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Is it the “junk DNA” that makes us human?

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Skin cells repurposed into brain cells were studied:

Our DNA is very similar to that of the chimpanzee, which in evolutionary terms is our closest living relative. Stem cell researchers at Lund University in Sweden have now found a previously overlooked part of our DNA, so-called non-coded DNA, that appears to contribute to a difference which, despite all our similarities, may explain why our brains work differently. The study is published in the journal Cell Stem Cell…

Using the stem cells, the researchers specifically grew brain cells from humans and chimpanzees and compared the two cell types. The researchers then found that humans and chimpanzees use a part of their DNA in different ways, which appears to play a considerable role in the development of our brains.

“The part of our DNA identified as different was unexpected. It was a so-called structural variant of DNA that were previously called “junk DNA,” a long repetitive DNA string which has long been deemed to have no function. Previously, researchers have looked for answers in the part of the DNA where the protein-producing genes are — which only makes up about two per cent of our entire DNA — and examined the proteins themselves to find examples of differences.”

The new findings thus indicate that the differences appear to lie outside the protein-coding genes in what has been labelled as “junk DNA,” which was thought to have no function and which constitutes the majority of our DNA.

“This suggests that the basis for the human brain’s evolution are genetic mechanisms that are probably a lot more complex than previously thought, as it was supposed that the answer was in those two per cent of the genetic DNA. Our results indicate that what has been significant for the brain’s development is instead perhaps hidden in the overlooked 98 per cent, which appears to be important. This is a surprising finding.”

Lund University, “What makes us human? The answer may be found in overlooked DNA” at ScienceDaily (October 8, 2021)

The question “What makes us human?” is problematic in principle. It seems as if researchers are looking for a switch: Click! Now it’s human. There’s a lot that that approach won’t account for.

The paper is open access.

You may also wish to read: Term “junk DNA” critiqued at journal. But now remember the history! “The days of ‘junk DNA’ are over…”? So the house is clearly supporting this move away from the Darwinian position. Oh yes, let’s not forget that “junk DNA” was very much a Darwinian position. Most or all of the Darwinian Bigs signed onto junk DNA as part of their thesis about the unguided nature of life. The big question will doubtless be put off for now: Why does it only count if Darwinian predictions are right but never if they are wrong?

Casey Luskin reflects on the “official” demise of the term “junk DNA.” Luskin: “these authors remember a day when ‘the common doctrine was that the nonprotein coding part of eukaryotic genome’ consisted of ‘“useless sequences, often organized in repetitive elements.’” Good. Keep the history alive. It won’t be very long before Darwinians start claiming that they never thought it was junk. Then they will start insinuating that WE said it was junk. No, that doesn’t make any sense but if the history is forgotten, it doesn’t need to either.

and

And now … Transposable elements (junk DNA) shape the evolution of mammalian development. No wonder people are backing away from the Darwinian staple of junk DNA. We wonder, when will the pop science articles start to appear, claiming that junk DNA was never really an argument used by Darwinian evolutionists in support of their cause and that, in any event, they were right to use such an argument.

Comments
ET: And yet if he can’t answer that then his book is just nonsense. No, it's not nonsense. He was spending a lot of time and effort to address some issues about how we know that certain evolutionary processes are valid. Learn how to read. It’s his take that is rubbish. Right. So you cannot point to a particular bit of research that you think was rubbish. Noted. There isn’t anything in peer review that says fish can evolve into tetrapods. There aren’t any experiments showing it is possible. There aren’t any known mechanisms capable of producing the transformations required. Get specific. Point to particular results you think are questionable. That's how science works. YOU can’t point to any of his references that demonstrate otherwise. Can you find a result or research outcome that is wrong? CAN YOU?JVL
October 22, 2021
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Origenes: It seems like you have indeed misrepresented Shubin. Hard to say if you haven't actually read the book. According to him, the proteins know how to build brain and bodies. They are directing and instructing the cells during development. Why don't you actually read the full argument and explanation? Cell A to cell B: “Go divide neighbour!” Cell B: “How do you know?” Cell A: “A protein told me that you need to divide” Cell B: “How does that protein know that I need to divide? Does it follow a body plan?” Cell A:” Of course not. Experts do not see a need for body plans.” If you're not going to even bother to read the background and justification then is there a point trying to have a discussion?JVL
October 22, 2021
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If you want to read an honest Darwinist, look at the brief description I posted on Wilcox. He tentatively accepts evolution through Darwin's ideas.
Much of this variation has been generated by transposon-driven mutation (ALUs— or jumping genes). As to how this pattern evolved, it seems obvious to point to a selective regime favoring neural complexity. But that is an empty description. The real question for evolution would be, what circumstances would produce such a regime?
He is pointing to a micro evolutionary explanation for human brain development. Not to the creation of new proteins or organs. Where the real debate on evolution is.jerry
October 22, 2021
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Shubin:
These proteins both hold cells together, as in the skin, and serve as a way for cells to communicate chemically, telling one another when to divide, die, or make other proteins.
Cell A to cell B: "Go divide neighbour!" Cell B: "How do you know?" Cell A: "A protein told me that you need to divide" Cell B: "How does that protein know that I need to divide? Does it follow a body plan?" Cell A:" Of course not. Experts do not see a need for body plans."Origenes
October 22, 2021
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JVL:
Was that the point of his book? I don’t think so.
And yet if he can't answer that then his book is just nonsense.
So, you can’t point to a piece of peer-reviewed research that Dr Shubin references in his book that you think is rubbish.
Learn how to read. It’s his take that is rubbish. There isn't anything in peer review that says fish can evolve into tetrapods. There aren't any experiments showing it is possible. There aren't any known mechanisms capable of producing the transformations required. YOU can't point to any of his references that demonstrate otherwise.ET
October 22, 2021
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JVL:
Why don’t you read it and find out? Maybe I have misrepresented what it says.
It seems like you have indeed misrepresented Shubin. According to him, the proteins know how to build brain and bodies. They are directing and instructing the cells during development. Where these proteins got their insight into higher-level structures and patterns, which is obviously necessary for succesful building, Shubin does not say. Shubin:
A special molecular machinery gives cells the ability to work together and make bodies. Different cells have to be able to stick together. It would be challenging to have a solid body in which the cells did not adhere to one another in very precise ways. Skin cells, for example, have special mechanical properties that allow them to attach to one another to make sheets of tissue. They make the collagens, keratins, and other proteins that give the tissue its characteristic feel. Finally, cells in bodies need ways to communicate with one another, to coordinate their reproduction, death, and gene activity. And again, proteins are the way this happens: different proteins convey messages to cells that tell them where and when to divide, die, or secrete more proteins. The genetic machinery that makes this possible is the gene families we discussed in Chapter 5. Each gene in the family makes a protein that is subtly different from its cousins. For example, one class of protein, cadherins, resides in one hundred different kinds of cells, each specific to a different kind of tissue—skin, nerve, bone, and so forth. These proteins both hold cells together, as in the skin, and serve as a way for cells to communicate chemically, telling one another when to divide, die, or make other proteins.
Origenes
October 22, 2021
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It looks like we will have to read Shubin’s book to see what it says. My guess nothing relevant. Dawkins’ book, “The Greatest Show…” is about micro evolution. He punts when he gets near anything major. Wells’ thesis is that Darwin is about an argument without evidence to support it. So are all of Dawkins’ books and anyone else of Darwin’s disciples who have written anything. All they provide is speculation. Why is Shubin different? My guess, he isn’t. Aside: there will be a Nobel prize for anyone who can demonstrate an instance of macro evolution.jerry
October 22, 2021
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ET: It’s his take that is rubbish. There isn’t any peer review that shows blind and mindless processes can produce eukaryotes. Was that the point of his book? I don't think so. The same goes for developmental biology. And our knowledge of DNA refutes his claims. As I said, get an education. So, you can't point to a piece of peer-reviewed research that Dr Shubin references in his book that you think is rubbish. Fine.JVL
October 22, 2021
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JVL:
Be specific, give an example of one bit of work he references that you think is rubbish.
It's his take that is rubbish. There isn't any peer review that shows blind and mindless processes can produce eukaryotes. The same goes for developmental biology. And our knowledge of DNA refutes his claims. As I said, get an education.ET
October 22, 2021
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@JVL The problem of coding-decoding of information is insuperable.Sandy
October 22, 2021
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Shubin didn't reference any peer reviewed material that supports his claims. He doesn't have any idea how developmental biology arose. He doesn't have any idea how eukaryotes arose.ET
October 22, 2021
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Shubin's heavily biased books and unscientific views are NOT data.ET
October 22, 2021
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ET: I read it last year. It’s full of unscientific BS. He doesn’t address anything with actual science. That you are too dense to understand that says it all, really. What, specifically, does he relate that you think is BS? Which peer-review bit of work that he references do you think is rubbish? Shubin’s book is devoid of science. And it is refuted by actual science. Be specific, give an example of one bit of work he references that you think is rubbish.JVL
October 22, 2021
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Shubin's book is devoid of science. And it is refuted by actual science.ET
October 22, 2021
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Origenes: General instructions are sufficient to build a brain or an eye? No need for precision? No. Look, I've suggestion a good, general book discussing how this all works. It's recent, it's not expensive and you can probably find it in your local library. IF you're really interested. Ok. Whatever. And those general instructions are in the genes which also contain the code for proteins? Is that the great insight you obtained from Shubin’s book? Why don't you read it and find out? Maybe I have misrepresented what it says. You can find out. IF you really want to. OR you can just prejudge something which might address your questions. Only one way to find out . . . If you don't read it then you won't know whether or not it explains the issues you're bringing up. And you'll be ignoring something that might be informative. And surely anyone who is interested in scientific truth would like to consider all the data.JVL
October 22, 2021
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JVL:
His book Some Assembly Required is almost totally about work not his own. But, since you’ve already decided it’s rubbish and therefore you won’t read it you’ll never know that for yourself.
I read it last year. It's full of unscientific BS. He doesn't address anything with actual science. That you are too dense to understand that says it all, really.ET
October 22, 2021
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JVL:
No because you do not need specific instructions like a blueprint for every minor structure.
General instructions are sufficient to build a brain or an eye? No need for precision? Ok. Whatever. And those general instructions are in the genes which also contain the code for proteins? Is that the great insight you obtained from Shubin's book?Origenes
October 22, 2021
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ET: Shubin is full of it. He doesn’t know what makes a fish a fish. He has no idea how animals evolved. He can’t even say how blind and mindless processes produced HOX genes. He has no idea how developmental biology evolved. His book Some Assembly Required is almost totally about work not his own. But, since you've already decided it's rubbish and therefore you won't read it you'll never know that for yourself. I thought good scientists considered all the data. Here's a good, well written book that addresses some of the questions you have and you won't read it because you've prejudged it to be rubbish. Science knowledge is provisional based on our current best data. If you ignore some of the data then how do you know if your view is up-to-date?JVL
October 22, 2021
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Shubin is full of it. He doesn't know what makes a fish a fish. He has no idea how animals evolved. He can't even say how blind and mindless processes produced HOX genes. He has no idea how developmental biology evolved.ET
October 22, 2021
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Origenes: Do you now see the storage problem if the rest of DNA is junk? No because you do not need specific instructions like a blueprint for every minor structure. Again, I would highly recommend Dr Shubin's book Some Assembly Required if you're really interested in finding out some of the work being done in that area over the last century or more. It puts it into context and explains the reasoning and data and results.JVL
October 22, 2021
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JVL:
Origenes: If a brain is built succesfully, massive information is needed. This information does not have to be in the form of blueprint, as you pointed out, it can be in the form of Instructions “a cooking recipe”. However, the amount of information, remains massive.
It’s all in the DNA. (...) I can’t remember the exact value but it’s estimated that there are something like 30,000 genes in the human genome. Apparently, that’s enough when the right ones are activated at the right time.
You do not seem to grasp the problem. Those 30.000 genes you are talking about code for proteins. They are already occupied by information about proteins. IOWs they are not a blank sheet, they are not (also) available as a basis for your "cooking instructions". Do you now see the storage problem if the rest of DNA is junk?Origenes
October 22, 2021
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From: https://3quarksdaily.com/3quarksdaily/2020/03/some-assembly-required-by-neil-shubin-review.html
It turns out that genes can be switched on and off depending on the environment that a cell finds itself in. In development, the switches are produced by genes which are themselves responsive to their environment, giving rise to complex causal networks. If that sounds complicated, that’s because it is. The molecular mechanisms of development, and how they themselves evolved, are among the most exciting areas of current research, and Shubin devotes considerable space to describing for us the current state of play. Some features turn out to be common across the entire animal kingdom. Worms have segments, insects and other arthropods have segments, and at a very fundamental level our backbone is a series of segments. The control genes in worms, crabs and insects are directly related to the Hox genes of vertebrates, including fish, and the same Hox genes that are active in the development of toes are also active in the development of the terminal ends of fishes’ fins. Everywhere, we see the redeployment of similar subroutines. Repurposing also takes place within the DNA itself, by means of duplication, as well as by transfer of genetic material between different species. The existence of two separate subunits within the haemoglobin molecule is the result of an ancient duplication. Vertebrates show a fourfold repetition of their Hox genes, as the result of two episodes in each of which the entire genome was duplicated. Colour vision is a much quoted example of the possibilities created by gene duplication. Old world monkeys and their close relatives (including us) have three-colour vision, unlike the two-colour vision of most mammals. This arose through duplication of the gene for green-sensitive visual pigment, allowing one copy, by a minor change in its protein sequence, to evolve sensitivity for red.
We can understand major changes in body form, even such major changes as those between fish and land animal, or between running dinosaur and bird, in terms of a sequence of small interlocking adaptations. The appearance of a new kind of cell, such as bone cells, presents a much more difficult problem, since it entails an entire new suite of proteins, so that it looks as if many different things would have had to happen at once. One way in which this can occur is by the incorporation of multiple copies of a sequence at different sites, as sometimes happens with jumping DNA derived ultimately from a virus. This has happened in the cells responsible for forming the mammalian placenta.
JVL
October 22, 2021
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I will stay with actual science as opposed to the unscientific words of a very biased person. If Shubin says he knows how metazoans arose then he should have it in peer review. Yet he doesn't publish that. So he writes a book for rubes, like you.ET
October 22, 2021
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ET: I am sure that you think so. However peer review refutes your claim. It's a book for general readers; it wasn't peer reviewed. Look, if you don't want to read it fine but if you don't know what's in the book then you can't really comment about it.JVL
October 22, 2021
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JVL:
When cells reproduce certain genes are activated or inactivated which then dictates what kind of cell they turn out to be.
There isn't any evidence for that, just a need.ET
October 22, 2021
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JVL:
You should read Dr Shubin’s book; I’m sure you could get it from your local library if you don’t want to put money in his pocket. He does address a lot of your concerns.
I am sure that you think so. However peer review refutes your claim. I bet that you don't even know what DNA does. DNA isn't a recipe. At best it's just a template for making copies of itself and different RNAs. With mRNA, DNA doesn't even say how its processed. DNA doesn't have a say in how proteins fold nor how they are configured into structures. You don't know anything about biology and it shows.ET
October 22, 2021
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Origenes: Where is the information stored which tells the cells which genes to activate or inactivate? You cannot leave those decisions to the individual genes. It's all in the DNA. Ok. So you say there are “control genes”, which activate the genes. And these control genes are getting their (partial) instructions from the environment you say. In a former post you wrote that the control genes contain instructions; “like a cooking recipe: when this is true do this, etc”, to which my question was: “where is this “cooking recipe” information stored?” It's best to think of the DNA in total as being more of a recipe than a blueprint. But it is just a metaphor so not completely 'correct'. If a brain is built succesfully, massive information is needed. This information does not have to be in the form of blueprint, as you pointed out, it can be in the form of Instructions “a cooking recipe”. However, the amount of information, remains massive. I can't remember the exact value but it's estimated that there are something like 30,000 genes in the human genome. Apparently, that's enough when the right ones are activated at the right time. You should read Dr Shubin's book; it's quite interesting.JVL
October 22, 2021
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JVL:
When cells reproduce certain genes are activated or inactivated which then dictates what kind of cell they turn out to be.
Where is the information stored which tells the cells which genes to activate or inactivate? You cannot leave those decisions to the individual genes. JVL:
Origenes: So my question remains essentially the same: given that 98% of our genome is junk, where is this “cooking recipe” information stored?
All the genes (which create proteins) and the control genes (which activate genes) are in the DNA of course. But they get input from the environment.
Ok. So you say there are "control genes", which activate the genes. And these control genes are getting clues from the environment you say. In a former post you wrote that the control genes contain instructions; "like a cooking recipe: when this is true do this, etc", [when the environment is like that do this] to which my question was: "where is this “cooking recipe” information stored?" If a brain is built succesfully, massive information is needed. This information does not have to be in the form of blueprint, as you pointed out, it can be in the form of Instructions "a cooking recipe". However, the amount of information, remains massive. A collection of [if this do that] instructions does not require less storage than a blueprint. So, my question remains the same:
If most of our genome is junk, then where is the information stored for the (adult) body plan? Where is the information stored for e.g. the brain?
Origenes
October 22, 2021
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Origenes: The information on how to build a brain must reside somewhere, right? And, obviously, you are not saying that it is stored in ‘exterior influences’. No, but it's not written down like a blueprint either. When cells reproduce certain genes are activated or inactivated which then dictates what kind of cell they turn out to be. This makes no difference to the problem. In the cooking recipe scenario, the information on how to build a brain is in the instructions [when this is true do this, etc]. So my question remains essentially the same: given that 98% of our genome is junk, where is this “cooking recipe” information stored? All the genes (which create proteins) and the control genes (which activate genes) are in the DNA of course. But they get input from the environment. And BTW how do we get the right ‘cooking-instructions’ to the right cells, at the right time? It's in the DNA so it's in most body cells. If I remember correctly, red blood cells have no DNA.JVL
October 22, 2021
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ET: Neither Dawkins nor Shubin know what makes an organism what it is. They are just liars for evolutionism. They don’t have any idea how metazoans arose. They have nothing beyond a narrative based on their very biased, but untestable, ideas. You should read Dr Shubin's book; I'm sure you could get it from your local library if you don't want to put money in his pocket. He does address a lot of your concerns.JVL
October 22, 2021
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