'Junk DNA'

Anything I Remove Without Causing Immediate Catastrophe Must Be Junk

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I was in the server room with my system administrator the other day, discussing how we could cut costs in the server room.

I told him that the budget for the server room was too big, and we needed to implement some cost-saving measures. He said that everything he bought was necessary. That is so like a system administrator – to overbuy and just pretend that it is necessary.

What I told him is this – if I can remove it and the servers still function, then it was a waste and we can at least resell the extra pieces.

So, I took a big bin with me and started walking around. The first thing I noticed was that every server was plugged into the wall twice into different circuits. Not only that, but the machines themselves had two power supplies. So I went to each machine and physically removed one of the power supplies and put it in the bin. The machines continued to run, so I was satisfied with what I had done. In fact, removing one power supply from each machine opened up an entire circuit path on each rack, so that was removed as well.

Then, I went to the an area labelled “backups”. There was a giant, expensive-looking machine that was moving tapes back-and-forth. There were numerous servers, each sucking up a huge amount of electricity. I asked the system administrator if this data existed anywhere else. “Yes,” he said. “Well, then we don’t need it.”

I unplugged all of the devices. I put all the servers in the bin. The tape library was too big for the bin, but I had some people remove it and take it to the curb.

Next, I noticed that the cables connecting everything were attached to various nodes. I asked the system administrator, “what do these things do?” “Cable management” he said. Cable management? “Do the wires carry the same amount of data without cable management?” “Yes.” “Then get rid of them.” So we removed all of the armatures and supports of the cabling.

Then, I got to a section that had an endless array of batteries. “What do these batteries power?” “Right now, nothing” said the system administrator. “So why did we buy them?” I said angrily as I threw them into the bin. I also noticed an unused generator in the corner. I told the men carrying out the tape machine to get the generator as well. “What is that, from the 1800s? We’ve been connected to the grid for years, and that generator is just sitting in the corner doing nothing. Get rid of it.”

Then I realized – I had been concentrating on the center of the room. There was all sorts of equipment on the outer walls of the room as well. “What are these big units? How much data do they process?” “They don’t process any data, sir” said the administrator. “They are air conditioners” he said. I responded, “the building is already air-conditioned! You don’t need special air conditioners just because you are well-paid.” So we removed the air conditioners.

“Is there anything else that can be removed?” I asked. “Well,” the administrator said nervously. “The hard drives are in a RAID configuration. That means that at least one hard drive from each machine can be removed.” So we went around and removed a hard drive from each machine.

Then there were a bunch of machines labelled “staging”. “What do these do?” I asked. “They are the machines that we use to test code before we release it.” “Get rid of them.” I said.

Then I noticed a lot of machines labelled “Secondary”. There was a “Secondary DNS” machine, a “secondary database” machine, and so forth. “Are these needed?” “Only if the main one goes down.” “So they just sit here and eat up electricity and bandwidth without doing anything?” Get rid of them.

I then called up to the operations center and had them test all of our systems to make sure they are all still online. “Yes, sir!” They said. “In fact, you are using significantly less electricity as well – sounds like you are doing a great job over there!”

So, pleased with my work, I told the system administrator – “see, I told you that we could cut this stuff down. We removed over half of the server room and it is still functional!”

(note – this post is a more satirized version of a comment I made on a previous post)

——————–end of story

I should also note that instead of removing the secondary DNS and secondary databases, we actually could have removed the primary DNS and the primary database without any immediate issue if the site was not under load. Additionally, if the hard drives were in a RAID5 configuration, removing a hard drive would actually increase performance.

In case you didn’t notice, the goal of this is to illustrate the idiocy of saying that the “functional fraction” of the genome is equivalent to the amount of the genome for which there are no detrimental effects to removing or to mutation. Under this criteria, all of the things that we removed from the server room would not be considered “functional”.

And yes, if the server is well built, you can remove active power supplies and hard drives from running servers without them even hiccuping.

72 Replies to “Anything I Remove Without Causing Immediate Catastrophe Must Be Junk

  1. 1
    polistra says:

    It’s not just the genome.

    I’m putting together courseware based on a Neurology book, and in the process I’m learning all sorts of stuff that wasn’t known 10 years ago. The glial cells were considered to be padding until somebody looked closely. Now the glia are turning out to be a skilled and varied army of technicians taking care of the neurons.

    Just one example: Oligodendrocytes spend their time knitting myelin sleeves around axons. Most of their work is done in childhood, but they remain around in case the sleeves start to unravel. If you wiped them out, you’d guarantee MS.

  2. 2
    LocalMinimum says:

    Excellent post, thank you.

  3. 3
    harry says:

    johnnyb,

    (note – this post is a more satirized version of a comment I made on a previous post)

    I am glad you added that, as, having spent most of my adult life working in IT, your story sounded far fetched. ;o)

    We are in a no better position to decide what is really functional and what isn’t, what is necessary and what isn’t, in the nanotechnology of life than jungle savages are to make such judgments about the functionality of a laptop PC.

    The technology is beyond us. We can’t even design and build a small package that can be buried in the earth that will, using the resources in the ground, grow into something the size of, say, a small bush, and produce more packages like the one we started with. Why can’t we do something like that? Because we are nowhere near understanding the nanotechnology of life.

    We have learned a lot. So would savages poking around with laptop PCs, but they would still have no idea how to build one from scratch. Nor do we have any idea how to build life from scratch.

    Just as it would be for the savages poking around with PCs, it is ridiculous for us to be making pronouncements about the functionality or necessity of the components of nanotechnology that is light years beyond our own.

  4. 4
    Seversky says:

    It’s a nice little parable but there is one point missing. Nothing is perfect, things break down. So around the server room, tucked away in various odd spaces and in neighboring storage rooms. are piles of crashed hard drives, burnt-out monitors, broken keyboards and spent batteries, They take up a bit of space but they don’t impede the operation of the servers in any way. they all have a function, it’s just that they can no longer perform it. Maybe you could still get some fragments of information off the damaged drives if you hooked them up right or a splutter of power from the batteries. Would you say they are still functional or would you say they are junk?

  5. 5
  6. 6
    Dionisio says:

    johnnyb,
    I like this. Thanks.
    Unfortunately some politely dissenting interlocutors won’t understand the meaning of the story.
    Oh, well. What else is new?

  7. 7
    PaV says:

    johnnyb:

    I just posted on the original OP concerning Graur’s assertion. You might be interested.

  8. 8

    Seversky @ 4: Your analogy breaks down at almost every point, as if you have no idea about how DNA works or how miserably a/mats failed when trying to use the junk DNA myth against design arguments. I don’t hear many a/mats talking about junk DNA anymore, save for a few diehards (like yourself?) still clinging to the myth.

  9. 9
    Kal says:

    If the criteria for junk is the ability to to remove anything without causing immediate catastrophic failure, then I guess we could all lose a few fingers and toes, a kidney, gallbladder, a lung, and who knows what else…..

  10. 10
    EricMH says:

    Seversky and harry make johnnyb’s point. Without understanding the server room, we have no way of knowing what is functional or not merely by removing it and nothing crashing.

  11. 11
    harry says:

    EricMH @ 9,

    Seversky is saying that stuff wears out, which wasn’t really my point.

    Any agreement with Seversky on my part was purely accidental, coincidental, and unintended. :o)

  12. 12
    Dionisio says:

    Perhaps the comment posted @1030 in the thread titled “A third way of evolution?” in the following link relates to this OP?

    http://www.uncommondescent.com.....ent-612770

  13. 13
    Kal says:

    Spetner says that when determining the minimum amount of DNA needed for a living thing to survive, one has to take into account that the elimination of code may make the organism less robust and unable to adapt to changing conditions. Although the experiment he refers to speaks about ‘gene’ elimination, one wonders what regulatory effects non-gene coding DNA would have upon genes and their proper function.

    He writes –

    “There is experimental evidence that there are DNA sequences that have no effect on the functioning of the organism under ordinary circumstances but which play a role under extraordinary conditions.

    An experiment was performed on yeast in which each of its 6,000 genes was deleted, one by one (Hillenmeyer et al. 2008). Of these 6,000 genes, 34% were found to be necessary for the proper functioning of the cells under normal conditions because their deletion was either lethal or led to growth defects. The remaining 66% of the deletions showed no effect under normal conditions!

    Almost all of these (63% of the total), however, showed growth defects under various environmental changes! The remaining 3% showed no effects in this experiment. It is possible, though, they would have shown some growth defects under some other environmental conditions that were not tested.

    Thus, some two-thirds of the genes studied are likely to be the part of the genome containing the yeast cell’s built-in ability to adapt to environmental changes. There is thus good evidence that a significant fraction of the genome is dedicated to adapting the organism to changing environmental conditions.”

    Quoted from – ‘The Evolution Revolution: Why Thinking People are Rethinking the Theory of Evolution’ by Dr Lee Spetner.

  14. 14
    Dionisio says:

    @11 addendum:
    This comment was posted @1029 in the thread titled “A third way of evolution?”

    I would refrain from classifying anything as either functional or non-functional prematurely.

    One thing is clear, though: had we stayed in Eden, there wouldn’t have been any non-functional parts. However, that’s not the case, hence it is expected that some messy/noisy stuff resides in the biological systems.
    Actually, it’s possible that more garbage is being added these days.

    Still, the presence of that undesired stuff testifies to the robustness of the biological systems, which can operate under adverse thermodynamic noise in stochastic environments.

  15. 15
  16. 16
    Dionisio says:

    @11 & @13 addendum

    Here’s the example:

    Testing for functionality could be misleading in some cases.

    For example, let’s assume we don’t know what the small dark screens attached to back of many airline seats in economy class (mainly long routes) are for.

    Now let’s say we want to thoroughly test their functionality regarding several important criteria:

    1. The airplanes capability to take off and land.
    2. The fuel efficiency of the airplanes.
    3. The maximum number of passengers that can be transported on every flight.
    4. The maximum altitude the airplane can reach.
    5. The maximum speed the airplanes can fly at.
    6. The easiness of boarding and deplaning at the terminals.
    7. The ruggedness and reliability of the cockpit instruments.
    8. The experience of the pilots.
    9. The flight schedules.
    10. The airport fees.

    At the end of the thorough examination -performed redundantly by several teams of experts- we conclude -without any doubt- that the small dark screens attached to the back of the economy seats are definitely non-functional.

    Would such a conclusion be accurate?

  17. 17
    Dionisio says:

    @14 follow-up

    Please, note that in the current johnnyb’s thread several things are knocked out and one test is performed: the server runs.

    In the example @14, one thing is knocked out and several tests are performed.

    Several knocked outs with one test
    One knocked out with several tests

    In both cases the conclusion is wrong.

    The lack of comprehensiveness seems like a common issue here. Isn’t it?

  18. 18
    LocalMinimum says:

    Seversky:

    Yes, junk exists within engineered, maintained systems. Even should we locate actual “junk” DNA, we still would have to determine if it wasn’t degraded, previously functional DNA. Good contribution to Johnny’s post.

  19. 19
    Dionisio says:

    @15 follow-up

    Please, note that in both cases, the right test wasn’t done.

    Sometimes it may be very difficult to figure out every possible situation or scenario to test.

    Also, the functional effect of different components of a system –or of their combinations– may vary depending on the circumstances.

    Basically, the old Harvard University “look at the fish” anecdote comes to mind, doesn’t it?
    Keep studying the system, refrain from drawing conclusions prematurely.

  20. 20
    Mung says:

    This OP could be removed without causing immediate catastrophe.

  21. 21
    gpuccio says:

    Mung, you are an artist. 🙂

  22. 22
    Seversky says:

    Are you saying that the OP is junk?

  23. 23
    Seversky says:

    I would assume that with any knock-out experiments sufficient time is allowed for any delayed effects to become apparent.

  24. 24
    Seversky says:

    Truth Will Set You Free @ 8

    Seversky @ 4: Your analogy breaks down at almost every point, as if you have no idea about how DNA works or how miserably a/mats failed when trying to use the junk DNA myth against design arguments. I don’t hear many a/mats talking about junk DNA anymore, save for a few diehards (like yourself?) still clinging to the myth

    “Junk” DNA is hardly a myth. You have only to read Larry Moran’s blog to see the concept is taken seriously in evolutionary biology. There is certainly debate about the how much of the genome is “junk” but there is little doubt that some of it is. It’s inevitable. DNA is vulnerable to damage from a number of different causes. That damage can disable genes permanently in spite of sophisticated repair mechanisms. That’s why we are no longer able to manufacture vitamin C internally. It’s reasonable to assume that over billions of years there will be a gradual accumulation of no-longer-functional genetic material and it will stay there so long as it doesn’t become an insupportable burden to the organism. All that says about design is that, if it was designed, the designer had a very different approach to the process than contemporary human designers.

  25. 25
    LocalMinimum says:

    Seversky @ 22:

    All that says about design is that, if it was designed, the designer had a very different approach to the process than contemporary human designers.

    We cannot make any designs that are independent of an external infrastructure, which is primarily composed of and even still almost completely operated by humans, and thus is subject to our external infrastructure (the general ecosystem).

    So, humans haven’t reached a level of engineering that can emulate the wind-up-and-go reliability/independence of biology, as we cannot build anything that doesn’t constantly rely on it.

    Our engineering may look a lot different once/if we ever get there.

  26. 26
    aarceng says:

    Seversky @ 4 has a good point. It is likely that due to genetic entropy some parts of the genome have been damaged and are no longer functional. If these had no or little immediate impact they could have been fixed by genetic drift.This is consistent with ID or YEC.

  27. 27
    critical rationalist says:

    In case you didn’t notice, the goal of this is to illustrate the idiocy of saying that the “functional fraction” of the genome is equivalent to the amount of the genome for which there are no detrimental effects to removing or to mutation. Under this criteria, all of the things that we removed from the server room would not be considered “functional”.

    The flaw in your argument is assuming that cells are actually an equivalent to server rooms or that all server rooms are actually well built and maintained by professionals.

    Unfortunately, I’ve seen my fair share of “server rooms” that are organically built by amateurs (such as the owner’s son) which has plenty of equipment that can be removed or optimized. In many cases, functionality incrementally gets pushed into the cloud until, eventually, the number of services actually in use on a server goes to zero and the server becomes redundant. Yet, it’s still sitting there drawing power.

    For example, design department moves file sharing to Dropbox or engineering moves repositories to GitHub instead of an on site server. This can happen without informing IT, so hardware ends up going unused until, if your systems administrator is good, they notice traffic has gone to zero due to monitoring logs.

    Furthermore, RAID arrays and DNA repair mechanisms in a cell are both means of dealing with errors. I don’t think that biologists would say that the latter is not a function. So would means of storing energy for potential shortages or the ability to use multiple sources for energy, if one becomes scarce, etc.

  28. 28
    critical rationalist says:

    Our engineering may look a lot different once/if we ever get there.

    Unless something is prohibited by the laws of physics, the only thing that would prevent us from achieving it is knowing how. Current day 3D printers can already print some of their parts. And this trend will continue.

    It happens in organisms because the requisite knowledge necessary is present there. So, it’s a matter of knowledge. Unless we chose not to create the necessary knowledge or do not create it in time needed to prevent the human race from going extinct, it will happen.

  29. 29
    Dionisio says:

    The deeper we look into the biological systems, the more we know about them, the more they look designed. That’s an undeniable fact.

  30. 30
    johnnyb says:

    Seversky – the issue isn’t whether “some” of it is – there probably is some somewhere. The issue is a matter of degree. According to Graur and others, the minimum amount of junk is 75%. That is, quite simply, a ridiculous figure. There would be no argument if the question was over 1%. It wouldn’t necessarily be correct, but who would really care?

    critical rationalist – you missed the point. The point is that the test being used to determine function or non-function – whether or not the object continues to function upon removal – is completely irrational. It is simply not a valid test of function. There *may* be junk, but you won’t find it this way. It isn’t a matter of whether or not biologists allow for redundant systems in their thinking. The fact is that the tests don’t allow for this.

    Someone (possibly on a different thread) mentioned timeframe. The problem is, we don’t know what timeframe we should be looking for. If a given mechanism operates on timeframes of a thousand years, we won’t be able to determine this using ordinary fitness tests.

    The default assumption, given what we know about biology, should be function. The tests used for determining that something is junk are beyond ridiculous.

  31. 31
    gpuccio says:

    Seversky:

    “I would assume that with any knock-out experiments sufficient time is allowed for any delayed effects to become apparent.”

    What about a few million years? Those are evolutionary times, you know.

  32. 32
    Bob O'H says:

    TWSYF @ 8 & EricMH @ 10 – Fortunately we do know what a lot of the junk DNA is, and what it does (SINEs, LINEs and the like).

    johnnyb @ 30 – why do you think 75% is a ridiculous figure?

  33. 33
    Dionisio says:

    johnnyb @30:

    “The point is that the test being used to determine function or non-function – whether or not the object continues to function upon removal – is completely irrational.”

    Exactly.

  34. 34
    Dionisio says:

    johnnyb @30:

    “The tests used for determining that something is junk are beyond ridiculous.”

    Exactly.

  35. 35
    gpuccio says:

    Bob O’H:

    In what sense we know what id does?

  36. 36
    Dionisio says:

    LocalMinimum @25:

    You referred to Seversky @ 22
    but shouldn’t it be
    Seversky @ 24 instead?

    Or maybe johnnyb inserted a couple of posts before 22 and shifted the numbers up?

    Anyway, this quote seems taken from Seversky @ 24:

    “…the designer had a very different approach to the process than contemporary human designers.”

    Duh! Of course!

    The Designer made the human designers!
    The Maker made us in Imago Dei.
    That is with rational creative minds.
    But who knows more about design, the Creator or His creatures?
    The first Designer or the product of His design?

  37. 37
    Bob O'H says:

    gpiccio @ 35 – I’m afraid I can’t parse your question, can you re-pharse (or chase away any tyops)?

  38. 38
    Dionisio says:

    Bob O’H @32:

    “Fortunately we do know what a lot of the junk DNA is, and what it does (SINEs, LINEs and the like).”

    Do we? Really?

    How?

    Using the ridiculous approach so well described by johnnyb in the OP or by the airline analogy comments posted in this thread?

  39. 39
    Dionisio says:

    Bob O’H @37:

    gpiccio @ 35 – I’m afraid I can’t parse your question, can you re-pharse (or chase away any tyops)?

    Huh? Say what?

    🙂

    [emphasis added]

  40. 40
    Bob O'H says:

    Dionosio – a lot of research has been done on them, e.g. sequencing and functional work. You could start by reading the wikipedia article.

  41. 41
    Dionisio says:

    Bob O’H:

    If that research was done in the style described by johnnyb in his OP or in my comments posted @12, 14-17, 19, then we can sweep and mop the floor with all those tests.

    Ok?

  42. 42
    gpuccio says:

    Bob O’H:

    It should have been:

    In what sense we know what it does?

    Referring to your statement:

    Fortunately we do know what a lot of the junk DNA is, and what it does (SINEs, LINEs and the like

    Then you wrote:

    “a lot of research has been done on them, e.g. sequencing and functional work.”

    True. But still a lot is to be understood, I believe.

    So, do you agree with Sal, That SINEs and LINEs are functional?

  43. 43
    gpuccio says:

    Bob O’H:

    Do you mean stuff like this?

    A c-Myc regulatory subnetwork from human transposable element sequences

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850603/pdf/nihms182319.pdf

    I need not emphasize what c-Myc regulation implies!

  44. 44
    LocalMinimum says:

    Dionisio @ 36:

    You referred to Seversky @ 22
    but shouldn’t it be
    Seversky @ 24 instead?

    Yes, that was the intent, if not the action. I wish I actually knew how I did that.

  45. 45
    Dionisio says:

    Bob O’H @40:

    You could start by reading the wikipedia article.

    After watching online biology-related courses from MIT or the Weizmann Institute and after reading many peer-reviewed biology-related research papers –some of which I’ve shared here in other threads within this website– I don’t have much time left for Wikipedia stuff. 🙂

    BTW, a substantial proportion of the peer-reviewed literature frequently shows words like “surprisingly” or “unexpectedly” which seem associated with the reductionist bottom-up reverse engineering approach taken by many researchers that were taught the archaic pseudoscientific hogwash of Darwinian ideas, thus graduating as scientists that lack open-mindedness, hence don’t know how to think out of wrongly preconceived paradigms. If we add that pathetic situation to the sad fact that we humans lack the humility required to do serious science, then the outcome is certainly a bunch of stuff said and/or written that is partially useful in the best cases, but still could be used to sweep and mop the floor. 🙂

  46. 46
    Dionisio says:

    LocalMinimum @44:

    Yes, that was the intent, if not the action. I wish I actually knew how I did that.

    Join the club! Been there, done that!

    🙂

    BTW, if the thread moderator added a couple of posts before the one @22, the numbering went up by two.

    I’ve seen that happen before here.

    But it doesn’t seem like that was the case this time.

    Have a good day.

  47. 47
    Dionisio says:

    gpuccio @43:

    That’s very interesting! Thanks!

    However, do you expect your politely dissenting interlocutor to understand the meaning and humbly accept the importance of your comment?

  48. 48
    critical rationalist says:

    The deeper we look into the biological systems, the more we know about them, the more they look designed. That’s an undeniable fact.

    It’s not in question whether organisms exhibit the appearance of design. What is in question is, what exactly is the appearance of design and is it actually the result of conscious, intelligent agents in the case of our biosphere.

  49. 49
    Dionisio says:

    Seversky @ 24:

    “…the designer had a very different approach to the process than contemporary human designers.”

    Duh! Of course!

    The Designer made the human designers!
    The Maker made us in Imago Dei.
    That is with rational creative minds.
    But who knows more about design, the Creator or His creatures?
    The first Designer or the product of His design?

  50. 50
    critical rationalist says:

    @Dionisio

    So how is it that the first designer became a “expert” on design in the first place? What is the foundation of its rationality and knowledge? If we need such a foundation, it seems that you have the same problem in the case of your designer.

    Also, wouldn’t said designer be well adapted for the purpose of designing things? Is it possible to vary that designer without it becoming less capable of that purpose? If so, it seems it has the very same property that you claim needs a designer.

  51. 51
    Dionisio says:

    critical rationalist @48:

    There’s no doubt that it is designed.

    Most Darwinian ideas are just archaic pseudoscientific hogwash based on gross extrapolation of the observed phenotypic results of the embedded variability framework associated with the biological systems.
    The Galapagos birds remain birds. The turtles remain turtles. The antibiotic resistant bacteria remain bacteria.

    I prefer the Cinderella story where a pumpkin became a carriage, mice turned into beautiful horses and the grasshopper was hired as a cochero. But at midnight it all got back to where they once belonged. 🙂

    At least that makes more sense than the Darwinian just-so fairytales.

  52. 52
    Dionisio says:

    critical rationalist @50:

    You won’t understand it anyway I could explain it, because you don’t want to understand it.
    The day you will desire to understand it, the explanation will be given to you. It’s written for all who truly want to know it.
    For many years I did not care about that knowledge either. I was educated in the most atheistic environment one could think of back then: very close to the Red Square in the capital of the Soviet Union. There I graduated as electrical engineer. You could not find a stronger atheist than me in those years.
    But a marvelous day came when I was pointed in the right direction.
    And the desire to know was ignited in my soul.
    I pray that the same happens to you, so you also can rejoice in the revelation of the Truth.

  53. 53
    johnnyb says:

    I think there is a small amount of confusion. Oftentimes we are presented as if all of biology was on the same page, and then there are those crazy ID’ers and creationists on the other side. That is not the case. There is quite a bit of diversity of opinion and research within the biological community. Just take as an example the feud between Graur and ENCODE.

    Yes, many biologists have found numerous functions for LINEs and SINEs. By and large, these are not the same people who say that 75% of the genome is junk! The biology community is not a homogenous kumbaya community – there are a lot of differences of opinion. Those who are searching for purposes are often different than the ones claiming junk. That isn’t to say that they aren’t aware of each other’s research, just the nature of their research programs are drastically different.

    As for retrotransposition, though it is an unpopular view, I tend to think that Blanden and Steele’s “somatic selection” concept may eventually make a comeback once we have the ability to investigate it well. It makes good sense of the mechanism.

    It looks like it is a very interesting plugin system for the genome.

  54. 54
    johnnyb says:

    By the way, don’t forget to check out my latest Dan Graur post here.

  55. 55
    Dionisio says:

    critical rationalist @50:

    We have radically opposite worldview positions.

    To me the ultimate reality is summarily defined in the first few verses of the first chapter of the Gospel according to the Apostle John (4th in the NT). Read it yourself if you want to. Just make sure you don’t use a version used by the JW cult, because they altered the first verse of that first chapter. Use a translation that corresponds to the oldest extant manuscripts in Greek.
    I read it in Russian, Polish, Spanish and English. I don’t understand other languages, but the oldest extant manuscripts were written in ancient Greek language.
    I like the ESV, but other translations are fine too. They all are equivalent in the bottom line meaning of the fundamental ideas.

  56. 56
    Dionisio says:

    johnnyb @53:

    There is quite a bit of diversity of opinion and research within the biological community.

    My wife and I are good friends with a couple of very seriously dedicated biology researchers who were not excited when I told them that I had watched two courses on Systems Biology, one by professor Uri Alon @ the Weizmann Institute in Rehovot and another by professor Jeff Gore @ MIT. BTW, both professors have PhD degrees in Physics.
    My classic biology friends made not too friendly comments about Systems Biology.

  57. 57
    Bob O'H says:

    Dionisio @ 41 – no, that isn’t the approach used.

    gpuccio @ 42 – if you mean by “functional” that they do something, then yes. But, as far as I know, most of the functional SINEs and LINEs are selfish genetic elements, i.e. they don’t improve the fitness of the organism.

    gpuccio @ 43 – Indeed. I’m always careful not to say that not all junk DNA is useless for the organism!

  58. 58
    johnnyb says:

    “selfish genetic elements” is another holdover from neo-Darwinian assumptions. Transposable elements have been directly implicated in the genome’s ability to remodel itself as needed in times of stress. This has been known since Barbara McClintock, but the Darwinists shot it down, and no one investigated them for 2-3 decades. Now interest is back, and, it turns out, McClintock was right, not the Darwinists.

  59. 59
    es58 says:

    Dio@56: Re “Systems Biology”

    This whole article is relevant to the discussion here, but, one particular quote :

    Systems Biology as a Research Program for Intelligent Design
    David Snoke

    http://www.bio-complexity.org/.....O-C.2014.3

    Optimization

    That we expect living things to have a purpose is part of a broader assumption, namely that living systems are nearly optimized for their expected modes of operation. In other words, in looking at any given part or unknown operation, one assumes that it has some purpose. This presumes that just about everything in the cell does indeed have a role, i.e., that there is very little “junk.”

  60. 60
    gpuccio says:

    critical rationalist at #48:

    It’s not in question whether organisms exhibit the appearance of design. What is in question is, what exactly is the appearance of design and is it actually the result of conscious, intelligent agents in the case of our biosphere.

    One thing is the appearance of design, which was already obvious in Darwin’s times. All another thing is a constantly increasing appearance of an increasingly complex design.

    You could maybe agree that the complexity of the design that “appears” to our eyes has increased esponentially from Darwin’s times to now, and is increasing daily with all the new facts that are discovered.

    Can you remember 10-15 years ago, when we knew almost nothing, or very little, of all the epigenetic mechanisms that control cell development?

    Can you remember a few years ago, when the regulation of chromatin states was practically a mystery? (Not that it is particularly clear even today!)

    Who would have anticipated, 15 years ago, the existence of “a c-Myc regulatory subnetwork from human transposable element sequences”?

    And so on, and so on.

    Certainly, this “appearance of design” is very well articulated, and organized in apparently endless tiers of complexity, probably in order to constantly surprise the researchers and us.

    Unfortunately our human life has unpredictable time limits, but it would be fun to take again this discussion with you in, say, 15 years! 🙂

  61. 61
    gpuccio says:

    Bob O’H:

    “gpuccio @ 43 – Indeed. I’m always careful not to say that not all junk DNA is useless for the organism!”

    Is it just me, or there are too many “not” here? Is it intentional?

  62. 62
    Dionisio says:

    gpuccio @60:

    Certainly, this “appearance of design” is very well articulated, and organized in apparently endless tiers of complexity, probably in order to constantly surprise the researchers and us.

    Exactly!

    The politely dissenting interlocutor reacted at this comment @29:

    The deeper we look into the biological systems, the more we know about them, the more they look designed. That’s an undeniable fact.

    Notice a subtle increment of the “design appearance” as we get deeper into the biological systems.
    You stated it very precisely. As we look deeper, because –as you well said– modern technology is allowing us to do things we couldn’t even imagine a decade or two ago, we are seeing more clearly elaborate choreographies orchestrated within those biological systems at cellular and even molecular levels. Hence we’re seeing choreographies that look more and more written by a choreographer that doesn’t seem to leave many details out of control.

    At this point, once we get to this kind of realization, the appearance turns more and more into a strong confirmation.
    When a detective is investigating a difficult case, there is a moment when he has gathered so much evidence, that even an outsider would clearly see the solution to the problem.

    🙂

  63. 63
    Dionisio says:

    gpuccio @61:

    Is it just me, or there are too many “not” here? Is it intentional?

    I don’t know if that’s intentional, but it’s definitely interesting:

    careful not to say “something”

    where “something” in this case is:
    “that not all junk DNA is useless for the organism”

    which could also be interpreted as
    “some junk DNA is useful for the organism”

    Therefore the whole statement could be rewritten as:

    careful not to say that some junk DNA is useful for the organism.

    which means that

    all junk DNA is useless for the organism

    But isn’t that what the interlocutor believes in anyway?

    Why going so much around to end up in the same?

    Did I understand this right?

  64. 64
    Dionisio says:

    gpuccio @60:

    Unfortunately our human life has unpredictable time limits, but it would be fun to take again this discussion with you in, say, 15 years!

    I think i’d enjoy watching that discussion too. 🙂

    However, I think we shall enjoy this discussion every day from now on.

    We ain’t seen nothin’ yet.
    The most fascinating discoveries, specially for gpuccio and other folks in this online forum, are still ahead.
    And they are coming from the wet and dry labs at increasing numbers.

    That’s one of the reasons I have sneaked out of my project for longer breaks, under the valid excuse of gathering more information for the case scenarios, because the avalanche of research papers is becoming literally overwhelming.
    It’s hard to keep up with everything being published even using a very strict filtering criteria. Sometimes it’s really mind boggling. I have a huge list of papers waiting to be reviewed after they were initially preselected and placed in a tentative queue. We need more help with this in the project, but so far I’m the only one taking care of this. But I’m enjoying it, though it’s keeping me from making progress in the other fronts of the project.

    So I would say that in few months I would like to watch a similar discussion here.

  65. 65
    gpuccio says:

    Dionisio:

    Well, a few months is probably reasonable… But, as we say, God’s will be done! 🙂

  66. 66
    Dionisio says:

    es58 @59:

    Thanks for referencing that book.

    It’s strange that it does not mention the textbook on Systems Biology by Uri Alon, which includes the word “design” in its title. The first edition was published in 2006. The second edition is expected in January 2018.

    An Introduction to Systems Biology: Design Principles of Biological Circuits, Second Edition (Chapman & Hall/CRC Mathematical & Computational Biology)

    Check this out:

    https://www.amazon.com/s/ref=nb_sb_noss_1?url=search-alias%3Daps&field-keywords=systems+biology

    https://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1439837171/ref=dp_ob_title_bk

    In this link the Systems Biology course by professor Alon is mentioned several times in the discussion:

    https://uncommondescent.com/intelligent-design/alternatives-to-methodological-naturalism-online-conference-preview-today/#comment-601838

  67. 67
    Eugene S says:

    GP #21,

    Yes 😉

  68. 68
    Seversky says:

    johnnyb @ 30

    Seversky – the issue isn’t whether “some” of it is – there probably is some somewhere. The issue is a matter of degree. According to Graur and others, the minimum amount of junk is 75%. That is, quite simply, a ridiculous figure. There would be no argument if the question was over 1%. It wouldn’t necessarily be correct, but who would really care?

    If 1% could be junk, why not 75% or 90%? If we look at Larry Moran’s post on his blog Sandwalk he writes

    There’s a huge literature on mutation rates in humans. We don’t know the exact value because there’s a fair bit of controversy in the scientific literature. The values range from about 70 new mutations per generation to about 150 [see: Human mutation rates – what’s the right number?]. Graur uses a range of mutation rates covering these values. He expresses them as mutations per site per generation which translates to values from 1.0 × 10-8 to 2.5 × 10-8. As we shall see, he calculates the genetic load for a range of mutation rates order to get an upper limit to the amount of functional DNA in our genome.

    The most difficult part of these calculations is estimating the percentage of mutations that are beneficial, neutral, and deleterious. Population geneticists have rightly assumed that the number of beneficial (selected) mutations is insignificant so they concentrate on the number of deleterious mutations. The estimates range from about 4% of the total mutations to about 40% of the total based on the analysis of mutations in coding regions.

    Most scientists assume that the correct value is about 10% of the total. What this means is that if there are 100 new mutations in every newborn there will be about 10 deleterious mutations if the entire genome is functional. If only 10% is functional then there will be only 1 deleterious mutation per generation. A mutation load of about one deleterious mutation per generation is the limit that a population can tolerate. Graur assumes 0.99. Others have proposed that the mutation load could be higher (Lynch, 2010; Agrawal and Whitlock, 2012) but it’s unlikely to be more than 1.5. The difference isn’t important.

    That alone looks like a very good argument for why most of the human genome could be junk.

  69. 69
    Dionisio says:

    Seversky:

    A couple of years ago the professor you referred to @68 answered “Yes” to a simple question that had “NO” as the only logically acceptable answer. Later he blamed it on a dishonest question containing a tricky word (“exactly”) that was not in bold text. Are your arguments based on that professor’s opinion?

  70. 70
    Dionisio says:

    Bob O’H @57:

    Dionisio @ 41 – no, that isn’t the approach used.

    How do you know that?

    BTW, see gpuccio @61.

  71. 71
    Dionisio says:

    critical rationalist has several comments with questions he might want to answer.

  72. 72
    EricMH says:

    @68 Seversky, the argument misses the point, he defines the tolerable genetic load by catastrophe. OP’s point is catastrophe is not a sufficient metric of functionality. I can remove many functional pieces from my car before it catastrophically fails.

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