together.”
    http://www.genomenewsnetwork.o.....ccus.shtml

    Of related interest, RecA is one of the primary proteins that Dr. Durston studied:

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.
    http://powertochange.com/wp-co.....Myers_.pdf

    How can RecA proteins reconstruct fragmented DNA? i.e. If the Genetic/Molecular reductionism model of neo-Darwinism were actually true, how can RecA possibly ‘know’ the correct sequence? Needless to say, this is NOT what reductive materialism, which undergirds neo-Darwinian thought, expects. ,,, This all plays into epigenetic information and its falsification of neo-Darwinism:

    “Live memory” of the cell, the other hereditary memory of living systems – 2005
    Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.
    http://www.ncbi.nlm.nih.gov/pubmed/15888340

    “The genome is an ‘organ of the cell’, not its dictator”
    – Denis Nobel – President of the International Union of Physiological Sciences

    Modern Synthesis Of Neo-Darwinism Is False – Denis Nobel – video
    http://www.metacafe.com/w/10395212
    ,, In the preceding video, Dr Nobel states that around 1900 there was the integration of Mendelian (discrete) inheritance with evolutionary theory, and about the same time Weismann established what was called the Weismann barrier, which is the idea that germ cells and their genetic materials are not in anyway influenced by the organism itself or by the environment. And then about 40 years later, circa 1940, a variety of people, Julian Huxley, R.A. Fisher, J.B.S. Haldane, and Sewell Wright, put things together to call it ‘The Modern Synthesis’. So what exactly is the ‘The Modern Synthesis’? It is sometimes called neo-Darwinism, and it was popularized in the book by Richard Dawkins, ‘The Selfish Gene’ in 1976. It’s main assumptions are, first of all, is that it is a gene centered view of natural selection. The process of evolution can therefore be characterized entirely by what is happening to the genome. It would be a process in which there would be accumulation of random mutations, followed by selection. (Now an important point to make here is that if that process is genuinely random, then there is nothing that physiology, or physiologists, can say about that process. That is a very important point.) The second aspect of neo-Darwinism was the impossibility of acquired characteristics (mis-called “Larmarckism”). And there is a very important distinction in Dawkins’ book ‘The Selfish Gene’ between the replicator, that is the genes, and the vehicle that carries the replicator, that is the organism or phenotype. And of course that idea was not only buttressed and supported by the Weissman barrier idea, but later on by the ‘Central Dogma’ of molecular biology. Then Dr. Nobel pauses to emphasize his point and states “All these rules have been broken!”.
    Professor Denis Noble is President of the International Union of Physiological Sciences.

    Of related interest, bacteria are exquisitely designed to ‘detoxify’ the earth of dangerous levels of heavy metal:

    Unexpected allies help bacteria clean uranium from groundwater – March 8, 2013
    Excerpt: Since 2009, SLAC scientist John Bargar has led a team using synchrotron-based X-ray techniques to study bacteria that help clean uranium from groundwater in a process called bioremediation. Their initial goal was to discover how the bacteria do it and determine the best way to help, but during the course of their research the team made an even more important discovery: “Nature” thinks bigger than that.
    The researchers discovered that bacteria don’t necessarily go straight for the uranium, as was often thought to be the case. The bacteria make their own, even tinier allies – nanoparticles of a common mineral called iron sulfide. Then, working together, the bacteria and the iron sulfide grab molecules of a highly soluble form of uranium known as U(VI), or hexavalent uranium, and transform them into U(IV), a less-soluble form that’s much less likely to spread through the water table. According to Barger, this newly discovered partnership may be the basis of a global geochemical process that forms deposits of uranium ore.,,
    Discovering that bacteria work together with minerals to transform uranium was a surprise, said Bargar.,,,
    But as a scientist, he appreciates the glimpse he’s been given into “Nature’s” abilities to multitask. “Originally we wanted to see what happened to uranium and how it could help bioremediation technology to be successful,” he said. “But scientifically the results are much deeper than that.” And since their original hypothesis focused on bacteria alone, it’s a little humbling, too.
    http://phys.org/news/2013-03-u.....water.html

    Bacterial Heavy Metal Detoxification and Resistance Systems:
    Excerpt: Bacterial plasmids contain genetic determinants for resistance systems for Hg2+ (and organomercurials), Cd2+, AsO2, AsO43-, CrO4 2-, TeO3 2-, Cu2+, Ag+, Co2+, Pb2+, and other metals of environmental concern.,, Recombinant DNA analysis has been applied to mercury, cadmium, zinc, cobalt, arsenic, chromate, tellurium and copper resistance systems.
    http://www.int-res.com/article.....26p203.pdf

    Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides.
    – Paul G. Falkowski – Professor Geological Sciences – Rutgers

  55. 55
    bornagain77 says:

    As to testing ‘evolutionary drift’, this is what I have so far:

    The consequences of genetic drift for bacterial genome complexity – Howard Ochman – 2009
    Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.
    http://genome.cshlp.org/conten.....091785.109

    To the disbelieving shock of many evolutionary scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence. According to prevailing evolutionary dogma, there ‘HAS’ to be ‘significant genetic drift’ to the DNA of modern bacteria from 250 million years ago.

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    That certainly is not what neo-Darwinists expected!

    Of related interest:

    Bacteria ‘invest’ wisely to survive uncertain times, scientists report – December 1, 2009
    Excerpt: “When conditions are highly variable, some individual bacteria are equipped to thrive in the highs or lows, while others tank,” he said. “It’s like the stock market. If you invest all your money in just one stock, and conditions change to lessen or completely eliminate its value, you won’t survive financially. Similarly, in the case of these bacteria, if all the cells were adapted to only a small, rigid set of environmental factors, the population would be wiped out if conditions unexpectedly changed.
    “There seems to be an optimization going on in these organisms,” he added.,,,
    Essentially, variability of bacterial cells appears to match the variability in the environment, thereby increasing the chances of bacterial survival, he said.
    http://www.sciencedaily.com/re.....112102.htm

    Verse and a little ‘Heavy Metal’ music:

    Isaiah 6:3
    And they were calling to one another: “Holy, holy, holy is the LORD Almighty; the whole earth is full of his glory.”

    Alter Bridge – Rise Today
    http://www.youtube.com/watch?v=ZYG3BPvFOgs

  56. 56
    Jehu says:

    Piotr,

    There was no explanation at the time when orphan genes were discovered.

    I remember when these things were first discovered and the official party line was that the parents were yet to be discovered and that there were so-called “deep” homolgies that would explain their existence. We IDiots correctly called BS and pointed out that orphans were being discovered faster than parents, and of course “deep” homolgies can’t explain absence in supposedly closely related species.

    The talking points now are that orphans evolved quickly and entire genes were deleted from related species. Even the advocates of these “explanations” admit they are “improbable” and “kind of nutty.”

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