Cell biology Genetics Intelligent Design

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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64 Replies to “Pond scum smashes genome into over 225k parts, then rebuilds it

  1. 1
    Dionisio says:

    The organism’s ability to take apart and quickly reassemble its own genes is unusually elaborate for any form of life,…

    unusually elaborate?

    well, it’s also kind of cool, isn’t it?

    😉

  2. 2
    Dionisio says:

    That such intricacy exists in a seemingly simple organism accentuates the “true diversity of life on our planet,”

    is that all it accentuates?

    does another word come to mind besides ‘diversity’?

  3. 3
    BM40 says:

    You should be aware, that on the one hand Oxytricha’s germline micro-nucleus is transcriptionally silent. On the other hand its transcriptionally-active somatic macronucleus eliminates repetitive elements such as transposons during the process of its development. Differently phrased,~96% of Oxytricha’s micronuclear complexity is eliminated during the macronuclear formation. Thus, at least with regard to the regulation of gene expression the eliminated sequences have to be regarded as junk.

  4. 4
    Dionisio says:

    It may take time, but we’re slowly getting there:

    How specific transcription programs are established during vertebrate embryogenesis, however, remains poorly understood.

    functional understanding of chromatin in transcriptional regulation during development is very limited.

    http://www.uncommondescent.com.....ent-513843

    Briefings in Functional Genomics (2014)
    13 (2): 106-120.
    doi: 10.1093/bfgp/elt045

  5. 5
    News says:

    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%. …

  6. 6
    Dionisio says:

    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:

    http://www.uncommondescent.com.....ent-513810

  7. 7
    Andre says:

    And when it scrambles it’s DNA it also encypts it… Friggin awesone!!!!!!!!!

  8. 8
    Eric Anderson says:

    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?

  9. 9
    Dionisio says:

    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

    http://www.uncommondescent.com.....ent-513907

  10. 10
  11. 11
  12. 12
    wd400 says:

    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.

  13. 13
    BM40 says:

    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.

  14. 14
    Dionisio says:

    #13 BM40

    Dionisio, could your second name be BA77?

    No, why?

  15. 15
    Axel says:

    He feels you’re threatening his world-view? A world made and sustained by zillions of impossible coincidences.

  16. 16
    Acartia_bogart says:

    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?

  17. 17
    bornagain77 says:

    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.o.....ccus.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/pm.....MC3319128/

    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/edu.....ucation.uk

  18. 18
    Dionisio says:

    #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)

    😉

  19. 19
    Dionisio says:

    #13 BM40

    Dionisio, could your second name be BA77?

    No, that’s not my second name, but why did you ask such a question?

  20. 20
    Mung says:

    That such intricacy exists in a seemingly simple organism accentuates the “true idiocy of the neo-darwinian story,” he said.

  21. 21
    Mung says:

    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.

  22. 22
    Dionisio says:

    #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?

  23. 23
    Mung says:

    Arcatia_bogart:

    Did I ever mention that I love silly hats?

    No, I don’t believe you did.

  24. 24
    bornagain77 says:

    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/2.....89651.html

  25. 25
    Acartia_bogart says:

    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.

  26. 26
    bornagain77 says:

    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/2.....89421.html

  27. 27
    Axel says:

    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.

  28. 28
    Heartlander says:

    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…

  29. 29
    Dionisio says:

    #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.

  30. 30
    Dionisio says:

    #27 Axel

    I see your point. Thanks.

    🙂

  31. 31
    Dionisio says:

    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.biosciencetechnolog.....8;type=cta

  32. 32
    Acartia_bogart says:

    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..,

  33. 33
    Acartia_bogart says:

    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.

  34. 34
    Dionisio says:

    #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.

  35. 35
    Dionisio says:

    #33 Acartia_bogart

    (in reference to #16, #18, #25 and #29)

    You may read the posts in the indicated sequence again.

  36. 36
    CalvinsBulldog says:

    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.

  37. 37
    Axel says:

    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!

  38. 38
    Acartia_bogart says:

    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).

  39. 39
    wd400 says:

    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.

  40. 40
    Dionisio says:

    #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.

  41. 41
    Dionisio says:

    #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.

  42. 42
    tjguy says:

    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!

  43. 43
    Acartia_bogart says:

    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.

  44. 44
    Eric Anderson says:

    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).

  45. 45
    Heartlander says:

    A-B @ 32

    Just saying – Ciliate masturbation forum

  46. 46
    Dionisio says:

    #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.

  47. 47
    Acartia_bogart says:

    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.

  48. 48
    Dionisio says:

    #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.

  49. 49
    Acartia_bogart says:

    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.

  50. 50
    Dionisio says:

    #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.

  51. 51
    Silver Asiatic says:

    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.

  52. 52
    Axel says:

    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?

  53. 53
    Dionisio says:

    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.
    🙂

  54. 54
    Dionisio says:

    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.

  55. 55
    Mung says:

    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.

  56. 56
    Acartia_bogart says:

    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.

  57. 57
    Mung says:

    And what a variety there are!

  58. 58
    tjguy says:

    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.

  59. 59
    Acartia_bogart says:

    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.

  60. 60
    Joe says:

    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.

  61. 61
    Joe says:

    BTW Acartia_bogart- I agree that evolution does not have a direction wrt complexity.

  62. 62
    alan777 says:

    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.

  63. 63
    Silver Asiatic says:

    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.

  64. 64
    Dionisio says:

    #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.

    🙂

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