• Can Mutation Cause Changes – Part 2

    I’m an odd person. When I see some clown on the internet make a claim and the very next issue of Science has a paper that utterly demolishes that claim, I get all excited.

    After the debates, I’ve had several conversations with creationists who make the claim that mutations can’t do something. Mutations can’t create new structures. Mutations change the gene and make it non-functional. Mutations can’t create new information. Blah blah blah. The simple truth is that they can. The paper in question is by Camille Sayou et. al. (It took 14 people to do this research.)

    As always, if something I say is unclear or doesn’t make sense, please let me know.

    Most genes in any organism actually don’t make proteins that build the organism or make muscles or whatever else. Most genes make proteins that regulate other genes, turning them on or off or speeding up or slowing down their transcription. This changes the amount of that protein in the organism and will have some kind of effect.

    These regulatory proteins are called transcription factors. They are important drivers in evolution. A mutation in a transcription factor can result in a longer than normal body or more of a particular blood protein. This may provide an advantage or may kill the organism before it gets past the blastula stage.

    People often wonder how mutations can cause extra limbs (for example) to form. Well, it’s not a change in the muscle proteins and the bone proteins and the skin proteins. It’s one change in the regulatory protein that controls all the others. Small changes, in the right spot can have massive effects on the final organism.

    These leads to the question of how can these genes evolve at all? If they are so fraught with danger, changing those regulatory proteins should almost universally be bad right? Well… pretty much. Yeah. But (and there’s always a ‘but’ isn’t there?), many of these genes have multiple copies in each organism. This often results from DNA copy errors or chromosome separation errors.  Regardless of how it happens, the organism now has two copies of the gene.  One of which fulfills the essential function of the gene and one is free to mutate without harming the organism.

    The gene Dr. Sayou (and the others) looked at is called LEAFY. This gene codes for a transcription factor that is a major regulator of flower development and cell division in land plants. What is interesting though, is that the vast majority of species of plants have only a single copy of LEAFY. What’s even more interesting is that there are three distinct types of LEAFY. I will refer to these as Type 1, Type 2, and Type 3.

    Most land plants are Type 1. This includes flowering plants, cone bearing plants (which happens to have a parlogue called NEEDLY), the ferns, and the liverworts. Type 2 includes the mosses. Type 3 includes the hornworts and, curiously, algae.  Yep, this gene goes way back.

    They are obviously the same gene with only minor mutational differences.  In fact all the differences occur because of changes at 3 different points. So, the question is, how do we get these wildly different versions of a gene that is very specific and very conserved?

    The answer is, biochemistry. The authors analyzed the protein that LEAFY makes in many plants and analyzed the results.

    LEAFY

     

    This cladogram is the result. The three boxes labeled “312”, “345”, and “387” t each junction represent the mutations in the transcription factor at those numbered positions (it’s a big protein). By analyzing even algal samples, they were able to determine the ancestral version (to a high confidence).  That ancestral version is on the upper left, QCS.

    The algae version is most like the ancestral version, which is to be expected. The split at QCH is what is interesting to us, because that’s where the Type 2 and Type 3 versions come from.  But if this is so particular, how can it change?

    Because that one mutation, changing position 387 from an S amino acid to a H amino acid (yes, I could go look them up, no I don’t care right now) results in a version of the transcription factor that the authors call “Promiscuous”. That promiscuous version of the transcription factor is capable of performing the functions of Type 1 AND type 2 AND Type 3 LEAFY.

    It’s transitional!

    But, if it’s so cool that it can function as all three versions, why did the other version appear (Type 2 and Type 1)? Because it’s not quite as efficient at all of the functions as the versions on the right are. It’s like having a phone that’s also a camera that’s also a tablet computer. That’s very cool, but try to whip out your phone and take that super awesome snapshot.  You’ll probably miss because the phone just isn’t as efficient as a point and shoot camera.

    In fact, the authors specifically mention that they missed noticing that the promiscuous version could even act as Type 1 or TYpe 2 because it was less efficient at them.

    So there you have it. Not only can mutations change genes so we get new effects on the organisms, but in at least one case (LEAFY) we know that mutations in important transcription factors don’t even have to disrupt the organisms that much.

    This is very, very cool research and puts another nail in the “mutations can’t” myth.

    _______________________________

    C. Sayou et al., A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity.Science (New York, N.Y.) (2014), doi:10.1126/science.1247660

    Category: featuredGeneticsResearchScience

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    Article by: Smilodon's Retreat

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    • John Farrell

      Wait–where is Part 1? 🙂

    • Pingback: Morsels For The Mind – 07/02/2014 › Six Incredible Things Before Breakfast()

    • Void L. Walker

      Awesome and informative, thanks for this

    • RexTugwell

      So this is supposed to solve the mystery of the Cambrian Explosion, huh? I guess mutating drosophila these past few decades hasn’t delivered such promising results. So we turn to plants to figure out how we get from small shellys to anomalocaris in just 6 million years. Good one. Hey, Smilodon, you asked for page references from Darwin’s Doubt for you to comment on. How about pages 50 to 335 (Kindle edition location 962 to 6269)? Too bad you didn’t get Censor of the Year. Maybe next year.

      • SmilodonsRetreat

        And yet, new species are found all the time. In much, much less time than 30,000 years.

        As far as the page numbers, so you don’t have a clue either. Good to know.

        • RexTugwell

          Speaking of new species, when are we going to get new species out of Lenski’s project? Fifty thousand plus generations later and no Lenski coli yet? or Smilodon coli?

          • SmilodonsRetreat

            My understanding (which is just rumor) is that the cit+ E. coli will be classified as a new species. There, done.

            Since the inability to metabolize citrate is a defining feature of E. coli, a bacteria that is like E. coli, but can utilize citrate is not e. coli.

            • RexTugwell

              bacterium

            • SmilodonsRetreat

              Is that a goal post shift I hear?

              “Bacterium” is not a formal classification. Indeed, there are two entire kingdoms in taxonomy that cover ‘bacteria’ and arguably, some members of protista are more bacteria-like than anything else.

              So saying something is ‘bacteria’ is roughly akin to saying something is ‘solid’.

              What you seem to be asking is, has it changed a higher taxonomic level than species? The answer depends.
              1) The people actually doing this research (instead of whining about it on the internet) may determine that cit+ represents a new genus, or even family. In which case, a higher taxonomic level would have happened.
              2) I do know of at least one case in the literature in which a new genus was formed.
              3) See how easy it is to make a new genus, family, etc? These distinctions (and this is something that creationists truly do not understand) are completely artificial. Things like this ONLY happen at the species level in the real world, even though scientists might determine that the result deserves a higher taxonomic category.
              4) We both know that dogs have been dogs for about 30,000 years. So that sets something of a timeframe in which you would expect something like that to occur.
              5) Finally, what’s truly funny is that creationists yell at evolution because things don’t happen quickly yet they are the ones who require that all evolution (including at multiple taxonomic levels) have occurred in the last 6,000 years.

            • RexTugwell

              The only sound you hear is me laughing at you. Fear not. The goalposts are firmly in place. In your eager attempt to “educate” me in the ways of taxonomy, you failed to notice I was merely correcting your speech. You said “a bacteria that is like E. coli” when you should have said “a bacterium that is like E. coli”. You mixed a singular, indefinite article with a plural subject. Tsk, tsk. Real scientists don’t talk like that.

              I accept the universe to be 13.7 billion years old, the earth to be 4.5 billion and life to be 3.8 billion. After all, an eternal God is in no hurry to have His creation run its course in the quickest time possible. Your constant attempt to conflate YECs with ID proponents simply shows your narrow mindedness and inability to distinguish the two. No worries.

            • SmilodonsRetreat

              OK. Maybe you should be more specific. Tell you what, why don’t you go talk to Ken Ham and explain to him why he’s wrong?

              Tell, does your god meet the level of evidence you require of evolution? If so, please detail that evidence. Because I haven’t seen any.

            • RexTugwell

              For someone who believes the universe created itself from nothing, no evidence will be convincing enough for you. Your motives for disbelief are strictly emotional and psychological. Just my humble opinion yet not unfounded. Let me know when you get some empirical evidence for string theory.

            • SmilodonsRetreat

              Again, the actual evidence is that the universe is nothing. Therefore nothing came from nothing.

              There are no motives for belief as I don’t believe in things. If you were able to present any evidence, then I would take that evidence and determine if it resulted in a better explanation. Since you nor any other creationist has ever presented actual evidence, then it’s a moot point.

              My understanding is that String theory is pretty much dead. It was internally mathematically consistent, but never really offered much empirical support or predictions (much like creationism). Many people think it wasn’t even really science. I can see where those people are coming from and they have a good case.

              Let me know if you ever get any empirical evidence for creationism (any form of it).

            • RexTugwell

              “The universe is nothing”. Did you verify that from the sources listed in Krauss’ bibliography? Oh wait. There was no bib.

            • SmilodonsRetreat

              Better no bibliography than fundamentally misrepresenting the papers in one’s bibliography.

              You never have answered the question as to whether Meyer is a liar or the worst researcher ever. Why is that? Because he’s one or the other.

            • RexTugwell

              Uh oh! Smiley the Boy Wonder and his sidekick Doc Bill have mounted a formidable defense of nothing. LMAO! Hey, Doc Bill, provide me with a reference of how 0 + 1 = 0 Thanks. Explain how if it’s not true in the abstract, how it can be true in the physical world? Smiley, in your equations for calculating the emergence of the universe from nothing, what’s the Greek symbol you use for nothing? N? How would that equation look? N + (wishful thinking) = 10^80 baryons?

              And here’s a little something extra: My favorite Lawrence Krauss quote, “By nothing I don’t mean nothing. I mean nothing.” (no doubt you’ll accuse me of quotemining. That’ll amuse me even more) That’s a keeper. I just hope the popcorn holds out while we watch atheists spiral downward into intellectual idiocy.

              As for Meyer…if he’s a liar and the worst researcher ever, why didn’t you directly address Part 2 of his book instead of spending 5 months and 30,000 words on introductory paragraphs? Now all your time and effort will be nothing more than another example of the deafening silence that has characterized the so-called criticism of his book’s two main arguments since it was published.

            • SmilodonsRetreat

              You were asked specific question, why don’t you give a specific answer.

              If a liar spends the first three chapters of his book lying, why would you even read the rest of it? Because he supports the notion you wish was true?

            • Doc Bill

              Since Rex is an authoritarian, unable to think on his own, and must be told the answer by an authority, let me introduce Dr. Charles Marshall, who Meyer (mis) quotes in “Doubt.” Unlike Meyer, Marshall is a working scientist, professor of integrative biology at Berkeley, who studies the change in biodiversity over geological time and has performed physical research (that is, not high school level reading about stuff like Meyer), published in scientific journals (unlike Meyer), and studies new genomic data as it pertains to the Cambrian Explosion (again, unlike Meyer).

              In a review of “Doubt,” Marshall summarizes Meyer’s work in this insightful and (for me) too polite statement: This work demonstrates a systematic failure of scholarship.

              In terms more blunt: Meyer is a deliberate liar.

              I’ll await Rex’s apology.

            • SmilodonsRetreat

              Let me dd that I had the pleasure of having Dr. Marshall contact me after I pointed out another misquote by Meyer of Marshall’s work.
              Here: http://www.skepticink.com/smilodonsretreat/2013/11/20/darwins-doubt-another-quote-another-mine/

            • RexTugwell

              Let’s see. Doc Bill starts off by calling me an IDiot followed by some sniveling about how I insulted him. Then proceeds to insult my non-working brain. I see I’m back in 3rd grade. No surprise there. Since you’re now the Dynamic Duo, I’ll reply to you both in one post.

              OK, I get the “net energy of the universe is zero” thing. Kinda like when I have a zero balance in my savings account. I then add $1 million and then withdraw $1 million. My net balance is zero. Understood. Now along comes the IRS and it’s gonna want some taxes. Will the IRS be satisfied with the “but my net balance is zero so I don’t owe you any taxes” exuse? I think not. You guys haven’t explained how something comes from nothing. You make a category error with your net energy feint. The net energy of the universe is merely descriptive but it’s not explanatory. Try again.

              I’m guessing you didn’t read Meyer’s 4-part response to Marshall’s critique of his book. It’s here if you want to read it. Meyer points to no less than three self-contradictions Marshall makes regarding the duration of the Cambrian explosion, the significance of the small shellys and the need for new genetic information.

              Refresh my memory, Doc Bill. Why do I owe you an apology?

            • SmilodonsRetreat

              Shockingly, Marshall is not the determinant of the length of Cambrian.

              Regardless, Meyer lied about the content of Marshall;s paper and numerous others. Is he a liar or the worst researcher ever?

              Again, you were asked specific questions and you ignore them to go on this tangent using an inappropriate analogy and then a ‘well he did too’ kind of attack on Marshall. None of which matters.

              You were asked specific questions and you chose, multiple times, to not answer them. Why is that?

            • RexTugwell

              Boy Wonder, you’re using words; even forming sentences. However, there’s nothing substantive to your replies.

              Marshall is not the determinant of the length of Cambrian.

              You may want to confer with your sidekick because it sounds like Doc Bill worships at the altar of Charles Marshall. Judging from what he said, Marshall is more than qualified to determine the length of the Cambrian. Did either of you guys muster up the courage to read Meyer’s 4-part reply? While you’re at it, read this. A Taxonomy of Evasion: Reviewing the Reviewers of Darwin’s Doubt You have your own phylum, Smilodon!

              I’m pretty sure my analogy holds but you’re welcome to show me where it breaks down. Also, the subject of nothing may be tangential to the thread but you did engage the topic with your faith-based “the universe is nothing” fantasy.

              Finally, I don’t know if you suffer from short-term memory loss or what but why do you continue to ask me questions when I’ve told you over and over that you’ll not get any answers from me until you fix your math. Gosh!!! 😉

            • Doc Bill

              You’d make a great sideshow act in a circus, Rex, “The Man Who Can Dodge Points!” The point is, my dear demented little authoritarian, is that Scientist Marshall countered Liar Meyer with actual science while Meyer could only “rebut” with rhetoric. Furthermore, Meyer did not address his “systematic failure in scholarship,” by far Marshall’s most devastating rebuke simply because Marshall is manifestly and demonstrably correct in his assessment.

              You needed an authority so I gave you one. You ignored it. I pointed you to the math of Randall and Carroll, but you came back with a childishly inane and totally irrelevant analogy that really did not address the price of tin in Bolivia.

              And, now, you’re going to do the Creationist Pout and refuse to eat your porridge. I think it’s nap time for ‘ittle Wexy.

            • RexTugwell

              Woopsie! Seems like I hit a nerve with Doc Bill. (Are you a real doctor or did you just play one as a child?) You’re also welcome to show me where my analogy breaks down. I haven’t heard from Smiley yet so all eyes are on you.

            • Doc Bill

              Your analogy breaks down starting with the word, “Kinda.”

            • Doc Bill

              Taunts, insults and more taunts, Rex. Is that all you are capable of? I realize, Rex, that as an authoritarian you don’t have use of a working brain but do try to follow. What can be called positive energy (matter) can be balanced by what can be called negative energy (gravity) such that if they are equal the net energy of the Universe is zero.

              If there is a cosmologist of whom you are aware whose demonstration of such a calculation is one you would accept, name the person and I’ll dig up a reference. How about Lisa Randall or Sean Carroll?

            • Dkennedy

              So then… nothing is here? Correct Bill? I mean.. the universe is empty – we are phantoms. Or was all of that “positive energy” in existence previous to the big bang? If it wasn’t – it’s irrelevant how you want to frame it – there’s stuff here, there wasn’t before.

              It’s sad of you to try to defend an inane nothing universe concept — it’s frankly the most desperate act I’ve seen.

            • SmilodonsRetreat

              You need to understand the difference between nothing and summing up all the energy in the universe and it equaling zero.

            • Doc Bill

              You want a bibliography, Rex, to demonstrate your wrongness? What exactly would you like to see? How about an energy balance of the Universe? Upon whose authority would you accept as factual and correct? Let me know and I’ll dig up a reference for you.

            • Doc Bill

              ID proponent Paul Nelson is a YEC. No conflation there.

              Secondly, since Rex is such a precise IDiot, he should have written that the universe is “about” 13.7 billion years given that the most accurate estimate at this moment in time is 13.798±0.037 billion years.

              Such sloppiness, however, is the hallmark of creationists like Rex who don’t understand the big picture nor the details for that matter.

            • RexTugwell

              Genius…pure genius.

            • Void L. Walker

              Rex, you make me giggle. 🙂