Wednesday, March 08, 2017

What's in Your Genome? Chapter 4: Pervasive Transcription

I'm working (slowly) on a book called What's in Your Genome?: 90% of your genome is junk! The first chapter is an introduction to genomes and DNA [What's in Your Genome? Chapter 1: Introducing Genomes ]. Chapter 2 is an overview of the human genome. It's a summary of known functional sequences and known junk DNA [What's in Your Genome? Chapter 2: The Big Picture]. Chapter 3 defines "genes" and describes protein-coding genes and alternative splicing [What's in Your Genome? Chapter 3: What Is a Gene?].

Chapter 4 is all about pervasive transcription and genes for functional noncoding RNAs.
Chapter 4: Pervasive Transcription
  • How much of the genome is transcribed?
  • How do we know about pervasive transcription?
  • Different kinds of noncoding RNAs
  •         Box 4-1: Long noncoding RNAs (lncRNAs)
  • Understanding transcription
  •         Box 4-2: Revisiting the Central Dogma
  • What the scientific papers don’t tell you
  •         Box 4-3: John Mattick proves his hypothesis?
  • On the origin of new genes
  • The biggest blow to junk?
  •         Box 4-4: How do you tell if it’s functional?
  • Biochemistry is messy
  • Evolution as a tinkerer
  •         Box 4-5: Dealing with junk RNA
  • Change your worldview


198 comments :

  1. "Evolution as a tinkerer"

    Just like Thomas Edison.

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    1. Perhaps you can name something Edison "invented" without 6000 tinkers. Or 99 percent perspiration.

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    2. Evolution as tinkering is a reference to this 1977 paper by Francois Jacob. A classic paper, best read without preconceptions about evolution being "just like Thomas Edison" though, as much of what he describes is very much not like human tinkering.

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    1. Evolution doesn't predict future events. It predicts past events, and that's usually good enough. Reasoning is certainly not your strong suit.

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    2. Except evolution can't predict past events.

      http://tiktaalik.uchicago.edu/

      You were saying...?

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    3. LoL! Tetrapods existed before Tiktaalik.

      Right. Your point being...?

      I don't want to insult you by recounting information already well-known to anyone even slightly interested in the evolution/creationism "debate". But for the benefit of anyone who might less informed than you or I: The physical features and location of the Tiktaalik fossil were predicted on the basis of the date (and hence the geographical stratum) in which a fish-tetrapod transitional form would be expected to have existed. Paleontologists then went into the field and found the fossil exactly where expected.

      I'd be interested in hearing about the fossils whose appearance and location have been predicted by creationism. Thanks in advance, Joe.

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    4. "Let’s return to our problem of how to find relatives of the first fish to walk on land. In our grouping scheme, these creatures are somewhere between the “Everythungs” and the “Everythings with limbs”. Map this to what we know of the rocks, and there is strong geological evidence that the period from 380 million to 365 million years ago is the critical time. The younger rocks in that range, those about 360 million years old, include diverse kinds of fossilized animals that we would recognize as amphibians or reptiles. My colleague Jenny Clark at Cambridge University and others have uncovered amphibians from rocks in Greenland that are about 365 million years old. With their necks, their ears, and their four legs, they do not look like fish. But in rocks that are about 385 million years old, we find whole fish that look like, well, fish. They have fins. conical heads, and scales; and they have no necks. Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals."- Neil Subin

      So his rationale and conclusions (and his iconic promotion amongst the clergy) are meaningless. Tiktaalik was a fish, antecedent to nothing.

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    5. "I'd be interested in hearing about the fossils whose appearance and location have been predicted by creationism"

      No, you would not. You do not like the idea of an incomprehensibly violent flood burying countless billions of animals in sedimentary deposits. It's a "not being able to see the forest for the trees" deal.

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    6. "So his rationale and conclusions (and his iconic promotion amongst the clergy) are meaningless. Tiktaalik was a fish, antecedent to nothing."

      This is literally the opposite of what he says. Did you even read what you quoted? He gives the rationale for searching 375 million year old strata for a species with specific morphological features. If the method used to date that strata is flawed and the age is false, or if there really did not a morphological evolutionary transition take place during that time, then there'd be no reason to expect organisms like Tiktaalik to exist there.

      Simply put, the only way that can all make sense is if the stratum really is 375 million years old, and if there really did evolve lots of species of fish into amphibian and tetrapod-like animals around that time.

      A prediction was made, they went to the field to test it, and found what was predicted to exist. Your response to this amounts to brainless denialism. You are mindlessly declaring with no supporting evidence or reasoning, the diametrically opposite of what the data implies.

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    7. "No, you would not. You do not like the idea of an incomprehensibly violent flood burying countless billions of animals in sedimentary deposits. It's a "not being able to see the forest for the trees" deal."

      This has nothing to do with what anyone "likes". Every time I read you creationist morons blathering about "liking" something it looks to me like textbook psychological projection.

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    8. You do not like the idea of an incomprehensibly violent flood burying countless billions of animals in sedimentary deposits.

      So let me get this straight: You are saying that the highly specific prediction of creationism is "We'll find a whole bunch of fossils buried all over the place." Honestly, why do I even bother?

      OTOH, at least you tried, txpiper. I'm betting that's more than I'll get from Mr. Security Clearance.

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    9. You are mindlessly declaring with no supporting evidence or reasoning, the diametrically opposite of what the data implies.

      Yes. I read and re-read that post from txpiper and honestly cannot fathom how he drew that conclusion from what Subin wrote. My only explanation is that txpiper suffers a peculiar perceptual deficit that, whenever he reads something that supports evolution, causes him to read it as "GoddiditGoddiditGoddidit..."

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    10. The best way to understand folks like txpiper:

      https://www.theatlantic.com/science/archive/2017/03/this-article-wont-change-your-mind/519093/

      Money quote from the article (among many, but for our present purposes the one on point: "Kahan has previously written that whether people 'believe' in evolution or not has nothing to do with whether they understand the theory of it — saying you don’t believe in evolution is just another way of saying you’re religious."

      If tx gives in to the huge weight of scientific evidence rather than all the "flood geology" and all the other nonsense that goes along with creationism, that is the same for him as asking him to lose his faith, which he will not do. And it is likely no good to talk to him about the Christians who are also scientists who understand the science of evolution, because my guess is he wouldn't consider them true Christians.

      This is a matter for tx of his identity as a religious person. He sees things so much in these terms that in fact he can't conceive of the scientific enterprise around evolutionary theory as anything but religious also. Just like many of us think if we just marshall more facts we can show tx he's wrong, he thinks he can convince us the religion we're following is the wrong one. Each side of the argument is making the points the other considers "not even wrong," completely dismissable. In other words, we (and tx) are wasting our time.

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    11. Well, you always have to wonder a bit about how far "gone" they are on the spectrum. There are many former creationists in the world, but sure there are definitely also some who simply can't. I wasn't invovled in these discussions at the time, but someone like Glenn Morton of 'Morton's Demon' fame managed to open his mind up well enough that he could suddenly see where he'd been wrong for so long. It can happen.

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    12. Agreed, Mikkel. (Of course I'm sure the religious folks have stories of "conversions" from the heresy of Darwinism, too. :) )

      But as the article goes into some detail in recounting, (1) coming out of a cult/religious mindset is a long, slow process that is likely reliant on the individual to first begin questioning on his or her own; (2) if the individual is not questioning his or her present beliefs, then providing mountains of evidence very likely will have the paradoxical effect of making them believe even more strongly, because it's perceived as an attack (which it is) on the thing that makes them belong to their social group, and social groups have always been tremendously important - vital, really - to humans.

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    13. No, you would not. You do not like the idea of an incomprehensibly violent flood burying countless billions of animals in sedimentary deposits.

      I'd love the idea if there were any evidence for it. All the Tiktaaliks killed by the flood ending up at the same narrow set of strata seems something of a streeeeetch. Not to mention the problem of where tens of kms of fine sediment actually comes from in the first place.

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    14. Not to mention the problem of where tens of kms of fine sediment actually comes from in the first place.

      Well, remember, txpiper says the flood was "incomprehensibly violent." If the sediment pattern made any sense in that model, that would mean the flood was comprehensibly violent. Heresy!

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    15. Money quote from the article (among many, but for our present purposes the one on point: "Kahan has previously written that whether people 'believe' in evolution or not has nothing to do with whether they understand the theory of it — saying you don’t believe in evolution is just another way of saying you’re religious."

      To my mind, the creationist who best exemplifies that quote is Todd C. Wood. He actually understands and accepts that the scientific evidence supporting evolution is overwhelming and unrefuted. He simply, and admittedly, continues to believe in creationism because his faith demands it. As he puts it:

      We believe that we understand only a tiny portion of God’s creation, and we believe that God called us to accept Him by faith. We believe that our own ignorance has brought us to a crisis point where science seems to contradict our faith in God’s creation. We believe this “contradiction” is only an appearance, because God’s truth is one truth and cannot contradict itself when we properly understand it.

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    16. Mr. Security Clearance thinks Tiktaalik is claimed to have been the first tetrapod that ever existed. Honestly, you couldn't make it up.

      Anyway, I didn't ask you for evidence that you have shit for brains. That, we already know. I asked you for an example of a paleontological prediction made by creationism that was subsequently confirmed. Still working on it, Joe?

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    17. Let me try explain this in itsy, bitsy baby words so you can follow along, Joe.

      In rocks younger than 365 millions years, true tetrapods abound.

      In rocks older than 385 million years, no evidence of tetrapods was known to exist.

      Now, if you want to find evidence of transitional forms between the two, where are you going to look? In the period when those transitional forms would be most abundant i.e. the period just before 365 mya.

      Even if the 395 myo tracks had been found previously, that would not have changed this. The odds of finding an actual transitional fossil would still be greater when the transitional species were most common, not at the time when they were first emerging.

      In any event, the finding of the earlier tracks does not change the sequence of events of the transition. It only lengthens the time frame over which it occurred.

      I hope that's clear now. I apologize to other readers for belaboring this blatantly obvious point.

      So, Joe, when can I expect an answer to my question?

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    18. No one predicted a transitional form would exist twenty million years plus after the transition.

      Hee hee. You're so funny. Are next going to ask why monkeys don't give birth to human babies?

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    19. Monkeys are not transitional forms.

      Correct. On the other hand, everything not at an endpoint here is a transitional form: http://www.nature.com/nrg/journal/v15/n5/fig_tab/nrg3707_F1.html

      And only an imbecile would intentionally look for a transitional form twenty million years AFTER the alleged transition

      Perhaps only someone whose beliefs steadfastly prevented any curiosity about evolution wouldn't. Speciation doesn't necessarily result in die-off of the ancestral form. And while twenty million years is an awfully long time for stasis, perhaps it isn't unknown in the long history of life on the planet.

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    20. What a moron. Monkeys are not transitional forms.

      Really? How would one know this? Are you a visitor from 20 million years into the future?

      And only an imbecile would intentionally look for a transitional form twenty million years AFTER the alleged transition.

      Interesting. You seem to have quite certain ideas regarding how long the period of transition should be from when all vertebrates were fully aquatic to when tetrapods would be expected to be commonly found in the fossil record. How long do you calculate that period of time to be? How did you calculate this? Please show your work.

      This is all a very round about way to avoid answering the question about verified predictions of ID. I'm beginning to suspect you might actually not have an answer to that question.

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    21. Actually, my global statement that "monkeys are not transitional forms" might be incorrect, and we might not have to wait 20 million years to find out.

      I'm not an expert on the phylogenetics of anything, so I don't know the answer, but nothing necessarily precludes a current monkey species from having been the ancestral form of another current monkey species.

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    22. (Of course, strictly speaking, monkeys are already transitional forms. Between humans and lemurs, for instance. As well as between humans and bumblebees, or humans and fig trees, etc. But I don't want to confuse poor ol' Mr. Security Clearance more than he already is.)

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    23. Maybe Joe is a transitional form. Towards what, I can't guess. But I envision a world where there is not a single malfunctioning toaster.

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    24. Of course, strictly speaking, monkeys are already transitional forms. Between humans and lemurs, for instance.

      Not all the current monkey species, and maybe not any of them. We definitely shared an LCA, though.

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    25. How does it sound when you say humans are transitional forms between primitive primates and monkeys? If that doesn't seem right then think about whether monkeys are really transitional forms between humans and primitive primates.

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    26. Only in Joe G land does actually finding Tiktaalik, an organism within the expected anatomical range, in the correct chronological position, constitute NOT finding Tiktaalik. Apparently they weren't looking for something like Tiktaalik.

      Kids, Joe G is your brain on creationism. Just say no!

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    27. Here's my understanding of how the term "transitional" is used in phylogenetics, (with the caveat of course that I am not by any means an expert).

      First of all, as I'm sure most here already know, "transitional" does not mean the same thing as "ancestral". For to say one organism is transitional between two others does not mean it was directly descended from nor was ancestral to either of them.

      I said earlier that monkeys are transitional between humans and bumblebees. Here's what I mean by that: Look at a phylogenetic tree and find the branch that contains humans. Follow the tree back from that branch until you arrive at the point indicating the MRCA of human beings and bumblebees (That would be the point where deuterostomes and protostomes diverge, IIUC). From that point, go back up the tree until you arrive at the bumble bee.

      Every single branch that comes off from the path you just traced indicates a transitional form between humans and bumblebees. That is to say, all the branches from earlier than the MRCA indicate the common lineage between the two of us. So there is no transition occurring there. However, after the divergence from the MRCA, the descendents from every other branch along the way will demonstrate the genomic changes that have occurred to give rise to the two species. That is to say, by examining the genomes of present day organisms and determining the chronological place of their MRCA with either humans or bumblees, we can obtain a partial account of the series of genomic changes resulted in the two species.

      This is really no different than the sense in which earlier hominids are said to be transitional between humans and chimps. It is just over a much longer time scale.

      So since both old world and new world monkeys branch off between humans and our MRCA with bumblebees, they are transitional between the two of us. By the same token, it would not be correct to say that humans are transitional between primitive primates and monkeys because if we trace back the phylogenetic tree we arrive at the MRCA of humans and monkeys before we reach the MRCA of all primates.

      Hope that makes sense. I'm sure someone here will correct me if anything I wrote is inaccurate or misleading.

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    28. "OK please show me the evolutionary theory that says transitional forms can persist 20+ million years after the transition. And why don't we see that today with all organisms?"

      Joe, there is no requirement that the transition only takes place once, in one lineage, nor is there any requirement that the transitional lineage die out. Some species remain in the water, as lobe-finned fish, others gradually adapt to life in shallow waters, and others further go on to fully adapt to life on land.
      All three "stages" there can go on to coexist for a long time, doing just fine where they are.

      Even now, today, we still have many organisms showing gradual adaptation to life on land and in the water. Think of all the different speces of aquatic mammals, from everything to otters and beavers, to seals, sea-lions, walruses, manatees, sea-cows, hippos and so on. Google them, look at them, their fins and flippers, toes, arms and so on. They are clearly all in various stages of adaptation to life in the water. They all coexist. One did not evolve INTO the other, but they share common ancestry.

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    29. I wonder if Joe realizes the point he is trying to make is the same as "If evolution is true, why are there still monkeys?" I wonder if he thinks that, too, is a knockdown great argument. I also wonder if he has the neural capacity to even tie his own shoes.

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    30. For that matter, Joe, to you agree that there are still fish around? Or do you think that's also conspiracy promoted by Big Evo?

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    31. It has only been allegedly 7 million years since the chimps and human lineages split. Yet there aren't any living transitions. And yet Tiktaalik was found at least 20 million years after the alleged transition and that is OK.

      And it's been over 395 million years since tetrapods and fish split. Examples of both still abound. Nothing in evolutionary theory requires that any particular line must go extinct after any particular length of time, nor that any particular line must persist for any particular length of time. As anyone with even a rudimentary understanding of the theory knows.

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    32. Joe G has one thing right and as a result seems to miss the point. Tiktaalik was not the first tetrapod. However, it was found by thinking about the fossil record and evolution and predicting a time when species with morphology intermediate between (and truly transitional between) fish and amphibians should be found. This is, it was predicted.

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    33. The finding of tetrapod style trackways 20 million years before Tiktaalik is very interesting, but not a problem for our understanding of the transition between fish and amphibians, for two reasons.

      First, organisms morphologically intermediate between fish and amphibians no doubt existed long before Tiktaalik and long after.

      Second, fish that walk, do so with the tetrapod pattern. Consider living frogfish. Consider this little cave fish: https://www.nytimes.com/2016/03/25/science/researchers-find-fish-that-walks-the-way-land-vertebrates-do.html?_r=0

      How far along on the path between fish and amphibians were the animals that made the trackways? We don't know. Might have been fish. Might have been fully formed tetrapods. Interesting question, but not actually a problem.

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    34. Shubin said he was looking for evidence for the transition which had to occur BEFORE tetrapods existed

      Ah, so that's your elementary logical error. I was kind of wondering.

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    35. Also no one knows if any amount of genetic change can account for the transition from fic\sh to tetrapods.

      Another fascinating example of creationist "logic". Fish exist. Tetrapods exist. And they all have genomes which differ from one another. Are those differences the wrong amount, or the wrong type of differences? Joe seems to think so. It'd be interesting to learn of the thought process, if one could call it that, that leads him to that conclusion.

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    36. Wrong- tetrapods existed before Tiktaalik which means they did NOT find what they were looking for.

      Hee hee. Yes, they were looking for a fossil that looked pretty much exactly like Tiktaalik. And then they found a fossil that looked exactly like Tiktaalik. But, in so doing, they failed to find a fossil that looked like Tiktaalik. That what you're saying, Joe?

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    37. What part of that don't evos understand?

      It's quite clear. The marvel is that you somehow have made yourself unable to understand it. But then, I'm supposing you figure God hit the fish with his magic wand and gave 'em the genes for legs. (Just two, or a whole bunch? And if only two, did he create both, or create the male fish first and do the rib trick?)

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    38. No one can link the anatomical and physiological differences to the genetic differences.

      So you either haven't done any of the relevant reading, or have managed to do so and remain bravely ignorant.

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    39. Wow... Joe, not only do you show you have no clue about science and the scientific method, nor about evolutionary theory. You're also incapable of reading.

      Which part is so difficult to understand??
      "385 and 360 million years ago toward the end of the period of time known as the Devonian. The Devonian is often referred to as the 'Age of Fishes,'"

      and

      "Given this, it is probably no great surprise that we should focus on rocks about 375 million years old to find evidence of the transition between fish and land-living animals"

      Should we try google translate for you? Translate to Chinese? Would that help you comprehend how incredibly stupid you look posting this??

      Here you go:
      "鑑於這一點,可能沒有什麼大驚奇,我們應該集中在約3.75億歲的岩石,以找到魚和陸生動物之間的過渡的證據"

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    40. Hey,Ed, want some fun? Ask Joe what the word "prediction" means.

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    41. Wait, you mean 375 is between 360 and 385?

      Who knew math could be so complicated?

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    42. And only evoTARDs think that 395 is between 360 and 385

      Insulting people by using a term for mental disability. How very Christian of you, Joe.

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    43. And if you don't want to read a whole book (in fact I doubt you even can), read this webpage instead: Homeotic Genes and Body Patterns.

      And if you're too stupid to even read anything more than titles and blog comments (which seems plausible), just look at this picture.

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    44. “…read this webpage instead: Homeotic Genes and Body Patterns.”

      The issue isn’t shared genes. It is the assumption that DNA replication errors are responsible for the sharing. You are looking at results and assuming a cause. If you find a corpse with a knife stuck in it, it doesn’t warrant an automatic conclusion that it was an accident.

      True to form, the page you refer to provides two mutant examples, both of them failures. Your perception of mutations is in accordance with what your theory requires, but it does not line up with reality.

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    45. both of them failures

      Yep, it ain't like there's any jellyfish, worms, insects, mollusks, starfish, or 4-limbed land vertebrates around anymore, is it?

      The will to ignorance is strong in this one.

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    46. Stop being an ignoramus, read books.

      Normally a sound prescription, but for someone who said a float trip through the Grand Canyon helped convince them geology was nonsense and the Bible had it right, likely ineffective in this case.

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    47. "The issue isn’t shared genes. It is the assumption that DNA replication errors are responsible for the sharing. You are looking at results and assuming a cause."

      No. The particular patterns of the shared genes (and the particular patterns of mutations IN those genes) is what implies the cause of those patterns is evolution by mutation, drift and natural selection.

      You creationists keep not getting this fundamental point. You constantly speak of mere similarities, while totally ignoring the nesting hierarchical patterns in those shared similarities.

      "True to form, the page you refer to provides two mutant examples, both of them failures."

      Failures in what way? What were they supposed to be and why? Let me guess, you think all mutations with morphological or phenotypic effect have to be adaptive and confer the carrier increased fitness, right?

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    48. “just look at this picture”

      No, don’t just frickin look at it. Think about it.

      -Ancestral Hox-like gene

      Where did this gene come from, and how and for what reason did it originate?

      -Hox-like gene is duplicated

      How wonderfully convenient.

      -The two genes change and take on different functions

      Of course they do, because that’s how evolution works. Cool things just randomly happen.

      -Additional duplication events lead to an ancestor with 4 Hox genes

      You bet. All it takes is imagination. Accidental duplications, and natural selection will tidy everything up.

      I know this all sounds perfectly normal and rational to you. But you should at least be able to comprehend why there are people who see this as preposterous nonsense, and cannot understand why you don’t.

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    49. "convince them geology was nonsense"

      The same geology that thinks that swamps grow on top of each other and result in coal seams.

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    50. "Where did this gene come from, and how and for what reason did it originate? "

      It's a gene regulatory element. It evolved from DNA binding proteins. Either because it was beneficial, or by mere chance.

      "How wonderfully convenient."

      Why is that convenient?

      "Of course they do, because that’s how evolution works. Cool things just randomly happen. "

      Yes, demonstrably so. The citrate transporter was randomly duplicated into a region of the E coli genome under control of a promoter active under aerobic conditions, conferring the bacteria the ability to transport citrate into the cell when oxygen is present. It happened randomly. Get over it.

      "You bet. All it takes is imagination. Accidental duplications, and natural selection will tidy everything up. "

      It's not imagination, it's actual data. You aren't even arguing against it, you are just finding new and inventive ways to express your volitional denial. Everything you've said amounts to "bla bla I don't believe it".

      "I know this all sounds perfectly normal and rational to you. But you should at least be able to comprehend why there are people who see this as preposterous nonsense, and cannot understand why you don’t."

      I do, you were brainwashed with a religious upbringing at a pre-rational age and you have trouble letting go. Your every post reeks with righteous indignation and a desire to express how filthy and disgusting you find the whole thing.

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    51. I do, you were brainwashed with a religious upbringing at a pre-rational age

      Actually, if I recall/understand some of txpiper's previous comments correctly, it was an adult conversion experience.

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    52. The same geology that thinks that swamps grow on top of each other and result in coal seams.


      Sorry, is the coal not there, being mined, looked for and found by geologists trained in what you think is nonsense? You figure it's all just luck, and the multibillion-dollar resource extraction industry hires geologists on a whim?

      That's the thing about science that's so problematic for anyone who doubts: it works.

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    53. Cool things just randomly happen.

      Probably the fundamental conceptual piece that's hardest for someone looking at this with teleology in mind, I'd guess:

      Random things randomly happen. Some of them are bad, resulting in death, inability to reproduce, or failure to thrive. Bye-bye. Some of them are neutral or even slightly bad, and are fixed anyway due to genetic drift or other factors. A very, very few are really good, so those who have them benefit and the good things stand a very good chance of being fixed in the population.

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    54. He has no idea what makes an organism what it is

      How could he possibly, all he ever did was get an excellent education in the field and do real scientific work for decades.

      You, on the other hand, know more because...well, just because.

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    55. “It's not imagination, it's actual data.”

      No, the data is the data. Everyone can access what is actually known. What you are doing is proposing untested (and untestable) interpretations. There is nothing empirically true about the ‘steps’ in the picture you linked to. That is just invoking miracles on an as-needed basis. It is not the scientific method.

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    56. Tx, cool! What predictions did your bible make about coal in the ground? Do tell, when geologists learn their trade, do they:
      - read the bible and pray to find coal?
      or
      - use knowledge about how geological formations were formed in the last hundreds of millions of years to find coal or oil?

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    57. Everyone can access what is actually known.

      You can lead a horse to water, but you can't make him read a science book and understand it. :-)

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    58. Geologists don't rely on the untestable claims of evolutionism, that's for sure

      'Course not, they know just where to look for hydrocarbons 'cause God tells 'em! (Don't forget to tip your waiters, I'll be here all week....)

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    59. "That is your opinion and only your opinion. Too bad evolution by means of blind and mindless processes couldn't produce regulatory networks if your life depended on it."

      Evolution of a regulated operon in the laboratory.

      "Hall BG.
      Abstract
      The evolution of new metabolic functions is being studied in the laboratory using the EBG system of E. coli as a model system. It is demonstrated that the evolution of lactose utilization by lacZ deletion strains requires a series of structural and regulatory gene mutations. Two structural gene mutations act to increase the activity of ebg enzyme toward lactose, and to permit ebg enzyme to convert lactose into allolactose, and inducer of the lac operon. A regulatory mutation increases the sensitivity of the ebg repressor of lactose, and permits sufficient ebg enzyme activity for growth. The resulting fully evolved ebg operon regulates its own expression, and also regulates the synthesis of the lactose permease."

      "Again that is only your opinion.

      So if science were done by untestable opinions Mikkel would have something"


      There are 12 strains in the LTEE, one of them evolved the cit+ mutation. Others evolved other mutations. Because they're random.

      Joe, what's it like to be constantly wrong? Why are you here just mindlessly stating demonstrable falsehoods? Grow up, accept the evidence, change your mind and move on with your life. Stop being wrong and stop being angry, you are wasting your life on this shit.

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    60. "No, the data is the data. Everyone can access what is actually known. What you are doing is proposing untested (and untestable) interpretations. There is nothing empirically true about the ‘steps’ in the picture you linked to. That is just invoking miracles on an as-needed basis. It is not the scientific method."

      All false. Read this:http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence.

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    61. Joe G wrote:
      "'-Hox-like gene is duplicated'
      How wonderfully convenient. "

      As if gene duplication were really rare. Genes get duplicated, Joe G. We even know some different ways the duplication can happen. It can be observed within a single species. The results can be seen between species. It's not surprising that a given gene might be duplicated many times in a given lineage, though most of those duplication would just mutate away to uselessness.

      Mutations that make the duplicated gene beneficial are rarer. Gene duplication happens, though.

      Acting like it's an extraordinary event doesn't make it seem extraordinary; it just makes you look uninformed.

      Delete
    62. MRR-
      You link to this-
      http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence

      The argument presented isn’t all that convincing to me because it seems to make some basic errors. Perhaps I’m mistaken about that, but the errors include—

      1) The opening quote is an argument from ignorance.
      2) He compares the difficulties of measuring the gravitational constant with alignment of DNA sequences. This is apples to oranges.
      3) There are other observed mechanisms that produce similar genetics besides common ancestry. (GMO tech depends on one, for example).
      4) He fails to note different genes can give different trees (ignoring contrary evidence).

      I’m not sure if I’m just picking nits and missing the ‘big picture’, but those seem real problems for the argument as presented to me.

      Delete
    63. Jack,

      "The argument presented isn’t all that convincing to me because it seems to make some basic errors. Perhaps I’m mistaken about that, but the errors include—"

      I think you missed the boat on some of these critiques.

      1. The opening quote is a testable hypothesis, one that has been supported by mountains of molecular data.

      2. The article sites the lack of molecular data for many species as leading to a less accurate phylogeny for all life. This is very much like lacking sensitive and numerous measurements for the gravitational constant.

      3. GMO technology results in gross and obvious violations of the expected phylogeny as genes are moved from one distantly related species to another, without any change in sequence. GMO technology only highlights how the evidence strongly supports evolution and not intelligent design since we can observe that intelligent design does not produce a nested hierarchy.

      4. The article goes into depth about statistical tests. While the tree topologies between two genes may differ, they don't differ by much. That is stressed again and again. The prediction isn't a perfect match for every single gene. The prediction is a statistically significant phylogenetic signal.

      Delete
    64. While the tree topologies between two genes may differ, they don't differ by much. That is stressed again and again. The prediction isn't a perfect match for every single gene.

      To elaborate, Jack:

      Do you accept that it is possible a random person who is not a close relative could share an allele with your mother, that you do not possess yourself?

      Do you accept that, despite this, it will still be possible to determine thru genetic testing that you are more closely related to your mother than to this other person?

      Delete
    65. Eric-
      You make a good point about the GMO type inserts not necessarily producing a nested hierarchy.
      Because of that I realized I had confused a couple of different articles-
      Allow me to better state my difficulties-

      Regarding the use of the gravitational constant as an analogy-

      Evolutionary theory predicts the trees using different genes will be more or less the same but not completely the same. Evolution is on going and includes a stochastic aspect, so one assumes he will occasionally find something unusual or improbable because the process will produce such artifacts. Because the process can yield different results, the best we can do is infer the process from the fact the differences between what we find and what is expected is predicted. (When I rolled the die I got a 6 three times in a row— but this difference from what I expected and what I got is predicted— so I did not conclude the die was ‘fixed’, I thought I had observed a slightly improbable sequence).
      So we get 'statistically significant' matches.

      General relativity is not a stochastic process and there is no known reason the measurements of the constant should differ other than it is difficult to make precise measurements of some things.

      These are not similar situations.

      The observation the opening quote is based on is the evidence is in agreement with the theory (more or less),
      The claim ‘only the theory of evolution,…, could reasonably account…’ is what I’m calling an argument from ignorance because it overstates the inference.
      Am I misusing the term?

      Delete
    66. Yes, you are.

      An argument from ignorance would be something like, "No one has proven that God created life. Therefore, evolution is true."

      Delete
    67. lutesuite-
      The way it is stated it comes across as-
      "Since nobody has come up with another explanation, there isn't one."
      That is over stating the inference and seems like an argument from ignorance to me.

      Delete
    68. By that reasoning, it's an argument from ignorance to say that gravity exists, since we haven't ruled out the option that things fall because they're pulled to the ground by invisible pixies.

      Delete
    69. "Since nobody has come up with another explanation, there isn't one."

      But of course that's not the situation at all, is it? Many people have come up with other explanations that don't work. Evolutionary theory works, as shown by the huge amount of supporting facts from multiple scientific disciplines resulting from a century and a half of research. More is published every week from all over the world. You're not unaware of the shelves and shelves and petabytes of files full of this research in universities, corporate and foundation research facilities, and libraries everywhere, right?

      Delete
    70. lutesuite-
      No, gravity exists because things fall. It doesn’t matter if our explanations are correct or not, things fall = gravity.
      It would be an argument from ignorance to say our current theory is the only possible explanation and that no evidence will ever be found contrary to that theory.
      To say gravity doesn’t exist would an indication the person making the claim doesn’t know what the word means— that is not the same as an argument from ignorance.
      That’s an ignorant argument.

      judmarc-
      I thought I was talking about how the comparison between making evolutionary trees and measuring the gravitational constant is apples to oranges.

      Delete
    71. No, gravity exists because things fall. It doesn’t matter if our explanations are correct or not, things fall = gravity.

      Wrong. There is no such thing as gravity. It is physically impossible for things to fall down. What happens when we see things "fall" is that the invisible pixies, who possess supernatural powers, pull things to the ground, making it appear as if they are "falling". It is only ignorance that causes some to believe in "gravity."

      You disagree? Prove me wrong.

      Delete
    72. lutesuite-
      Problems-
      1) I have no desire to prove you wrong about anything.
      2) Even if I decided to make the attempt to prove you wrong for some reason, I have no idea what you would consider evidence, so I have no means to go forward.
      3) Even if I decide to guess at what you think is evidence, it seems you use English in a manner that I am incapable of understanding.
      4) Even if I decide to guess at what you are talking about, I have no way to tell what I’m saying to you means to you, as I’m only guessing at the language you use.

      I’m guessing you know this list better than I based on your exploits on this site.

      Delete
    73. I don't actually believe in invisible supernatural pixies that trick us into thinking gravity exists, Jack. Sorry to have confused you.

      Delete
  3. This entire series of comments is based on a misunderstanding of my first response to the first comment from Jass, now removed, a misunderstanding by some creationist whose very existence has been removed by Larry. And then everyone ran with that. Evolution doesn't predict Tiktaalik. An evolutionary biologist predicted Tiktaalik. Evolution, specifically natural selection, predicts the past in the sense that selection is a response to past conditions, and it works because those conditions often continue for many generations. That's what I was talking about before the unknown creationist derailed the whole thing.

    ReplyDelete
    Replies
    1. Evolution doesn't predict Tiktaalik. An evolutionary biologist predicted Tiktaalik.

      Evolutionary biologists can use evolutionary theory and associated scientific theory and evidence (e.g., geology) to predict where certain historic life forms might show up, even historic life forms that were previously unknown.

      Delete
    2. Natural selection, metaphorically speaking, predicts what environment the current generation will encounter based on what happened to the previous generation. Why is that so hard to understand?

      Delete
    3. Why is that so hard to understand?

      It isn't, if what you are doing is actually trying to understand. That Atlantic article I cited is pretty relevant, I think. (Of course I'm in the mode of having read an article I think is good and applying it overbroadly, but it's still a good article.)

      Delete
    4. Evolution by means of blind and mindless processes doesn't make any predictions beyond change, stasis, disease and deformities.

      I'm still waiting to hear of the predictions made by creationism, or IDiocy, or whatever the name for the hypothesis you espouse. Soon, I hope?

      Delete
    5. So an example of an ID prediction that was fulfilled...? I'm getting a bit impatient.

      Delete
    6. Joe Gallien, the Idiot Savant, minus the savant part.

      Delete
    7. Natural selection, metaphorically speaking, predicts what environment the current generation will encounter based on what happened to the previous generation. Why is that so hard to understand?

      Well, I guess when you don't have anything interesting to say when you are a devout Darwinist, you might as well say shit in hopes it passes through as evidence with the support of shit loving buddies...

      I gotta tell you Harsh, ...the metaphorically speaking, natural selection's predictions just killed it. If it wasn't such a waste of my goddamn time, I would recommend you for a Noble Prize... Keep spreading shit Harsh! You are very good at it...Some of it might stick. Science first as you indicated above..lol

      Delete
    8. Good metaphor, John Harshman, but used in a thread full of people trained from an early age to misinterpret metaphors. Understanding would not be predicted.

      Delete
    9. “That Atlantic article I cited is pretty relevant, I think. (Of course I'm in the mode of having read an article I think is good and applying it overbroadly, but it's still a good article.)”

      No, it isn’t relevant at all. Beck is just another fup, unaware of the absurdities that a person has to believe in order to believe the things that they like.

      Delete
    10. Thank you for so unambigously stating your mere opinion. Showed us you did.

      Delete
    11. Sorry, evolutionists beat IDiots to that prediction by a few decades.

      http://www.talkorigins.org/faqs/comdesc/ICsilly.html

      Delete
    12. So what are you saying, Joe? That some IDiot "predicted" Irreducible Complexity after it had already been described by an evolutionary biologist in 1939? By what definition does that count as a prediction?

      Delete
    13. People here are still having problems with the meaning of "evolution". Some are using it to mean "evolutionary biologists" and others "evolutionary theory", when the meaning that started this discussion was "evolutionary processes", specifically natural selection.

      The meaning of "prediction" is another problem. Now of course only human beings actually predict anything. Evolutionary theory can entail certain predictions. But the original meaning in this thread was, again, about the ability of natural selection to confer advantage on future populations, as long as the future environment resembles that of the recent past. No actual prediction involved.

      I ask again whether this is hard to understand.

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

      Delete
    15. lutey- in 1939 no one knew the internal workings of the cell. DNA wasn't elucidated until 1953.

      Exactly.

      Your homework, now, is to go learn the definition of the word "prediction." There's a good boy.

      Delete
    16. I ask again whether this is hard to understand

      No, it isn't. But the discussion just seems to have veered into other terrain.

      Delete
    17. “People here are still having problems with the meaning of "evolution". Some are using it to mean "evolutionary biologists" and others "evolutionary theory", when the meaning that started this discussion was "evolutionary processes", specifically natural selection.”

      Actually, what they are having problems with is sticking to the baseline principles of the theory. Natural selection does not make the changes. DNA replication errors make the changes. If those errors do not occur, there is no variation for selection to act on. Things don’t just evolve. It’s your theory. The least you could do is use it.

      Delete
    18. txpiper,

      You have confused individuals with populations. Mutation introduces variation into a population, but natural selection does make the change in the population, resulting in fixation. The least you could do is try to understand how that works.

      Delete
    19. “Mutation introduces variation into a population, but natural selection does make the change in the population, resulting in fixation.”

      Right. And that’s how fish acquired another heart chamber so that they could utilize the adult-phase lung and cutaneous gas exchange circuits that were being introduced into the population, so they could become amphibs, and so on.
      -
      “The least you could do is try to understand how that works.”

      Oh, I get that part. Error fixation is an absolute necessity, but the actual game changers are the errors themselves. And that part, for anyone actually trying to imagine any kind of system developing, is very difficult to comprehend. That’s why you’d rather talk about natural selection.

      Delete
    20. And that part, for anyone actually trying to imagine any kind of system developing, is very difficult to comprehend.

      For some people, evidently.

      Delete
    21. "For some people"

      No, for anyone who doesn't let their atheism interfere with their objectivity. There is a list of reasons why a long sequence of replication failures won't lead up to hyper-complex systems.

      Delete
    22. txpiper,

      As usual, you understand nothing. Lungs are a primitive feature of Osteichthyes, not Tetrapoda. Heart evolution was gradual: many steps, not one. Each step was advantageous at the time, and so was selected. Any comparative anatomy text will explain some of the steps. The creative power of natural selection lies in the cumulative addition of small changes resulting in big changes.

      Delete
    23. The creative power of natural selection lies in the cumulative addition of small changes resulting in big changes.

      And/or small changes (in genes responsible for some aspect of morphology/development) with big (morphological/genetic) results.

      Throw in a huge dose of contingency (I'm under the impression the big extinctions have been followed by relatively rapid speciation)....

      Delete
  4. Am I alone in finding Jass' "contributions" near valueless, seldom if ever rising beyond mere attempted insult? At least some of our other frequent folks from ID/creationist land attempt to put together subject matter arguments a fair amount of the time.

    ReplyDelete
  5. Joe G said: "Tiktaalik lived AFTER tetrapods already existed."

    And then he said it again in bold face.

    Quite apart from the fact that it's irrelevant if Tiktaalik is found a little later in time than the very first tetrapod (because it's still a form with intermediate morphology, and the fossil record is sufficiently spotty in the Late Devonian to extend the statistical probabilities of the relevant "window", see Freeman and Brazeau, Proceedings of the Royal Society B 2010), two salient points remain.

    1. Those "tetrapod" footprints have yet to be confirmed by a body fossil, and we've found out a lot since then about other types of fish locomotion that might leave similar trackways (e.g., lungfishes using their head to pivot around -- see Falkingham & Horner, Science Reports 2016). The general consensus among my colleagues these days is that those trackways were not made by tetrapods after all.

    2. It always amuses me how creationists have glommed on to that single set of dubious footprints as firm evidence that dethrones Tiktaalik. Yet they assiduously ignore or deny all of the trace fossil records of bilaterians in the Ediacaran that shows that the Cambrian "explosion" was in large part a taphonomic event, not a biological one.

    ReplyDelete
    Replies
    1. Don't need a mechanism as long as there's a nice transitional series, e.g. Eusthenopteron, Panderichthys, Tiktaalik, Acanthostega, etc.

      (Note that this is not a claim of direct ancestry and descent, just of intermediate forms, which is enough to privide evidence of a transition and make it credible. Phylogenetics is what shows us that such a transition actually happened.)

      Delete
    2. CMJ, I think Joe thinks his LOL trumps your Royal Society paper.

      Delete
    3. Hey, Joe. Does that mean you IDiots have finally come up with a mechanism by which your "designer" created all those critters? One which explains the existing fossil record better than common descent? Cool. We've been waiting decades for this. Let's hear it.

      Delete
    4. "LoL! The footprints are only "dubious" to evos. What lungfish could make those tracks?"

      The footprints are dubious to people who study fossil trackways. Also, I gave the reference to the lungfish work, look it up.

      Delete
    5. "As for Tiktaalik, you still don't have a mechanism capable of producing it starting from a regular fish."

      You certainly couldn't turn any fish living today into Tiktaalik, and most certainly not a "regular fish", but which I presume you mean a teleost. And your point is?

      Delete
    6. They have projections which have been interpreted as digits, but it's not all that clear. I can just imagine what creationists would make of those fuzzy impressions if they disagreed with the interpretation. Why, they'd probably dismiss them the same way that they dismiss the Ediacaran trace fossils of bilaterians.


      Did you read the original paper, or did you just read what creationist websites say about it?

      Those footprints may be real, although many people have doubts. But until we have a body fossil they remain enigmatic. And, even if there was a real tetrapod 18 Ma earlier than Tiktaalik, all that means is that Tiktaalik wasn't the actual ancestor. Nobody ever said it was: it's a form with intermediate morphology at approximately the right time.

      Delete
    7. "And it still remains that evolution by means of blind and mindless process cannot account for metazoans in the first place."

      Why don't you do the infinite regression, Joe, and tell us that blind and mindless processes can't account for the atoms that make up the chemicals that make up the biochemistry that make up the organisms?

      Delete
    8. "Incomplete references. Are you sure you are an academic? "

      I never claimed I was. Have you been stalking?

      Delete
    9. That's a different context entirely from this blog site (not to mention a couple of years ago). So my comment was not totally inappropriate.

      But, now you mention it. Yes, I am an academic, and a lot more informed about what is going on in evolutionary biology than you are.

      Delete
  6. I thought that readers of this blog you might like to read these articles:

    The Origins of Life
    Editors: David Deamer and Jack W. Szostak

    Not all of them are free, but many are.

    ReplyDelete
    Replies
    1. Has Szostak been able to replicate life?

      Even if he did, which he didn't, would that prove that random, natural processes can create life? Or would it rather prove that the creation of life requires an intelligent designer who can foresee how life would form?

      As far as I know, there is a great prize beyond what Noble has ever imagined for anyone who would replicate life...
      There are many smart people working on it because the prize is very tempting...
      I'll make prediction though about this thing and I feel very comfortable about it; no human being will ever replicate life! Never! I have very small means, but I'm willing to give them all away for whoever does it...

      Delete
    2. You're actually correct for once, Jass.

      It is highly unlikely that any intelligent agent will create life in the foreseeable future. Certainly no intelligent agent to date has even come close to doing so.

      Someone whose mind is operating correctly would understand that this is a very strong argument that life has not been created by an intelligent agent.

      I somehow suspect your mind undertands things differently.

      Delete
    3. You're actually correct for once, Jass.

      It is highly unlikely that any intelligent agent will create life in the foreseeable future. Certainly no intelligent agent to date has even come close to doing so.

      Someone whose mind is operating correctly would understand that this is a very strong argument that life has not been created by an intelligent agent.

      I somehow suspect your mind undertands things differently.

      I'm sure Szostak, Venter and man and others share your view...

      Well, I do have a slightly different view than yours, because what you are claiming is very simple to me; all science is worthless if it can't even come close to what dumb luck had accomplished. In other words, human endeavors, including science, are pointless because they can never match what accidents have accomplished...

      If that's how you feel, and I'm pretty sure I understand you correctly, why would anybody give a Nobel Prize in science to anyone if the people who get them only discover what dumb luck, spontaneous eruptions and random assemblies are doing better than them? There goes their intelligence and effort to discover what dummies have accomplished and left no message with it

      Delete
    4. If that's how you feel, and I'm pretty sure I understand you correctly, why would anybody give a Nobel Prize in science to anyone if the people who get them only discover what dumb luck, spontaneous eruptions and random assemblies are doing better than them?

      To what should be absolutely no one's surprise, you do not understand me correctly. Human designers don't have the luxury of taking hundreds of thousands of years to gradually develop something. So we have to make do with the more time efficient method of "intelligent design."

      Delete
    5. Interesting view:

      Intelligence cannot do it, therefore intelligence did it.
      If intelligence gets to do it, then intelligence did it.

      Heads I win, tails you lose.

      Delete
  7. This is a very interesting thread to try to follow, not so much for the content as it is much like other long threads on Sandwalk, a mix of science and creationist nonsense with loads of vitriol. Rather it is for the varying numbers of comments: the totals have risen and fallen as some nutcases post and the comments seem to be subsequently deleted. Reading some subthreads now, the comments seem to hang in space without context, where only a day ago they made some sense. It seems almost a shame to delete any of the worst of the comments, if only so that a sort of sense could be preserved.

    ReplyDelete
    Replies
    1. Joe G has been banned from this blog but Blogger does not have a mechanism for banning individuals. I delete all of his posts as soon as I see them but I don't check the comments more than a few times a day. If someone chooses to reply to Joe G then that response may remain visible. Please don't respond to him or to any other idiot that spams this blog.

      Delete
    2. I am never tempted to reply to the nuts who post here, partly as I don't have the expertise of many of the others who reply and partly because some of these people seem to reach a special level of unimpeachable lunacy it seems utterly pointless. I am always surprised and impressed by the indefatigable efforts of you and others in your responses.

      Delete
    3. some of these people seem to reach a special level of unimpeachable lunacy

      You have a way with words. :-)

      Delete
  8. Our body or mind contains no Junk. Can anybody explain why the genome should be full of it? My guess is that whole genome appears step by step functional and it will by nature be completely different from current opinion.. see eg.
    http://www.pnas.org/content/111/45/16112.full.pdf

    ReplyDelete
    Replies
    1. One question: have you ever read anything Larry has ever posted on this site?

      Delete
    2. And let me point out that your link shows that you have managed to commit the primary error of a lot of ignorant folks: confusing "non-coding" with "considered junk".

      Delete
    3. And let me point out that your link shows that you have managed to commit the primary error

      Either that, or the link was repeated, unexamined, from another website/blog authored by someone who made that error.

      Delete
    4. Pentti S. Varis, I found the idea of junk DNA odd at first, and then I thought about it a different way. Considering mutations and viruses, useless (junk) DNA will form pretty often in a genome. How can it be removed?

      Having a little extra, useless DNA isn't good for an organism, but it isn't very harmful, either. Selection pressure to remove it will be tiny, much less than the selection pressure on many more important traits. So that little bit of DNA is likely to remain. What about another bit of extra, useless DNA? Same thing. And another? Same thing.

      For organisms like humans that seem to have 90% junk, removing all the junk would make us much more efficient. But how to do it? We humans do differ in the presence or absence of small bits of junk DNA, and it seem to make no difference to the chance that we will reproduce, so natural selection can't effect it. And the cell has no mechanism to read through DNA and find out which sequences are totally useless in all tissue types. So we're stuck with extra, junk DNA.

      Delete
  9. Larry´s intresting blogs are my favourite reading, specially his vision and knowledge about the genome, even though I don’t understand or believe all. Reason for my unbelieving is, that I prefer “much functional” –opinion. Some time before I gave a summary (in finnish) of about hundred new scientific articles on genes written by the “much functional –group”-members.
    I have not found some binding cause not to believe almost every gene having some task in the genome. The reason of that ensues most from my belief, that knowledge of physics of the genome is wery primitive jet..
    What physics is necessary for eg. that? http://www.pnas.org/content/111/45/16112.full.pdf
    Anyhow, I have a positive attitude towards my belief perhaps being in the wrong..

    ReplyDelete
    Replies
    1. Once more, you are confusing "non-coding DNA" with "supposed junk DNA". Nobody who knows anything about junk DNA thinks that the two are synonymous. There is quite a bit of functional, non-coding DNA in your genome, and a small amount in the typical bacterial genome. But that functional stuff is counted within the 10% of your genome that isn't junk, and in fact makes up around 4/5 of it.

      Larry has written extensively on the reasons for believing that most of your genome is junk. Have you read any of it? Do you have any reason to reject any of his reasoning other than that you would like to disagree?

      Delete
  10. ”In summary, the notion that the majority of eukaryotic noncoding DNA is functional is very difficult to reconcile with the massive diversity in genome size observed among species, including among some closely related taxa.”
    I thought 1963 to attend a computer course in our university, but when I saw the clattering and puffing thresher-like computer, I went away. The genome of the onion reminds me of that old computer. Forthcoming physics of the genome will perhaps clarify the problem.

    ReplyDelete
    Replies
    1. How exactly is the genome of the onion like that computer? It may be because of the language barrier, but your analogy does not actually say much.

      I also doubt anyone knows what you mean by "physics of the genome." I include you in that.

      Maybe try stating your answer to the onion test in plain terms. Why is its genome so much larger than yours, if all of it is functional?

      Delete
    2. My idea is that a big, tresher-like computer is not more effective than a modern minor computer. The same holds to the large and little genomes.
      Especially quantum physics, eg. entanglement and different oscillations can have place in the genome.
      Information is wery important to take in to consideration too
      http://www.space.com/29477-did-information-create-the-cosmos.html

      Delete
  11. “Do you have any reason to reject any of his reasoning other than that you would like to disagree?”
    I have only a couple of reasons why to disagree that most genes in our genome have no piece of work.
    One reason is my opinion that other places of our body do not have any “junk”. Why should it all center to the genome? Somehow the evolution-centered arguments do not convince me in that question. Other reason is our minor knowledge about the physics of the genome. Forthcoming physics will uncover many secrets..
    Different brains, different thinking. My genome produces my brain with different thoughts.. https://www.sciencedaily.com/releases/2013/02/130206131048.htm
    Comprehending well me possibly having the wrong belief..

    ReplyDelete
    Replies
    1. Actually, all genes in your genome are functional. That's part of the definition of "gene". But most of your genome isn't genes.

      There are important reasons why other parts of the body have less junk (bu still some) than the genome does. Morphology is more subject to selection than the genome. Not sure what physics you're talking about, but we certainly know the physics we need to know to understand how the genome works. And your genome doesn't produce your thoughts.

      Delete
    2. Pentti S. Varis, your body does have some junk. We call the "junk" things vestigial structures. Things that we inherited from our distant ancestors that do not work for us.

      Many people have an extra tendon in the forearm that isn't needed. We have muscles some people can use to wiggle their ears, but wiggling our ears isn't helpful for us. There's a little bump at the edge of the outer ear that corresponds to the place many mammals have to fold their ears.

      Other animals have vestigial structures, too. Consider the wings of the kiwi (scientific name Apteryx).

      As John Harshman said, "junk" structures are less common than "junk" DNA, but they do exist.

      Delete
  12. We in Finland have argued much vestigial structures and I have got the next opinion.
    Ostrich´s and penguin´s wings have many functions, why then kiwi´s not? My hands are balance organs too, test says, minor hand movements help me keep my balance when walking.
    Wiggling our ears with muscles belongs to healthy smiling, test says. Recently found lymphatic circulation to the brain can became more effective too.
    Tragus can direct the current of air and likely help hearing
    https://www.quora.com/Whats-the-functional-role-of-the-tragus
    Evolution has given “vestigial structures” some , perhaps minor function.

    ReplyDelete
    Replies
    1. Those examples are all debatable. However, you have yet to demonstrate that you are familiar with the evidence for junk DNA. If you want to make an argument that all of the genome is functional, you need to address that evidence. Not just base your position on half-assed analogies.

      Delete
    2. My visions and motives are perhaps wery dilettantish.
      Recently I gave a summary (in finnish) of about hundred new scientific articles on the genome mostly written by my favourite group, “much functional –group”-members. I don’t remember any article having found a piece of genome which had not some job. Maybe it is infantile, but I began thinking the same holds to the whole genome.
      Secondly I have formed in my mind continuously changing picture of the genome trying to apply other knowledge to it, which I feel pleasant.
      https://www.google.fi/#q=how+much+junk+in+my+genome+2016+2017&*&spf=1
      http://www.kurzweilai.net/no-longer-junk-dna-shedding-light-on-the-dark-matter-of-the-genome

      Delete
    3. Of course, Ray Kurzweil. *He* certainly knows a thing or two about DNA (but most of it's probably junk! ;-) ).

      Delete
    4. Pentti,

      None of those things demonstrate that any of those traits aren't vestigial. In fact, they are evidence that those structures are in fact vestigial.

      Delete
    5. The non-flying wings of Ostriches have some use in balance, and penguin wings function for swimming. However, kiwi wings are smaller than the body feathers that hide them. Also, they are oddly variable. Vestigial structures are often variable. (No selection preserves one form over another.) Kiwi wings probably have no function.

      Delete
    6. Vestigial structures do not work for us. Maybe kiwi wings are really such one. 150 years ago the number of vestigial organs was as far as I know more than 100. That should be evidence of evolution.
      Nowadays we do not need such evidence. Rudiments are in my opinion results of evolution like all other living things. But I do not favour "standard" evolution.
      Sorry for needless words...

      Delete
    7. "Vestigial structures are often variable. (No selection preserves one form over another.)"

      Selection seems to have been really agitated at Moa wings.

      Delete
    8. I experimented possible function of kiwi wings and tightened my hands muscles. I observed that my voice changed a little.

      Delete
    9. "None of those things demonstrate that any of those traits aren't vestigial. In fact, they are evidence that those structures are in fact vestigial."

      But, what came first? The loss of flight muscles, the altered sternum or the ruination of the wings? Where did the devolution start?

      Delete
    10. "But, what came first? The loss of flight muscles, the altered sternum or the ruination of the wings? Where did the devolution start?"

      I don't know. It would be interesting to know how the wings of kiwis became essentially without function. However, that is extra information not needed to answer the basic question, are there vestigial organs.

      Delete
    11. "that is extra information not needed to answer the basic question, are there vestigial organs."

      Right. Unnecessary information. But surely you must have some vestigial curiosity about numerous DNA replication errors being selected for because they dismantled the systems necessary for flight.

      No, you don't.

      Delete
    12. He just said it would be interesting, so he does have some curiosity. He merely said that that knowledge isn't necessary to have in order to show that there are, in fact, such things as vestigial organs.

      Sooner or later you're going to have to come to terms with what people actually say instead of what your religious cognitive biases reads into things.

      Delete
    13. "But surely you must have some vestigial curiosity about numerous DNA replication errors being selected for because they dismantled the systems necessary for flight"

      It's more probable that mutations "dismantling" those systems were not selected against.

      Delete
    14. TX, I am curious about very many things. Unfortunately, life is too short to figure out all of them. I am delving deeply into the patterns of diversity in certain plants, so I will have to leave some other questions unanswered.

      I agree with Gabriel M-H that the mutations "dismantling" wings were probably just not selected against, since the kiwi ancestors didn't need functional wings because they didn't fly much if at all. (Why? Because there were no terrestrial mammalian predators in New Zealand.) However, there may have been some selection favoring traits that resulted in energy being available for other uses rather than the growing and maintaining of wings.

      (My botany friends and I, pedants all, find we mostly argue when we agree but with slightly different shades of meaning.)

      Delete
    15. tx,

      "But, what came first? The loss of flight muscles, the altered sternum or the ruination of the wings?"

      Well, loss of flight evolved independently 5 or 6 times in the Palaeognaths alone, so there are different evolutionary pathways there.

      "Where did the devolution start?"
      There is no such thing as 'devolution'. That implies evolution is purposefully heading somewhere, or that evolution leads only inexorably toward 'improvement'. Neither is true.

      Delete
    16. "Well, loss of flight evolved independently 5 or 6 times..."

      Yes, it's quite a tale of coincidence. Convergent Evolution stories always are.
      -
      "Neither is true"

      Neither is permissible. There are rules.

      Delete
    17. That "Intelligent Designer", such a joker. Putting useless vestigial wings on flightless birds, when it would be so much more "intelligent" to give them hands, or something else that might actually serve a purpose.

      Y'know, it's weird. I've never noticed a shrivelled up, vestigial choke valve left behind by automobile designers in a modern fuel injection engine. I guess those guys are just more intelligent than whatever doofus "designed" the kiwi bird.

      Delete
    18. ls, the ID is quite a sick joker at that. Nipples on guys, in which we get cancer, are just the start.

      Delete
    19. "Yes, it's quite a tale of coincidence. Convergent Evolution stories always are."

      No, not coincidence, but rather facts and evidence. Intelligent design creationism on flightlessness in Palaeognaths says.....nothing.


      "Neither is permissible."
      Of course its permissible. wahtever could you mean here?

      Delete
    20. Chris B,

      “Of course its permissible. wahtever could you mean here?”

      What I mean is that you have to think according to the rules. You said:

      “That implies evolution is purposefully heading somewhere, or that evolution leads only inexorably toward ‘improvement’."

      Those are not facts. Those are allowable theoretical parameters….rules that force you to think and draw acceptable conclusions. You have to believe that every cave species that loses sight and pigment does so because random mutations and natural selection because the rules say that evolution is aimless and cannot make plans for contingency. The belief that “loss of flight evolved independently 5 or 6 times” is the same thing.

      Delete
    21. TX: In some cases, convergent evolution is amazing and impressive, e.g. the evolution of flippers in icthyosaurs, plesiosaurs, whales, seals, and penguins. Your inability to understand that these all evolved, though mistaken, would be understandable to me.

      However, I don't understand your opposing multiple of losses of sight or loss of flight. After all, many different mutations can cause these losses. For an animals that isn't seeing anyway because it lives in the dark, mutations destroying sight are not harmful. And obviously their ancestors used to see (or fly) because we can see remnants of the eyes (or wings) in the currently blind (or flightless) organisms.

      Delete
    22. Scientists can best make an enduring name for ourselves if we can go beyond the limits of our theories. If we can provide better explanations for the phenomena we see. That's why so many papers talk about overturning the old ideas, developing new paradigms, etc., even if they have to exaggerate a lot to do so. Successfully presenting really new ideas is rare (having good evidence for them and explaining it well is rare), but thinking those new thoughts, and mistaken thoughts, is certainly "permissible."

      Delete
    23. "You have to believe that every cave species that loses sight and pigment does so because random mutations and natural selection "

      We don't have to believe that. We can also hypothesize that those species lost sight and pigment because, once more, the mutations behind those loses were not selected against.

      Most creationists insist that mutations can only destroy. Yet, when confronted with examples of independent "destructions," they forget their own prejudices.

      Delete
    24. "Most creationists insist that mutations can only destroy. Yet, when confronted with examples of independent "destructions," they forget their own prejudices."

      Sometimes I wish this blog had "like" buttons.

      Delete
    25. bwilson295,

      “I don't understand your opposing multiple of losses of sight or loss of flight.”

      I don’t oppose those things. What I would question is the randomness of the mechanism that causes those things. Similar cave environment adaptations occur in all kinds of animals. I don’t think it is reasonable to conclude that they occur because of random mutations and natural selection. It looks like a planned response.

      “Standing Genetic Variation” is a proposal that tries to work around the idea that purpose is involved. I think it is absurd, but there are people who recognize the problem for the mutations/selection paradigm. I’ve posted this article before:

      ”The classical view of evolution holds that organisms experience spontaneous, or de novo, genetic mutations that produce various novel traits. Nature then selects for the most beneficial, and those get passed along to subsequent generations. It’s an elegant model, but it’s also extremely time-consuming and doesn’t help species that need to cope with sudden, potentially life-threatening changes in their environments.

      With standing genetic variation, by contrast, genetic mutations arise and are passed along within a given population but are normally kept silent. The physical manifestations of the mutations don’t emerge unless a population encounters stressful conditions, like being forced to live in a dark cave instead of a vibrant river.

      “De novo mutations occur after an organism arrives in its new environment. They’re slow, and they favor dominant traits,” explained Rohner. “Standing variation provides a pool of mutations that are already available in the whole population. When organisms find themselves in a new environment, the silent variations are released and nature can select the ones that help.” “

      https://hms.harvard.edu/news/evolutions-fast-track-12-16-13

      A pool of mutations. Saving up DNA replication errors for a rainy day.
      -
      “And obviously their ancestors used to see (or fly) because we can see remnants of the eyes (or wings) in the currently blind (or flightless) organisms.”

      In the case of the ratites, the currently accepted idea is that their flight-capable ancestors left somewhere and flew to Africa, Australia, South America, New Zealand and Madagascar, and evolved into, respectively, ostriches, emus, rheas, moas and elephant birds. (The old idea that a ratite ancestor evolved and radiated before Gondwana broke up made a lot more sense. I don’t buy that either, but they preferred that notion for very practical reasons.)

      To say that after their arrival they became flightless birds is a gross understatement. They are all completely different from flighted birds, but but they share some striking and similar features, like gigantism. All of them make very interesting reading, but I don’t think ‘convergent evolution’ is anywhere near an adequate explanation. In my view, it is just a cop-out.

      Delete
    26. "Scientists can best make an enduring name for ourselves if we can go beyond the limits of our theories. If we can provide better explanations for the phenomena we see. That's why so many papers talk about overturning the old ideas, developing new paradigms, etc., even if they have to exaggerate a lot to do so."

      This is exactly the mental path that people walk in order to believe that meteorites or deep sea vents produced your ancestral elements, dinosaur soft tissue can last for tens of millions of years, and DNA replication errors coated your teeth with enamel. It is willful, deliberate blindness. Lewontin hit it right in the pills.

      Delete
    27. TX, lets stay on topic, which is, or was, the evolution of LOSS of a feature, e.g. sight in cave animals and ability to fly in many birds (including not only ratites but ducks, many rails, pigeons, a cormorant and a parrot, among others).

      Many, many genes can damage or destroy a complex trait. At least one and probably more alleles that cause blindness probably exist in the "standing variation" of every common animal species. Two handy examples: alleles causing blindness exist now in both humans and dogs.

      There are so many different mutations that contribute to the loss of sight or the loss of flight, that it is also entirely reasonable to expect that new ones would also turn up after the animal enters conditions where sight or flight is no longer beneficial.

      Evolution of LOSS of a complex trait is not all that difficult.

      Delete
    28. Our understanding of ratite evolution has improved in several steps. Current thinking definitely is that ancestral members of the clade could fly, as their descendants and tinamous can now. And many of them have convergently become gigantic. Too late at night to write more about that, but this blog (https://blogs.scientificamerican.com/tetrapod-zoology/ratites-in-trees-the-evolution-of-ostriches-and-kin-and-the-repeated-evolution-of-flightlessness-ratite-evolution-part-ii/) links to both previous blogs on ratite evolution and to scientific papers on the topic.

      Delete
    29. What I mean is that you have to think according to the rules.

      Of logic and evidence, as opposed to making shit up, yeah.

      Delete
    30. I don’t oppose those things. What I would question is the randomness of the mechanism that causes those things. Similar cave environment adaptations occur in all kinds of animals. I don’t think it is reasonable to conclude that they occur because of random mutations and natural selection. It looks like a planned response.

      Since we can point to the specific mutations that are selected against in environments where sight is an advantage in surviving and reproducing, but are no longer selected against where sight is not an advantage, what external planning is needed? If the city puts in new underground water pipes and the old unused ones corrode and waste away, do we need a planning commission in charge of corrosion?

      Delete
    31. BWilson
      "There are so many different mutations that contribute to the loss of sight or the loss of flight, that it is also entirely reasonable to expect that new ones would also turn up after the animal enters conditions where sight or flight is no longer beneficial.

      Evolution of LOSS of a complex trait is not all that difficult."

      Can you identify the mutations that caused the loss of flight in any of these birds?

      Delete
    32. I think we've been wasting time with txpiper. She or he keeps repeating arguments. I think that he or she prefers to ignore corrections than understand them. I quit.

      Delete
    33. "Can you identify the mutations that caused the loss of flight in any of these birds?"

      I don't know about those birds. but I found a bit about the loss of sight. We'd expect that, if the mutations behind the loss are random, then different mutations would be present in different populations. Guess what?

      Delete
    34. Nah, what Bill wants is a play by play replay of the events leading to loss of sight, or else goddidit.

      Delete
    35. Take a look at this picture showing the location of different kinds of mutations in the CTFR gene, the gene that can cause cystic fibrosis if mutated (depending on what effect the mutation has).

      http://www.genet.sickkids.on.ca/PicturePage.html

      The top line is a simplified map of the gene. The other lines show locations of mutations that have been detected in humans. The bottom line ("seq. var.") are harmless mutations. The others cause mild to severe disease.

      Many, many mutations can occur in this one gene in humans!

      Complex organs, like eyes or wings, involve input from many genes, and each can mutate at any point.

      Evolution of LOSS of a complex organ or function is not difficult, assuming the organism can survive without it.

      Delete
    36. @ Bill Cole

      Can you identify the mutations that caused the loss of flight in any of these birds?

      What do you think happens instead, Bill? Does Baby Jesus sneak about in the night plucking the feathers from the wings of each individual bird so they can't fly?

      Delete
    37. G M-H, it's clear that responding to TX has no direct good effect, but still I respond sometimes, for two reasons. First, writing this stuff is fun. Second, others who aren't commenting may be learning at lot more than TX.

      Delete
    38. bw,
      Sounds reasonable. I like reading those answers myself. I've learned a thing or two about studies I had not checked before.

      Delete
    39. bwilson295,

      “Many, many genes can damage or destroy a complex trait.”

      “Our understanding of ratite evolution has improved in several steps. Current thinking definitely is that ancestral members of the clade could fly…”

      Yeah, but don’t you see what all you’re dealing with here? In the first place, the mutations that you believe produced those many, many flight associated genes (you want to talk about how random mutations produced those genes?) are now credited with fantastic coincidental failures. And more accidental genes, or accidentally altered genes, are supposed to have popped the hell up out of nowhere in descendants in Africa, Australia, South America, New Zealand and Madagascar to produce giant flightless birds with all kinds of variant traits. Thickened bones, increased body mass, foot alterations, etc.

      You have matchless faith in DNA replication errors occurring in the same genes, that might occur in the rarest of germ cells which might be involved in reproduction and might wind up fixed in a population. All ridiculously low-probability events, but you believe things like this happened billions of times with monotonous regularity. Really impressive faith and reverence, but not at all believable.

      Delete
    40. LS
      "What do you think happens instead, Bill? Does Baby Jesus sneak about in the night plucking the feathers from the wings of each individual bird so they can't fly?"

      So the current explanation, based on circular reasoning sucks, but it's the best we have :-)

      Delete
    41. So, Bill, are you saying we have no direct evidence that heritable morphological change is due to mutations? You're even more ignorant than I feared.

      Delete
    42. fantastic coincidental failures

      Neither. Random failures at well established rates. And nothing coincidental about them. Different loss-of-function failures, as the study that G M-H referenced demonstrated so well.

      Delete
    43. So, Bill, are you saying we have no direct evidence that heritable morphological change is due to mutations?

      Not Bill, but my supposition is this is the well worn trope we've gone over before, that eventually evolution reduces to a tautology. So of course the folks who make much of this trope call it a "mere" tautology, or "circular reasoning."

      The major problem with this way of thinking is that *any* true statement logically reduces to a tautology. (E.g., two squared equals four, which reduces to four equals four.)

      So ability to reduce something to a tautology simply proves a statement is true. (Bill, you paying attention?) The much more better question is whether one or more of the various ways in which the truth can be stated are enlightening, and that is surely true of evolution.

      Delete
    44. TX, mutations that reduce or eliminate the ability to fly occur in all populations of flying birds. If the individuals showing such mutations really need to fly, what happens to them?

      They die. They're eaten by predators or they can't find food. Their flight-reducing mutations never become common in the population (though if these mutations are recessive, they may remain in the population, as "standing variation").

      However, if the birds don't need to fly, individuals showing such mutations don't die. They can reproduce. The mutations can become common in the population. In fact, they may be favored because the birds save the energy used to make big wings.

      Therefore, the evolution of flightlessness in ratites, ducks, a parrot, a cormorant, and several rails is not a spooky coincidence. It's a likely result of the many different mutations that can cause flightlessness, under situations where flightlessness is harmless.

      Delete
    45. Once again, we see the intellectual inconsistency of creationism. "Evolution can't happen, 'cuz all mutations are destructive. Beneficial mutations never happen." That's what they usually say. Except when confronted with something like the loss of flight or vision. Then the story suddenly becomes "How could such destructive mutations happen?"

      One wonder how their brains don't explode from holding so many mutually contradictory beliefs.

      Delete
  13. John Harshman, Yes, I should have written "junk DNA".
    Yes, brain needs outer and inner influences when thinking and when changing too. Activity of the genome is the modifiable ground to the net of the brain cells and eg. consciousness.
    “we certainly know the physics we need to know to understand how the genome works”.
    But, what physics is necessary for eg. that? (it is not evolution..) http://www.pnas.org/content/111/45/16112.full.pdf

    ReplyDelete
    Replies
    1. This the third time you've linked that article. You clearly have not the faintest idea what it means if you think it somehow presents a challenge to the current understanding of physics (Never mind genetics or evolution).

      I'm going to be charitable and presume that is a result of English not being your 1st language. Why don't you summarize the main points of that article in your own words, and we can help correct what you got so terribly wrong.

      Delete
    2. I feel revolutionary the ability of genes or gene collectives to choose new, totally different regulation genes and therefore new expression

      Delete
    3. They don't "choose" anything. There's nothing strange or mysterious about the process described there. It's just a variant of horizontal gene transfer. Since you seem unfamiliar with the concept, this short video might help:

      https://www.youtube.com/watch?v=Nunq1yg9Ea0

      Basically, bacteria are exchanging bits of DNA all the time. Every so often, one of these bits happen to be useful to the recipient organism. The only novel thing about the paper you cite is that this applies to regulatory elements as well as to genes.

      Delete
  14. I found it wery difficult to understand how recipients DNA and foreign DNA can adapt to a new situation, and more diffcult to understand, that regulatory elements can change too. In reality I do not understand that at all.

    ReplyDelete
    Replies
    1. What are you having difficulty following? Do you understand what mutations are? Do you understand what natural selection is?

      Delete
  15. Answering to your questions not only "yes" I put on display one of my threads unfortunately in finnish but after some comments I have borrowed some english publications about the physics which I thought explains evolution..
    The physics choosen could be interessant..
    http://www.tiede.fi/keskustelu/20186/ketju/nykydarwinismi_heikkoa_tiedetta?changed=1489362519

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    Replies
    1. That's not much help to me. Did you watch that video I suggested? Do you now understand the mechanisms behind horizontal gene transfer? What part of that do you think defies the current understanding of physics?

      Delete
  16. Video is excellent. However I did not get that supplementary knowledge which I needed: how donors DNA and recipient DNA can form a functioning unit. Or I did not perceive it.
    I have only fantasy of physics which clarifies evolution and many other things in biology: Nambu-Goldstone bosons (Nambu, Nobel 2008), Principle of Least Action, self organization et.al. and especially topological defect dynamics. I would say that we are topological defects. But it all would perhaps be only imagination..

    ReplyDelete
    Replies
    1. Video is excellent. However I did not get that supplementary knowledge which I needed: how donors DNA and recipient DNA can form a functioning unit.

      If a gene serves a function in one organism, why would it not be possible for it to also serve a function in a different organism?

      Delete
    2. The DNA sequence from one species (which is actually a molecule), is physically inserted into another organisms's DNA. So the molecules are linked together, so now the recipient species can "use" the new DNA.

      Delete
    3. how donors DNA and recipient DNA can form a functioning unit"

      If parts of some incorporated DNA happen to look enough like a promoter, or enough like a transcription factor binding site, then they might act like one and thus "rewire" gene expression. Promoters and transcription binding sites tend to be short and variable. Thus, the probability for some random piece of DNA to look and act like one is somewhat high.

      Some friends of mine found, for example, that it's likely that some low GC DNA pieces fail to be cloned into E coli, because their low GC content results in lots of spurious transcription (lots of pieces in those sequences look like E coli's promoters).

      Delete