Monday, November 23, 2015

The Dark Proteome and Dark Evolution

Evolution Did It

A new PNAS paper published last week on the dark proteome has some interesting implications for the theory of evolution. The paper presents a survey of protein sequences, focusing on the many sequences for which the corresponding three dimensional protein structure is not known, and cannot be inferred from any remotely similar sequence. Why is this so-called “dark proteome” so large? The survey finds that the various hypotheses to explain this—that the dark proteins are intrinsically disordered, or their sequences are compositionally biased, or they are transmembrane proteins, all reasons that can confound structure determination—don’t work very well. The paper concludes that “a surprisingly large fraction of dark proteins … cannot be easily accounted for by these conventional explanations.” And not surprisingly, these dark proteins are less common across the species. So where did all these dark protein sequences come from? Well evolution did it. As the paper explains, “dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches.”

We might call this dark evolution. Once again, the pattern is not one of common descent, but of unique structures.

The results also have implications for the so-called orphans, open reading frames found only in a particular species. Such genetic sequences contradict evolution and when they were first discovered evolutionists predicted they would be found in other species as more genomes were decoded. Instead the number of orphans just continued to grow.

Evolutionists next predicted that orphan sequences were probably not part of a mature protein coding gene and did not form functional proteins. That has not been found to be true, and this new survey provides further evidence for this. As the authors conclude, “Thus, our results suggest that many of the uncharacterized orphan sequences … are indeed real proteins.”

Protein science, however, is clear that blind mutations cannot form real proteins this fast from scratch (or at all for that matter). Hence we must believe that built-in cellular processes must have created these proteins—processes that are complex and require, among other things, proteins.

Real ones.

74 comments:

  1. Here is the pdf

    Unexpected features of the dark proteome - Oct. 2015
    Excerpt: Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions,,,
    We deliberately chose this stringent definition of “darkness,” so we can be confident that the dark proteome has completely unknown structure.,,,
    ,,,in eukaryotes and viruses, about half (44–54%) of the proteome was dark (Fig. 1B). Of the total dark proteome, nearly half (34–52%) comprised dark proteins.
    We repeated the above analysis using an even more stringent definition for darkness—combining PMP (2) and Aquaria (SI Methods) — but this had little effect (Fig. S1).,,,
    Lower Evolutionary Reuse.
    For each protein, we calculated how frequently any part of its sequence has been reused across all other known proteins (SI Methods). Dark proteins were reused much less frequently than nondark proteins (Fig. 4 C and Fig. S8), suggesting that dark proteins may be newly evolved proteins or rare proteins adapted to specific functional niches. This result was partly expected, given how darkness was defined and given the progress of structural genomics in targeting large protein families with unknown structure (8). Low evolutionary reuse also partly explains why dark proteins have few known interactions (Fig. 4 B and Fig. S8), because many interactions are inferred by homology (33).
    http://www.pnas.org/content/early/2015/11/16/1508380112.full.pdf

    as to this comment from you Dr. Hunter:

    "Protein science, however, is clear that blind mutations cannot form real proteins this fast from scratch (or at all for that matter)."

    Here are a few notes in that regards:

    Yockey and a Calculator Versus Evolutionists - Cornelius Hunter PhD - September 25, 2015
    Excerpt: In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein.,,,
    Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”
    Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.
    A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.
    These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.
    Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had.,,,
    http://darwins-god.blogspot.com/2015/09/yockey-and-calculator-versus.html

    ReplyDelete
    Replies
    1. Evolution vs. Functional Protein Domains ("Mount Improbable") - Doug Axe and Stephen Meyer – Video
      https://www.youtube.com/watch?v=7rgainpMXa8

      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/index.php/main/article/view/BIO-C.2010.1

      Quantum criticality in a wide range of important biomolecules
      Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
      That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
      The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
      “what exactly is the advantage that criticality confers?”
      https://medium.com/the-physics-arxiv-blog/the-origin-of-life-and-the-hidden-role-of-quantum-criticality-ca4707924552

      Delete
  2. Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    "Biologist Douglas Axe on Evolution's (non) Ability to Produce New (Protein) Functions " - video
    Quote: It turns out once you get above the number six [changes in amino acids] -- and even at lower numbers actually -- but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.
    https://www.youtube.com/watch?v=8ZiLsXO-dYo

    Doug Axe PhD. on the Rarity and 'non-Evolvability' of Functional Proteins - video (notes in video description)
    https://www.youtube.com/watch?v=8ZiLsXO-dYo

    Can Even One Polymer Become a Protein in 13 billion Years? – Dr. Douglas Axe, Biologic Institute - June 20, 2013 - audio
    http://radiomaria.us/discoveringintelligentdesign/2013/06/20/june-20-2013-can-even-one-polymer-become-a-protein-in-13-billion-years-dr-douglas-axe-biologic-institute/

    Creating Life in the Lab: How New Discoveries in Synthetic Biology Make a Case for the Creator - Fazale Rana
    Excerpt of Review: ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?”
    - per Amazon

    ReplyDelete
  3. BA77, I was going to read your comments and then realized that I had a life.

    Could you summarize your points in two or three sentences rather than trying to overwhelm us with copy pasta? Do you honestly think that anyone reads your nonsense?

    ReplyDelete
    Replies
    1. WS
      You didn't read it but you know it's nonsense?

      Delete
    2. Phillymike

      WS
      You didn't read it but you know it's nonsense?


      BA77 has been C&Ping the same Creationist walls of text garbage for almost a decade. It's like a Pavlov's dog reaction with him. He sees some key word that sets him off and out pops thousands of words of copypasta vomit.

      BA77 didn't earn the nickname "the scroll wheel killer" for nothing.

      Delete
    3. I guess one has to resort to name calling when There are no scientific findings to refute the material.

      Delete
    4. BA77, William Spearshake says, "Do you honestly think that anyone reads your nonsense?" I for one TOTALLY disagree with him. Your links are one of my favorite features. Your sources are so rich. Love it!

      Delete
    5. bFast

      BA77, William Spearshake says, "Do you honestly think that anyone reads your nonsense?" I for one TOTALLY disagree with him. Your links are one of my favorite features. Your sources are so rich. Love it!


      Well then, since you get all your "science" from heavily spun Creationist websites instead of the primary scientific literature don't act so surprised when real scientists laugh at you.

      Delete
    6. I just want to know if BA77 can take part in a real discussion. I thought my request was quite reasonable. He posted three copy pasta comments. All I ask is that he summarize them, in three sentences, in his own words.

      Personally, I don't think that he is capable. Any more than Gordon Mullings (Kairosfocus) is capable of writing an intelligible sentence, or Barry being capable of not being an arrogant, pompous ass.

      Delete
  4. I read it always, the parts pasted anyway. It's too good to miss. BA77's ability to fly documentation immediately to the front line and deliver it exactly on target time and again is truly amazing. It's a gift.

    Often I get as much out of the excerpts as I do from the original.article.

    ReplyDelete
  5. Thanks, Dr. Hunter, for posting this. This is getting little play on Uncommon Descent, though the findings are profound. I think that the issue is that the other side is baffled as to how to defend their theory. If naturalistic evolution is to work, there can be very little change between species. There certainly can't be new advanced function, or multiple new necessary proteins. This "dark proteome" and its sister de-novo genes are going to be the death knell to naturalistic evolution.

    ReplyDelete
    Replies
    1. bFast

      This "dark proteome" and its sister de-novo genes are going to be the death knell to naturalistic evolution.


      LOL! Another case of the "imminent demise of evolution". Creationists have only been predicting that for over 160 straight years now.

      Delete
    2. Cool comment, but you fail to conjure up an explanation for the data -- again.

      Delete
    3. bFast

      Cool comment, but you fail to conjure up an explanation for the data -- again.


      So? There's lots of things that science can't explain yet. That doesn't invalidate the huge amount of things in evolutionary biology it can explain, and it doesn't mean you get to fill in the gaps with whatever supernatural POOFING suits your fancy.

      Maybe some day you Creationists will realize that.

      Delete
  6. bFast
    "Cool comment, but you fail to conjure up an explanation for the data -- again."

    And again and again.
    All I hear from the evolutionists are insults, name calling and demeaning comments for anyone who isn't in agreement with their beliefs. I don't seem to see any refuting the blog's point with any hard science.

    ReplyDelete
    Replies
    1. Phillymike

      I don't seem to see any refuting the blog's point with any hard science.


      What is the blog's point? I all see is one more boring case of "here's some things science doesn't know yet, therefore GAWDDIDIT!".

      That sort of faulty reasoning is less than impressive to anyone with even the smallest bit of scientific knowledge.

      Delete
    2. Ghost
      So sorry to question your sacred doctrine!!! Please forgive my "faulty reasoning " and how I have such a difficult time believing that the chaotic forces of nature created information and intelligence.

      Delete
    3. Phillymike

      So sorry to question your sacred doctrine!!! Please forgive my "faulty reasoning " and how I have such a difficult time believing that the chaotic forces of nature created information and intelligence


      Empirically verified reality isn't affected by your inability to understand it.

      Delete
    4. ghostrider, "Empirically verified reality isn't affected by your inability to understand it"

      Oooh, there you have it. Empirically verified, yup. Where? First life? We haven't an empirical clue. Origin of new gene families? We haven't an empirical clue -- but there's not very many of 'em, that's been empirically verified. Has it? This data says that there's bunches of genes that are species specific. I'm with empirically verified all the way. I just don't find empirically verified in the evolutionary myth.

      Delete
    5. bFast

      Origin of new gene families? We haven't an empirical clue -- but there's not very many of 'em, that's been empirically verified.


      THE ORIGIN OF NEW GENES: GLIMPSES FROM THE YOUNG AND OLD

      You really should try doing at least a teeny bit of research before popping off.

      Delete
    6. Interesting find. Rude presentation (You really should try ...) I'll read the paper, but so far I am seeing, "the details of which are understood to varying degrees." Ie, we know how some new genes are made, but others baffle us.

      My understanding is that de novo is a title given to genes that have no apparent predecessor pattern. In any case, I'll read the paper.

      Delete
    7. bFast

      Interesting find. Rude presentation


      You get the civility you earn bfast. You didn't politely ask for information. You made the rude assertion that there was no evidence "we haven't an empirical clue". As it turns out there's quite a bit of empirical evidence for the origin of gene families. See the work of molecular biologist Joe Thornton for some good recent publications. Such research is easily found by anyone who bothers to look. But like most internet Creationist you didn't bother. You just KNOW you're right because GOD told you so.

      When you start acting like an interested civil adult you'll get civil adult replies.

      Delete
    8. ghostrider, I read your paper. It discusses well known mechanisms of novel genes: exon shuffling, gene duplication, retroposition, mobile elements, lateral (horizontal) gene transfer and gene fusion. These are well known mechanisms that are irrelevant to the study that started this thread.

      It also discusses "de novo" genes. It says, "Although the true de novo origination of new genes from previously non-coding sequences is rare." This study refutes this position.

      Now, quit pompously claiming superiority.

      Delete
    9. bfast

      Now, quit pompously claiming superiority.


      You pompously claimed there was no evidence of gene family evolution at all, not just the ones discussed in the OP. Now you just look silly.

      I didn't claim superiority BTW. I merely showed you're ignorant of the actual evidence available in evolutionary biology. Arguing from ignorance won't make you any points with the scientific community I'm afraid.

      Delete
    10. "You pompously claimed there was no evidence of gene family evolution at all"

      No, I pompously claimed that there was no evidence of the "Origin of new gene families". Every one of the mechanisms listed, except de novo, does not originate a new family, but produces new varieties within existing families.

      Now, quit pompously misquoting me.

      Delete
    11. bFast

      No, I pompously claimed that there was no evidence of the "Origin of new gene families". Every one of the mechanisms listed, except de novo, does not originate a new family, but produces new varieties within existing families.


      LOL! So you lied about reading the paper. That or you just skimmed it and didn't understand the words. What a surprise.

      Delete
  7. Ghostrider, you dare to accuse me of GAWDDIDIT? In the same breath you declare, "here's some things science doesn't know yet". How do you say EVOLUTIONDIDIT?

    The question is, are the goddidits being chipped off faster than new goddidits are growing? The answer, found here, is that goddidit is rapidly increasing in support, not diminishing. Have no fear, evolutiondidit?

    ReplyDelete
  8. PhillyMike: "All I hear from the evolutionists are insults, name calling and demeaning comments for anyone who isn't in agreement with their beliefs."

    Really? Have you not read the comments at Uncommon Descent? If you think that it is the evolutionists who resort to abisive language and name calling, you are delusional. And that isn't an insult, it is a diagnosis.

    It is moderated by someone who frequently calls anyone who disagrees with him a liar, insane, pathetic, a coward, etc. and then you have Virgil Cain (Joe), Mapou (Louis) and KairosFocus (Gordon Mullings). Can you honestly say that they treat the opposition with respect?

    ReplyDelete
    Replies
    1. Thanks WS. Where should I mail the payment for your concerned diagnosis? Lol
      Sorry but I've never visited that site.
      I guess should have been more specific naming the guilty parties.
      It's sad when people resort to name calling and disrespect. I'd much rather see the science backing up their claims.

      Delete
    2. Phillymike

      I'd much rather see the science backing up their claims


      Me too. I'd love to see some positive scientific evidence for the Intelligent Design of life you guys keep claiming. That's positive evidence, not the usual negative fallacy "Feature XYZ is soooo complex I just can't imagine how it could have evolved, therefore ID wins by default".

      Have at it.

      Delete
    3. William Spearshake says, "If you think that it is the evolutionists who resort to abisive language ..."

      When I ask Ghostrider to back up his position with evidence, he finds some, and says, "You really should try doing at least a teeny bit of research before popping off." What ever happened to "Hey, how 'bout this?"

      Spearshake, some UDers are significantly quicker to insult than they should be. But to imply that the IDiots are the one with the problem is the pot calling the kettle black. I know, the kettle calls the pot black too. Please don't participate, and I'll try to do the same.

      Delete
    4. BFast, many ID proponents have been civil, as you always have. I don't deny that. But to claim that evolutionists are bad behaved, as claimed above, is just not supported by the evidence.

      Let's go back to UD. Can you find me some comments by ID opponents that even come close to the abusive comments made by the site's moderator? Keep in mind that Barry frequently calls people liars, insane, asshats, etc. and he bans anyone who uses logic and good argument to make him look foolish.

      Not everyone at UD is like him, but any impartial observer can see that the bulk of the abusive behaviour comes from the ID side.

      Delete
    5. William Spearshake, I think I would agree with you that the most abusive language on UD comes from IDers, and most notably from a couple of moderators.

      That said, the moderators at UD are FAMOUS for kicking out abusive descent. They have a little bit of a point, after all, this is IDs back yard, the outsiders do need to respect where they are at. That said, the ID community does need to deal with a fair hand.

      However

      I tried posting on one site, forget its name, something about after dark, or pub at night or something. It is a forum that is a subset of something bigger. Ho, the abuse I faced! Nothing I have ever seen on UD comes close!

      I have posted on sandwalk, Larry Moran's site. I faced solidly more abuse there than anyone faces on UD. Lastly, there's that skeptic zone site. Its another abusive world.

      Do I wish that the moderators of UD could be honest enough to treat themselves like they demand of others? You bet I do. Do I support your general thesis that the IDers are the abusive ones. Not close.

      Delete
    6. BFast, I never intended to claim that ID opponents were without fault. But you have to take into account the venue. After The Bar Closes does not pretend to be a site for open and fair discussion. I comment there on occasion, but I don't expect to learn anything there.

      The Sandwalk often has comments from ID proponents. Yes, their views are often torn apart, but usually based on the science. But the Sandwalk is different in that it is the personal blog of a U of T professor. He doesn't pretend that it is anything else.

      I am surprised at your view of TSZ. They have a very clear set of rules. One is that you can attack a view or an opinion, but not the person. It does not always work perfectly, but at least they make an attempt. In addition, they do not delete comments (although they will move the abusive ones to a different thread) and they never edit or insert comments into anyone's comments. I think the only one they have banned was Joe. Big surprise.

      UD however, claims that they encourage opposing views, which we know is not true. The tactics used by Barry are reprehensible. As the moderator, he sets the tone for the blog. I have been banned there under several guises. I admit that I deserved a couple of them, but the majority were simply the result of disagreeing with him.

      Delete
  9. GW at 4;09:

    Okay, I'll try. Organism have charateristics that we know from experience are characteristics of designed things only.

    ReplyDelete
    Replies
    1. "Okay, I'll try. Organism have charateristics that we know from experience are characteristics of designed things only."

      And of other organisms. Your logic is so circular that we could use it to derive pi.

      Delete
    2. natschuster

      Organism have charateristics that we know from experience are characteristics of designed things only.


      You've got it bass ackwards. Humans often design things that mimic naturally occurring features found in life forms. That's because the laws of chemistry and physics limit the number of solutions to many design problems.

      Nature was here first, not humans. Just because humans design lawn sprinklers doesn't mean the rain clouds which water your lawn are designed.

      Delete
    3. We can explain the existance of rainclouds wothout coming on to design. Lawn sprinklers have characteristics that we know could not have come about without design. I'm not talkin about teleology, by the way. I'm talking about things like irreducible complexity, highly specified complexity. We know form makinghtings that these charaterisctics only come about when you use intelligence,

      Delete
    4. natschuster

      We know form making htings that these charaterisctics only come about when you use intelligence,


      No, we don't know that. That's merely what the IDiots claim. In fact all the evidence we have says the exact opposite, that natural processes can produce complexity and IC.

      Delete
    5. Has anyone ever made something as complex as a slingshot without designing ? How about a flint knife shaped like leaf with two sharp egdes> Whenever we see there, we assume design ,because it is very hard to make someting like a flint knire or slingshot without design. Has anypne ver seen natrual processe actually created anything as complex as a slingshot?

      Delete
  10. See; it'dlike this.When we make thngsthat have cetain charateristics, we see that it is really really hard to make these things without intelligent design. I;m talking abou things like computers,outboard motors, ars, crossbows, meras, telescopes, slingshots, trebuchets, sliderules, etc.

    ReplyDelete
    Replies
    1. There we have it. Evolutionists can't see design in creation even though as some top evolutionists admit that it's impossible for the blind forces of nature to have brought about the intricacies of life.
      The evolutionist and Nobel Prize winner George Wald demonstrates this inconsistency very clearly: “Spontaneous generation of a living organism is impossible. Yet here we [human beings] are, as a result, I believe, of spontaneous generation.”

      Jason Rosenhouse writes:

      "Personally, I find it incredible that the four fundamental forces of physics, operating from the moment after the Big Bang, could rearrange matter into everything that we see today. That unintelligent causes can ultimately lead to the creation of intelligent creatures, who can then rearrange matter and energy in clever ways, is, I entirely agree, hard to believe. And Darwinian evolution strains credulity as well. I am very sympathetic to the view that natural forces do not construct delicate, biomolecular machines."
      But the obstacle in the way of you ever seeing ID is as he states:
      "However superficially implausible they seem, the only alternative on offer is much harder to believe."
      So no matter how much science shows that XYZ and ABC is impossible by chance your "religion" i.e. Naturalism, will never allow you to see it.

      Delete
  11. This comment has been removed by the author.

    ReplyDelete
  12. I could never get Dr Hunter's point of this blog before and why he always ends with the same statement as I was here for the cool science. But I get it now.

    (From Dr Hunter's earlier blog)
    "Like Ray’s seventeenth century findings about biology, today’s physicists are finding what seems to be a capricious creation. There is no natural explanation as the world seems to consist of a long list of ad hoc, randomly selected designs. One thing they know for sure: no creator would have done this. It must have arisen by chance.

    Religion drives science, and it matters."

    ReplyDelete
    Replies
    1. Phillymike

      "Religion drives science, and it matters".


      Religion's fear of becoming irrelevant drives its baseless and scurrilous attacks on science.

      Delete
    2. ghostrider, you are a religious zealot, but you don't know it. You think that atheism is somehow not religion. But religion is defined by dictionary.com as: "a set of beliefs concerning the cause, nature, and purpose of the universe" Philosophical naturalism provides this. It does so with no better evidence, I would say much poorer evidence, than monotheistic theism has.

      Philosophical naturalism generally begins with the emphatic premise that there is no god, any gaps in this explanation are filled with "we don't know yet", and concludes that there is no god. The fact that the gaps are monstrously huge is beside the point.

      Delete
    3. "It does so with no better evidence, I would say much poorer evidence, than monotheistic theism has."

      Why do you rule out polytheistic theism? Or Buddhism? Why must it be mono-theistic?

      Delete
    4. Um, the evidence my dear man. The scientific consensus holds that our universe was caused by exactly 1 big bang. If the big bang isn't an accident, and there's stunningly strong evidence that it wasn't, then it was caused by a unity of thought. That unity could possibly be a group of gods acting as a unity, or it could be a single god. Occam's razor supports the single god hypothesis. Even if the unified group is correct, because they act as one, they should likely be treated as one.

      The same goes for life on earth. The scientific consensus holds that there was exactly one universal common ancestor -- that one model of life has survived (though it is conceivable that others once existed.) With this singularity the same analysis holds as with the big bang.

      The evidence supports a monotheistic god, not any other jumble thereof.

      Delete
    5. bFast

      ghostrider, you are a religious zealot, but you don't know it.


      You're a religious zealot and an anti-science Luddite and you do know it.

      Philosophical naturalism generally begins with the emphatic premise that there is no god, any gaps in this explanation are filled with "we don't know yet", and concludes that there is no god. The fact that the gaps are monstrously huge is beside the point.

      Twaddle. Evolution like all sciences doesn't say anything about the existence or non-existence of any God or Gods. That's just you projecting your own religious beliefs.

      Delete
  13. Replies
    1. Sorry for laughing but Scurrilous? Really? For reporting the scientific problems of your theory?
      i can understand how your religion won't permit you to stray from it. But it takes more faith than I have to believe it all these marvels we see created themselves.

      Delete
    2. Phillymike

      Sorry for laughing but Scurrilous? Really? For reporting the scientific problems of your theory?


      Unknowns in science aren't problems for a theory. They're unknowns, interesting challenges to be investigated.

      Some religious people are scared spitless by the idea they weren't specially created by their God. That's why they level these baseless attacks on evolutionary science and the honest scientists who study the topic.

      Delete
    3. GW:

      The problems aren't ust unknows, The problems are things like the fact that it uit very unlikely that accidents can make e.g. a protein or something like that. We have teh problem of time contraints. Evolution just takes too long.

      Delete
    4. natschuster

      The problems aren't ust unknows, The problems are things like the fact that it uit very unlikely that accidents can make e.g. a protein or something like that.


      Evolutionary theory doesn't posit a protein formed all by accident so we can ignore that critique.

      We have teh problem of time contraints. Evolution just takes too long.

      You have no idea of the time required and no clue how to even guesstimate it.

      Delete
    5. Evolution starts with accidents, y'konw, the mutations.

      According to this:

      http://www.genetics.org/content/180/3/1501.short

      it would take ~100,000,000 years for an adaptation that requires. That's two long.

      And then there's the real problems of epistasis.

      Delete
    6. According to this:

      http://www.genetics.org/content/180/3/1501.short

      it would take ~100,000,000 years for an adaptation that requires. That's two long.


      That's the time for two prespecified mutations to occur, like saying the time for one prespecified lottery number to come up is very long. Evolution doesn't have to wait for prespecified mutations. It gets as raw material some 150 new ones in every person in every generation and uses selection to amass the ones that work. Someone wins the lottery every week.

      BTW at the end of the paper the authors offer a nice smackdown of Behe's errors and stupidity in Edge of Evolution. Is that what you wanted us to see nat?

      Sorry nat, you're still a clueless boob. Try actually reading the paper for once.

      Delete
    7. I understand that Behe also smackdown the smackdown. He also corrected the math error.

      And I not sure what difference prespecified makes, or what it means. There are lots of mutations, true, but sometimes there is nothing for natural selectiom to work on, until you get two specific (prespecified?)mutations. Sometimes they even have to happen simultaniously, since, it one mutations miht lead to an unstable protein, which requires a compensatory mutation. The way I dee it, you said there is no problem with evolution. I mentioend time constraints. Seems that that is a real issue. It seems to me that if you want to say that evolution is even possible, the burden of proof is on you to show that it can happen in the given time.

      Oh, and don't forget epistasis.

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    8. Here's Behe rebuttal of the rebuttal:

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253464/

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    9. Shevi S

      And I not sure what difference prespecified makes, or what it means.


      That sums up your whole relationship with science. You're as ignorant as a box of rocks, don't understand what anything means but you're sure science has everything wrong.

      Don't worry about it though nat. That big red nose looks good on you.

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    10. Is your name Thornton? He also compared me to box of rocks.

      Anyway,I think that science has a whole lot right. The thing is that I don't think that evolution and science have a whole lot to do with each other.

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    11. Shevi S

      Is your name Thornton? He also compared me to box of rocks.


      No, but given your scientific cluelessness I'm sure lots of people have made that comparison with you.

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    12. Natshuster

      Ghost totally sounds like Thorton. The ghost of Thorton is haunting us :D

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    13. Natshuster

      Ghost totally sounds like Thorton. The ghost of Thorton is haunting us :D

      Delete
  14. Is it too late to wish everyone a happy thanksgiving?

    ReplyDelete
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    1. You can be the first for next year's Thanksgiving. :)
      Hope you had a nice Thanksgiving

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  15. The various methods for the development of "new" genes according to "science" as illustrated using an automotive analogy.

    Exon Shuffling - we took the transmission and frame from this car and bolted it up to the engine and exhaust from another car - this is where new cars can come from.

    Gene Duplication - We made another assembly line just like the first one and then changed some small things. We found that the result was also... cars. So now we have 2 examples of cars coming from cars. How can the creationists stand up to this?

    Retroposition and transposons - Some cars are moved to different states and used at different times in different contexts. We know it used to be a Taurus, but since it's also being driven one state over, we need to find another name, since we need to find a way to describe this new car creation process.

    HGT - One way cars are made is to import them from another country. How can you still have questions? You must not want to understand..

    Gene Fusion/Fission - sometimes a tractor backs up to a trailer. You guessed it, that's how tractor trailers are made.

    Denovo - Some people theorize that if any genes evolved, at some point they might have to come into being whole cloth. This theory accounts for that. We're not sure how but it's obviously pretty rare, so the details are fuzzy. We don't rely on it very much because of all the above explanations.

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    1. John

      The various methods for the development of "new" genes according to "science" as illustrated using an automotive analogy.


      LOL! It wouldn't be the internet if we didn't have some know-nothing Creationist making an argument by lame analogy.

      notice how all the "explanations" for "new" genes all describe basically one event or mutation that happened to something whose precursors are basically structurally the same?

      Gene families show phylogenetic trees with evolutionary branching descent over time too.

      Myosin phylogenetic tree

      Only know-nothing Creationists think they all just POOFED into existence.

      How do you expect these "explanations" to satisfy people once they learn what proteins are and how they move and operate like machinery?

      Frankly John the scientific community doesn't care if willfully ignorant Creationists stay ignorant or not.

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    2. "Gene families show phylogenetic trees with evolutionary branching descent over time too."

      yeah, everyone knows we share a more recent common ancestor with yeast than with round worms. Nice link. Can you articulate even one clear indication of common ancestry from the tree that isn't violated on another branch?

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  16. This comment has been removed by the author.

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  17. notice how all the "explanations" for "new" genes all describe basically one event or mutation that happened to something whose precursors are basically structurally the same?

    Sorry, but that's not a characterization of a mechanism. That's not a process characterized OVER TIME. It doesn't explain anything compelling about proteins. In fact, it's worse than the analogy above.

    How do you expect these "explanations" to satisfy people once they learn what proteins are and how they move and operate like machinery? Good luck.

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    Replies
    1. Here's a great quote I found on the Discovery site.
      "One of the insurmountable problems that Darwinists face is this: There are no analogies to living things that are not intelligently designed."

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  18. Mine was great. Over one month ago, when civilized people celebrate it๐Ÿ˜€

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    Replies
    1. Canuck Thanksgiving! So you are the first for next year. :)

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