Friday, July 24, 2015

John Parrington and modern evolutionary theory

We are continuing our discussion of John Parrington's book The Deeper Genome: Why there is more to the human genome than meets the eye. This is the third of five posts on: Five Things You Should Know if You Want to Participate in the Junk DNA Debate

1. Genetic load
John Parrington and the genetic load argument
2. C-Value paradox
John Parrington and the c-value paradox
3. Modern evolutionary theory (this post)
John Parrington and modern evolutionary theory
4. Pseudogenes and broken genes are junk
John Parrington discusses pseudogenes and broken genes
5. Most of the genome is not conserved
John Parrington discusses genome sequence conservation

3. Modern evolutionary theory

You can't understand the junk DNA debate unless you've read Michael Lynch's book The Origins of Genome Architecture. That means you have to understand modern population genetics and the role of random genetic drift in the evolution of genomes. There's no evidence in Parrington's book that he has read The Origins of Genome Architecture and no evidence that he understands modern evolutionary theory. The only evolution he talks about is natural selection (Chapter 1).

Here's an example where he demonstrates adaptationist thinking and the fact that he hasn't read Lynch's book ...
At first glance, the existence of junk DNA seems to pose another problem for Crick's central dogma. If information flows in a one-way direction from DNA to RNA to protein, then there would appear to be no function for such noncoding DNA. But if 'junk DNA' really is useless, then isn't it incredibly wasteful to carry it around in our genome? After all, the reproduction of the genome that takes place during each cell division uses valuable cellular energy. And there is also the issue of packaging the approximately 3 billion base pairs of the human genome into the tiny cell nucleus. So surely natural selection would favor a situation where both genomic energy requirements and packaging needs are reduced fiftyfold?1
Nobody who understands modern evolutionary theory would ask such a question. They would have read all the published work on the issue and they would know about the limits of natural selection and why species can't necessarily get rid of junk DNA even if it seems harmful.

People like that would also understand the central dogma of molecular biology.


1. He goes on to propose a solution to this adaptationist paradox. Apparently, most of our genome consists of parasites (transposons), an idea he mistakenly attributes to Richard Dawkins' concept of The Selfish Gene. Parrington seems to have forgotten that most of the sequence of active transposons consists of protein-coding genes so it doesn't work very well as an explanation for excess noncoding DNA.

88 comments :

  1. Who is John Parrington?:

    "Dr Parrington was educated at Downing College, Cambridge and received a BA in Natural Sciences (Zoology) in 1986. He obtained his PhD in 1992 from the Imperial Cancer Research Fund and London University, having worked on the molecular mechanisms underlying the interferon signalling pathway in Ian Kerr's laboratory. Dr Parrington moved to the MRC National Institute for Medical Research where he begun studying the molecular events underlying fertilization, a theme which he continued at University College London as an MRC Career Development Fellow. He currently holds an MRC Senior Non-Clinical Fellowship. Dr Parrington was elected to a joint Tutorial Fellowship and College Lectureship at Worcester and Exeter Colleges, respectively, in 2002 and will take up a University Lectureship in Pharmacology in 2006.

    Since joining the Department, Dr Parrington's principal research interest has been in studying how calcium signalling governs key physiological events. He has been centrally involved in demonstrating that the physiological agent of egg activation in mammals appears to be a novel, sperm-derived phospholipase C with distinctive properties - PLCzeta. Recently he has identified an avian orthologue of PLCzeta, which suggests that this signalling protein may play a universal role in vertebrate egg activation. Dr Parrington is also studying how signalling molecules of the phosphoinositide pathway are involved in gametogenesis and development of the early embryo. He is currently involved in identifying and characterising the NAADP receptor and other components of the cADPR and NAADP signalling pathways at the molecular level. A strong theme of Dr Parrington’s research is in using biochemical and molecular strategies within a multidisciplinary approach. Most recently, his group have been developing a way to express recombinant proteins in the sperm using in vivo gene transfer, which could provide a novel way to study testis and sperm function.

    Dr Parrington is General Secretary of the Society for Reproduction and Fertility, upon whose Education Committee he also sits, and a Member of the British Society for Andrology and the US Society for the Study of Reproduction. He also has a diploma with distinction in Science Communication from Birkbeck College, London. He has written articles about science for The Guardian and New Scientist as well as preparing reports about scientific issues for the public for the Wellcome Trust, the Royal Society and the British Council. He presented the Charles Darwin Award Lecture at the BA Festival of Science 2003 at the University of Salford."

    L. Moran: "There's no evidence in Parrington's book....that he understands modern evolutionary theory."

    Imagine that; a man with said credentials doesn't understand modern evolutionary theory! Of course that observation is applied to any worker who is perceived as opposing the status quo.

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    1. I bet there are a lot of carpenters who don't understand botany too. Is there any clue in all that stuff that Parrington has been educated in evolutionary biology or that he ever took as much as one course or read one book or paper on the subject? His work seems to concern only how various systems function in the present, without any concern about how they got to be that way.

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    2. Senior Martinez

      We don't take credentials seriously here. I definitely don't. We, or us, like evidence, preferably experimental, like John H is going to present as will Larry and Dio's new sock puppet.

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    3. You've missed the other point (implied). If a man with Parrington's credentials doesn't, then who can?

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    4. I'm not going to get sucked into this debate. I don't think it would be polite to point that out as to why. I suspected you were Piotr G's sock puppet for a while but then it all became obvious.

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    5. Ray,

      So, which of those credentials make this guy an undeniable expert in evolutionary biology and genome organization? I couldn't find anything like that in this description, so help me out.

      In any event, as Septic Mind said, credentials don't necessarily mean that someone knows what they're talking about. I take proper credentials seriously. For example, if I say something about biochemistry, and Larry tells me that I'm mistaken, I sure would revise and check and recheck my sources and many more sources before challenging Larry on such a thing (more often I should discover that Larry was right, since he works and has written textbooks on biochemistry). I have to assume that I might have missed something, rather than assume that I know everything. But notice that I focused on Larry's expertise to think how much weight I would give to his opinion.

      But a fertilization expert writing about genome evolution and genomic functional organization? Not too impressed. Sorry.

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    6. Septic Mind,

      "I'm not going to get sucked into this debate. I don't think it would be polite to point that out as to why. I suspected you were Piotr G's sock puppet for a while but then it all became obvious."

      And so we discover that Septic is Quest's sock-puppet.

      When will you go back to ellipses Septic?

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    7. Ray,

      If a man with Parrington's credentials doesn't, then who can?

      That's simple enough. A person who knows something about evolutionary biology. Credentials aren't everything, but Parrington's credentials in the subject of evolutionary biology as given in what you posted are nonexistent. There is no mention of evolutionary biology or anything associated with it in all that. Lacking evidence from credentials, we have to go with performance, and that's what Larry is doing.

      Of course I do have formal credentials in the field. I have a PhD specifically in evolutionary biology, I took quite a few courses in the subject, and I've published extensively on it. While none of that proves I know much about it (you'd have to actually read my publications to find out if I do), it would certainly be the way to bet if you had to choose sight unseen.

      I don't know what Larry's formal credentials are here, though his textbook on biochemistry sure has a lot about evolution in it, but more importantly you can see that he knows what he's talking about by reading his posts and following his arguments.

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    8. So, which one of all his credentials make him a qualified authority in evolution? All I see there is some medicine and general genetics.

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  2. JH: All you and Larry are saying is that the modern theory is esoteric.

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    1. A Ray Martinez Dictionary doesn't define the meaning of "esoteric" in the Martinezian language. Does anyone happen to know it?

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    2. Are you the authority to comment on this? Tell us why.

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  3. What "modern theory of evolution"? Why can't anyone link to it?

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  4. A Google search for:

    theory of evolution produces about 340,000,000 results

    evolutionary theory produces about 41,600,000 results

    theory of evolution definition produces about 169,000,000 results

    And of course there are many other places where the ToE/Evolutionary Theory is defined, explained, discussed, debated, etc. such as books, scientific papers, schools, TV shows, scientific conferences, etc.

    YEC joey-virgil, your attention seeking demonstrations of your willful ignorance and arrogance are childish and boring.

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    1. Not one of those results links to an actual theory of evolution. You are an imbecile who wouldn't know a theory if it was handed to you.

      A Google search for bigfoot produces 22,500,000 results. Bigfoot is real

      Loch Ness monster produces 3,540,000 results

      When I ask about gravity I will find Einstein's scientific theory, complete with equations. I will also find Newton's treatise, again complete with equations.

      Darwin had an idea but didn't have anything beyond that.

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    2. YEC joey-virgil, your goal post moving comparison of a scientific theory to the existence, or not, of two mythical creatures is amusing.

      By the way, lots of equations are used and published by scientists who study evolution. If it's equations you want, you should read the proper materials.

      "Darwin had an idea but didn't have anything beyond that.'

      Darwin actually had a lot beyond an idea, and then there's the fact that evolutionary theory (aka the ToE) has been revised in some substantial ways since Darwin, and further revisions/refinements will be done if or as necessary. Focusing on and denigrating Darwin just shows that you aren't even close to being up to date on evolutionary theory.

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    3. The alleged scientific theory of evolution is a myth, moron. And there aren't any equations for the evolution of any bacterial flagellum. None for the evolution of eukaryotes from prokaryotes. Obviously you are just an ignorant ass,

      It is very telling that you cannot link to this alleged theory of evolution. You are a pathetic loser.

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    4. There you go moving the goal posts, as usual. First you demanded equations for the "theory of evolution" but now you're demanding equations for "the evolution of any bacterial flagellum" and "the evolution of eukaryotes from prokaryotes".

      So, absolutely everything, no matter how big or small, that pertains to evolution and/or evolutionary theory has to be expressed or expressible by an equation, eh YEC muslim joey-virgil?

      Hmm, let's see you do the same for your version of ID-creationism. Start with an equation for the creation of allah, and then an equation for allah-did-it, and then equations for absolutely every detail of everything, no matter how big or small, that allah has ever done and will ever do. You can do that, can't you?

      Oh, and I and others have shown you many times how and where to find the ToE/evolutionary theory. That you're too IDiotic and incorrigible to follow the leads you've been given and actually learn something is your problem.

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    5. Asking for an "equation for the bacterial flagellum", in order to insinuate that without such a thing there cannot be a theory of evolution, is like asking for an "equation" for a specific pebble in the himalayas, otherwise there wouldn't be a theory of plate tectonics.

      What idiocy.

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    6. I can link you at least 10 books on the theory of evolution. Start with Douglas Futuyma's "Evolution".
      (This is where Joe G just mindlessly declares this isn't a theory of evolution).

      The bacterial flagellum is explained by gene duplication and exaptation.

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    7. "So Futuyma is the author of the theory of evolution?"

      He simply wrote a book about the theory of evolution. The book contains the theory of evolution.

      The bacterial flagellum is made up of many homologous proteins. They evolved through gene duplication and subsequent mutations. Obviously, the same is true for any necessary chaperones. Obviously, the bacterial flagellum went through several stages of exaptation before it became a flagellum.

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    8. The alleged scientific theory of evolution is a myth, moron. And there aren't any equations for the evolution of any bacterial flagellum.

      Oh my. The stupid is strong in this one. I do hope that he never did run for school board.

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    9. Darwin had an idea but didn't have anything beyond that.

      Never read anything he wrote on the subject, eh?

      By the way, there are enough equations about evolution to boggle your mind under the topic of population genetics. You're about 90 years too late complaining about lack of equations.

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    10. @N.Manning : Joe is one of the most infamous creationist morons on the Web. He posts copiously, but you've seen pretty much all he's got.

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  5. Photosynthesis:

    "So, which of those credentials make this guy an undeniable expert in evolutionary biology and genome organization?"

    I didn't say Parrington was an expert in the genetical theory; rather, I questioned how a man with the credentials he has could not understand the genetical theory as Larry Moran claimed?

    I think Larry needs to revise his criticism.

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    1. Jonathan Wells has a Ph.D. in molecular biology from UC Berkeley. It was pretty easy to show where he didn't understand genomics and junk DNA [The Myth of Junk DNA by Jonathan Wells]. Wells probably had a better understanding of the issues than John Parrington.

      There are people with "credentials" on both sides of the issue. You need to judge whether they are right or wrong based on the quality of their logic and the evidence they present. Feel free to show me where I've gone wrong and Parrington is correct.

      Waiting ....

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    2. I just saw your reply yesterday. And I'm glad you brought up Wells because he helps with the point I'm making.

      Both Wells and Parrington are highly credentialed, yet according to you both men do not understand the modern theory and/or genetics. How can this be? How can two persons with doctorates not UNDERSTAND the modern genetical theory? Surely based on their credentials both have the capacity to understand, so what's the problem or real issue here?

      Concerning Parrington:

      Larry Moran: "Here's an example where he demonstrates adaptationist thinking...." And: "He goes on to propose a solution to this adaptationist paradox. Apparently, most of our genome consists of parasites (transposons), an idea he mistakenly attributes to Richard Dawkins' concept of The Selfish Gene. Parrington seems to have forgotten that...."

      Last I checked Dawkins, like Parrington, is an adaptationist. So your criticism is against the Adapatationist interpretation of evidence, which renders your "don"t understand" criticism invalid. In short: Parrington subscribes to a different explanatory model (adaptationism). So, to say he doesn't understand the modern theory is inaccurate. In response to your criticism Parrington could say that you are the one who doesn't understand and my points here could be reversed on him.




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    3. For John Harshman:

      Larry Moran: "You need to judge whether they are right or wrong based on the quality of their logic...."

      I've been saying the same thing for years; it's all about logic and nothing else.

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    4. Ray,

      This is what Larry said:

      "You need to judge whether they are right or wrong based on the quality of their logic and the evidence they present."

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    5. Rule of thumb for creotards: When they use an ellipsis in a quotation, assume they are doing so to conceal a quote mine. Thanks for confirming this, Ray,

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    6. Ray, logic is only one of the tools unavailable to you.

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    7. Wells either purposefully or via ignorance quote mined and/or misrepresented a number of sources in his 'Icons' book. That means that he either does not understand evolution (for he would have been able to recognized the errors of his misrepresentations) or he does not care. Which do you prefer in your creationists?

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    8. Ray, are you the Ray Martinez who calls himself a "Protestant Evangelical, Old Earth-Young Biosphere Creationist-species immutabilist, Paleyan Designist"?

      And are you the Ray Martinez who said:

      "It is of no surprise that a Darwinist asserts the Bible does not mean what it says. How convenient. Does the desire to validate your theory have anything to do with asserting what anyone can read does not mean what it says? How would anyone expect to obtain accurate information about the Bible from a Darwinist/atheist?", and added this this: "Darwinists and the Bible = Catholic priests and young boys."

      So, Ray, if you're that Ray Martinez I'm curious about why you're an "Old Earth-Young Biosphere Creationist", not a full blown OEC or a full blown YEC. Does the bible say that Earth is old and the "Biosphere" is young? If so, how old, and how young? If the bible doesn't say or if it says something other than what you believe then how did you come to your beliefs? Surely you can support your beliefs with specific and indisputable (accurate) wording from the bible, right? If you can't, it would appear that you're conveniently young-boy-raping the bible in your desire to validate your non-biblical beliefs.

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    9. That's me; and the Bible clearly implies an old Earth. There's an immense gap of time between Genesis 1:1 and Genesis 1:2, which should read "And the earth became a waste and a desolation," and the fact of the Flood (3140 BC) means the present biosphere is young, about 5000 years old.

      IF you think the Bible conveys a young earth then cough up any verse, statement, phrase, or word that says so....waiting.

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    10. Of course Ray will re-interpret any verse or set of verses that says any such thing (just as he has Genesis 1:2), so there's no way to win that one.

      Ray: by "present biosphere", do you mean all life? Does that include marine organisms and bacteria? If so, how did the flood kill the previous batch?

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    11. Given that there are some still living stands of clonal trees known to be 10-80 thousand years old, and regionally unbroken dendrochronological sequences spanning more than 10,000 years, all that nonsense can be dismissed out of hand.

      Earth to Ray: the Bible is neither a scientific treatise nor a live chronicle.

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    12. Ray Martinez

      That's me; and the Bible clearly implies an old Earth. There's an immense gap of time between Genesis 1:1 and Genesis 1:2, which should read "And the earth became a waste and a desolation," and the fact of the Flood (3140 BC) means the present biosphere is young, about 5000 years old.

      Can you explain further how you connected Gen 1:1 , 1:2 with the flood making the present biosphere young? While I can agree that there may be a great time gap between Gen 1:1 and 1:2, I fail to see the connection with those verses, and the flood making it 5000 years young.

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    13. They've have discovered fossils of four legged snake. The bible was right again when it stated that the snake will be going on its belly from then on.

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    14. From when on? Unfortunately, there were no humans or apples around when proto-snakes lost their legs (or for the next 100 million years). There are also a number of Cretaceous snakes with well-developed hind legs but no forelimbs. Does the Bible say that the snake was cursed gradually?

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    15. I'm sure that those tiny legs in that long snake body were enough to make the snake walk upright. It's a biped snake Piotr. The Bible can't be wrong! It's the ultimate scientific book. I don't know why Larry bothered writing a textbook on biochemistry. Students should just use their bibles for everything.

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    16. Besides, as Septic insists, The Bible doesn't imply a young Earth. So when The Bible says that "God" said "from now on," it means that "God" said "within the next million years your descendants will lose their legs." Did you check the time it took for snakes to lose their legs? Well, that's what The Bible meant exactly!

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    17. Hum. It was Ray. I don't remember if Septic is too an old earth creationist. But you get the idea. "From now on" doesn't necessarily mean "from now on." It can mean any period of time, just like "extending a tent" really truly authentically means "making a universe that expands really really really fast."

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    18. Ray Martinez said:

      "That's me; and the Bible clearly implies an old Earth. There's an immense gap of time between Genesis 1:1 and Genesis 1:2, which should read "And the earth became a waste and a desolation," ..."

      Implies? Does the bible specifically say that there was "an immense gap of time between Genesis 1:1 and Genesis 1:2"? How about a specific or even an approximate number of years?

      "...and the fact of the Flood (3140 BC) means the present biosphere is young, about 5000 years old."

      The "fact of the Flood"? What "fact"? And where in the bible does it say that "the Flood" occurred in 3140 BC and that the present biosphere is young, about 5000 years old?

      "IF you think the Bible conveys a young earth then cough up any verse, statement, phrase, or word that says so....waiting."

      I think that the bible is a contradictory, poorly written, variously edited, variously interpreted, mind deadening batch of ridiculous, despicable, impossible fairy tales.

      You, like other thumpers, interpret it to say whatever you want it to say, mean whatever you want it to mean, and imply whatever you want it to imply. The fact that the bible is gibberish makes it easy to do that.

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    19. What was going on in 3140 BC?

      King Narmer had just unified Upper and Lower Egypt and had been ruling the country for ten years. His scribes were busy developing a writing system for Old Egyptian.

      In Ireland, megalithic builders were finishing the vast complex of Newgrange. They would complete it a little later, flood or no flood.

      Advanced neolithic farming flourished from Mesopotamia to Europe. Someone had just invented the wheel. In Anatolia, they were already in the Copper Age.

      Meanwhile in Australia people were doing their regular business: huntin', gath'rin', fishin', and of course playing the didgeridoo.

      Nobody noticed the flood.

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    20. But Piotr, that's why they had to build with megaliths, so everything wouldn't be washed away.

      And of course to stand on top of with their thumbs out, hoping Noah would be by to pick them up.

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    21. I was just thinking how curious that before the blog era I never thought there would be people who really think that Noah's flood happened. It's like expecting that someone would think that there's really a Neverland, or a Hogwarts.

      I was so surprised. It's plainly ridiculous. Yet, now I'm so used to it that I no longer stare in disbelief.

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    22. Tle late Polish writer Stanisław Lem put it like this:

      "Before the advent of the Internet I had no idea there were so many idiots in the world."

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    23. And KevNick chimes in, right on cue. At least he remembered to use the correct name this time....

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    24. Yep. Call the idiot and the idiot will come.

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    25. Piotr Gąsiorowski:

      "King Narmer had just unified Upper and Lower Egypt and had been ruling the country for ten years. His scribes were busy developing a writing system for Old Egyptian."

      Egyptian civilization was founded no earlier than 3000 BC.

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    26. During the Naqada II period (between 3500 and 3200 BC) the Egyptians already built cities with thousands of inhabitants. The hieroglyphic writing system was invented at the end of that period. They obviously had a civilisaton even well before the First Dynasty. And of course they had a much longer prehistory, preserved in the archaeological record.

      People who ignore history, archeology, geology, linguistics, genetics, radiocarbon dating, dendrochronology, etc., but accept fairy tales from the mid-first millennium BC as their source of information about the history of the Universe, of life on Earth, and of the human race, must be either extremely stupid or insane. Possibly both.

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    27. Ray Martinez: he fact of the Flood (3140 BC) means the present biosphere is young, about 5000 years old.

      Well, Ken Ham says it's "a fact" that Noah's Flood happened in 2348 BC, so you two disagree in your interpretations of the Bible by about 800 years.

      You see this guy? He's Enkheftykai, an acquaintance of the Pharoah, seen in a seated tomb statue, ca. 2494-2345 BC, 5th Dynasty. Most likely older than Ken Ham's flood, but younger than yours. You'd say the dating of this statue is a little wrong, Ken Ham would say the dating is wrong by 1,000+ years. Who's right?

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    28. Ray Martinez tries: Egyptian civilization was founded no earlier than 3000 BC.

      The Early Dynastic Period started about 3100 BC, and as Piotr points out, was preceded by Predynastic cultures.

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    29. Regarding Ken Ham's claim that Noah's Flood happened in precisely 2348 BC, and buried all the fossils, here are some real captions of exhibits from the Creation Museum.

      The caption for the Ornitholestes exhibit says: "Layer found in: Upper Jurassic (~2348BC)"

      This is the caption for Triceratops, which says "Layer found in: Upper Cretaceous (~2348 BC)".

      Like a kind of comedy sketch, in all the museum captions, all the geological strata are seriously given the same precise date.

      And it's 800 years off from Ray's date. Oh, who to believe.

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    30. Like Photosynthesis, I have to thank the Internet for making me aware that such people still exist.

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    31. Both Piotr Gasiorowski and Diogenes re-assert their claim that Egyptian civilization existed prior to 3140 BC.

      My date (3140 BC) is based on Biblical chronology and corresponding ANE chronology. IF a catastrophic flood had interrupted Egyptian civilization it surely would have been recorded in their annals. The fact that it wasn't supports my claim of fact that Egyptian civilization came into existence after the Flood. And a person is not obligated to account for everything that a living contradiction says, an evolution accepting YEC.

      Ray (Old Earth, Paleyan IDist-species immutabilist)

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    32. We all agree that Egyptian civilization existed in the 25th century BC, so the Ken Ham date is falsified by the fact that Egyptian annals do not mention a catastrophic flood.

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    33. Gen 1:1 "In the beginning"- clearly refers to the beginning of the universe.

      "God created the heavens and the earth". Just like scientists recently discovered, the many stars, just like our the Sun had formed before the earth. How would life on earth be possible without light? How did a simple man few thousand years ago know this scientific fact? It can't be another of coincidences could it?
      Gen 1:2 gives as a further scientific clue:

      "When the earth was as yet unformed and desolate, with the surface of the ocean depths shrouded in darkness, and while the Spirit of God was hovering over the surface of the waters"

      This statements tells us that there was a significant time gap between the formations of the heavens and the earth and at the end of the verse 2.The earth was still covered in darkness and there was no life on it because? There was no light penetrating the earth's atmosphere. This is just as the recent scientific discoveries confirmed. While the bible doesn't give the exact timeline, neither does science, the sequence of the events related to the formation of the universe and the earthe are scientifically accurate.

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    34. My date (3140 BC) is based on Biblical chronology and corresponding ANE chronology.

      'Nuff said.

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    35. 3140 BCE? Let us see your Biblical chronology. The way I see it, you are only about 600 years off, which is nothing in comparison with the calculations of the "evidence" some call evolutionary.

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    36. "God created the heavens and the earth". Just like scientists recently discovered, the many stars, just like our the Sun had formed before the earth.

      The sentence from the Bible, however, clearly says that they came into existence at the same time. If I say "I'll have a peanut butter and jelly sandwich", I don't mean I'll first eat the peanut butter and then, 10 billion years later, the jelly.

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    37. Don't make me lol. You have no evidence. I should say you got nothing. Just because you don't like the comparison, it doesn't make your lack of evidence true. It may put you at ease, but it is a false sense of relief.

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    38. Skeptical Mind: You are misreading the story. Light wasn't created until Genesis 1:3, after the verses you quoted from that odd translation (JW?). And the moon, sun, and stars were created after the earth, not until Genesis 1:14-16. I know you will rationalize that to say that it was just from the viewpoint of an earthbound observer, and really just clouds parting, but of course that makes no sense at all given the text. I will also note that the story has plants being created before the sun, moon, and stars.

      Your story doesn't match reality at all.

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    39. It's the "International Standard Version" -- an odd translation indeed. Let's see how it works. Genesis 1:1 goes like this:

      In the beginning, God created the universe.

      And they add a footnote:

      Lit.[erally] the heavens and the earth; i.e. space and matter

      So the Hebrew words meaning 'heavens' and 'earth' really mean 'space' and 'matter', and this is supposed to justify the ISV translation (universe). Things are not what they seem to be.

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    40. "IF a catastrophic flood had interrupted Egyptian civilization it surely would have been recorded in their annals."

      Yep.

      "The fact that it wasn't supports my claim of fact that Egyptian civilization came into existence after the Flood."

      Nope.

      The alleged 'worldwide biblical flood' never occurred.

      By the way, Ray, sceptical mind, and other theobots, you do realize, don't you, that by choosing to believe in, worship, and promote a so-called 'God' that would commit such a heinous, genocidal, ecocidal act as 'the flood' (and all of the other horrors that are attributable to your so-called 'God'), you are revealing how despicable you are.

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    41. John Harshman

      Skeptical Mind: You are misreading the story. Light wasn't created until Genesis 1:3, after the verses you quoted from that odd translation (JW?).
      And the moon, sun, and stars were created after the earth, not until Genesis 1:14-16.


      Nope. Bible text in Genesis 1:1 uses the word "bara" which is used to describe the process of creation, which is not used in Genesis 1:3 and Genesis 1:14-16.

      I know you will rationalize that to say that it was just from the viewpoint of an earthbound observer, and really just clouds parting, but of course that makes no sense at all given the text.

      This is a really good observation John. I've never thought about the text being written from the point of view of the writer rather than Creator. Now, since Gen 1:3 and 1:14-16 is not talking about creating light, it does make sense.

      I will also note that the story has plants being created before the sun, moon, and stars.Your story doesn't match reality at all.

      Well, it does make sense now considering my argument above, but you will not accept it. You will move on to the next point of a deliberately sceptical mind.

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    42. Genesis 1:1 does not mention light. Genesis 1:3 is the creation of light, even if it doesn't use the word "bara"; "And god said 'let there be light'; and there was light". What does that mean to you?

      Nothing you say makes sense, and seems only to be an attempt to avoid talking about the subject.

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    43. Gen 1:1 refers to the creation (bara) of the physical universe--the heavens with all the stars like the Sun--the source of light-- and then the earth.

      Gen 1:2 clearly states that the light didn't penetrate through to the earth even though the heaves had been created that were the source of light.

      " Now the earth was formless and empty, darkness was over the surface of the deep, and the Spirit of God was hovering over the waters."
      Gen 1:3 clearly describes the process of the earth transformation for light to be visible. "Let there be light". If the creator were "creating light (the source of light)", the word "bara" would have to be used in Gen 1:3 but it is not. Gen 1:14-16 does't use the word "bara" either with relation to light, so it could not describe the creation process of light.

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    44. Gen 1:1 refers to the creation (bara) of the physical universe--the heavens with all the stars like the Sun--the source of light-- and then the earth.

      No. Everything mentioned in that verse was created "in the beginning". There is no mention of one thing being created, and then another. Why do you insist on distorting the text of your Holy Book? Isn't that blasphemous or something?

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    45. Also, on Day 4, this is what God was allegedly up to:

      And God made two great lights; the greater light to rule the day, and the lesser light to rule the night: he made the stars also.

      What was this "greater light to rule the day", if the sun had already been created on Day 1. And why is God creating the stars again, when he already did that on Day 1 as well? Let's see that "skeptical mind" at work, now.....

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    46. Clearly, words don't mean what they mean. They mean what Skeptical Mind (and his JW predecessors) want them to mean. It's the Humpty Dumpty view of biblical exegesis.

      Nowhere does Genesis 1:1 mention light, or the sun, or the moon, or stars. They are all mentioned later, at the times they are said to be created, or made, or called into being, depending. "Made two great lights" doesn't mean "let two previously existing lights become visible"; it means "made two great lights". And so on.

      In other words, Genesis 1 is seriously wrong about the ordering of events in the history of the universe and of the earth. You can fudge and reinterpret the language all you want, but it's a dishonest exercise.

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    47. John Harshaman

      I accept your view because it is true that some of these things are a matter of interpretation but keen minds are able to see beyond the actual evidence. You do it every day. I'm not going to insult you because you don't see it as convincing.

      I'm just surprised that you didn't take the lead in doing the same when some of us here demanded evidence for evolution of prokaryotes to eukaryotes with the same skepticism. I fear that you are either withholding some revolutionary information on the subject, or ? You finish the sentence yourself.

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    48. Piotr

      Did you finally get your own bible chronology straight?

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    49. keen minds are able to see beyond the actual evidence

      You can't make this stuff up.

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    50. Oh yeah. Let's see. Where did the genes come from that are found in eukaryotes that are not found in prokaryotes or anywhere else for that matter? Please tell me you've always had the answer for it but you were hiding it until today. If you do, you can resolve one of the greatest mysteries of science after the first cause, origins of life and this; not only how it happened but were did the missing genes come from. I bet you will get a Noble Prize if you reveal your secret today and I will be the first one to nominate you. Go ahead! Make me cry!

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    51. Septic Mind,

      "Oh yeah. Let's see. Where did the genes come from that are found in eukaryotes that are not found in prokaryotes or anywhere else for that matter?"

      How could anybody possibly know that those genes are not found in any prokaryotes or anywhere else for that matter? Do you have any idea how much we haven't explored? How much we could not have possibly explored?

      Also, of course, there's also such thing as de novo gene formation. Lots of articles about that.

      "Please tell me you've always had the answer for it but you were hiding it until today."

      Nobody has The Answer you idiot. Each of the genes you're referring to will have a different history. Obviously.

      "If you do, you can resolve one of the greatest mysteries of science after the first cause,"

      "Cause" is but an obsolete way of understanding phenomena. "First cause" is a poor excuse to argue for gods.

      "origins of life"

      Meh.

      "not only how it happened but were did the missing genes come from. I bet you will get a Noble Prize if you reveal your secret today and I will be the first one to nominate you."

      You're such an idiot. The history of some genes has been figured out. For others there is not enough information. You're just uninformed and misinformed (not a surprise), besides you're too much of a fool not to be able to understand, all by yourself, that we are far from having explored the vast prokaryotic, eukaryotic, and viral worlds. Man you're such an idiot it's hard to believe that you can write.

      "Go ahead! Make me cry!"

      Sure guys. If we don't know everything, it surely means that gods-did-it! When will we all learn?

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    52. Let's see. Where did the genes come from.

      Btw: I didn't read your post except for the first two words.

      I'm was confident you had no answer, so why should waste time and read the rest of your pointless post?

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    53. "Evolution did it. We don't know how and don't ask us about the mechanisms. The evidence is still to be found"

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    54. "Evolution did it. We don't know how and don't ask us about the mechanisms. The evidence is still to be found"

      But we know how, even if you don't. The mechanisms are quite clear. The evidence has been found. There is still much to be learned, but this is the way the human quest for knowledge works, when magic thinking fails (as it always has throughout human history).

      Now replace the word "evolution' in your statement with the word "God", and you will be making some sense.

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    55. Btw: I didn't read your post except for the first two words.

      I'm was confident you had no answer, so why should waste time and read the rest of your pointless post?


      Well, that's good way of keeping oneself ignorant. I imagine you did the same with all the scientific publications and articles that answer your question.

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    56. Septic Mind:

      Did you finally get your own bible chronology straight?

      The biblical cosmogony has no consistent chronology. It all happened in the Middle Eastern Dreamtime.


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    57. Actually, the chronology of the Bible makes a certain amount of sense (as a story in reference to itself, that is. Not in relation to current scientific knowledge) if the authors did not know that daylight was produced by the sun. They could have thought "light" was just something that permeated the atmosphere, like air. People were pretty ignorant back then. No knock on them intended, of course. Science was at a rather primitive stage then, that's not their fault.

      Anyway, that might explain why they would have written something as blatantly absurd (to most of rational contemporary minds today, as opposed to "Sceptical Minds") as the sun and moon being created three days after "light" was.

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    58. Three of the ways eukaryotes can get genes that were not present in their prokaryote ancestors:

      1. After polyploidy or duplication of a single gene, the extra copy of a gene mutates, coding for a protein that functions in a different way.

      2. Mutations leave a little DNA sequence functioning as a promoter that leads to transcription of a DNA sequence that wasn't transcribed before but produces a more or less functional protein. (Rare, but has apparently happened.)

      3. Virus infects a cell and becomes part of the cell's DNA. Mutations trap it there. However, one or more of its genes remain functional.

      Yes, examples are known (though examples of #2 may remain controversial). And no doubt other methods are known, but not by me.

      Though related to Sceptical Mind's question, this obviously isn't written for Sceptical Mind, who won't read it.

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  6. Photosynthesis:

    "But a fertilization expert writing about genome evolution and genomic functional organization? Not too impressed. Sorry."

    Does the person who wrote "Evolution is a fact, fact, FACT" (Michael Ruse) understand the genetical theory?

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    1. I don't know. I've never read anything by the guy.

      As Larry said, you should follow the evidence and the reasoning.

      Did you read my comment beyond those two sentences you quoted?

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    2. Ray,

      Evolution is a fact. Evolution occurred - species over long time were replaced by other species, which in many cases were very similar, or went extinct, or both.

      Evolution is also a theory, which deals with the mechanisms causing evolution as a fact to occur.

      ID could be a theory of evolution too - one with a serial incompetent creator (as Ken Miller put it), creating tens of thousands species of trilobites over hundreds of millions of years before allowing the last trilobites to go extinct 250 MYA at the end of Permian mass extinction (the mother of all mass extinctions) for unknown reasons.

      It's just simpler to assume that species originated by natural undirected means. And if you're a believer, to shoehorn your belief system into reality by asserting that your choice of deity inserted some intangible quality, such as the soul, into humans in the recent past.

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    3. Kev,

      Well, evolution is a fact and a theory. Evolution is a fact, because it happened. Evolution as a theory explains how it happened.

      Stephen Meyer doesn't deny that evolution happened, at least not to his non-creationist audience. He just attempts to replace it with his ID nonsense.

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    4. This comment has been removed by the author.

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