Sep 03 2009

What’s Your Mutant Power

The unavoidable truth is that we are all mutants. This doesn’t mean that some of us can control magnetic fields at will while others have claws protruding from their knuckles (although it is fun to fantasize about what you would like your mutant power to be).

Rather, it means that mutations – random changes in the base pair sequence of our DNA brought about by copying errors in the reproductive process – are common. This is old news, but scientists have been trying to nail down exactly how common for years.

Now a new study, using the latest genetic sequencing techniques, gives us a more accurate estimate of the mutation rate in humans – 3 x10 -8 mutations per nucleotide per generation. This translates to 100-200 mutations per person. That means that you have  100-200 new mutations not present in either of your parents.

The paper concludes:

Twelve mutations were confirmed in not, vert, similar10.15 Mb; eight of these had occurred in vitro and four in vivo. The latter could be placed in different positions on the pedigree and led to a mutation-rate measurement of 3.0 × 10−8 mutations/nucleotide/generation (95% CI: 8.9 × 10−9–7.0 × 10−8), consistent with estimates of 2.3 × 10−8–6.3 × 10−8 mutations/nucleotide/generation for the same Y-chromosomal region from published human-chimpanzee comparisons [5] depending on the generation and split times assumed.

What this means, as Larry Moran explains quite nicely, is that there is nice agreement between the theoretical mutation rate based upon the rate of copy error, the mutation rate we calculate when we compare two people separated by 13 generations, and the rate we calculate when we compare humans to chimpanzees.

What this further means is that most mutations are neutral.

For some quick background, each strand of DNA contains a sequence of four different base pairs (GTCA). Each triplet of three base pairs (in a coding region) codes for either an amino acid or a basic command, like “stop coding here.” There is redundancy in this code in that there are more triplet combinations (4^3 = 64) than amino acids (20). So each amino acid on average has about three triplet combinations that code for it.

Therefore, some mutations are completely silent in that they shift from one triplet code to another for the same amino acid – therefore the amino acid sequence and the resultant protien are identical. Actually, recent research shows that silent mutations, while they do not affect the resulting protein, can affect the transcription rate and therefore the amount of that protein cells make. There’s always another layer of complexity to biology.

A mutation may also change one amino acid to another, but the new amino acid may be chemically interchangeable with the old one, and again the three dimensional structure of the resulting protein may be unchanged. Or, there may be a slight change in the protein structure, but not one that affects function. Or, function may be altered but in a way that does not affect health and survival (let’s say it has a small effect on hair color).

These are all neutral mutations – they do not make the organism more or less fit, but they do add genetic diversity to the population.

Mutations may also be harmful or beneficial if they result in a change of protein structure that alters its function, or changes signals that alter the developmental pathways. Also, not all mutations swap one amino acid for another. A point mutation may change a triplet code to a stop codon, telling the cell’s machinery to stop the process of making the protein prematurely and resulting in a truncated protein. Or, there may be a frame-shift mutation – a base pair can be added or deleted which will shift the three letter code, essentially scrambling the amino acid sequence from that point forward.

If most mutations were harmful then many of these mutations would be lost to spontaneous abortions – embryos that are just not viable and therefore die in the womb. If the measured rate of mutations were far less than the theoretical rate, we could infer that most mutations may be harmful. However, this new study and other evidence supports the conclusion that most mutations are neutral, and only a few that are harmful, and also a few that are beneficial.

Creationists, as they often do, habitually misunderstand the nature of “mutations.” They see them as deviations from a perfect “normal” state. But in reality, all gene variations are just that – variations. No one variation is any more perfect or normal than another. There is likely, for most proteins, a large variety of base pair and amino acid sequences that function just fine, or may have only subtle differences. There is also context – one sequence may have a survival advantage in one environment but be a detriment in another.

We can actually infer the degree to which protein variations are tolerated by how well they are conserved in evolution. If peas and humans have the same version of the same protein, than that protein is highly conserved, which means that evolutionary pressures select against change. The most highly conserved proteins are the histones (also the nerdy name of my medical school acapella group) – proteins that wrap up and control the long DNA strand. This makes sense as this is a very basic function to the machinery of cells.

This is similar to the creationist misunderstanding of transitional species – all species are transitional just as all individuals are mutants. Life is a continuum of variation, although an uneven one, and much of the variation extinct.

Understanding the nature of variation, mutation, and diversity is critical to conceptualizing evolution, and a misunderstanding of these things is often a part of creationist denial of evolution.

60 responses so far

60 thoughts on “What’s Your Mutant Power”

  1. Mark Entel says:

    A very nice reminder that there is a difference between typical & normal.

  2. Enzo says:

    I feel this is a key concept for the public to understand as we move into the age of advanced genetics and genetics-guided medicine.

    An understanding of genetic diversity provides a lot of answers for some of the questions that people attack medicine with…Such as why cancer is so difficult to treat and why some people don’t have cholesterol problems despite scary diets. I’ve seen a lot of mistrust and skepticism directed toward medicine because of misconceptions like this.

    Hopefully, as more and more research continues to inform us of our current understanding, attitudes will change and excitement will follow.

  3. artfulD says:

    “Understanding the nature of variation, mutation, and diversity is critical to conceptualizing evolution, and a misunderstanding of these things is often a part of creationist denial of evolution.”

    Unfortunately, you and perhaps the sandwalker seem to feel the mutations bring the strategic changes to the organism with them.
    Mutations themselves thus causing the differences between species and especially between humans and chimpanzees. Yeah, that’ll work.
    Creationists will love the concept of the gods routinely and regularly sending down evolutionary strategies.

  4. artfulD says:

    Speaking as I just did of humans and chimpanzees, check this out:
    http://www.newscientist.com/article/mg20327244.100-three-human-genes-evolved-from-junk.html

    Especially note this paragraph:
    “Part of the explanation might be that biological systems are very noisy: even though most of our DNA is junk, most of it still gets transcribed into RNA at times, and some of that RNA probably reaches cells’ protein-making machinery. This means that when mutations do throw up sequences capable of encoding proteins, some may get “tested” and useful ones selected for. As more primate genome data becomes available, McLysaght estimates a further 15 human genes will turn out to have evolved de novo.”

    Now what is this about testing and useful ones selected for, if those noisy biological systems aren’t really doing it?

  5. weing says:

    “Now what is this about testing and useful ones selected for, if those noisy biological systems aren’t really doing it?”

    What do you think it means?

  6. artfulD says:

    It means biological systems are recognized as being functionally involved in the choices of selecting for useful mutations. Thanks for asking.

  7. weing says:

    How does this happen?

  8. artfulD says:

    Through one of the myriad of trial and error processes developed over millions of years of incremental steps by countless variations on the original form of life that came to earth either spontaneously or through panspermial seedlings.
    In other words, how the hell would I know?

  9. CertifiedCyborg says:

    This is one of the most frustrating general misunderstandings of evolution. I was talking to a woman last night who seemed to think mutations were by definition an imperfection in the genome. It was hard to convince her that every gene is a mutant in its own right.

    artfulD – The newscientists article is not a criticism of natural selection, but an acknowledgement that our “junk” dna may indeed be the potential source of mutations which can actually code for proteins. Again, its got squat to say about whether or not behavioural strategies are selectionariy pressures.

  10. artfulD says:

    CertifiedCyborg,
    I say again, it shows biological systems are recognized as being functionally involved in the choices of selecting for useful mutations.

    Behavioral strategies were mentioned with respect to the previous topic, You will note I referred to evolutionary strategies to help start this one off. In one case we were dealing with behaviors attributed to mutation. In this case it’s the potential for beneficial change that the organism is concerned with.

    This tactic of twice asking me to clear up a misunderstanding of what I actually never said to begin with is getting a bit old. I can see little point in responding to it a third time.

  11. CertifiedCyborg says:

    I’m not asking you to clear anything up this time artfulD, I just jumped the gun and assumed you were applying the same argument to this topic. My mistake.

  12. artfulD says:

    Well,Cyborg, it wasn’t your responsibility to offer a response to my observations anyway. But was it also your mistake to assume I cited the article as criticism of natural selection when my criticism has always been about the failure of its current advocates not only to propose a theory for the selective mechanism, but to consider that any such mechanism exists as far as the organism is concerned?

    Here we have some acknowledgement that such a mechanism exists. Any ideas on how it might work? That’s all I’m really interested in.
    To use your terminology, you’ve had squat to contribute in that respect. Unless somehow you can expand on the notion that the sexual selection feedback loop you mentioned earlier could be determinant when it comes to testing for useful mutations.

  13. Ryan261357 says:

    artfulD, CertifiedCyborg just apoligized for not understanding you. Why do you need bring the hostility again.

  14. artfulD says:

    Pro forma apologies are for when you get caught at something.

  15. Ryan261357 says:

    artfulD

    Since you post on this forum I think we will all take the “responsibility to offer a response to [your] observations” How could we not! You bring up some fascinating topics. I disagree with most of them but I really like the discussion. Great article that you linked to, by the way.

    I still do not understand your theory. Maybe there won’t be any confusion if you would just state it.

    You should give a detailed description of what you believe is not being described by the standard model of evolution.

    You should state a hypothesis that is testable.

    You should provide a protocol that tests of your hypothesis, or provide relevant resources that support your hypothesis.

    If it requires a lot of time then fine. We will wait. Write a paper and direct us to it when you are done. See if Dr. Novella will let you post it here.

  16. Ryan261357 says:

    artfulD

    If you believe that CertifiedCyborg gave a pro forma apology then that’s up to you. I don’t see how you read that though. An apology for not understanding a position is not the same thing as being “caught at something”. Stop taking criticism personally.

  17. artfulD says:

    I’ll consider writing the paper when anyone of you comes up with a positive idea on something that isn’t simply a reinforcement of the ideas presented by Dr. Novella. So far the only one that does this with any distinction is daedalus2u. Even though we both consider each other to be bonkers – but the guy gives it a hell of try.

    What I meant by the responsibility comment was that the onus wasn’t on Cyborg to do so. Thus any appreciation I may have had for the effort was offset by the tactics that I did not appreciate.

    Not that it was intended that I appreciate it, or that I should appreciate your condescension in advising me on how to prepare a paper that I am confident you have never succeeded doing yourself on this or any related subject.

    Lets see now, should I call it Evolution for Dummies? Nah, that’s supposed to be an ironic reference that wouldn’t apply here.

  18. Ryan261357 says:

    Who wants to name all the logical fallicies in artfulD’s last statment?

  19. Ryan261357 says:

    [A repeat with proper spelling] Who wants to name all the logical fallacies in artfulD’s last statement?!

  20. Michael Kingsford Gray says:

    # artfulD:

    Are you habitually posting whilst intoxicated?
    Yes or No.

  21. artfulD says:

    Well, I suppose it might appear that way to someone who, say, believes in memes and wears funny hats.

  22. SteveA says:

    Ryan261357: “Who wants to name all the logical fallacies in artfulD’s last statement?!”

    Moving the goalposts might be one:

    artfulD: “I’ll consider writing the paper when anyone of you comes up with a positive idea on something that isn’t simply a reinforcement of the ideas presented by Dr. Novella.”

    Most people asked to explain an idea, would just do so, not make vague caveats about the conditions under which they’d do so. (I say vague because fulfilling the conditions would depend on artfulD’s idea of what is ‘positive’ or not).

    Also, the ‘ideas presented by Dr. Novella’ are simply conventional evolutionary theory. I’m sure this kind of misrepresentation is a logical fallacy, but I’m not sure how to label it. Any ideas?

  23. weing says:

    I think ArtfulD himself may be logical phallus. See?

  24. JeffG says:

    Geez, you stepped on the joke I was about to make, weing! which was:

    The most highly conserved proteins are the histones (also the nerdy name of my medical school acapella group)

    I can just imagine “The Histones” battling it out with their cross-campus rivals, the “Logical Phalluses”.

  25. artfulD says:

    Gee, you can’t leave those three blind mice alone for a minute can you. Come back and there they are, playing with their low hanging fruit. With nary a testicle in any vesicle. Weing especially fond of his goalpost, moving it to and fro, as if it will somehow help him think. Look, someone has put dunce caps on their little heads and they don’t know they’re there!
    And hey, they’re begging for help to pass out an idea. But little mice, that’s not an idea you’re expecting. You’ve looked in the wrong place all this time, haven’t you. But that just can’t be, they cry, that’s the place our ideas have always come from. Can’t you see, they cry, that’s where we’re talking from. Why, we’ve even been employed because of our particular skills!
    We are the designated flalulaters, the front ranks of the surrogate squad.
    You must be so proud, I respond, as I’m forced to leave the room by the darkening cloud of what passes for them as wisdom.

    And they so wanted me to light a match! Why do I feel such guilt? Because I secretly wanted to see them fry? Perhaps I should punish myself, dumb down a bit, maybe go snowbaording or hicking in Colorado.

  26. weing says:

    Aw, come on. Lighten up.

  27. tmac57 says:

    Captain: ” Progress report”

    1st Officer: ” The subject has received sufficient rope now Captain”

    Captain:” And what is the status of phase two?”

    1st Officer:” Phase two is now in progress sir, and looks to be near it’s final stage”

    Captain:” Excellent ! Carry on”

    1st Officer: “Aye, captain!”

  28. artfulD says:

    tmac57,
    Speaking of ropes, or in your case strings, don’t look now, but you’re a puppet. You’re the main dummy in the rope a dope show.

  29. artfulD says:

    weing, about that phallus envy of yours, you might back off a bit with the search for enlightenment. You could already be a bit too light for your loafers. Not that there’s anything wrong with that.

  30. CertifiedCyborg says:

    Directed mutation as opposed to directed adaptation; how much of a difference one word makes! All you comments suddenly fall into place artfulD.

  31. artfulD says:

    Prepare for the philistines to sound the alarm.

  32. Draal says:

    You should give a detailed description of what you believe is not being described by the standard model of evolution.
    You should state a hypothesis that is testable.
    You should provide a protocol that tests of your hypothesis, or provide relevant resources that support your hypothesis.

    Hey Artie, when you getting around to this? You can wax poetic ’till the cows come home or are you going to put your money where your mouth is?

  33. Draal says:

    at the very least, “You should state a hypothesis that is testable”.

  34. artfulD says:

    Hey Draal, or should I call you sonic the philistine, I destroyed your argumentation the last time we met, and I could easily do it again, so you are hardly one to advise me what I should or should not do, based on what some other dummy thought was the best way to cover up his own ignorance – one who has yet to write any papers of his own, or even present the germ of any alternate hypotheses.

    And of course, the theories I’ve endorsed are not exclusively mine and are not only plausible and testable, I’ve made reference to the results of such tests numerous times on this forum.

    That’s the last detailed answer I’ll bother to give you on this forum.

  35. Ryan261357 says:

    Thanks Draal for restating the hypothesis question. Once again artfulD has no answer but to insult everyone on this forum.

  36. Ryan261357 says:

    “And of course, the theories I’ve endorsed are not exclusively mine and are not only plausible and testable, I’ve made reference to the results of such tests numerous times on this forum.”

    Well I guess you are going to have to do it again. Sending us references to all of the “plausible and testable” studies. With there being so many it might take long time. Dont worry we will wait.

    By the way I am reading your book you suggested called “The Life and Behavior of Living Organisms” So far it is very interesting. Ill let you know what I think you crazy loon!

  37. artfulD says:

    Dumb.

  38. Ryan261357 says:

    “I’ll consider writing the paper when anyone of you comes up with a positive idea on something that isn’t simply a reinforcement of the ideas presented by Dr. Novella”

    artfulD; You do not understand skepticism at all. Skepticism is a method and may have its leaders like Steve Novella or Phil Plait, but it is not a belief system. It is a way to systematicaly test ideas. We use science to test those ideas becaues it has been proven over time to repeatedly demontrate it effectivness. It is important that scientists look at your ideas and evaluate them. We have tried to give you constructive criticism on this forum but yiou have not taken it

  39. artfulD says:

    But you’re not a scientist, you’re basically a bum. My guess would be you have serious mental problems. How do I know? The pattern of paranoia is clear, as I’m sure you’ve been told before. They used to call it delusions of grandeur and it’s classified in the DSM as megalomania. There’s often a psychopathic element involved as well, which has caused you to pretend you actually are part of this operation, and that you actually know these other people you’re naming, when of course you don’t have a clue as to who they are or what they do. You should shut up now but of course you can’t, so you won’t.
    But I can stop responding to you and I will. I found that for some odd reason I like to see you beg.

  40. Ryan261357 says:

    Holy Sh*t you are crazy as hell.

  41. Ryan261357 says:

    Why are you on this forum? It wasnt to make fun of people?

  42. Ryan261357 says:

    Really why are you here!

  43. Draal says:

    heh, Artie you crazy coot. For one that prides himself on reasoning, you fail. You inject your posts full of logical fallacies and insults. You are unable to substantiate your views except by posting links to reviews. REVIEWS. Ain’t nothin’ about your arguments are scientific. Put down the WoW and get your butt into a wet lab to get some real life perspective.

  44. artfulD says:

    Dumb and dumber.

  45. Draal says:

    Point, set, match, there Professor.

  46. artfulD says:

    Reminds me of one of you dummies that thinks it a logical fallacy to play in a game with more than one goalpost. Saves coming up with a strategy when you have no game. And no direction.

    We reviewed the game film and you stunk up the field:
    http://www.theness.com/neurologicablog/?s=evolving+useful+bacteria

    You have not been selected for further training. We use a level playing filed, and you’re not on the level. Neither is that other dummy.

    Talk randomly amongst yourselves. Good luck with the adaptation.

    Oh yeah, and this is for the psychopathic ski bum, remember the old adage, beggars can’t be choosers. (Exit laughing my ass off.)

  47. artfulD says:

    Poor spelling must be catching – should be playing field.

  48. artfulD says:

    Actually I’ve said all I feel the need to about direction, although directed selection would have been another topic if I thought I had a receptive audience. Also to be discussed would have been more about the actual mechanisms we’ve been testing.
    In that connection I would have also been discussing the basics of evolutionary and behavioral strategies, and their common elements across species, but the naysayers will be happy to know I’ve chosen not to. If you can’t accept that there actually are such strategic mechanisms, the nature of the strategies will have no relevance here.

  49. weing says:

    Artie,
    Don’t be so touchy. I’m receptive, but I’m like the guy at heaven’s gate who has to be dragged in because he’s not convinced it’s heaven he’s going to. I can accept that such strategic mechanisms have evolved. Which ones and how have you been testing them? What have you learned so far?

  50. artfulD says:

    Well, we’ve learned that game theory doesn’t apply all that well to biological algorithms, so we have had to construct a different model (or models) and test that model’s predictive capabilities with respect to why things happen rather than how.
    That’s really all I want to say about the process as it’s largely in the realm of proprietary information at present. And there’s an analytical aspect to this process that some of you will surely not approve of. The patterns involved are not the usual table top level variety. You might have been interested in some of the results, as a lot of what I’ve discussed already has been based on those experiments.
    But wait, you didn’t much care for those findings, and that means I’d have to run anything new through the same old gauntlet. I think I’ll pass on that.

    .

  51. weing says:

    I can understand your reticence in divulging your model(s). Let us know when you publish them. What is the analytical aspect that you are referring to? Describe, if you can, the patterns involved. BTW, once you publish, be ready for everyone to try and tear your work apart. Don’t take it personal. If your work is sound, it will survive the process.

  52. artfulD says:

    Assumptions involving a hierarchy of consequences. Simulations of symbolic algorithms. The holography is a bitch to simulate. The inconsistencies of parasitic morphology are driving us nuts.

  53. artfulD says:

    Controversial analytical aspect? Here’s a clue:
    http://www.springerlink.com/content/h4514rqu414h3774/

  54. HHC says:

    I believe the concept of mutant power and generations of separate variation may be an apt explaination for the cultural arts. View a work by Leonardo DaVinci and then a work by Jackson Pollack. Pollack’s lifestyle was a perfection in mutation, alcoholism, cigarettes, and mental disorder. His work is a reflection of his internal chaos.

  55. artfulD says:

    Researchers have discovered that Pollock’s patterns could be characterized as fractals–shapes that repeat themselves on different scales within the same object. Each smaller structure is a miniature version of the larger form. Fractals often occur in nature, and a fractal pattern, whether in nature or in a Pollock painting, is subconciously pleasing.
    Fractal geometry is strategic, and represents, as one example, an
    adaptive synchronization strategy based on active control for demodulating message hidden in chaotic signals.
    The functional mechanism of the God of the zaps perhaps.

  56. HHC says:

    artfulD, your example suggests ending a synchronized signal to impact chaotic signals, extracting waves? How would this apply to molecular vibration?

  57. artfulD says:

    Harnessing the molecular energy by strategic intervention, such as in frequency modulation and multiplexing systems first used for telegraphy and now for FM radio, etc. Some of the towers used for these purposes are in the Nebraska Sand Hills.

  58. HHC says:

    artfulD, So there are t.v., radio, telephone, and cell towers in the Nebraska Sand Hills. The Sand Hills satellite dishes receive the multiplex signals.

  59. artfulD says:

    God willing.

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