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Pond scum smashes genome into over 225k parts, then rebuilds it

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Oxytricha trifallax/John Bracht, American University, and Robert Hammersmith, Ball State University

From ScienceDaily:

The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it’s time to mate, the researchers report in the journal Cell. The organism internally stores its genome as thousands of scrambled, encrypted gene pieces. Upon mating with another of its kind, the organism rummages through these jumbled genes and DNA segments to piece together more than 225,000 tiny strands of DNA. This all happens in about 60 hours.

The organism’s ability to take apart and quickly reassemble its own genes is unusually elaborate for any form of life, explained senior author Laura Landweber, a Princeton professor of ecology and evolutionary biology. That such intricacy exists in a seemingly simple organism accentuates the “true diversity of life on our planet,” she said.

“It’s one of nature’s early attempts to become more complex despite staying small in the sense of being unicellular,” Landweber said. “There are other examples of genomic jigsaw puzzles, but this one is a leader in terms of complexity. People might think that pond-dwelling organisms would be simple, but this shows how complex life can be, that it can reassemble all the building blocks of chromosomes.”

HALT! Say the science semantic police. Nature doesn’t “attempt”to become more complex. Nature is not supposed to have purpose, remember? Evolution is blind. And life forms are supposed to progress from being simple to being complex.

But

An individual Oxytricha cell, however, keeps its active DNA in one working nucleus and uses the second to store an archive of the genetic material it will pass along to the next generation, Landweber said. The genome of this second nucleus — known as the germ-line nucleus — undergoes the dismantling and reconstruction to produce a new working nucleus in the offspring.

Oxytricha uses sex solely to exchange DNA rather than to reproduce, Landweber said — like plant cuttings, new Oxytricha populations spawn from a single organism. During sex, two organisms fuse together to share half of their genetic information. The object is for each cell to replace aging genes with new genes and DNA parts from its partner. Together, both cells construct new working nuclei with a fresh set of chromosomes. This rejuvenates them and diversifies their genetic material, which is good for the organism, Landweber said.

“It’s kind of like science fiction — they stop aging by trading in their old parts,” she said.

And, according to theory, it all just sort of happened by natural selection acting on random mutations. Note: Probability calculations are not permitted in Darwinclass! Elsewhere, they are fine. Be elsewhere.

Here’s the abstract:

Programmed DNA rearrangements in the single-celled eukaryote Oxytricha trifallax completely rewire its germline into a somatic nucleus during development. This elaborate, RNA-mediated pathway eliminates noncoding DNA sequences that interrupt gene loci and reorganizes the remaining fragments by inversions and permutations to produce functional genes. Here, we report the Oxytricha germline genome and compare it to the somatic genome to present a global view of its massive scale of genome rearrangements. The remarkably encrypted genome architecture contains >3,500 scrambled genes, as well as >800 predicted germline-limited genes expressed, and some posttranslationally modified, during genome rearrangements. Gene segments for different somatic loci often interweave with each other. Single gene segments can contribute to multiple, distinct somatic loci. Terminal precursor segments from neighboring somatic loci map extremely close to each other, often overlapping. This genome assembly provides a draft of a scrambled genome and a powerful model for studies of genome rearrangement. Registration required to view article.

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Comments
#63 Silver Asiatic Agree, there's only one way, the first way. The other ways are simply open rejections of the true way. The so called 'third way' is just a materialistic way of admitting that the second way (i.e. n-D e) can't explain many biological things that have been discovered in the last couple of decades. But still they don't want to accept the first way. :)Dionisio
September 11, 2014
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Dionisio #54 Thanks. I don't think there really is a third way, as such. There are a number of non-Darwinian ideas like self-organization but none of it has as much support as ID does, for example - if that means anything about how significant they are.Silver Asiatic
September 11, 2014
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This artice reminds me of an old problem programers that used punch cards used to have. You would be rushing to the computer room, when you would accidently drop your cards. If this happened, you would have to go back to your office and hopefully be able to put all the cards back in the same order. As a programmer myself, I assure you this is a very difficult process, and necessitated the invention of the sequence number. It is ironic to me that an organism without a brain could do something simiar in 60 hours.alan777
September 11, 2014
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BTW Acartia_bogart- I agree that evolution does not have a direction wrt complexity.Joe
September 11, 2014
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Acartia_bogart 16:
Evolution is NOT supposed to progress from being simple to being complex. It can go both ways.
Just another reason why evolution does NOT predict a nested hierarchy.Joe
September 11, 2014
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TGuy: "What we want is evidence for the simple to the complex. Does evolution really go both ways? That’s the million dollar question. Evolutionists believe it does, but many of us aren’t so easily persuaded." I am really baffled. The one time that I had no intention of picking a fight with the UD crowd because of my awe for ciliates (silly hats, silly idiots, yes, I have heard them all), I manage to pick a fight. I strongly urge everyone to do a little google research on ciliates (Mung, you can research silly hats). Here is a single celled organism that can do almost everything a complex metazoan can do. Ingest, egest, move, detect light, have sex, encyst to ride out poor conditions, produce armour, etc. I am willing to argue on any other OP thread, but please allow me my zen moment.Acartia_bogart
September 10, 2014
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Acartia says:
HALT! say the science semantic police. Evolution is NOT supposed to progress from being simple to being complex. It can go both ways.
Calvinsbulldog made an excellent point in post number 36. At some point or other evolution had to produce a heck of a lot of complexity. Dawkins didn't name his book "Climbing Mt. Improbable" for nothing! It's a heck of a mountain! It had to progress from the simple to the extremely complex and do it in a really short amount of time too. We all agree with you about evolution progressing from the complex to the simple! No argument here about that. That is normal! It's what we all experience every day of our lives. So examples of that don't impress us or make us change our minds. What we want is evidence for the simple to the complex. Does evolution really go both ways? That's the million dollar question. Evolutionists believe it does, but many of us aren't so easily persuaded. Examples like this little amazing creature are part of the reason why. Now if your faith can stretch to the point of encompassing things like this, fine. Go for it. Just don't expect everyone to have the same amount of faith as you.tjguy
September 10, 2014
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And what a variety there are!Mung
September 10, 2014
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Axel #37: "But it’s common for people who have no substance to their views to disparage opponents they fear, whose arguments they cannot counter, in an oblique way, as A_b seemed to be seeking to do to BA." Am I missing something here? I haven't said anything here about BA (or BA77). I just commented on how amazing ciliates are.Acartia_bogart
September 10, 2014
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NEWS: Boats are supposed to float. A_b: Sometimes boats sink. It is an error to say boats are supposed to float simply because some times boats sink. oooh kaaaay Whatever floats your boat A_b.Mung
September 10, 2014
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SA #51 Thank you for writing the commentary you posted. It certainly clarifies things more than my posts did. :) Perhaps this time AB will understand the situation better. PS. I'm benefiting from participating in this blog, because it helps me improve my reading comprehension level and also helps me acquire some writing skills. The over 300 bio examples I've posted in the 'third way' thread are some of the many materials I'm reviewing for my current studies. The main idea is to show examples of biological complexity so that the third way folks could try to explain its origin. As you can imagine, over 300 posts could keep them busy for quite some time. ;-) The second way 'n-D e' crowd already failed to explain things. The First Way, which is The Only Way, and was known as The Way in the first century of this age, already knows the origin of everything, including the biological systems.Dionisio
September 10, 2014
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Axel, Agree. You and I may have different points of view on certain subjects, and sometimes even misunderstandings, but our discussions flow smoothly. However, most discussions between persons with opposite irreconcilable worldview positions lead nowhere, unless both parties are willing to understand the other side's point, though without having to agree. I think the latter occurs very rarely. As it has been said by others in this blog, some lurkers may benefit from reading the discussions, and we can benefit too, from learning to discuss, to think, to analyze, to respect, and as you wrote, to receive offensive messages and still react graciously. Because we can't forget that even those who strongly disagree with us, and even may resort to personal attacks, are also human beings made in the "Imago Dei" hence they are to be treated with dignity by those who profess to love God. On many occasions I have not done as I should, and I regret it. Many times I do things I don't want to do, or don't do things I would like to do. It's a constant battle with the old 'I' and all his legacies. BTW, we haven't heard back from BM40. It would be interesting to read his opinion on this. I'm starting to use Mind Meister to map the materials I'm studying, hence I might gradually fade away from these discussions in the near future, as I will spend more time studying and will rely more on Mind Meister to bookmark and organize my ideas. But I don't expect to disappear completely from this blog. :)Dionisio
September 10, 2014
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Thanks Dionisio. I suspected that, but wasn't 100% sure, so thought I'd better leave it in. And yes, BA knows the brickbats and slurs he receives on here from atheists are the highest form of compliment in their gift. The mind and heart of the speaker are so pivotal in evaluating insults - and likewise compliments from benighted atheist dingbats, aren't they?Axel
September 10, 2014
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AB #49 Yes, that's true, and this is a good example of the wonder of life, but in fairness the OP was referring to a single-celled organism. The whole point of Darwinian theory is to explain the move from simple (bacteria) to complex life. It supposedly explains why there is so much variety of life on earth. It's very much harder to explain how evolution developed organisms which are immensely more complex than a single-cell when we hear that evolution can also make things less complex. Even forgetting that, this OP is about a single celled organism that is already incredibly complex on its own. Evolutionary theory, in whatever modified form of Darwin's thought exists today, somehow has to explain all of this. We have an incredibly sophisticated and complex single-celled organism. What hope is there that a plausible evolutionary path of mutations and selection can be invented to explain that? How many transitions are required and where are they? What ancestral process came before this? I think the OP is merely pointing to the impossible task of trying to offer a reasonable evolutionary explanation for this one organism. What steps created this "genomic jigsaw puzzle"? Why was it necessary at all? How many mutations does it take to have a process that arranges "thousands of scrambled, encrypted gene pieces"? How many species went extinct before this arrangement reached its final form? Why did the ancestors to this not require the process? How does the organism know what to do when it "rummages through these jumbled genes and DNA segments to piece together more than 225,000 tiny strands of DNA"? I don't think anyone in the evolutionary community can offer a reasonable answer for any of this. Do you really wonder why people think that evolutionary theory is laughable and absurd? I don't think anyone even pretends to have a Darwinian solution to this. They just walk away with conviction that evolution did it somehow.Silver Asiatic
September 10, 2014
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#49 Acartia_bogart It seems like the OP text that you reacted to in your post #16 is related to this part of the quoted ScienceDaily text “It’s one of nature’s early attempts to become more complex..." which is only about the alleged capacity of natural processes to produce higher levels of complexity or functional specified information. I don't think News or anybody else, except you, was talking about decreasing complexity in the offending piece of text referred above. But I could be wrong. I'm not good expressing ideas, but I want to make sure you understand this. Feedback is an effective method to verify that the message has been received and understood correctly. Let me know if you see my point this time. Seeing my point does not imply agreeing with it. We still can disagree, but at least we should see each other's message. Do you see that the whole argument here is about increasing complexity? No one is arguing about decreasing complexity, which may imply losing functionality. Apparently the OP statement your post #16 reacted to was about increasing complexity, or what our beloved friends gpuccio and KF refer to as dFCSI and FSCO/I respectively, although the two terms are not exactly equivalent, but very related. As I wrote before, my comment on your post was also referring to all the explanations that appear in the pop-sic literature out there, which miss the point because they are full of poetic descriptions without many functional and operational details. You may go back and read what I wrote to verify this. Do you see my point now? Do I have to explain it differently? Let me know. Thank you.Dionisio
September 10, 2014
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Dionisio: "Can you highlight the text in the OP that is wrong and then explain what is wrong with it?" I did that in my first comment. #16. But if you insist, here is the statement from the OP: "And life forms are supposed to progress from being simple to being complex." it is an error simply because evolution can also go from complex to less complex. Many parasites exhibit this.Acartia_bogart
September 9, 2014
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#47 Acartia_bogart
factual error in the OP.
Ok, since you insist, then can you describe that error? Can you highlight the text in the OP that is wrong and then explain what is wrong with it? Thank you.Dionisio
September 9, 2014
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Dionisio, I just find it odd that the one comment string where I agree with everybody else on the wonder of life, in this case ciliophora, I am called to task for one throw away sentence that was just a correction of a factual error in the OP.Acartia_bogart
September 9, 2014
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#43 Acartia_bogart
Let me remind you that it was just one sentence correcting a factual error in the OP.
My comment was related to your reaction at the OP. That was all. But you did not like it, so here we are. Agree, since this discussion is not going anywhere, maybe we should leave it right here. Remember, even if we disagree on fundamental issues, I still want the best for you. My Master asked me to love Him with all my mind and all my strength, and to love my neighbors, including you. Have a good night, or a good day, depending on the time zone you're in.Dionisio
September 9, 2014
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A-B @ 32 Just saying - Ciliate masturbation forumHeartlander
September 9, 2014
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wd400 @12:
There are ~40 recombination per meiosis in females, fewer (less than 30) in males.
Thanks. Interesting. So is that suggesting that most human chromosomes undergo, on average, less than 2 recombinations per generation? Which would also suggest that it is quite common to inherit an entire chromosome intact, without any recombination having taken place?
And of course recombination is an exchange of homologous regions, these guys build their somatic genome from bits and pieces from all over the germ-line.
Fair enough. It just reminded me of the fact that our chromosomes aren't static either. The question of what to snip apart and sew back together, even in recombination, still remains. The facile "well it just happens" doesn't cut it; not saying you've said anything of the sort, just that it seems we still have very little understanding of exactly what controls concatenation of DNA (or RNA).Eric Anderson
September 9, 2014
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Dionisio: "Well, let me remind you that your first post in this thread (#16) did start with a very explicit comment about evolution, as a direct confrontational reply to the OP." Let me remind you that it was just one sentence correcting a factual error in the OP. There was nothing else that I commented that could be construed as being critical of ID (I don't think). I was simply providing information on an amazing group of critters that I happen to have considerable experience with. But feel free to ignore me if you choose.Acartia_bogart
September 9, 2014
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The organism’s ability to take apart and quickly reassemble its own genes is unusually elaborate for any form of life, explained senior author Laura Landweber, a Princeton professor of ecology and evolutionary biology. That such intricacy exists in a seemingly simple organism accentuates the “true diversity of life on our planet,” she said.
What it accentuates is the impossibility of the evolutionary story. Anyone want to try and come up with a just so story that attempts to explain how such a system could have evolved? Seems like an irriducibly complex system if you ask me. I mean, if it didn't work right the first time, the organism would not have been able to reproduce, right? How can something that has to be right from the beginning and yet is so unbelievably complex have evolved by chance random mutations? The fortunate thing for evolutionists is that they only need to come up with a "plausible" sounding just so story. They don't need to test their story - they can't test their story. How fortunate for them!tjguy
September 9, 2014
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#38 Acartia_bogart
My comments did not say anything about ID/evolution
Well, let me remind you that your first post in this thread (#16) did start with a very explicit comment about evolution, as a direct confrontational reply to the OP. Here's exactly what you wrote:
HALT! say the science semantic police. Evolution is NOT supposed to progress from being simple to being complex. It can go both ways.
BTW, what you wrote seems to show that you misunderstood the OP. Hence, I'm not surprised you misunderstood my posts. The OP is written much better than my posts.Dionisio
September 9, 2014
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#37 Axel Sorry for the confusion my message created. I still don't know how to express my ideas clearly enough. My message to you was a follow-up to your comments, but the references to BA were only related to BM40's question, which you commented on very well. What you wrote about BA was fine. It was BM40 who made the wrong comparison.Dionisio
September 9, 2014
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This is some new definition of "very early" CalvinsBulldog, cilliates arose about halfway through the (current) history of life, a little over 2 billion years ago. This particular cilliate is among the weirdest of the group, so the degree of genome rearrangement here is the product of even more evolution.wd400
September 9, 2014
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Dionisio: "(in reference to #16, #18, #25 and #29) You may read the posts in the indicated sequence again." As with Axel, I don't understand your point. My comments did not say anything about ID/evolution (or, almost nothing).Acartia_bogart
September 9, 2014
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Dionisio #34 I'm afraid I don't follow you. Are you under the impression that I said something disrespectful about BA? Because my intention was precisely the opposite! But it's common for people who have no substance to their views to disparage opponents they fear, whose arguments they cannot counter, in an oblique way, as A_b seemed to be seeking to do to BA. If it's simply that you feel BA should feel insulted by comparison with you, I suspect you are being far, far too modest and sensitive. The amount of flak that BA takes of a far, far more vicious nature, from rabid atheists enraged by his evangelism, would be enormous, and he must have developed a hide like a rhino. In fact, I think B-A's jibe fired BA up a bit, as he chimed in, to shoot him down in flames again, with a detailed, technical post or two. Am I right, BA? I hope so. And as you said, yourself, Dionisio, everyone is unique and special, so that must include you. And I don't expect a prize for my logic in saying that!Axel
September 9, 2014
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Evolution is NOT supposed to progress from being simple to being complex. It can go both ways.
This strikes me as somewhat disingenuous. An organism can only evolve from the complex to the simple if first it had evolved to the level of complexity. An example of "simple" unicellular life that allegedly appeared very early in the development of life displays remarkable features that enable it to manipulate its genetic material in very sophisticated ways. The chance of this being the product of a largely random and unguided process, building upwards one mutation at a time, is so remote as to constitute a miracle.CalvinsBulldog
September 9, 2014
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#33 Acartia_bogart (in reference to #16, #18, #25 and #29) You may read the posts in the indicated sequence again.Dionisio
September 9, 2014
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