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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
#27 Axel (in reference to #13, #14, #15, #19 and #22) I see your point. Thanks. BTW, BA77 and every person is unique and special, therefore such a comparison is disrespectful at the best. Really a bad choice of words. Besides that, in this particular case, BA77 does a very commendable work, providing interesting information to the discussions. I can't do what BA77 does. Simply I don't know that much, not even close. Hence, again, the comparison was poor and totally tasteless at the best. We all should learn a lesson from this incident and be atert, so we don't make a similar embarrassing mistake in the future.Dionisio
September 9, 2014
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Dionisio: "You can’t make any valid point, because even the serious research scientists who understand the biological systems more than all of the participants in this blog combined," Really? How many participants here have published papers on ciliates? Just asking. I know of one.Acartia_bogart
September 9, 2014
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Heartlander: "What you do in private is your business, but this may not be the right forum… Just saying…" Why? I thought that ID was about the science, not religious based prohibitions...just saying..,Acartia_bogart
September 9, 2014
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Team Finds Cancer Oncogene in 'Junk DNA'?! Over the years researchers have made tremendous strides in the understanding and treatment of cancer by searching genomes for links between genetic alterations and disease. Most of those studies have focused on the portion of the human genome that encodes protein– a fraction that accounts for just 2 percent of human DNA overall. Yet the vast majority of genomic alterations associated with cancer lie outside protein-coding genes, in what traditionally has been derided as “junk DNA.” Researchers today know that “junk DNA” is anything but– much of it is transcribed into RNA, for instance- but finding meaning in those sequences remains a challenge. http://www.biosciencetechnology.com/news/2014/09/team-finds-ovarian-cancer-oncogene-junk-dna?et_cid=4144089&et_rid=653535995&type=ctaDionisio
September 9, 2014
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#27 Axel I see your point. Thanks. :)Dionisio
September 9, 2014
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#25 Acartia_bogart
I wasn’t trying to make any point.
You can't make any valid point, because even the serious research scientists who understand the biological systems more than all of the participants in this blog combined, humbly admit their ignorance when it comes to the point of providing detailed explanations for the processes they observe in their labs. I was referring not only to your post, but also to any pop-sci publication out there, which does not reveal to the commoners like me the mind-boggling complexity of the biological systems, the lack of detailed coherent explanations for many intricate processes occurring in biology, and the highly speculative nature of the officially accepted vague explanations for the OOL. As scientific research continues to produce the growing information avalanche we are witnessing these days, the big picture of biology should seem more understandable to the scientists and to the rest of us too. I believe we are approaching a big 'told you so' moment in science. That's why I look forward, with so much anticipation, to reading the newest reports on scientific discoveries, which shed more light on the wonderful beauty of the biological systems.Dionisio
September 9, 2014
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A-B @ 16
...Essentially, this is like sex without the need of the partner. Ciliate masturbation, if you will. During this process, the micronucleus undergoes the meiotic process without the exchange of genetic material with another ciliate. Did I ever mention that I love ciliates?
What you do in private is your business, but this may not be the right forum… Just saying…Heartlander
September 9, 2014
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You don't have to address BN40 or any of them, specifically, for them to feel threatened by truths inimical to their world-view, Dionisio. They still get the colly-wobbles, and a jibe at BA is a sure sign they're 'losing it'. I can't know the details of his fears, but that was what his tone, in invoking BA suggested to me. And yes, why shouldn't he answer your question...? I suspect I've given the answer to that question, so he'd need to think up some more specific, but not too specific, twaddle about BA.Axel
September 9, 2014
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UH OH, now not only does Darwinian evolution outclass our best computer programmers in programming, but it seems Darwinian evolution has now figured out, (figured out in an unguided way of course :) , how to edit better than the film editors of Hollywood do,,, Alternative Splicing: The Film Editor of the Genome - September 9, 2014 Excerpt: The story compares alternative splicing (performed by a sophisticated molecular machine, the spliceosome) to what a movie editor does: "Film editors play a critical role by helping shape raw footage into a narrative. Part of the challenge is that their work can have a profound impact on the finished product -- with just a few cuts in the wrong places, comedy can become tragedy, or vice versa. A similar process, "alternative splicing," is at work inside the bodies of billions of creatures -- including humans. Just as a film editor can change the story with a few cuts, alternative splicing allows cells to stitch genetic information into different formations, enabling a single gene to produce up to thousands of different proteins." http://www.evolutionnews.org/2014/09/alternative_spl089421.htmlbornagain77
September 9, 2014
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Dionisio #18
Lots of nice scenery descriptions, but missing many important operational details and definitely not much about how to get there. ????
I wasn't trying to make any point. I just find ciliates very interesting. They are unlike prokaryotes, and they are unlike most other eukaryotes. The live almost everywhere, including in interstitial sea ice. And some of them beautiful. I recommend googling for images of tintinnids, a group of mostly marine ciliates.Acartia_bogart
September 9, 2014
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Of note: Biology's Quiet Revolution - Jonathan Wells - September 8, 2014 Excerpt: In 1996, biologists discovered a protein that does not fold into a unique shape but can assume different shapes when it interacts with other molecules. Since then, many such proteins have been found; they are called "intrinsically disordered proteins," or IDPs. IDPs are surprisingly common, and their disordered regions play important functional roles.,,, So it is not true that biologists know all the basic features of living cells and are merely filling in the details. Nor is it true that Darwinian evolution is a settled scientific "fact," as its defenders claim. Huge unanswered questions remain, and they will only be answered by going beyond the discredited myth that "DNA makes RNA makes protein makes us." http://www.evolutionnews.org/2014/09/biologys_quiet_089651.htmlbornagain77
September 9, 2014
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Arcatia_bogart:
Did I ever mention that I love silly hats?
No, I don't believe you did.Mung
September 9, 2014
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#15 Axel Why would he feel I'm threatening his worldview? What did I do that could justify such a feeling? I did not mention his name. I did not refer to his posts. Since I responded his question, shouldn't he respond mine?Dionisio
September 9, 2014
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Arcatia_bogart:
Evolution is NOT supposed to progress from being simple to being complex. It can go both ways.
Yep. Evolution from the simple to the even more simple. Arcatia_bogart:
Evolution is NOT supposed to progress from being simple to being complex. It can go both ways.
For once I have to agree with A_b. Just look at how a dead body evovles from complex to simple.Mung
September 9, 2014
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That such intricacy exists in a seemingly simple organism accentuates the “true idiocy of the neo-darwinian story,” he said.Mung
September 9, 2014
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#13 BM40
Dionisio, could your second name be BA77?
No, that's not my second name, but why did you ask such a question?Dionisio
September 9, 2014
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#16 Acartia_bogart Lots of nice scenery descriptions, but missing many important operational details and definitely not much about how to get there. ???? Is that the best you can do? ???? Remember the most fundamental philosophical requirements in serious science discussions: Where's the beef? (http://youtu.be/Ug75diEyiA0) Show me the money! (http://youtu.be/OaiSHcHM0PA) ;-)Dionisio
September 9, 2014
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Per BM40 at post 3,,, if I may take a few liberties with what he said,,,
"News, it does not really matter that the Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces because, you see News, I deem most of the sequences to be junk"
If that is what BM40 is trying to get at, and it seems that he is, then that is to miss the point completely. The point News is making is that this is a level of complexity beyond anything man has ever built. Imagine your computer breaking its hard drive into a quarter million pieces and then putting it back together again. That would be roughly similar to what is happening here (save for the fact that the computer cannot replicate itself :) ). Moreover, another point that is completely missed, in BM40's rush to declare anything that he doesn't understand as useless junk, is that Oxytricha trifallax breaking its own DNA into nearly a quarter-million pieces and then rapidly reassembling those pieces is completely antithetical to the 'bottom up' framework of neo-Darwinism in which the DNA sequences are presupposed to have dominion over all the other information in the cell. Yet here we have something outside of the DNA that is dictating the sequence of DNA to reassemble in a certain order. From whence is this information coming? How does it know how to reassemble the DNA into the proper sequence. All these questions apparently go by the wayside for BM40 since some of the sequences are junk... It would be hillarious if he were not dead serious! And Oxytricha trifallax is not alone in its ability to reassemble its genome:
The World’s Toughest Bacterium - 2002 Excerpt: “When subjected to high levels of radiation, the Deinococcus genome is reduced to fragments,” (…) “RecA proteins may play role in finding overlapping fragments and splicing them together.” http://www.genomenewsnetwork.org/articles/07_02/deinococcus.shtml Extreme Genome Repair - 2009 Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319128/
If neo-Darwinism were actually true, how can the cell possibly ‘know’ the correct sequence? How can RecA proteins possibly reconstruct fragmented DNA? Where is the information coming from to accomplish the task?
In the lab, scientists coax E. coli to resist radiation damage - March 17, 2014 Excerpt: ,,, John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. "We blasted the cultures until 99 percent of the bacteria were dead. Then we'd grow up the survivors and blast them again. We did that twenty times," explains Cox. The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human. http://www.news.wisc.edu/22641
It would be nice if Darwinists on UD were ever to get honest with the astonishing complexity that we are dealing with in life.
DNA - Replication, Wrapping & Mitosis http://vimeo.com/33882804 How we could create life - The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 11 December 2002 Excerpt: Instead, the living cell is best thought of as a supercomputer - an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff - hardware - but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won't work because it addresses the problem at the wrong conceptual level. http://www.theguardian.com/education/2002/dec/11/highereducation.uk
bornagain77
September 9, 2014
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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.
HALT! say the science semantic police. Evolution is NOT supposed to progress from being simple to being complex. It can go both ways. For whatever reason, genetic exchange is required in almost all eukaryotic animals in order to rejuvenate the strain/cell line. Even organisms that we often refer to as parthenogenetic (e.g., rotifers) still undergo the exchange of genetic material. Ciliates are no exception. For ciliates (and rotifers), the trigger for sex is often environmental stress (e.g., the coming of winter). No ciliate reproduces sexually, but cell division almost always follows conjugation. It is possible, in culture, to maintain conditions such that conjugation does not occur. But in these situations, the cell line eventually senesces and dies. Even though most ciliates undergo conjugation in order to rejuvenate the line, genetic exchange is not always necessary. There are some ciliates (e.g., oligotrichs) that undergo a process of autogamy. Essentially, this is like sex without the need of the partner. Ciliate masturbation, if you will. During this process, the micronucleus undergoes the meiotic process without the exchange of genetic material with another ciliate. Did I ever mention that I love ciliates?Acartia_bogart
September 9, 2014
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He feels you're threatening his world-view? A world made and sustained by zillions of impossible coincidences.Axel
September 9, 2014
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#13 BM40
Dionisio, could your second name be BA77?
No, why?Dionisio
September 9, 2014
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Dionisio, could your second name be BA77? Regarding meiosis: IIRC it's about one homologous exchange per chromosome pair per meiosis. Between alligned paired homologous chromosomes which after the initial strand breaks took place stay interconnected rather then being really broken in separate pieces.BM40
September 9, 2014
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Isn’t it the case that our genome is also broken into, if not thousands, then at least hundreds, of different parts and then reassembled. Nah. There are ~40 recombination per meiosis in females, fewer (< 30) in males. 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.wd400
September 9, 2014
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Chromosomes in Mitosis video https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-513919Dionisio
September 9, 2014
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Fertilization video https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-513914Dionisio
September 9, 2014
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Slowly but surely we seem to be getting there... at least we see light at the end of the tunnel... let's just hope it's not a fast approaching train ???? Here's an illustration of what's going on in serious biological research these days: Epigenetic genome marking and chromatin regulation are central to establishing tissue-specific gene expression programs, and hence to several biological processes. Until recently, the only known epigenetic mark on DNA in mammals was 5-methylcytosine, established and propagated by DNA methyltransferases and generally associated with gene repression. All of a sudden, a host of new actors—novel cytosine modifications and the ten eleven translocation (TET) enzymes—has appeared on the scene, sparking great interest. The challenge is now to uncover the roles they play and how they relate to DNA demethylation. Knowledge is accumulating at a frantic pace, linking these new players to essential biological processes Briefings in Functional Genomics (2013) 12 (3): 191-204. doi: 10.1093/bfgp/elt010 https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-513907Dionisio
September 9, 2014
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Isn't it the case that our genome is also broken into, if not thousands, then at least hundreds, of different parts and then reassembled. It happens as a regular part of meiosis. That is not to diminish the remarkable nature of this feat. It is thoroughly dumbfounding how any organism could possibly do this, particularly under the "all information for an organism is contained in its DNA" school of thought. BTW, does anyone have a sense of how many pieces our DNA is broken into during meiosis?Eric Anderson
September 9, 2014
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And when it scrambles it's DNA it also encypts it... Friggin awesone!!!!!!!!!Andre
September 9, 2014
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Kind of OT? Slowly but surely we're getting there... aren't we?
Figuring out how blank slate stem cells decide which kind of cell they want to be when they grow up — a muscle cell, a bone cell, a neuron — has been no small task for science.
Many posts in the thread about 'the third way' are related to the 'cell fate determination' issues: https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-513810Dionisio
September 9, 2014
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BM40, not sure I understand the point you are making. Re junk, just in general: 99% of all the paper in my file cabinets will never really be needed again. Now, if I just knew which of the pieces of paper were the 1%, I could store wrapping paper and bows in all the freed-up space in my file cabinets. (I almost always end up eventually needing that stuff.) Sadly, neither I nor anyone else knows which pieces are the 1%. ...News
September 9, 2014
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